@article {pmid39466404,
year = {2024},
author = {Ortjohann, M and Schönheit, P},
title = {Sugar alcohol degradation in Archaea: uptake and degradation of mannitol and sorbitol in Haloarcula hispanica.},
journal = {Extremophiles : life under extreme conditions},
volume = {28},
number = {3},
pages = {48},
pmid = {39466404},
issn = {1433-4909},
mesh = {*Haloarcula/metabolism/genetics ; *Sorbitol/metabolism ; *Mannitol/metabolism ; Archaeal Proteins/metabolism/genetics ; Fructokinases/metabolism/genetics ; Fructose/metabolism ; ATP-Binding Cassette Transporters/metabolism/genetics ; },
abstract = {The halophilic archaeon Haloarcula hispanica utilizes the sugar alcohols mannitol and sorbitol as carbon and energy sources. Genes, enzymes, and transcriptional regulators involved in uptake and degradation of these sugar alcohols were identified by growth experiments with deletion mutants and enzyme characterization. It is shown that both mannitol and sorbitol are taken up via a single ABC transporter of the CUT1 transporter family. Then, mannitol and sorbitol are oxidized to fructose by two distinct dehydrogenases. Fructose is further phosphorylated to fructose-1-phosphate by a haloarchaeal ketohexokinase, providing the first evidence for a physiological function of ketohexokinase in prokaryotes. Finally, fructose-1-phosphate is phosphorylated via fructose-1-phosphate kinase to fructose-1,6-bisphosphate, which is cleaved to triosephosphates by a Class I fructose-1,6-bisphosphate aldolase. Two distinct transcriptional regulators, acting as activators, have been identified: an IclR-like regulator involved in activating genes for sugar alcohol uptake and oxidation to fructose, and a GfcR-like regulator that likely activates genes involved in the degradation of fructose to pyruvate. This is the first comprehensive analysis of a sugar alcohol degradation pathway in Archaea.},
}
@article {pmid39455151,
year = {2024},
author = {Pan, YC and Zhao, JW and Niu, HJ and Huang, YL and Wang, Y and Zhang, XX},
title = {[Effects of Vegetable Planting Ages on Community Structure of Ammonia-oxidizing Archaea and Ammonia-oxidizing Bacteria in Greenhouse Vegetable Fields].},
journal = {Huan jing ke xue= Huanjing kexue},
volume = {45},
number = {10},
pages = {6077-6085},
doi = {10.13227/j.hjkx.202310135},
pmid = {39455151},
issn = {0250-3301},
mesh = {*Archaea/metabolism/growth & development/classification ; *Ammonia/metabolism ; *Soil Microbiology ; *Bacteria/classification/growth & development/metabolism ; *Oxidation-Reduction ; *Vegetables/growth & development ; Soil/chemistry ; China ; Nitrous Oxide/metabolism/analysis ; Time Factors ; Agriculture/methods ; Nitrogen/metabolism ; },
abstract = {The ammonia oxidation process driven by microorganisms is a dominant source for nitrous oxide （N2O） emissions. Here, we examined the influence of greenhouse vegetable planting ages on soil ammonia-oxidizing archaea （AOA） and ammonia-oxidizing bacteria （AOB）, which is of great significance for assessing the soil quality status and greenhouse gas transformations. A field study was conducted at different times （1, 5, 10, and 20 a） in greenhouse vegetable soils of Gaoyi, Hebei Province. Chemical analysis and Illumina NovaSeq high-throughput sequencing were used to analyze the soil physicochemical properties and community structures and diversity of AOA and AOB. The variation in AOA and AOB communities and the driving factors in greenhouse soils at different ages were also investigated. The results showed that the contents of total nitrogen, organic matter, alkali-hydrolyzable nitrogen, available phosphorus, and available potassium first increased and then decreased with the prolongation of growth. The contents of nitrate nitrogen, ammonium nitrogen, and electrical conductivity first decreased and then increased with the prolongation of growth. The pH value of soils decreased with the prolongation of growth. The abundance and diversity index of AOA and AOB first decreased and then increased with the prolongation of growth. Nitrososphaeria, unclassified Thaumarchaeota, and Candidatus Nitrosocaldus were the dominant species of AOA, while Betaproteobacteria and Nitrosospira were the dominant species of AOB. The composition of the soil AOA community varied greatly compared to that of AOB with the prolongation of growth. Correlation analysis showed that the changes in soil nutrient factors had a significant correlation with AOA and AOB communities. Redundancy analysis indicated that ammonium nitrogen, alkali-hydrolyzable nitrogen, and nitrate nitrogen were key factors of AOA communities, while electrical conductivity, available potassium, and nitrate nitrogen were key factors for AOB. In summary, long-term planting of greenhouse vegetables significantly affected the abundance and composition of soil AOA and AOB communities. Our results provide a theoretical basis for further studies on the greenhouse gas transformation and microbial mechanisms of the nitrogen cycle in greenhouse soils.},
}
@article {pmid39437693,
year = {2024},
author = {Zhang, L and Yang, J and Ge, AH and Xie, W and Yao, R and Wang, X},
title = {Salinity drives niche differentiation of soil bacteria and archaea in Hetao Plain, China.},
journal = {Journal of environmental management},
volume = {370},
number = {},
pages = {122977},
doi = {10.1016/j.jenvman.2024.122977},
pmid = {39437693},
issn = {1095-8630},
abstract = {Soil salinization is a critical environmental issue that limits plant productivity and disrupts ecosystem functions. As important indicators of soil environment, soil microbes play essential roles in driving nutrient cycling and sustaining ecosystem services. Therefore, understanding how microbial communities and their functional potentials respond to varying levels of soil salinization across different land use types is crucial for the restoration and management of salt-affected ecosystems. In this study, we randomly selected 63 sites across the Hetao Plain, covering an area of ∼2500 km[2]. Our results showed that both salinity- and fertility-related soil parameters were significantly correlated with bacterial and archaeal diversities, with soil salinity emerging as the stronger predictor of prokaryotic diversity. Intriguingly, bacterial and archaeal communities were tightly interlinked but displayed opposite trends in response to environmental factors, indicating a clear microbial niche differentiation driven by soil salinity. Moreover, the generalist functions of bacteria and archaea (e.g., chemoheterotrophy) exhibited contrasting responses to environmental parameters, while their specialist functions (e.g., nitrification) responded consistently. These findings highlight the pivotal role of soil salinity in shaping the niche differentiation of bacterial and archaeal communities in saline soils, providing insights to guide salinity-centered restoration strategies for effective marginal land management.},
}
@article {pmid39436425,
year = {2024},
author = {Dong, XY and Mao, YL and Zhang, QK and Zhu, LR and Hou, J and Cui, HL},
title = {Genome‑based classification of the family Natrialbaceae and description of four novel halophilic archaea from three saline lakes and a saline-alkaline land.},
journal = {Extremophiles : life under extreme conditions},
volume = {28},
number = {3},
pages = {47},
pmid = {39436425},
issn = {1433-4909},
support = {32070003//National Natural Science Foundation of China/ ; },
mesh = {*Phylogeny ; *Genome, Archaeal ; *Lakes/microbiology ; Halobacteriales/genetics/classification ; Salt Tolerance ; Salinity ; },
abstract = {The current representatives of the family Natrialbaceae within the class Halobacteria were subjected to phylogenetic, phylogenomic, and comparative genomic analyses. The current species of Halobiforma and Halomontanus were found to be related to those of Natronobacterium and Natronoglomus, respectively. According to the cutoff value of average amino acid identity (AAI) (≤ 76%) proposed to differentiate genera within the family Natrialbaceae, Halobiforma, and Natronoglomus should be merged with Natronobacterium and Halomontanus, respectively. Beyond these, four novel halophilic archaeal strains, CCL63[T], AD-5[T], CG52[T], and KLK7[T], isolated from three saline lakes and a saline-alkaline land in China, were simultaneously subjected to polyphasic classification. The phenotypic, phylogenetic, phylogenomic, and comparative genomic analyses indicated that strain CCL63[T] (= CGMCC 1.18663[T] = JCM 35096[T]) represents a novel genus of the family Natrialbaceae, strains AD-5[T] (= CGMCC 1.13783[T] = JCM 33734[T]) and CG52[T] (= CGMCC 1.17139[T] = JCM 34160[T]) represent two novel species of the genus Natronococcus, and strain KLK7[T] (= MCCC 4K00128[T] = KCTC 4307[T]) represents a novel species of Haloterrigena. Halovalidus salilacus gen. nov., sp. nov., Natronococcus wangiae sp. nov., Natronococcus zhouii sp. nov., and Haloterrigena salinisoli sp. nov. are further proposed based on these type strains accordingly.},
}
@article {pmid39433727,
year = {2024},
author = {Lemaire, ON and Wegener, G and Wagner, T},
title = {Ethane-oxidising archaea couple CO2 generation to F420 reduction.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {9065},
pmid = {39433727},
issn = {2041-1723},
support = {WA 4053/2-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; WE 5492/1-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; WA 4053/1-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; },
mesh = {*Oxidation-Reduction ; *Carbon Dioxide/metabolism ; *Ethane/metabolism/chemistry ; Archaea/metabolism/genetics ; Aldehyde Oxidoreductases/metabolism/genetics/chemistry ; Multienzyme Complexes/metabolism/genetics/chemistry ; Crystallography, X-Ray ; Archaeal Proteins/metabolism/genetics/chemistry ; Anaerobiosis ; Ferredoxins/metabolism ; Riboflavin/analogs & derivatives ; },
abstract = {The anaerobic oxidation of alkanes is a microbial process that mitigates the flux of hydrocarbon seeps into the oceans. In marine archaea, the process depends on sulphate-reducing bacterial partners to exhaust electrons, and it is generally assumed that the archaeal CO2-forming enzymes (CO dehydrogenase and formylmethanofuran dehydrogenase) are coupled to ferredoxin reduction. Here, we study the molecular basis of the CO2-generating steps of anaerobic ethane oxidation by characterising native enzymes of the thermophile Candidatus Ethanoperedens thermophilum obtained from microbial enrichment. We perform biochemical assays and solve crystal structures of the CO dehydrogenase and formylmethanofuran dehydrogenase complexes, showing that both enzymes deliver electrons to the F420 cofactor. Both multi-metalloenzyme harbour electronic bridges connecting CO and formylmethanofuran oxidation centres to a bound flavin-dependent F420 reductase. Accordingly, both systems exhibit robust coupled F420-reductase activities, which are not detected in the cell extract of related methanogens and anaerobic methane oxidisers. Based on the crystal structures, enzymatic activities, and metagenome mining, we propose a model in which the catabolic oxidising steps would wire electron delivery to F420 in this organism. Via this specific adaptation, the indirect electron transfer from reduced F420 to the sulphate-reducing partner would fuel energy conservation and represent the driving force of ethanotrophy.},
}
@article {pmid39413712,
year = {2024},
author = {Wang, M and Peñuelas, J and Sardans, J and Zeng, Q and Song, Z and Zhou, J and Xu, X and Zhou, X and Fang, Y and Vancov, T and Wang, W},
title = {Conversion of coastal marsh to aquaculture ponds decreased the potential of methane production by altering soil chemical properties and methanogenic archaea community structure.},
journal = {Water research},
volume = {268},
number = {Pt A},
pages = {122608},
doi = {10.1016/j.watres.2024.122608},
pmid = {39413712},
issn = {1879-2448},
abstract = {Coastal wetlands are among the most productive and dynamic ecosystems globally, contributing significantly to atmospheric methane (CH4) emissions. The widespread conversion of these wetlands into aquaculture ponds degrades these ecosystems, yet its effects on CH4 production and associated microbial mechanisms are not well understood. This study aimed to assess the impact of land conversion on CH4 production potential, total and active soil organic C (SOC) content, and microbial communities. We conducted a comparative study on three brackish marshes and adjacent aquaculture ponds in southeastern China. Compared to costal marshes, aquaculture ponds exhibited significantly (P < 0.05) lower CH4 production potential (0.05 vs. 0.02 μg kg[-1] h[-1]), SOC (17.64 vs. 6.97 g kg[-1]), total nitrogen (TN) content (1.62 vs. 1.24 g kg[-1]) and carbon/nitrogen (C/N) ratio (10.85 vs. 5.66). CH4 production potential in aquaculture ponds was influenced by both microbial and abiotic factors. Specifically, the relative abundance of Methanosarcina slightly decreased in aquaculture ponds, while the potential for CH4 production declined with lower SOC contents and C/N ratio. Overall, our findings demonstrate that converting natural coastal marshes into aquaculture ponds reduces CH4 production by altering key soil properties and the structure and diversity of methanogenic archaea communities. These results provide empirical evidence to enhance global carbon models, improving predictions of carbon feedback from wetland land conversion in the context of climate change.},
}
@article {pmid39406503,
year = {2024},
author = {Valentin-Alvarado, LE and Shi, LD and Appler, KE and Crits-Christoph, A and De Anda, V and Adler, BA and Cui, ML and Ly, L and Leão, P and Roberts, RJ and Sachdeva, R and Baker, BJ and Savage, DF and Banfield, JF},
title = {Complete genomes of Asgard archaea reveal diverse integrated and mobile genetic elements.},
journal = {Genome research},
volume = {},
number = {},
pages = {},
doi = {10.1101/gr.279480.124},
pmid = {39406503},
issn = {1549-5469},
abstract = {Asgard archaea are of great interest as the progenitors of Eukaryotes, but little is known about the mobile genetic elements (MGEs) that may shape their ongoing evolution. Here, we describe MGEs that replicate in Atabeyarchaeia, a wetland Asgard archaea lineage represented by two complete genomes. We used soil depth-resolved population metagenomic data sets to track 18 MGEs for which genome structures were defined and precise chromosome integration sites could be identified for confident host linkage. Additionally, we identified a complete 20.67 kbp circular plasmid and two family-level groups of viruses linked to Atabeyarchaeia, via CRISPR spacer targeting. Closely related 40 kbp viruses possess a hypervariable genomic region encoding combinations of specific genes for small cysteine-rich proteins structurally similar to restriction-homing endonucleases. One 10.9 kbp integrative conjugative element (ICE) integrates genomically into the Atabeyarchaeum deiterrae-1 chromosome and has a 2.5 kbp circularizable element integrated within it. The 10.9 kbp ICE encodes an expressed Type IIG restriction-modification system with a sequence specificity matching an active methylation motif identified by Pacific Biosciences (PacBio) high-accuracy long-read (HiFi) metagenomic sequencing. Restriction-modification of Atabeyarchaeia differs from that of another coexisting Asgard archaea, Freyarchaeia, which has few identified MGEs but possesses diverse defense mechanisms, including DISARM and Hachiman, not found in Atabeyarchaeia. Overall, defense systems and methylation mechanisms of Asgard archaea likely modulate their interactions with MGEs, and integration/excision and copy number variation of MGEs in turn enable host genetic versatility.},
}
@article {pmid39404452,
year = {2024},
author = {Villa, EA and Escalante-Semerena, JC},
title = {Corrinoid salvaging and cobamide remodeling in bacteria and archaea.},
journal = {Journal of bacteriology},
volume = {},
number = {},
pages = {e0028624},
doi = {10.1128/jb.00286-24},
pmid = {39404452},
issn = {1098-5530},
abstract = {Cobamides (Cbas) are cobalt-containing cyclic tetrapyrroles used by cells from all domains of life as co-catalyst of diverse reactions. There are several structural features that distinguish Cbas from one another. The most relevant of those features discussed in this review is the lower ligand, which is the nucleobase of a ribotide located in the lower face of the cyclic tetrapyrrole ring. The above-mentioned ribotide is known as the nucleotide loop, which is attached to the ring by a short linker. In Cbas, the nucleobase of the ribotide can be benzimidazole or derivatives of it, purine or derivatives of it, or phenolic compounds. Given the importance of Cbas in prokaryotic metabolism, it is not surprising that prokaryotes have evolved enzymes that cleave part or the entire nucleotide loop. This function is advantageous when Cbas contain nucleobases that somehow interfere with the function of Cba-dependent enzymes in the organism. After cleavage, Cbas are rebuilt via the nucleotide loop assembly (NLA) pathway, which includes enzymes that activate the nucleobase and the ring intermediate, followed by condensation of activated intermediates and a final dephosphorylation reaction. This exchange of nucleobases is known as Cba remodeling. The NLA pathway is used to salvage Cba precursors from the environment.},
}
@article {pmid39402493,
year = {2024},
author = {Bobbo, T and Biscarini, F and Yaddehige, SK and Alberghini, L and Rigoni, D and Bianchi, N and Taccioli, C},
title = {Machine learning classification of archaea and bacteria identifies novel predictive genomic features.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {955},
pmid = {39402493},
issn = {1471-2164},
mesh = {*Archaea/genetics/classification ; *Machine Learning ; *Bacteria/genetics/classification ; *Genomics/methods ; *Genome, Archaeal ; Genome, Bacterial ; RNA, Transfer/genetics ; Phylogeny ; },
abstract = {BACKGROUND: Archaea and Bacteria are distinct domains of life that are adapted to a variety of ecological niches. Several genome-based methods have been developed for their accurate classification, yet many aspects of the specific genomic features that determine these differences are not fully understood. In this study, we used publicly available whole-genome sequences from bacteria (N = 2546) and archaea (N = 109). From these, a set of genomic features (nucleotide frequencies and proportions, coding sequences (CDS), non-coding, ribosomal and transfer RNA genes (ncRNA, rRNA, tRNA), Chargaff's, topological entropy and Shannon's entropy scores) was extracted and used as input data to develop machine learning models for the classification of archaea and bacteria.<br><br>RESULTS: The classification accuracy ranged from 0.993 (Random Forest) to 0.998 (Neural Networks). Over the four models, only 11 examples were misclassified, especially those belonging to the minority class (Archaea). From variable importance, tRNA topological and Shannon's entropy, nucleotide frequencies in tRNA, rRNA and ncRNA, CDS, tRNA and rRNA Chargaff's scores have emerged as the top discriminating factors. In particular, tRNA entropy (both topological and Shannon's) was the most important genomic feature for classification, pointing at the complex interactions between the genetic code, tRNAs and the translational machinery.<br><br>CONCLUSIONS: tRNA, rRNA and ncRNA genes emerged as the key genomic elements that underpin the classification of archaea and bacteria. In particular, higher nucleotide diversity was found in tRNA from bacteria compared to archaea. The analysis of the few classification errors reflects the complex phylogenetic relationships between bacteria, archaea and eukaryotes.},
}
@article {pmid39390113,
year = {2024},
author = {Nagar, DN and Mani, K and Braganca, JM},
title = {Author Correction: Genomic insights on carotenoid synthesis by extremely halophilic archaea Haloarcularubripromontorii BS2, Haloferaxlucentense BBK2 and Halogeometricumborinquense E3 isolated from the solar salterns of India.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {23750},
doi = {10.1038/s41598-024-74079-z},
pmid = {39390113},
issn = {2045-2322},
}
@article {pmid39383165,
year = {2024},
author = {, },
title = {Correction: A Versatile Medium for Cultivating Methanogenic Archaea.},
journal = {PloS one},
volume = {19},
number = {10},
pages = {e0312093},
pmid = {39383165},
issn = {1932-6203},
abstract = {[This corrects the article DOI: 10.1371/journal.pone.0061563.].},
}
@article {pmid39363002,
year = {2024},
author = {Mühling, L and Baur, T and Molitor, B},
title = {Methanothermobacter thermautotrophicus and Alternative Methanogens: Archaea-Based Production.},
journal = {Advances in biochemical engineering/biotechnology},
volume = {},
number = {},
pages = {},
pmid = {39363002},
issn = {0724-6145},
abstract = {Methanogenic archaea convert bacterial fermentation intermediates from the decomposition of organic material into methane. This process has relevance in the global carbon cycle and finds application in anthropogenic processes, such as wastewater treatment and anaerobic digestion. Furthermore, methanogenic archaea that utilize hydrogen and carbon dioxide as substrates are being employed as biocatalysts for the biomethanation step of power-to-gas technology. This technology converts hydrogen from water electrolysis and carbon dioxide into renewable natural gas (i.e., methane). The application of methanogenic archaea in bioproduction beyond methane has been demonstrated in only a few instances and is limited to mesophilic species for which genetic engineering tools are available. In this chapter, we discuss recent developments for those existing genetically tractable systems and the inclusion of novel genetic tools for thermophilic methanogenic species. We then give an overview of recombinant bioproduction with mesophilic methanogenic archaea and thermophilic non-methanogenic microbes. This is the basis for discussing putative products with thermophilic methanogenic archaea, specifically the species Methanothermobacter thermautotrophicus. We give estimates of potential conversion efficiencies for those putative products based on a genome-scale metabolic model for M. thermautotrophicus.},
}
@article {pmid39360821,
year = {2024},
author = {Han, S and Kim, S and Sedlacek, CJ and Farooq, A and Song, C and Lee, S and Liu, S and Brüggemann, N and Rohe, L and Kwon, M and Rhee, S-K and Jung, M-Y},
title = {Adaptive traits of Nitrosocosmicus clade ammonia-oxidizing archaea.},
journal = {mBio},
volume = {},
number = {},
pages = {e0216924},
doi = {10.1128/mbio.02169-24},
pmid = {39360821},
issn = {2150-7511},
abstract = {UNLABELLED: Nitrification is a core process in the global nitrogen (N) cycle mediated by ammonia-oxidizing microorganisms, including ammonia-oxidizing archaea (AOA) as a key player. Although much is known about AOA abundance and diversity across environments, the genetic drivers of the ecophysiological adaptations of the AOA are often less clearly defined. This is especially true for AOA within the genus Nitrosocosmicus, which have several unique physiological traits (e.g., high substrate tolerance, low substrate affinity, and large cell size). To better understand what separates the physiology of Nitrosocosmicus AOA, we performed comparative genomics with genomes from 39 cultured AOA, including five Nitrosocosmicus AOA. The absence of a canonical high-affinity type ammonium transporter and typical S-layer structural genes was found to be conserved across all Nitrosocosmicus AOA. In agreement, cryo-electron tomography confirmed the absence of a visible outermost S-layer structure, which has been observed in other AOA. In contrast to other AOA, the cryo-electron tomography highlighted the possibility that Nitrosocosmicus AOA may possess a glycoprotein or glycolipid-based glycocalyx cell covering outer layer. Together, the genomic, physiological, and metabolic properties revealed in this study provide insight into niche adaptation mechanisms and the overall ecophysiology of members of the Nitrosocosmicus clade in various terrestrial ecosystems.<br><br>IMPORTANCE: Nitrification is a vital process within the global biogeochemical nitrogen cycle but plays a significant role in the eutrophication of aquatic ecosystems and the production of the greenhouse gas nitrous oxide (N2O) from industrial agriculture ecosystems. While various types of ammonia-oxidizing microorganisms play a critical role in the N cycle, ammonia-oxidizing archaea (AOA) are often the most abundant nitrifiers in natural environments. Members of the genus Nitrosocosmicus are one of the prevalent AOA groups detected in undisturbed terrestrial ecosystems and have previously been reported to possess a range of physiological characteristics that set their physiology apart from other AOA species. This study provides significant progress in understanding these unique physiological traits and their genetic drivers. Our results highlight how physiological studies based on comparative genomics-driven hypotheses can contribute to understanding the unique niche of Nitrosocosmicus AOA.},
}
@article {pmid39359677,
year = {2024},
author = {Pereira, O and Qin, W and Galand, PE and Debroas, D and Lami, R and Hochart, C and Zhou, Y and Zhou, J and Zhang, C},
title = {Metabolic activities of marine ammonia-oxidizing archaea orchestrated by quorum sensing.},
journal = {mLife},
volume = {3},
number = {3},
pages = {417-429},
pmid = {39359677},
issn = {2770-100X},
abstract = {Ammonia-oxidizing archaea (AOA) play crucial roles in marine carbon and nitrogen cycles by fixing inorganic carbon and performing the initial step of nitrification. Evaluation of carbon and nitrogen metabolism popularly relies on functional genes such as amoA and accA. Increasing studies suggest that quorum sensing (QS) mainly studied in biofilms for bacteria may serve as a universal communication and regulatory mechanism among prokaryotes; however, this has yet to be demonstrated in marine planktonic archaea. To bridge this knowledge gap, we employed a combination of metabolic activity markers (amoA, accA, and grs) to elucidate the regulation of AOA-mediated nitrogen, carbon processes, and their interactions with the surrounding heterotrophic population. Through co-transcription investigations linking metabolic markers to potential key QS genes, we discovered that QS molecules could regulate AOA's carbon, nitrogen, and lipid metabolisms under different conditions. Interestingly, specific AOA ecotypes showed a preference for employing distinct QS systems and a distinct QS circuit involving a typical population. Overall, our data demonstrate that QS orchestrates nitrogen and carbon metabolism, including the exchange of organic metabolites between AOA and surrounding heterotrophic bacteria, which has been previously overlooked in marine AOA research.},
}
@article {pmid39348174,
year = {2024},
author = {Lehtovirta-Morley, LE and Ge, C and Ross, J and Yao, H and Hazard, C and Gubry-Rangin, C and Prosser, JI and Nicol, GW},
title = {Nitrosotalea devaniterrae gen. nov., sp. nov. and Nitrosotalea sinensis sp. nov., two acidophilic ammonia oxidising archaea isolated from acidic soil, and proposal of the new order Nitrosotaleales ord. nov. within the class Nitrososphaeria of the phylum Nitrososphaerota.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {74},
number = {9},
pages = {},
doi = {10.1099/ijsem.0.006387},
pmid = {39348174},
issn = {1466-5034},
mesh = {*Soil Microbiology ; *Phylogeny ; *Base Composition ; *RNA, Ribosomal, 16S/genetics ; *Sequence Analysis, DNA ; *Ammonia/metabolism ; *DNA, Archaeal/genetics ; *Oxidation-Reduction ; China ; Archaea/classification/genetics/isolation &amp; purification ; Hydrogen-Ion Concentration ; Nitrites/metabolism ; Chemoautotrophic Growth ; },
abstract = {Two obligately acidophilic, mesophilic and aerobic soil ammonia-oxidising archaea were isolated from a pH 4.5 arable sandy loam (UK) and pH 4.7 acidic sulphate paddy soil (PR China) and designated strains Nd1[T] and Nd2[T], respectively. The strains shared more than 99 % 16S rRNA gene sequence identity and their genomes were both less than 2 Mb in length, sharing 79 % average nucleotide identity, 81 % average amino acid identity and a DNA G+C content of approximately 37 mol%. Both strains were chemolithotrophs that fixed carbon dioxide and gained energy by oxidising ammonia to nitrite, with no evidence of mixotrophic growth. Neither strain was capable of using urea as a source of ammonia. Both strains were non-motile in culture, although Nd1[T] does possess genes encoding flagella components and therefore may be motile under certain conditions. Cells of Nd1[T] were small angular rods 0.5-1 µm in length and grew at pH 4.2-5.6 and at 20-30 °C. Cells of Nd1[T] were small angular rods 0.5-1 µm in length and grew at pH 4.0-6.1 and at 20-42 °C. Nd1[T] and Nd2[T] are distinct with respect to genomic and physiological features and are assigned as the type strains for the species Nitrosotalea devaniterrae sp. nov. (type strain, Nd1[T]=NCIMB 15248[T]=DSM 110862[T]) and Nitrosotalea sinensis sp. nov. (type strain, Nd2[T]=NCIMB 15249[T]=DSM 110863[T]), respectively, within the genus Nitrosotalea gen. nov. The family Nitrosotaleaceae fam. nov. and order Nitrosotaleales ord. nov. are also proposed officially.},
}
@article {pmid39304533,
year = {2024},
author = {Zhang, QK and Zhu, LR and Dong, XY and Yang, XY and Hou, J and Cui, HL},
title = {Salinirarus marinus gen. nov., sp. nov., Haloplanus salilacus sp. nov., Haloplanus pelagicus sp. nov., Haloplanus halophilus sp. nov., Haloplanus halobius sp. nov., halophilic archaea isolated from commercial coarse salts with potential as starter cultures for salt-fermented foods.},
journal = {FEMS microbiology letters},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsle/fnae075},
pmid = {39304533},
issn = {1574-6968},
abstract = {Five halophilic archaeal strains, XH8T, CK5-1T, GDY1T, HW8-1T, and XH21T, were isolated from commercial coarse salt produced in different regions of China. Their 16S rRNA and rpoB' gene sequences indicated that four of the strains (CK5-1T, GDY1T, HW8-1T, and XH21T) represent distinct species within the genus Haloplanus (family Haloferacaceae), while strain XH8T represents a novel genus within the same family. These assignments were supported by phylogenetic and phylogenomic analyses, which showed that strains CK5-1T, GDY1T, HW8-1T, and XH21T cluster with the current species of the genus Haloplanus, while strain XH8T forms a separate branch from the genus Haloplanus. The digital DNA-DNA hybridization and average amino acid identity (AAI) values among these four strains and the current members of the genus Haloplanus were 23.1-35.2% and 75.9-83.8%, respectively; and those values between strain XH8T and other genera in the family Haloferacaceae were 18.8-33.6% and 59.8-66.6%, respectively, much lower than the threshold values for species demarcation. Strain XH8T may represent a novel genus of the family Haloferacaceae according to the cut-off value of AAI (≤72.1%) proposed to differentiate genera within the family Haloferacaceae. These five strains could be distinguished from the related species according to differential phenotypic characteristics. Based on these results, it is proposed that strain XH8T represents a novel genus within the family Haloferacaceae, and strains CK5-1T, GDY1T, HW8-1T, and XH21T represent four novel species of the genus Haloplanus, respectively. Additionally, these five strains possess genes encoding enzymes critical for the fermentation process in salt-fermented foods, indicating their potential as starter cultures for these applications.},
}
@article {pmid39300577,
year = {2024},
author = {Lezcano, M&#xc1; and Bornemann, TLV and Sánchez-García, L and Carrizo, D and Adam, PS and Esser, SP and Cabrol, NA and Probst, AJ and Parro, V},
title = {Hyperexpansion of genetic diversity and metabolic capacity of extremophilic bacteria and archaea in ancient Andean lake sediments.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {176},
pmid = {39300577},
issn = {2049-2618},
support = {FJC2018-037246-I//Spanish Ministry of Science and Innovation/State Agency of Research/ ; RYC2018-023943-I//Spanish Ministry of Science and Innovation/State Agency of Research/ ; RYC-2014-19446//Spanish Ministry of Science and Innovation/State Agency of Research/ ; RTI2018-094368-B-I0//Spanish Ministry of Science and Innovation/State Agency of Research/ ; PEJD-2017- POST/TIC-4119//Spanish Ministry of Science and Innovation/State Agency of Research (EU Youth Employment Initiative)/ ; NAI-CAN7, 13NAI7_2-0018//NASA Astrobiology Institute/ ; DFG PR1603/2-1//German Research Foundation/ ; 161L0285E//German Federal Ministry of Education and Research/ ; },
mesh = {*Lakes/microbiology ; *Archaea/genetics/metabolism/classification ; *Geologic Sediments/microbiology ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; *Genetic Variation ; Chile ; Phylogeny ; Microbiota ; Extremophiles/metabolism/genetics/classification ; RNA, Ribosomal, 16S/genetics ; },
abstract = {BACKGROUND: The Andean Altiplano hosts a repertoire of high-altitude lakes with harsh conditions for life. These lakes are undergoing a process of desiccation caused by the current climate, leaving terraces exposed to extreme atmospheric conditions and serving as analogs to Martian paleolake basins. Microbiomes in Altiplano lake terraces have been poorly studied, enclosing uncultured lineages and a great opportunity to understand environmental adaptation and the limits of life on Earth. Here we examine the microbial diversity and function in ancient sediments (10.3-11 kyr BP (before present)) from a terrace profile of Laguna Lejía, a sulfur- and metal/metalloid-rich saline lake in the Chilean Altiplano. We also evaluate the physical and chemical changes of the lake over time by studying the mineralogy and geochemistry of the terrace profile.<br><br>RESULTS: The mineralogy and geochemistry of the terrace profile revealed large water level fluctuations in the lake, scarcity of organic carbon, and high concentration of SO4[2-]-S, Na, Cl and Mg. Lipid biomarker analysis indicated the presence of aquatic/terrestrial plant remnants preserved in the ancient sediments, and genome-resolved metagenomics unveiled a diverse prokaryotic community with still active microorganisms based on in silico growth predictions. We reconstructed 591 bacterial and archaeal metagenome-assembled genomes (MAGs), of which 98.8% belonged to previously unreported species. The most abundant and widespread metabolisms among MAGs were the reduction and oxidation of S, N, As, and halogenated compounds, as well as aerobic CO oxidation, possibly as a key metabolic trait in the organic carbon-depleted sediments. The broad redox and CO2 fixation pathways among phylogenetically distant bacteria and archaea extended the knowledge of metabolic capacities to previously unknown taxa. For instance, we identified genomic potential for dissimilatory sulfate reduction in Bacteroidota and &#x3b1;- and &#x3b3;-Proteobacteria, predicted an enzyme for ammonia oxidation in a novel Actinobacteriota, and predicted enzymes of the Calvin-Benson-Bassham cycle in Planctomycetota, Gemmatimonadota, and Nanoarchaeota.<br><br>CONCLUSIONS: The high number of novel bacterial and archaeal MAGs in the Laguna Lej&#xed;a indicates the wide prokaryotic diversity discovered. In addition, the detection of genes in unexpected taxonomic groups has significant implications for the expansion of microorganisms involved in the biogeochemical cycles of carbon, nitrogen, and sulfur. Video Abstract.},
}
@article {pmid39299940,
year = {2024},
author = {Obayori, OS and Salam, LB and Ashade, AO and Oseni, TD and Kalu, MD and Mustapha, FM},
title = {An animal charcoal contaminated cottage industry soil highlighted by halophilic archaea dominance and decimation of bacteria.},
journal = {World journal of microbiology &amp; biotechnology},
volume = {40},
number = {10},
pages = {327},
pmid = {39299940},
issn = {1573-0972},
mesh = {*Metals, Heavy/analysis ; *Soil Microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; *Archaea/classification/genetics/isolation &amp; purification/metabolism ; *Charcoal ; *Soil Pollutants/analysis ; *Soil/chemistry ; Nigeria ; High-Throughput Nucleotide Sequencing ; Animals ; Hydrocarbons/metabolism/analysis ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; },
abstract = {An animal charcoal contaminated cottage industry soil in Lagos, Nigeria (ACGT) was compared in an ex post facto study with a nearby unimpacted soil (ACGC). Hydrocarbon content was higher than regulatory limits in ACGT (180.2 mg/kg) but lower in ACGC (19.28 mg/kg). Heavy metals like nickel, cadmium, chromium and lead were below detection limit in ACGC. However, all these metals, except cadmium, were detected in ACGT, but at concentrations below regulatory limits. Furthermore, copper (253.205 mg/kg) and zinc (422.630 mg/kg) were above regulatory limits in ACGT. Next generation sequencing revealed that the procaryotic community was dominated by bacteria in ACGC (62%) while in ACGT archaea dominated (76%). Dominant phyla in ACGC were Euryarchaeota (37%), Pseudomonadota (16%) and Actinomycetota (12%). In ACGT it was Euryarchaeota (76%), Bacillota (9%), Pseudomonadota (7%) and Candidatus Nanohaloarchaeota (5%). Dominant Halobacteria genera in ACGT were Halobacterium (16%), Halorientalis (16%), unranked halophilic archaeon (13%) Salarchaeum (6%) and Candidatus Nanohalobium (5%), whereas ACGC showed greater diversity dominated by bacterial genera Salimicrobium (7%) and Halomonas (3%). Heavy metals homeostasis genes, especially for copper, were fairly represented in both soils but with bacterial taxonomic affiliations. Sites like ACGT, hitherto poorly studied and understood, could be sources of novel bioresources.},
}
@article {pmid39296579,
year = {2024},
author = {Vershinin, Z and Zaretsky, M and Eichler, J},
title = {N-glycosylation in Archaea - Expanding the process, components and roles of a universal post-translational modification.},
journal = {BBA advances},
volume = {6},
number = {},
pages = {100120},
pmid = {39296579},
issn = {2667-1603},
abstract = {While performed by all three domains of life, N-glycosylation in Archaea is less well described than are the parallel eukaryal and bacterial processes. Still, what is known of the archaeal version of this universal post-translational modification reveals numerous seemingly domain-specific traits. Specifically, the biosynthesis of archaeal N-linked glycans relies on distinct pathway steps and components, rare sugars and sugar modifications, as well as unique lipid carriers upon which N-linked glycans are assembled. At the same time, Archaea possess the apparently unique ability to simultaneously modify their glycoproteins with very different N-linked glycans. In addition to these biochemical aspects of archaeal N-glycosylation, such post-translational modification has been found to serve a wide range of roles possibly unique to Archaea, including allowing these microorganisms to not only cope with the harsh physical conditions of the niches they can inhabit but also providing the ability to adapt to transient changes in such environments.},
}
@article {pmid39296305,
year = {2024},
author = {Hernández-Magaña, E and Kraft, B},
title = {Nitrous oxide production and consumption by marine ammonia-oxidizing archaea under oxygen depletion.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1410251},
pmid = {39296305},
issn = {1664-302X},
abstract = {Ammonia-oxidizing archaea (AOA) are key players in the nitrogen cycle and among the most abundant microorganisms in the ocean, thriving even in oxygen-depleted ecosystems. AOA produce the greenhouse gas nitrous oxide (N2O) as a byproduct of ammonia oxidation. Additionally, the recent discovery of a nitric oxide dismutation pathway in the AOA isolate Nitrosopumilus maritimus points toward other N2O production and consumption pathways in AOA. AOA that perform NO dismutation when exposed to oxygen depletion, produce oxygen and dinitrogen as final products. Based on the transient accumulation of N2O coupled with oxygen accumulation, N2O has been proposed as an intermediate in this novel archaeal pathway. In this study, we spiked N2O to oxygen-depleted incubations with pure cultures of two marine AOA isolates that were performing NO dismutation. By using combinations of N compounds with different isotopic signatures ([15]NO2 [-] pool +[44]N2O spike and [14]NO2 [-] pool +[46]N2O spike), we evaluated the N2O spike effects on the production of oxygen and the isotopic signature of N2 and N2O. The experiments confirmed that N2O is an intermediate in NO dismutation by AOA, distinguishing it from similar pathways in other microbial clades. Furthermore, we showed that AOA rapidly reduce high concentrations of spiked N2O to N2. These findings advance our understanding of microbial N2O production and consumption in oxygen-depleted settings and highlight AOA as potentially important key players in N2O turnover.},
}
@article {pmid39287442,
year = {2024},
author = {Mattick, JSA and Bromley, RE and Watson, KJ and Adkins, RS and Holt, CI and Lebov, JF and Sparklin, BC and Tyson, TS and Rasko, DA and Dunning Hotopp, JC},
title = {Deciphering transcript architectural complexity in bacteria and archaea.},
journal = {mBio},
volume = {15},
number = {10},
pages = {e0235924},
pmid = {39287442},
issn = {2150-7511},
abstract = {RNA transcripts are potential therapeutic targets, yet bacterial transcripts have uncharacterized biodiversity. We developed an algorithm for transcript prediction called tp.py using it to predict transcripts (mRNA and other RNAs) in Escherichia coli K12 and E2348/69 strains (Bacteria:gamma-Proteobacteria), Listeria monocytogenes strains Scott A and RO15 (Bacteria:Firmicute), Pseudomonas aeruginosa strains SG17M and NN2 strains (Bacteria:gamma-Proteobacteria), and Haloferax volcanii (Archaea:Halobacteria). From >5 million E. coli K12 and >3 million E. coli E2348/69 newly generated Oxford Nanopore Technologies direct RNA sequencing reads, 2,487 K12 mRNAs and 1,844 E2348/69 mRNAs were predicted, with the K12 mRNAs containing more than half of the predicted E. coli K12 proteins. While the number of predicted transcripts varied by strain based on the amount of sequence data used, across all strains examined, the predicted average size of the mRNAs was 1.6-1.7 kbp, while the median size of the 5'- and 3'-untranslated regions (UTRs) were 30-90 bp. Given the lack of bacterial and archaeal transcript annotation, most predictions were of novel transcripts, but we also predicted many previously characterized mRNAs and ncRNAs, including post-transcriptionally generated transcripts and small RNAs associated with pathogenesis in the E. coli E2348/69 LEE pathogenicity islands. We predicted small transcripts in the 100-200 bp range as well as >10 kbp transcripts for all strains, with the longest transcript for two of the seven strains being the nuo operon transcript, and for another two strains it was a phage/prophage transcript. This quick, easy, and reproducible method will facilitate the presentation of transcripts, and UTR predictions alongside coding sequences and protein predictions in bacterial genome annotation as important resources for the research community.IMPORTANCEOur understanding of bacterial and archaeal genes and genomes is largely focused on proteins since there have only been limited efforts to describe bacterial/archaeal RNA diversity. This contrasts with studies on the human genome, where transcripts were sequenced prior to the release of the human genome over two decades ago. We developed software for the quick, easy, and reproducible prediction of bacterial and archaeal transcripts from Oxford Nanopore Technologies direct RNA sequencing data. These predictions are urgently needed for more accurate studies examining bacterial/archaeal gene regulation, including regulation of virulence factors, and for the development of novel RNA-based therapeutics and diagnostics to combat bacterial pathogens, like those with extreme antimicrobial resistance.},
}
@article {pmid39281633,
year = {2024},
author = {Ben Hamad Bouhamed, S and Chaari, M and Baati, H and Zouari, S and Ammar, E},
title = {Extreme halophilic Archaea: Halobacterium salinarum carotenoids characterization and antioxidant properties.},
journal = {Heliyon},
volume = {10},
number = {17},
pages = {e36832},
pmid = {39281633},
issn = {2405-8440},
abstract = {Important marine microorganisms are resources of renewable energy that may face global population growth and needs. The application of biomass metabolites, such as carotenoids and their derivatives, may solve some agro-food health problems. Herein, a new halophilic Archaea Halobacterium salinarum producing carotenoid was screened from a Tunisian solar Saltworks (Sfax). The identification of the carotenoid pigments was carried out using HPLC-MS/MS. The predominant pigments produced by this Halobacterium were bacterioruberin and its derivatives and the carotenoids production was found to be of 21.51 mg/mL. Moreover, the data revealed that the carotenoids extract exhibited a high antioxidant activity across four oxidizing assays. The present results suggested that carotenoids extracted from halophilic Archaea are interesting sources of natural antioxidants for future innovative applications in agro-food, cosmetic and health fields.},
}
@article {pmid39215524,
year = {2024},
author = {Chatziargyri, AG and Stasi, EA and Tsirigos, KI and Litou, ZI and Iconomidou, VA and Bagos, PG},
title = {CW-PRED: Prediction of C-terminal surface anchoring sorting signals in bacteria and Archaea.},
journal = {Journal of bioinformatics and computational biology},
volume = {22},
number = {4},
pages = {2450021},
doi = {10.1142/S0219720024500215},
pmid = {39215524},
issn = {1757-6334},
mesh = {*Protein Sorting Signals ; *Bacterial Proteins/metabolism/chemistry/genetics ; *Archaeal Proteins/metabolism/chemistry/genetics ; Archaea/metabolism/genetics ; Computational Biology/methods ; Cell Wall/metabolism/chemistry ; Markov Chains ; Amino Acid Motifs ; Software ; Bacteria/metabolism/genetics ; Algorithms ; },
abstract = {Sorting signals are crucial for the anchoring of proteins to the cell surface in archaea and bacteria. These proteins often feature distinct motifs at their C-terminus, cleaved by sortase or sortase-like enzymes. Gram-positive bacteria exhibit the LPXTGX consensus motif, cleaved by sortases, while Gram-negative bacteria employ exosortases recognizing motifs like PEP. Archaea utilize exosortase homologs known as archaeosortases for signal anchoring. Traditionally identification of such C-terminal sorting signals was performed with profile Hidden Markov Models (pHMMs). The Cell-Wall PREDiction (CW-PRED) method introduced for the first time a custom-made class HMM for proteins in Gram-positive bacteria that contain a cell wall sorting signal which begins with an LPXTG motif, followed by a hydrophobic domain and a tail of positively charged residues. Here we present a new and updated version of CW-PRED for predicting C-terminal sorting signals in Archaea, Gram-positive, and Gram-negative bacteria. We used a large training set and several model enhancements that improve motif identification in order to achieve better discrimination between C-terminal signals and other proteins. Cross-validation demonstrates CW-PRED's superiority in sensitivity and specificity compared to other methods. Application of the method in reference proteomes reveals a large number of potential surface proteins not previously identified. The method is available for academic use at http://195.251.108.230/apps.compgen.org/CW-PRED/ and as standalone software.},
}
@article {pmid39215388,
year = {2024},
author = {Tejedor-Sanz, S and Song, YE and Sundstrom, ER},
title = {Utilization of formic acid by extremely thermoacidophilic archaea species.},
journal = {Microbial biotechnology},
volume = {17},
number = {9},
pages = {e70003},
pmid = {39215388},
issn = {1751-7915},
support = {CW367480//Energy Biosciences Institute/ ; },
mesh = {*Formates/metabolism ; Sulfolobales/metabolism/genetics ; },
abstract = {The exploration of novel hosts with the ability to assimilate formic acid, a C1 substrate that can be produced from renewable electrons and CO2, is of great relevance for developing novel and sustainable biomanufacturing platforms. Formatotrophs can use formic acid or formate as a carbon and/or reducing power source. Formatotrophy has typically been studied in neutrophilic microorganisms because formic acid toxicity increases in acidic environments below the pKa of 3.75 (25°C). Because of this toxicity challenge, utilization of formic acid as either a carbon or energy source has been largely unexplored in thermoacidophiles, species that possess the ability to produce a variety of metabolites and enzymes of high biotechnological relevance. Here we investigate the capacity of several thermoacidophilic archaea species from the Sulfolobales order to tolerate and metabolize formic acid. Metallosphaera prunae, Sulfolobus metallicus and Sulfolobus acidocaldarium were found to metabolize and grow with 1-2 mM of formic acid in batch cultivations. Formic acid was co-utilized by this species alongside physiological electron donors, including ferrous iron. To enhance formic acid utilization while maintaining aqueous concentrations below the toxicity threshold, we developed a bioreactor culturing method based on a sequential formic acid feeding strategy. By dosing small amounts of formic acid sequentially and feeding H2 as co-substrate, M. prunae could utilize a total of 16.3 mM of formic acid and grow to higher cell densities than when H2 was supplied as a sole electron donor. These results demonstrate the viability of culturing thermoacidophilic species with formic acid as an auxiliary substrate in bioreactors to obtain higher cell densities than those yielded by conventional autotrophic conditions. Our work underscores the significance of formic acid metabolism in extreme habitats and holds promise for biotechnological applications in the realm of sustainable energy production and environmental remediation.},
}
@article {pmid39215047,
year = {2024},
author = {Nagar, DN and Mani, K and Braganca, JM},
title = {Genomic insights on carotenoid synthesis by extremely halophilic archaea Haloarcula rubripromontorii BS2, Haloferax lucentense BBK2 and Halogeometricum borinquense E3 isolated from the solar salterns of India.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {20214},
pmid = {39215047},
issn = {2045-2322},
support = {(Level III) BT/INF/22/SP2543/2021//Department of Biotechnology, Ministry of Science and Technology, India/ ; 2023-24//DSTE&amp;WM, Government of Goa/ ; },
mesh = {*Carotenoids/metabolism ; India ; *Phylogeny ; *Haloferax/genetics/metabolism ; *Haloarcula/genetics/metabolism ; Genome, Archaeal ; Whole Genome Sequencing ; RNA, Ribosomal, 16S/genetics ; Halobacteriaceae/genetics/metabolism/isolation &amp; purification/classification ; Genomics/methods ; Base Composition ; },
abstract = {Haloarchaeal cultures were isolated from solar salterns of Goa and Tamil Nadu and designated as BS2, BBK2 and E3. These isolates grew with a characteristic bright orange to pink pigmentation and were capable of growing in media containing upto 25% (w/vol) NaCl. Whole genome sequencing (WGS) of the three haloarchaeal strains BS2, BBK2 and E3 indicated an assembled genomic size of 4.1 Mb, 3.8 Mb and 4 Mb with G + C content of 61.8, 65.6 and 59.8% respectively. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that the archaeal isolates belong to Haloarcula, Haloferax and Halogeometricum genera. Haloarcula rubripromontorii BS2 was predicted to have 4292 genes with 4242 CDS regions, 46 tRNAs, 6 rRNAs and 3 misc_RNAs. In case of Haloferax lucentense BBK2,, 3840 genes with 3780 CDS regions were detected along with 52 tRNAs, 5 rRNAs and 3 misc_RNAs. Halogeometricum borinquense E3 contained 4101 genes, 4043 CDS regions, 52 tRNAs, 4 rRNAs, and 2 misc_RNAs. The functional annotation and curation of the haloarchaeal genome, revealed C50 carotenoid biosynthetic genes like phytoene desaturase/carotenoid 3' -4' desaturase (crtI), lycopene elongase (ubiA/lyeJ) and carotenoid biosynthesis membrane protein (cruF) in the three isolates. Whereas crtD (C-3',4' desaturase), crtY (lycopene cyclase) and brp/blh (β-carotene dioxygenase) genes were identified only in BS2.},
}
@article {pmid39210225,
year = {2024},
author = {da Costa Soares, S and Vezzani, FM and Favaretto, N and Auler, AC and da Silva Coelho, I and de Sousa Pires, A and Cruz, LM and de Souza, EM and Barth, G},
title = {Effect of long-term liquid dairy manure application on activity and structure of bacteria and archaea in no-till soils depends on plant in development.},
journal = {Environmental science and pollution research international},
volume = {31},
number = {42},
pages = {54713-54728},
pmid = {39210225},
issn = {1614-7499},
mesh = {*Soil Microbiology ; *Manure/microbiology ; *Archaea ; *Bacteria ; *Soil/chemistry ; RNA, Ribosomal, 16S ; Brazil ; Agriculture/methods ; Dairying ; },
abstract = {This study aimed to evaluate the impact of long-term liquid dairy manure (LDM) application on the activity and structure of soil bacterial and archaea communities in two cropping seasons over 1 year of a no-till crop rotation system. The experiment was run in a sandy clay loam texture Oxisol, in Brazil, including LDM doses of 60, 120, and 180 m[3] ha[-1] year[-1], installed in 2005. Soil sampling was conducted during spring 2018 and autumn 2019 at 0-10-cm depth. Microbial biomass carbon and nitrogen, 16S rRNA gene sequencing, microbial respiration and quotient were performed. Over the 14-year period, LDM application increased soil microbial community activity. Analysis of 16S rRNA gene sequencing revealed dominance by Proteobacteria, Acidobacteria, and Actinobacteria phyla (67% in spring and 70% in autumn). Genera Pirulla and Nitrososphaera showed enrichment at LDM doses of 120 and 180 m[3] ha[-1] year[-1] doses, respectively. During spring, following black oat cropping, shifts in the relative abundance of Bacteroidetes, Proteobacteria, Firmicutes, Gemmatimonadetes, Verrucomicrobia, Chloroflexi, Actinobacteria, and AD3 phyla were observed due to LDM application, correlating with soil chemical indicators such as pH, K, Ca, Mn, and Zn. Our findings indicate that plant development strongly influences microbial community composition, potentially outweighing the impact of LDM. Our findings indicate that the application of liquid dairy manure alters the soil bacterial activity and community; however, this effect depends on the developing plant.},
}
@article {pmid39207169,
year = {2024},
author = {Baker, BJ and Sarno, N},
title = {Small archaea may form intimate partnerships to maximize their metabolic potential.},
journal = {mBio},
volume = {15},
number = {10},
pages = {e0034724},
pmid = {39207169},
issn = {2150-7511},
abstract = {DPANN archaea have characteristically small cells and unique genomes that were long overlooked in diversity surveys. Their reduced genomes often lack essential metabolic pathways, requiring symbiotic relationships with other archaeal and bacterial hosts for survival. Yet a long-standing question remains, what is the advantage of maintaining ultrasmall cells. A recent study by Zhang et al. examined genomes of DPANN archaea from marine oxygen deficient zones (ODZs) (I. H. Zhang, B. Borer, R. Zhao, S. Wilbert, et al., mBio 15:e02918-23, 2024, https://doi.org/10.1128/mbio.02918-23). Surprisingly, these genomes contain a broad array of metabolic pathways including genes predicted to be involved in nitrous oxide (N2O) reduction. However, N2O levels are likely too low in ODZs to make this metabolically feasible. Modeling co-localization of DPANN archaea (N2O consumers) with other larger cells (N2O producers) demonstrates that N2O uptake rates can be optimized by maximizing the producer-to-consumer size ratio and proximity of consumer cells to producers. This may explain why such a diversity of archaea maintain extremely small cell sizes.},
}
@article {pmid39203380,
year = {2024},
author = {Bai, C and Wang, Q and Xu, J and Zhang, H and Huang, Y and Cai, L and Zheng, X and Yang, M},
title = {Impact of Nutrient Enrichment on Community Structure and Co-Occurrence Networks of Coral Symbiotic Microbiota in Duncanopsammia peltata: Zooxanthellae, Bacteria, and Archaea.},
journal = {Microorganisms},
volume = {12},
number = {8},
pages = {},
pmid = {39203380},
issn = {2076-2607},
support = {2022YFC3102003//the National Key Research and Development Program of China/ ; 2022ZD01//the Fund of Fujian Key Laboratory of Island Monitoring and Ecological Development (Island Research Center, MNR)/ ; 2019017//the Scientific Research Foundation of the Third Institute of Oceanography, Ministry of Natural Resources of China/ ; 41976127//the National Natural Science Foundation of China/ ; 2023J06043//the Fujian Provincial Natural Science Funds for Distinguished Young Scholar/ ; },
abstract = {Symbiotic microorganisms in reef-building corals, including algae, bacteria, archaea, fungi, and viruses, play critical roles in the adaptation of coral hosts to adverse environmental conditions. However, their adaptation and functional relationships in nutrient-rich environments have yet to be fully explored. This study investigated Duncanopsammia peltata and the surrounding seawater and sediments from protected and non-protected areas in the summer and winter in Dongshan Bay. High-throughput sequencing was used to characterize community changes, co-occurrence patterns, and factors influencing symbiotic coral microorganisms (zooxanthellae, bacteria, and archaea) in different environments. The results showed that nutrient enrichment in the protected and non-protected areas was the greatest in December, followed by the non-protected area in August. In contrast, the August protected area had the lowest nutrient enrichment. Significant differences were found in the composition of the bacterial and archaeal communities in seawater and sediments from different regions. Among the coral symbiotic microorganisms, the main dominant species of zooxanthellae is the C1 subspecies (42.22-56.35%). The dominant phyla of bacteria were Proteobacteria, Cyanobacteria, Firmicutes, and Bacteroidota. Only in the August protected area did a large number (41.98%) of SAR324_cladeMarine_group_B exist. The August protected and non-protected areas and December protected and non-protected areas contained beneficial bacteria as biomarkers. They were Nisaea, Spiroplasma, Endozoicomonas, and Bacillus. No pathogenic bacteria appeared in the protected area in August. The dominant phylum in Archaea was Crenarchaeota. These symbiotic coral microorganisms' relative abundances and compositions vary with environmental changes. The enrichment of dissolved inorganic nitrogen in environmental media is a key factor affecting the composition of coral microbial communities. Co-occurrence analysis showed that nutrient enrichment under anthropogenic disturbances enhanced the interactions between coral symbiotic microorganisms. These findings improve our understanding of the adaptations of coral holobionts to various nutritional environments.},
}
@article {pmid39194224,
year = {2024},
author = {Nakagawa, S and Sakai, HD and Shimamura, S and Takamatsu, Y and Kato, S and Yagi, H and Yanaka, S and Yagi-Utsumi, M and Kurosawa, N and Ohkuma, M and Kato, K and Takai, K},
title = {N-linked protein glycosylation in Nanobdellati (formerly DPANN) archaea and their hosts.},
journal = {Journal of bacteriology},
volume = {206},
number = {9},
pages = {e0020524},
pmid = {39194224},
issn = {1098-5530},
support = {JP 20H03322//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JP 23K20307//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; //MEXT | National Institutes of Natural Sciences (NINS)/ ; 22EXC601//MEXT | NINS | Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences (ExCELLS)/ ; },
mesh = {Glycosylation ; *Archaeal Proteins/metabolism/genetics/chemistry ; Nanoarchaeota/metabolism/genetics ; Glycoproteins/metabolism/genetics/chemistry ; Archaea/metabolism/genetics ; Polysaccharides/metabolism ; Membrane Glycoproteins ; },
abstract = {Members of the kingdom Nanobdellati, previously known as DPANN archaea, are characterized by ultrasmall cell sizes and reduced genomes. They primarily thrive through ectosymbiotic interactions with specific hosts in diverse environments. Recent successful cultivations have emphasized the importance of adhesion to host cells for understanding the ecophysiology of Nanobdellati. Cell adhesion is often mediated by cell surface carbohydrates, and in archaea, this may be facilitated by the glycosylated S-layer protein that typically coats their cell surface. In this study, we conducted glycoproteomic analyses on two co-cultures of Nanobdellati with their host archaea, as well as on pure cultures of both host and non-host archaea. Nanobdellati exhibited various glycoproteins, including archaellins and hypothetical proteins, with glycans that were structurally distinct from those of their hosts. This indicated that Nanobdellati autonomously synthesize their glycans for protein modifications probably using host-derived substrates, despite the high energy cost. Glycan modifications on Nanobdellati proteins consistently occurred on asparagine residues within the N-X-S/T sequon, consistent with patterns observed across archaea, bacteria, and eukaryotes. In both host and non-host archaea, S-layer proteins were commonly modified with hexose, N-acetylhexosamine, and sulfonated deoxyhexose. However, the N-glycan structures of host archaea, characterized by distinct sugars such as deoxyhexose, nonulosonate sugar, and pentose at the nonreducing ends, were implicated in enabling Nanobdellati to differentiate between host and non-host cells. Interestingly, the specific sugar, xylose, was eliminated from the N-glycan in a host archaeon when co-cultured with Nanobdella. These findings enhance our understanding of the role of protein glycosylation in archaeal interactions.IMPORTANCENanobdellati archaea, formerly known as DPANN, are phylogenetically diverse, widely distributed, and obligately ectosymbiotic. The molecular mechanisms by which Nanobdellati recognize and adhere to their specific hosts remain largely unexplored. Protein glycosylation, a fundamental biological mechanism observed across all domains of life, is often crucial for various cell-cell interactions. This study provides the first insights into the glycoproteome of Nanobdellati and their host and non-host archaea. We discovered that Nanobdellati autonomously synthesize glycans for protein modifications, probably utilizing substrates derived from their hosts. Additionally, we identified distinctive glycosylation patterns that suggest mechanisms through which Nanobdellati differentiate between host and non-host cells. This research significantly advances our understanding of the molecular basis of microbial interactions in extreme environments.},
}
@article {pmid39134651,
year = {2024},
author = {Gutiérrez-Preciado, A and Dede, B and Baker, BA and Eme, L and Moreira, D and López-García, P},
title = {Extremely acidic proteomes and metabolic flexibility in bacteria and highly diversified archaea thriving in geothermal chaotropic brines.},
journal = {Nature ecology &amp; evolution},
volume = {8},
number = {10},
pages = {1856-1869},
pmid = {39134651},
issn = {2397-334X},
support = {doi.org/10.37807/GBMF9739//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; 787904//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; },
mesh = {*Proteome ; *Archaea/genetics/metabolism ; *Bacteria/metabolism/genetics/classification ; Lakes/microbiology ; Metagenome ; Salinity ; Archaeal Proteins/genetics/metabolism ; Genome, Archaeal ; Hot Springs/microbiology ; },
abstract = {Few described archaeal, and fewer bacterial, lineages thrive under salt-saturating conditions, such as solar saltern crystallizers (salinity above 30% w/v). They accumulate molar K[+] cytoplasmic concentrations to maintain osmotic balance ('salt-in' strategy) and have proteins adaptively enriched in negatively charged acidic amino acids. Here we analysed metagenomes and metagenome-assembled genomes from geothermally influenced hypersaline ecosystems with increasing chaotropicity in the Danakil Depression. Normalized abundances of universal single-copy genes confirmed that haloarchaea and Nanohaloarchaeota encompass 99% of microbial communities in the near-life-limiting conditions of the Western-Canyon Lakes. Danakil metagenome- and metagenome-assembled-genome-inferred proteomes, compared with those of freshwater, seawater and solar saltern ponds up to saturation (6-14-32% salinity), showed that Western-Canyon Lake archaea encode the most acidic proteomes ever observed (median protein isoelectric points ≤4.4). We identified previously undescribed haloarchaeal families as well as an Aenigmatarchaeota family and a bacterial phylum independently adapted to extreme halophily. Despite phylum-level diversity decreasing with increasing salinity-chaotropicity, and unlike in solar salterns, adapted archaea exceedingly diversified in Danakil ecosystems, challenging the notion of decreasing diversity under extreme conditions. Metabolic flexibility to utilize multiple energy and carbon resources generated by local hydrothermalism along feast-and-famine strategies seemingly shapes microbial diversity in these ecosystems near life limits.},
}
@article {pmid39128722,
year = {2024},
author = {Carilo, I and Senju, Y and Yokoyama, T and Robinson, RC},
title = {Intercompatibility of eukaryotic and Asgard archaea ribosome-translocon machineries.},
journal = {The Journal of biological chemistry},
volume = {300},
number = {9},
pages = {107673},
pmid = {39128722},
issn = {1083-351X},
mesh = {*Ribosomes/metabolism ; *Endoplasmic Reticulum/metabolism ; *Archaeal Proteins/metabolism/genetics ; Membrane Proteins/metabolism/genetics ; Archaea/metabolism/genetics ; Protein Transport ; Eukaryota/metabolism/genetics ; Phylogeny ; Protein Sorting Signals/physiology ; Eukaryotic Cells/metabolism ; },
abstract = {In all domains of life, the ribosome-translocon complex inserts nascent transmembrane proteins into, and processes and transports signal peptide-containing proteins across, membranes. Eukaryotic translocons are anchored in the endoplasmic reticulum, while the prokaryotic complexes reside in cell membranes. Phylogenetic analyses indicate the inheritance of eukaryotic Sec61/oligosaccharyltransferase/translocon-associated protein translocon subunits from an Asgard archaea ancestor. However, the mechanism for translocon migration from a peripheral membrane to an internal cellular compartment (the proto-endoplasmic reticulum) during eukaryogenesis is unknown. Here we show compatibility between the eukaryotic ribosome-translocon complex and Asgard signal peptides and transmembrane proteins. We find that Asgard translocon proteins from Candidatus Prometheoarchaeum syntrophicum strain Candidatus Prometheoarchaeum syntrophicum strain MK-D1, a Lokiarchaeon confirmed to contain no internal cellular membranes, are targeted to the eukaryotic endoplasmic reticulum on ectopic expression. Furthermore, we show that the cytoplasmic domain of Candidatus Prometheoarchaeum syntrophicum strain MK-D1 oligosaccharyltransferase 1 (ribophorin I) can interact with eukaryotic ribosomes. Our data indicate that the location of existing ribosome-translocon complexes, at the protein level, determines the future placement of yet-to-be-translated translocon subunits. This principle predicts that during eukaryogenesis, under positive selection pressure, the relocation of a few translocon complexes to the proto-endoplasmic reticulum will have contributed to propagating the new translocon location, leading to their loss from the cell membrane.},
}
@article {pmid39115222,
year = {2024},
author = {Zhao, Z and Qin, W and Li, L and Zhao, H and Ju, F},
title = {Discovery of Candidatus Nitrosomaritimum as a New Genus of Ammonia-Oxidizing Archaea Widespread in Anoxic Saltmarsh Intertidal Aquifers.},
journal = {Environmental science &amp; technology},
volume = {58},
number = {36},
pages = {16040-16054},
doi = {10.1021/acs.est.4c02321},
pmid = {39115222},
issn = {1520-5851},
mesh = {*Ammonia/metabolism ; *Archaea/metabolism/genetics ; Phylogeny ; Oxidation-Reduction ; },
abstract = {Ammonia-oxidizing archaea (AOA) are widely distributed in marine and terrestrial habitats, contributing significantly to global nitrogen and carbon cycles. However, their genomic diversity, ecological niches, and metabolic potentials in the anoxic intertidal aquifers remain poorly understood. Here, we discovered and named a novel AOA genus, Candidatus Nitrosomaritimum, from the intertidal aquifers of Yancheng Wetland, showing close metagenomic abundance to the previously acknowledged dominant Nitrosopumilus AOA. Further construction of ammonia monooxygenase-based phylogeny demonstrated the widespread distribution of Nitrosomaritimum AOA in global estuarine-coastal niches and marine sediment. Niche differentiation among sublineages of this new genus in anoxic intertidal aquifers is driven by salinity and dissolved oxygen gradients. Comparative genomics revealed that Candidatus Nitrosomaritimum has the genetic capacity to utilize urea and possesses high-affinity phosphate transporter systems (phnCDE) for surviving phosphorus-limited conditions. Additionally, it contains putative nosZ genes encoding nitrous-oxide (N2O) reductase for reducing N2O to nitrogen gas. Furthermore, we gained first genomic insights into the archaeal phylum Hydrothermarchaeota populations residing in intertidal aquifers and revealed their potential hydroxylamine-detoxification mutualism with AOA through utilizing the AOA-released extracellular hydroxylamine using hydroxylamine oxidoreductase. Together, this study unravels the overlooked role of priorly unknown but abundant AOA lineages of the newly discovered genus Candidatus Nitrosomaritimum in biological nitrogen transformation and their potential for nitrogen pollution mitigation in coastal environments.},
}
@article {pmid39097239,
year = {2024},
author = {Manesh, MJH and Willard, DJ and John, KM and Kelly, RM},
title = {Chalcopyrite bioleaching efficacy by extremely thermoacidophilic archaea leverages balanced iron and sulfur biooxidation.},
journal = {Bioresource technology},
volume = {408},
number = {},
pages = {131198},
pmid = {39097239},
issn = {1873-2976},
support = {T32 GM008776/GM/NIGMS NIH HHS/United States ; T32 GM133366/GM/NIGMS NIH HHS/United States ; },
mesh = {*Sulfur/metabolism ; *Oxidation-Reduction ; *Copper/metabolism ; *Iron/metabolism ; Archaea/metabolism ; Hydrogen-Ion Concentration ; Temperature ; Sulfolobales/metabolism ; },
abstract = {Factors that contribute to optimal chalcopyrite bioleaching by extremely thermoacidophilic archaea were examined for ten species belonging to the order Sulfolobales from the genera Acidianus (A. brierleyi), Metallosphaera (M. hakonensis, M. sedula, M. prunae), Sulfuracidifex (S. metallicus, S. tepriarius), Sulfolobus (S. acidocaldarius), Saccharlobus (S. solfataricus) and Sulfurisphaera (S. ohwakuensis, S. tokodaii). Only A. brierleyi, M. sedula, S. metallicus, S. tepriarius, S. ohwakuensis, and S. tokodai exhibited significant amounts of bioleaching and were investigated further. At 70-75 °C, Chalcopyrite loadings of 10 g/l were leached for 21 days during which pH, redox potential, planktonic cell density, iron concentrations and sulfate levels were monitored, in addition to copper mobilization. S. ohwakuensis proved to be the most prolific bioleacher. This was attributed to balanced iron and sulfur oxidation, thereby reducing by-product (e.g., jarosites) formation and minimizing surface passivation. Comparative genomics suggest markers for bioleaching potential, but the results here point to the need for experimental verification.},
}
@article {pmid39096085,
year = {2024},
author = {Blombach, F and Werner, F},
title = {Chromatin and gene regulation in archaea.},
journal = {Molecular microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/mmi.15302},
pmid = {39096085},
issn = {1365-2958},
support = {207446/Z/17/Z/WT_/Wellcome Trust/United Kingdom ; },
abstract = {The chromatinisation of DNA by nucleoid-associated proteins (NAPs) in archaea 'formats' the genome structure in profound ways, revealing both striking differences and analogies to eukaryotic chromatin. However, the extent to which archaeal NAPs actively regulate gene expression remains poorly understood. The dawn of quantitative chromatin mapping techniques and first NAP-specific occupancy profiles in different archaea promise a more accurate view. A picture emerges where in diverse archaea with very different NAP repertoires chromatin maintains access to regulatory motifs including the gene promoter independently of transcription activity. Our re-analysis of genome-wide occupancy data of the crenarchaeal NAP Cren7 shows that these chromatin-free regions are flanked by increased Cren7 binding across the transcription start site. While bacterial NAPs often form heterochromatin-like regions across islands with xenogeneic genes that are transcriptionally silenced, there is little evidence for similar structures in archaea and data from Haloferax show that the promoters of xenogeneic genes remain accessible. Local changes in chromatinisation causing wide-ranging effects on transcription restricted to one chromosomal interaction domain (CID) in Saccharolobus islandicus hint at a higher-order level of organisation between chromatin and transcription. The emerging challenge is to integrate results obtained at microscale and macroscale, reconciling molecular structure and function with dynamic genome-wide chromatin landscapes.},
}
@article {pmid39085212,
year = {2024},
author = {Leão, P and Little, ME and Appler, KE and Sahaya, D and Aguilar-Pine, E and Currie, K and Finkelstein, IJ and De Anda, V and Baker, BJ},
title = {Asgard archaea defense systems and their roles in the origin of eukaryotic immunity.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {6386},
pmid = {39085212},
issn = {2041-1723},
support = {73592LPI//Simons Foundation/ ; F-1808//Welch Foundation/ ; },
mesh = {*Phylogeny ; *Archaea/genetics/immunology/virology ; *Archaeal Proteins/metabolism/genetics ; Argonaute Proteins/metabolism/genetics ; Eukaryota/genetics/immunology ; Bacteriophages/genetics/physiology ; Evolution, Molecular ; },
abstract = {Dozens of new antiviral systems have been recently characterized in bacteria. Some of these systems are present in eukaryotes and appear to have originated in prokaryotes, but little is known about these defense mechanisms in archaea. Here, we explore the diversity and distribution of defense systems in archaea and identify 2610 complete systems in Asgardarchaeota, a group of archaea related to eukaryotes. The Asgard defense systems comprise 89 unique systems, including argonaute, NLR, Mokosh, viperin, Lassamu, and CBASS. Asgard viperin and argonaute proteins have structural homology to eukaryotic proteins, and phylogenetic analyses suggest that eukaryotic viperin proteins were derived from Asgard viperins. We show that Asgard viperins display anti-phage activity when heterologously expressed in bacteria. Eukaryotic and bacterial argonaute proteins appear to have originated in Asgardarchaeota, and Asgard argonaute proteins have argonaute-PIWI domains, key components of eukaryotic RNA interference systems. Our results support that Asgardarchaeota played important roles in the origin of antiviral defense systems in eukaryotes.},
}
@article {pmid39085194,
year = {2024},
author = {Valentin-Alvarado, LE and Appler, KE and De Anda, V and Schoelmerich, MC and West-Roberts, J and Kivenson, V and Crits-Christoph, A and Ly, L and Sachdeva, R and Greening, C and Savage, DF and Baker, BJ and Banfield, JF},
title = {Asgard archaea modulate potential methanogenesis substrates in wetland soil.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {6384},
pmid = {39085194},
issn = {2041-1723},
support = {INV-037174/GATES/Bill &amp; Melinda Gates Foundation/United States ; LI-SIAME-00002001//Simons Foundation/ ; },
mesh = {*Wetlands ; *Methane/metabolism ; *Soil Microbiology ; *Archaea/genetics/metabolism ; *Carbon Cycle ; *Soil/chemistry ; Phylogeny ; Genome, Archaeal ; Oxidation-Reduction ; },
abstract = {The roles of Asgard archaea in eukaryogenesis and marine biogeochemical cycles are well studied, yet their contributions in soil ecosystems remain unknown. Of particular interest are Asgard archaeal contributions to methane cycling in wetland soils. To investigate this, we reconstructed two complete genomes for soil-associated Atabeyarchaeia, a new Asgard lineage, and a complete genome of Freyarchaeia, and predicted their metabolism in situ. Metatranscriptomics reveals expression of genes for [NiFe]-hydrogenases, pyruvate oxidation and carbon fixation via the Wood-Ljungdahl pathway. Also expressed are genes encoding enzymes for amino acid metabolism, anaerobic aldehyde oxidation, hydrogen peroxide detoxification and carbohydrate breakdown to acetate and formate. Overall, soil-associated Asgard archaea are predicted to include non-methanogenic acetogens, highlighting their potential role in carbon cycling in terrestrial environments.},
}
@article {pmid39085041,
year = {2024},
author = {Hayashi, M and Wada, Y and Yamamura, A and Inoue, H and Yamashita, N and Ichimura, S and Iida, Y},
title = {Evaluation of the enzymatic properties of DNA (cytosine-5)-methyltransferase M.ApeKI from archaea in the presence of metal ions.},
journal = {Bioscience, biotechnology, and biochemistry},
volume = {88},
number = {10},
pages = {1155-1163},
doi = {10.1093/bbb/zbae106},
pmid = {39085041},
issn = {1347-6947},
mesh = {*Metals/pharmacology/metabolism ; DNA-Cytosine Methylases/metabolism ; DNA/metabolism ; Archaea/enzymology/genetics ; Copper/metabolism/pharmacology ; Archaeal Proteins/metabolism/genetics ; },
abstract = {We previously identified M.ApeKI from Aeropyum pernix K1 as a highly thermostable DNA (cytosine-5)-methyltransferase. M.ApeKI uses the type II restriction-modification system (R-M system), among the best-studied R-M systems. Although endonucleases generally utilize Mg (II) as a cofactor, several reports have shown that MTases exhibit different reactions in the presence of metal ions. This study aim was to evaluate the enzymatic properties of DNA (cytosine-5)-methyltransferase M.ApeKI from archaea in the presence of metal ions. We evaluated the influence of metal ions on the catalytic activity and DNA binding of M.ApeKI. The catalytic activity was inhibited by Cu (II), Mg (II), Mn (II), and Zn (II), each at 5 m m. DNA binding was more strongly inhibited by 5 m m Cu (II) and 10 m m Zn (II). To our knowledge, this is the first report showing that DNA binding of type II MTase is inhibited by metal ions.},
}
@article {pmid39081362,
year = {2024},
author = {Kaneko, M and Omori, T and Igai, K and Mabuchi, T and Sakai-Tazawa, M and Nishihara, A and Kihara, K and Yoshimura, T and Ohkuma, M and Hongoh, Y},
title = {Facultative endosymbiosis between cellulolytic protists and methanogenic archaea in the gut of the Formosan termite Coptotermes formosanus.},
journal = {ISME communications},
volume = {4},
number = {1},
pages = {ycae097},
pmid = {39081362},
issn = {2730-6151},
abstract = {Anaerobic protists frequently harbour methanogenic archaea, which apparently contribute to the hosts' fermentative metabolism by consuming excess H2. However, the ecological properties of endosymbiotic methanogens remain elusive in many cases. Here we investigated the ecology and genome of the endosymbiotic methanogen of the Cononympha protists in the hindgut of the termite Coptotermes formosanus. Microscopic and 16S rRNA amplicon sequencing analyses revealed that a single species, designated here "Candidatus Methanobrevibacter cononymphae", is associated with both Cononympha leidyi and Cononympha koidzumii and that its infection rate in Cononympha cells varied from 0.0% to 99.8% among termite colonies. Fine-scale network analysis indicated that multiple 16S rRNA sequence variants coexisted within a single host cell and that identical variants were present in both Cononympha species and also on the gut wall. Thus, "Ca. Methanobrevibacter cononymphae" is a facultative endosymbiont, transmitted vertically with frequent exchanges with the gut environment. Indeed, transmission electron microscopy showed escape or uptake of methanogens from/by a Cononympha cell. The genome of "Ca. Methanobrevibacter cononymphae" showed features consistent with its facultative lifestyle: i.e., the genome size (2.7 Mbp) comparable to those of free-living relatives; the pseudogenization of the formate dehydrogenase gene fdhA, unnecessary within the non-formate-producing host cell; the dependence on abundant acetate in the host cell as an essential carbon source; and the presence of a catalase gene, required for colonization on the microoxic gut wall. Our study revealed a versatile endosymbiosis between the methanogen and protists, which may be a strategy responding to changing conditions in the termite gut.},
}
@article {pmid39077992,
year = {2024},
author = {Rasmussen, AN and Francis, CA},
title = {Dynamics and activity of an ammonia-oxidizing archaea bloom in South San Francisco Bay.},
journal = {The ISME journal},
volume = {18},
number = {1},
pages = {},
pmid = {39077992},
issn = {1751-7370},
support = {DE-AC02-05CH11231//Department of Energy/ ; //Stanford Data Science Scholars Program/ ; },
mesh = {*Ammonia/metabolism ; San Francisco ; *Archaea/genetics/classification/metabolism/isolation &amp; purification ; *Bays/microbiology ; *Oxidation-Reduction ; *Nitrification ; Metagenome ; Seasons ; Metagenomics ; },
abstract = {Transient or recurring blooms of ammonia-oxidizing archaea (AOA) have been reported in several estuarine and coastal environments, including recent observations of AOA blooms in South San Francisco Bay. Here, we measured nitrification rates, quantified AOA abundance, and analyzed both metagenomic and metatranscriptomic data to examine the dynamics and activity of nitrifying microorganisms over the course of an AOA bloom in South San Francisco Bay during the autumn of 2018 and seasonally throughout 2019. Nitrification rates were correlated with AOA abundance in quantitative polymerase chain reaction (PCR) data, and both increased several orders of magnitude between the autumn AOA bloom and spring and summer seasons. From bloom samples, we recovered an extremely abundant, high-quality Candidatus Nitrosomarinus catalina-like AOA metagenome-assembled genome that had high transcript abundance during the bloom and expressed >80% of genes in its genome. We also recovered a putative nitrite-oxidizing bacteria metagenome-assembled genome from within the Nitrospinaceae that was of much lower abundance and had lower transcript abundance than AOA. During the AOA bloom, we observed increased transcript abundance for nitrogen uptake and oxidative stress genes in non-nitrifier metagenome-assembled genomes. This study confirms AOA are not only abundant but also highly active during blooms oxidizing large amounts of ammonia to nitrite-a key intermediate in the microbial nitrogen cycle-and producing reactive compounds that may impact other members of the microbial community.},
}
@article {pmid39077943,
year = {2024},
author = {Lin, MG and Yen, CY and Shen, YY and Huang, YS and Ng, IW and Barillà, D and Sun, YJ and Hsiao, CD},
title = {Unraveling the structure and function of a novel SegC protein interacting with the SegAB chromosome segregation complex in Archaea.},
journal = {Nucleic acids research},
volume = {52},
number = {16},
pages = {9966-9977},
pmid = {39077943},
issn = {1362-4962},
support = {NSTC 111-2311-B-001-001//National Science and Technology Council/ ; RPG-245//Leverhulme Trust/ ; BB/X00645X/1//BBSRC/ ; },
mesh = {*Chromosome Segregation ; *Archaeal Proteins/chemistry/metabolism/genetics ; *Models, Molecular ; Protein Binding ; Crystallography, X-Ray ; Adenosine Diphosphate/metabolism/chemistry ; Binding Sites ; DNA, Archaeal/metabolism/chemistry/genetics ; DNA-Binding Proteins/chemistry/metabolism/genetics/ultrastructure ; },
abstract = {Genome segregation is a fundamental process that preserves the genetic integrity of all organisms, but the mechanisms driving genome segregation in archaea remain enigmatic. This study delved into the unknown function of SegC (SSO0033), a novel protein thought to be involved in chromosome segregation in archaea. Using fluorescence polarization DNA binding assays, we discovered the ability of SegC to bind DNA without any sequence preference. Furthermore, we determined the crystal structure of SegC at 2.8 Å resolution, revealing the multimeric configuration and forming a large positively charged surface that can bind DNA. SegC has a tertiary structure folding similar to those of the ThDP-binding fold superfamily, but SegC shares only 5-15% sequence identity with those proteins. Unexpectedly, we found that SegC has nucleotide triphosphatase (NTPase) activity. We also determined the SegC-ADP complex structure, identifying the NTP binding pocket and relative SegC residues involved in the interaction. Interestingly, images from negative-stain electron microscopy revealed that SegC forms filamentous structures in the presence of DNA and NTPs. Further, more uniform and larger SegC-filaments are observed, when SegA-ATP was added. Notably, the introduction of SegB disrupts these oligomers, with ATP being essential for regulating filament formation. These findings provide insights into the functional and structural role of SegC in archaeal chromosome segregation.},
}
@article {pmid39071849,
year = {2024},
author = {Sakoula, D and Schatteman, A and Blom, P and Jetten, MSM and van Kessel, MAHJ and Lehtovirta-Morley, L and Lücker, S},
title = {Activity-based labelling of ammonia- and alkane-oxidizing microorganisms including ammonia-oxidizing archaea.},
journal = {ISME communications},
volume = {4},
number = {1},
pages = {ycae092},
pmid = {39071849},
issn = {2730-6151},
abstract = {Recently, an activity-based labelling protocol for the in vivo detection of ammonia- and alkane-oxidizing bacteria became available. This functional tagging technique enabled targeted studies of these environmentally widespread functional groups, but it failed to capture ammonia-oxidizing archaea (AOA). Since their first discovery, AOA have emerged as key players within the biogeochemical nitrogen cycle, but our knowledge regarding their distribution and abundance in natural and engineered ecosystems is mainly derived from PCR-based and metagenomic studies. Furthermore, the archaeal ammonia monooxygenase is distinctly different from its bacterial counterparts and remains poorly understood. Here, we report on the development of an activity-based labelling protocol for the fluorescent detection of all ammonia- and alkane-oxidizing prokaryotes, including AOA. In this protocol, 1,5-hexadiyne is used as inhibitor of ammonia and alkane oxidation and as bifunctional enzyme probe for the fluorescent labelling of cells via the Cu(I)-catalyzed alkyne-azide cycloaddition reaction. Besides efficient activity-based labelling of ammonia- and alkane-oxidizing microorganisms, this method can also be employed in combination with deconvolution microscopy for determining the subcellular localization of their ammonia- and alkane-oxidizing enzyme systems. Labelling of these enzymes in diverse ammonia- and alkane-oxidizing microorganisms allowed their visualization on the cytoplasmic membranes, the intracytoplasmic membrane stacks of ammonia- and methane-oxidizing bacteria, and, fascinatingly, on vesicle-like structures in one AOA species. The development of this novel activity-based labelling method for ammonia- and alkane-oxidizers will be a valuable addition to the expanding molecular toolbox available for research of nitrifying and alkane-oxidizing microorganisms.},
}
@article {pmid39060562,
year = {2024},
author = {Harada, M and Endo, A and Wada, S and Watanabe, T and Epron, D and Asakawa, S},
title = {Ubiquity of methanogenic archaea in the trunk of coniferous and broadleaved tree species in a mountain forest.},
journal = {Antonie van Leeuwenhoek},
volume = {117},
number = {1},
pages = {107},
pmid = {39060562},
issn = {1572-9699},
support = {24K01797//Japan Society for the Promotion of Science/ ; },
mesh = {*RNA, Ribosomal, 16S/genetics ; *Forests ; *Methane/metabolism ; *Phylogeny ; Trees/microbiology ; Archaea/classification/genetics/metabolism/isolation &amp; purification ; Wood/microbiology ; DNA, Archaeal/genetics ; },
abstract = {Wetwood of living trees is a habitat of methanogenic archaea, but the ubiquity of methanogenic archaea in the trunk of various trees has not been revealed. The present study analysed methanogenic archaeal communities inside coniferous and broadleaved trees in a cold temperate mountain forest by culture-dependent or independent techniques. Heartwood and sapwood segments were obtained from the trunk of seven tree species, Cryptomeria japonica, Quercus crispula, Fraxinus mandshurica, Acer pictum, Aesculus turbinata, Magnolia obovata, and Populus tremula. Amplicon sequencing analysis of 16S rRNA genes showed that Methanobacteriaceae predominated the archaeal communities and Methanomassiliicoccaceae also inhabited some trees. Real-time PCR analysis detected methanogenic archaeal mcrA genes from all the tree species, with a maximum of 10[7] copies g[-1] dry wood. Digital PCR analysis also detected mcrA genes derived from Methanobacterium spp. and Methanobrevibacter spp. from several samples, with a maximum of 10[5] and 10[4] copies g[-1] dry wood. The enumeration by the most probable number method demonstrated the inhabitation of viable methanogenic archaea inside the trees; 10[6] cells g[-1] dry wood was enumerated from a heartwood sample of C. japonica. Methanogenic archaea related to Methanobacterium beijingense were cultivated from a heartwood sample of Q. crispula and F. mandshurica. The present study demonstrated that the inside of various trees is a common habitat for methanogenic archaeal communities and a potential source of methane in forest ecosystems.},
}
@article {pmid39053544,
year = {2024},
author = {Yan, A and Pan, Z and Liang, Y and Mo, X and Guo, T and Li, J},
title = {Archaea communities in aerobic granular sludge: A mini-review.},
journal = {The Science of the total environment},
volume = {949},
number = {},
pages = {174974},
doi = {10.1016/j.scitotenv.2024.174974},
pmid = {39053544},
issn = {1879-1026},
mesh = {*Sewage/microbiology ; *Archaea/physiology ; Aerobiosis ; Waste Disposal, Fluid/methods ; Bioreactors/microbiology ; },
abstract = {Recent research on the archaea community in aerobic granular sludge (AGS) has attracted considerable attention. This review summarizes the existing literature on composition, distribution, and related functions of archaea community in AGS. Furthermore, the effects of granulation, substrate, temperature, process types, and aeration models on the archaea community were discussed. Significantly, the layered structure of AGS facilitates the enrichment of archaea, including methanogenic archaea and ammonia-oxidizing archaea. Archaea engage in metabolic interactions with other microorganisms, enhancing the ecological functionalities of AGS and its tolerance to adverse conditions. Future investigations should focus on minimizing greenhouse gas emissions and exploring the roles and interactive mechanisms of archaea and other microorganisms within AGS.},
}
@article {pmid39052173,
year = {2024},
author = {Tenorio-Salgado, S and Villalpando-Aguilar, JL and Hernandez-Guerrero, R and Poot-Hernández, AC and Perez-Rueda, E},
title = {Exploring the enzymatic repertoires of Bacteria and Archaea and their associations with metabolic maps.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {},
number = {},
pages = {},
pmid = {39052173},
issn = {1678-4405},
abstract = {The evolution, survival, and adaptation of microbes are consequences of gene duplication, acquisition, and divergence in response to environmental challenges. In this context, enzymes play a central role in the evolution of organisms, because they are fundamental in cell metabolism. Here, we analyzed the enzymatic repertoire in 6,467 microbial genomes, including their abundances, and their associations with metabolic maps. We found that the enzymes follow a power-law distribution, in relation to the genome sizes. Therefore, we evaluated the total proportion enzymatic classes in relation to the genomes, identifying a descending-order proportion: transferases (EC:2.-), hydrolases (EC:3.-), oxidoreductases (EC:1.-), ligases (EC:6.-), lyases (EC:4.-), isomerases (EC:5.-), and translocases (EC:7-.). In addition, we identified a preferential use of enzymatic classes in metabolism pathways for xenobiotics, cofactors and vitamins, carbohydrates, amino acids, glycans, and energy. Therefore, this analysis provides clues about the functional constraints associated with the enzymatic repertoire of functions in Bacteria and Archaea.},
}
@article {pmid39043438,
year = {2024},
author = {Gemler, BT and Warner, BR and Bundschuh, R and Fredrick, K},
title = {Identification of leader-trailer helices of precursor ribosomal RNA in all phyla of bacteria and archaea.},
journal = {RNA (New York, N.Y.)},
volume = {30},
number = {10},
pages = {1264-1276},
pmid = {39043438},
issn = {1469-9001},
support = {R01 GM072528/GM/NIGMS NIH HHS/United States ; },
mesh = {*Nucleic Acid Conformation ; *RNA, Archaeal/genetics/chemistry/metabolism ; *Archaea/genetics ; *RNA, Bacterial/genetics/chemistry/metabolism ; RNA, Ribosomal/genetics/chemistry/metabolism ; Bacteria/genetics ; RNA Precursors/genetics/metabolism/chemistry ; RNA, Ribosomal, 23S/genetics/chemistry/metabolism ; Base Sequence ; RNA, Ribosomal, 16S/genetics/chemistry ; Base Pairing ; },
abstract = {Ribosomal RNAs are transcribed as part of larger precursor molecules. In Escherichia coli, complementary RNA segments flank each rRNA and form long leader-trailer (LT) helices, which are crucial for subunit biogenesis in the cell. A previous study of 15 representative species suggested that most but not all prokaryotes contain LT helices. Here, we use a combination of in silico folding and covariation methods to identify and characterize LT helices in 4464 bacterial and 260 archaeal organisms. Our results suggest that LT helices are present in all phyla, including Deinococcota, which had previously been suspected to lack LT helices. In very few organisms, our pipeline failed to detect LT helices for both 16S and 23S rRNA. However, a closer case-by-case look revealed that LT helices are indeed present but escaped initial detection. Over 3600 secondary structure models, many well supported by nucleotide covariation, were generated. These structures show a high degree of diversity. Yet, all exhibit extensive base-pairing between the leader and trailer strands, in line with a common and essential function.},
}
@article {pmid39043386,
year = {2024},
author = {Duller, S and Moissl-Eichinger, C},
title = {Archaea in the Human Microbiome and Potential Effects on Human Infectious Disease.},
journal = {Emerging infectious diseases},
volume = {30},
number = {8},
pages = {1505-1513},
pmid = {39043386},
issn = {1080-6059},
mesh = {Humans ; *Archaea/genetics ; *Microbiota ; Communicable Diseases/microbiology ; },
abstract = {Archaea represent a separate domain of life, next to bacteria and eukarya. As components of the human microbiome, archaea have been associated with various diseases, including periodontitis, endodontic infections, small intestinal bacterial overgrowth, and urogenital tract infections. Archaea are generally considered nonpathogenic; the reasons are speculative because of limited knowledge and gene annotation challenges. Nevertheless, archaeal syntrophic principles that shape global microbial networks aid both archaea and potentially pathogenic bacteria. Evaluating archaea interactions remains challenging, requiring clinical studies on inflammatory potential and the effects of archaeal metabolism. Establishing a culture collection is crucial for investigating archaea functions within the human microbiome, which could improve health outcomes in infectious diseases. We summarize potential reasons for archaeal nonpathogenicity, assess the association with infectious diseases in humans, and discuss the necessary experimental steps to enable mechanistic studies involving archaea.},
}
@article {pmid39030685,
year = {2024},
author = {Echeveste Medrano, MJ and Leu, AO and Pabst, M and Lin, Y and McIlroy, SJ and Tyson, GW and van Ede, J and Sánchez-Andrea, I and Jetten, MSM and Jansen, R and Welte, CU},
title = {Osmoregulation in freshwater anaerobic methane-oxidizing archaea under salt stress.},
journal = {The ISME journal},
volume = {18},
number = {1},
pages = {},
pmid = {39030685},
issn = {1751-7370},
support = {VI.Vidi.223.012//NWO-VIDI/ ; FT190100211//Australian Research Council/ ; 854088//ERC/ ; 024.002.002//NWO/ ; },
mesh = {*Methane/metabolism ; *Fresh Water/microbiology ; Anaerobiosis ; *Archaea/metabolism/genetics/classification ; *Salt Stress ; *Phylogeny ; *Osmoregulation ; Oxidation-Reduction ; },
abstract = {Climate change-driven sea level rise threatens freshwater ecosystems and elicits salinity stress in microbiomes. Methane emissions in these systems are largely mitigated by methane-oxidizing microorganisms. Here, we characterized the physiological and metabolic response of freshwater methanotrophic archaea to salt stress. In our microcosm experiments, inhibition of methanotrophic archaea started at 1%. However, during gradual increase of salt up to 3% in a reactor over 12 weeks, the culture continued to oxidize methane. Using gene expression profiles and metabolomics, we identified a pathway for salt-stress response that produces the osmolyte of anaerobic methanotrophic archaea: N(ε)-acetyl-β-L-lysine. An extensive phylogenomic analysis on N(ε)-acetyl-β-L-lysine-producing enzymes revealed that they are widespread across both bacteria and archaea, indicating a potential horizontal gene transfer and a link to BORG extrachromosomal elements. Physicochemical analysis of bioreactor biomass further indicated the presence of sialic acids and the consumption of intracellular polyhydroxyalkanoates in anaerobic methanotrophs during salt stress.},
}
@article {pmid38967634,
year = {2024},
author = {Imachi, H and Nobu, MK and Kato, S and Takaki, Y and Miyazaki, M and Miyata, M and Ogawara, M and Saito, Y and Sakai, S and Tahara, YO and Takano, Y and Tasumi, E and Uematsu, K and Yoshimura, T and Itoh, T and Ohkuma, M and Takai, K},
title = {Promethearchaeum syntrophicum gen. nov., sp. nov., an anaerobic, obligately syntrophic archaeon, the first isolate of the lineage 'Asgard' archaea, and proposal of the new archaeal phylum Promethearchaeota phyl. nov. and kingdom Promethearchaeati regn. nov.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {74},
number = {7},
pages = {},
pmid = {38967634},
issn = {1466-5034},
mesh = {*Phylogeny ; *RNA, Ribosomal, 16S/genetics ; *Base Composition ; *Sequence Analysis, DNA ; *DNA, Archaeal/genetics ; Geologic Sediments/microbiology ; Anaerobiosis ; Seawater/microbiology ; Vitamin K 2/analogs &amp; derivatives ; },
abstract = {An anaerobic, mesophilic, syntrophic, archaeon strain MK-D1[T], was isolated as a pure co-culture with Methanogenium sp. strain MK-MG from deep-sea methane seep sediment. This organism is, to our knowledge, the first cultured representative of 'Asgard' archaea, an archaeal group closely related to eukaryotes. Here, we describe the detailed physiology and phylogeny of MK-D1[T] and propose Promethearchaeum syntrophicum gen. nov., sp. nov. to accommodate this strain. Cells were non-motile, small cocci, approximately 300-750 nm in diameter and produced membrane vesicles, chains of blebs and membrane-based protrusions. MK-D1[T] grew at 4-30 °C with optimum growth at 20 °C. The strain grew chemoorganotrophically with amino acids, peptides and yeast extract with obligate dependence on syntrophy with H2-/formate-utilizing organisms. MK-D1[T] showed the fastest growth and highest maximum cell yield when grown with yeast extract as the substrate: approximately 3 months to full growth, reaching up to 6.7×10[6] 16S rRNA gene copies ml[-1]. MK-D1[T] had a circular 4.32 Mb chromosome with a DNA G+C content of 31.1 mol%. The results of phylogenetic analyses of the 16S rRNA gene and conserved marker proteins indicated that the strain is affiliated with 'Asgard' archaea and more specifically DHVC1/DSAG/MBG-B and 'Lokiarchaeota'/'Lokiarchaeia'. On the basis of the results of 16S rRNA gene sequence analysis, the most closely related isolated relatives were Infirmifilum lucidum 3507LT[T] (76.09 %) and Methanothermobacter tenebrarum RMAS[T] (77.45 %) and the closest relative in enrichment culture was Candidatus 'Lokiarchaeum ossiferum' (95.39 %). The type strain of the type species is MK-D1[T] (JCM 39240[T] and JAMSTEC no. 115508). We propose the associated family, order, class, phylum, and kingdom as Promethearchaeaceae fam. nov., Promethearchaeales ord. nov., Promethearchaeia class. nov., Promethearchaeota phyl. nov., and Promethearchaeati regn. nov., respectively. These are in accordance with ICNP Rules 8 and 22 for nomenclature, Rule 30(3)(b) for validation and maintenance of the type strain, and Rule 31a for description as a member of an unambiguous syntrophic association.},
}
@article {pmid38953360,
year = {2024},
author = {Willard, DJ and H Manesh, MJ and Bing, RG and Alexander, BH and Kelly, RM},
title = {Phenotype-driven assessment of the ancestral trajectory of sulfur biooxidation in the thermoacidophilic archaea Sulfolobaceae.},
journal = {mBio},
volume = {15},
number = {8},
pages = {e0103324},
pmid = {38953360},
issn = {2150-7511},
support = {T32 GM008776/GM/NIGMS NIH HHS/United States ; CBET-1802939//National Science Foundation (NSF)/ ; T32 GM008776-16//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; FA9550-20-1-0216//US Air Force Office of Sponsored Projects/ ; },
mesh = {*Sulfur/metabolism ; *Oxidation-Reduction ; *Sulfolobaceae/metabolism/genetics ; Phenotype ; Phylogeny ; Gene Expression Profiling ; Genome, Archaeal ; },
abstract = {Certain members of the family Sulfolobaceae represent the only archaea known to oxidize elemental sulfur, and their evolutionary history provides a framework to understand the development of chemolithotrophic growth by sulfur oxidation. Here, we evaluate the sulfur oxidation phenotype of Sulfolobaceae species and leverage comparative genomic and transcriptomic analysis to identify the key genes linked to sulfur oxidation. Metabolic engineering of the obligate heterotroph Sulfolobus acidocaldarius revealed that the known cytoplasmic components of sulfur oxidation alone are not sufficient to drive prolific sulfur oxidation. Imaging analysis showed that Sulfolobaceae species maintain proximity to the sulfur surface but do not necessarily contact the substrate directly. This indicates that a soluble form of sulfur must be transported to initiate cytoplasmic sulfur oxidation. Conservation patterns and transcriptomic response implicate an extracellular tetrathionate hydrolase and putative thiosulfate transporter in a newly proposed mechanism of sulfur acquisition in the Sulfolobaceae.IMPORTANCESulfur is one of the most abundant elements on earth (2.9% by mass), so it makes sense that the earliest biology found a way to use sulfur to create and sustain life. However, beyond evolutionary significance, sulfur and the molecules it comprises have important technological significance, not only in chemicals such as sulfuric acid and in pyritic ores containing critical metals but also as a waste product from oil and gas production. The thermoacidophilic Sulfolobaceae are unique among the archaea as sulfur oxidizers. The trajectory for how sulfur biooxidation arose and evolved can be traced using experimental and bioinformatic analyses of the available genomic data set. Such analysis can also inform the process by which extracellular sulfur is acquired and transported by thermoacidophilic archaea, a phenomenon that is critical to these microorganisms but has yet to be elucidated.},
}
@article {pmid38951176,
year = {2024},
author = {Martínez-Espinosa, RM},
title = {Halophilic archaea as tools for bioremediation technologies.},
journal = {Applied microbiology and biotechnology},
volume = {108},
number = {1},
pages = {401},
pmid = {38951176},
issn = {1432-0614},
support = {VIGROB-309//Universidad de Alicante/ ; PROMETEO/2021/055//Conselleria de Cultura, Educaci&#xf3;n y Ciencia, Generalitat Valenciana/ ; },
mesh = {*Biodegradation, Environmental ; Archaea/metabolism ; Halobacteriaceae/metabolism/genetics ; Metals, Heavy/metabolism ; Soil Pollutants/metabolism ; Soil Microbiology ; },
abstract = {Haloarchaea are extremophilic microorganisms belonging to the Archaea domain that require high salt concentrations to be alive, thus inhabiting ecosystems like salty ponds, salty marshes, or extremely salty lagoons. They are more abundantly and widely distributed worldwide than initially expected. Most of them are grouped into two families: Halobacteriaceae and Haloferacaceae. The extreme conditions under which haloarchaea survive contribute to their metabolic and molecular adaptations, thus making them good candidates for the design of bioremediation strategies to treat brines, salty water, and saline soils contaminated with toxic compounds such as nitrate, nitrite, oxychlorates such as perchlorate and chlorate, heavy metals, hydrocarbons, and aromatic compounds. New advances in understanding haloarchaea physiology, metabolism, biochemistry, and molecular biology suggest that biochemical pathways related to nitrogen and carbon, metals, hydrocarbons, or aromatic compounds can be used for bioremediation proposals. This review analyses the novelty of the most recent results showing the capability of some haloarchaeal species to assimilate, modify, or degrade toxic compounds for most living beings. Several examples of the role of these microorganisms in the treatment of polluted brine or salty soils are also discussed in connection with circular economy-based processes. KEY POINTS: • Haloarchaea are extremophilic microorganisms showing genuine metabolism • Haloarchaea can metabolise compounds that are highly toxic to most living beings • These metabolic capabilities are useful for designing soil and water bioremediation strategies.},
}
@article {pmid38926353,
year = {2024},
author = {Schoelmerich, MC and Ly, L and West-Roberts, J and Shi, LD and Shen, C and Malvankar, NS and Taib, N and Gribaldo, S and Woodcroft, BJ and Schadt, CW and Al-Shayeb, B and Dai, X and Mozsary, C and Hickey, S and He, C and Beaulaurier, J and Juul, S and Sachdeva, R and Banfield, JF},
title = {Borg extrachromosomal elements of methane-oxidizing archaea have conserved and expressed genetic repertoires.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {5414},
pmid = {38926353},
issn = {2041-1723},
support = {INV-037174/GATES/Bill &amp; Melinda Gates Foundation/United States ; },
mesh = {*Genome, Archaeal ; *Methane/metabolism ; *Phylogeny ; Oxidation-Reduction ; Archaea/genetics/metabolism ; Nanopore Sequencing/methods ; DNA Methylation ; Soil Microbiology ; },
abstract = {Borgs are huge extrachromosomal elements (ECE) of anaerobic methane-consuming "Candidatus Methanoperedens" archaea. Here, we used nanopore sequencing to validate published complete genomes curated from short reads and to reconstruct new genomes. 13 complete and four near-complete linear genomes share 40 genes that define a largely syntenous genome backbone. We use these conserved genes to identify new Borgs from peatland soil and to delineate Borg phylogeny, revealing two major clades. Remarkably, Borg genes encoding nanowire-like electron-transferring cytochromes and cell surface proteins are more highly expressed than those of host Methanoperedens, indicating that Borgs augment the Methanoperedens activity in situ. We reconstructed the first complete 4.00 Mbp genome for a Methanoperedens that is inferred to be a Borg host and predicted its methylation motifs, which differ from pervasive TC and CC methylation motifs of the Borgs. Thus, methylation may enable Methanoperedens to distinguish their genomes from those of Borgs. Very high Borg to Methanoperedens ratios and structural predictions suggest that Borgs may be capable of encapsulation. The findings clearly define Borgs as a distinct class of ECE with shared genomic signatures, establish their diversification from a common ancestor with genetic inheritance, and raise the possibility of periodic existence outside of host cells.},
}
@article {pmid38922750,
year = {2024},
author = {Lawruk-Desjardins, C and Storck, V and Ponton, DE and Amyot, M and Walsh, DA},
title = {A genome catalogue of mercury-methylating bacteria and archaea from sediments of a boreal river facing human disturbances.},
journal = {Environmental microbiology},
volume = {26},
number = {6},
pages = {e16669},
doi = {10.1111/1462-2920.16669},
pmid = {38922750},
issn = {1462-2920},
support = {ALLRP 560330 - 20//Natural Sciences and Engineering Research Council of Canada/ ; RDCPJ493474-15//Natural Sciences and Engineering Research Council of Canada/ ; },
mesh = {*Geologic Sediments/microbiology ; *Rivers/microbiology ; *Archaea/genetics/metabolism/classification ; *Bacteria/genetics/classification/metabolism ; *Mercury/metabolism ; *Methylmercury Compounds/metabolism ; Metagenomics ; Humans ; Genome, Bacterial ; Genome, Archaeal ; Ecosystem ; Microbiota ; },
abstract = {Methyl mercury, a toxic compound, is produced by anaerobic microbes and magnifies in aquatic food webs, affecting the health of animals and humans. The exploration of mercury methylators based on genomes is still limited, especially in the context of river ecosystems. To address this knowledge gap, we developed a genome catalogue of potential mercury-methylating microorganisms. This was based on the presence of hgcAB from the sediments of a river affected by two run-of-river hydroelectric dams, logging activities and a wildfire. Through the use of genome-resolved metagenomics, we discovered a unique and diverse group of mercury methylators. These were dominated by members of the metabolically versatile Bacteroidota and were particularly rich in microbes that ferment butyrate. By comparing the diversity and abundance of mercury methylators between sites subjected to different disturbances, we found that ongoing disturbances, such as the input of organic matter related to logging activities, were particularly conducive to the establishment of a mercury-methylating niche. Finally, to gain a deeper understanding of the environmental factors that shape the diversity of mercury methylators, we compared the mercury-methylating genome catalogue with the broader microbial community. The results suggest that mercury methylators respond to environmental conditions in a manner similar to the overall microbial community. Therefore, it is crucial to interpret the diversity and abundance of mercury methylators within their specific ecological context.},
}
@article {pmid38918468,
year = {2024},
author = {Shi, LD and West-Roberts, J and Schoelmerich, MC and Penev, PI and Chen, L and Amano, Y and Lei, S and Sachdeva, R and Banfield, JF},
title = {Methanotrophic Methanoperedens archaea host diverse and interacting extrachromosomal elements.},
journal = {Nature microbiology},
volume = {9},
number = {9},
pages = {2422-2433},
pmid = {38918468},
issn = {2058-5276},
support = {INV-037174/GATES/Bill &amp; Melinda Gates Foundation/United States ; INV-037174/GATES/Bill &amp; Melinda Gates Foundation/United States ; },
mesh = {*Methane/metabolism ; *Phylogeny ; Genome, Archaeal ; DNA Transposable Elements/genetics ; Euryarchaeota/genetics/metabolism ; Genetic Variation ; },
abstract = {Methane emissions are mitigated by anaerobic methane-oxidizing archaea, including Methanoperedens. Some Methanoperedens host huge extrachromosomal genetic elements (ECEs) called Borgs that may modulate their activity, yet the broader diversity of Methanoperedens ECEs is understudied. Here we report small enigmatic linear ECEs, circular viruses and unclassified ECEs that are predicted to replicate within Methanoperedens. Linear ECEs have inverted terminal repeats, tandem repeats and coding patterns that are strongly reminiscent of Borgs, but they are only 52-145 kb in length. As they share proteins with Borgs and Methanoperedens, we refer to them as mini-Borgs. Mini-Borgs are genetically diverse and can be assigned to at least five family-level groups. We identify eight families of Methanoperedens viruses, some of which encode multi-haem cytochromes, and circular ECEs encoding transposon-associated TnpB genes with proximal population-heterogeneous CRISPR arrays. These ECEs exchange genetic information with each other and with Methanoperedens, probably impacting their archaeal host activity and evolution.},
}
@article {pmid38918384,
year = {2024},
author = {Dueholm, MKD and Andersen, KS and Korntved, AC and Rudkjøbing, V and Alves, M and Bajón-Fernández, Y and Batstone, D and Butler, C and Cruz, MC and Davidsson, &#xc5; and Erijman, L and Holliger, C and Koch, K and Kreuzinger, N and Lee, C and Lyberatos, G and Mutnuri, S and O'Flaherty, V and Oleskowicz-Popiel, P and Pokorna, D and Rajal, V and Recktenwald, M and Rodríguez, J and Saikaly, PE and Tooker, N and Vierheilig, J and De Vrieze, J and Wurzbacher, C and Nielsen, PH},
title = {MiDAS 5: Global diversity of bacteria and archaea in anaerobic digesters.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {5361},
pmid = {38918384},
issn = {2041-1723},
support = {Dark Matter and grant 13351//Villum Fonden (Villum Foundation)/ ; 6111-00617 A//Det Frie Forskningsr&#xe5;d (Danish Council for Independent Research)/ ; },
mesh = {*Archaea/genetics/classification/metabolism ; *RNA, Ribosomal, 16S/genetics ; Anaerobiosis ; *Bacteria/genetics/classification/metabolism ; *Microbiota/genetics ; *Biodiversity ; *Phylogeny ; Wastewater/microbiology ; Bioreactors/microbiology ; Methane/metabolism ; Sequence Analysis, DNA ; },
abstract = {Anaerobic digestion of organic waste into methane and carbon dioxide (biogas) is carried out by complex microbial communities. Here, we use full-length 16S rRNA gene sequencing of 285 full-scale anaerobic digesters (ADs) to expand our knowledge about diversity and function of the bacteria and archaea in ADs worldwide. The sequences are processed into full-length 16S rRNA amplicon sequence variants (FL-ASVs) and are used to expand the MiDAS 4 database for bacteria and archaea in wastewater treatment systems, creating MiDAS 5. The expansion of the MiDAS database increases the coverage for bacteria and archaea in ADs worldwide, leading to improved genus- and species-level classification. Using MiDAS 5, we carry out an amplicon-based, global-scale microbial community profiling of the sampled ADs using three common sets of primers targeting different regions of the 16S rRNA gene in bacteria and/or archaea. We reveal how environmental conditions and biogeography shape the AD microbiota. We also identify core and conditionally rare or abundant taxa, encompassing 692 genera and 1013 species. These represent 84-99% and 18-61% of the accumulated read abundance, respectively, across samples depending on the amplicon primers used. Finally, we examine the global diversity of functional groups with known importance for the anaerobic digestion process.},
}
@article {pmid38900790,
year = {2024},
author = {Murali, R and Pace, LA and Sanford, RA and Ward, LM and Lynes, MM and Hatzenpichler, R and Lingappa, UF and Fischer, WW and Gennis, RB and Hemp, J},
title = {Diversity and evolution of nitric oxide reduction in bacteria and archaea.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {26},
pages = {e2316422121},
pmid = {38900790},
issn = {1091-6490},
support = {U12AB123456//National Institute of Health (NIH)/ ; 503546//Joint Genome Institute (JGI)/ ; DE-AC02-05CH11231//Joint Genome Institute (JGI)/ ; DE-AC05-76RL01830//DOE | SC | PNNL | Environmental Molecular Sciences Laboratory (EMSL)/ ; },
mesh = {*Nitric Oxide/metabolism ; *Oxidoreductases/metabolism/genetics ; *Phylogeny ; *Oxidation-Reduction ; Archaea/metabolism/genetics ; Rhodothermus/metabolism/enzymology/genetics ; Evolution, Molecular ; Bacteria/metabolism/genetics ; Bacterial Proteins/metabolism/genetics/chemistry ; },
abstract = {Nitrous oxide is a potent greenhouse gas whose production is catalyzed by nitric oxide reductase (NOR) members of the heme-copper oxidoreductase (HCO) enzyme superfamily. We identified several previously uncharacterized HCO families, four of which (eNOR, sNOR, gNOR, and nNOR) appear to perform NO reduction. These families have novel active-site structures and several have conserved proton channels, suggesting that they might be able to couple NO reduction to energy conservation. We isolated and biochemically characterized a member of the eNOR family from the bacterium Rhodothermus marinus and found that it performs NO reduction. These recently identified NORs exhibited broad phylogenetic and environmental distributions, greatly expanding the diversity of microbes in nature capable of NO reduction. Phylogenetic analyses further demonstrated that NORs evolved multiple times independently from oxygen reductases, supporting the view that complete denitrification evolved after aerobic respiration.},
}
@article {pmid38898040,
year = {2024},
author = {Li, Y and Yu, T and Feng, X and Zhao, B and Chen, H and Yang, H and Chen, X and Zhang, XH and Anderson, HR and Burns, NZ and Zeng, F and Tao, L and Zeng, Z},
title = {Biosynthesis of GMGT lipids by a radical SAM enzyme associated with anaerobic archaea and oxygen-deficient environments.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {5256},
pmid = {38898040},
issn = {2041-1723},
support = {92351301//National Science Foundation of China | National Natural Science Foundation of China-Yunnan Joint Fund (NSFC-Yunnan Joint Fund)/ ; },
mesh = {*S-Adenosylmethionine/metabolism ; *Archaea/genetics/metabolism/enzymology ; *Oxygen/metabolism ; Anaerobiosis ; Archaeal Proteins/metabolism/genetics ; Glycerol/metabolism ; Metagenome ; Phylogeny ; },
abstract = {Archaea possess characteristic membrane-spanning lipids that are thought to contribute to the adaptation to extreme environments. However, the biosynthesis of these lipids is poorly understood. Here, we identify a radical S-adenosyl-L-methionine (SAM) enzyme that synthesizes glycerol monoalkyl glycerol tetraethers (GMGTs). The enzyme, which we name GMGT synthase (Gms), catalyzes the formation of a C(sp[3])-C(sp[3]) linkage between the two isoprenoid chains of glycerol dialkyl glycerol tetraethers (GDGTs). This conclusion is supported by heterologous expression of gene gms from a GMGT-producing species in a methanogen, as well as demonstration of in vitro activity using purified Gms enzyme. Additionally, we show that genes encoding putative Gms homologs are present in obligate anaerobic archaea and in metagenomes obtained from oxygen-deficient environments, and appear to be absent in metagenomes from oxic settings.},
}
@article {pmid38896033,
year = {2024},
author = {Huang, B and Xiao, Y and Zhang, Y},
title = {Asgard archaeal selenoproteome reveals a roadmap for the archaea-to-eukaryote transition of selenocysteine incorporation machinery.},
journal = {The ISME journal},
volume = {18},
number = {1},
pages = {},
pmid = {38896033},
issn = {1751-7370},
support = {32270680//National Natural Science Foundation of China/ ; 2023SHIBS0003//Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions/ ; },
mesh = {*Selenocysteine/metabolism/genetics ; *Archaea/genetics/metabolism/classification ; *Selenoproteins/genetics/metabolism ; *Eukaryota/genetics/classification/metabolism ; Genome, Archaeal ; Proteome ; Codon, Terminator/genetics ; Archaeal Proteins/genetics/metabolism ; Evolution, Molecular ; Gene Transfer, Horizontal ; Phylogeny ; },
abstract = {Selenocysteine (Sec) is encoded by the UGA codon that normally functions as a stop signal and is specifically incorporated into selenoproteins via a unique recoding mechanism. The translational recoding of UGA as Sec is directed by an unusual RNA structure, the SECIS element. Although archaea and eukaryotes adopt similar Sec encoding machinery, the SECIS elements have no similarities to each other with regard to sequence and structure. We analyzed >400 Asgard archaeal genomes to examine the occurrence of both Sec encoding system and selenoproteins in this archaeal superphylum, the closest prokaryotic relatives of eukaryotes. A comprehensive map of Sec utilization trait has been generated, providing the most detailed understanding of the use of this nonstandard amino acid in Asgard archaea so far. By characterizing the selenoproteomes of all organisms, several selenoprotein-rich phyla and species were identified. Most Asgard archaeal selenoprotein genes possess eukaryotic SECIS-like structures with varying degrees of diversity. Moreover, euryarchaeal SECIS elements might originate from Asgard archaeal SECIS elements via lateral gene transfer, indicating a complex and dynamic scenario of the evolution of SECIS element within archaea. Finally, a roadmap for the transition of eukaryotic SECIS elements from archaea was proposed, and selenophosphate synthetase may serve as a potential intermediate for the generation of ancestral eukaryotic SECIS element. Our results offer new insights into a deeper understanding of the evolution of Sec insertion machinery.},
}
@article {pmid38890479,
year = {2024},
author = {Du Toit, A},
title = {Gassy archaea.},
journal = {Nature reviews. Microbiology},
volume = {22},
number = {8},
pages = {456},
pmid = {38890479},
issn = {1740-1534},
mesh = {*Archaea/genetics ; Genome, Archaeal ; Phylogeny ; },
}
@article {pmid38890178,
year = {2024},
author = {Cui, L and Hu, Y and Li, XX and Ma, X and Cheng, M and Tan, S and Hou, J and Cui, HL},
title = {Halobacterium yunchengense sp. nov., Natronomonas amylolytica sp. nov., Halorientalis halophila sp. nov., Halobellus salinisoli sp. nov., halophilic archaea isolated from a saline lake and inland saline soil.},
journal = {Extremophiles : life under extreme conditions},
volume = {28},
number = {2},
pages = {28},
pmid = {38890178},
issn = {1433-4909},
support = {32070003//National Natural Science Foundation of China/ ; },
mesh = {*Lakes/microbiology ; *Phylogeny ; Soil Microbiology ; Halobacterium/genetics/isolation &amp; purification ; Genome, Archaeal ; Halobacteriaceae/genetics/isolation &amp; purification/classification ; },
abstract = {Four halophilic archaeal strains YCN1[T], YCN58[T], LT38[T], and LT62[T] were isolated from Yuncheng Salt Lake (Shanxi, China) and Tarim Basin (Xinjiang, China), respectively. Phylogenetic and phylogenomic analyses showed that these four strains tightly cluster with related species of Halobacterium, Natronomonas, Halorientalis, and Halobellus, respectively. The AAI, ANI, and dDDH values between these four strains and their related species of respective genera were lower than the proposed threshold values for species delineation. Strains YCN1[T], YCN58[T], LT38[T], and LT62[T] could be differentiated from the current species of Halobacterium, Natronomonas, Halorientalis, and Halobellus, respectively, based on the comparison of diverse phenotypic characteristics. The polar lipid profiles of these four strains were closely similar to those of respective relatives within the genera Halobacterium, Natronomonas, Halorientalis, and Halobellus, respectively. The phenotypic, phylogenetic, and genome-based analyses indicated that strains YCN1[T], YCN58[T], LT38[T], and LT62[T] represent respective novel species within the genera Halobacterium, Natronomonas, Halorentalis, and Halobellus, for which the names Halobacterium yunchengense sp. nov., Natronomonas amylolytica sp. nov., Halorientalis halophila sp. nov., and Halobellus salinisoli sp. nov. are proposed, respectively.},
}
@article {pmid38887712,
year = {2024},
author = {Rekadwad, BN and Gonzalez, JM and Li, WJ},
title = {Editorial: Last universal common ancestor and origin of life: what uncultivated Bacteria, Archaea, and extremophiles can tell us.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1412625},
pmid = {38887712},
issn = {1664-302X},
}
@article {pmid38885730,
year = {2024},
author = {Lv, PL and Jia, C and Wei, CH and Zhao, HP and Chen, R},
title = {Biochar modulates intracellular electron transfer for nitrate reduction in denitrifying anaerobic methane oxidizing archaea.},
journal = {Bioresource technology},
volume = {406},
number = {},
pages = {130998},
doi = {10.1016/j.biortech.2024.130998},
pmid = {38885730},
issn = {1873-2976},
mesh = {*Methane/metabolism ; *Archaea/metabolism ; *Charcoal/metabolism ; *Nitrates/metabolism ; Electron Transport ; *Oxidation-Reduction ; Anaerobiosis ; *Denitrification/physiology ; Biofilms ; Extracellular Polymeric Substance Matrix/metabolism ; },
abstract = {Denitrifying anaerobic methane oxidizing (DAMO) archaea plays a significant role in simultaneously nitrogen removal and methane mitigation, yet its limited metabolic activity hinders engineering applications. This study employed biochar to explore its potential for enhancing the metabolic activity and nitrate reduction capacity of DAMO microorganisms. Sawdust biochar (7 g/L) was found to increase the nitrate reduction rate by 2.85 times, although it did not affect the nitrite reduction rate individually. Scanning electron microscopy (SEM) and fluorescence excitation-emission matrix (EEM) analyses revealed that biochar promoted microbial aggregation, and stimulated the secretion of extracellular polymeric substances (EPS). Moreover, biochar bolstered the redox capacity and conductivity of the biofilm, notably enhancing the activity of the electron transfer system by 1.65 times. Key genes involved in intracellular electron transport (Hdr, MHC, Rnf) and membrane transport proteins (BBP, ABC, NDH) of archaea were significantly up-regulated. These findings suggest that biochar regulates electrons generated by reverse methanogenesis to the membrane for nitrate reduction.},
}
@article {pmid38884810,
year = {2024},
author = {Hu, Y and Ma, X and Tan, S and Li, XX and Cheng, M and Hou, J and Cui, HL},
title = {Correction: Genome-based classification of genera Halosegnis and Salella, and description of four novel halophilic archaea isolated from a tidal flat.},
journal = {Antonie van Leeuwenhoek},
volume = {117},
number = {1},
pages = {90},
doi = {10.1007/s10482-024-01983-9},
pmid = {38884810},
issn = {1572-9699},
}
@article {pmid38866018,
year = {2024},
author = {Greening, C and Cabotaje, PR and Valentin Alvarado, LE and Leung, PM and Land, H and Rodrigues-Oliveira, T and Ponce-Toledo, RI and Senger, M and Klamke, MA and Milton, M and Lappan, R and Mullen, S and West-Roberts, J and Mao, J and Song, J and Schoelmerich, M and Stairs, CW and Schleper, C and Grinter, R and Spang, A and Banfield, JF and Berggren, G},
title = {Minimal and hybrid hydrogenases are active from archaea.},
journal = {Cell},
volume = {187},
number = {13},
pages = {3357-3372.e19},
pmid = {38866018},
issn = {1097-4172},
mesh = {*Archaea/genetics/enzymology ; Archaeal Proteins/metabolism/chemistry/genetics ; Genome, Archaeal ; *Hydrogen/metabolism ; *Hydrogenase/metabolism/genetics/chemistry ; Iron-Sulfur Proteins/metabolism/genetics/chemistry ; Models, Molecular ; *Phylogeny ; Protein Structure, Tertiary ; },
abstract = {Microbial hydrogen (H2) cycling underpins the diversity and functionality of diverse anoxic ecosystems. Among the three evolutionarily distinct hydrogenase superfamilies responsible, [FeFe] hydrogenases were thought to be restricted to bacteria and eukaryotes. Here, we show that anaerobic archaea encode diverse, active, and ancient lineages of [FeFe] hydrogenases through combining analysis of existing and new genomes with extensive biochemical experiments. [FeFe] hydrogenases are encoded by genomes of nine archaeal phyla and expressed by H2-producing Asgard archaeon cultures. We report an ultraminimal hydrogenase in DPANN archaea that binds the catalytic H-cluster and produces H2. Moreover, we identify and characterize remarkable hybrid complexes formed through the fusion of [FeFe] and [NiFe] hydrogenases in ten other archaeal orders. Phylogenetic analysis and structural modeling suggest a deep evolutionary history of hybrid hydrogenases. These findings reveal new metabolic adaptations of archaea, streamlined H2 catalysts for biotechnological development, and a surprisingly intertwined evolutionary history between the two major H2-metabolizing enzymes.},
}
@article {pmid38852635,
year = {2024},
author = {Kong, L and Wang, Y and Cui, D and He, W and Zhang, C and Zheng, C},
title = {Application of single-cell Raman-deuterium isotope probing to reveal the resistance of marine ammonia-oxidizing archaea SCM1 against common antibiotics.},
journal = {Chemosphere},
volume = {362},
number = {},
pages = {142500},
doi = {10.1016/j.chemosphere.2024.142500},
pmid = {38852635},
issn = {1879-1298},
mesh = {*Anti-Bacterial Agents/pharmacology ; *Archaea/genetics/drug effects/metabolism ; Ammonia/metabolism ; Microbial Sensitivity Tests ; Oxidation-Reduction ; Single-Cell Analysis ; Spectrum Analysis, Raman ; Drug Resistance, Microbial/genetics ; },
abstract = {Antimicrobial resistance (AMR) in oceans poses a significant threat to human health through the seafood supply chain. Ammonia-oxidizing archaea (AOA) are important marine microorganisms and play a key role in the biogeochemical nitrogen cycle around the world. However, the AMR of marine AOA to aquicultural antibiotics is poorly explored. Here, Raman-deuterium isotope probing (Raman-DIP), a single-cell tool, was developed to reveal the AMR of a typical marine species of AOA, Nitrosopumilus maritimus (designated SCM1), against six antibiotics, including erythromycin, tetracycline, novobiocin, neomycin, bacitracin, and vancomycin. The D2O concentration (30% v/v) and culture period (9 days) were optimized for the precise detection of metabolic activity in SCM1 cells through Raman-DIP. The relative metabolic activity of SCM1 upon exposure to antibiotics was semi-quantitatively calculated based on single-cell Raman spectra. SCM1 exhibited high resistance to erythromycin, tetracycline, novobiocin, neomycin, and vancomycin, with minimum inhibitory concentration (MIC) values between 100 and 400 mg/L, while SCM1 is very sensitive to bacitracin (MIC: 0.8 mg/L). Notably, SCM1 cells were completely inactive under the metabolic activity minimum inhibitory concentration conditions (MA-MIC: 1.6-800 mg/L) for the six antibiotics. Further genomic analysis revealed the antibiotic resistance genes (ARGs) of SCM1, including 14 types categorized into 33 subtypes. This work increases our knowledge of the AMR of marine AOA by linking the resistant phenome to the genome, contributing to the risk assessment of AMR in the underexplored ocean environment. As antibiotic resistance in marine microorganisms is significantly affected by the concentration of antibiotics in coastal environments, we encourage more studies concentrating on both the phenotypic and genotypic antibiotic resistance of marine archaea. This may facilitate a comprehensive evaluation of the capacity of marine microorganisms to spread AMR and the implementation of suitable control measures to protect environmental safety and human health.},
}
@article {pmid38829054,
year = {2024},
author = {Ma, Y and Sun, Z and Yang, H and Xie, W and Song, M and Zhang, B and Sui, L},
title = {The biosynthesis mechanism of bacterioruberin in halophilic archaea revealed by genome and transcriptome analysis.},
journal = {Applied and environmental microbiology},
volume = {90},
number = {7},
pages = {e0054024},
pmid = {38829054},
issn = {1098-5336},
support = {42306106//MOST | National Natural Science Foundation of China (NSFC)/ ; EMTUST-21-01//Key laboratory of Marine Resource Chemistry and Food Technology, Ministry of Education/ ; 2019KJ220//Tianjin Municipal Education Commission/ ; },
mesh = {*Genome, Archaeal ; *Carotenoids/metabolism ; *Gene Expression Profiling ; Halorubrum/genetics/metabolism/growth &amp; development ; Transcriptome ; Archaeal Proteins/genetics/metabolism ; },
abstract = {UNLABELLED: Halophilic archaea are promising microbial cell factories for bacterioruberin (BR) production. BR is a natural product with multi-bioactivities, allowing potential application in many fields. In the previous work, a haloarchaeon Halorubrum sp. HRM-150 with a high proportion of BR (about 85%) was isolated, but the low yield impeded its large-scale production. This work figured out BR synthesis characteristics and mechanisms, and proposed strategies for yield improvement. First, glucose (10 g/L) and tryptone (15 g/L) were tested to be better sources for BR production. Besides, the combination of glucose and starch achieved the diauxic growth, and the biomass and BR productivity increased by 85% and 54% than using glucose. Additionally, this work first proposed the BR synthesis pattern, which differs from that of other carotenoids. As a structural component of cell membranes, the BR synthesis is highly coupled with growth, which was most active in the logarithm phase. Meanwhile, the osmotic down shock at the logarithm phase could increase the BR productivity without sacrificing the biomass. Moreover, the de-novo pathway for BR synthesis with a key gene of lyeJ, and its competitive pathways (notably tetraether lipids and retinal) were revealed through genome, transcriptome, and osmotic down shock. Therefore, the BR yield is expected to be improved through mutant construction, such as the overexpression of key gene lyeJ and the knockout of competitive genes, which need to be further explored. The findings will contribute to a better understanding of the metabolism mechanism in haloarchaea and the development of haloarchaea as microbial cell factories.<br><br>IMPORTANCE: Recent studies have revealed that halophilic microorganism is a promising microbial factory for the next-generation industrialization. Among them, halophilic archaea are advantageous as microbial factories due to their low contamination risk and low freshwater consumption. The halophilic archaea usually accumulate long chain C50 carotenoids, which are barely found in other organisms. Bacterioruberin (BR), the major C50 carotenoid, has multi-bioactivities, allowing potential application in food, cosmetic, and biomedical industries. However, the low yield impedes its large-scale application. This work figured out the BR synthesis characteristics and mechanism, and proposed several strategies for BR yield improvement, encouraging halophilic archaea to function as microbial factories for BR production. Meanwhile, the archaea have special evolutionary status and unique characteristics in taxonomy, the revelation of BR biosynthesis mechanism is beneficial for a better understanding of archaea.},
}
@article {pmid38825783,
year = {2024},
author = {Orgler, E and Baumgartner, M and Duller, S and Kumptisch, C and Hausmann, B and Moser, D and Khare, V and Lang, M and Köcher, T and Frick, A and Muttenthaler, M and Makristathis, A and Moissl-Eichinger, C and Gasche, C},
title = {Archaea influence composition of endoscopically visible ileocolonic biofilms.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2359500},
pmid = {38825783},
issn = {1949-0984},
mesh = {Humans ; *Biofilms/growth &amp; development ; *Gastrointestinal Microbiome ; *Archaea/classification/metabolism/genetics/isolation &amp; purification ; Adult ; Middle Aged ; Female ; Male ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; *Feces/microbiology ; Colon/microbiology ; Methanobrevibacter/metabolism/genetics/growth &amp; development/isolation &amp; purification ; Colitis, Ulcerative/microbiology/metabolism ; Irritable Bowel Syndrome/microbiology/metabolism ; Aged ; Intestinal Mucosa/microbiology/metabolism ; Ileum/microbiology ; Fatty Acids, Volatile/metabolism ; Young Adult ; Bile Acids and Salts/metabolism ; },
abstract = {The gut microbiota has been implicated as a driver of irritable bowel syndrome (IBS) and inflammatory bowel disease (IBD). Recently we described, mucosal biofilms, signifying alterations in microbiota composition and bile acid (BA) metabolism in IBS and ulcerative colitis (UC). Luminal oxygen concentration is a key factor in the gastrointestinal (GI) ecosystem and might be increased in IBS and UC. Here we analyzed the role of archaea as a marker for hypoxia in mucosal biofilms and GI homeostasis. The effects of archaea on microbiome composition and metabolites were analyzed via amplicon sequencing and untargeted metabolomics in 154 stool samples of IBS-, UC-patients and controls. Mucosal biofilms were collected in a subset of patients and examined for their bacterial, fungal and archaeal composition. Absence of archaea, specifically Methanobrevibacter, correlated with disrupted GI homeostasis including decreased microbial diversity, overgrowth of facultative anaerobes and conjugated secondary BA. IBS-D/-M was associated with absence of archaea. Presence of Methanobrevibacter correlated with Oscillospiraceae and epithelial short chain fatty acid metabolism and decreased levels of Ruminococcus gnavus. Absence of fecal Methanobrevibacter may indicate a less hypoxic GI environment, reduced fatty acid oxidation, overgrowth of facultative anaerobes and disrupted BA deconjugation. Archaea and Ruminococcus gnavus could distinguish distinct subtypes of mucosal biofilms. Further research on the connection between archaea, mucosal biofilms and small intestinal bacterial overgrowth should be performed.},
}
@article {pmid38814265,
year = {2024},
author = {Rahn, HP and Sun, J and Li, Z and Waymouth, RM and Levy, R and Wender, PA},
title = {Isoprenoid CARTs: In Vitro and In Vivo mRNA Delivery by Charge-Altering Releasable Transporters Functionalized with Archaea-inspired Branched Lipids.},
journal = {Biomacromolecules},
volume = {25},
number = {7},
pages = {4305-4316},
doi = {10.1021/acs.biomac.4c00373},
pmid = {38814265},
issn = {1526-4602},
mesh = {Animals ; Mice ; *RNA, Messenger/genetics ; *Lipids/chemistry ; Humans ; Terpenes/chemistry ; Archaea/genetics/chemistry ; Nanoparticles/chemistry ; },
abstract = {The delivery of oligonucleotides across biological barriers is a challenge of unsurpassed significance at the interface of materials science and medicine, with emerging clinical utility in prophylactic and therapeutic vaccinations, immunotherapies, genome editing, and cell rejuvenation. Here, we address the role of readily available branched lipids in the design, synthesis, and evaluation of isoprenoid charge-altering releasable transporters (CARTs), a pH-responsive oligomeric nanoparticle delivery system for RNA. Systematic variation of the lipid block reveals an emergent relationship between the lipid block and the neutralization kinetics of the polycationic block. Unexpectedly, iA21A11, a CART with the smallest lipid side chain, isoamyl-, was identified as the lead isoprenoid CART for the in vitro transfection of immortalized lymphoblastic cell lines. When administered intramuscularly in a murine model, iA21A11-mRNA complexes induce higher protein expression levels than our previous lead CART, ONA. Isoprenoid CARTs represent a new delivery platform for RNA vaccines and other polyanion-based therapeutics.},
}
@article {pmid38811725,
year = {2024},
author = {von Kügelgen, A and Cassidy, CK and van Dorst, S and Pagani, LL and Batters, C and Ford, Z and Löwe, J and Alva, V and Stansfeld, PJ and Bharat, TAM},
title = {Membraneless channels sieve cations in ammonia-oxidizing marine archaea.},
journal = {Nature},
volume = {630},
number = {8015},
pages = {230-236},
pmid = {38811725},
issn = {1476-4687},
mesh = {*Ammonia/chemistry/metabolism ; *Aquatic Organisms/chemistry/metabolism/ultrastructure ; *Archaea/chemistry/metabolism/ultrastructure ; Cations/chemistry/metabolism ; *Cell Membrane ; Cryoelectron Microscopy ; Models, Molecular ; Oxidation-Reduction ; Polysaccharides/metabolism/chemistry ; },
abstract = {Nitrosopumilus maritimus is an ammonia-oxidizing archaeon that is crucial to the global nitrogen cycle[1,2]. A critical step for nitrogen oxidation is the entrapment of ammonium ions from a dilute marine environment at the cell surface and their subsequent channelling to the cell membrane of N. maritimus. Here we elucidate the structure of the molecular machinery responsible for this process, comprising the surface layer (S-layer), using electron cryotomography and subtomogram averaging from cells. We supplemented our in situ structure of the ammonium-binding S-layer array with a single-particle electron cryomicroscopy structure, revealing detailed features of this immunoglobulin-rich and glycan-decorated S-layer. Biochemical analyses showed strong ammonium binding by the cell surface, which was lost after S-layer disassembly. Sensitive bioinformatic analyses identified similar S-layers in many ammonia-oxidizing archaea, with conserved sequence and structural characteristics. Moreover, molecular simulations and structure determination of ammonium-enriched specimens enabled us to examine the cation-binding properties of the S-layer, revealing how it concentrates ammonium ions on its cell-facing side, effectively acting as a multichannel sieve on the cell membrane. This in situ structural study illuminates the biogeochemically essential process of ammonium binding and channelling, common to many marine microorganisms that are fundamental to the nitrogen cycle.},
}
@article {pmid38806737,
year = {2024},
author = {Cheng, M and Li, XX and Hou, J and Cui, HL},
title = {Halomarina litorea sp. nov., Halomarina pelagica sp. nov., Halomarina halobia sp. nov., and Halomarina ordinaria sp. nov., Halophilic Archaea Isolated from Coastal and Inland Saline Soil.},
journal = {Current microbiology},
volume = {81},
number = {7},
pages = {194},
pmid = {38806737},
issn = {1432-0991},
support = {32070003//National Natural Science Foundation of China/ ; },
mesh = {*Phylogeny ; *Soil Microbiology ; *RNA, Ribosomal, 16S/genetics ; *DNA, Archaeal/genetics/chemistry ; Halobacteriaceae/classification/genetics/isolation &amp; purification ; Base Composition ; Phospholipids/analysis ; Sequence Analysis, DNA ; },
abstract = {Four halophilic archaeal strains, BCD28[T], BND7[T], PSR21[T], and PSRA2[T], were isolated from coastal and inland saline soil, respectively. The 16S rRNA and rpoB' gene sequence similarities among these four strains and current species of Halomarina were 95.9-96.6% and 86.9-90.3%, respectively. Phylogenetic and phylogenomic analyses revealed that these four strains tightly cluster with the current species of the genus Halomarina. The AAI, ANI, and dDDH values among these four strains and current species of Halomarina were 65.3-68.4%, 75.8-77.7%, and 20.3-22.0%, respectively, clearly below the threshold values for species demarcation. Strains BCD28[T], BND7[T], PSR21[T], and PSRA2[T] could be differentiated from the current species of Halomarina based on the comparison of diverse phenotypic characteristics. The major polar lipids of these four strains were phosphatidylglycerol (PG), phosphatidylglycerol phosphate methyl ester (PGP-Me), and four to five glycolipids. Phosphatidylglycerol sulfate (PGS) was only detected in strain BND7[T]. The phenotypic, phylogenetic, and genome-based analyses suggested that strains BCD28[T] (= CGMCC 1.18776[T] = JCM 34908[T]), BND7[T] (= CGMCC 1.18778[T] = JCM 34910[T]), PSR21[T] (= CGMCC 1.17027[T] = JCM 34147[T]), and PSRA2[T] (= CGMCC 1.17214[T] = JCM 34148[T]) represent four novel species of the genus Halomarina, for which the names Halomarina litorea sp. nov., Halomarina pelagica sp. nov., Halomarina halobia sp. nov., and Halomarina ordinaria sp. nov. are proposed.},
}
@article {pmid38799924,
year = {2024},
author = {},
title = {Expression of Concern: Haloferax massiliensis sp. nov., the first human-associated halophilic archaea.},
journal = {New microbes and new infections},
volume = {59},
number = {},
pages = {101323},
pmid = {38799924},
issn = {2052-2975},
}
@article {pmid38765610,
year = {2024},
author = {Basu, S and Kurgan, L},
title = {Taxonomy-specific assessment of intrinsic disorder predictions at residue and region levels in higher eukaryotes, protists, archaea, bacteria and viruses.},
journal = {Computational and structural biotechnology journal},
volume = {23},
number = {},
pages = {1968-1977},
pmid = {38765610},
issn = {2001-0370},
abstract = {Intrinsic disorder predictors were evaluated in several studies including the two large CAID experiments. However, these studies are biased towards eukaryotic proteins and focus primarily on the residue-level predictions. We provide first-of-its-kind assessment that comprehensively covers the taxonomy and evaluates predictions at the residue and disordered region levels. We curate a benchmark dataset that uniformly covers eukaryotic, archaeal, bacterial, and viral proteins. We find that predictive performance differs substantially across taxonomy, where viruses are predicted most accurately, followed by protists and higher eukaryotes, while bacterial and archaeal proteins suffer lower levels of accuracy. These trends are consistent across predictors. We also find that current tools, except for flDPnn, struggle with reproducing native distributions of the numbers and sizes of the disordered regions. Moreover, analysis of two variants of disorder predictions derived from the AlphaFold2 predicted structures reveals that they produce accurate residue-level propensities for archaea, bacteria and protists. However, they underperform for higher eukaryotes and generally struggle to accurately identify disordered regions. Our results motivate development of new predictors that target bacteria and archaea and which produce accurate results at both residue and region levels. We also stress the need to include the region-level assessments in future assessments.},
}
@article {pmid38753237,
year = {2024},
author = {Zhang, Y and Xiang, Y and Yang, Z and Xu, R},
title = {Co-occurrence of dominant bacteria and methanogenic archaea and their metabolic traits in a thermophilic anaerobic digester.},
journal = {Environmental science and pollution research international},
volume = {31},
number = {25},
pages = {36716-36727},
pmid = {38753237},
issn = {1614-7499},
support = {42007357//National Natural Science Foundation of China/ ; },
mesh = {*Archaea/genetics/metabolism ; *Bacteria/metabolism/genetics ; Anaerobiosis ; *Methane/metabolism ; Phylogeny ; Bioreactors/microbiology ; },
abstract = {Thermophilic anaerobic digestion (TAD) represents a promising biotechnology for both methane energy production and waste stream treatment. However, numerous critical microorganisms and their metabolic characteristics involved in this process remain unidentified due to the limitations of culturable isolates. This study investigated the phylogenetic composition and potential metabolic traits of bacteria and methanogenic archaea in a TAD system using culture-independent metagenomics. Predominant microorganisms identified in the stable phase of TAD included hydrogenotrophic methanogens (Methanothermobacter and Methanosarcina) and hydrogen-producing bacteria (Coprothermobacter, Acetomicrobium, and Defluviitoga). Nine major metagenome-assembled genomes (MAGs) associated with the dominant genera were selected to infer their metabolic potentials. Genes related to thermal resistance were widely found in all nine major MAGs, such as the molecular chaperone genes, Clp protease gene, and RNA polymerase genes, which may contribute to their predominance under thermophilic condition. Thermophilic temperatures may increase the hydrogen partial pressure of Coprothermobacter, Acetomicrobium, and Defluviitoga, subsequently altering the primary methanogenesis pathway from acetoclastic pathway to hydrogenotrophic pathway in the TAD. Consequently, genes encoding the hydrogenotrophic methanogenesis pathway were the most abundant in the recovered archaeal MAGs. The potential interaction between hydrogen-producing bacteria and hydrogenotrophic methanogens may play critical roles in TAD processes.},
}
@article {pmid38744628,
year = {2024},
author = {Liu, X and Su, D and Huan, H and Zhang, J and Zhen, H and Jia, Q and Zhao, M},
title = {Corrigendum to "Rice-fish coculture without phosphorus addition improves paddy soil nitrogen availability by shaping ammonia-oxidizing archaea and bacteria in subtropical regions of South China" [Sci. Total Environ. 927 (2024): 171642].},
journal = {The Science of the total environment},
volume = {933},
number = {},
pages = {172946},
doi = {10.1016/j.scitotenv.2024.172946},
pmid = {38744628},
issn = {1879-1026},
}
@article {pmid38733792,
year = {2024},
author = {Musat, F and Kjeldsen, KU and Rotaru, AE and Chen, SC and Musat, N},
title = {Archaea oxidizing alkanes through alkyl-coenzyme M reductases.},
journal = {Current opinion in microbiology},
volume = {79},
number = {},
pages = {102486},
doi = {10.1016/j.mib.2024.102486},
pmid = {38733792},
issn = {1879-0364},
mesh = {*Alkanes/metabolism ; *Archaea/enzymology/genetics/metabolism ; *Oxidation-Reduction ; *Oxidoreductases/metabolism/genetics ; *Phylogeny ; Electron Transport ; Archaeal Proteins/metabolism/genetics/chemistry ; Gene Transfer, Horizontal ; Bacteria/enzymology/genetics/metabolism/classification ; },
abstract = {This review synthesizes recent discoveries of novel archaea clades capable of oxidizing higher alkanes, from volatile ones like ethane to longer-chain alkanes like hexadecane. These archaea, termed anaerobic multicarbon alkane-oxidizing archaea (ANKA), initiate alkane oxidation using alkyl-coenzyme M reductases, enzymes similar to the methyl-coenzyme M reductases of methanogenic and anaerobic methanotrophic archaea (ANME). The polyphyletic alkane-oxidizing archaea group (ALOX), encompassing ANME and ANKA, harbors increasingly complex alkane degradation pathways, correlated with the alkane chain length. We discuss the evolutionary trajectory of these pathways emphasizing metabolic innovations and the acquisition of metabolic modules via lateral gene transfer. Additionally, we explore the mechanisms by which archaea couple alkane oxidation with the reduction of electron acceptors, including electron transfer to partner sulfate-reducing bacteria (SRB). The phylogenetic and functional constraints that shape ALOX-SRB associations are also discussed. We conclude by highlighting the research needs in this emerging research field and its potential applications in biotechnology.},
}
@article {pmid38700364,
year = {2024},
author = {Padalko, A and Nair, G and Sousa, FL},
title = {Fusion/fission protein family identification in Archaea.},
journal = {mSystems},
volume = {9},
number = {6},
pages = {e0094823},
pmid = {38700364},
issn = {2379-5077},
support = {VRG15-007//Wien Wissenschafts- Forschungs- und TechnologieFonds/ ; },
mesh = {*Archaea/genetics ; *Archaeal Proteins/genetics/chemistry/metabolism ; *Genome, Archaeal/genetics ; *Phylogeny ; },
abstract = {The majority of newly discovered archaeal lineages remain without a cultivated representative, but scarce experimental data from the cultivated organisms show that they harbor distinct functional repertoires. To unveil the ecological as well as evolutionary impact of Archaea from metagenomics, new computational methods need to be developed, followed by in-depth analysis. Among them is the genome-wide protein fusion screening performed here. Natural fusions and fissions of genes not only contribute to microbial evolution but also complicate the correct identification and functional annotation of sequences. The products of these processes can be defined as fusion (or composite) proteins, the ones consisting of two or more domains originally encoded by different genes and split proteins, and the ones originating from the separation of a gene in two (fission). Fusion identifications are required for proper phylogenetic reconstructions and metabolic pathway completeness assessments, while mappings between fused and unfused proteins can fill some of the existing gaps in metabolic models. In the archaeal genome-wide screening, more than 1,900 fusion/fission protein clusters were identified, belonging to both newly sequenced and well-studied lineages. These protein families are mainly associated with different types of metabolism, genetic, and cellular processes. Moreover, 162 of the identified fusion/fission protein families are archaeal specific, having no identified fused homolog within the bacterial domain. Our approach was validated by the identification of experimentally characterized fusion/fission cases. However, around 25% of the identified fusion/fission families lack functional annotations for both composite and split states, showing the need for experimental characterization in Archaea.IMPORTANCEGenome-wide fusion screening has never been performed in Archaea on a broad taxonomic scale. The overlay of multiple computational techniques allows the detection of a fine-grained set of predicted fusion/fission families, instead of rough estimations based on conserved domain annotations only. The exhaustive mapping of fused proteins to bacterial organisms allows us to capture fusion/fission families that are specific to archaeal biology, as well as to identify links between bacterial and archaeal lineages based on cooccurrence of taxonomically restricted proteins and their sequence features. Furthermore, the identification of poorly characterized lineage-specific fusion proteins opens up possibilities for future experimental and computational investigations. This approach enhances our understanding of Archaea in general and provides potential candidates for in-depth studies in the future.},
}
@article {pmid38673759,
year = {2024},
author = {Dobryakova, NV and Dumina, MV and Zhgun, AA and Pokrovskaya, MV and Aleksandrova, SS and Zhdanov, DD and Kudryashova, EV},
title = {L-Asparaginase Conjugates from the Hyperthermophilic Archaea Thermococcus sibiricus with Improved Biocatalytic Properties.},
journal = {International journal of molecular sciences},
volume = {25},
number = {8},
pages = {},
pmid = {38673759},
issn = {1422-0067},
support = {project No. 22-74-10100//Russian Science Foundation/ ; },
mesh = {*Asparaginase/chemistry/metabolism ; *Thermococcus/enzymology ; Hydrogen-Ion Concentration ; *Enzyme Stability ; *Biocatalysis ; Polyethylene Glycols/chemistry ; Temperature ; Archaeal Proteins/chemistry/metabolism ; },
abstract = {This study investigated the effect of polycationic and uncharged polymers (and oligomers) on the catalytic parameters and thermostability of L-asparaginase from Thermococcus sibiricus (TsA). This enzyme has potential applications in the food industry to decrease the formation of carcinogenic acrylamide during the processing of carbohydrate-containing products. Conjugation with the polyamines polyethylenimine and spermine (PEI and Spm) or polyethylene glycol (PEG) did not significantly affect the secondary structure of the enzyme. PEG contributes to the stabilization of the dimeric form of TsA, as shown by HPLC. Furthermore, neither polyamines nor PEG significantly affected the binding of the L-Asn substrate to TsA. The conjugates showed greater maximum activity at pH 7.5 and 85 °C, 10-50% more than for native TsA. The pH optima for both TsA-PEI and TsA-Spm conjugates were shifted to lower pH ranges from pH 10 (for the native enzyme) to pH 8.0. Additionally, the TsA-Spm conjugate exhibited the highest activity at pH 6.5-9.0 among all the samples. Furthermore, the temperature optimum for activity at pH 7.5 shifted from 90-95 °C to 80-85 °C for the conjugates. The thermal inactivation mechanism of TsA-PEG appeared to change, and no aggregation was observed in contrast to that of the native enzyme. This was visually confirmed and supported by the analysis of the CD spectra, which remained almost unchanged after heating the conjugate solution. These results suggest that TsA-PEG may be a more stable form of TsA, making it a potentially more suitable option for industrial use.},
}
@article {pmid38664262,
year = {2024},
author = {Mukherjee, D and Selvi, VA and Ganguly, J and Masto, RE},
title = {New insights into the coal-associated methane architect: the ancient archaebacteria.},
journal = {Archives of microbiology},
volume = {206},
number = {5},
pages = {234},
pmid = {38664262},
issn = {1432-072X},
mesh = {*Methane/metabolism ; *Coal ; *Archaea/metabolism/genetics ; Ecosystem ; Phylogeny ; },
abstract = {Exploration and marketable exploitation of coalbed methane (CBM) as cleaner fuel has been started globally. In addition, incidence of methane in coal basins is an imperative fraction of global carbon cycle. Significantly, subsurface coal ecosystem contains methane forming archaea. There is a rising attention in optimizing microbial coal gasification to exploit the abundant or inexpensive coal reserves worldwide. Therefore, it is essential to understand the coalbeds in geo-microbial perspective. Current review provides an in-depth analysis of recent advances in our understanding of how methanoarchaea are distributed in coal deposits globally. Specially, we highlight the findings on coal-associated methanoarchaeal existence, abundance, diversity, metabolic activity, and biogeography in diverse coal basins worldwide. Growing evidences indicates that we have arrived an exciting era of archaeal research. Moreover, gasification of coal into methane by utilizing microbial methanogenesis is a considerable way to mitigate the energy crisis for the rising world population.},
}
@article {pmid38659982,
year = {2024},
author = {Li, Q and Cheng, X and Liu, X and Gao, P and Wang, H and Su, C and Huang, Q},
title = {Ammonia-oxidizing archaea adapted better to the dark, alkaline oligotrophic karst cave than their bacterial counterparts.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1377721},
pmid = {38659982},
issn = {1664-302X},
abstract = {Subsurface karst caves provide unique opportunities to study the deep biosphere, shedding light on microbial contribution to elemental cycling. Although ammonia oxidation driven by both ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) is well explored in soil and marine environments, our understanding in the subsurface biosphere still remained limited to date. To address this gap, weathered rock and sediment samples were collected from the Xincuntun Cave in Guilin City, an alkaline karst cave, and subjected to high-throughput sequencing and quantification of bacterial and archaeal amoA, along with determination of the potential nitrification rates (PNR). Results revealed that AOA dominated in ammonia oxidation, contributing 48-100% to the PNR, and AOA amoA gene copies outnumbered AOB by 2 to 6 orders. Nitrososphaera dominated in AOA communities, while Nitrosopira dominated AOB communities. AOA demonstrated significantly larger niche breadth than AOB. The development of AOA communities was influenced by deterministic processes (50.71%), while AOB communities were predominantly influenced by stochastic processes. TOC, NH4[+], and Cl[-] played crucial roles in shaping the compositions of ammonia oxidizers at the OTU level. Cross-domain co-occurrence networks highlighted the dominance of AOA nodes in the networks and positive associations between AOA and AOB, especially in the inner zone, suggesting collaborative effort to thrive in extreme environments. Their high gene copies, dominance in the interaction with ammonia oxidizing bacteria, expansive niche breadth and substantial contribution to PNR collectively confirmed that AOA better adapted to alkaline, oligotrophic karst caves environments, and thus play a fundamental role in nitrogen cycling in subsurface biosphere.},
}
@article {pmid38655083,
year = {2024},
author = {van Wolferen, M and Ithurbide, S and Santiago-Martínez, MG and Charles-Orszag, A},
title = {Editorial: Molecular Biology of Archaea - 2022.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1393932},
pmid = {38655083},
issn = {1664-302X},
}
@article {pmid38644887,
year = {2024},
author = {Gulati, P and Singh, A and Patra, S and Bhat, S and Verma, A},
title = {Restriction modification systems in archaea: A panoramic outlook.},
journal = {Heliyon},
volume = {10},
number = {8},
pages = {e27382},
pmid = {38644887},
issn = {2405-8440},
abstract = {Restriction modification (RM) systems are one of the ubiquitous yet primitive defense responses employed by bacteria and archaea with the primary role of safeguarding themselves against invading bacteriophages. Protection of the host occurs by the cleavage of the invading foreign DNA via restriction endonucleases with concomitant methylation of host DNA with the aid of a methyltransferase counterpart. RM systems have been extensively studied in bacteria, however, in the case of archaea there are limited reports of RM enzymes that are investigated to date owing to their inhospitable growth demands. This review aims to broaden the knowledge about what is known about the diversity of RM systems in archaea and encapsulate the current knowledge on restriction and modification enzymes characterized in archaea so far and the role of RM systems in the milieu of archaeal biology.},
}
@article {pmid38640671,
year = {2024},
author = {Wang, Q and Zheng, G and Ni, L and Wang, H and Li, W and Guo, P and Wang, Y and Zheng, D and Wu, J and Zhang, D},
title = {Colonization characteristics and dynamic transition of archaea communities on polyethylene and polypropylene microplastics in the sediments of mangrove ecosystems.},
journal = {Journal of hazardous materials},
volume = {471},
number = {},
pages = {134343},
doi = {10.1016/j.jhazmat.2024.134343},
pmid = {38640671},
issn = {1873-3336},
mesh = {*Polyethylene ; *Archaea/drug effects/metabolism ; *Geologic Sediments/microbiology/chemistry ; *Microplastics/toxicity ; *Polypropylenes ; *Wetlands ; *Biofilms/drug effects ; Water Pollutants, Chemical/toxicity/analysis ; Ecosystem ; },
abstract = {Microplastics are a growing concern in mangrove ecosystems; however, their effects on archaeal communities and related ecological processes remain unclear. We conducted in situ biofilm-enrichment experiments to investigate the ecological influence of polyethylene (PE) and polypropylene microplastics on archaeal communities in the sediments of mangrove ecosystems. The archaeal community present on microplastics was distinct from that of the surrounding sediments at an early stage but became increasingly similar over time. Bathyarchaeota, Thaumarchaeota, Euryarchaeota, and Asgardaeota were the most abundant phyla. Methanolobus, an archaeal biomarker, was enriched in PE biofilms, and significantly controlled by homogeneous selection in the plastisphere, indicating an increased potential risk of methane emission. The dominant archaeal assembly process in the sediments was deterministic (58.85%-70.47%), while that of the PE biofilm changed from stochastic to deterministic during the experiment. The network of PE plastispheres showed less complexity and competitive links, and higher modularity and stability than that of sediments. Functional prediction showed an increase in aerobic ammonia oxidation during the experiment, whereas methanogenesis and chemoheterotrophy were significantly higher in the plastisphere. This study provides novel insights into the impact of microplastic pollution on archaeal communities and their mediating ecological functions in mangrove ecosystems.},
}
@article {pmid38593165,
year = {2024},
author = {Price, MN and Arkin, AP},
title = {A fast comparative genome browser for diverse bacteria and archaea.},
journal = {PloS one},
volume = {19},
number = {4},
pages = {e0301871},
pmid = {38593165},
issn = {1932-6203},
mesh = {*Archaea/genetics ; *Bacteria/genetics ; Genomics ; Proteins/genetics ; Chromosome Mapping ; },
abstract = {Genome sequencing has revealed an incredible diversity of bacteria and archaea, but there are no fast and convenient tools for browsing across these genomes. It is cumbersome to view the prevalence of homologs for a protein of interest, or the gene neighborhoods of those homologs, across the diversity of the prokaryotes. We developed a web-based tool, fast.genomics, that uses two strategies to support fast browsing across the diversity of prokaryotes. First, the database of genomes is split up. The main database contains one representative from each of the 6,377 genera that have a high-quality genome, and additional databases for each taxonomic order contain up to 10 representatives of each species. Second, homologs of proteins of interest are identified quickly by using accelerated searches, usually in a few seconds. Once homologs are identified, fast.genomics can quickly show their prevalence across taxa, view their neighboring genes, or compare the prevalence of two different proteins. Fast.genomics is available at https://fast.genomics.lbl.gov.},
}
@article {pmid38593075,
year = {2024},
author = {Michimori, Y and Izaki, R and Su, Y and Fukuyama, Y and Shimamura, S and Nishimura, K and Miwa, Y and Hamakita, S and Shimosaka, T and Makino, Y and Takeno, R and Sato, T and Beppu, H and Cann, I and Kanai, T and Nunoura, T and Atomi, H},
title = {Removal of phosphoglycolate in hyperthermophilic archaea.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {16},
pages = {e2311390121},
pmid = {38593075},
issn = {1091-6490},
support = {JP19H05679//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JP19H05684//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JPNP22010//New Energy and Industrial Technology Development Organization (NEDO)/ ; },
mesh = {*Ribulose-Bisphosphate Carboxylase/genetics/metabolism ; *Archaea/metabolism ; Photosynthesis ; Glycolates/metabolism ; Phosphoric Monoester Hydrolases/metabolism ; Oxygenases/metabolism ; Pentoses ; },
abstract = {Many organisms that utilize the Calvin-Benson-Bassham (CBB) cycle for autotrophic growth harbor metabolic pathways to remove and/or salvage 2-phosphoglycolate, the product of the oxygenase activity of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco). It has been presumed that the occurrence of 2-phosphoglycolate salvage is linked to the CBB cycle, and in particular, the C2 pathway to the CBB cycle and oxygenic photosynthesis. Here, we examined 2-phosphoglycolate salvage in the hyperthermophilic archaeon Thermococcus kodakarensis, an obligate anaerobe that harbors a Rubisco that functions in the pentose bisphosphate pathway. T. kodakarensis harbors enzymes that have the potential to convert 2-phosphoglycolate to glycine and serine, and their genes were identified by biochemical and/or genetic analyses. 2-phosphoglycolate phosphatase activity increased 1.6-fold when cells were grown under microaerobic conditions compared to anaerobic conditions. Among two candidates, TK1734 encoded a phosphatase specific for 2-phosphoglycolate, and the enzyme was responsible for 80% of the 2-phosphoglycolate phosphatase activity in T. kodakarensis cells. The TK1734 disruption strain displayed growth impairment under microaerobic conditions, which was relieved upon addition of sodium sulfide. In addition, glycolate was detected in the medium when T. kodakarensis was grown under microaerobic conditions. The results suggest that T. kodakarensis removes 2-phosphoglycolate via a phosphatase reaction followed by secretion of glycolate to the medium. As the Rubisco in T. kodakarensis functions in the pentose bisphosphate pathway and not in the CBB cycle, mechanisms to remove 2-phosphoglycolate in this archaeon emerged independent of the CBB cycle.},
}
@article {pmid38592380,
year = {2024},
author = {Gao, X and Wang, S and Kong, W and Li, G and Zhang, L and Yin, X},
title = {Floristic changes and environmental drivers of soil fungi and archaea in different salt-tolerant plant communities in the intertidal habitat of coastal wetlands.},
journal = {Environmental geochemistry and health},
volume = {46},
number = {5},
pages = {167},
pmid = {38592380},
issn = {1573-2983},
support = {2022YSKY-41//Fundamental Research Funds for Central Public Welfare Scientific Research Institutes of China/ ; },
mesh = {*Ecosystem ; *Wetlands ; Salt-Tolerant Plants ; RNA, Ribosomal, 16S ; Archaea/genetics ; Poaceae ; Soil ; Fungi/genetics ; },
abstract = {Microorganisms are crucial elements of terrestrial ecosystems, which play significant roles in improving soil physicochemical properties, providing plant growth nutrients, degrading toxic and harmful chemicals, and biogeochemical cycling. Variations in the types and quantities of root exudates among different plants greatly alter soil physicochemical properties and result in variations in the diversity, structure, and function of soil microorganisms. Not much is understood about the differences of soil fungi and archaea communities for different plant communities in coastal wetlands, and their response mechanisms to environmental changes. In this study, fungal and archaea communities in soils of Suaeda salsa, Phragmites australis, and Spartina alterniflora in the intertidal habitat of coastal wetlands were selected for research. Soil fungi and archaea were analyzed for diversity, community structure, and function using high throughput ITS and 16S rRNA gene sequencing. The study revealed significant differences in fungi and archaea's diversity and community structure in the rhizosphere soil of three plant communities. At the same time, there is no significant difference in the functional groups. SOM, TP, AP, MC, EC and SOM, TN, TP, AP, MC, EC are the primary environmental determinants affecting changes in soil fungal and archaeal communities, respectively. Variations in the diversity, community structure, and ecological functions of fungi and archaea can be used as indicators characterizing the impact of external disturbances on the soil environment, providing a theoretical foundation for the effective utilization of soil microbial resources, thereby achieving the goal of environmental protection and health promotion.},
}
@article {pmid38570877,
year = {2024},
author = {Yin, X and Zhou, G and Cai, M and Richter-Heitmann, T and Zhu, QZ and Maeke, M and Kulkarni, AC and Nimzyk, R and Elvert, M and Friedrich, MW},
title = {Physiological versatility of ANME-1 and Bathyarchaeotoa-8 archaea evidenced by inverse stable isotope labeling.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {68},
pmid = {38570877},
issn = {2049-2618},
support = {49926684//Cluster of Excellence EXC 309/ ; 49926684//Cluster of Excellence EXC 309/ ; 390741601//Cluster of Excellence EXC 2077/ ; 390741601//Cluster of Excellence EXC 2077/ ; },
mesh = {*Archaea/genetics ; Isotope Labeling ; Oxidation-Reduction ; *Methane/metabolism ; Carbon/metabolism ; DNA ; Anaerobiosis ; Geologic Sediments ; Phylogeny ; },
abstract = {BACKGROUND: The trophic strategy is one key principle to categorize microbial lifestyles, by broadly classifying microorganisms based on the combination of their preferred carbon sources, electron sources, and electron sinks. Recently, a novel trophic strategy, i.e., chemoorganoautotrophy-the utilization of organic carbon as energy source but inorganic carbon as sole carbon source-has been specifically proposed for anaerobic methane oxidizing archaea (ANME-1) and Bathyarchaeota subgroup 8 (Bathy-8).<br><br>RESULTS: To further explore chemoorganoautotrophy, we employed stable isotope probing (SIP) of nucleic acids (rRNA or DNA) using unlabeled organic carbon and [13]C-labeled dissolved inorganic carbon (DIC), i.e., inverse stable isotope labeling, in combination with metagenomics. We found that ANME-1 archaea actively incorporated [13]C-DIC into RNA in the presence of methane and lepidocrocite when sulfate was absent, but assimilated organic carbon when cellulose was added to incubations without methane additions. Bathy-8 archaea assimilated [13]C-DIC when lignin was amended; however, their DNA was derived from both inorganic and organic carbon sources rather than from inorganic carbon alone. Based on SIP results and supported by metagenomics, carbon transfer between catabolic and anabolic branches of metabolism is possible in these archaeal groups, indicating their anabolic versatility.<br><br>CONCLUSION: We provide evidence for the incorporation of the mixed organic and inorganic carbon by ANME-1 and&#xa0;Bathy-8 archaea in the environment. Video Abstract.},
}
@article {pmid38530473,
year = {2024},
author = {Fry, M},
title = {The discovery of archaea: from observed anomaly to consequential restructuring of the phylogenetic tree.},
journal = {History and philosophy of the life sciences},
volume = {46},
number = {2},
pages = {16},
pmid = {38530473},
issn = {1742-6316},
support = {/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Phylogeny ; *Archaea/genetics ; Biological Evolution ; *Biological Science Disciplines ; },
abstract = {Observational and experimental discoveries of new factual entities such as objects, systems, or processes, are major contributors to some advances in the life sciences. Yet, whereas discovery of theories was extensively deliberated by philosophers of science, very little philosophical attention was paid to the discovery of factual entities. This paper examines historical and philosophical aspects of the experimental discovery by Carl Woese of archaea, prokaryotes that comprise one of the three principal domains of the phylogenetic tree. Borrowing Kuhn's terminology, this discovery of a major biological entity was made during a 'normal science' project of building molecular taxonomy for prokaryotes. Unexpectedly, however, an observed anomaly instigated the discovery of archaea. Substantiation of the existence of the new archaeal entity and consequent reconstruction of the phylogenetic tree prompted replacement of a long-held model of a prokarya and eukarya bipartite tree of life by a new model of a tripartite tree comprising of bacteria, archaea, and eukarya. This paper explores the history and philosophical implications of the progression of Woese's project from normal science to anomaly-instigated model-changing discovery. It is also shown that the consequential discoveries of RNA splicing and of ribozymes were similarly prompted by unexpected irregularities during normal science activities. It is thus submitted that some discoveries of factual biological entities are triggered by unforeseen observational or experimental anomalies.},
}
@article {pmid38519541,
year = {2024},
author = {Baker, BA and Gutiérrez-Preciado, A and Rodríguez Del Río, &#xc1; and McCarthy, CGP and López-García, P and Huerta-Cepas, J and Susko, E and Roger, AJ and Eme, L and Moreira, D},
title = {Expanded phylogeny of extremely halophilic archaea shows multiple independent adaptations to hypersaline environments.},
journal = {Nature microbiology},
volume = {9},
number = {4},
pages = {964-975},
pmid = {38519541},
issn = {2058-5276},
support = {787904//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; 803151//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; },
mesh = {Phylogeny ; *Salinity ; Archaea/genetics ; *Euryarchaeota/genetics ; Metagenome ; },
abstract = {Extremely halophilic archaea (Haloarchaea, Nanohaloarchaeota, Methanonatronarchaeia and Halarchaeoplasmatales) thrive in saturating salt concentrations where they must maintain osmotic equilibrium with their environment. The evolutionary history of adaptations enabling salt tolerance remains poorly understood, in particular because the phylogeny of several lineages is conflicting. Here we present a resolved phylogeny of extremely halophilic archaea obtained using improved taxon sampling and state-of-the-art phylogenetic approaches designed to cope with the strong compositional biases of their proteomes. We describe two uncultured lineages, Afararchaeaceae and Asbonarchaeaceae, which break the long branches at the base of Haloarchaea and Nanohaloarchaeota, respectively. We obtained 13 metagenome-assembled genomes (MAGs) of these archaea from metagenomes of hypersaline aquatic systems of the Danakil Depression (Ethiopia). Our phylogenomic analyses including these taxa show that at least four independent adaptations to extreme halophily occurred during archaeal evolution. Gene-tree/species-tree reconciliation suggests that gene duplication and horizontal gene transfer played an important role in this process, for example, by spreading key genes (such as those encoding potassium transporters) across extremely halophilic lineages.},
}
@article {pmid38500564,
year = {2024},
author = {Batista, M and Langendijk-Genevaux, P and Kwapisz, M and Canal, I and Phung, DK and Plassart, L and Capeyrou, R and Moalic, Y and Jebbar, M and Flament, D and Fichant, G and Bouvier, M and Clouet-d'Orval, B},
title = {Evolutionary and functional insights into the Ski2-like helicase family in Archaea: a comparison of Thermococcales ASH-Ski2 and Hel308 activities.},
journal = {NAR genomics and bioinformatics},
volume = {6},
number = {1},
pages = {lqae026},
pmid = {38500564},
issn = {2631-9268},
abstract = {RNA helicases perform essential housekeeping and regulatory functions in all domains of life by binding and unwinding RNA molecules. The Ski2-like proteins are primordial helicases that play an active role in eukaryotic RNA homeostasis pathways, with multiple homologs having specialized functions. The significance of the expansion and diversity of Ski2-like proteins in Archaea, the third domain of life, has not yet been established. Here, by studying the phylogenetic diversity of Ski2-like helicases among archaeal genomes and the enzymatic activities of those in Thermococcales, we provide further evidence of the function of this protein family in archaeal metabolism of nucleic acids. We show that, in the course of evolution, ASH-Ski2 and Hel308-Ski2, the two main groups of Ski2-like proteins, have diverged in their biological functions. Whereas Hel308 has been shown to mainly act on DNA, we show that ASH-Ski2, previously described to be associated with the 5'-3' aRNase J exonuclease, acts on RNA by supporting an efficient annealing activity, but also an RNA unwinding with a 3'-5' polarity. To gain insights into the function of Ski2, we also analyse the transcriptome of Thermococcus barophilus ΔASH-Ski2 mutant strain and provide evidence of the importance of ASH-Ski2 in cellular metabolism pathways related to translation.},
}
@article {pmid38499200,
year = {2024},
author = {Guo, K and Li, D and Hao, T and Teng, L and Li, S and Zeng, H and Zhang, J},
title = {Potential directions for future development of mainstream partial nitrification-anammox processes: Ammonia-oxidizing archaea as novel functional microorganisms providing nitrite.},
journal = {Bioresource technology},
volume = {399},
number = {},
pages = {130605},
doi = {10.1016/j.biortech.2024.130605},
pmid = {38499200},
issn = {1873-2976},
mesh = {*Archaea/genetics ; *Nitrification ; Ammonia ; Nitrites ; Anaerobic Ammonia Oxidation ; Wastewater ; Oxidation-Reduction ; Nitrogen/analysis ; Oxygen ; },
abstract = {The application of ammonia-oxidizing archaea (AOA)-based partial nitrification-anammox (PN-A) for mainstream wastewater treatment has attracted research interest because AOA can maintain higher activity in low-temperature environments and they have higher affinity for oxygen and ammonia-nitrogen compared with ammonia-oxidizing bacteria (AOB), thus facilitating stabilized nitrite production, deep removal of low-ammonia, and nitrite-oxidizing bacteria suppression. Moreover, the low affinity of AOA for ammonia makes them more tolerant to N-shock loading and more efficiently integrated with anaerobic ammonium oxidation (anammox). Based on the limitations of the AOB-based PN-A process, this review comprehensively summarizes the potential and significance of AOA for nitrite supply, then gives strategies and influencing factors for replacing AOB with AOA. Additionally, the methods and key influences on the coupling of AOA and anammox are explored. Finally, this review proposes four AOA-based oxygen- or ammonia-limited autotrophic nitritation/denitrification processes to address the low effluent quality and instability of mainstream PN-A processes.},
}
@article {pmid38486239,
year = {2024},
author = {Alghamrawy, BT and Hegazy, GE and Sabry, SA and Ghozlan, H},
title = {Production, characterization and biomedical potential of biosurfactants produced by haloalkaliphilic archaea from Wadi El-Natrun, Egypt.},
journal = {Microbial cell factories},
volume = {23},
number = {1},
pages = {84},
pmid = {38486239},
issn = {1475-2859},
mesh = {*Sodium Chloride/pharmacology/metabolism ; Egypt ; Antioxidants/metabolism ; *Halobacteriaceae/metabolism ; Anti-Inflammatory Agents/metabolism ; },
abstract = {Extreme halophilic archaea that can live in high saline environments can offer potential applications in different biotechnological fields. This study delves into the fascinating field of halophilic archaea and their ability to produce biosurfactants. Some strains of haloarchaea were isolated from Wadi El-Natrun and were screened for biosurfactants production in a standard basal medium using emulsification index assay. Two strains were chosen as the potential strains for surface tension reduction. They were identified as Natrialba sp. BG1 and N3. The biosurfactants production was optimized and the produced emulsifiers were partially purified and identified using FTIR and NMR. Sequential statistical optimization, Plackett-Burman (PB) and Box-Behnken Designs (BBD) were carried out using 5 factors: oil, NaCl, casamino acids, pH, and inoculum size. The most significant factors were used for the next Response Surface Methodology experiment. The final optimal conditions for biosurfactants production were the inoculum size 2% pH 11 and NaCl 250 g/L, for Natrialba sp. BG1 and inoculum size 2.2%, pH 10 and NaCl 100 g/L for Natrialba sp. N3. The produced biosurfactants were tested for wound healing and the results indicated that Natrialba sp. BG1 biosurfactants is more efficient than Natrialba sp. N3 biosurfactants. Biosurfactants extracts were tested for their cytotoxic effects on normal cell line as well as on different cancer cells using MTT assay. The findings demonstrated that varying concentrations of the biosurfactants (31.25, 62.5, 125, 250, 500 and 1000 µg/mL) exhibited cytotoxic effects on the cell lines being tested. Additionally, the outcomes unveiled the presence of anti-inflammatory and antioxidant properties for both biosurfactants. Consequently, they could potentially serve as natural, safe, and efficient novel agents for combating cancer, promoting wound healing, and providing anti-inflammatory and antioxidant benefits.},
}
@article {pmid38479518,
year = {2024},
author = {Liu, X and Sun, D and Huang, H and Zhang, J and Zheng, H and Jia, Q and Zhao, M},
title = {Rice-fish coculture without phosphorus addition improves paddy soil nitrogen availability by shaping ammonia-oxidizing archaea and bacteria in subtropical regions of South China.},
journal = {The Science of the total environment},
volume = {927},
number = {},
pages = {171642},
doi = {10.1016/j.scitotenv.2024.171642},
pmid = {38479518},
issn = {1879-1026},
mesh = {*Archaea/metabolism ; *Phosphorus ; China ; *Bacteria/metabolism ; *Soil Microbiology ; *Nitrogen ; *Ammonia/metabolism ; *Soil/chemistry ; *Oryza ; *Oxidation-Reduction ; Animals ; Fishes ; Fertilizers/analysis ; Agriculture/methods ; },
abstract = {Rice-fish coculture (RFC), as a traditional agricultural strategy in China, can optimally utilize the scarce resource, especially in subtropical regions where phosphorus (P) deficiency limits agricultural production. However, ammonia-oxidizing archaea (AOA) and bacteria (AOB) are involved in the ammonia oxidation, but it remains uncertain whether their community compositions are related to the RFC combined with and without P addition that improves soil nitrogen (N) use efficiency. Here, a microcosm experiment was conducted to assess the impacts of RFC combined with and without inorganic P (0 and 50 mg P kg[-1] as KH2PO4) addition on AOA and AOB community diversities, enzyme activities and N availability. The results showed that RFC significantly increased available N content without P addition compared with P addition. Moreover, RFC significantly increased urease activity and AOA shannon diversity, and reduced NAG activity and AOB shannon diversity without P addition, respectively. Higher diversity of AOA compared with that of AOB causes greater competition for resources and energy within their habitats, thereby resulting in lower network complexity. Our findings indicated that the abundances of AOA and AOB are influenced through the introduction of fish and/or P availability, of which AOB is linked to N availability. Overall, RFC could improve paddy soil N availability without P addition in subtropical region, which provides a scientific reference for promoting the practices that reduce N fertilizer application in RFC.},
}
@article {pmid38476944,
year = {2024},
author = {von Hoyningen-Huene, AJE and Bang, C and Rausch, P and Rühlemann, M and Fokt, H and He, J and Jensen, N and Knop, M and Petersen, C and Schmittmann, L and Zimmer, T and Baines, JF and Bosch, TCG and Hentschel, U and Reusch, TBH and Roeder, T and Franke, A and Schulenburg, H and Stukenbrock, E and Schmitz, RA},
title = {The archaeome in metaorganism research, with a focus on marine models and their bacteria-archaea interactions.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1347422},
pmid = {38476944},
issn = {1664-302X},
abstract = {Metaorganism research contributes substantially to our understanding of the interaction between microbes and their hosts, as well as their co-evolution. Most research is currently focused on the bacterial community, while archaea often remain at the sidelines of metaorganism-related research. Here, we describe the archaeome of a total of eleven classical and emerging multicellular model organisms across the phylogenetic tree of life. To determine the microbial community composition of each host, we utilized a combination of archaea and bacteria-specific 16S rRNA gene amplicons. Members of the two prokaryotic domains were described regarding their community composition, diversity, and richness in each multicellular host. Moreover, association with specific hosts and possible interaction partners between the bacterial and archaeal communities were determined for the marine models. Our data show that the archaeome in marine hosts predominantly consists of Nitrosopumilaceae and Nanoarchaeota, which represent keystone taxa among the porifera. The presence of an archaeome in the terrestrial hosts varies substantially. With respect to abundant archaeal taxa, they harbor a higher proportion of methanoarchaea over the aquatic environment. We find that the archaeal community is much less diverse than its bacterial counterpart. Archaeal amplicon sequence variants are usually host-specific, suggesting adaptation through co-evolution with the host. While bacterial richness was higher in the aquatic than the terrestrial hosts, a significant difference in diversity and richness between these groups could not be observed in the archaeal dataset. Our data show a large proportion of unclassifiable archaeal taxa, highlighting the need for improved cultivation efforts and expanded databases.},
}
@article {pmid38472444,
year = {2024},
author = {Hu, Y and Ma, X and Tan, S and Li, XX and Cheng, M and Hou, J and Cui, HL},
title = {Genome-based classification of genera Halosegnis and Salella, and description of four novel halophilic archaea isolated from a tidal flat.},
journal = {Antonie van Leeuwenhoek},
volume = {117},
number = {1},
pages = {51},
pmid = {38472444},
issn = {1572-9699},
support = {2021FY100900//National Science and Technology Fundamental Resources Investigation Program of China/ ; 32070003//National Natural Science Foundation of China/ ; },
mesh = {Sequence Analysis, DNA ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Halobacteriaceae/genetics ; China ; DNA ; DNA, Archaeal/genetics ; Fatty Acids/chemistry ; DNA, Bacterial/genetics ; },
abstract = {The current species of Halosegnis and Salella within the class Halobacteria are closely related based on phylogenetic, phylogenomic, and comparative genomic analyses. The Halosegnis species showed 99.8-100.0% 16S rRNA and 96.6-99.6% rpoB' gene similarities to the Salella species, respectively. Phylogenetic and phylogenomic analyses showed that Salella cibi CBA1133[T], the sole species of Salella, formed a single tight cluster with Halosegnis longus F12-1[T], then with Halosegnis rubeus F17-44[T]. The average nucleotide identity (ANI), digital DNA-DNA hybridization (dDDH), and average amino acid identity (AAI) values between Salella cibi CBA1133[T] and Halosegnis longus F12-1[T] were 99.2, 94.2, and 98.6%, respectively, much higher than the thresholds for species demarcation. This genome-based classification revealed that the genus Salella should be merged with Halosegnis, and Salella cibi should be a later heterotypic synonym of Halosegnis longus. Halophilic archaeal strains DT72[T], DT80[T], DT85[T], and DT116[T], isolated from the saline soil of a tidal flat in China, were subjected to polyphasic taxonomic characterization. The phenotypic, chemotaxonomic, phylogenetic, and phylogenomic features indicated that strains DT72[T] (= CGMCC 1.18925[T] = JCM 35418[T]), DT80[T] (= CGMCC 1.18926[T] = JCM 35419[T]), DT85[T] (= CGMCC 1.19049[T] = JCM 35605[T]), and DT116[T] (= CGMCC 1.19045[T] = JCM 35606[T]) represent four novel species of the genera Halorussus, Halosegnis and Haloglomus, respectively, for which the names, Halorussus caseinilyticus sp. nov., Halorussus lipolyticus sp. nov., Halosegnis marinus sp. nov., and Haloglomus litoreum sp. nov., are proposed.},
}
@article {pmid38472392,
year = {2024},
author = {Tran, LT and Akıl, C and Senju, Y and Robinson, RC},
title = {The eukaryotic-like characteristics of small GTPase, roadblock and TRAPPC3 proteins from Asgard archaea.},
journal = {Communications biology},
volume = {7},
number = {1},
pages = {273},
pmid = {38472392},
issn = {2399-3642},
support = {JPMJCR19S5//MEXT | JST | Core Research for Evolutional Science and Technology (CREST)/ ; JP20H00476//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JP19K23727//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JP23K05718//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JP23H04423//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; GBMF9743//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; GBMF9743//Simons Foundation/ ; },
mesh = {*Monomeric GTP-Binding Proteins/chemistry ; Archaea/metabolism ; Protein Transport ; },
abstract = {Membrane-enclosed organelles are defining features of eukaryotes in distinguishing these organisms from prokaryotes. Specification of distinct membranes is critical to assemble and maintain discrete compartments. Small GTPases and their regulators are the signaling molecules that drive membrane-modifying machineries to the desired location. These signaling molecules include Rab and Rag GTPases, roadblock and longin domain proteins, and TRAPPC3-like proteins. Here, we take a structural approach to assess the relatedness of these eukaryotic-like proteins in Asgard archaea, the closest known prokaryotic relatives to eukaryotes. We find that the Asgard archaea GTPase core domains closely resemble eukaryotic Rabs and Rags. Asgard archaea roadblock, longin and TRAPPC3 domain-containing proteins form dimers similar to those found in the eukaryotic TRAPP and Ragulator complexes. We conclude that the emergence of these protein architectures predated eukaryogenesis, however further adaptations occurred in proto-eukaryotes to allow these proteins to regulate distinct internal membranes.},
}
@article {pmid38471592,
year = {2024},
author = {Chisholm, C and Di, H and Cameron, K and Podolyan, A and Shen, J and Zhang, L and Sirisena, K and Godsoe, W},
title = {Contrasting response of comammox Nitrospira, ammonia oxidising bacteria, and archaea to soil pH and nitrogen inputs.},
journal = {The Science of the total environment},
volume = {924},
number = {},
pages = {171627},
doi = {10.1016/j.scitotenv.2024.171627},
pmid = {38471592},
issn = {1879-1026},
mesh = {*Archaea ; Ammonia ; Soil/chemistry ; Nitrogen ; Phylogeny ; Oxidation-Reduction ; Soil Microbiology ; Bacteria ; Nitrification ; *Betaproteobacteria ; Hydrogen-Ion Concentration ; },
abstract = {This study aimed to investigate the effect of soil pH change, and nitrogen amendment on ammonia oxidiser abundance and comammox Nitrospira community composition. The experimental design used soil mesocosms placed in a temperature-controlled incubator for 90 days. A Templeton silt loam was used as its physiochemical properties are typical of the region's dairy farms. The results showed that comammox Nitrospira clade B preferred the natural (pH 6.1-6.2) soil pH with no applied nitrogen. Furthermore, synthetic urine (N700) decreased the abundance of comammox Nitrospira clade B. This may have been because the large amounts of available ammonia in the N700 treatments inhibited the growth of comammox Nitrospira. These results suggest that while comammox Nitrospira clade B are present in New Zealand dairy farm soils, but their role in nitrification in the very high nitrogen environment under a urine patch in grazed pastures may be limited. Further research is needed to confirm this. In contrast to comammox, the AOB community (dominated by Nitrosospira) responded positively to the application of synthetic urine. The response was greatest in the high pH soil (7.1), followed by the natural and then the low pH (4.9) soils. This may be due to the difference in ammonia availability. At high pH, the ammonia/ammonium equilibrium favours ammonia production. Calculated ammonia availability in the N700 treatments accurately predicted the AOB amoA gene abundance. Interestingly, the AOA community abundance (which was predominantly made up of Thaumarchaeota group I.1b clade E) seemed to prefer the natural and high pH soils over the low pH. This may be due to the specific lineage of AOA present. AOA did not respond to the application of nitrogen.},
}
@article {pmid38466496,
year = {2024},
author = {Huda, N and Rana, MR and Huq, MA and Al-Mamun, A and Rahman, ST and Alam, MK and Rahman, MM},
title = {Understanding vermicompost and organic manure interactions: impact on toxic elements, nitrification activity, comammox Nitrospira inopinata, and archaea/bacteria.},
journal = {Environmental monitoring and assessment},
volume = {196},
number = {4},
pages = {355},
pmid = {38466496},
issn = {1573-2959},
mesh = {*Archaea ; *Nitrification ; Manure ; Ammonia ; Carbon ; Oxidation-Reduction ; Soil/chemistry ; Phylogeny ; Soil Microbiology ; Environmental Monitoring ; Bacteria ; Nitrites ; },
abstract = {Vermicompost is a substantial source of nutrients, promotes soil fertility, and maintains or increases soil organic matter levels. Potentially toxic elements (PTEs) in vermicompost impact on nitrification activity. However, it is yet unknown how vermicompost affects nitrifying bacteria and archaea, comammox Nitrospira inopinata (complete ammonia oxidizers), net nitrification rates (NNRs), and PTEs. The effects of vermicompost application on NNRs, potential nitrification rates (NPs), PTEs, and the abundances of comammox N. inopinata bacteria, nitrite-oxidizing bacteria (NOB), and ammonia-oxidizing bacteria (AOB)/archaea (AOA) were studied. NNRs and NPs were significantly higher (p < 0.05) in fresh cow-dung vermicompost (stored for 40 days) as compared with other organic manure. The level of PTEs (Cu[2+], Fe[2+], Pb[2+], Cd[2+], and Zn[2+]) was significantly lower (p < 0.05) in vermicompost as compared with compost of waste material with Trichoderma and cow dung. Comammox N. inopinata, NOB, AOB, and AOA were significantly higher (p < 0.05) in stored cow-dung vermicompost (more than 1 year) as compared with other organic manure. The results of the scatterplot matrix analysis suggested that Fe[2+], total nitrogen (TN), soil organic carbon (SOC), and total carbon (TC) were linearly correlated (p < 0.001) with NNRs and NPs in vermicompost and organic manure. Similarly, comammox N. inopinata bacteria, NOB, AOB, and AOA were linearly correlated (p < 0.001) with NNR and NP. These results indicated that vermicompost promoted nitrification activity by increasing microbial diversity and abundance, supplying nutrients and organic matter for microbial growth, and facilitating complex microbial interactions. It may be concluded that the influence of vermicompost, which played a great role in PTE concentration reduction, increased chemical, and biological properties, increased the growth rate of nitrifying bacteria/archaea and the nitrogen cycle.},
}
@article {pmid38458444,
year = {2024},
author = {Peng, L and Jia, M and Li, S and Wang, X and Liang, C and Xu, Y},
title = {Developing antibiotics-based strategies to efficiently enrich ammonia-oxidizing archaea from wastewater treatment plants.},
journal = {The Science of the total environment},
volume = {923},
number = {},
pages = {171479},
doi = {10.1016/j.scitotenv.2024.171479},
pmid = {38458444},
issn = {1879-1026},
mesh = {*Archaea/genetics ; *Ammonia ; Anti-Bacterial Agents ; Nitrites ; Oxidation-Reduction ; Bacteria/genetics ; Phylogeny ; Soil Microbiology ; },
abstract = {The effects of five antibiotics (i.e., ampicillin, streptomycin, carbenicillin, kanamycin and tetracycline) on ammonia-oxidizing archaea (AOA) enrichment from anoxic activated sludge were investigated. The combined use of five antibiotics during 90-day cultivation could selectively inhibit nitrite-oxidizing bacteria (NOB) and ammonia-oxidizing bacteria (AOB) with AOA unaffected, as evidenced by the nitrite accumulation ratio of 100 % and the proportion of AOA in ammonia-oxidizing microbes over 91 %. The alternative use of five antibiotics was the optimal approach to screening for AOA during 348-day cultivation, which inhibited AOB growth at a level equivalent to the combined use of five antibiotics (the AOB-amoA gene decreased by over 99.90 %), further promoted AOA abundance (the much higher AOA-amoA to AOB-amoA gene copy number ratio (1453.30) than that in the groups with the combined use of five antibiotics (192.94)), eliminated bacterial adaptation to antibiotics and reduced antibiotic-resistant bacteria to form Nitrocosmicus-dominant community (42.35 % in abundance).},
}
@article {pmid38444950,
year = {2024},
author = {Sun, D and Rozmoš, M and Kotianová, M and Hršelová, H and Jansa, J},
title = {Arbuscular mycorrhizal fungi suppress ammonia-oxidizing bacteria but not archaea across agricultural soils.},
journal = {Heliyon},
volume = {10},
number = {4},
pages = {e26485},
pmid = {38444950},
issn = {2405-8440},
abstract = {Arbuscular mycorrhizal (AM) fungi are supposedly competing with ammonia-oxidizing microorganisms (AO) for soil nitrogen in form of ammonium. Despite a few studies directly addressing AM fungal and AO interactions, mostly in artificial cultivation substrates, it is not yet clear whether AM fungi can effectively suppress AO in field soils containing complex indigenous microbiomes. To fill this knowledge gap, we conducted compartmentalized pot experiments using four pairs of cropland and grassland soils with varying physicochemical properties. To exclude the interference of roots, a fine nylon mesh was used to separate the rhizosphere and mesh bags, with the latter being filled with unsterile field soils. Inoculation of plants with AM fungus Rhizophagus irregularis LPA9 suppressed AO bacteria (AOB) but not archaea (AOA) in the soils, indicating how soil nitrification could be suppressed by AM fungal presence/activity. In addition, in rhizosphere filled with artificial substrate, AM inoculation did suppress both AOB and AOA, implying more complex interactions between roots, AO, and AM fungi. Besides, we also observed that indigenous AM fungi contained in the field soils eventually did colonize the roots of plants behind the root barrier, and that the extent of such colonization was higher if the soil has previously been taken from cropland than from grassland. Despite this, the effect of experimental AM fungal inoculation on suppression of indigenous AOB in the unsterile field soils did not vanish. It seems that studying processes at a finer temporal scale, using larger buffer zones between rhizosphere and mesh bags, and/or detailed characterization of indigenous AM fungal and AO communities would be needed to uncover further details of the biotic interactions between the AM fungi and indigenous soil AO.},
}
@article {pmid38436843,
year = {2024},
author = {Wang, J and Wen, X and Fang, Z and Gao, P and Wu, P and Li, X and Zeng, G},
title = {Impact of salinity and organic matter on the ammonia-oxidizing archaea and bacteria in treating hypersaline industrial wastewater: amoA gene abundance and ammonia removal contributions.},
journal = {Environmental science and pollution research international},
volume = {31},
number = {16},
pages = {24099-24112},
pmid = {38436843},
issn = {1614-7499},
support = {52000019//National Natural Science Foundation of China/ ; KJQN202101526//Chongqing Municipal Education Commission/ ; YS2021089//Chongqing Bayu Scholars Young Scholars Project/ ; },
mesh = {*Archaea/genetics ; *Wastewater ; Ammonia ; Salinity ; Sodium Chloride ; Oxidation-Reduction ; Bacteria/genetics ; Nitrification ; Phylogeny ; Soil Microbiology ; },
abstract = {Studies published recently proposed that ammonia-oxidizing archaea (AOA) may be beneficial for hypersaline (salinity > 50 g NaCl L[-1]) industrial wastewater treatment. However, knowledge of AOA activity in hypersaline bioreactors is limited. This study investigated the effects of salinity, organic matter, and practical pickled mustard tuber wastewater (PMTW) on AOA and ammonia-oxidizing bacteria (AOB) in two sequencing batch biofilm reactors (SBBRs). Results showed that despite observed salinity inhibition (p < 0.05), both AOA and AOB contributed to high ammonia removal efficiency at a salinity of 70 g NaCl L[-1] in the two SBBRs. The ammonia removal efficiency of SBBR2 did not significantly differ from that of SBBR1 in the absence of organic matter (p > 0.05). Batch tests and quantitative real-time PCR (qPCR) reveal that salinity and organic matter inhibition resulted in a sharp decline in specific ammonia oxidation rates and amoA gene copy numbers of AOA and AOB (p < 0.05). AOA demonstrated higher abundance and more active ammonia oxidation activity in hypersaline and high organic matter environments. Salinity was positively correlated with the potential ammonia oxidation contribution of AOA (p < 0.05), resulting in a potential transition from AOB dominance to AOA dominance in SBBR1 as salinity levels rose. Moreover, autochthonous AOA in PMTW promoted the abundance and ammonia oxidation activities of AOA in SBBR2, further elevating the nitrification removal efficiency after feeding the practical PMTW. AOA demonstrates greater tolerance to the challenging hypersaline environment, making it a valuable candidate for the treatment of practical industrial wastewater with high salinity and organic content.},
}
@article {pmid38435527,
year = {2024},
author = {Liu, Y and Qian, Y and Fu, L and Zhu, C and Li, X and Wang, Q and Ling, H and Du, H and Zhou, S and Kong, XY and Jiang, L and Wen, L},
title = {Archaea-Inspired Switchable Nanochannels for On-Demand Lithium Detection by pH Activation.},
journal = {ACS central science},
volume = {10},
number = {2},
pages = {469-476},
pmid = {38435527},
issn = {2374-7943},
abstract = {With the rapid development of the lithium ion battery industry, emerging lithium (Li) enrichment in nature has attracted ever-growing attention due to the biotoxicity of high Li levels. To date, fast lithium ion (Li[+]) detection remains urgent but is limited by the selectivity, sensitivity, and stability of conventional technologies based on passive response processes. In nature, archaeal plasma membrane ion exchangers (NCLX_Mj) exhibit Li[+]-gated multi/monovalent ion transport behavior, activated by different stimuli. Inspired by NCLX_Mj, we design a pH-controlled biomimetic Li[+]-responsive solid-state nanochannel system for on-demand Li[+] detection using 2-(2-hydroxyphenyl)benzoxazole (HPBO) units as Li[+] recognition groups. Pristine HPBO is not reactive to Li[+], whereas negatively charged HPBO enables specific Li[+] coordination under alkaline conditions to decrease the ion exchange capacity of nanochannels. On-demand Li[+] detection is achieved by monitoring the decline in currents, thereby ensuring precise and stable Li[+] recognition (>0.1 mM) in the toxic range of Li[+] concentration (>1.5 mM) for human beings. This work provides a new approach to constructing Li[+] detection nanodevices and has potential for applications of Li-related industries and medical services.},
}
@article {pmid38428597,
year = {2024},
author = {Lee, KC and Archer, SDJ and Kansour, MK and Al-Mailem, DM},
title = {Bioremediation of oily hypersaline soil via autochthonous bioaugmentation with halophilic bacteria and archaea.},
journal = {The Science of the total environment},
volume = {922},
number = {},
pages = {171279},
doi = {10.1016/j.scitotenv.2024.171279},
pmid = {38428597},
issn = {1879-1026},
mesh = {Archaea/metabolism ; Biodegradation, Environmental ; Soil ; Soil Microbiology ; Oils ; Bacteria/metabolism ; *Petroleum/analysis ; Hydrocarbons/metabolism ; *Soil Pollutants/analysis ; },
abstract = {Kuwaiti hypersaline soil samples were contaminated with 5 % (w/w) weathered Kuwaiti light crude oil and bioaugmented with autochthonous halophilic hydrocarbonoclastic archaeal and bacterial strains, two each, individually and as consortia. Residual oil contents were determined, and microbial communities were analyzed by culture-dependent and culture-independent approaches initially and seasonally for one year. After one year of the bioremediation process, the mean oil degradation rate was similar across all treated soils including the controlled unbioaugmented one. Oil hydrocarbons were drastically reduced in all soil samples with values ranging from 82.7 % to 93 %. During the bioremediation process, the number of culturable oil-degrading bacteria increased to a range of 142 to 344 CFUx10[4] g[-1] after 12 months of bioaugmentation. Although culture-independent analysis showed a high proportion of inoculants initially, none could be cultured throughout the bioremediation procedure. Within a year, microbial communities changed continually, and 33 species of halotolerant/halophilic hydrocarbonoclastic bacteria were isolated and identified belonged mainly to the three major bacterial phyla Actinobacteria, Proteobacteria, and Firmicutes. The archaeal phylum Halobacterota represented <1 % of the microbial community's relative abundance, which explains why none of its members were cultured. Improving the biodegradability of an already balanced environment by autochthonous bioaugmentation is more involved than just adding the proper oil degraders. This study emphasizes the possibility of a relatively large resistant population, a greater diversity of oil-degrading microorganisms, and the highly selective impacts of oil contamination on hypersaline soil bacterial communities.},
}
@article {pmid38422909,
year = {2024},
author = {Cena, JA and Belmok, A and Kyaw, CM and Dame-Teixeira, N},
title = {The Archaea domain: Exploring historical and contemporary perspectives with in silico primer coverage analysis for future research in Dentistry.},
journal = {Archives of oral biology},
volume = {161},
number = {},
pages = {105936},
doi = {10.1016/j.archoralbio.2024.105936},
pmid = {38422909},
issn = {1879-1506},
mesh = {Humans ; *Archaea/genetics ; Bacteria ; *Microbiota ; Mouth ; Dentistry ; Phylogeny ; },
abstract = {OBJECTIVE: The complete picture of how the human microbiome interacts with its host is still largely unknown, particularly concerning microorganisms beyond bacteria. Although existing in very low abundance and not directly linked to causing diseases, archaea have been detected in various sites of the human body, including the gastrointestinal tract, oral cavity, skin, eyes, respiratory and urinary systems. But what exactly are these microorganisms? In the early 1990 s, archaea were classified as a distinct domain of life, sharing a more recent common ancestor with eukaryotes than with bacteria. While archaea's presence and potential significance in Dentistry remain under-recognized, there are concerns that they may contribute to oral dysbiosis. However, detecting archaea in oral samples presents challenges, including difficulties in culturing, the selection of DNA extraction methods, primer design, bioinformatic analysis, and databases.<br><br>DESIGN: This is a comprehensive review on the oral archaeome, presenting an in-depth in silico analysis of various primers commonly used for detecting archaea in human body sites.<br><br>RESULTS: Among several primer pairs used for detecting archaea in human samples across the literature, only one specifically designed for detecting methanogenic archaea in stool samples, exhibited exceptional coverage levels for the domain and various archaea phyla.<br><br>CONCLUSIONS: Our in silico analysis underscores the need for designing new primers targeting not only methanogenic archaea but also nanoarchaeal and thaumarchaeota groups to gain a comprehensive understanding of the archaeal oral community. By doing so, researchers can pave the way for further advancements in the field of oral archaeome research.},
}
@article {pmid38392629,
year = {2024},
author = {Cisek, AA and Szymańska, E and Aleksandrzak-Piekarczyk, T and Cukrowska, B},
title = {The Role of Methanogenic Archaea in Inflammatory Bowel Disease-A Review.},
journal = {Journal of personalized medicine},
volume = {14},
number = {2},
pages = {},
pmid = {38392629},
issn = {2075-4426},
abstract = {Methanogenic archaea are a part of the commensal gut microbiota responsible for hydrogen sink and the efficient production of short-chain fatty acids. Dysbiosis of methanogens is suspected to play a role in pathogenesis of variety of diseases, including inflammatory bowel disease (IBD). Unlike bacteria, the diversity of archaea seems to be higher in IBD patients compared to healthy subjects, whereas the prevalence and abundance of gut methanogens declines in IBD, especially in ulcerative colitis. To date, studies focusing on methanogens in pediatric IBD are very limited; nevertheless, the preliminary results provide some evidence that methanogens may be influenced by the chronic inflammatory process in IBD. In this review, we demonstrated the development and diversity of the methanogenic community in IBD, both in adults and children.},
}
@article {pmid38380943,
year = {2024},
author = {Zhang, IH and Borer, B and Zhao, R and Wilbert, S and Newman, DK and Babbin, AR},
title = {Uncultivated DPANN archaea are ubiquitous inhabitants of global oxygen-deficient zones with diverse metabolic potential.},
journal = {mBio},
volume = {15},
number = {3},
pages = {e0291823},
pmid = {38380943},
issn = {2150-7511},
support = {R01 HL152190/HL/NHLBI NIH HHS/United States ; },
mesh = {*Archaea/genetics ; Nitrous Oxide/metabolism ; Phylogeny ; Metagenome ; *Microbiota ; Methane/metabolism ; Oxygen/metabolism ; Carbon/metabolism ; Nitrogen/metabolism ; Sulfur/metabolism ; Water/metabolism ; },
abstract = {UNLABELLED: Archaea belonging to the DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaeota) superphylum have been found in an expanding number of environments and perform a variety of biogeochemical roles, including contributing to carbon, sulfur, and nitrogen cycling. Generally characterized by ultrasmall cell sizes and reduced genomes, DPANN archaea may form mutualistic, commensal, or parasitic interactions with various archaeal and bacterial hosts, influencing the ecology and functioning of microbial communities. While DPANN archaea reportedly comprise a sizeable fraction of the archaeal community within marine oxygen-deficient zone (ODZ) water columns, little is known about their metabolic capabilities in these ecosystems. We report 33 novel metagenome-assembled genomes (MAGs) belonging to the DPANN phyla Nanoarchaeota, Pacearchaeota, Woesearchaeota, Undinarchaeota, Iainarchaeota, and SpSt-1190 from pelagic ODZs in the Eastern Tropical North Pacific and the Arabian Sea. We find these archaea to be permanent, stable residents of all three major ODZs only within anoxic depths, comprising up to 1% of the total microbial community and up to 25%-50% of archaea as estimated from read mapping to MAGs. ODZ DPANN appear to be capable of diverse metabolic functions, including fermentation, organic carbon scavenging, and the cycling of sulfur, hydrogen, and methane. Within a majority of ODZ DPANN, we identify a gene homologous to nitrous oxide reductase. Modeling analyses indicate the feasibility of a nitrous oxide reduction metabolism for host-attached symbionts, and the small genome sizes and reduced metabolic capabilities of most DPANN MAGs suggest host-associated lifestyles within ODZs.<br><br>IMPORTANCE: Archaea from the DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaeota) superphylum have diverse metabolic capabilities and participate in multiple biogeochemical cycles. While metagenomics and enrichments have revealed that many DPANN are characterized by ultrasmall genomes, few biosynthetic genes, and episymbiotic lifestyles, much remains unknown about their biology. We report 33 new DPANN metagenome-assembled genomes originating from the three global marine oxygen-deficient zones (ODZs), the first from these regions. We survey DPANN abundance and distribution within the ODZ water column, investigate their biosynthetic capabilities, and report potential roles in the cycling of organic carbon, methane, and nitrogen. We test the hypothesis that nitrous oxide reductases found within several ODZ DPANN genomes may enable ultrasmall episymbionts to serve as nitrous oxide consumers when attached to a host nitrous oxide producer. Our results indicate DPANN archaea as ubiquitous residents within the anoxic core of ODZs with the potential to produce or consume key compounds.},
}
@article {pmid38368447,
year = {2024},
author = {Ouboter, HT and Mesman, R and Sleutels, T and Postma, J and Wissink, M and Jetten, MSM and Ter Heijne, A and Berben, T and Welte, CU},
title = {Mechanisms of extracellular electron transfer in anaerobic methanotrophic archaea.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {1477},
pmid = {38368447},
issn = {2041-1723},
support = {024.002.002//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (Netherlands Organisation for Scientific Research)/ ; VI.Vidi.223.012//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (Netherlands Organisation for Scientific Research)/ ; 854088//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; },
mesh = {*Archaea/genetics/metabolism ; Electron Transport ; *Bacteria/metabolism ; Anaerobiosis ; Electrons ; Oxidation-Reduction ; Methane/metabolism ; },
abstract = {Anaerobic methanotrophic (ANME) archaea are environmentally important, uncultivated microorganisms that oxidize the potent greenhouse gas methane. During methane oxidation, ANME archaea engage in extracellular electron transfer (EET) with other microbes, metal oxides, and electrodes through unclear mechanisms. Here, we cultivate ANME-2d archaea ('Ca. Methanoperedens') in bioelectrochemical systems and observe strong methane-dependent current (91-93% of total current) associated with high enrichment of 'Ca. Methanoperedens' on the anode (up to 82% of the community), as determined by metagenomics and transmission electron microscopy. Electrochemical and metatranscriptomic analyses suggest that the EET mechanism is similar at various electrode potentials, with the possible involvement of an uncharacterized short-range electron transport protein complex and OmcZ nanowires.},
}
@article {pmid38366050,
year = {2024},
author = {Baquero, DP and Bignon, EA and Krupovic, M},
title = {Pleomorphic viruses establish stable relationship with marine hyperthermophilic archaea.},
journal = {The ISME journal},
volume = {18},
number = {1},
pages = {},
pmid = {38366050},
issn = {1751-7370},
support = {ANR-20-CE20-009//l'Agence Nationale de la Recherche/ ; },
mesh = {Archaea/genetics ; Phylogeny ; Ecosystem ; *Viruses/genetics ; Virion ; *Euryarchaeota ; *Archaeal Viruses/genetics ; },
abstract = {Non-lytic viruses with enveloped pleomorphic virions (family Pleolipoviridae) are ubiquitous in hypersaline environments across the globe and are associated with nearly all major lineages of halophilic archaea. However, their existence in other ecosystems remains largely unknown. Here, we show that evolutionarily-related viruses also infect hyperthermophilic archaea thriving in deep-sea hydrothermal vents. Archaeoglobus veneficus pleomorphic virus 1 (AvPV1), the first virus described for any member of the class Archaeoglobi, encodes a morphogenetic module typical of pleolipoviruses, including the characteristic VP4-like membrane fusion protein. We show that AvPV1 is a non-lytic virus chronically produced in liquid cultures without substantially affecting the growth dynamics of its host with a stable virus-to-host ratio of ~1. Mining of genomic and metagenomic databases revealed broad distribution of AvPV1-like viruses in geographically remote hydrothermal vents. Comparative genomics, coupled with phylogenetic analysis of VP4-like fusogens revealed deep divergence of pleomorphic viruses infecting halophilic, methanogenic, and hyperthermophilic archaea, signifying niche separation and coevolution of the corresponding virus-host pairs. Hence, we propose a new virus family, "Thalassapleoviridae," for classification of the marine hyperthermophilic virus AvPV1 and its relatives. Collectively, our results provide insights into the diversity and evolution of pleomorphic viruses beyond hypersaline environments.},
}
@article {pmid38365232,
year = {2024},
author = {Zheng, Y and Wang, B and Gao, P and Yang, Y and Xu, B and Su, X and Ning, D and Tao, Q and Li, Q and Zhao, F and Wang, D and Zhang, Y and Li, M and Winkler, MH and Ingalls, AE and Zhou, J and Zhang, C and Stahl, DA and Jiang, J and Martens-Habbena, W and Qin, W},
title = {Novel order-level lineage of ammonia-oxidizing archaea widespread in marine and terrestrial environments.},
journal = {The ISME journal},
volume = {18},
number = {1},
pages = {},
pmid = {38365232},
issn = {1751-7370},
support = {548565//Simons Postdoctoral Fellowship in Marine Microbial Ecology/ ; //Florida Agricultural Experiment Station Hatch project/ ; //National Natural Science Foundation of China/ ; 2020Z01//Shanghai Sheshan National Geophysical Observatory/ ; 20200925173954005//Stable Support Plan Program of Shenzhen Natural Science Fund/ ; ZDSYS201802081843490//Southern University of Science and Technology/ ; //Shenzhen Key Laboratory of Marine Archaea Geo-Omics/ ; 2020KCXTD023//the Innovation Team Project of Universities/ ; //National Natural Science Foundation of China/ ; //Fundamental Research Funds for the Central Universities of China/ ; 92051114//National Natural Science Foundation of China/ ; },
mesh = {*Archaea ; *Ammonia/metabolism ; Ecosystem ; RNA, Ribosomal, 16S/genetics/metabolism ; Oxidation-Reduction ; Phylogeny ; Soil ; Soil Microbiology ; },
abstract = {Ammonia-oxidizing archaea (AOA) are among the most ubiquitous and abundant archaea on Earth, widely distributed in marine, terrestrial, and geothermal ecosystems. However, the genomic diversity, biogeography, and evolutionary process of AOA populations in subsurface environments are vastly understudied compared to those in marine and soil systems. Here, we report a novel AOA order Candidatus (Ca.) Nitrosomirales which forms a sister lineage to the thermophilic Ca. Nitrosocaldales. Metagenomic and 16S rRNA gene-read mapping demonstrates the abundant presence of Nitrosomirales AOA in various groundwater environments and their widespread distribution across a range of geothermal, terrestrial, and marine habitats. Terrestrial Nitrosomirales AOA show the genetic capacity of using formate as a source of reductant and using nitrate as an alternative electron acceptor. Nitrosomirales AOA appear to have acquired key metabolic genes and operons from other mesophilic populations via horizontal gene transfer, including genes encoding urease, nitrite reductase, and V-type ATPase. The additional metabolic versatility conferred by acquired functions may have facilitated their radiation into a variety of subsurface, marine, and soil environments. We also provide evidence that each of the four AOA orders spans both marine and terrestrial habitats, which suggests a more complex evolutionary history for major AOA lineages than previously proposed. Together, these findings establish a robust phylogenomic framework of AOA and provide new insights into the ecology and adaptation of this globally abundant functional guild.},
}
@article {pmid38358888,
year = {2024},
author = {Lu, Z and Zhang, S and Liu, Y and Xia, R and Li, M},
title = {Origin of eukaryotic-like Vps23 shapes an ancient functional interplay between ESCRT and ubiquitin system in Asgard archaea.},
journal = {Cell reports},
volume = {43},
number = {2},
pages = {113781},
doi = {10.1016/j.celrep.2024.113781},
pmid = {38358888},
issn = {2211-1247},
mesh = {*Ubiquitin ; Ubiquitination ; *Archaea/genetics ; Cell Movement ; Endosomal Sorting Complexes Required for Transport ; },
abstract = {Functional interplay between the endosomal sorting complexes required for transport (ESCRT) and the ubiquitin system underlies the ubiquitin-dependent cargo-sorting pathway of the eukaryotic endomembrane system, yet its evolutionary origin remains unclear. Here, we show that a UEV-Vps23 protein family, which contains UEV and Vps23 domains, mediates an ancient ESCRT and ubiquitin system interplay in Asgard archaea. The UEV binds ubiquitin with high affinity, making the UEV-Vps23 a sensor for sorting ubiquitinated cargo. A steadiness box in the Vps23 domain undergoes ubiquitination through an Asgard E1, E2, and RING E3 cascade. The UEV-Vps23 switches between autoinhibited and active forms, regulating the ESCRT and ubiquitin system interplay. Furthermore, the shared sequence and structural homology among the UEV-Vps23, eukaryotic Vps23, and archaeal CdvA suggest a common evolutionary origin. Together, this work expands our understanding of the ancient ESCRT and ubiquitin system interplay that likely arose antedating divergent evolution between Asgard archaea and eukaryotes.},
}
@article {pmid38354884,
year = {2024},
author = {Ju, H and Zhang, J and Zou, Y and Xie, F and Tang, X and Zhang, S and Li, J},
title = {Bacteria undergo significant shifts while archaea maintain stability in Pocillopora damicornis under sustained heat stress.},
journal = {Environmental research},
volume = {250},
number = {},
pages = {118469},
doi = {10.1016/j.envres.2024.118469},
pmid = {38354884},
issn = {1096-0953},
mesh = {*Anthozoa/microbiology/physiology ; Animals ; *Archaea/genetics/physiology ; *Bacteria/genetics/classification ; Heat-Shock Response ; Microbiota ; Hot Temperature ; Coral Reefs ; },
abstract = {Global warming reportedly poses a critical risk to coral reef ecosystems. Bacteria and archaea are crucial components of the coral holobiont. The response of archaea associated with warming is less well understood than that of the bacterial community in corals. Also, there have been few studies on the dynamics of the microbial community in the coral holobiont under long-term heat stress. In order to track the dynamic alternations in the microbial communities within the heat-stressed coral holobiont, three-week heat-stress monitoring was carried out on the coral Pocillopora damicornis. The findings demonstrate that the corals were stressed at 32 °C, and showed a gradual decrease in Symbiodiniaceae density with increasing duration of heat stress. The archaeal community in the coral holobiont remained relatively unaltered by the increasing temperature, whereas the bacterial community was considerably altered. Sustained heat stress exacerbated the dissimilarities among parallel samples of the bacterial community, confirming the Anna Karenina Principle in animal microbiomes. Heat stress leads to more complex and unstable microbial networks, characterized by an increased average degree and decreased modularity, respectively. With the extension of heat stress duration, the relative abundances of the gene (nifH) and genus (Tistlia) associated with nitrogen fixation increased in coral samples, as well as the potential pathogenic bacteria (Flavobacteriales) and opportunistic bacteria (Bacteroides). Hence, our findings suggest that coral hosts might recruit nitrogen-fixing bacteria during the initial stages of suffering heat stress. An environment that is conducive to the colonization and development of opportunistic and pathogenic bacteria when the coral host becomes more susceptible as heat stress duration increases.},
}
@article {pmid38349190,
year = {2024},
author = {Ghimire-Kafle, S and Weaver, ME and Kimbrel, MP and Bollmann, A},
title = {Competition between ammonia-oxidizing archaea and complete ammonia oxidizers from freshwater environments.},
journal = {Applied and environmental microbiology},
volume = {90},
number = {3},
pages = {e0169823},
pmid = {38349190},
issn = {1098-5336},
support = {IOS1755270//National Science Foundation (NSF)/ ; },
mesh = {*Archaea ; Ammonia ; Nitrites ; Nitrates ; Bacteria ; Nitrification ; Oxidation-Reduction ; Lakes ; *Ammonium Compounds ; Phylogeny ; },
abstract = {UNLABELLED: Aerobic ammonia oxidizers (AOs) are prokaryotic microorganisms that contribute to the global nitrogen cycle by performing the first step of nitrification, the oxidation of ammonium to nitrite and nitrate. While aerobic AOs are found ubiquitously, their distribution is controlled by key environmental conditions such as substrate (ammonium) availability. Ammonia-oxidizing archaea (AOA) and complete ammonia oxidizers (comammox) are generally found in oligotrophic environments with low ammonium availability. However, whether AOA and comammox share these habitats or outcompete each other is not well understood. We assessed the competition for ammonium between an AOA and comammox enriched from the freshwater Lake Burr Oak. The AOA enrichment culture (AOA-BO1) contained Nitrosarchaeum sp. BO1 as the ammonia oxidizer and Nitrospira sp. BO1 as the nitrite oxidizer. The comammox enrichment BO4 (cmx-BO4) contained the comammox strain Nitrospira sp. BO4. The competition experiments were performed either in continuous cultivation with ammonium as a growth-limiting substrate or in batch cultivation with initial ammonium concentrations of 50 and 500 µM. Regardless of the ammonium concentration, Nitrospira sp. BO4 outcompeted Nitrosarchaeum sp. BO1 under all tested conditions. The dominance of Nitrospira sp. BO4 could be explained by the ability of comammox to generate more energy through the complete oxidation of ammonia to nitrate and their more efficient carbon fixation pathway-the reductive tricarboxylic acid cycle. Our results are supported by the higher abundance of comammox compared to AOA in the sediment of Lake Burr Oak.<br><br>IMPORTANCE: Nitrification is a key process in the global nitrogen cycle. Aerobic ammonia oxidizers play a central role in the nitrogen cycle by performing the first step of nitrification. Ammonia-oxidizing archaea (AOA) and complete ammonia oxidizers (comammox) are the dominant nitrifiers in environments with low ammonium availability. While AOA have been studied for almost 20 years, comammox were only discovered 8 years ago. Until now, there has been a gap in our understanding of whether AOA and comammox can co-exist or if one strain would be dominant under ammonium-limiting conditions. Here, we present the first study characterizing the competition between freshwater AOA and comammox under varying substrate concentrations. Our results will help in elucidating the niches of two key nitrifiers in freshwater lakes.},
}
@article {pmid38323857,
year = {2024},
author = {Kuroda, K and Nakajima, M and Nakai, R and Hirakata, Y and Kagemasa, S and Kubota, K and Noguchi, TQP and Yamamoto, K and Satoh, H and Nobu, MK and Narihiro, T},
title = {Microscopic and metatranscriptomic analyses revealed unique cross-domain parasitism between phylum Candidatus Patescibacteria/candidate phyla radiation and methanogenic archaea in anaerobic ecosystems.},
journal = {mBio},
volume = {15},
number = {3},
pages = {e0310223},
pmid = {38323857},
issn = {2150-7511},
support = {JP16H07403, JP21H01471//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; G-2019-1-052//Institute for Fermentation, Osaka (IFO)/ ; G-2022-1-014//Institute for Fermentation, Osaka (IFO)/ ; //A matching fund between National Institute of Advanced Industrial Science and Technology (AIST) and Tohoku University/ ; },
mesh = {Humans ; *Archaea/genetics ; Anaerobiosis ; Ecosystem ; In Situ Hybridization, Fluorescence ; Phylogeny ; Bacteria/genetics ; *Euryarchaeota/genetics ; },
abstract = {To verify whether members of the phylum Candidatus Patescibacteria parasitize archaea, we applied cultivation, microscopy, metatranscriptomic, and protein structure prediction analyses on the Patescibacteria-enriched cultures derived from a methanogenic bioreactor. Amendment of cultures with exogenous methanogenic archaea, acetate, amino acids, and nucleoside monophosphates increased the relative abundance of Ca. Patescibacteria. The predominant Ca. Patescibacteria were families Ca. Yanofskyibacteriaceae and Ca. Minisyncoccaceae, and the former showed positive linear relationships (r[2] ≥ 0.70) Methanothrix in their relative abundances, suggesting related growth patterns. Methanothrix and Methanospirillum cells with attached Ca. Yanofskyibacteriaceae and Ca. Minisyncoccaceae, respectively, had significantly lower cellular activity than those of the methanogens without Ca. Patescibacteria, as extrapolated from fluorescence in situ hybridization-based fluorescence. We also observed that parasitized methanogens often had cell surface deformations. Some Methanothrix-like filamentous cells were dented where the submicron cells were attached. Ca. Yanofskyibacteriaceae and Ca. Minisyncoccaceae highly expressed extracellular enzymes, and based on structural predictions, some contained peptidoglycan-binding domains with potential involvement in host cell attachment. Collectively, we propose that the interactions of Ca. Yanofskyibacteriaceae and Ca. Minisyncoccaceae with methanogenic archaea are parasitisms.IMPORTANCECulture-independent DNA sequencing approaches have explored diverse yet-to-be-cultured microorganisms and have significantly expanded the tree of life in recent years. One major lineage of the domain Bacteria, Ca. Patescibacteria (also known as candidate phyla radiation), is widely distributed in natural and engineered ecosystems and has been thought to be dependent on host bacteria due to the lack of several biosynthetic pathways and small cell/genome size. Although bacteria-parasitizing or bacteria-preying Ca. Patescibacteria have been described, our recent studies revealed that some lineages can specifically interact with archaea. In this study, we provide strong evidence that the relationship is parasitic, shedding light on overlooked roles of Ca. Patescibacteria in anaerobic habitats.},
}
@article {pmid38314098,
year = {2023},
author = {Tirumalai, MR and Sivaraman, RV and Kutty, LA and Song, EL and Fox, GE},
title = {Ribosomal Protein Cluster Organization in Asgard Archaea.},
journal = {Archaea (Vancouver, B.C.)},
volume = {2023},
number = {},
pages = {5512414},
pmid = {38314098},
issn = {1472-3654},
mesh = {*Archaea/genetics/metabolism ; *Ribosomal Proteins/genetics/metabolism ; Escherichia coli/genetics ; Bacteria/genetics ; Genome, Bacterial ; Phylogeny ; },
abstract = {It has been proposed that the superphylum of Asgard Archaea may represent a historical link between the Archaea and Eukarya. Following the discovery of the Archaea, it was soon appreciated that archaeal ribosomes were more similar to those of Eukarya rather than Bacteria. Coupled with other eukaryotic-like features, it has been suggested that the Asgard Archaea may be directly linked to eukaryotes. However, the genomes of Bacteria and non-Asgard Archaea generally organize ribosome-related genes into clusters that likely function as operons. In contrast, eukaryotes typically do not employ an operon strategy. To gain further insight into conservation of the r-protein genes, the genome order of conserved ribosomal protein (r-protein) coding genes was identified in 17 Asgard genomes (thirteen complete genomes and four genomes with less than 20 contigs) and compared with those found previously in non-Asgard archaeal and bacterial genomes. A universal core of two clusters of 14 and 4 cooccurring r-proteins, respectively, was identified in both the Asgard and non-Asgard Archaea. The equivalent genes in the E. coli version of the cluster are found in the S10 and spc operons. The large cluster of 14 r-protein genes (uS19-uL22-uS3-uL29-uS17 from the S10 operon and uL14-uL24-uL5-uS14-uS8-uL6-uL18-uS5-uL30-uL15 from the spc operon) occurs as a complete set in the genomes of thirteen Asgard genomes (five Lokiarchaeotes, three Heimdallarchaeotes, one Odinarchaeote, and four Thorarchaeotes). Four less conserved clusters with partial bacterial equivalents were found in the Asgard. These were the L30e (str operon in Bacteria) cluster, the L18e (alpha operon in Bacteria) cluster, the S24e-S27ae-rpoE1 cluster, and the L31e, L12..L1 cluster. Finally, a new cluster referred to as L7ae was identified. In many cases, r-protein gene clusters/operons are less conserved in their organization in the Asgard group than in other Archaea. If this is generally true for nonribosomal gene clusters, the results may have implications for the history of genome organization. In particular, there may have been an early transition to or from the operon approach to genome organization. Other nonribosomal cellular features may support different relationships. For this reason, it may be important to consider ribosome features separately.},
}
@article {pmid38302496,
year = {2024},
author = {Tang, SK and Zhi, XY and Zhang, Y and Makarova, KS and Liu, BB and Zheng, GS and Zhang, ZP and Zheng, HJ and Wolf, YI and Zhao, YR and Jiang, SH and Chen, XM and Li, EY and Zhang, T and Chen, PR and Feng, YZ and Xiang, MX and Lin, ZQ and Shi, JH and Chang, C and Zhang, X and Li, R and Lou, K and Wang, Y and Chang, L and Yin, M and Yang, LL and Gao, HY and Zhang, ZK and Tao, TS and Guan, TW and He, FC and Lu, YH and Cui, HL and Koonin, EV and Zhao, GP and Xu, P},
title = {Addendum: Cellular differentiation into hyphae and spores in halophilic archaea.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {523},
pmid = {38302496},
issn = {2041-1723},
mesh = {*Hyphae ; Spores, Fungal ; *Archaea/genetics ; Phylogeny ; Cell Differentiation ; },
}
@article {pmid38299815,
year = {2024},
author = {Scott, KM and Payne, RR and Gahramanova, A},
title = {Widespread dissolved inorganic carbon-modifying toolkits in genomes of autotrophic Bacteria and Archaea and how they are likely to bridge supply from the environment to demand by autotrophic pathways.},
journal = {Applied and environmental microbiology},
volume = {90},
number = {2},
pages = {e0155723},
pmid = {38299815},
issn = {1098-5336},
support = {NSF-MCB-1952676//National Science Foundation (NSF)/ ; },
mesh = {*Archaea/genetics/metabolism ; *Bacteria/genetics/metabolism ; Autotrophic Processes/genetics ; Carbon/metabolism ; Hydroxybutyrates/metabolism ; Carbon Dioxide/metabolism ; Carbon Cycle/genetics ; },
abstract = {Using dissolved inorganic carbon (DIC) as a major carbon source, as autotrophs do, is complicated by the bedeviling nature of this substance. Autotrophs using the Calvin-Benson-Bassham cycle (CBB) are known to make use of a toolkit comprised of DIC transporters and carbonic anhydrase enzymes (CA) to facilitate DIC fixation. This minireview provides a brief overview of the current understanding of how toolkit function facilitates DIC fixation in Cyanobacteria and some Proteobacteria using the CBB and continues with a survey of the DIC toolkit gene presence in organisms using different versions of the CBB and other autotrophic pathways (reductive citric acid cycle, Wood-Ljungdahl pathway, hydroxypropionate bicycle, hydroxypropionate-hydroxybutyrate cycle, and dicarboxylate-hydroxybutyrate cycle). The potential function of toolkit gene products in these organisms is discussed in terms of CO2 and HCO3[-] supply from the environment and demand by the autotrophic pathway. The presence of DIC toolkit genes in autotrophic organisms beyond those using the CBB suggests the relevance of DIC metabolism to these organisms and provides a basis for better engineering of these organisms for industrial and agricultural purposes.},
}
@article {pmid38297167,
year = {2024},
author = {Qin, W and Wei, SP and Zheng, Y and Choi, E and Li, X and Johnston, J and Wan, X and Abrahamson, B and Flinkstrom, Z and Wang, B and Li, H and Hou, L and Tao, Q and Chlouber, WW and Sun, X and Wells, M and Ngo, L and Hunt, KA and Urakawa, H and Tao, X and Wang, D and Yan, X and Wang, D and Pan, C and Weber, PK and Jiang, J and Zhou, J and Zhang, Y and Stahl, DA and Ward, BB and Mayali, X and Martens-Habbena, W and Winkler, MH},
title = {Ammonia-oxidizing bacteria and archaea exhibit differential nitrogen source preferences.},
journal = {Nature microbiology},
volume = {9},
number = {2},
pages = {524-536},
pmid = {38297167},
issn = {2058-5276},
support = {DE-SC0020356//DOE | Advanced Research Projects Agency - Energy (Advanced Research Projects Agency - Energy - U.S. Department of Energy)/ ; 675459//Simons Foundation/ ; DEB-1664052//National Science Foundation (NSF)/ ; HR0011-17-2-0064//United States Department of Defense | Defense Advanced Research Projects Agency (DARPA)/ ; },
mesh = {*Archaea/metabolism ; *Bacteria/metabolism ; Ammonia/metabolism ; Nitrogen/metabolism ; Oxidation-Reduction ; Nitrification ; Phylogeny ; Soil Microbiology ; Urea/metabolism ; },
abstract = {Ammonia-oxidizing microorganisms (AOM) contribute to one of the largest nitrogen fluxes in the global nitrogen budget. Four distinct lineages of AOM: ammonia-oxidizing archaea (AOA), beta- and gamma-proteobacterial ammonia-oxidizing bacteria (β-AOB and γ-AOB) and complete ammonia oxidizers (comammox), are thought to compete for ammonia as their primary nitrogen substrate. In addition, many AOM species can utilize urea as an alternative energy and nitrogen source through hydrolysis to ammonia. How the coordination of ammonia and urea metabolism in AOM influences their ecology remains poorly understood. Here we use stable isotope tracing, kinetics and transcriptomics experiments to show that representatives of the AOM lineages employ distinct regulatory strategies for ammonia or urea utilization, thereby minimizing direct substrate competition. The tested AOA and comammox species preferentially used ammonia over urea, while β-AOB favoured urea utilization, repressed ammonia transport in the presence of urea and showed higher affinity for urea than for ammonia. Characterized γ-AOB co-utilized both substrates. These results reveal contrasting niche adaptation and coexistence patterns among the major AOM lineages.},
}
@article {pmid38297006,
year = {2024},
author = {Maza-Márquez, P and Lee, MD and Bebout, BM},
title = {Community ecology and functional potential of bacteria, archaea, eukarya and viruses in Guerrero Negro microbial mat.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {2561},
pmid = {38297006},
issn = {2045-2322},
mesh = {Archaea/genetics ; Bacteria/genetics ; Eukaryota/genetics ; Phylogeny ; Viruses/genetics ; *Microbiota ; },
abstract = {In this study, the microbial ecology, potential environmental adaptive mechanisms, and the potential evolutionary interlinking of genes between bacterial, archaeal and viral lineages in Guerrero Negro (GN) microbial mat were investigated using metagenomic sequencing across a vertical transect at millimeter scale. The community composition based on unique genes comprised bacteria (98.01%), archaea (1.81%), eukarya (0.07%) and viruses (0.11%). A gene-focused analysis of bacteria archaea, eukarya and viruses showed a vertical partition of the community. The greatest coverages of genes of bacteria and eukarya were detected in first layers, while the highest coverages of genes of archaea and viruses were found in deeper layers. Many genes potentially related to adaptation to the local environment were detected, such as UV radiation, multidrug resistance, oxidative stress, heavy metals, salinity and desiccation. Those genes were found in bacterial, archaeal and viral lineages with 6477, 44, and 1 genes, respectively. The evolutionary histories of those genes were studied using phylogenetic analysis, showing an interlinking between domains in GN mat.},
}
@article {pmid38292760,
year = {2024},
author = {Candeliere, F and Sola, L and Raimondi, S and Rossi, M and Amaretti, A},
title = {Good and bad dispositions between archaea and bacteria in the human gut: New insights from metagenomic survey and co-occurrence analysis.},
journal = {Synthetic and systems biotechnology},
volume = {9},
number = {1},
pages = {88-98},
pmid = {38292760},
issn = {2405-805X},
abstract = {Archaea are an understudied component of the human microbiome. In this study, the gut archaeome and bacteriome of 60 healthy adults from different region were analyzed by whole-genome shotgun sequencing. Archaea were ubiquitously found in a wide range of abundances, reaching up to 7.2 %. The dominant archaeal phylum was Methanobacteriota, specifically the family Methanobacteriaceae, encompassing more than 50 % of Archaea in 50 samples. The previously underestimated Thermoplasmatota, mostly composed of Methanomassiliicoccaceae, dominated in 10 subjects (>50 %) and was present in all others except one. Halobacteriota, the sole other archaeal phylum, occurred in negligible concentration, except for two samples (4.6-4.8 %). This finding confirmed that the human gut archaeome is primarily composed of methanogenic organisms and among the known methanogenic pathway: i) hydrogenotrophic reduction of CO2 is the predominant, being the genus Methanobrevibacter and the species Methanobrevibacter smithii the most abundant in the majority of the samples; ii) the second pathway, that involved Methanomassiliicoccales, was the hydrogenotrophic reduction of methyl-compounds; iii) dismutation of acetate or methyl-compounds seemed to be absent. Co-occurrence analysis allowed to unravel correlations between Archaea and Bacteria that shapes the overall structure of the microbial community, allowing to depict a clearer picture of the human gut archaeome.},
}
@article {pmid38280122,
year = {2024},
author = {Rao, A and Driessen, AJM},
title = {Unraveling the multiplicity of geranylgeranyl reductases in Archaea: potential roles in saturation of terpenoids.},
journal = {Extremophiles : life under extreme conditions},
volume = {28},
number = {1},
pages = {14},
pmid = {38280122},
issn = {1433-4909},
support = {024.003.019//BaSyC - Building a Synthetic Cell/ ; },
mesh = {*Terpenes/metabolism ; *Archaea/genetics/metabolism ; Phospholipids/metabolism ; Oxidoreductases/genetics/chemistry/metabolism ; },
abstract = {The enzymology of the key steps in the archaeal phospholipid biosynthetic pathway has been elucidated in recent years. In contrast, the complete biosynthetic pathways for proposed membrane regulators consisting of polyterpenes, such as carotenoids, respiratory quinones, and polyprenols remain unknown. Notably, the multiplicity of geranylgeranyl reductases (GGRs) in archaeal genomes has been correlated with the saturation of polyterpenes. Although GGRs, which are responsible for saturation of the isoprene chains of phospholipids, have been identified and studied in detail, there is little information regarding the structure and function of the paralogs. Here, we discuss the diversity of archaeal membrane-associated polyterpenes which is correlated with the genomic loci, structural and sequence-based analyses of GGR paralogs.},
}
@article {pmid38263861,
year = {2024},
author = {Ni, Y and Xu, T and Yan, S and Chen, L and Wang, Y},
title = {Hiding in plain sight: The discovery of complete genomes of 11 hypothetical spindle-shaped viruses that putatively infect mesophilic ammonia-oxidizing archaea.},
journal = {Environmental microbiology reports},
volume = {16},
number = {1},
pages = {e13230},
pmid = {38263861},
issn = {1758-2229},
support = {32370151//National Natural Science Foundation of China/ ; 41376135//National Natural Science Foundation of China/ ; },
mesh = {*Archaea/genetics/metabolism ; Ammonia/metabolism ; Capsid Proteins/chemistry/genetics/metabolism ; *Archaeal Viruses/genetics/metabolism ; Oxidation-Reduction ; Phylogeny ; },
abstract = {The genome of a putative Nitrosopumilaceae virus with a hypothetical spindle-shaped particle morphology was identified in the Yangshan Harbour metavirome from the East China Sea through protein similarity comparison and structure analysis. This discovery was accompanied by a set of 10 geographically dispersed close relatives found in the environmental virus datasets from typical locations of ammonia-oxidizing archaeon distribution. Its host prediction was supported by iPHoP prediction and protein sequence similarity. The structure of the predicted major capsid protein, together with the overall N-glycosylation site, the transmembrane helices prediction, the hydrophilicity profile, and the docking simulation of the major capsid proteins, indicate that these viruses resemble spindle-shaped viruses. It suggests a similarly assembled structure and, consequently, a possibly spindle-shaped morphology of these newly discovered archaeal viruses.},
}
@article {pmid38261994,
year = {2024},
author = {},
title = {Correction to 'Rare ribosomal RNA sequences from archaea stabilize the bacterial ribosome'.},
journal = {Nucleic acids research},
volume = {52},
number = {4},
pages = {2092},
doi = {10.1093/nar/gkae047},
pmid = {38261994},
issn = {1362-4962},
}
@article {pmid38259951,
year = {2023},
author = {Beeckman, F and Drozdzecki, A and De Knijf, A and Audenaert, D and Beeckman, T and Motte, H},
title = {High-throughput assays to identify archaea-targeting nitrification inhibitors.},
journal = {Frontiers in plant science},
volume = {14},
number = {},
pages = {1283047},
pmid = {38259951},
issn = {1664-462X},
abstract = {Nitrification is a microbial process that converts ammonia (NH3) to nitrite (NO2 [-]) and then to nitrate (NO3 [-]). The first and rate-limiting step in nitrification is ammonia oxidation, which is conducted by both bacteria and archaea. In agriculture, it is important to control this process as high nitrification rates result in NO3 [-] leaching, reduced nitrogen (N) availability for the plants and environmental problems such as eutrophication and greenhouse gas emissions. Nitrification inhibitors can be used to block nitrification, and as such reduce N pollution and improve fertilizer use efficiency (FUE) in agriculture. Currently applied inhibitors target the bacteria, and do not block nitrification by ammonia-oxidizing archaea (AOA). While it was long believed that nitrification in agroecosystems was primarily driven by bacteria, recent research has unveiled potential significant contributions from ammonia-oxidizing archaea (AOA), especially when bacterial activity is inhibited. Hence, there is also a need for AOA-targeting nitrification inhibitors. However, to date, almost no AOA-targeting inhibitors are described. Furthermore, AOA are difficult to handle, hindering their use to test or identify possible AOA-targeting nitrification inhibitors. To address the need for AOA-targeting nitrification inhibitors, we developed two miniaturized nitrification inhibition assays using an AOA-enriched nitrifying community or the AOA Nitrosospaera viennensis. These assays enable high-throughput testing of candidate AOA inhibitors. We here present detailed guidelines on the protocols and illustrate their use with some examples. We believe that these assays can contribute to the discovery of future AOA-targeting nitrification inhibitors, which could complement the currently applied inhibitors to increase nitrification inhibition efficiency in the field and as such contribute to a more sustainable agriculture.},
}
@article {pmid38246077,
year = {2024},
author = {Tang, M and Chen, Q and Zhong, H and Liu, S and Sun, W},
title = {CPR bacteria and DPANN archaea play pivotal roles in response of microbial community to antibiotic stress in groundwater.},
journal = {Water research},
volume = {251},
number = {},
pages = {121137},
doi = {10.1016/j.watres.2024.121137},
pmid = {38246077},
issn = {1879-2448},
mesh = {Archaea/genetics/metabolism ; Anti-Bacterial Agents/pharmacology/metabolism ; Bacteria/genetics/metabolism ; *Microbiota ; *Groundwater/microbiology ; Phylogeny ; },
abstract = {The accumulation of antibiotics in the natural environment can disrupt microbial population dynamics. However, our understanding of how microbial communities adapt to the antibiotic stress in groundwater ecosystems remains limited. By recovering 2675 metagenome-assembled genomes (MAGs) from 66 groundwater samples, we explored the effect of antibiotics on bacterial, archaeal, and fungal communities, and revealed the pivotal microbes and their mechanisms in coping with antibiotic stress. The results indicated that antibiotics had the most significant influence on bacterial and archaeal communities, while the impact on the fungal community was minimal. Analysis of co-occurrence networks between antibiotics and microbes revealed the critical roles of Candidate Phyla Radiation (CPR) bacteria and DPANN archaea, two representative microbial groups in groundwater ecosystem, in coping with antibiotic resistance and enhancing network connectivity and complexity. Further genomic analysis demonstrated that CPR bacteria carried approximately 6 % of the identified antibiotic resistance genes (ARGs), indicating their potential to withstand antibiotics on their own. Meanwhile, the genomes of CPR bacteria and DPANN archaea were found to encode diverse biosynthetic gene clusters (BGCs) responsible for producing antimicrobial metabolites, which could not only assist CPR and DPANN organisms but also benefit the surrounding microbes in combating antibiotic stress. These findings underscore the significant impact of antibiotics on prokaryotic microbial communities in groundwater, and highlight the importance of CPR bacteria and DPANN archaea in enhancing the overall resilience and functionality of the microbial community in the face of antibiotic stress.},
}
@article {pmid38243071,
year = {2024},
author = {Müller, MC and Lemaire, ON and Kurth, JM and Welte, CU and Wagner, T},
title = {Differences in regulation mechanisms of glutamine synthetases from methanogenic archaea unveiled by structural investigations.},
journal = {Communications biology},
volume = {7},
number = {1},
pages = {111},
pmid = {38243071},
issn = {2399-3642},
support = {KU 3768/1-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; },
mesh = {*Glutamine/metabolism ; *Archaea/genetics/metabolism ; Glutamate-Ammonia Ligase/metabolism ; Ketoglutaric Acids ; Bacteria/metabolism ; Nitrogen/metabolism ; },
abstract = {Glutamine synthetases (GS) catalyze the ATP-dependent ammonium assimilation, the initial step of nitrogen acquisition that must be under tight control to fit cellular needs. While their catalytic mechanisms and regulations are well-characterized in bacteria and eukaryotes, only limited knowledge exists in archaea. Here, we solved two archaeal GS structures and unveiled unexpected differences in their regulatory mechanisms. GS from Methanothermococcus thermolithotrophicus is inactive in its resting state and switched on by 2-oxoglutarate, a sensor of cellular nitrogen deficiency. The enzyme activation overlays remarkably well with the reported cellular concentration for 2-oxoglutarate. Its binding to an allosteric pocket reconfigures the active site through long-range conformational changes. The homolog from Methermicoccus shengliensis does not harbor the 2-oxoglutarate binding motif and, consequently, is 2-oxoglutarate insensitive. Instead, it is directly feedback-inhibited through glutamine recognition by the catalytic Asp50'-loop, a mechanism common to bacterial homologs, but absent in M. thermolithotrophicus due to residue substitution. Analyses of residue conservation in archaeal GS suggest that both regulations are widespread and not mutually exclusive. While the effectors and their binding sites are surprisingly different, the molecular mechanisms underlying their mode of action on GS activity operate on the same molecular determinants in the active site.},
}
@article {pmid38227606,
year = {2024},
author = {Hackley, RK and Vreugdenhil-Hayslette, A and Darnell, CL and Schmid, AK},
title = {A conserved transcription factor controls gluconeogenesis via distinct targets in hypersaline-adapted archaea with diverse metabolic capabilities.},
journal = {PLoS genetics},
volume = {20},
number = {1},
pages = {e1011115},
pmid = {38227606},
issn = {1553-7404},
mesh = {*Transcription Factors/genetics/metabolism ; *Gluconeogenesis/genetics ; Archaea/genetics ; Gene Expression Regulation, Archaeal ; Carbohydrates ; Carbon/metabolism ; },
abstract = {Timely regulation of carbon metabolic pathways is essential for cellular processes and to prevent futile cycling of intracellular metabolites. In Halobacterium salinarum, a hypersaline adapted archaeon, a sugar-sensing TrmB family protein controls gluconeogenesis and other biosynthetic pathways. Notably, Hbt. salinarum does not utilize carbohydrates for energy, uncommon among Haloarchaea. We characterized a TrmB-family transcriptional regulator in a saccharolytic generalist, Haloarcula hispanica, to investigate whether the targets and function of TrmB, or its regulon, is conserved in related species with distinct metabolic capabilities. In Har. hispanica, TrmB binds to 15 sites in the genome and induces the expression of genes primarily involved in gluconeogenesis and tryptophan biosynthesis. An important regulatory control point in Hbt. salinarum, activation of ppsA and repression of pykA, is absent in Har. hispanica. Contrary to its role in Hbt. salinarum and saccharolytic hyperthermophiles, TrmB does not act as a global regulator: it does not directly repress the expression of glycolytic enzymes, peripheral pathways such as cofactor biosynthesis, or catabolism of other carbon sources in Har. hispanica. Cumulatively, these findings suggest rewiring of the TrmB regulon alongside metabolic network evolution in Haloarchaea.},
}
@article {pmid38225278,
year = {2024},
author = {Lu, Z and Xia, R and Zhang, S and Pan, J and Liu, Y and Wolf, YI and Koonin, EV and Li, M},
title = {Evolution of optimal growth temperature in Asgard archaea inferred from the temperature dependence of GDP binding to EF-1A.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {515},
pmid = {38225278},
issn = {2041-1723},
mesh = {*Archaea/growth &amp; development ; Phylogeny ; Temperature ; *Guanosine Diphosphate/metabolism ; *Peptide Elongation Factor 1/metabolism ; },
abstract = {The archaeal ancestor of eukaryotes apparently belonged to the phylum Asgardarchaeota, but the ecology and evolution of Asgard archaea are poorly understood. The optimal GDP-binding temperature of a translation elongation factor (EF-1A or EF-Tu) has been previously shown to correlate with the optimal growth temperature of diverse prokaryotes. Here, we reconstruct ancestral EF-1A sequences and experimentally measure the optimal GDP-binding temperature of EF-1A from ancient and extant Asgard archaea, to infer the evolution of optimal growth temperatures in Asgardarchaeota. Our results suggest that the Asgard ancestor of eukaryotes was a moderate thermophile, with an optimal growth temperature around 53 °C. The origin of eukaryotes appears to coincide with a transition from thermophilic to mesophilic lifestyle during the evolution of Asgard archaea.},
}
@article {pmid38203843,
year = {2024},
author = {Cisek, AA and Szymańska, E and Wierzbicka-Rucińska, A and Aleksandrzak-Piekarczyk, T and Cukrowska, B},
title = {Methanogenic Archaea in the Pediatric Inflammatory Bowel Disease in Relation to Disease Type and Activity.},
journal = {International journal of molecular sciences},
volume = {25},
number = {1},
pages = {},
pmid = {38203843},
issn = {1422-0067},
support = {M34/2019//Children's Memorial Health Institute/ ; 2017/25/N/NZ7/02905//National Science Center/ ; },
mesh = {Humans ; Child ; Archaea/genetics ; *Euryarchaeota ; *Inflammatory Bowel Diseases ; *Colitis, Ulcerative ; *Crohn Disease ; Leukocyte L1 Antigen Complex ; },
abstract = {The inflammatory bowel disease (IBD) is associated with gut microbiota dysbiosis; however, studies on methanogens-especially those focused on children-are extremely limited. The aim of this study was to determine the abundance of total methanogenic archaea and their three subgroups: Methanobrevibacter (Mb.) smithii, Methanosphaera (Ms.) stadtmanae, and Methanomassiliicoccales, in the feces of children with both active and inactive Crohn's disease (CD) and ulcerative colitis (UC). The results of a quantitative real-time PCR were cross-referenced with the disease type (CD vs. UC) and activity assessed with the use of Pediatric Crohn's Disease Activity Index (PCDAI) and Pediatric Ulcerative Colitis Activity Index (PUCAI) indices, and fecal calprotectin (FCP) concentration, and compared with controls. There was a significant decrease in the number of total methanogens in CD and UC compared to controls. The prevalence of total methanogens was also lower in UC compared to controls. Furthermore, patients from the inactive UC group were colonized by a lower number of Mb. smithii, and demonstrated the most pronounced positive correlation between the number of Ms. stadtmanae and the FCP concentration. Our results demonstrate that gut methanogens are related to the type and activity of pediatric IBD.},
}
@article {pmid38197785,
year = {2024},
author = {Hu, Y and Ma, X and Li, XX and Tan, S and Cheng, M and Hou, J and Cui, HL},
title = {Halomicrococcus gelatinilyticus sp. nov. and Halosimplex aquaticum sp. nov., halophilic archaea isolated from saline soil and an inland solar saltern.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {74},
number = {1},
pages = {},
doi = {10.1099/ijsem.0.006231},
pmid = {38197785},
issn = {1466-5034},
mesh = {RNA, Ribosomal, 16S/genetics ; Phylogeny ; Sequence Analysis, DNA ; DNA, Bacterial/genetics ; Bacterial Typing Techniques ; Base Composition ; Fatty Acids/chemistry ; *Halobacteriaceae/genetics ; *Halobacteriales ; Phosphatidylglycerols ; Soil ; Sulfates ; },
abstract = {Two extremely halophilic archaeal strains, GSLN9[T] and XZYJT29[T], were isolated from the saline soil in different regions of western China. Both strains GSLN9[T] and XZYJT29[T] have two 16S rRNA genes with similarities of 95.1 and 94.8 %, respectively. Strain GSLN9[T] was mostly related to the genus Halomicrococcus based on 16S rRNA (showing 91.0-96.0 % identities) and rpoB' genes (showing 92.0 % identity). Strain XZYJT29[T] showed 92.1-97.6 % (16S rRNA gene) and 91.4-93.1 % (rpoB' gene) sequence similarities to its relatives in the genus Halosimplex, respectively. The polar lipid profile of strain GSLN9[T] included phosphatidic acid (PA), phosphatidylglycerol (PG), phosphatidylglycerol phosphate methyl ester (PGP-Me), phosphatidylglycerol sulphate (PGS), sulphated mannosyl glucosyl diether (S-DGD-1) and sulphated galactosyl mannosyl glucosyl diether (S-TGD-1), mostly similar to that of Halomicrococcus hydrotolerans H22[T]. PA, PG, PGP-Me, S-DGD-1 (S-DGD-PA), S2-DGD, S-TGD-1 and an unidentified glycolipid were detected in strain XZYJT29[T]; this polar lipid composition is similar to those of members of the genus Halosimplex. The average nucleotide identity, digital DNA-DNA hybridization and average amino acid identity values between these two strains and their relatives of the genera Halomicrococcus and Halosimplex were no more than 82, 27 and 80 %, respectively, much lower than the thresholds for species demarcation. Other phenotypic characterization results indicated that strains GSLN9[T] and XZYJT29[T] can be differentiated from the current species of the genera Halomicrococcus and Halosimplex, respectively. These results revealed that strains GSLN9[T] (=CGMCC 1.15215[T]=JCM 30842[T]) and XZYJT29[T] (=CGMCC 1.15828[T]=JCM 31853[T]) represent novel species of Halomicrococcus and Halosimplex, for which the names Halomicrococcus gelatinilyticus sp. nov. and Halosimplex aquaticum sp. nov. are proposed.},
}
@article {pmid38194256,
year = {2024},
author = {Li, XX and Tan, S and Cheng, M and Hu, Y and Ma, X and Hou, J and Cui, HL},
title = {Halospeciosus flavus gen. nov., sp. nov. and Haladaptatus caseinilyticus sp. nov., halophilic archaea isolated from saline soil of an inland solar saltern and offshore sediment.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {74},
number = {1},
pages = {},
doi = {10.1099/ijsem.0.006220},
pmid = {38194256},
issn = {1466-5034},
mesh = {Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; DNA, Bacterial/genetics ; Bacterial Typing Techniques ; Base Composition ; Fatty Acids/chemistry ; *Halobacteriaceae/genetics ; *Halobacteriales ; Phosphatidylglycerols ; },
abstract = {Two novel halophilic archaeal strains (XZGYJ-43[T] and ZJ1[T]) were isolated from Mangkang ancient solar saltern (Tibet, PR China) and Zhujiang river inlet (Guangdong, PR China), respectively. The comparison of the 16S rRNA gene sequences revealed that strain XZGYJ-43[T] is related to the current species of the family Halobacteriaceae (89.2-91.7% similarity) and strain ZJ1[T] showed 94.7-98.3% similarity to the current species of the genus Haladaptatus. Phylogenetic analyses based on 16S rRNA genes, rpoB' genes and genomes indicated that strain XZGYJ-43[T] is separate from the related genera, Halocalculus, Salarchaeum and Halarchaeum of the family Halobacteriaceae, and strain ZJ1[T] tightly clusters with the current species of the genus Haladaptatus. The average nucleotide identity, digital DNA-DNA hybridization and average amino acid identity values between strain XZGYJ-43[T] and the current species of the family Halobacteriaceae were 71-75, 20-25 and 59-68 %, and these values between strain ZJ1[T] and the current species of the genus Haladaptatus were 77-81, 27-32 and 76-82 %, respectively, clearly below the thresholds for prokaryotic species demarcation. These two strains could be distinguished from their relatives according to differential phenotypic characteristics. The major polar lipids of strain XZGYJ-43[T] were phosphatidic acid (PA), phosphatidylglycerol (PG), phosphatidylglycerol phosphate methyl ester (PGP-Me), mannosyl glucosyl diether (DGD-1; DGD-PA) and sulphated mannosyl glucosyl diether (S-DGD-1; S-DGD-PA), and those of strain ZJ1[T] were PA, PG, PGP-Me, DGD-PA, S-DGD-1 (S-DGD-PA) and sulphated galactosyl mannosyl glucosyl diether. Based on phenotypic, phylogenetic and genomic data, strain XZGYJ-43[T] (=CGMCC 1.13890[T]=JCM 33735[T]) represents a novel species of a new genus within the family Halobacteriaceae, and strain ZJ1[T] (=CGMCC 1.18785[T]=JCM 34917[T]) represents a novel species of the genus Haladaptatus, for which the names Halospeciosus flavus gen. nov., sp. nov. and Haladaptatus caseinilyticus sp. nov. are proposed, respectively.},
}
@article {pmid38189270,
year = {2024},
author = {Makarova, KS and Zhang, C and Wolf, YI and Karamycheva, S and Whitaker, RJ and Koonin, EV},
title = {Computational analysis of genes with lethal knockout phenotype and prediction of essential genes in archaea.},
journal = {mBio},
volume = {15},
number = {2},
pages = {e0309223},
pmid = {38189270},
issn = {2150-7511},
support = {//HHS | National Institutes of Health (NIH)/ ; 1656869//National Science Foundation (NSF)/ ; GBMF9195//Gordon and Betty Moore Foundation (GBMF)/ ; 1656869//National Science Foundation (NSF)/ ; GBMF9195//Gordon and Betty Moore Foundation (GBMF)/ ; },
mesh = {*Archaea/genetics/metabolism ; Genes, Essential ; Genome, Archaeal ; Genomics ; Phenotype ; *Archaeal Proteins/genetics/metabolism ; },
abstract = {The identification of microbial genes essential for survival as those with lethal knockout phenotype (LKP) is a common strategy for functional interrogation of genomes. However, interpretation of the LKP is complicated because a substantial fraction of the genes with this phenotype remains poorly functionally characterized. Furthermore, many genes can exhibit LKP not because their products perform essential cellular functions but because their knockout activates the toxicity of other genes (conditionally essential genes). We analyzed the sets of LKP genes for two archaea, Methanococcus maripaludis and Sulfolobus islandicus, using a variety of computational approaches aiming to differentiate between essential and conditionally essential genes and to predict at least a general function for as many of the proteins encoded by these genes as possible. This analysis allowed us to predict the functions of several LKP genes including previously uncharacterized subunit of the GINS protein complex with an essential function in genome replication and of the KEOPS complex that is responsible for an essential tRNA modification as well as GRP protease implicated in protein quality control. Additionally, several novel antitoxins (conditionally essential genes) were predicted, and this prediction was experimentally validated by showing that the deletion of these genes together with the adjacent genes apparently encoding the cognate toxins caused no growth defect. We applied principal component analysis based on sequence and comparative genomic features showing that this approach can separate essential genes from conditionally essential ones and used it to predict essential genes in other archaeal genomes.IMPORTANCEOnly a relatively small fraction of the genes in any bacterium or archaeon is essential for survival as demonstrated by the lethal effect of their disruption. The identification of essential genes and their functions is crucial for understanding fundamental cell biology. However, many of the genes with a lethal knockout phenotype remain poorly functionally characterized, and furthermore, many genes can exhibit this phenotype not because their products perform essential cellular functions but because their knockout activates the toxicity of other genes. We applied state-of-the-art computational methods to predict the functions of a number of uncharacterized genes with the lethal knockout phenotype in two archaeal species and developed a computational approach to predict genes involved in essential functions. These findings advance the current understanding of key functionalities of archaeal cells.},
}
@article {pmid38188570,
year = {2023},
author = {Hanišáková, N and Vítězová, M and Vítěz, T and Kushkevych, I and Kotrlová, E and Novák, D and Lochman, J and Zavada, R},
title = {Microbiological insight into various underground gas storages in Vienna Basin focusing on methanogenic Archaea.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1293506},
pmid = {38188570},
issn = {1664-302X},
abstract = {In recent years, there has been a growing interest in extending the potential of underground gas storage (UGS) facilities to hydrogen and carbon dioxide storage. However, this transition to hydrogen storage raises concerns regarding potential microbial reactions, which could convert hydrogen into methane. It is crucial to gain a comprehensive understanding of the microbial communities within any UGS facilities designated for hydrogen storage. In this study, underground water samples and water samples from surface technologies from 7 different UGS objects located in the Vienna Basin were studied using both molecular biology methods and cultivation methods. Results from 16S rRNA sequencing revealed that the proportion of archaea in the groundwater samples ranged from 20 to 58%, with methanogens being the predominant. Some water samples collected from surface technologies contained up to 87% of methanogens. Various species of methanogens were isolated from individual wells, including Methanobacterium sp., Methanocalculus sp., Methanolobus sp. or Methanosarcina sp. We also examined water samples for the presence of sulfate-reducing bacteria known to be involved in microbially induced corrosion and identified species of the genus Desulfovibrio in the samples. In the second part of our study, we contextualized our data by comparing it to available sequencing data from terrestrial subsurface environments worldwide. This allowed us to discern patterns and correlations between different types of underground samples based on environmental conditions. Our findings reveal presence of methanogens in all analyzed groups of underground samples, which suggests the possibility of unintended microbial hydrogen-to-methane conversion and the associated financial losses. Nevertheless, the prevalence of methanogens in our results also highlights the potential of the UGS environment, which can be effectively leveraged as a bioreactor for the conversion of hydrogen into methane, particularly in the context of Power-to-Methane technology.},
}
@article {pmid38185001,
year = {2024},
author = {Mao, Y and Wu, J and Yang, R and Ma, Y and Ye, J and Zhong, J and Deng, N and He, X and Hong, Y},
title = {Novel database for accA gene revealed a vertical variability pattern of autotrophic carbon fixation potential of ammonia oxidizing archaea in a permeable subterranean estuary.},
journal = {Marine environmental research},
volume = {194},
number = {},
pages = {106342},
doi = {10.1016/j.marenvres.2024.106342},
pmid = {38185001},
issn = {1879-0291},
mesh = {*Archaea/genetics ; *Ammonia/metabolism ; Estuaries ; RNA, Ribosomal, 16S/genetics ; Oxidation-Reduction ; Carbon Cycle ; Phylogeny ; },
abstract = {The autotrophic carbon fixation pathway of ammonia-oxidizing archaea (AOA) was the 3-hydroxypropionate/4-hydroxybutyrate (3-HP/4-HB) cycle, of which the acetyl-CoA carboxylase α-submit (accA) gene is widely recognized as the indicator. To date, there is no reference database or suitable cut-off value for operational taxonomic unit (OTU) clustering to analyze the diversity of AOA based on the accA gene. In this study, a reference database with 489 sequences was constructed, all the accA gene sequences was obtained from the AOA enrichment culture, pure culture and environmental samples. Additionally, the 79% was determined as the cut-off value for OTU clustering by comparing the similarity between the accA gene and the 16S rRNA gene. The developed method was verified by analyzing samples from the subterranean estuary and a vertical variation pattern of autotrophic carbon fixation potential of AOA was revealed. This study provided an effective method to analyze the diversity and autotrophic carbon fixation potential of AOA based on accA gene.},
}
@article {pmid38181064,
year = {2024},
author = {Zhao, H and Wu, H and Guseman, A and Abeykoon, D and Camara, CM and Dalal, Y and Fushman, D and Papoian, GA},
title = {The role of cryptic ancestral symmetry in histone folding mechanisms across Eukarya and Archaea.},
journal = {PLoS computational biology},
volume = {20},
number = {1},
pages = {e1011721},
pmid = {38181064},
issn = {1553-7358},
support = {R01 GM065334/GM/NIGMS NIH HHS/United States ; U54 CA272220/CA/NCI NIH HHS/United States ; },
mesh = {Humans ; *Histones/chemistry ; *Archaea/genetics ; Molecular Dynamics Simulation ; DNA ; Eukaryota/genetics ; Protein Folding ; },
abstract = {Histones compact and store DNA in both Eukarya and Archaea, forming heterodimers in Eukarya and homodimers in Archaea. Despite this, the folding mechanism of histones across species remains unclear. Our study addresses this gap by investigating 11 types of histone and histone-like proteins across humans, Drosophila, and Archaea through multiscale molecular dynamics (MD) simulations, complemented by NMR and circular dichroism experiments. We confirm and elaborate on the widely applied "folding upon binding" mechanism of histone dimeric proteins and report a new alternative conformation, namely, the inverted non-native dimer, which may be a thermodynamically metastable configuration. Protein sequence analysis indicated that the inverted conformation arises from the hidden ancestral head-tail sequence symmetry underlying all histone proteins, which is congruent with the previously proposed histone evolution hypotheses. Finally, to explore the potential formations of homodimers in Eukarya, we utilized MD-based AWSEM and AI-based AlphaFold-Multimer models to predict their structures and conducted extensive all-atom MD simulations to examine their respective structural stabilities. Our results suggest that eukaryotic histones may also form stable homodimers, whereas their disordered tails bring significant structural asymmetry and tip the balance towards the formation of commonly observed heterotypic dimers.},
}
@article {pmid38179456,
year = {2023},
author = {Medina-Chávez, NO and Torres-Cerda, A and Chacón, JM and Harcombe, WR and De la Torre-Zavala, S and Travisano, M},
title = {Disentangling a metabolic cross-feeding in a halophilic archaea-bacteria consortium.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1276438},
pmid = {38179456},
issn = {1664-302X},
abstract = {Microbial syntrophy, a cooperative metabolic interaction among prokaryotes, serves a critical role in shaping communities, due to the auxotrophic nature of many microorganisms. Syntrophy played a key role in the evolution of life, including the hypothesized origin of eukaryotes. In a recent exploration of the microbial mats within the exceptional and uniquely extreme Cuatro Cienegas Basin (CCB), a halophilic isolate, designated as AD140, emerged as a standout due to its distinct growth pattern. Subsequent genome sequencing revealed AD140 to be a co-culture of a halophilic archaeon from the Halorubrum genus and a marine halophilic bacterium, Marinococcus luteus, both occupying the same ecological niche. This intriguing coexistence hints at an early-stage symbiotic relationship that thrives on adaptability. By delving into their metabolic interdependence through genomic analysis, this study aims to uncover shared characteristics that enhance their symbiotic association, offering insights into the evolution of halophilic microorganisms and their remarkable adaptations to high-salinity environments.},
}
@article {pmid38172371,
year = {2024},
author = {Guerra, A},
title = {Human associated Archaea: a neglected microbiome worth investigating.},
journal = {World journal of microbiology &amp; biotechnology},
volume = {40},
number = {2},
pages = {60},
pmid = {38172371},
issn = {1573-0972},
mesh = {Animals ; Female ; Humans ; Pregnancy ; *Archaea ; Colostrum/microbiology ; Infectious Disease Transmission, Vertical ; *Microbiota ; Milk ; Infant ; Infant, Newborn ; },
abstract = {The majority of research in the field of human microbiota has predominantly focused on bacterial and fungal communities. Conversely, the human archaeome has received scant attention and remains poorly studied, despite its potential role in human diseases. Archaea have the capability to colonize various human body sites, including the gastrointestinal tract, skin, vagina, breast milk, colostrum, urinary tract, lungs, nasal and oral cavities. This colonization can occur through vertical transmission, facilitated by the transfer of breast milk or colostrum from mother to child, as well as through the consumption of dairy products, organic produce, salty foods, and fermented items. The involvement of these microorganisms in diseases, such as periodontitis, might be attributed to their production of toxic compounds and the detoxification of growth inhibitors for pathogens. However, the precise mechanisms through which these contributions occur remain incompletely understood, necessitating further studies to assess their impact on human health.},
}
@article {pmid38138100,
year = {2023},
author = {Hinkle, JE and Mara, P and Beaudoin, DJ and Edgcomb, VP and Teske, AP},
title = {A PCR-Based Survey of Methane-Cycling Archaea in Methane-Soaked Subsurface Sediments of Guaymas Basin, Gulf of California.},
journal = {Microorganisms},
volume = {11},
number = {12},
pages = {},
pmid = {38138100},
issn = {2076-2607},
support = {512580/NASA/NASA/United States ; },
abstract = {The Guaymas Basin in the Gulf of California is characterized by active seafloor spreading, the rapid deposition of organic-rich sediments, steep geothermal gradients, and abundant methane of mixed thermogenic and microbial origin. Subsurface sediment samples from eight drilling sites with distinct geochemical and thermal profiles were selected for DNA extraction and PCR amplification to explore the diversity of methane-cycling archaea in the Guaymas Basin subsurface. We performed PCR amplifications with general (mcrIRD), and ANME-1 specific primers that target the alpha (α) subunit of methyl coenzyme M reductase (mcrA). Diverse ANME-1 lineages associated with anaerobic methane oxidation were detected in seven out of the eight drilling sites, preferentially around the methane-sulfate interface, and in several cases, showed preferences for specific sampling sites. Phylogenetically, most ANME-1 sequences from the Guaymas Basin subsurface were related to marine mud volcanoes, seep sites, and the shallow marine subsurface. The most frequently recovered methanogenic phylotypes were closely affiliated with the hyperthermophilic Methanocaldococcaceae, and found at the hydrothermally influenced Ringvent site. The coolest drilling site, in the northern axial trough of Guaymas Basin, yielded the greatest diversity in methanogen lineages. Our survey indicates the potential for extensive microbial methane cycling within subsurface sediments of Guaymas Basin.},
}
@article {pmid38138015,
year = {2023},
author = {Wu, X and Zhang, W and Liu, G and Chen, T and Li, Z},
title = {Changes in Diversity and Abundance of Ammonia-Oxidizing Archaea and Bacteria along a Glacier Retreating Chronosequence in the Tianshan Mountains, China.},
journal = {Microorganisms},
volume = {11},
number = {12},
pages = {},
pmid = {38138015},
issn = {2076-2607},
abstract = {Glaciers retreating due to global warming create important new habitats, particularly suitable for studying ecosystem development where nitrogen is a limiting factor. Nitrogen availability mainly results from microbial decomposition and transformation processes, including nitrification. AOA and AOB perform the first and rate-limiting step of nitrification. Investigating the abundance and diversity of AOA and AOB is essential for understanding early ecosystem development. The dynamics of AOA and AOB community structure along a soil chronosequence in Tianshan No. 1 Glacier foreland were analyzed using qPCR and clone library methods. The results consistently showed low quantities of both AOA and AOB throughout the chronosequence. Initially, the copy numbers of AOB were higher than those of AOA, but they decreased in later stages. The AOB community was dominated by "Nitrosospira cluster ME", while the AOA community was dominated by "the soil and sediment 1". Both communities were potentially connected to supra- and subglacial microbial communities during early stages. Correlation analysis revealed a significant positive correlation between the ratios of AOA and AOB with soil ammonium and total nitrogen levels. These results suggest that variations in abundance and diversity of AOA and AOB along the chronosequences were influenced by ammonium availability during glacier retreat.},
}
@article {pmid38135695,
year = {2023},
author = {Trouche, B and Schauberger, C and Bouderka, F and Auguet, JC and Belser, C and Poulain, J and Thamdrup, B and Wincker, P and Arnaud-Haond, S and Glud, RN and Maignien, L},
title = {Distribution and genomic variation of ammonia-oxidizing archaea in abyssal and hadal surface sediments.},
journal = {ISME communications},
volume = {3},
number = {1},
pages = {133},
pmid = {38135695},
issn = {2730-6151},
abstract = {Ammonia-oxidizing archaea of the phylum Thaumarchaeota play a central role in the biogeochemical cycling of nitrogen in benthic sediments, at the interface between pelagic and subsurface ecosystems. However, our understanding of their niche separation and of the processes controlling their population structure in hadal and abyssal surface sediments is still limited. Here, we reconstructed 47 AOA metagenome-assembled genomes (MAGs) from surface sediments of the Atacama and Kermadec trench systems. They formed deep-sea-specific groups within the family Nitrosopumilaceae and were assigned to six amoA gene-based clades. MAGs from different clades had distinct distribution patterns along oxygen-ammonium counter gradients in surface sediments. At the species level, MAGs thus seemed to form different ecotypes and follow deterministic niche-based distributions. In contrast, intraspecific population structure, defined by patterns of Single Nucleotide Variants (SNV), seemed to reflect more complex contributions of both deterministic and stochastic processes. Firstly, the bathymetric range had a strong effect on population structure, with distinct populations in abyssal plains and hadal trenches. Then, hadal populations were clearly separated by trench system, suggesting a strong isolation-by-topography effect, whereas abyssal populations were rather controlled by sediment depth or geographic distances, depending on the clade considered. Interestingly, genetic variability between samples was lowest in sediment layers where the mean MAG coverage was highest, highlighting the importance of selective pressure linked with each AOA clade's ecological niche. Overall, our results show that deep-sea AOA genome distributions seem to follow both deterministic and stochastic processes, depending on the genomic variability scale considered.},
}
@article {pmid38132325,
year = {2023},
author = {Rafiq, M and Hassan, N and Rehman, M and Hayat, M and Nadeem, G and Hassan, F and Iqbal, N and Ali, H and Zada, S and Kang, Y and Sajjad, W and Jamal, M},
title = {Challenges and Approaches of Culturing the Unculturable Archaea.},
journal = {Biology},
volume = {12},
number = {12},
pages = {},
pmid = {38132325},
issn = {2079-7737},
abstract = {Since Carl Woese's discovery of archaea as a third domain of life, numerous archaeal species have been discovered, yet archaeal diversity is poorly characterized. Culturing archaea is complicated, but several queries about archaeal cell biology, evolution, physiology, and diversity need to be solved by culturing and culture-dependent techniques. Increasing interest in demand for innovative culturing methods has led to various technological and methodological advances. The current review explains frequent hurdles hindering uncultured archaea isolation and discusses features for more archaeal cultivation. This review also discusses successful strategies and available media for archaeal culturing, which might be helpful for future culturing practices.},
}
@article {pmid38098882,
year = {2023},
author = {Xiang, Y and Zhou, T and Deng, S and Shao, Z and Liu, Y and He, Q and Chai, H},
title = {Nitrite improved nitrification efficiency and enriched ammonia-oxidizing archaea and bacteria in the simultaneous nitrification and denitrification process.},
journal = {Water research X},
volume = {21},
number = {},
pages = {100204},
pmid = {38098882},
issn = {2589-9147},
abstract = {Simultaneous nitrification and denitrification (SND) is effective and energy-saving for wastewater treatment. As an inevitable intermediate product in the SND process, nitrite affects the efficiency of ammonia oxidation and the composition of nitrifiers. To investigate the impact of nitrite on ammonia oxidation efficiency, two reactors performing SND were respectively operated without nitrite (R1 as control) and with 20 mg N/L nitrite addition (R2 as experimental). The total nitrogen removal efficiency was 74.5% in R1 while 99.0% in R2. With nitrite addition (i.e., 20 mg N/L), the ammonia removal rate in R2 increased to 4.5 times of that in R1. The ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) contributed to respective around 46.9% and 41.8% ammonia removal in R2 based on the results of experiments with specific inhibitors. The number of respective AOA and AOB ammonia monooxygenase gene (amoA) copies increased by 280 and 30 times due to nitrite addition, according to the qPCR results. The high-throughput sequencing results illustrated the increase of dominant AOB species from 0.40% in R1 to 1.59% in R2 and the phylogenetic tree analysis revealed a close link to Nitrosospira multiformis. These results indicated that the ammonia removal efficiency was improved and AOA/AOB were enriched by nitrite addition. The specific nitrite reductases in AOA and AOB boosted the adaptation of nitrite addition. This study demonstrated the positive impacts of nitrite addition on the ammonia removal efficiency and rate in the SND process.},
}
@article {pmid38075885,
year = {2023},
author = {Boswinkle, K and Dinh, TA and Allen, KD},
title = {Biochemical and genetic studies define the functions of methylthiotransferases in methanogenic and methanotrophic archaea.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1304671},
pmid = {38075885},
issn = {1664-302X},
abstract = {Methylthiotransferases (MTTases) are radical S-adenosylmethionine (SAM) enzymes that catalyze the addition of a methylthio (-SCH3) group to an unreactive carbon center. These enzymes are responsible for the production of 2-methylthioadenosine (ms[2]A) derivatives found at position A37 of select tRNAs in all domains of life. Additionally, some bacteria contain the RimO MTTase that catalyzes the methylthiolation of the S12 ribosomal protein. Although the functions of MTTases in bacteria and eukaryotes have been established via detailed genetic and biochemical studies, MTTases from the archaeal domain of life are understudied and the substrate specificity determinants of MTTases remain unclear. Here, we report the in vitro enzymatic activities of an MTTase (C4B56_06395) from a thermophilic Ca. Methanophagales anaerobic methanotroph (ANME) as well as the MTTase from a hyperthermophilic methanogen - MJ0867 from Methanocaldococcus jannaschii. Both enzymes catalyze the methylthiolation of N[6]-threonylcarbamoyladenosine (t[6]A) and N[6]-hydroxynorvalylcarbamoyladenosine (hn[6]A) residues to produce 2-methylthio-N[6]-threonylcarbamoyladenosine (ms[2]t[6]A) and 2-methylthio-N[6]-hydroxynorvalylcarbamoyladenosine (ms[2]hn[6]A), respectively. To further assess the function of archaeal MTTases, we analyzed select tRNA modifications in a model methanogen - Methanosarcina acetivorans - and generated a deletion of the MTTase-encoding gene (MA1153). We found that M. acetivorans produces ms[2]hn[6]A in exponential phase of growth, but does not produce ms[2]t[6]A in detectable amounts. Upon deletion of MA1153, the ms[2]A modification was absent, thus confirming the function of MtaB-family MTTases in generating ms[2]hn[6]A modified nucleosides in select tRNAs.},
}
@article {pmid38062210,
year = {2024},
author = {Zhang, J and Zhou, M and Shi, F and Lei, Z and Wang, Y and Hu, M and Zhao, J},
title = {The abundance of comammox bacteria was higher than that of ammonia-oxidizing archaea and bacteria in rhizosphere of emergent macrophytes in a typical shallow lake riparian.},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {27},
number = {1},
pages = {67-79},
pmid = {38062210},
issn = {1618-1905},
support = {92047204//National Natural Science Foundation of China/ ; 42177383//National Natural Science Foundation of China/ ; U1802241//National Natural Science Foundation of China/ ; U2040211//National Natural Science Foundation of China/ ; 51679258//National Natural Science Foundation of China/ ; SKL2020TS07//the State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin/ ; },
mesh = {*Archaea/genetics ; *Ammonia ; Rhizosphere ; Ecosystem ; Lakes/microbiology ; Oxidation-Reduction ; Phylogeny ; Bacteria ; Soil Microbiology ; },
abstract = {Complete ammonia oxidation (comammox) bacteria can complete the whole nitrification process independently, which not only challenges the classical two-step nitrification theory but also updates long-held perspective of microbial ecological relationship in nitrification process. Although comammox bacteria have been found in many ecosystems in recent years, there is still a lack of research on the comammox process in rhizosphere of emergent macrophytes in lakeshore zone. Sediment samples were collected in this study from rhizosphere, far-rhizosphere, and non-rhizosphere of emergent macrophytes along the shore of Lake Liangzi, a shallow lake. The diversity of comammox bacteria and amoA gene abundance of comammox bacteria, ammonia-oxidizing archaea (AOA), and ammonia-oxidizing bacteria (AOB) in these samples were measured. The results showed that comammox bacteria widely existed in the rhizosphere of emergent macrophytes and fell into clade A.1, clade A.2, and clade B, and clade A was the predominant community in all sampling sites. The abundance of comammox amoA gene (6.52 × 10[6]-2.45 × 10[8] copies g[-1] dry sediment) was higher than that of AOB amoA gene (6.58 × 10[4]-3.58 × 10[6] copies g[-1] dry sediment), and four orders of magnitude higher than that of AOA amoA gene (7.24 × 10[2]-6.89 × 10[3] copies g[-1] dry sediment), suggesting that the rhizosphere of emergent macrophytes is more favorable for the growth of comammox bacteria than that of AOB and AOA. Our study indicated that the comammox bacteria may play important roles in ammonia-oxidizing processes in all different rhizosphere regions.},
}
@article {pmid38047693,
year = {2024},
author = {Qu, L and Li, M and Gong, F and He, L and Li, M and Zhang, C and Yin, K and Xie, W},
title = {Oxygen-driven divergence of marine group II archaea reflected by transitions of superoxide dismutases.},
journal = {Microbiology spectrum},
volume = {12},
number = {1},
pages = {e0203323},
pmid = {38047693},
issn = {2165-0497},
support = {92051117, 41776137//MOST | National Natural Science Foundation of China (NSFC)/ ; 91851210//MOST | National Natural Science Foundation of China (NSFC)/ ; 2021B1515120080//GDSTC | Basic and Applied Basic Research Foundation of Guangdong Province ()/ ; 2021B1515120080//GDSTC | Basic and Applied Basic Research Foundation of Guangdong Province ()/ ; ZDSYS201802081843490//Shenzhen Municipal Science and Technology Innovation Council | Shenzhen Key Laboratory Fund ()/ ; },
mesh = {*Archaea/genetics ; Reactive Oxygen Species ; *Oxygen ; Superoxide Dismutase/genetics ; Superoxides ; },
abstract = {Reactive oxygen species (ROS), including superoxide anion, is a series of substances that cause oxidative stress for all organisms. Marine group II (MGII) archaea are mainly live in the surface seawater and exposed to considerable ROS. Therefore, it is important to understand the antioxidant capacity of MGII. Our research found that Fe/Mn- superoxide dismutase (Fe/MnSOD) may be more suitable for MGII to resist oxidative damage, and the changes in oxygen concentrations and SOD metallic cofactors play an important role in the selection of SOD by the 17 clades of MGII, which in turn affects the species differentiation of MGII. Overall, this study provides insight into the co-evolutionary history of these uncultivated marine archaea with the earth system.},
}
@article {pmid38042190,
year = {2024},
author = {Wu, Y and Zhou, S and Li, Y and Niu, L and Wang, L},
title = {Climate and local environment co-mediate the taxonomic and functional diversity of bacteria and archaea in the Qinghai-Tibet Plateau rivers.},
journal = {The Science of the total environment},
volume = {912},
number = {},
pages = {168968},
doi = {10.1016/j.scitotenv.2023.168968},
pmid = {38042190},
issn = {1879-1026},
mesh = {*Archaea ; Tibet ; Ecosystem ; Rivers/microbiology ; Bacteria ; Soil ; *Microbiota ; Water ; },
abstract = {Understanding the environmental response patterns of riverine microbiota is essential for predicting the potential impact of future environmental change on river ecosystems. Vulnerable plateau ecosystems are particularly sensitive to climate and local environmental changes, however, the environmental response patterns of the taxonomic and functional diversity of riverine microbiota remain unclear. Here, we conducted a systematic investigation of the taxonomic and functional diversity of bacteria and archaea from riparian soils, sediments, and water across the elevation of 1800- 4800 m in the Qinghai-Tibet Plateau rivers. We found that within the elevation range of 1800 to 3800 m, riparian soils and sediments exhibited similarities and stabilities in microbial taxonomic and functional diversity, and water microbiomes were more sensitive with great fluctuations in microbial diversity. Beyond the elevation of 3800 m, microbial diversity declined across all riverine matrixes. Local environmental conditions can influence the sensitivity of microbiomes to climate change. The combination of critical climate and local environmental factors, including total nitrogen, total organic carbon, as well as climate variables associated with temperature and precipitation, provided better explanations for microbial diversity than single-factor analyses. Under the extremely adverse scenario of high greenhouse gas emission concentrations (SSP585), we anticipate that by the end of this century, the bacterial, archaeal, and microbial functional diversity across the river network of the Yangtze and Yellow source basin would potentially change by -16.9- 5.2 %, -16.1- 5.7 %, and -9.3- 6.4 %, respectively. Overall, climate and local environments jointly shaped the microbial diversity in plateau river ecosystems, and water microbiomes would provide early signs of environmental changes. Our study provides effective theoretical foundations for the conservation of river biodiversity and functional stability under environmental changes.},
}
@article {pmid38041127,
year = {2023},
author = {Diaz, GR and Gaire, TN and Ferm, P and Case, L and Caixeta, LS and Goldsmith, TJ and Armstrong, J and Noyes, NR},
title = {Effect of castration timing and weaning strategy on the taxonomic and functional profile of ruminal bacteria and archaea of beef calves.},
journal = {Animal microbiome},
volume = {5},
number = {1},
pages = {61},
pmid = {38041127},
issn = {2524-4671},
support = {Grantee No. GNT-20212290//Fulbright Scholarship/ ; Contract No. 085-2020-FONDECYT//Consejo Nacional de Ciencia, Tecnologia e Innovacion Tecnologica from Peru/ ; MnDRIVE Graduate Student Professional Development award//MnDRIVE Global Food Ventures Program/ ; },
abstract = {BACKGROUND: Beef cattle experience several management challenges across their lifecycle. Castration and weaning, two major interventions in the early life of beef cattle, can have a substantial impact on animal performance. Despite the key role of the rumen microbiome on productive traits of beef cattle, the effect of castration timing and weaning strategy on this microbial community has not been formally described. We assessed the effect of four castration time windows (at birth, turnout, pre-weaning and weaning) and two weaning strategies (fence-line and truck transportation) on the rumen microbiome in a randomized controlled study with 32 male calves across 3 collection days (i.e., time points). Ruminal fluid samples were submitted to shotgun metagenomic sequencing and changes in the taxonomic (microbiota) and functional profile (metagenome) of the rumen microbiome were described.<br><br>RESULTS: Using a comprehensive yet stringent taxonomic classification approach, we identified 10,238 unique taxa classified under 40 bacterial and 7 archaeal phyla across all samples. Castration timing had a limited long-term impact on the rumen microbiota and was not associated with changes in alpha and beta diversity. The interaction of collection day and weaning strategy was associated with changes in the rumen microbiota, which experienced a significant decrease in alpha diversity and shifts in beta diversity within 48&#xa0;h post-weaning, especially in calves abruptly weaned by truck transportation. Calves weaned using a fence-line weaning strategy had lower relative abundance of Bacteroides, Lachnospira, Fibrobacter and Ruminococcus genera compared to calves weaned by truck transportation. Some genes involved in the hydrogenotrophic methanogenesis pathway (fwdB and fwdF) had higher relative abundance in fence-line-weaned calves post-weaning. The antimicrobial resistance gene tetW consistently represented more than 50% of the resistome across time, weaning and castration groups, without significant changes in relative abundance.<br><br>CONCLUSIONS: Within the context of this study, castration timing had limited long-term effects on the rumen microbiota, while weaning strategy had short-term effects on the rumen microbiota and methane-associated metagenome, but not on the rumen resistome.},
}
@article {pmid38033561,
year = {2023},
author = {Protasov, E and Nonoh, JO and Kästle Silva, JM and Mies, US and Hervé, V and Dietrich, C and Lang, K and Mikulski, L and Platt, K and Poehlein, A and Köhler-Ramm, T and Miambi, E and Boga, HI and Feldewert, C and Ngugi, DK and Plarre, R and Sillam-Dussès, D and Šobotník, J and Daniel, R and Brune, A},
title = {Diversity and taxonomic revision of methanogens and other archaea in the intestinal tract of terrestrial arthropods.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1281628},
pmid = {38033561},
issn = {1664-302X},
abstract = {Methane emission by terrestrial invertebrates is restricted to millipedes, termites, cockroaches, and scarab beetles. The arthropod-associated archaea known to date belong to the orders Methanobacteriales, Methanomassiliicoccales, Methanomicrobiales, and Methanosarcinales, and in a few cases also to non-methanogenic Nitrososphaerales and Bathyarchaeales. However, all major host groups are severely undersampled, and the taxonomy of existing lineages is not well developed. Full-length 16S rRNA gene sequences and genomes of arthropod-associated archaea are scarce, reference databases lack resolution, and the names of many taxa are either not validly published or under-classified and require revision. Here, we investigated the diversity of archaea in a wide range of methane-emitting arthropods, combining phylogenomic analysis of isolates and metagenome-assembled genomes (MAGs) with amplicon sequencing of full-length 16S rRNA genes. Our results allowed us to describe numerous new species in hitherto undescribed taxa among the orders Methanobacteriales (Methanacia, Methanarmilla, Methanobaculum, Methanobinarius, Methanocatella, Methanoflexus, Methanorudis, and Methanovirga, all gen. nova), Methanomicrobiales (Methanofilum and Methanorbis, both gen. nova), Methanosarcinales (Methanofrustulum and Methanolapillus, both gen. nova), Methanomassiliicoccales (Methanomethylophilaceae fam. nov., Methanarcanum, Methanogranum, Methanomethylophilus, Methanomicula, Methanoplasma, Methanoprimaticola, all gen. nova), and the new family Bathycorpusculaceae (Bathycorpusculum gen. nov.). Reclassification of amplicon libraries from this and previous studies using this new taxonomic framework revealed that arthropods harbor only CO2 and methyl-reducing hydrogenotrophic methanogens. Numerous genus-level lineages appear to be present exclusively in arthropods, suggesting long evolutionary trajectories with their termite, cockroach, and millipede hosts, and a radiation into various microhabitats and ecological niches provided by their digestive tracts (e.g., hindgut compartments, gut wall, or anaerobic protists). The distribution patterns among the different host groups are often complex, indicating a mixed mode of transmission and a parallel evolution of invertebrate and vertebrate-associated lineages.},
}
@article {pmid38029671,
year = {2024},
author = {Sun, F and Wang, Y and Wang, Y and Sun, C and Cheng, H and Wu, M},
title = {Insights into the spatial distributions of bacteria, archaea, ammonia-oxidizing bacteria and archaea communities in sediments of Daya Bay, northern South China Sea.},
journal = {Marine pollution bulletin},
volume = {198},
number = {},
pages = {115850},
doi = {10.1016/j.marpolbul.2023.115850},
pmid = {38029671},
issn = {1879-3363},
mesh = {*Archaea/metabolism ; *Ammonia/metabolism ; Bays ; Oxidation-Reduction ; Geologic Sediments/chemistry ; Bacteria/metabolism ; China ; Nitrogen/metabolism ; Phylogeny ; Soil Microbiology ; },
abstract = {Microbe plays an important role in the biogeochemical cycles of the coastal waters. However, comprehensive information about the microbe in the gulf waters is lacking. This study employed high-throughput sequencing and quantitative PCR (qPCR) to investigate the distribution patterns of bacterial, archaeal, ammonia-oxidizing bacterial (AOB), and archaeal (AOA) communities in Daya Bay. Community compositions and principal coordinates analysis (PCoA) exhibited significant spatial characteristics in the diversity and distributions of bacteria, archaea, AOB, and AOA. Notably, various microbial taxa (bacterial, archaeal, AOB, and AOA) exhibited significant differences in different regions, playing crucial roles in nitrogen, sulfur metabolism, and organic carbon mineralization. Canonical correlation analysis (CCA) or redundancy analysis (RDA) indicated that environmental parameters such as temperature, salinity, nitrate, total nitrogen, silicate, and phosphate strongly influenced the distributions of bacterial, archaeal, AOB, and AOA. This study deepens the understanding of the composition and ecological function of prokaryotes in the bay.},
}
@article {pmid38029211,
year = {2023},
author = {Huber, M and Vogel, N and Borst, A and Pfeiffer, F and Karamycheva, S and Wolf, YI and Koonin, EV and Soppa, J},
title = {Unidirectional gene pairs in archaea and bacteria require overlaps or very short intergenic distances for translational coupling via termination-reinitiation and often encode subunits of heteromeric complexes.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1291523},
pmid = {38029211},
issn = {1664-302X},
abstract = {Genomes of bacteria and archaea contain a much larger fraction of unidirectional (serial) gene pairs than convergent or divergent gene pairs. Many of the unidirectional gene pairs have short overlaps of -4 nt and -1 nt. As shown previously, translation of the genes in overlapping unidirectional gene pairs is tightly coupled. Two alternative models for the fate of the post-termination ribosome predict either that overlaps or very short intergenic distances are essential for translational coupling or that the undissociated post-termination ribosome can scan through long intergenic regions, up to hundreds of nucleotides. We aimed to experimentally resolve the contradiction between the two models by analyzing three native gene pairs from the model archaeon Haloferax volcanii and three native pairs from Escherichia coli. A two reporter gene system was used to quantify the reinitiation frequency, and several stop codons in the upstream gene were introduced to increase the intergenic distances. For all six gene pairs from two species, an extremely strong dependence of the reinitiation efficiency on the intergenic distance was unequivocally demonstrated, such that even short intergenic distances of about 20 nt almost completely abolished translational coupling. Bioinformatic analysis of the intergenic distances in all unidirectional gene pairs in the genomes of H. volcanii and E. coli and in 1,695 prokaryotic species representative of 49 phyla showed that intergenic distances of -4 nt or -1 nt (= short gene overlaps of 4 nt or 1 nt) were by far most common in all these groups of archaea and bacteria. A small set of genes in E. coli, but not in H. volcanii, had intergenic distances of around +10 nt. Our experimental and bioinformatic analyses clearly show that translational coupling requires short gene overlaps, whereas scanning of intergenic regions by the post-termination ribosome occurs rarely, if at all. Short overlaps are enriched among genes that encode subunits of heteromeric complexes, and co-translational complex formation requiring precise subunit stoichiometry likely confers an evolutionary advantage that drove the formation and conservation of overlapping gene pairs during evolution.},
}
@article {pmid38012208,
year = {2023},
author = {Mara, P and Geller-McGrath, D and Edgcomb, V and Beaudoin, D and Morono, Y and Teske, A},
title = {Metagenomic profiles of archaea and bacteria within thermal and geochemical gradients of the Guaymas Basin deep subsurface.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {7768},
pmid = {38012208},
issn = {2041-1723},
support = {OCE-2046799//National Science Foundation (NSF)/ ; OCE-1829903//National Science Foundation (NSF)/ ; OCE-2046799//National Science Foundation (NSF)/ ; OCE-1829903//National Science Foundation (NSF)/ ; OCE-1829903//National Science Foundation (NSF)/ ; OCE-2046799//National Science Foundation (NSF)/ ; OCE-1829903//National Science Foundation (NSF)/ ; JP19H00730//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JP23H00154//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; },
mesh = {*Archaea/genetics ; Metagenome/genetics ; Geologic Sediments/chemistry ; Phylogeny ; Bacteria/genetics ; *Crenarchaeota ; RNA, Ribosomal, 16S ; },
abstract = {Previous studies of microbial communities in subseafloor sediments reported that microbial abundance and diversity decrease with sediment depth and age, and microbes dominating at depth tend to be a subset of the local seafloor community. However, the existence of geographically widespread, subsurface-adapted specialists is also possible. Here, we use metagenomic and metatranscriptomic analyses of the hydrothermally heated, sediment layers of Guaymas Basin (Gulf of California, Mexico) to examine the distribution and activity patterns of bacteria and archaea along thermal, geochemical and cell count gradients. We find that the composition and distribution of metagenome-assembled genomes (MAGs), dominated by numerous lineages of Chloroflexota and Thermoproteota, correlate with biogeochemical parameters as long as temperatures remain moderate, but downcore increasing temperatures beyond ca. 45 ºC override other factors. Consistently, MAG size and diversity decrease with increasing temperature, indicating a downcore winnowing of the subsurface biosphere. By contrast, specific archaeal MAGs within the Thermoproteota and Hadarchaeota increase in relative abundance and in recruitment of transcriptome reads towards deeper, hotter sediments, marking the transition towards a specialized deep, hot biosphere.},
}
@article {pmid38007550,
year = {2023},
author = {Yang, Y and Liu, H and Zhang, Y and Fang, X and Zhong, X and Lv, J},
title = {Contribution of ammonia-oxidizing archaea and bacteria to nitrogen transformation in a soil fertilized with urea and organic amendments.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {20722},
pmid = {38007550},
issn = {2045-2322},
support = {2452021124//Talent Special Fund Grant from Northwest A&amp;F university/ ; S202210712582//Innovation and entrepreneurship training program for College Students from Northwest A&amp;F university/ ; A314021402-202218//Foundation of the State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau/ ; 42077135//National natural science foundation of China/ ; },
mesh = {Animals ; Swine ; *Archaea ; Ammonia ; Soil ; Urea ; Nitrogen ; Dissolved Organic Matter ; Oxidation-Reduction ; Soil Microbiology ; Phylogeny ; Bacteria/genetics ; *Betaproteobacteria ; Nitrification ; },
abstract = {The contribution of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) is crucial for nitrogen transformation. The effects of four organic amendments (OAs) plus urea on soil nitrogen transformation and the contribution of the ammonia-oxidizing microbial community were investigated using an incubation experiment. The OAs plus urea treatments included pig manure plus urea (PM + U), wheat straw plus urea (WS + U), compost plus urea (CP + U) and improved-compost plus urea (IC + U), while no OAs and urea amended control was noted as CK. The abundance and composition of AOA and AOB were determined using high through-put sequencing. Compared with CK, the OA plus urea treatments significantly enhanced the amount of total mineralized nitrogen released during the incubation process. After incubation, the highest mineralized nitrogen and net nitrogen mineralization was under the PM + U treatment and the lowest was in the WS + U treatment. In conclusion, among all OA plus urea treatments, the microbial biomass nitrogen content was the highest in WS + U treatment and dissolved organic nitrogen content was the highest with the PM + U treatment. Additionally, the abundance of AOB was inhibited in comparison to that of AOA; however, AOB contributed more to nitrification than AOA. Soil NO3[-]-N and dissolved organic nitrogen were the principal components influencing the distribution of AOA and AOB. The result illustrated that the OAs plus urea, especially PM plus urea promoted mineralization to produce more dissolved organic nitrogen and NH4[+]-N, thus accelerating the growth of AOB to strengthen nitrification in soil.},
}
@article {pmid38007076,
year = {2024},
author = {Zhang, Z and Bo, L and Wang, S and Li, C and Zhang, X and Xue, B and Yang, X and He, X and Shen, Z and Qiu, Z and Zhao, C and Wang, J},
title = {Multidrug-resistant plasmid RP4 inhibits the nitrogen removal capacity of ammonia-oxidizing archaea, ammonia-oxidizing bacteria, and comammox in activated sludge.},
journal = {Environmental research},
volume = {242},
number = {},
pages = {117739},
doi = {10.1016/j.envres.2023.117739},
pmid = {38007076},
issn = {1096-0953},
mesh = {*Archaea/genetics/metabolism ; Sewage/microbiology ; Ammonia ; Nitrogen/metabolism ; Denitrification ; In Situ Hybridization, Fluorescence ; Oxidation-Reduction ; Bacteria/genetics/metabolism ; Plasmids/genetics ; *Betaproteobacteria/genetics/metabolism ; Anti-Bacterial Agents ; Phylogeny ; Soil Microbiology ; },
abstract = {In wastewater treatment plants (WWTPs), ammonia oxidation is primarily carried out by three types of ammonia oxidation microorganisms (AOMs): ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), and comammox (CMX). Antibiotic resistance genes (ARGs), which pose an important public health concern, have been identified at every stage of wastewater treatment. However, few studies have focused on the impact of ARGs on ammonia removal performance. Therefore, our study sought to investigate the effect of the representative multidrug-resistant plasmid RP4 on the functional microorganisms involved in ammonia oxidation. Using an inhibitor-based method, we first evaluated the contributions of AOA, AOB, and CMX to ammonia oxidation in activated sludge, which were determined to be 13.7%, 41.1%, and 39.1%, respectively. The inhibitory effects of C2H2, C8H14, and 3,4-dimethylpyrazole phosphate (DMPP) were then validated by qPCR. After adding donor strains to the sludge, fluorescence in situ hybridization (FISH) imaging analysis demonstrated the co-localization of RP4 plasmids and all three AOMs, thus confirming the horizontal gene transfer (HGT) of the RP4 plasmid among these microorganisms. Significant inhibitory effects of the RP4 plasmid on the ammonia nitrogen consumption of AOA, AOB, and CMX were also observed, with inhibition rates of 39.7%, 36.2%, and 49.7%, respectively. Moreover, amoA expression in AOB and CMX was variably inhibited by the RP4 plasmid, whereas AOA amoA expression was not inhibited. These results demonstrate the adverse environmental effects of the RP4 plasmid and provide indirect evidence supporting plasmid-mediated conjugation transfer from bacteria to archaea.},
}
@article {pmid38004804,
year = {2023},
author = {Borrel, G and Fadhlaoui, K and Ben Hania, W and Gaci, N and Pehau-Arnaudet, G and Chaudhary, PP and Vandekerckove, P and Ballet, N and Alric, M and O'Toole, PW and Fardeau, ML and Ollivier, B and Brugère, JF},
title = {Methanomethylophilus alvi gen. nov., sp. nov., a Novel Hydrogenotrophic Methyl-Reducing Methanogenic Archaea of the Order Methanomassiliicoccales Isolated from the Human Gut and Proposal of the Novel Family Methanomethylophilaceae fam. nov.},
journal = {Microorganisms},
volume = {11},
number = {11},
pages = {},
pmid = {38004804},
issn = {2076-2607},
support = {NA/SFI_/Science Foundation Ireland/Ireland ; },
abstract = {The methanogenic strain Mx-05[T] was isolated from the human fecal microbiome. A phylogenetic analysis based on the 16S rRNA gene and protein marker genes indicated that the strain is affiliated with the order Methanomassiliicoccales. It shares 86.9% 16S rRNA gene sequence identity with Methanomassiliicoccus luminyensis, the only member of this order previously isolated. The cells of Mx-05[T] were non-motile cocci, with a diameter range of 0.4-0.7 μm. They grew anaerobically and reduced methanol, monomethylamine, dimethylamine, and trimethylamine into methane, using H2 as an electron donor. H2/CO2, formate, ethanol, and acetate were not used as energy sources. The growth of Mx-05[T] required an unknown medium factor(s) provided by Eggerthella lenta and present in rumen fluid. Mx-05[T] grew between 30 °C and 40 °C (optimum 37 °C), over a pH range of 6.9-8.3 (optimum pH 7.5), and between 0.02 and 0.34 mol.L[-1] NaCl (optimum 0.12 mol.L[-1] NaCl). The genome is 1.67 Mbp with a G+C content of 55.5 mol%. Genome sequence annotation confirmed the absence of the methyl branch of the H4MPT Wood-Ljungdahl pathway, as described for other Methanomassiliicoccales members. Based on an average nucleotide identity analysis, we propose strain Mx-05[T] as being a novel representative of the order Methanomassiliicoccales, within the novel family Methanomethylophilaceae, for which the name Methanomethylophilus alvi gen. nov, sp. nov. is proposed. The type strain is Mx-05[T] (JCM 31474T).},
}
@article {pmid37996939,
year = {2023},
author = {Tao, S and Veen, GFC and Zhang, N and Yu, T and Qu, L},
title = {Tree and shrub richness modifies subtropical tree productivity by regulating the diversity and community composition of soil bacteria and archaea.},
journal = {Microbiome},
volume = {11},
number = {1},
pages = {261},
pmid = {37996939},
issn = {2049-2618},
mesh = {*Trees ; *Ecosystem ; Archaea/genetics ; Soil ; Biodiversity ; Bacteria/genetics ; Plants ; },
abstract = {BACKGROUND: Declines in plant biodiversity often have negative consequences for plant community productivity, and it becomes increasingly acknowledged that this may be driven by shifts in soil microbial communities. So far, the role of fungal communities in driving tree diversity-productivity relationships has been well assessed in forests. However, the role of bacteria and archaea, which are also highly abundant in forest soils and perform pivotal ecosystem functions, has been less investigated in this context. Here, we investigated how tree and shrub richness affects stand-level tree productivity by regulating bacterial and archaeal community diversity and composition. We used a landscape-scale, subtropical tree biodiversity experiment (BEF-China) where tree (1, 2, or 4 species) and shrub richness (0, 2, 4, 8 species) were modified.<br><br>RESULTS: Our findings indicated a noteworthy decline in soil bacterial &#x3b1;-diversity as tree species richness increased from monoculture to 2- and 4- tree species mixtures, but a significant increase in archaeal &#x3b1;-diversity. Additionally, we observed that the impact of shrub species richness on microbial &#x3b1;-diversity was largely dependent on the level of tree species richness. The increase in tree species richness greatly reduced the variability in bacterial community composition and the complexity of co-occurrence network, but this effect was marginal for archaea. Both tree and shrub species richness increased the stand-level tree productivity by regulating the diversity and composition of bacterial community and archaeal diversity, with the effects being mediated via increases in soil C:N ratios.<br><br>CONCLUSIONS: Our findings provide insight into the importance of bacterial and archaeal communities in driving the relationship between plant diversity and productivity in subtropical forests and highlight the necessity for a better understanding of prokaryotic communities in forest soils. Video Abstract.},
}
@article {pmid37989750,
year = {2023},
author = {Gomes-Filho, JV and Breuer, R and Morales-Filloy, HG and Pozhydaieva, N and Borst, A and Paczia, N and Soppa, J and Höfer, K and Jäschke, A and Randau, L},
title = {Identification of NAD-RNA species and ADPR-RNA decapping in Archaea.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {7597},
pmid = {37989750},
issn = {2041-1723},
support = {882789//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; },
mesh = {*RNA ; *NAD/metabolism ; Adenosine Diphosphate Ribose/metabolism ; Archaea/metabolism ; Chromatography, Liquid ; Tandem Mass Spectrometry ; },
abstract = {NAD is a coenzyme central to metabolism that also serves as a 5'-terminal cap for bacterial and eukaryotic transcripts. Thermal degradation of NAD can generate nicotinamide and ADP-ribose (ADPR). Here, we use LC-MS/MS and NAD captureSeq to detect and identify NAD-RNAs in the thermophilic model archaeon Sulfolobus acidocaldarius and in the halophilic mesophile Haloferax volcanii. None of the four Nudix proteins of S. acidocaldarius catalyze NAD-RNA decapping in vitro, but one of the proteins (Saci_NudT5) promotes ADPR-RNA decapping. NAD-RNAs are converted into ADPR-RNAs, which we detect in S. acidocaldarius total RNA. Deletion of the gene encoding the 5'-3' exonuclease Saci-aCPSF2 leads to a 4.5-fold increase in NAD-RNA levels. We propose that the incorporation of NAD into RNA acts as a degradation marker for Saci-aCPSF2. In contrast, ADPR-RNA is processed by Saci_NudT5 into 5'-p-RNAs, providing another layer of regulation for RNA turnover in archaeal cells.},
}
@article {pmid37987001,
year = {2023},
author = {Sarkar, S and Kazarina, A and Hansen, PM and Ward, K and Hargreaves, C and Reese, N and Ran, Q and Kessler, W and de Souza, LFT and Loecke, TD and Sarto, MVM and Rice, CW and Zeglin, LH and Sikes, BA and Lee, STM},
title = {Ammonia-oxidizing archaea and bacteria differentially contribute to ammonia oxidation in soil under precipitation gradients and land legacy.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {37987001},
issn = {2692-8205},
support = {P30 GM122731/GM/NIGMS NIH HHS/United States ; S10 OD021743/OD/NIH HHS/United States ; U54 HD090216/HD/NICHD NIH HHS/United States ; UL1 TR002366/TR/NCATS NIH HHS/United States ; },
abstract = {BACKGROUND: Global change has accelerated the nitrogen cycle. Soil nitrogen stock degradation by microbes leads to the release of various gases, including nitrous oxide (N2O), a potent greenhouse gas. Ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) participate in the soil nitrogen cycle, producing N2O. There are outstanding questions regarding the impact of environmental processes such as precipitation and land use legacy on AOA and AOB structurally, compositionally, and functionally. To answer these questions, we analyzed field soil cores and soil monoliths under varying precipitation profiles and land legacies.<br><br>RESULTS: We resolved 28 AOA and AOB metagenome assembled genomes (MAGs) and found that they were significantly higher in drier environments and differentially abundant in different land use legacies. We further dissected AOA and AOB functional potentials to understand their contribution to nitrogen transformation capabilities. We identified the involvement of stress response genes, differential metabolic functional potentials, and subtle population dynamics under different environmental parameters for AOA and AOB. We observed that AOA MAGs lacked a canonical membrane-bound electron transport chain and F-type ATPase but possessed A/A-type ATPase, while AOB MAGs had a complete complex III module and F-type ATPase, suggesting differential survival strategies of AOA and AOB.<br><br>CONCLUSIONS: The outcomes from this study will enable us to comprehend how drought-like environments and land use legacies could impact AOA- and AOB-driven nitrogen transformations in soil.},
}
@article {pmid37973213,
year = {2023},
author = {Wolff, P and Lechner, A and Droogmans, L and Grosjean, H and Westhof, E},
title = {Corrigendum: Identification of U[p]47 in three thermophilic archaea, one mesophilic archaeon, and one hyperthermophilic bacterium.},
journal = {RNA (New York, N.Y.)},
volume = {29},
number = {12},
pages = {1973},
doi = {10.1261/rna.079812.123},
pmid = {37973213},
issn = {1469-9001},
}
@article {pmid37961710,
year = {2023},
author = {Zhang, IH and Borer, B and Zhao, R and Wilbert, S and Newman, DK and Babbin, AR},
title = {Uncultivated DPANN archaea are ubiquitous inhabitants of global oxygen deficient zones with diverse metabolic potential.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {37961710},
issn = {2692-8205},
support = {R01 HL152190/HL/NHLBI NIH HHS/United States ; },
abstract = {Archaea belonging to the DPANN superphylum have been found within an expanding number of environments and perform a variety of biogeochemical roles, including contributing to carbon, sulfur, and nitrogen cycling. Generally characterized by ultrasmall cell sizes and reduced genomes, DPANN archaea may form mutualistic, commensal, or parasitic interactions with various archaeal and bacterial hosts, influencing the ecology and functioning of microbial communities. While DPANN archaea reportedly comprise 15-26% of the archaeal community within marine oxygen deficient zone (ODZ) water columns, little is known about their metabolic capabilities in these ecosystems. We report 33 novel metagenome-assembled genomes belonging to DPANN phyla Nanoarchaeota, Pacearchaeota, Woesarchaeota, Undinarchaeota, Iainarchaeota, and SpSt-1190 from pelagic ODZs in the Eastern Tropical North Pacific and Arabian Sea. We find these archaea to be permanent, stable residents of all 3 major ODZs only within anoxic depths, comprising up to 1% of the total microbial community and up to 25-50% of archaea. ODZ DPANN appear capable of diverse metabolic functions, including fermentation, organic carbon scavenging, and the cycling of sulfur, hydrogen, and methane. Within a majority of ODZ DPANN, we identify a gene homologous to nitrous oxide reductase. Modeling analyses indicate the feasibility of a nitrous oxide reduction metabolism for host-attached symbionts, and the small genome sizes and reduced metabolic capabilities of most DPANN MAGs suggest host-associated lifestyles within ODZs.},
}
@article {pmid37955638,
year = {2023},
author = {Krawczyk, A and Gosiewski, T and Zapała, B and Kowalska-Duplaga, K and Salamon, D},
title = {Alterations in intestinal Archaea composition in pediatric patients with Crohn's disease based on next-generation sequencing - a pilot study.},
journal = {Gut microbes},
volume = {15},
number = {2},
pages = {2276806},
pmid = {37955638},
issn = {1949-0984},
mesh = {Humans ; Child ; Archaea/genetics ; Pilot Projects ; *Crohn Disease/genetics ; *Gastrointestinal Microbiome/genetics ; High-Throughput Nucleotide Sequencing ; },
abstract = {Intestinal dysbiosis can lead to the induction of systemic immune-mediated inflammatory diseases, such as Crohn's disease Although archaea are part of the commensal microbiota, they are still one of the least studied microorganisms. The aim of our study was the standardization of the optimal conditions and primers for sequencing of the gut archaeome using Next Generation Sequencing, and evaluation of the differences between the composition of archaea in patients and healthy volunteers, as well as analysis of the changes that occur in the archaeome of patients depending on disease activity. Newly diagnosed patients were characterized by similar archeal profiles at every taxonomic level as in healthy individuals (the dominance of Methanobacteria at the class level, and Methanobrevibacter at the genus level). In turn, in patients previously diagnosed with Crohn's disease (both in active and remission phase), an increased prevalence of Thermoplasmata, Thermoprotei, Halobacteria (at the class level), and Halococcus, Methanospaera or Picrophilus (at the genus level) were observed. Furthermore, we have found a significant correlation between the patient's parameters and the individual class or species of Archaea. Our study confirms changes in archaeal composition in pediatric patients with Crohn's disease, however, only in long-standing disease. At the beginning of the disease, the archeal profile is similar to that of healthy people. However, in the chronic form of the disease, significant differences in the composition of archaeome begin to appear. It seems that some archaea may be a good indicator of the chronicity and activity of Crohn's disease.},
}
@article {pmid37954235,
year = {2023},
author = {Zhang, T and He, W and Liang, Q and Zheng, F and Xiao, X and Zeng, Z and Zhou, J and Yao, W and Chen, H and Zhu, Y and Zhao, J and Zheng, Y and Zhang, C},
title = {Lipidomic diversity and proxy implications of archaea from cold seep sediments of the South China Sea.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1241958},
pmid = {37954235},
issn = {1664-302X},
abstract = {Cold seeps on the continental margins are characterized by intense microbial activities that consume a large portion of methane by anaerobic methanotrophic archaea (ANME) through anaerobic oxidation of methane (AOM). Although ANMEs are known to contain unique ether lipids that may have an important function in marine carbon cycling, their full lipidomic profiles and functional distribution in particular cold-seep settings are still poorly characterized. Here, we combined the 16S rRNA gene sequencing and lipidomic approaches to analyze archaeal communities and their lipids in cold seep sediments with distinct methane supplies from the South China Sea. The archaeal community was dominated by ANME-1 in the moderate seepage area with strong methane emission. Low seepage area presented higher archaeal diversity covering Lokiarchaeia, Bathyarchaeia, and Thermoplasmata. A total of 55 core lipids (CLs) and intact polar lipids (IPLs) of archaea were identified, which included glycerol dialkyl glycerol tetraethers (GDGTs), hydroxy-GDGTs (OH-GDGTs), archaeol (AR), hydroxyarchaeol (OH-AR), and dihydroxyarchaeol (2OH-AR). Diverse polar headgroups constituted the archaeal IPLs. High concentrations of dissolved inorganic carbon (DIC) with depleted δ[13]CDIC and high methane index (MI) values based on both CLs (MICL) and IPLs (MIIPL) indicate that ANMEs were active in the moderate seepage area. The ANME-2 and ANME-3 clades were characterized by enhanced glycosidic and phosphoric diether lipids production, indicating their potential role in coupling carbon and phosphurus cycling in cold seep ecosystems. ANME-1, though representing a smaller proportion of total archaea than ANME-2 and ANME-3 in the low seepage area, showed a positive correlation with MIIPL, indicating a different mechanism contributing to the IPL-GDGT pool. This also suggests that MIIPL could be a sensitive index to trace AOM activities performed by ANME-1. Overall, our study expands the understanding of the archaeal lipid composition in the cold seep and improves the application of MI using intact polar lipids that potentially link to extent ANME activities.},
}
@article {pmid37949149,
year = {2024},
author = {Manesh, MJH and Willard, DJ and Lewis, AM and Kelly, RM},
title = {Extremely thermoacidophilic archaea for metal bioleaching: What do their genomes tell Us?.},
journal = {Bioresource technology},
volume = {391},
number = {Pt B},
pages = {129988},
doi = {10.1016/j.biortech.2023.129988},
pmid = {37949149},
issn = {1873-2976},
mesh = {*Archaea/genetics/metabolism ; Oxidation-Reduction ; *Metals/metabolism ; Copper/metabolism ; Minerals ; },
abstract = {Elevated temperatures favor bioleaching processes through faster kinetics, more favorable mineral chemistry, lower cooling requirements, and less surface passivation. Extremely thermoacidophilic archaea from the order Sulfolobales exhibit novel mechanisms for bioleaching metals from ores and have great potential. Genome sequences of many extreme thermoacidophiles are now available and provide new insights into their biochemistry, metabolism, physiology and ecology as these relate to metal mobilization from ores. Although there are some molecular genetic tools available for extreme thermoacidophiles, further development of these is sorely needed to advance the study and application of these archaea for bioleaching applications. The evolving landscape for bioleaching technologies at high temperatures merits a closer look through a genomic lens at what is currently possible and what lies ahead in terms of new developments and emerging opportunities. The need for critical metals and the diminishing primary deposits for copper should provide incentives for high temperature bioleaching.},
}
@article {pmid37918493,
year = {2024},
author = {Lv, PL and Jia, C and Guo, X and Zhao, HP and Chen, R},
title = {Microbial stratification protects denitrifying anaerobic methane oxidation archaea and bacteria from external oxygen shock in membrane biofilm reactor.},
journal = {Bioresource technology},
volume = {391},
number = {Pt A},
pages = {129966},
doi = {10.1016/j.biortech.2023.129966},
pmid = {37918493},
issn = {1873-2976},
mesh = {*Archaea/genetics/metabolism ; Anaerobiosis ; Methane/metabolism ; Bacteria/genetics/metabolism ; Oxidation-Reduction ; Biofilms ; Methanobacteriaceae/metabolism ; *Ammonium Compounds/metabolism ; Bioreactors/microbiology ; Denitrification ; },
abstract = {Different gradients of dissolved oxygen (DO) regulate the microbial community and nitrogen removal pathways of denitrifying anaerobic methane oxidation (DAMO) and anaerobic ammonium oxidation (Anammox) coupled process in a batch biofilm reactor. Under completely anaerobic condition, approximately 72 mg NO3[-]-N/L was removed at a daily rate of 6.55 mg N/L, whereas a peak accumulation of 95 mg NO3[-]-N/L was observed during DO reached 0.5 mg/L. There is a decrease in the abundance of Candidatus Methylomirabilis (24.1%), Candidatus Methanoperedens (23.3%), and Candidatus Kuenenia (22.6%) to below 5% when DO levels reached 0.2 mg/L. Moreover, key genes associated with the reverse methanogenesis (mcrA) and anaerobic ammonium oxidase (hzo) decreased. These findings indicate that during oxygen shock, methanotrophs and denitrifiers replace Anammox bacteria on the outer sphere of the biofilm, whereas DAMO bacteria and archaea are protected from external oxygen shock due to the microbial stratification of biofilm.},
}
@article {pmid37917544,
year = {2023},
author = {Cheng, M and Li, XX and Tan, S and Ma, X and Hu, Y and Hou, J and Cui, HL},
title = {Salinigranum marinum sp. nov. and Halohasta salina sp. nov., halophilic archaea isolated from sediment of a marine saltern and inland saline soil.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {73},
number = {11},
pages = {},
doi = {10.1099/ijsem.0.006143},
pmid = {37917544},
issn = {1466-5034},
mesh = {Sodium Chloride/analysis ; Phylogeny ; Fatty Acids/chemistry ; DNA, Archaeal/genetics ; RNA, Ribosomal, 16S/genetics ; Base Composition ; Sequence Analysis, DNA ; DNA, Bacterial/genetics ; Bacterial Typing Techniques ; *Euryarchaeota ; *Halobacteriales ; China ; Glycolipids/chemistry ; Phosphatidylglycerols/analysis ; *Halobacteriaceae ; },
abstract = {Two halophilic archaeal strains, ZS-10[T] and GSL13[T], were isolated from the Zhoushan marine saltern in Zhejiang, and an inland saline soil from the Tarim Basin, Xinjiang, PR China, respectively. The cells of strain ZS-10[T] were pleomorphic while those of strain GSL13[T] were rod-shaped. Both of them stained Gram-negative and formed red-pigmented colonies on agar plates and their cells lysed in distilled water. The optimum growth of strain ZS-10[T] was observed at 40 °C, 3.4 M NaCl, 0.03 M MgCl2 and pH 7.5, while that of strain GSL13[T] was at 37 °C, 3.1 M NaCl, 0.5 M MgCl2 and pH 7.5. Phylogenetic and phylogenomic analyses indicated that these two strains were related to Salinigranum and Halohasta, respectively. Strains ZS-10[T] and GSL13[T] could be differentiated from the current members of Salinigranum and Halohasta based on the comparison of diverse phenotypic characteristics. The average amino acid identity, average nucleotide identity and digital DNA-DNA hybridization values among strain ZS-10[T] and current species of Salinigranum were 75.8-78.6 %, 80.6-81.9 % and 24.3-26.1 %, respectively. These values between strain GSL13[T] and current species of Halohasta were 78.4-80.8 %, 79.8-82.8% and 22.7-25.7 %, respectively, clearly below the threshold values for species demarcation. The polar lipids of strain ZS-10[T] were phosphatidylglycerol (PG), phosphatidylglycerol phosphate methyl ester (PGP-Me) and sulphated mannosyl glucosyl diether (S-DGD-1), while those of strain GSL13[T] were phosphatidic acid, PG, PGP-Me, phosphatidylglycerol sulphate and S-DGD-1. The polar lipid profile of strain GSL13[T] was identical to those of Halohasta, whereas strain ZS-10[T] did not contain the minor glycolipids detected in the current Salinigranum species. The phenotypic, phylogenetic and genome-based results suggested that strains ZS-10[T] (=CGMCC 1.12868[T]=JCM 30241[T]) and GSL13[T] (=CGMCC 1.15214[T]=JCM 30841[T]) represent two novel species, for which the names Salinigranum marinum sp. nov. and Halohasta salina sp. nov. are proposed.},
}
@article {pmid37917005,
year = {2023},
author = {Prakash, O and Dodsworth, JA and Dong, X and Ferry, JG and L'Haridon, S and Imachi, H and Kamagata, Y and Rhee, SK and Sagar, I and Shcherbakova, V and Wagner, D and Whitman, WB},
title = {Corrigendum: Proposed minimal standards for description of methanogenic archaea.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {73},
number = {11},
pages = {},
doi = {10.1099/ijsem.0.006127},
pmid = {37917005},
issn = {1466-5034},
}
@article {pmid37907951,
year = {2023},
author = {Romero, P and Belanche, A and Jiménez, E and Hueso, R and Ramos-Morales, E and Salwen, JK and Kebreab, E and Yáñez-Ruiz, DR},
title = {Rumen microbial degradation of bromoform from red seaweed (Asparagopsis taxiformis) and the impact on rumen fermentation and methanogenic archaea.},
journal = {Journal of animal science and biotechnology},
volume = {14},
number = {1},
pages = {133},
pmid = {37907951},
issn = {1674-9782},
support = {RYC2019-027764-I//Agencia Nacional de Investigaci&#xf3;n y Desarrollo/ ; },
abstract = {BACKGROUND: The red macroalgae Asparagopsis is an effective methanogenesis inhibitor due to the presence of halogenated methane (CH4) analogues, primarily bromoform (CHBr3). This study aimed to investigate the degradation process of CHBr3 from A. taxiformis in the rumen and whether this process is diet-dependent. An in vitro batch culture system was used according to a 2 × 2 factorial design, assessing two A. taxiformis inclusion rates [0 (CTL) and 2% DM diet (AT)] and two diets [high-concentrate (HC) and high-forage diet (HF)]. Incubations lasted for 72 h and samples of headspace and fermentation liquid were taken at 0, 0.5, 1, 3, 6, 8, 12, 16, 24, 48 and 72 h to assess the pattern of degradation of CHBr3 into dibromomethane (CH2Br2) and fermentation parameters. Additionally, an in vitro experiment with pure cultures of seven methanogens strains (Methanobrevibacter smithii, Methanobrevibacter ruminantium, Methanosphaera stadtmanae, Methanosarcina barkeri, Methanobrevibacter millerae, Methanothermobacter wolfei and Methanobacterium mobile) was conducted to test the effects of increasing concentrations of CHBr3 (0.4, 2, 10 and 50 µmol/L).<br><br>RESULTS: The addition of AT significantly decreased CH4 production (P&#x2009;=&#x2009;0.002) and the acetate:propionate ratio (P&#x2009;=&#x2009;0.003) during a 72-h incubation. The concentrations of CHBr3 showed a rapid decrease with nearly 90% degraded within the first 3&#xa0;h of incubation. On the contrary, CH2Br2 concentration quickly increased during the first 6&#xa0;h and then gradually decreased towards the end of the incubation. Neither CHBr3 degradation nor CH2Br2 synthesis were affected by the type of diet used as substrate, suggesting that the fermentation rate is not a driving factor involved in CHBr3 degradation. The in vitro culture of methanogens showed a dose-response effect of CHBr3 by inhibiting the growth of M. smithii, M. ruminantium, M. stadtmanae, M. barkeri, M. millerae, M. wolfei, and M. mobile.<br><br>CONCLUSIONS: The present work demonstrated that CHBr3 from A. taxiformis is quickly degraded to CH2Br2 in the rumen and that the fermentation rate promoted by different diets is not a driving factor involved in CHBr3 degradation.},
}
@article {pmid37895260,
year = {2023},
author = {Ullah, N and Yang, N and Guan, Z and Xiang, K and Wang, Y and Diaby, M and Chen, C and Gao, B and Song, C},
title = {Comparative Analysis and Phylogenetic Insights of Cas14-Homology Proteins in Bacteria and Archaea.},
journal = {Genes},
volume = {14},
number = {10},
pages = {},
pmid = {37895260},
issn = {2073-4425},
mesh = {*Archaea/genetics ; Phylogeny ; Bacteria/genetics ; *CRISPR-Associated Proteins ; },
abstract = {Type-V-F Cas12f proteins, also known as Cas14, have drawn significant interest within the diverse CRISPR-Cas nucleases due to their compact size. This study involves analyzing and comparing Cas14-homology proteins in prokaryotic genomes through mining, sequence comparisons, a phylogenetic analysis, and an array/repeat analysis. In our analysis, we identified and mined a total of 93 Cas14-homology proteins that ranged in size from 344 aa to 843 aa. The majority of the Cas14-homology proteins discovered in this analysis were found within the Firmicutes group, which contained 37 species, representing 42% of all the Cas14-homology proteins identified. In archaea, the DPANN group had the highest number of species containing Cas14-homology proteins, a total of three species. The phylogenetic analysis results demonstrate the division of Cas14-homology proteins into three clades: Cas14-A, Cas14-B, and Cas14-U. Extensive similarity was observed at the C-terminal end (CTD) through a domain comparison of the three clades, suggesting a potentially shared mechanism of action due to the presence of cutting domains in that region. Additionally, a sequence similarity analysis of all the identified Cas14 sequences indicated a low level of similarity (18%) between the protein variants. The analysis of repeats/arrays in the extended nucleotide sequences of the identified Cas14-homology proteins highlighted that 44 out of the total mined proteins possessed CRISPR-associated repeats, with 20 of them being specific to Cas14. Our study contributes to the increased understanding of Cas14 proteins across prokaryotic genomes. These homologous proteins have the potential for future applications in the mining and engineering of Cas14 proteins.},
}
@article {pmid37890267,
year = {2023},
author = {Notaro, A and Zaretsky, M and Molinaro, A and De Castro, C and Eichler, J},
title = {N-glycosylation in Archaea: Unusual sugars and unique modifications.},
journal = {Carbohydrate research},
volume = {534},
number = {},
pages = {108963},
doi = {10.1016/j.carres.2023.108963},
pmid = {37890267},
issn = {1873-426X},
mesh = {Glycosylation ; *Archaea/metabolism ; Sugars ; Polysaccharides ; *Archaeal Proteins/metabolism ; },
abstract = {Archaea are microorganisms that comprise a distinct branch of the universal tree of life and which are best known as extremophiles, residing in a variety of environments characterized by harsh physical conditions. One seemingly universal trait of Archaea is the ability to perform N-glycosylation. At the same time, archaeal N-linked glycans present variety in terms of both composition and architecture not seen in the parallel eukaryal or bacterial processes. In this mini-review, many of the unique and unusual sugars found in archaeal N-linked glycans as identified by nuclear magnetic resonance spectroscopy are described.},
}
@article {pmid37876779,
year = {2023},
author = {Yang, J and Chen, R and Peng, Y and Chai, J and Li, Y and Deng, F},
title = {The role of gut archaea in the pig gut microbiome: a mini-review.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1284603},
pmid = {37876779},
issn = {1664-302X},
abstract = {The gastrointestinal microbiota of swine harbors an essential but often overlooked component: the gut archaea. These enigmatic microorganisms play pivotal roles in swine growth, health, and yield quality. Recent insights indicate that the diversity of gut archaea is influenced by various factors including breed, age, and diet. Such factors orchestrate the metabolic interactions within the porcine gastrointestinal environment. Through symbiotic relationships with bacteria, these archaea modulate the host's energy metabolism and digestive processes. Contemporary research elucidates a strong association between the abundance of these archaea and economically significant traits in swine. This review elucidates the multifaceted roles of gut archaea in swine and underscores the imperative for strategic interventions to modulate their population and functionality. By exploring the probiotic potential of gut archaea, we envisage novel avenues to enhance swine growth, health, and product excellence. By spotlighting this crucial, yet under-investigated, facet of the swine gut microbiome, we aim to galvanize further scientific exploration into harnessing their myriad benefits.},
}
@article {pmid37840747,
year = {2023},
author = {Liu, H and Jing, H and Wang, F},
title = {Archaea predominate in the ammonia oxidation process in the sediments of the Yap and Mariana Trenches.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1268790},
pmid = {37840747},
issn = {1664-302X},
abstract = {Ammonia-oxidizing archaea (AOA) and bacteria (AOB) play an important role in oxidizing ammonia to nitrite in different marine environments; however, their relative contribution to ammonia oxidation in the deep-sea sediments is still largely unknown. Sediment samples from seamounts and the Challenger Deep along the arc of the Yap Trench and the Mariana Trench were used for the investigation of the geographical distribution of AOA and AOB at the cDNA level, with associated potential nitrification rates (PNRs) being measured. AOA was predominated by Candidatus Nitrosopumilus and Nitrosopumilaceae, while Methylophaga was the major group of AOB. Significantly higher transcript abundance of the AOA amoA gene than that of AOB appeared in all samples, corresponding to the much higher RNRs contributed to AOA. Both the total and AOA PNRs were significantly higher in the deeper layers due to the high sensitivity of AOA to ammonia and oxygen than in AOB. In the surface layers, TN and TOC had significant positive and negative effects on the distribution of the AOA amoA gene transcripts, respectively, while NH4+ concentration was positively correlated with the AOB amoA gene transcripts. Our study demonstrated that AOA played a more important role than AOB in the ammonia-oxidizing process that occurred in the sediments of the Yap and Mariana Trenches and would expand the understanding of their ecological contribution to the nitrification process and nitrogen flux of trenches.},
}
@article {pmid37819981,
year = {2023},
author = {Cerna-Vargas, JP and Gumerov, VM and Krell, T and Zhulin, IB},
title = {Amine-recognizing domain in diverse receptors from bacteria and archaea evolved from the universal amino acid sensor.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {120},
number = {42},
pages = {e2305837120},
pmid = {37819981},
issn = {1091-6490},
support = {R35 GM131760/GM/NIGMS NIH HHS/United States ; },
mesh = {Humans ; *Archaea/genetics/metabolism ; *Amino Acids/metabolism ; Bacterial Proteins/metabolism ; Bacteria/genetics/metabolism ; Biogenic Amines/metabolism ; },
abstract = {Bacteria possess various receptors that sense different signals and transmit information to enable an optimal adaptation to the environment. A major limitation in microbiology is the lack of information on the signal molecules that activate receptors. Signals recognized by sensor domains are poorly reflected in overall sequence identity, and therefore, the identification of signals from the amino acid sequence of the sensor alone presents a challenge. Biogenic amines are of great physiological importance for microorganisms and humans. They serve as substrates for aerobic and anaerobic growth and play a role of neurotransmitters and osmoprotectants. Here, we report the identification of a sequence motif that is specific for amine-sensing sensor domains that belong to the Cache superfamily of the most abundant extracellular sensors in prokaryotes. We identified approximately 13,000 sensor histidine kinases, chemoreceptors, receptors involved in second messenger homeostasis and Ser/Thr phosphatases from 8,000 bacterial and archaeal species that contain the amine-recognizing motif. The screening of compound libraries and microcalorimetric titrations of selected sensor domains confirmed their ability to specifically bind biogenic amines. Mutants in the amine-binding motif or domains that contain a single mismatch in the binding motif had either no or a largely reduced affinity for amines. We demonstrate that the amine-recognizing domain originated from the universal amino acid-sensing Cache domain, thus providing insight into receptor evolution. Our approach enables precise "wet"-lab experiments to define the function of regulatory systems and therefore holds a strong promise to enable the identification of signals stimulating numerous receptors.},
}
@article {pmid37815851,
year = {2024},
author = {Laird, MG and Adlung, N and Koivisto, JJ and Scheller, S},
title = {Thiol-Disulfide Exchange Kinetics and Redox Potential of the Coenzyme M and Coenzyme B Heterodisulfide, an Electron Acceptor Coupled to Energy Conservation in Methanogenic Archaea.},
journal = {Chembiochem : a European journal of chemical biology},
volume = {25},
number = {1},
pages = {e202300595},
doi = {10.1002/cbic.202300595},
pmid = {37815851},
issn = {1439-7633},
support = {NNF19OC0054329//Novo Nordisk Foundation/ ; NNF19OC0055464//Novo Nordisk Foundation/ ; 326020//Academy of Finland/ ; },
mesh = {*Mesna/metabolism ; *Archaea/metabolism ; Sulfhydryl Compounds ; Mercaptoethanol ; Disulfides/metabolism ; Carbon Dioxide/metabolism ; Electrons ; Electron Transport ; Methane/metabolism ; Oxidation-Reduction ; },
abstract = {Methanogenic and methanotrophic archaea play important roles in the global carbon cycle by interconverting CO2 and methane. To conserve energy from these metabolic pathways that happen close to the thermodynamic equilibrium, specific electron carriers have evolved to balance the redox potentials between key steps. Reduced ferredoxins required to activate CO2 are provided by energetical coupling to the reduction of the high-potential heterodisulfide (HDS) of coenzyme M (2-mercaptoethanesulfonate) and coenzyme B (7-mercaptoheptanoylthreonine phosphate). While the standard redox potential of this important HDS has been determined previously to be -143 mV (Tietze et al. 2003 DOI: 10.1002/cbic.200390053), we have measured thiol disulfide exchange kinetics and reassessed this value by equilibrating thiol-disulfide mixtures of coenzyme M, coenzyme B, and mercaptoethanol. We determined the redox potential of the HDS of coenzyme M and coenzyme B to be -16.4±1.7 mV relative to the reference thiol mercaptoethanol (E[0] '=-264 mV). The resulting E[0] ' values are -281 mV for the HDS, -271 mV for the homodisulfide of coenzyme M, and -270 mV for the homodisulfide of coenzyme B. We discuss the importance of these updated values for the physiology of methanogenic and methanotrophic archaea and their implications in terms of energy conservation.},
}
@article {pmid37805516,
year = {2023},
author = {Hu, X and Huang, Y and Gu, G and Hu, H and Yan, H and Zhang, H and Zhang, R and Zhang, D and Wang, K},
title = {Distinct patterns of distribution, community assembly and cross-domain co-occurrence of planktonic archaea in four major estuaries of China.},
journal = {Environmental microbiome},
volume = {18},
number = {1},
pages = {75},
pmid = {37805516},
issn = {2524-6372},
support = {41977192//National Natural Science Foundation of China/ ; 2021J060//Natural Science Foundation of Ningbo/ ; SJLY2022001//Fundamental Research Funds for the Provincial Universities of Zhejiang/ ; },
abstract = {BACKGROUND: Archaea are key mediators of estuarine biogeochemical cycles, but comprehensive studies comparing archaeal communities among multiple estuaries with unified experimental protocols during the same sampling periods are scarce. Here, we investigated the distribution, community assembly, and cross-domain microbial co-occurrence of archaea in surface waters across four major estuaries (Yellow River, Yangtze River, Qiantang River, and Pearl River) of China cross climatic zones (~ 1,800 km) during the winter and summer cruises.<br><br>RESULTS: The relative abundance of archaea in the prokaryotic community and archaeal community composition varied with estuaries, seasons, and stations (reflecting local environmental changes such as salinity). Archaeal communities in four estuaries were overall predominated by ammonia-oxidizing archaea (AOA) (aka. Marine Group (MG) I; primarily Nitrosopumilus), while the genus Poseidonia of Poseidoniales (aka. MGII) was occasionally predominant in Pearl River estuary. The cross-estuary dispersal of archaea was largely limited and the assembly mechanism of archaea varied with estuaries in the winter cruise, while selection governed archaeal assembly in all estuaries in the summer cruise. Although the majority of archaea taxa in microbial networks were peripherals and/or connectors, extensive and distinct cross-domain associations of archaea with bacteria were found across the estuaries, with AOA as the most crucial archaeal group. Furthermore, the expanded associations of MGII taxa with heterotrophic bacteria were observed, speculatively indicating the endogenous demand for co-processing high amount and diversity of organic matters in the estuarine ecosystem highly impacted by terrestrial/anthropogenic input, which is worthy of further study.<br><br>CONCLUSIONS: Our results highlight the lack of common patterns in the dynamics of estuarine archaeal communities along the geographic gradient, expanding the understanding of roles of archaea in microbial networks of this highly dynamic ecosystem.},
}
@article {pmid37793447,
year = {2024},
author = {Salas, E and Gorfer, M and Bandian, D and Eichorst, SA and Schmidt, H and Horak, J and Rittmann, SKR and Schleper, C and Reischl, B and Pribasnig, T and Jansa, J and Kaiser, C and Wanek, W},
title = {Reevaluation and novel insights into amino sugar and neutral sugar necromass biomarkers in archaea, bacteria, fungi, and plants.},
journal = {The Science of the total environment},
volume = {906},
number = {},
pages = {167463},
doi = {10.1016/j.scitotenv.2023.167463},
pmid = {37793447},
issn = {1879-1026},
mesh = {*Archaea ; *Sugars ; Carbohydrates ; Amino Sugars/analysis ; Bacteria ; Carbon ; Fungi ; Soil/chemistry ; Biomarkers ; Soil Microbiology ; },
abstract = {Soil microbial necromass is an important contributor to soil organic matter (>50%) and it is largely composed of microbial residues. In soils, fragmented cell wall residues are mostly found in their polysaccharide forms of fungal chitin and bacterial peptidoglycan. Microbial necromass biomarkers, particularly amino sugars (AS) such as glucosamine (GlcN) and muramic acid (MurA) have been used to trace fungal and bacterial residues in soils, and to distinguish carbon (C) found in microbial residues from non-microbial organic C. Neutral sugars (NS), particularly the hexose/pentose ratio, have also been proposed as tracers of plant polysaccharides in soils. In our study, we extended the range of biomarkers to include AS and NS compounds in the biomass of 120 species belonging to archaea, bacteria, fungi, or plants. GlcN was the most common AS found in all taxa, contributing 42-91% to total AS content, while glucose was the most common NS found, contributing 56-79% to total NS. We identified talosaminuronic acid, found in archaeal pseudopeptidoglycan, as a new potential biomarker specific for Euryarchaeota. We compared the variability of these compounds between the different taxonomic groups using multivariate approaches, such as non-metric multidimensional scaling (NMDS) and partial least squares discriminant analysis (PLS-DA) and statistically evaluated their biomarker potential via indicator species analysis. Both NMDS and PLS-DA showcased the variability in the AS and NS contents between the different taxonomic groups, highlighting their potential as necromass residue biomarkers and allowing their extension from separating bacterial and fungal necromass to separating microbes from plants. Finally, we estimated new conversion factors where fungal GlcN is converted to fungal C by multiplying by 10 and MurA is converted to bacterial C by multiplying by 54. Conversion factors for talosaminuronic acid and galactosamine are also proposed to allow estimation of archaeal or all-microbial necromass residue C, respectively.},
}
@article {pmid37771611,
year = {2023},
author = {},
title = {Correction to: Putative nucleotide-based second messengers in archaea.},
journal = {microLife},
volume = {4},
number = {},
pages = {uqad039},
doi = {10.1093/femsml/uqad039},
pmid = {37771611},
issn = {2633-6693},
abstract = {[This corrects the article DOI: 10.1093/femsml/uqad027.].},
}
@article {pmid37759261,
year = {2023},
author = {Kowalewicz-Kulbat, M and Krawczyk, KT and Szulc-Kielbik, I and Rykowski, S and Denel-Bobrowska, M and Olejniczak, AB and Locht, C and Klink, M},
title = {Cytotoxic effects of halophilic archaea metabolites on ovarian cancer cell lines.},
journal = {Microbial cell factories},
volume = {22},
number = {1},
pages = {197},
pmid = {37759261},
issn = {1475-2859},
mesh = {Humans ; Female ; *Ovarian Neoplasms/drug therapy ; Cisplatin ; Cell Line, Tumor ; *Antineoplastic Agents/pharmacology ; HeLa Cells ; },
abstract = {BACKGROUND: Ovarian cancer is one of the most frequent and deadly gynaecological cancers, often resistant to platinum-based chemotherapy, the current standard of care. Halophilic microorganisms have been shown to produce a large variety of metabolites, some of which show toxicity to various cancer cell lines. However, none have yet been shown to be active against ovarian cancer cells. Here, we examined the effects of metabolites secreted by the halophilic archaea Halorhabdus rudnickae and Natrinema salaciae on various cancer cell lines, including ovarian cancer cell lines.<br><br>RESULTS: [1]H NMR analyses of Hrd. rudnickae and Nnm. salaciae culture supernatants contain a complex mixture of metabolites that differ between species, and even between two different strains of the same species, such as Hrd. rudnickae strains 64[T] and 66. By using the MTT and the xCELLigence RTCA assays, we found that the secreted metabolites of all three halophilic strains expressed cytotoxicity to the ovarian cancer cell lines, especially A2780, as well as its cisplatin-resistant derivative A2780cis, in a dose-dependent manner. The other tested cell lines A549, HepG2, SK-OV-3 and HeLa were only minimally, or not at all affected by the archaeal metabolites, and this was only seen with the MTT assay.<br><br>CONCLUSIONS: The halophilic archaea Hrd. rudnickae and Nnm. salaciae, isolated from a Polish salt mine and Lake Medee in the Mediterranean Sea, respectively, secrete metabolites that are active against ovarian cancer cells, including those that are resistant to cisplatin. This opens potential new possibilities for the treatment of these frequent and deadly gynaecological cancers.},
}
@article {pmid37754561,
year = {2023},
author = {Liu, WW and Pan, P and Zhou, NY},
title = {The presence of benzene ring activating CoA ligases for aromatics degradation in the ANaerobic MEthanotrophic (ANME) archaea.},
journal = {Microbiology spectrum},
volume = {11},
number = {5},
pages = {e0176623},
pmid = {37754561},
issn = {2165-0497},
abstract = {Petroleum-source and black carbon-source aromatic compounds are present in the cold seep environments, where ANaerobic MEthanotrophic (ANME) archaea as the dominant microbial community mediates the anaerobic oxidation of methane to produce inorganic and organic carbon. Here, by predicting the aromatics catabolic pathways in ANME metagenome-assembled genomes, we provide genomic and biochemical evidences that ANME have the potential of metabolizing aromatics via the strategy of CoA activation of the benzene ring using phenylacetic acid and benzoate as the substrates. Two ring-activating enzymes phenylacetate-CoA ligase (PaaKANME) and benzoate-CoA ligase (BadAANME) are able to convert phenylacetate to phenylacetyl-CoA and benzoate to benzoyl-CoA in vitro, respectively. They are mesophilic, alkali resistance, and with broad substrate spectra showing different affinity with various substrates. An exploration of the relative gene abundance in ANME genomes and cold seep environments indicates that about 50% of ANME genomes contain PCL genes, and various bacteria and archaea contain PCL and BCL genes. The results provide evidences for the capability of heterotrophic metabolism of aromatic compounds by ANME. This has not only enhanced our understanding of the nutrient range of ANME but also helped to explore the additional ecological and biogeochemical significance of this ubiquitous sedimentary archaea in the carbon flow in the cold seep environments. IMPORTANCE ANaerobic MEthanotrophic (ANME) archaea is the dominant microbial community mediating the anaerobic oxidation of methane in the cold seep environments, where aromatic compounds are present. Then it is hypothesized that ANME may be involved in the metabolism of aromatics. Here, we provide genomic and biochemical evidences for the heterotrophic metabolism of aromatic compounds by ANME, enhancing our understanding of their nutrient range and also shedding light on the ecological and biogeochemical significance of these ubiquitous sedimentary archaea in carbon flow within cold seep environments. Overall, this study offers valuable insights into the metabolic capabilities of ANME and their potential contributions to the global carbon cycle.},
}
@article {pmid37749252,
year = {2023},
author = {Medvedeva, S and Borrel, G and Krupovic, M and Gribaldo, S},
title = {A compendium of viruses from methanogenic archaea reveals their diversity and adaptations to the gut environment.},
journal = {Nature microbiology},
volume = {8},
number = {11},
pages = {2170-2182},
pmid = {37749252},
issn = {2058-5276},
support = {ANR-20-CE20-009-01//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-10-LABX-62-IBEID//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-19-CE02-0005-01//Agence Nationale de la Recherche (French National Research Agency)/ ; },
mesh = {Humans ; Animals ; Archaea/genetics ; *Euryarchaeota/metabolism ; Bacteria/metabolism ; Methane/metabolism ; *Viruses/metabolism ; },
abstract = {Methanogenic archaea are major producers of methane, a potent greenhouse gas and biofuel, and are widespread in diverse environments, including the animal gut. The ecophysiology of methanogens is likely impacted by viruses, which remain, however, largely uncharacterized. Here we carried out a global investigation of viruses associated with all current diversity of methanogens by assembling an extensive CRISPR database consisting of 156,000 spacers. We report 282 high-quality (pro)viral and 205 virus-like/plasmid sequences assigned to hosts belonging to ten main orders of methanogenic archaea. Viruses of methanogens can be classified into 87 families, underscoring a still largely undiscovered genetic diversity. Viruses infecting gut-associated archaea provide evidence of convergence in adaptation with viruses infecting gut-associated bacteria. These viruses contain a large repertoire of lysin proteins that cleave archaeal pseudomurein and are enriched in glycan-binding domains (Ig-like/Flg_new) and diversity-generating retroelements. The characterization of this vast repertoire of viruses paves the way towards a better understanding of their role in regulating methanogen communities globally, as well as the development of much-needed genetic tools.},
}
@article {pmid37747940,
year = {2023},
author = {Murali, R and Yu, H and Speth, DR and Wu, F and Metcalfe, KS and Crémière, A and Laso-Pèrez, R and Malmstrom, RR and Goudeau, D and Woyke, T and Hatzenpichler, R and Chadwick, GL and Connon, SA and Orphan, VJ},
title = {Physiological potential and evolutionary trajectories of syntrophic sulfate-reducing bacterial partners of anaerobic methanotrophic archaea.},
journal = {PLoS biology},
volume = {21},
number = {9},
pages = {e3002292},
pmid = {37747940},
issn = {1545-7885},
mesh = {*Archaea ; Anaerobiosis ; *Sulfates/metabolism ; Geologic Sediments/microbiology ; Bacteria/genetics ; Oxidation-Reduction ; Phylogeny ; },
abstract = {Sulfate-coupled anaerobic oxidation of methane (AOM) is performed by multicellular consortia of anaerobic methanotrophic archaea (ANME) in obligate syntrophic partnership with sulfate-reducing bacteria (SRB). Diverse ANME and SRB clades co-associate but the physiological basis for their adaptation and diversification is not well understood. In this work, we used comparative metagenomics and phylogenetics to investigate the metabolic adaptation among the 4 main syntrophic SRB clades (HotSeep-1, Seep-SRB2, Seep-SRB1a, and Seep-SRB1g) and identified features associated with their syntrophic lifestyle that distinguish them from their non-syntrophic evolutionary neighbors in the phylum Desulfobacterota. We show that the protein complexes involved in direct interspecies electron transfer (DIET) from ANME to the SRB outer membrane are conserved between the syntrophic lineages. In contrast, the proteins involved in electron transfer within the SRB inner membrane differ between clades, indicative of convergent evolution in the adaptation to a syntrophic lifestyle. Our analysis suggests that in most cases, this adaptation likely occurred after the acquisition of the DIET complexes in an ancestral clade and involve horizontal gene transfers within pathways for electron transfer (CbcBA) and biofilm formation (Pel). We also provide evidence for unique adaptations within syntrophic SRB clades, which vary depending on the archaeal partner. Among the most widespread syntrophic SRB, Seep-SRB1a, subclades that specifically partner ANME-2a are missing the cobalamin synthesis pathway, suggestive of nutritional dependency on its partner, while closely related Seep-SRB1a partners of ANME-2c lack nutritional auxotrophies. Our work provides insight into the features associated with DIET-based syntrophy and the adaptation of SRB towards it.},
}
@article {pmid37728966,
year = {2023},
author = {Tan, S and Cheng, M and Li, XX and Hu, Y and Ma, X and Hou, J and Cui, HL},
title = {Natronosalvus halobius gen. nov., sp. nov., Natronosalvus caseinilyticus sp. nov., Natronosalvus vescus sp. nov., Natronosalvus rutilus sp. nov. and Natronosalvus amylolyticus sp. nov., halophilic archaea isolated from salt lakes and soda lakes.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {73},
number = {9},
pages = {},
doi = {10.1099/ijsem.0.006036},
pmid = {37728966},
issn = {1466-5034},
mesh = {Animals ; Lakes ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; DNA, Bacterial/genetics ; Bacterial Typing Techniques ; Base Composition ; Fatty Acids/chemistry ; *Halobacteriales ; *Euryarchaeota ; Amino Acids ; *Cyprinidae ; },
abstract = {Five halophilic archaeal strains (AGai3-5[T], KZCA101[T], CGA3[T], WLHS1[T] and WLHSJ1[T]) were isolated from salt lakes and soda lakes in PR China. These strains had low 16S rRNA gene similarities (91.3-96.0 %) to closely related species of the family Natrialbaceae and may represent a new genus of the family. Phylogenetic and phylogenomic analyses revealed that these strains formed a distinct clade, separate from the nearby genera Natronobiforma and Saliphagus. The average nucleotide identity, digital DNA-DNA hybridization and average amino acid identity (AAI) values among these five strains and the current members of the family Natrialbaceae were 72-90, 20-42 and 62-91 %, respectively, clearly below the threshold values for species demarcation. According to the critical value of AAI (≤76 %) proposed to differentiate genera within the family Natrialbaceae, it was further indicated that these strains represented a novel genus within the family. These strains could be distinguished from the related genera according to differential phenotypic characteristics. The major lipids of these strains were phosphatidic acid (PA), phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, mannosyl glucosyl diether (DGD-PA), sulphated DGD-1 (S-DGD-PA) and sulphated galactosyl mannosyl glucosyl diether. The phenotypic, chemotaxonomic, phylogenetic and phylogenomic features indicated that strains AGai3-5[T] (=CGMCC 1.16078[T]=JCM 33549[T]), KZCA101[T] (=CGMCC 1.17431[T]=JCM 35074[T]), CGA3[T] (=CGMCC 1.17463[T]=JCM 34318[T]), WLHS1[T] (=CGMCC 1.13780[T]=JCM 33562[T]) and WLHSJ1[T] (=CGMCC 1.13784[T]=JCM 33563[T]) represent five novel species of a new genus within the family Natrialbaceae, named Natronosalvus halobius gen. nov., sp. nov., Natronosalvus caseinilyticus sp. nov., Natronosalvus vescus sp. nov., Natronosalvus rutilus sp. nov. and Natronosalvus amylolyticus sp. nov., respectively.},
}
@article {pmid37727289,
year = {2023},
author = {Volmer, JG and McRae, H and Morrison, M},
title = {The evolving role of methanogenic archaea in mammalian microbiomes.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1268451},
pmid = {37727289},
issn = {1664-302X},
abstract = {Methanogenic archaea (methanogens) represent a diverse group of microorganisms that inhabit various environmental and host-associated microbiomes. These organisms play an essential role in global carbon cycling given their ability to produce methane, a potent greenhouse gas, as a by-product of their energy production. Recent advances in culture-independent and -dependent studies have highlighted an increased prevalence of methanogens in the host-associated microbiome of diverse animal species. Moreover, there is increasing evidence that methanogens, and/or the methane they produce, may play a substantial role in human health and disease. This review addresses the expanding host-range and the emerging view of host-specific adaptations in methanogen biology and ecology, and the implications for host health and disease.},
}
@article {pmid37715368,
year = {2023},
author = {Soza-Bolaños, AI and Domínguez-Pérez, RA and Ayala-Herrera, JL and Pérez-Serrano, RM and Soto-Barreras, U and Espinosa-Cristóbal, LF and Rivera-Albarrán, CA and Zaldívar-Lelo de Larrea, G},
title = {Presence of methanogenic archaea in necrotic root canals of patients with or without type 2 diabetes mellitus.},
journal = {Australian endodontic journal : the journal of the Australian Society of Endodontology Inc},
volume = {49},
number = {3},
pages = {641-647},
doi = {10.1111/aej.12797},
pmid = {37715368},
issn = {1747-4477},
mesh = {Humans ; *Diabetes Mellitus, Type 2/complications ; Dental Pulp Cavity ; Archaea ; Root Canal Therapy ; *Periapical Periodontitis/diagnostic imaging/therapy ; Necrosis ; *Euryarchaeota ; },
abstract = {Theoretically, a necrotic root canal fulfils all requirements as a niche for methanogens to inhabit. However, their presence in it and its implication in apical periodontitis (AP) is controversial. Therefore, to contribute to ending the controversy, this study aimed to detect and compare methanogens' presence in two distinct niches with supposedly different microenvironments; both were necrotic root canals associated with AP but one from patients with type 2 diabetes mellitus (T2DM) while the other from non-diabetic patients. A clinical examination was performed on 65 T2DM patients and 73 non-diabetic controls. Samples from necrotic root canals were obtained, and methanogens were identified. The presence of methanogens was three times higher (27.6%) in the T2DM group than in non-diabetic patients (8.2%). In addition, methanogens' presence was associated with a higher prevalence of periapical symptoms.},
}
@article {pmid37714340,
year = {2023},
author = {Wang, W and Lei, J and Li, M and Zhang, X and Xiang, X and Wang, H and Lu, X and Ma, L and Liu, X and Tuovinen, OH},
title = {Archaea are better adapted to antimony stress than their bacterial counterparts in Xikuangshan groundwater.},
journal = {The Science of the total environment},
volume = {905},
number = {},
pages = {166999},
doi = {10.1016/j.scitotenv.2023.166999},
pmid = {37714340},
issn = {1879-1026},
mesh = {*Archaea/genetics ; Antimony/analysis ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; *Groundwater/chemistry ; },
abstract = {Archaea are important ecological components of microbial communities in various environments, but are currently poorly investigated in antimony (Sb) contaminated groundwater particularly on their ecological differences in comparison with bacteria. To address this issue, groundwater samples were collected from Xikuangshan aquifer along an Sb gradient and subjected to 16S rRNA gene amplicon sequencing and bioinformatic analysis. The results demonstrated that bacterial communities were more susceptibly affected by elevated Sb concentration than their archaeal counterparts, and the positive stimulation of Sb concentration on bacterial diversity coincided with the intermediate disturbance hypothesis. Overall, the balance of environmental variables (Sb, pH, and EC), competitive interactions, and stochastic events jointly regulated bacterial and archaeal communities. Linear fitting analysis revealed that Sb significantly drove the deterministic process (heterogeneous selection) of bacterial communities, whereas stochastic process (dispersal limitation) contributed more to archaeal community assembly. In contract, the assembly of Sb-resistant bacteria and archaea was dominated by the stochastic process (undominated), which implied the important role of diversification and drift instead of selection. Compared with Sb-resistant microorganisms, bacterial and archaeal communities showed lower niche width, which may result from the constraints of Sb concentration and competitive interaction. Moreover, Sb-resistant archaea had a higher niche than that of Sb-resistant bacteria via investing on flexible metabolic pathways such as organic metabolism, ammonia oxidation; and carbon fixation to enhance their competitiveness. Our results offered new insights into the ecological adaptation mechanisms of bacteria and archaea in Sb-contaminated groundwater.},
}
@article {pmid37707605,
year = {2023},
author = {Deore, KS and Dhakephalkar, PK and Dagar, SS},
title = {Phylogenetically and physiologically diverse methanogenic archaea inhabit the Indian hot spring environments.},
journal = {Archives of microbiology},
volume = {205},
number = {10},
pages = {332},
pmid = {37707605},
issn = {1432-072X},
support = {Ref. No. 23/06/2013(i)EU-V//University Grants Commission/ ; YSS/2015/000718//Science and Engineering Research Board/ ; },
mesh = {Humans ; Archaea/genetics ; *Hot Springs ; *Euryarchaeota ; Culture Media ; India ; },
abstract = {Mesophilic and thermophilic methanogens belonging to the hydrogenotrophic, methylotrophic, and acetotrophic groups were isolated from Indian hot spring environments using BY and BCYT growth media. Following initial Hinf I-based PCR-RFLP screening, 70 methanogens were sequenced to ascertain their identity. These methanogens were phylogenetically and physiologically diverse and represented different taxa distributed across three physiological groups, i.e., hydrogenotrophs (53), methylotrophs (14) and acetotrophs (3). Overall, methanogens representing three families, five genera, and ten species, including two putative novel species, were recognized. The highest number and diversity of methanogens was observed at 40 ℃, dominated by Methanobacterium (10; 3 species), Methanosarcina (9; 3 species), Methanothermobacter (7; 2 species), Methanomethylovorans (5; 1 species) and Methanoculleus (3; 1 species). Both putative novel methanogen species were isolated at 40 ℃ and belonged to the genera Methanosarcina and Methanobacterium. At 55 ℃, limited diversity was observed, and resulted in the isolation of only two genera of methanogens, i.e., Methanothermobacter (28; 2 species) and Methanosarcina (4; 1 species). At 70 ℃, only members of the genus Methanothermobacter (5; 2 species) were isolated, whereas no methanogen could be cultured at 85 ℃. Ours is the first study that documents the extensive range of cultivable methanogenic archaea inhabiting hot springs across various geothermal provinces of India.},
}
@article {pmid37702790,
year = {2023},
author = {Zou, D and Chen, J and Zhang, C and Kao, SJ and Liu, H and Li, M},
title = {Diversity and salinity adaptations of ammonia oxidizing archaea in three estuaries of China.},
journal = {Applied microbiology and biotechnology},
volume = {107},
number = {22},
pages = {6897-6909},
pmid = {37702790},
issn = {1432-0614},
support = {32225003//National Natural Science Foundation of China/ ; 31970105//National Natural Science Foundation of China/ ; 2022M722175//Postdoctoral Research Foundation of China/ ; JCYJ20200109105010363//Shenzhen Science and Technology Innovation Program/ ; },
abstract = {Ammonia-oxidizing archaea (AOA) are ubiquitously found in diverse habitats and play pivotal roles in the nitrogen and carbon cycle, especially in estuarine and coastal environments. Despite the fact that the diversity and distribution of AOA are thought to be tightly linked to habitats, little is known about the relationship that underpins their genomic traits, adaptive potentials, and ecological niches. Here, we have characterized and compared the AOA community in three estuaries of China using metagenomics. AOA were the dominant ammonia oxidizers in the three estuaries. Through phylogenetic analyses, five major AOA groups were identified, including the Nitrosomarinus-like, Nitrosopumilus-like, Aestuariumsis-like, Nitrosarchaeum-like, and Nitrosopelagicus-like groups. Statistical analyses showed that the aquatic and sedimentary AOA communities were mainly influenced by spatial factors (latitude and water depth) and environmental factors (salinity, pH, and dissolved oxygen) in estuaries, respectively. Compared to AOA dwelling in terrestrial and marine habitats, estuarine AOA encoded more genes involved in glucose and amino acid metabolism, transport systems, osmotic control, and cell motility. The low proteome isoelectric points (pI), high content of acidic amino acids, and the presence of potassium ion and mechanosensitive channels suggest a "salt-in" strategy for estuarine AOA to counteract high osmolarity in their surroundings. Our findings have indicated potential adaptation strategies and highlighted their importance in the estuarine nitrogen and carbon cycles. KEY POINTS: • Spatial and environmental factors influence water and sediment AOA respectively. • Estuarine AOA share low proteome isoelectric value and high acid amino acids content. • AOA adaptation to estuaries is likely resulted from their unique genomic features.},
}
@article {pmid37700049,
year = {2023},
author = {Spang, A},
title = {Uncovering the hidden world of nanosized archaea.},
journal = {Nature reviews. Microbiology},
volume = {21},
number = {10},
pages = {638},
pmid = {37700049},
issn = {1740-1534},
}
@article {pmid37698885,
year = {2023},
author = {Oudova-Rivera, B and Crombie, AT and Murrell, JC and Lehtovirta-Morley, LE},
title = {Alcohols as inhibitors of ammonia oxidizing archaea and bacteria.},
journal = {FEMS microbiology letters},
volume = {370},
number = {},
pages = {},
pmid = {37698885},
issn = {1574-6968},
mesh = {Humans ; *Archaea/physiology ; *Ammonia ; Nitrates ; Bacteria ; Oxidation-Reduction ; Ethanol ; Nitrification ; },
abstract = {Ammonia oxidizers are key players in the global nitrogen cycle and are responsible for the oxidation of ammonia to nitrite, which is further oxidized to nitrate by other microorganisms. Their activity can lead to adverse effects on some human-impacted environments, including water pollution through leaching of nitrate and emissions of the greenhouse gas nitrous oxide (N2O). Ammonia monooxygenase (AMO) is the key enzyme in microbial ammonia oxidation and shared by all groups of aerobic ammonia oxidizers. The AMO has not been purified in an active form, and much of what is known about its potential structure and function comes from studies on its interactions with inhibitors. The archaeal AMO is less well studied as ammonia oxidizing archaea were discovered much more recently than their bacterial counterparts. The inhibition of ammonia oxidation by aliphatic alcohols (C1-C8) using the model terrestrial ammonia oxidizing archaeon 'Candidatus Nitrosocosmicus franklandus' C13 and the ammonia oxidizing bacterium Nitrosomonas europaea was examined in order to expand knowledge about the range of inhibitors of ammonia oxidizers. Methanol was the most potent specific inhibitor of the AMO in both ammonia oxidizers, with half-maximal inhibitory concentrations (IC50) of 0.19 and 0.31 mM, respectively. The inhibition was AMO-specific in 'Ca. N. franklandus' C13 in the presence of C1-C2 alcohols, and in N. europaea in the presence of C1-C3 alcohols. Higher chain-length alcohols caused non-specific inhibition and also inhibited hydroxylamine oxidation. Ethanol was tolerated by 'Ca. N. franklandus' C13 at a higher threshold concentration than other chain-length alcohols, with 80 mM ethanol being required for complete inhibition of ammonia oxidation.},
}
@article {pmid37668803,
year = {2023},
author = {Vipindas, PV and Jabir, T and Venkatachalam, S and Yang, EJ and Jain, A and Krishnan, KP},
title = {Vertical segregation and phylogenetic characterization of archaea and archaeal ammonia monooxygenase gene in the water column of the western Arctic Ocean.},
journal = {Extremophiles : life under extreme conditions},
volume = {27},
number = {3},
pages = {24},
pmid = {37668803},
issn = {1433-4909},
mesh = {*Archaea/genetics ; Phylogeny ; *Euryarchaeota ; Water ; },
abstract = {Archaea constitute a substantial fraction of marine microbial biomass and play critical roles in the biogeochemistry of oceans. However, studies on their distribution and ecology in the Arctic Ocean are relatively scarce. Here, we studied the distributions of archaea and archaeal ammonia monooxygenase (amoA) gene in the western Arctic Ocean, using the amplicon sequencing approach from the sea surface to deep waters up to 3040 m depth. A total of five archaeal phyla, Nitrososphaerota, "Euryarchaeota", "Halobacteriota," "Nanoarchaeota", and Candidatus Thermoplasmatota, were detected. We observed a clear, depth-dependent vertical segregation among archaeal communities. Ca. Thermoplasmatota (66.8%) was the most dominant phylum in the surface waters. At the same time, Nitrososphaerota (55.9%) was dominant in the deep waters. Most of the amoA gene OTUs (99%) belonged to the Nitrosopumilales and were further clustered into five subclades ("NP-Alpha", "NP-Delta", "NP-Epsilon", "NP-Gamma", and "NP-Theta"). "NP-Epsilon" was the most dominant clade throughout the water column and "NP_Alpha" showed higher abundance only in the deeper water. Salinity and inorganic nutrient concentrations were the major factors that determined the vertical segregation of archaea. We anticipate that the observed differences in the vertical distribution of archaea might contribute to the compartmentalization of dark carbon fixation and nitrification in deeper water and organic matter degradation in surface waters of the Arctic Ocean.},
}
@article {pmid37652180,
year = {2023},
author = {Di Giulio, M},
title = {The absence of the evolutionary state of the Prokaryote would imply a polyphyletic origin of proteins and that LUCA, the ancestor of bacteria and that of archaea were progenotes.},
journal = {Bio Systems},
volume = {233},
number = {},
pages = {105014},
doi = {10.1016/j.biosystems.2023.105014},
pmid = {37652180},
issn = {1872-8324},
abstract = {I analysed the similarity gradient observed in protein families - of phylogenetically deep fundamental traits - of bacteria and archaea, ranging from cases such as the core of the DNA replication apparatus where there is no sequence similarity between the proteins involved, to cases in which, as in the translation initiation factors, only some proteins involved would be homologs, to cases such as for aminoacyl-tRNA synthetases in which most of the proteins involved would be homologs. This pattern of similarity between bacteria and archaea would seem to be a very clear indication of a transitional evolutionary stage that preceded both the Last Bacterial Common Ancestor and the Last Archaeal Common Ancestor, i.e. progenotic stages. Indeed, this similarity pattern would seem to exemplify an ongoing transition as all the evolutionary phases would be represented in it. Instead, in the cellular stage it is expected that these evolutionary phases should have already been overcome, i.e. completed, and therefore no longer detectable. In fact, if we had really been in the presence of the prokaryotic stage then we should not have observed this similarity pattern in proteins involved in defining the ancestral characters of bacteria and archaea, as the completion of the different cellular structures should have required a very low number of proteins to be late evolved in lineages leading to bacteria and archaea. Indeed, the already reached state of the Prokaryote would have determined complete cellular structures therefore a total absence of proteins to evolve independently in the two main phyletic lineages and able to complete the evolution of a particular character already evidently in a definitive state, which, on the other hand, does not appear to have been the case. All this would have prevented the formation of this pattern of similarity which instead would appear to be real. In conclusion, the existence of this pattern of similarity observed in the families of homologous proteins of bacteria and archaea would imply the absence of the evolutionary stage of the Prokaryote and consequently a progenotic status to be assigned to the LUCA. Indeed, the LUCA stage would have been a stage of evolutionary transition because it is belatedly marked by the presence of all the different evolutionary phases, evidently more easily interpretable within the definition of progenote than that of genote precisely because they are inherent in an evolutionary transition and not to an evolution that has already been achieved. Finally, I discuss the importance of these arguments for the polyphyletic origin of proteins.},
}
@article {pmid37630563,
year = {2023},
author = {Xie, L and Yu, S and Lu, X and Liu, S and Tang, Y and Lu, H},
title = {Different Responses of Bacteria and Archaea to Environmental Variables in Brines of the Mahai Potash Mine, Qinghai-Tibet Plateau.},
journal = {Microorganisms},
volume = {11},
number = {8},
pages = {},
pmid = {37630563},
issn = {2076-2607},
support = {DD20221703//China Geological Survey/ ; },
abstract = {Salt mines feature both autochthonous and allochthonous microbial communities introduced by industrialization. It is important to generate the information on the diversity of the microbial communities present in the salt mines and how they are shaped by the environment representing ecological diversification. Brine from Mahai potash mine (Qianghai, China), an extreme hypersaline environment, is used to produce potash salts for hundreds of millions of people. However, halophiles preserved in this niche during deposition are still unknown. In this study, using high-throughput 16S rRNA gene amplicon sequencing and estimation of physicochemical variables, we examined brine samples collected from locations with the gradient of industrial activity intensity and discrete hydrochemical compositions in the Mahai potash mine. Our findings revealed a highly diverse bacterial community, mainly composed of Pseudomonadota in the hypersaline brines from the industrial area, whereas in the natural brine collected from the upstream Mahai salt lake, most of the 16S rRNA gene reads were assigned to Bacteroidota. Halobacteria and halophilic methanogens dominated archaeal populations. Furthermore, we discovered that in the Mahai potash mining area, bacterial communities tended to respond to anthropogenic influences. In contrast, archaeal diversity and compositions were primarily shaped by the chemical properties of the hypersaline brines. Conspicuously, distinct methanogenic communities were discovered in sets of samples with varying ionic compositions, indicating their strong sensitivity to the brine hydrochemical alterations. Our findings provide the first taxonomic snapshot of microbial communities from the Mahai potash mine and reveal the different responses of bacteria and archaea to environmental variations in this high-altitude aquatic ecosystem.},
}
@article {pmid37629622,
year = {2023},
author = {Garcia-Bonete, MJ and Rajan, A and Suriano, F and Layunta, E},
title = {The Underrated Gut Microbiota Helminths, Bacteriophages, Fungi, and Archaea.},
journal = {Life (Basel, Switzerland)},
volume = {13},
number = {8},
pages = {},
pmid = {37629622},
issn = {2075-1729},
abstract = {The microbiota inhabits the gastrointestinal tract, providing essential capacities to the host. The microbiota is a crucial factor in intestinal health and regulates intestinal physiology. However, microbiota disturbances, named dysbiosis, can disrupt intestinal homeostasis, leading to the development of diseases. Classically, the microbiota has been referred to as bacteria, though other organisms form this complex group, including viruses, archaea, and eukaryotes such as fungi and protozoa. This review aims to clarify the role of helminths, bacteriophages, fungi, and archaea in intestinal homeostasis and diseases, their interaction with bacteria, and their use as therapeutic targets in intestinal maladies.},
}
@article {pmid37564293,
year = {2023},
author = {Naitam, MG and Ramakrishnan, B and Grover, M and Kaushik, R},
title = {Rhizosphere-dwelling halophilic archaea: a potential candidate for alleviating salinity-associated stress in agriculture.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1212349},
pmid = {37564293},
issn = {1664-302X},
abstract = {Salinity is a serious environmental factor that impedes crop growth and drastically reduces yield. This study aimed to investigate the potential of halophilic archaea isolated from the Rann of Kutch to alleviate the negative impact of salinity on crop growth and yield. The halophilic archaea, which demonstrated high tolerance to salinity levels up to 4.5 M, were evaluated for their ability to promote plant growth in both salt-tolerant and salt-susceptible wheat cultivars. Our assessment focused on their capacity to solubilize essential nutrients, including phosphorus (14-61 mg L[-1]), potassium (37-78 mg L[-1]), and zinc (8-17 mg L[-1]), as well as their production of the phytohormone IAA (17.30 to 49.3 μg ml[-1]). To conduct the experiments, five wheat cultivars (two salt-tolerant and three salt-susceptible) were grown in triplicates using soft MS agar tubes (50 ml) and pots containing 10 kg of soil with an electrical conductivity (EC) of 8 dSm[-1]. Data were collected at specific time points: 21 days after sowing (DAS) for the MS agar experiment, 45 DAS for the pot experiment, and at the time of harvest. In the presence of haloarchaea, the inoculated treatments exhibited significant increases in total protein (46%), sugar (27%), and chlorophyll (31%) levels compared to the un-inoculated control. Furthermore, the inoculation led to an elevated accumulation of osmolyte proline (31.51%) and total carbohydrates (27.85%) while substantially reducing the activity of antioxidant enzymes such as SOD, catalase, and peroxidase by 57-76%, respectively. Notably, the inoculated treatments also showed improved plant vegetative growth parameters compared to the un-inoculated treatments. Interestingly, the positive effects of the halophilic archaea were more pronounced in the susceptible wheat cultivars than in the tolerant cultivars. These findings highlight the growth-promoting abilities of the halophilic archaeon Halolamina pelagica CDK2 and its potential to mitigate the detrimental effects of salinity. Consequently, further evaluation of this halophilic archaeon under field conditions is warranted to explore its potential use in the development of microbial inoculants.},
}
@article {pmid37549709,
year = {2023},
author = {Ren, B and Wang, W and Shen, L and Yang, W and Yang, Y and Jin, J and Geng, C},
title = {Nitrogen fertilization rate affects communities of ammonia-oxidizing archaea and bacteria in paddy soils across different climatic zones of China.},
journal = {The Science of the total environment},
volume = {902},
number = {},
pages = {166089},
doi = {10.1016/j.scitotenv.2023.166089},
pmid = {37549709},
issn = {1879-1026},
mesh = {*Archaea/genetics ; Soil/chemistry ; Ammonia/chemistry ; Nitrogen/chemistry ; Oxidation-Reduction ; Soil Microbiology ; Phylogeny ; Bacteria/genetics ; *Betaproteobacteria/genetics ; Nitrification ; China ; Fertilization ; },
abstract = {Nitrogen fertilization has important effects on nitrification. However, how the rate of nitrogen fertilization affects nitrification potential, as well as the communities of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB), remains unclear. We performed a large-scale investigation of nitrification potential and ammonia-oxidizer communities in Chinese paddy fields at different nitrogen fertilization rates across different climatic zones. It was found that the nitrification potential at the high nitrogen fertilization rate (≥150 kg[-1] N ha[-1]) was 23.35 % higher than that at the intermediate rate (100-150 kg[-1] N ha[-1]) and 20.77 % higher than that at the low rate (< 100 kg[-1] N ha[-1]). The nitrification potential showed no significant variation among different nitrogen fertilization rates across climatic zones. Furthermore, the AOA and AOB amoA gene abundance at the high nitrogen fertilization rate was 481.67 % and 292.74 % higher (p < 0.05) than that at the intermediate rate, respectively. Correlation analysis demonstrated a significant positive correlation between AOB abundance and nitrification potential. AOA and AOB community composition differed significantly among nitrogen fertilization rates. Moreover, soil NH4[+] content, pH, water content, bulk density, and annual average temperature were regarded as key environmental factors influencing the community structure of ammonia-oxidizers. Taken together, the nitrogen fertilization rate had a significant impact on the communities of AOA and AOB but did not significantly alter the nitrification potential. Our findings provide new insights into the impact of nitrogen fertilization management on nitrification in rice paddy fields.},
}
@article {pmid37516446,
year = {2023},
author = {Manfredini, A and Malusà, E and Pinzari, F and Canfora, L},
title = {Quantification of nitrogen cycle functional genes from viable archaea and bacteria in paddy soil.},
journal = {Journal of applied microbiology},
volume = {134},
number = {8},
pages = {},
doi = {10.1093/jambio/lxad169},
pmid = {37516446},
issn = {1365-2672},
mesh = {*Archaea/genetics/metabolism ; *Soil/chemistry ; Bacteria/genetics/metabolism ; Nitrogen Cycle ; Soil Microbiology ; Ammonia/metabolism ; Oxidation-Reduction ; Nitrogen/metabolism ; },
abstract = {AIMS: One of the main challenges of culture-independent soil microbiology is distinguishing the microbial community's viable fraction from dead matter. Propidium monoazide (PMA) binds the DNA of dead cells, preventing its amplification. This dye could represent a robust means to overcome the drawbacks of other selective methods, such as ribonucleic acid-based analyses.<br><br>METHODS AND RESULTS: We quantified functional genes from viable archaea and bacteria in soil by combining the use of PMA and quantitative polymerase chain reaction. Four N-cycle-related functional genes (bacterial and archaeal ammonia monooxygenase, nitrate reductase, and nitrite reductase) were successfully quantified from the living fraction of bacteria and archaea of a paddy soil. The protocol was also tested with pure bacterial cultures and soils with different physical and chemical properties.<br><br>CONCLUSIONS: The experiment results revealed a contrasting impact of mineral and organic fertilizers on the abundance of microbial genes related to the N-cycle in paddy soil.},
}
@article {pmid37504286,
year = {2023},
author = {Marín-Paredes, R and Bolívar-Torres, HH and Coronel-Gaytán, A and Martínez-Romero, E and Servín-Garcidueñas, LE},
title = {A Metagenome from a Steam Vent in Los Azufres Geothermal Field Shows an Abundance of Thermoplasmatales archaea and Bacteria from the Phyla Actinomycetota and Pseudomonadota.},
journal = {Current issues in molecular biology},
volume = {45},
number = {7},
pages = {5849-5864},
pmid = {37504286},
issn = {1467-3045},
support = {IA210617 IA208019//PAPIIT-UNAM/ ; },
abstract = {Los Azufres National Park is a geothermal field that has a wide number of thermal manifestations; nevertheless, the microbial communities in many of these environments remain unknown. In this study, a metagenome from a sediment sample from Los Azufres National Park was sequenced. In this metagenome, we found that the microbial diversity corresponds to bacteria (Actinomycetota, Pseudomonadota), archaea (Thermoplasmatales and Candidatus Micrarchaeota and Candidatus Parvarchaeota), eukarya (Cyanidiaceae), and viruses (Fussellovirus and Caudoviricetes). The functional annotation showed genes related to the carbon fixation pathway, sulfur metabolism, genes involved in heat and cold shock, and heavy-metal resistance. From the sediment, it was possible to recover two metagenome-assembled genomes from Ferrimicrobium and Cuniculiplasma. Our results showed that there are a large number of microorganisms in Los Azufres that deserve to be studied.},
}
@article {pmid37500801,
year = {2023},
author = {Esser, SP and Rahlff, J and Zhao, W and Predl, M and Plewka, J and Sures, K and Wimmer, F and Lee, J and Adam, PS and McGonigle, J and Turzynski, V and Banas, I and Schwank, K and Krupovic, M and Bornemann, TLV and Figueroa-Gonzalez, PA and Jarett, J and Rattei, T and Amano, Y and Blaby, IK and Cheng, JF and Brazelton, WJ and Beisel, CL and Woyke, T and Zhang, Y and Probst, AJ},
title = {A predicted CRISPR-mediated symbiosis between uncultivated archaea.},
journal = {Nature microbiology},
volume = {8},
number = {9},
pages = {1619-1633},
pmid = {37500801},
issn = {2058-5276},
support = {DOC 69/FWF_/Austrian Science Fund FWF/Austria ; },
mesh = {*Archaea/genetics/metabolism ; *Symbiosis/genetics ; Genomics ; Plasmids ; DNA/metabolism ; },
abstract = {CRISPR-Cas systems defend prokaryotic cells from invasive DNA of viruses, plasmids and other mobile genetic elements. Here, we show using metagenomics, metatranscriptomics and single-cell genomics that CRISPR systems of widespread, uncultivated archaea can also target chromosomal DNA of archaeal episymbionts of the DPANN superphylum. Using meta-omics datasets from Crystal Geyser and Horonobe Underground Research Laboratory, we find that CRISPR spacers of the hosts Candidatus Altiarchaeum crystalense and Ca. A. horonobense, respectively, match putative essential genes in their episymbionts' genomes of the genus Ca. Huberiarchaeum and that some of these spacers are expressed in situ. Metabolic interaction modelling also reveals complementation between host-episymbiont systems, on the basis of which we propose that episymbionts are either parasitic or mutualistic depending on the genotype of the host. By expanding our analysis to 7,012 archaeal genomes, we suggest that CRISPR-Cas targeting of genomes associated with symbiotic archaea evolved independently in various archaeal lineages.},
}
@article {pmid37495052,
year = {2023},
author = {Cai, Y and Li, H and Qu, G and Hu, Y and Zou, H and Zhao, S and Cheng, M and Chu, X and Ren, N},
title = {Responses of applied voltages on the archaea microbial distribution in sludge digestion.},
journal = {Chemosphere},
volume = {339},
number = {},
pages = {139639},
doi = {10.1016/j.chemosphere.2023.139639},
pmid = {37495052},
issn = {1879-1298},
mesh = {*Sewage ; *Archaea ; Carbon Dioxide ; Anaerobiosis ; Methane ; Biofuels ; Digestion ; Bioreactors ; },
abstract = {As the development of urban population led to the increase of domestic water consumption, consequently the generation of surplus sludge (SS) produced increasingly during sewage treatment processes. In order to enhance the SS resource utilization efficiency, an electricity-assisted anaerobic digestion (EAAD) system was employed to examine the alterations in the digestion broth and the characteristics of gas production. Additionally, the response of applied voltages on the distribution of archaeal community near various electrodes within the sludge was explored. The results revealed that the application of high voltages exceeding 3.0 V hindered the CH4 production but stimulated the CO2 generation. Subsequently, both CH4 and CO2 production were impeded by the applied voltages. Furthermore, the increased voltages significantly decreased the abundance of Methanomicrobia, Methanosaeta, and Methanosarcina, which were crucial determinants of CH4 content in biogas. Notably, the excessively high voltages intensities caused the AD process to halt and even inactivate the microbial flora. Interestingly, the distribution characteristics of archaeal community were influenced not only by the voltages intensity but also exhibited variations between the anode and cathode regions. Moreover, as the applied voltage intensified, the discrepancy of responses between the cathode and anode regions became more pronounced, offering novel theoretical and technical foundations for the advancement of electricity-assisted with AD technology.},
}
@article {pmid37491319,
year = {2023},
author = {Williams, AM and Jolley, EA and Santiago-Martínez, MG and Chan, CX and Gutell, RR and Ferry, JG and Bevilacqua, PC},
title = {In vivo structure probing of RNA in Archaea: novel insights into the ribosome structure of Methanosarcina acetivorans.},
journal = {RNA (New York, N.Y.)},
volume = {29},
number = {10},
pages = {1610-1620},
pmid = {37491319},
issn = {1469-9001},
support = {R35 GM127064/GM/NIGMS NIH HHS/United States ; },
mesh = {*Archaea/genetics ; *RNA ; Methanosarcina/genetics ; Methanol ; Bacteria/genetics ; Ribosomes/genetics ; },
abstract = {Structure probing combined with next-generation sequencing (NGS) has provided novel insights into RNA structure-function relationships. To date, such studies have focused largely on bacteria and eukaryotes, with little attention given to the third domain of life, archaea. Furthermore, functional RNAs have not been extensively studied in archaea, leaving open questions about RNA structure and function within this domain of life. With archaeal species being diverse and having many similarities to both bacteria and eukaryotes, the archaea domain has the potential to be an evolutionary bridge. In this study, we introduce a method for probing RNA structure in vivo in the archaea domain of life. We investigated the structure of ribosomal RNA (rRNA) from Methanosarcina acetivorans, a well-studied anaerobic archaeal species, grown with either methanol or acetate. After probing the RNA in vivo with dimethyl sulfate (DMS), Structure-seq2 libraries were generated, sequenced, and analyzed. We mapped the reactivity of DMS onto the secondary structure of the ribosome, which we determined independently with comparative analysis, and confirmed the accuracy of DMS probing in M. acetivorans Accessibility of the rRNA to DMS in the two carbon sources was found to be quite similar, although some differences were found. Overall, this study establishes the Structure-seq2 pipeline in the archaea domain of life and informs about ribosomal structure within M. acetivorans.},
}
@article {pmid37474649,
year = {2023},
author = {Kim, YB and Whon, TW and Kim, JY and Kim, J and Kim, Y and Lee, SH and Park, SE and Kim, EJ and Son, HS and Roh, SW},
title = {In-depth metataxonomic investigation reveals low richness, high intervariability, and diverse phylotype candidates of archaea in the human urogenital tract.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {11746},
pmid = {37474649},
issn = {2045-2322},
mesh = {Humans ; Archaea/genetics ; RNA, Ribosomal, 16S/genetics ; Urogenital System ; *Microbiota/genetics ; *Euryarchaeota/genetics ; *Crenarchaeota ; Phylogeny ; },
abstract = {The urogenital microbiota is the potential principal factor in the pathophysiology of urinary tract infection and the protection of urinary tract health. Little is known about the urogenital archaeome although several reports have indicated that the archaeomes of various regions of the human body are associated with health. Accordingly, we aimed to determine the presence and diversity of archaeomes in the human urogenital tract. To explore the urogenital archaeome, voided urine specimens from 373 asymptomatic Korean individuals were used. No difference was observed in body mass index, age, or gender, according to presence of archaea. Analysis of archaeal 16S rRNA gene amplicons of archaea positive samples consisted of simple community structures, including diverse archaea, such as the phyla Methanobacteriota, Thermoproteota, and Halobacteriota. Asymptomatic individuals showed high participant-dependent intervariability in their urogenital archaeomes. The mean relative archaeal abundance was estimated to be 0.89%, and fluorescence in situ hybridisation micrographs provided evidence of archaeal cells in the human urogenital tract. In addition, the urogenital archaeome shared partial taxonomic compositional characteristics with those of the other body sites. In this study, Methanobacteriota, Thermoproteota, and Halobacteriota were suggested as inhabitants of the human urogenital tract, and a distinct human urogenital archaeome was characterised. These findings expand our knowledge of archaea-host associations in the human urogenital tract and may lead to novel insights into the role of archaea in urinary tract health.},
}
@article {pmid37468677,
year = {2023},
author = {Banas, I and Esser, SP and Turzynski, V and Soares, A and Novikova, P and May, P and Moraru, C and Hasenberg, M and Rahlff, J and Wilmes, P and Klingl, A and Probst, AJ},
title = {Spatio-functional organization in virocells of small uncultivated archaea from the deep biosphere.},
journal = {The ISME journal},
volume = {17},
number = {10},
pages = {1789-1792},
pmid = {37468677},
issn = {1751-7370},
support = {863664/ERC_/European Research Council/International ; },
mesh = {*Archaea/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Viruses/genetics ; DNA, Viral/genetics ; },
abstract = {Despite important ecological roles posited for virocells (i.e., cells infected with viruses), studying individual cells in situ is technically challenging. We introduce here a novel correlative microscopic approach to study the ecophysiology of virocells. By conducting concerted virusFISH, 16S rRNA FISH, and scanning electron microscopy interrogations of uncultivated archaea, we linked morphologies of various altiarchaeal cells to corresponding phylogenetic signals and indigenous virus infections. While uninfected cells exhibited moderate separation between fluorescence signals of ribosomes and DNA, virocells displayed complete cellular segregation of chromosomal DNA from viral DNA, the latter co-localizing with host ribosome signals. A similar spatial separation was observed in dividing cells, with viral signals congregating near ribosomes at the septum. These observations suggest that replication of these uncultivated viruses occurs alongside host ribosomes, which are used to generate the required proteins for virion assembly. Heavily infected cells sometimes displayed virus-like particles attached to their surface, which agree with virus structures in cells observed via transmission electron microscopy. Consequently, this approach is the first to link genomes of uncultivated viruses to their respective structures and host cells. Our findings shed new light on the complex ecophysiology of archaeal virocells in deep subsurface biofilms and provide a solid framework for future in situ studies of virocells.},
}
@article {pmid37464403,
year = {2023},
author = {Bargiela, R and Korzhenkov, AA and McIntosh, OA and Toshchakov, SV and Yakimov, MM and Golyshin, PN and Golyshina, OV},
title = {Evolutionary patterns of archaea predominant in acidic environment.},
journal = {Environmental microbiome},
volume = {18},
number = {1},
pages = {61},
pmid = {37464403},
issn = {2524-6372},
support = {N 810280//European Regional Development Fund/ ; N 810280//European Regional Development Fund/ ; N 810280//European Regional Development Fund/ ; RPG-2020-190//Leverhulme Trust/ ; RPG-2020-190//Leverhulme Trust/ ; RPG-2020-190//Leverhulme Trust/ ; },
abstract = {BACKGROUND: Archaea of the order Thermoplasmatales are widely distributed in natural acidic areas and are amongst the most acidophilic prokaryotic organisms known so far. These organisms are difficult to culture, with currently only six genera validly published since the discovery of Thermoplasma acidophilum in 1970. Moreover, known great diversity of uncultured Thermoplasmatales represents microbial dark matter and underlines the necessity of efforts in cultivation and study of these archaea. Organisms from the order Thermoplasmatales affiliated with the so-called "alphabet-plasmas", and collectively dubbed "E-plasma", were the focus of this study. These archaea were found predominantly in the hyperacidic site PM4 of Parys Mountain, Wales, UK, making up to 58% of total metagenomic reads. However, these archaea escaped all cultivation attempts.<br><br>RESULTS: Their genome-based metabolism revealed its peptidolytic potential, in line with the physiology of the previously studied Thermoplasmatales isolates. Analyses of the genome and evolutionary history reconstruction have shown both the gain and loss of genes, that may have contributed to the success of the "E-plasma" in hyperacidic environment compared to their community neighbours. Notable genes among them are involved in the following molecular processes: signal transduction, stress response and glyoxylate shunt, as well as multiple copies of genes associated with various cellular functions; from energy production and conversion, replication, recombination, and repair, to cell wall/membrane/envelope biogenesis and archaella production. History events reconstruction shows that these genes, acquired by putative common ancestors, may determine the evolutionary and functional divergences of "E-plasma", which is much more developed than other representatives of the order Thermoplasmatales. In addition, the ancestral hereditary reconstruction strongly indicates the placement of Thermogymnomonas acidicola close to the root of the Thermoplasmatales.<br><br>CONCLUSIONS: This study has analysed the metagenome-assembled genome of "E-plasma", which denotes the basis of their predominance in Parys Mountain environmental microbiome, their global ubiquity, and points into the right direction of further cultivation attempts. The results suggest distinct evolutionary trajectories of organisms comprising the order Thermoplasmatales, which is important for the understanding of their evolution and lifestyle.},
}
@article {pmid37461084,
year = {2023},
author = {Feehan, B and Ran, Q and Dorman, V and Rumback, K and Pogranichniy, S and Ward, K and Goodband, R and Niederwerder, MC and Lee, STM},
title = {Novel complete methanogenic pathways in longitudinal genomic study of monogastric age-associated archaea.},
journal = {Animal microbiome},
volume = {5},
number = {1},
pages = {35},
pmid = {37461084},
issn = {2524-4671},
support = {P30 GM122731/GM/NIGMS NIH HHS/United States ; U54 HD090216/HD/NICHD NIH HHS/United States ; S10 OD021743/OD/NIH HHS/United States ; UL1 TR002366/TR/NCATS NIH HHS/United States ; },
abstract = {BACKGROUND: Archaea perform critical roles in the microbiome system, including utilizing hydrogen to allow for enhanced microbiome member growth and influencing overall host health. With the majority of microbiome research focusing on bacteria, the functions of archaea are largely still under investigation. Understanding methanogenic functions during the host lifetime will add to the limited knowledge on archaeal influence on gut and host health. In our study, we determined lifelong archaea dynamics, including detection and methanogenic functions, while assessing global, temporal and host distribution of our novel archaeal metagenome-assembled genomes (MAGs). We followed 7 monogastric swine throughout their life, from birth to adult (1-156 days of age), and collected feces at 22 time points. The samples underwent gDNA extraction, Illumina sequencing, bioinformatic quality and assembly processes, MAG taxonomic assignment and functional annotation. MAGs were utilized in downstream phylogenetic analysis for global, temporal and host distribution in addition to methanogenic functional potential determination.<br><br>RESULTS: We generated 1130 non-redundant MAGs, representing 588 unique taxa at the species level, with 8 classified as methanogenic archaea. The taxonomic classifications were as follows: orders Methanomassiliicoccales (5) and Methanobacteriales (3); genera UBA71 (3), Methanomethylophilus (1), MX-02 (1), and Methanobrevibacter (3). We recovered the first US swine Methanobrevibacter UBA71 sp006954425 and Methanobrevibacter gottschalkii MAGs. The Methanobacteriales MAGs were identified primarily during the young, preweaned host whereas Methanomassiliicoccales primarily in the adult host. Moreover, we identified our methanogens in metagenomic sequences from Chinese swine, US adult humans, Mexican adult humans, Swedish adult humans, and paleontological humans, indicating that methanogens span different hosts, geography and time. We determined complete metabolic pathways for all three methanogenic pathways: hydrogenotrophic, methylotrophic, and acetoclastic. This study provided the first evidence of acetoclastic methanogenesis in archaea of monogastric hosts which indicated a previously unknown capability for acetate utilization in methanogenesis for monogastric methanogens. Overall, we hypothesized that the age-associated detection patterns were due to differential substrate availability via the host diet and microbial metabolism, and that these methanogenic functions are likely crucial to methanogens across hosts. This study provided a comprehensive, genome-centric investigation of monogastric-associated methanogens which will further improve our understanding of microbiome development and functions.},
}
@article {pmid37452095,
year = {2023},
author = {Wright, CL and Lehtovirta-Morley, LE},
title = {Nitrification and beyond: metabolic versatility of ammonia oxidising archaea.},
journal = {The ISME journal},
volume = {17},
number = {9},
pages = {1358-1368},
pmid = {37452095},
issn = {1751-7370},
mesh = {*Archaea/metabolism ; *Nitrification ; Ammonia/metabolism ; Nitrogen Cycle/physiology ; Oxidation-Reduction ; Soil Microbiology ; },
abstract = {Ammonia oxidising archaea are among the most abundant living organisms on Earth and key microbial players in the global nitrogen cycle. They carry out oxidation of ammonia to nitrite, and their activity is relevant for both food security and climate change. Since their discovery nearly 20 years ago, major insights have been gained into their nitrogen and carbon metabolism, growth preferences and their mechanisms of adaptation to the environment, as well as their diversity, abundance and activity in the environment. Despite significant strides forward through the cultivation of novel organisms and omics-based approaches, there are still many knowledge gaps on their metabolism and the mechanisms which enable them to adapt to the environment. Ammonia oxidising microorganisms are typically considered metabolically streamlined and highly specialised. Here we review the physiology of ammonia oxidising archaea, with focus on aspects of metabolic versatility and regulation, and discuss these traits in the context of nitrifier ecology.},
}
@article {pmid37446705,
year = {2023},
author = {Padilla-Vaca, F and de la Mora, J and García-Contreras, R and Ramírez-Prado, JH and Alva-Murillo, N and Fonseca-Yepez, S and Serna-Gutiérrez, I and Moreno-Galván, CL and Montufar-Rodríguez, JM and Vicente-Gómez, M and Rangel-Serrano, &#xc1; and Vargas-Maya, NI and Franco, B},
title = {Two-Component System Sensor Kinases from Asgardian Archaea May Be Witnesses to Eukaryotic Cell Evolution.},
journal = {Molecules (Basel, Switzerland)},
volume = {28},
number = {13},
pages = {},
pmid = {37446705},
issn = {1420-3049},
mesh = {*Archaea/genetics/metabolism ; *Eukaryotic Cells ; Bacteria/genetics ; Eukaryota/genetics ; Prokaryotic Cells ; Evolution, Molecular ; Phylogeny ; },
abstract = {The signal transduction paradigm in bacteria involves two-component systems (TCSs). Asgardarchaeota are archaea that may have originated the current eukaryotic lifeforms. Most research on these archaea has focused on eukaryotic-like features, such as genes involved in phagocytosis, cytoskeleton structure, and vesicle trafficking. However, little attention has been given to specific prokaryotic features. Here, the sequence and predicted structural features of TCS sensor kinases analyzed from two metagenome assemblies and a genomic assembly from cultured Asgardian archaea are presented. The homology of the sensor kinases suggests the grouping of Lokiarchaeum closer to bacterial homologs. In contrast, one group from a Lokiarchaeum and a meta-genome assembly from Candidatus Heimdallarchaeum suggest the presence of a set of kinases separated from the typical bacterial TCS sensor kinases. AtoS and ArcB homologs were found in meta-genome assemblies along with defined domains for other well-characterized sensor kinases, suggesting the close link between these organisms and bacteria that may have resulted in the metabolic link to the establishment of symbiosis. Several kinases are predicted to be cytoplasmic; some contain several PAS domains. The data shown here suggest that TCS kinases in Asgardian bacteria are witnesses to the transition from bacteria to eukaryotic organisms.},
}
@article {pmid37429213,
year = {2023},
author = {Sun, J and Zhang, A and Zhang, Z and Liu, Y and Zhou, H and Cheng, H and Chen, Z and Li, H and Zhang, R and Wang, Y},
title = {Distinct assembly processes and environmental adaptation of abundant and rare archaea in Arctic marine sediments.},
journal = {Marine environmental research},
volume = {190},
number = {},
pages = {106082},
doi = {10.1016/j.marenvres.2023.106082},
pmid = {37429213},
issn = {1879-0291},
mesh = {*Archaea/genetics ; Arctic Regions ; *Geologic Sediments ; },
abstract = {Revealing the ecological processes and environmental adaptation of abundant and rare archaea is a central, but poorly understood, topic in ecology. Here, abundant and rare archaeal diversity, community assembly processes and co-occurrence patterns were comparatively analyzed in Arctic marine sediments. Our findings revealed that the rare taxa exhibited significantly higher diversity compared to the abundant taxa. Additionally, the abundant taxa displayed stronger environmental adaptation than the rare taxa. The co-occurrence network analysis demonstrated that the rare taxa developed more interspecies interactions and modules in response to environmental disturbance. Furthermore, the community assembly of abundant and rare taxa in sediments was primarily controlled by stochastic and deterministic processes, respectively. These findings provide valuable insights into the archaeal community assembly processes and significantly contribute to a deeper understanding of the environmental adaptability of abundant and rare taxa in Arctic marine sediments.},
}
@article {pmid37404173,
year = {2023},
author = {Kiledal, EA and Shaw, M and Polson, SW and Maresca, JA},
title = {Metagenomic Analysis of a Concrete Bridge Reveals a Microbial Community Dominated by Halophilic Bacteria and Archaea.},
journal = {Microbiology spectrum},
volume = {11},
number = {4},
pages = {e0511222},
pmid = {37404173},
issn = {2165-0497},
support = {P20 GM103446/GM/NIGMS NIH HHS/United States ; },
mesh = {*Archaea/genetics ; *Microbiota/genetics ; Metagenome ; Sewage ; Sequence Analysis, DNA ; Metagenomics/methods ; Bacteria/genetics ; },
abstract = {Concrete hosts a small but diverse microbiome that changes over time. Shotgun metagenomic sequencing would enable assessment of both the diversity and function of the microbial community in concrete, but a number of unique challenges make this difficult for concrete samples. The high concentration of divalent cations in concrete interferes with nucleic acid extraction, and the extremely low biomass in concrete means that DNA from laboratory contamination may be a large fraction of the sequence data. Here, we develop an improved method for DNA extraction from concrete, with higher yield and lower laboratory contamination. To show that this method provides DNA of sufficient quality and quantity to do shotgun metagenomic sequencing, DNA was extracted from a sample of concrete obtained from a road bridge and sequenced with an Illumina MiSeq system. This microbial community was dominated by halophilic Bacteria and Archaea, with enriched functional pathways related to osmotic stress responses. Although this was a pilot-scale effort, we demonstrate that metagenomic sequencing can be used to characterize microbial communities in concrete and that older concrete structures may host different microbes than recently poured concrete. IMPORTANCE Prior work on the microbial communities of concrete focused on the surfaces of concrete structures such as sewage pipes or bridge pilings, where thick biofilms were easy to observe and sample. Because the biomass inside concrete is so low, more recent analyses of the microbial communities inside concrete used amplicon sequencing methods to describe those communities. However, to understand the activity and physiology of microbes in concrete, or to develop living infrastructure, we must develop more direct methods of community analysis. The method developed here for DNA extraction and metagenomic sequencing can be used for analysis of microbial communities inside concrete and can likely be adapted for other cementitious materials.},
}
@article {pmid37400737,
year = {2023},
author = {Li, XX and Tan, S and Cheng, M and Hu, Y and Ma, X and Hou, J and Cui, HL},
title = {Salinilacihabitans rarus gen. nov., sp. nov., Natrononativus amylolyticus gen. nov., sp. nov., Natronobeatus ordinarius gen. nov., sp. nov., and Halovivax gelatinilyticus sp. nov., halophilic archaea, isolated from a salt lake and soda lakes.},
journal = {Extremophiles : life under extreme conditions},
volume = {27},
number = {2},
pages = {15},
pmid = {37400737},
issn = {1433-4909},
support = {32070003//National Natural Science Foundation of China/ ; },
mesh = {Phylogeny ; Lakes ; RNA, Ribosomal, 16S/genetics ; DNA, Archaeal/genetics ; Sequence Analysis, DNA ; Nucleic Acid Hybridization ; *Halobacteriaceae ; China ; Glycolipids ; *Euryarchaeota/genetics ; },
abstract = {Four halophilic archaea strains, AD-4[T], CGA30[T], CGA73[T], and WLHSJ27[T], were isolated from a salt lake and two soda lakes located in different regions of China. The 16S rRNA and rpoB' gene sequence similarities among strains AD-4[T], CGA30[T], CGA73[T], WLHSJ27[T], and the current species of the family Natrialbaceae were 90.9-97.5% and 83.1-91.8%, respectively. The phylogenetic and phylogenomic analyses revealed that these four strains separated from existing genera in the family Natrialbaceae and formed distant branches. The ANI, isDDH, and AAI values among these four strains and the current members of the family Natrialbaceae were 72-79%, 20-25%, and 63-73%, respectively, much lower than the threshold values for species demarcation. Strains AD-4[T], CGA73[T], and WLHSJ27[T] may represent three novel genera of the family Natrialbaceae according to the cutoff value of AAI (≤ 76%) proposed to differentiate genera within the family Natrialbaceae. These four strains could be distinguished from the related genera according to differential phenotypic characteristics. The major phospholipids of these four strains were identical while their glycolipid profiles were diverse. DGD-1 is a major glycolipid found in strain AD-4[T], trace glycolipids, DGD-1, and S-DGD-1, and (or) S-TGD-1 was found in the other three strains. The major respiratory quinones detected in the four strains were menaquinone MK-8 and MK-8(H2). This polyphasic classification indicated that strains AD-4[T], CGA73[T], and WLHSJ27[T] represent three novel species of three new genera with the family Natrialbaceae, and strain CGA30[T] represents a novel species of Halovivax.},
}
@article {pmid37399976,
year = {2023},
author = {Li, B and Liang, J and Phillips, MA and Michael, AJ},
title = {Neofunctionalization of S-adenosylmethionine decarboxylase into pyruvoyl-dependent L-ornithine and L-arginine decarboxylases is widespread in bacteria and archaea.},
journal = {The Journal of biological chemistry},
volume = {299},
number = {8},
pages = {105005},
pmid = {37399976},
issn = {1083-351X},
support = {R01 AI034432/AI/NIAID NIH HHS/United States ; R37 AI034432/AI/NIAID NIH HHS/United States ; },
mesh = {*Adenosylmethionine Decarboxylase/genetics/metabolism ; Archaea/genetics/metabolism ; Ornithine ; Phylogeny ; *Carboxy-Lyases/genetics/metabolism ; Polyamines/metabolism ; Bacteria/metabolism ; Ornithine Decarboxylase/metabolism ; Arginine/genetics ; },
abstract = {S-adenosylmethionine decarboxylase (AdoMetDC/SpeD) is a key polyamine biosynthetic enzyme required for conversion of putrescine to spermidine. Autocatalytic self-processing of the AdoMetDC/SpeD proenzyme generates a pyruvoyl cofactor from an internal serine. Recently, we discovered that diverse bacteriophages encode AdoMetDC/SpeD homologs that lack AdoMetDC activity and instead decarboxylate L-ornithine or L-arginine. We reasoned that neofunctionalized AdoMetDC/SpeD homologs were unlikely to have emerged in bacteriophages and were probably acquired from ancestral bacterial hosts. To test this hypothesis, we sought to identify candidate AdoMetDC/SpeD homologs encoding L-ornithine and L-arginine decarboxylases in bacteria and archaea. We searched for the anomalous presence of AdoMetDC/SpeD homologs in the absence of its obligatory partner enzyme spermidine synthase, or the presence of two AdoMetDC/SpeD homologs encoded in the same genome. Biochemical characterization of candidate neofunctionalized genes confirmed lack of AdoMetDC activity, and functional presence of L-ornithine or L-arginine decarboxylase activity in proteins from phyla Actinomycetota, Armatimonadota, Planctomycetota, Melainabacteria, Perigrinibacteria, Atribacteria, Chloroflexota, Sumerlaeota, Omnitrophota, Lentisphaerota, and Euryarchaeota, the bacterial candidate phyla radiation and DPANN archaea, and the δ-Proteobacteria class. Phylogenetic analysis indicated that L-arginine decarboxylases emerged at least three times from AdoMetDC/SpeD, whereas L-ornithine decarboxylases arose only once, potentially from the AdoMetDC/SpeD-derived L-arginine decarboxylases, revealing unsuspected polyamine metabolic plasticity. Horizontal transfer of the neofunctionalized genes appears to be the more prevalent mode of dissemination. We identified fusion proteins of bona fide AdoMetDC/SpeD with homologous L-ornithine decarboxylases that possess two, unprecedented internal protein-derived pyruvoyl cofactors. These fusion proteins suggest a plausible model for the evolution of the eukaryotic AdoMetDC.},
}
@article {pmid37387308,
year = {2023},
author = {Johnsen, U and Ortjohann, M and Reinhardt, A and Turner, JM and Stratton, C and Weber, KR and Sanchez, KM and Maupin-Furlow, J and Davies, C and Schönheit, P},
title = {Discovery of a novel transcriptional regulator of sugar catabolism in archaea.},
journal = {Molecular microbiology},
volume = {120},
number = {2},
pages = {224-240},
pmid = {37387308},
issn = {1365-2958},
support = {R01 GM057498/GM/NIGMS NIH HHS/United States ; },
mesh = {*Archaea/metabolism ; *Pyruvate Kinase ; Glycerol ; Glucose/metabolism ; Fructose/metabolism ; Glyceraldehyde-3-Phosphate Dehydrogenases/metabolism ; },
abstract = {The haloarchaeon Haloferax volcanii degrades D-glucose via the semiphosphorylative Entner-Doudoroff pathway and D-fructose via a modified Embden-Meyerhof pathway. Here, we report the identification of GfcR, a novel type of transcriptional regulator that functions as an activator of both D-glucose and D-fructose catabolism. We find that in the presence of D-glucose, GfcR activates gluconate dehydratase, glyceraldehyde-3-phosphate dehydrogenase and pyruvate kinase and also acts as activator of the phosphotransferase system and of fructose-1,6-bisphosphate aldolase, which are involved in uptake and degradation of D-fructose. In addition, glyceraldehyde-3-phosphate dehydrogenase and pyruvate kinase are activated by GfcR in the presence of D-fructose and also during growth on D-galactose and glycerol. Electrophoretic mobility shift assays indicate that GfcR binds directly to promoters of regulated genes. Specific intermediates of the degradation pathways of the three hexoses and of glycerol were identified as inducer molecules of GfcR. GfcR is composed of a phosphoribosyltransferase (PRT) domain with an N-terminal helix-turn-helix motif and thus shows homology to PurR of Gram-positive bacteria that is involved in the transcriptional regulation of nucleotide biosynthesis. We propose that GfcR of H. volcanii evolved from a PRT-like enzyme to attain a function as a transcriptional regulator of central sugar catabolic pathways in archaea.},
}
@article {pmid37379385,
year = {2023},
author = {Wang, J and Qu, YN and Evans, PN and Guo, Q and Zhou, F and Nie, M and Jin, Q and Zhang, Y and Zhai, X and Zhou, M and Yu, Z and Fu, QL and Xie, YG and Hedlund, BP and Li, WJ and Hua, ZS and Wang, Z and Wang, Y},
title = {Evidence for nontraditional mcr-containing archaea contributing to biological methanogenesis in geothermal springs.},
journal = {Science advances},
volume = {9},
number = {26},
pages = {eadg6004},
pmid = {37379385},
issn = {2375-2548},
mesh = {*Archaea/genetics/metabolism ; Ecosystem ; *Hot Springs ; Methane/metabolism ; Temperature ; Phylogeny ; },
abstract = {Recent discoveries of methyl-coenzyme M reductase-encoding genes (mcr) in uncultured archaea beyond traditional euryarchaeotal methanogens have reshaped our view of methanogenesis. However, whether any of these nontraditional archaea perform methanogenesis remains elusive. Here, we report field and microcosm experiments based on [13]C-tracer labeling and genome-resolved metagenomics and metatranscriptomics, revealing that nontraditional archaea are predominant active methane producers in two geothermal springs. Archaeoglobales performed methanogenesis from methanol and may exhibit adaptability in using methylotrophic and hydrogenotrophic pathways based on temperature/substrate availability. A five-year field survey found Candidatus Nezhaarchaeota to be the predominant mcr-containing archaea inhabiting the springs; genomic inference and mcr expression under methanogenic conditions strongly suggested that this lineage mediated hydrogenotrophic methanogenesis in situ. Methanogenesis was temperature-sensitive , with a preference for methylotrophic over hydrogenotrophic pathways when incubation temperatures increased from 65° to 75°C. This study demonstrates an anoxic ecosystem wherein methanogenesis is primarily driven by archaea beyond known methanogens, highlighting diverse nontraditional mcr-containing archaea as previously unrecognized methane sources.},
}
@article {pmid37367666,
year = {2023},
author = {Mapelli-Brahm, P and Gómez-Villegas, P and Gonda, ML and León-Vaz, A and León, R and Mildenberger, J and Rebours, C and Saravia, V and Vero, S and Vila, E and Meléndez-Martínez, AJ},
title = {Microalgae, Seaweeds and Aquatic Bacteria, Archaea, and Yeasts: Sources of Carotenoids with Potential Antioxidant and Anti-Inflammatory Health-Promoting Actions in the Sustainability Era.},
journal = {Marine drugs},
volume = {21},
number = {6},
pages = {},
pmid = {37367666},
issn = {1660-3397},
mesh = {Carotenoids/pharmacology/metabolism ; Antioxidants/pharmacology/metabolism ; *Microalgae/metabolism ; Archaea ; *Seaweed ; Aquatic Organisms ; Anti-Inflammatory Agents/pharmacology/metabolism ; Bacteria ; Yeasts ; },
abstract = {Carotenoids are a large group of health-promoting compounds used in many industrial sectors, such as foods, feeds, pharmaceuticals, cosmetics, nutraceuticals, and colorants. Considering the global population growth and environmental challenges, it is essential to find new sustainable sources of carotenoids beyond those obtained from agriculture. This review focuses on the potential use of marine archaea, bacteria, algae, and yeast as biological factories of carotenoids. A wide variety of carotenoids, including novel ones, were identified in these organisms. The role of carotenoids in marine organisms and their potential health-promoting actions have also been discussed. Marine organisms have a great capacity to synthesize a wide variety of carotenoids, which can be obtained in a renewable manner without depleting natural resources. Thus, it is concluded that they represent a key sustainable source of carotenoids that could help Europe achieve its Green Deal and Recovery Plan. Additionally, the lack of standards, clinical studies, and toxicity analysis reduces the use of marine organisms as sources of traditional and novel carotenoids. Therefore, further research on the processing of marine organisms, the biosynthetic pathways, extraction procedures, and examination of their content is needed to increase carotenoid productivity, document their safety, and decrease costs for their industrial implementation.},
}
@article {pmid37349893,
year = {2023},
author = {Carré, L and Gonzalez, D and Girard, &#xc9; and Franzetti, B},
title = {Effects of chaotropic salts on global proteome stability in halophilic archaea: Implications for life signatures on Mars.},
journal = {Environmental microbiology},
volume = {25},
number = {11},
pages = {2216-2230},
doi = {10.1111/1462-2920.16451},
pmid = {37349893},
issn = {1462-2920},
mesh = {Proteome ; Salts ; Extraterrestrial Environment ; *Mars ; *Haloferax volcanii/genetics ; Biomarkers ; },
abstract = {Halophilic archaea thriving in hypersaline environments, such as salt lakes, offer models for putative life in extraterrestrial brines such as those found on Mars. However, little is known about the effect of the chaotropic salts that could be found in such brines, such as MgCl2 , CaCl2 and (per)chlorate salts, on complex biological samples like cell lysates which could be expected to be more representative of biomarkers left behind putative extraterrestrial life forms. We used intrinsic fluorescence to study the salt dependence of proteomes extracted from five halophilic strains: Haloarcula marismortui, Halobacterium salinarum, Haloferax mediterranei, Halorubrum sodomense and Haloferax volcanii. These strains were isolated from Earth environments with different salt compositions. Among the five strains that were analysed, H. mediterranei stood out as a results of its high dependency on NaCl for its proteome stabilization. Interestingly, the results showed contrasting denaturation responses of the proteomes to chaotropic salts. In particular, the proteomes of strains that are most dependent or tolerant on MgCl2 for growth exhibited higher tolerance towards chaotropic salts that are abundant in terrestrial and Martian brines. These experiments bridge together global protein properties and environmental adaptation and help guide the search for protein-like biomarkers in extraterrestrial briny environments.},
}
@article {pmid37341134,
year = {2023},
author = {Iacono, R and De Lise, F and Moracci, M and Cobucci-Ponzano, B and Strazzulli, A},
title = {Glycoside hydrolases from (hyper)thermophilic archaea: structure, function, and applications.},
journal = {Essays in biochemistry},
volume = {67},
number = {4},
pages = {731-751},
doi = {10.1042/EBC20220196},
pmid = {37341134},
issn = {1744-1358},
mesh = {*Glycoside Hydrolases/chemistry ; *Archaea/chemistry ; Hot Temperature ; Hydrolysis ; },
abstract = {(Hyper)thermophilic archaeal glycosidases are enzymes that catalyze the hydrolysis of glycosidic bonds to break down complex sugars and polysaccharides at high temperatures. These enzymes have an unique structure that allows them to remain stable and functional in extreme environments such as hot springs and hydrothermal vents. This review provides an overview of the current knowledge and milestones on the structures and functions of (hyper)thermophilic archaeal glycosidases and their potential applications in various fields. In particular, this review focuses on the structural characteristics of these enzymes and how these features relate to their catalytic activity by discussing different types of (hyper)thermophilic archaeal glycosidases, including β-glucosidases, chitinase, cellulases and α-amylases, describing their molecular structures, active sites, and mechanisms of action, including their role in the hydrolysis of carbohydrates. By providing a comprehensive overview of (hyper)thermophilic archaeal glycosidases, this review aims to stimulate further research into these fascinating enzymes.},
}
@article {pmid37332501,
year = {2022},
author = {Pessi, IS and Rutanen, A and Hultman, J},
title = {Candidatus Nitrosopolaris, a genus of putative ammonia-oxidizing archaea with a polar/alpine distribution.},
journal = {FEMS microbes},
volume = {3},
number = {},
pages = {xtac019},
pmid = {37332501},
issn = {2633-6685},
abstract = {Ammonia-oxidizing archaea (AOA) are key players in the nitrogen cycle of polar soils. Here, we analyzed metagenomic data from tundra soils in Rásttigáisá, Norway, and recovered four metagenome-assembled genomes (MAGs) assigned to the genus 'UBA10452', an uncultured lineage of putative AOA in the order Nitrososphaerales ('terrestrial group I.1b'), phylum Thaumarchaeota. Analysis of other eight previously reported MAGs and publicly available amplicon sequencing data revealed that the UBA10452 lineage is predominantly found in acidic polar and alpine soils. In particular, UBA10452 MAGs were more abundant in highly oligotrophic environments such as mineral permafrost than in more nutrient-rich, vegetated tundra soils. UBA10452 MAGs harbour multiple copies of genes related to cold tolerance, particularly genes involved in DNA replication and repair. Based on the phylogenetic, biogeographic, and ecological characteristics of 12 UBA10452 MAGs, which include a high-quality MAG (90.8% complete, 3.9% redundant) with a nearly complete 16S rRNA gene, we propose a novel Candidatus genus, Ca. Nitrosopolaris, with four species representing clear biogeographic/habitat clusters.},
}
@article {pmid37323904,
year = {2023},
author = {Elcheninov, AG and Ugolkov, YA and Elizarov, IM and Klyukina, AA and Kublanov, IV and Sorokin, DY},
title = {Cellulose metabolism in halo(natrono)archaea: a comparative genomics study.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1112247},
pmid = {37323904},
issn = {1664-302X},
abstract = {Extremely halophilic archaea are one of the principal microbial community components in hypersaline environments. The majority of cultivated haloarchaea are aerobic heterotrophs using peptides or simple sugars as carbon and energy sources. At the same time, a number of novel metabolic capacities of these extremophiles were discovered recently among which is a capability of growing on insoluble polysaccharides such as cellulose and chitin. Still, polysaccharidolytic strains are in minority among cultivated haloarchaea and their capacities of hydrolyzing recalcitrant polysaccharides are hardly investigated. This includes the mechanisms and enzymes involved in cellulose degradation, which are well studied for bacterial species, while almost unexplored in archaea and haloarchaea in particular. To fill this gap, a comparative genomic analysis of 155 cultivated representatives of halo(natrono)archaea, including seven cellulotrophic strains belonging to the genera Natronobiforma, Natronolimnobius, Natrarchaeobius, Halosimplex, Halomicrobium and Halococcoides was performed. The analysis revealed a number of cellulases, encoded in the genomes of cellulotrophic strains but also in several haloarchaea, for which the capacity to grow on cellulose was not shown. Surprisingly, the cellulases genes, especially of GH5, GH9 and GH12 families, were significantly overrepresented in the cellulotrophic haloarchaea genomes in comparison with other cellulotrophic archaea and even cellulotrophic bacteria. Besides cellulases, the genes for GH10 and GH51 families were also abundant in the genomes of cellulotrophic haloarchaea. These results allowed to propose the genomic patterns, determining the capability of haloarchaea to grow on cellulose. The patterns helped to predict cellulotrophic capacity for several halo(natrono)archaea, and for three of them it was experimentally confirmed. Further genomic search revealed that glucose and cellooligosaccharides import occurred by means of porters and ABC (ATP-binding cassette) transporters. Intracellular glucose oxidation occurred through glycolysis or the semi-phosphorylative Entner-Dudoroff pathway which occurrence was strain-specific. Comparative analysis of CAZymes toolbox and available cultivation-based information allowed proposing two possible strategies used by haloarchaea capable of growing on cellulose: so-called specialists are more effective in degradation of cellulose while generalists are more flexible in nutrient spectra. Besides CAZymes profiles the groups differed in genome sizes, as well as in variability of mechanisms of import and central metabolism of sugars.},
}
@article {pmid37322123,
year = {2023},
author = {Taglialegna, A},
title = {A plasmid to modify Archaea.},
journal = {Nature reviews. Microbiology},
volume = {21},
number = {8},
pages = {483},
pmid = {37322123},
issn = {1740-1534},
mesh = {*Archaea/genetics ; Plasmids/genetics ; },
}
@article {pmid37317245,
year = {2023},
author = {Thompson, TP and Busetti, A and Gilmore, BF},
title = {Quorum Sensing in Halorubrum saccharovorum Facilitates Cross-Domain Signaling between Archaea and Bacteria.},
journal = {Microorganisms},
volume = {11},
number = {5},
pages = {},
pmid = {37317245},
issn = {2076-2607},
abstract = {Quorum Sensing (QS) is a well-studied intercellular communication mechanism in bacteria, regulating collective behaviors such as biofilm formation, virulence, and antibiotic resistance. However, cell-cell signaling in haloarchaea remains largely unexplored. The coexistence of bacteria and archaea in various environments, coupled with the known cell-cell signaling mechanisms in both prokaryotic and eukaryotic microorganisms and the presence of cell-cell signaling mechanisms in both prokaryotic and eukaryotic microorganisms, suggests a possibility for haloarchaea to possess analogous cell-cell signaling or QS systems. Recently, N-acylhomoserine lactone (AHL)-like compounds were identified in haloarchaea; yet, their precise role-for example, persister cell formation-remains ambiguous. This study investigated the capacity of crude supernatant extract from the haloarchaeon Halorubrum saccharovorum CSM52 to stimulate bacterial AHL-dependent QS phenotypes using bioreporter strains. Our findings reveal that these crude extracts induced several AHL-dependent bioreporters and modulated pyocyanin and pyoverdine production in Pseudomonas aeruginosa. Importantly, our study suggests cross-domain communication between archaea and bacterial pathogens, providing evidence for archaea potentially influencing bacterial virulence. Using Thin Layer Chromatography overlay assays, lactonolysis, and colorimetric quantification, the bioactive compound was inferred to be a chemically modified AHL-like compound or a diketopiperazine-like molecule, potentially involved in biofilm formation in H. saccharovorum CSM52. This study offers new insights into putative QS mechanisms in haloarchaea and their potential role in interspecies communication and coordination, thereby enriching our understanding of microbial interactions in diverse environments.},
}
@article {pmid37317170,
year = {2023},
author = {Payá, G and Bautista, V and Camacho, M and Esclapez, J and Bonete, MJ},
title = {Comprehensive Bioinformatics Analysis of the Biodiversity of Lsm Proteins in the Archaea Domain.},
journal = {Microorganisms},
volume = {11},
number = {5},
pages = {},
pmid = {37317170},
issn = {2076-2607},
support = {ACIF/2018/200//Generalitat Valenciana/ ; VIGROB_016//University of Alicante/ ; },
abstract = {The Sm protein superfamily includes Sm, like-Sm (Lsm), and Hfq proteins. Sm and Lsm proteins are found in the Eukarya and Archaea domains, respectively, while Hfq proteins exist in the Bacteria domain. Even though Sm and Hfq proteins have been extensively studied, archaeal Lsm proteins still require further exploration. In this work, different bioinformatics tools are used to understand the diversity and distribution of 168 Lsm proteins in 109 archaeal species to increase the global understanding of these proteins. All 109 archaeal species analyzed encode one to three Lsm proteins in their genome. Lsm proteins can be classified into two groups based on molecular weight. Regarding the gene environment of lsm genes, many of these genes are located adjacent to transcriptional regulators of the Lrp/AsnC and MarR families, RNA-binding proteins, and ribosomal protein L37e. Notably, only proteins from species of the class Halobacteria conserved the internal and external residues of the RNA-binding site identified in Pyrococcus abyssi, despite belonging to different taxonomic orders. In most species, the Lsm genes show associations with 11 genes: rpl7ae, rpl37e, fusA, flpA, purF, rrp4, rrp41, hel308, rpoD, rpoH, and rpoN. We propose that most archaeal Lsm proteins are related to the RNA metabolism, and the larger Lsm proteins could perform different functions and/or act through other mechanisms of action.},
}
@article {pmid37308591,
year = {2023},
author = {Tong, Y and Wu, X and Liu, Y and Chen, H and Zhou, Y and Jiang, L and Li, M and Zhao, S and Zhang, Y},
title = {Alternative Z-genome biosynthesis pathway shows evolutionary progression from Archaea to phage.},
journal = {Nature microbiology},
volume = {8},
number = {7},
pages = {1330-1338},
pmid = {37308591},
issn = {2058-5276},
mesh = {*Bacteriophages/genetics ; Archaea/genetics ; Biosynthetic Pathways ; Phylogeny ; Guanosine Triphosphate ; Adenosine Triphosphate ; },
abstract = {Many bacteriophages evade bacterial immune recognition by substituting adenine with 2,6-diaminopurine (Z) in their genomes. The Z-genome biosynthetic pathway involves PurZ that belongs to the PurA (adenylosuccinate synthetase) family and bears particular similarity to archaeal PurA. However, how the transition of PurA to PurZ occurred during evolution is not clear; recapturing this process may shed light on the origin of Z-containing phages. Here we describe the computer-guided identification and biochemical characterization of a naturally existing PurZ variant, PurZ0, which uses guanosine triphosphate as the phosphate donor rather than the ATP used by PurZ. The atomic resolution structure of PurZ0 reveals a guanine nucleotide binding pocket highly analogous to that of archaeal PurA. Phylogenetic analyses suggest PurZ0 as an intermediate during the evolution of archaeal PurA to phage PurZ. Maintaining the balance of different purines necessitates further evolvement of guanosine triphosphate-using PurZ0 to ATP-using PurZ in adaptation to Z-genome life.},
}
@article {pmid37305433,
year = {2023},
author = {van der Does, C and Braun, F and Ren, H and Albers, SV},
title = {Putative nucleotide-based second messengers in archaea.},
journal = {microLife},
volume = {4},
number = {},
pages = {uqad027},
pmid = {37305433},
issn = {2633-6693},
abstract = {Second messengers transfer signals from changing intra- and extracellular conditions to a cellular response. Over the last few decades, several nucleotide-based second messengers have been identified and characterized in especially bacteria and eukaryotes. Also in archaea, several nucleotide-based second messengers have been identified. This review will summarize our understanding of nucleotide-based second messengers in archaea. For some of the nucleotide-based second messengers, like cyclic di-AMP and cyclic oligoadenylates, their roles in archaea have become clear. Cyclic di-AMP plays a similar role in osmoregulation in euryarchaea as in bacteria, and cyclic oligoadenylates are important in the Type III CRISPR-Cas response to activate CRISPR ancillary proteins involved in antiviral defense. Other putative nucleotide-based second messengers, like 3',5'- and 2',3'-cyclic mononucleotides and adenine dinucleotides, have been identified in archaea, but their synthesis and degradation pathways, as well as their functions as secondary messengers, still remain to be demonstrated. In contrast, 3'-3'-cGAMP has not yet been identified in archaea, but the enzymes required to synthesize 3'-3'-cGAMP have been found in several euryarchaeotes. Finally, the widely distributed bacterial second messengers, cyclic diguanosine monophosphate and guanosine (penta-)/tetraphosphate, do not appear to be present in archaea.},
}
@article {pmid37293225,
year = {2023},
author = {Jia, Z and Lipus, D and Burckhardt, O and Bussert, R and Sondermann, M and Bartholomäus, A and Wagner, D and Kallmeyer, J},
title = {Enrichment of rare methanogenic Archaea shows their important ecological role in natural high-CO2 terrestrial subsurface environments.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1105259},
pmid = {37293225},
issn = {1664-302X},
abstract = {INTRODUCTION: Long-term stability of underground CO2 storage is partially affected by microbial activity but our knowledge of these effects is limited, mainly due to a lack of sites. A consistently high flux of mantle-derived CO2 makes the Eger Rift in the Czech Republic a natural analogue to underground CO2 storage. The Eger Rift is a seismically active region and H2 is produced abiotically during earthquakes, providing energy to indigenous microbial communities.<br><br>METHODS: To investigate the response of a microbial ecosystem to high levels of CO2 and H2, we enriched microorganisms from samples from a 239.5 m long drill core from the Eger Rift. Microbial abundance, diversity and community structure were assessed using qPCR and 16S rRNA gene sequencing. Enrichment cultures were set up with minimal mineral media and H2/CO2 headspace to simulate a seismically active period with elevated H2.<br><br>RESULTS AND DISCUSSION: Methane headspace concentrations in the enrichments indicated that active methanogens were almost exclusively restricted to enrichment cultures from Miocene lacustrine deposits (50-60 m), for which we observed the most significant growth. Taxonomic assessment showed microbial communities in these enrichments to be less diverse than those with little or no growth. Active enrichments were especially abundant in methanogens of the taxa Methanobacterium and Methanosphaerula. Concurrent to the emergence of methanogenic archaea, we also observed sulfate reducers with the metabolic ability to utilize H2 and CO2, specifically the genus Desulfosporosinus, which were able to outcompete methanogens in several enrichments. Low microbial abundance and a diverse non-CO2 driven microbial community, similar to that in drill core samples, also reflect the inactivity in these cultures. Significant growth of sulfate reducing and methanogenic microbial taxa, which make up only a small fraction of the total microbial community, emphasize the need to account for rare biosphere taxa when assessing the metabolic potential of microbial subsurface populations. The observation that CO2 and H2-utilizing microorganisms could only be enriched from a narrow depth interval suggests that factors such as sediment heterogeneity may also be important. This study provides new insight on subsurface microbes under the influence of high CO2 concentrations, similar to those found in CCS sites.},
}
@article {pmid37277532,
year = {2023},
author = {Catchpole, RJ and Barbe, V and Magdelenat, G and Marguet, E and Terns, M and Oberto, J and Forterre, P and Da Cunha, V},
title = {A self-transmissible plasmid from a hyperthermophile that facilitates genetic modification of diverse Archaea.},
journal = {Nature microbiology},
volume = {8},
number = {7},
pages = {1339-1347},
pmid = {37277532},
issn = {2058-5276},
support = {R35 GM118160/GM/NIGMS NIH HHS/United States ; },
mesh = {*Archaea/genetics ; Plasmids/genetics ; *DNA/genetics ; Bacteria/genetics ; Genome, Archaeal ; },
abstract = {Conjugative plasmids are self-transmissible mobile genetic elements that transfer DNA between host cells via type IV secretion systems (T4SS). While T4SS-mediated conjugation has been well-studied in bacteria, information is sparse in Archaea and known representatives exist only in the Sulfolobales order of Crenarchaeota. Here we present the first self-transmissible plasmid identified in a Euryarchaeon, Thermococcus sp. 33-3. The 103 kbp plasmid, pT33-3, is seen in CRISPR spacers throughout the Thermococcales order. We demonstrate that pT33-3 is a bona fide conjugative plasmid that requires cell-to-cell contact and is dependent on canonical, plasmid-encoded T4SS-like genes. Under laboratory conditions, pT33-3 transfers to various Thermococcales and transconjugants propagate at 100 °C. Using pT33-3, we developed a genetic toolkit that allows modification of phylogenetically diverse Archaeal genomes. We demonstrate pT33-3-mediated plasmid mobilization and subsequent targeted genome modification in previously untransformable Thermococcales species, and extend this process to interphylum transfer to a Crenarchaeon.},
}
@article {pmid37264141,
year = {2023},
author = {Zehnle, H and Laso-Pérez, R and Lipp, J and Riedel, D and Benito Merino, D and Teske, A and Wegener, G},
title = {Candidatus Alkanophaga archaea from Guaymas Basin hydrothermal vent sediment oxidize petroleum alkanes.},
journal = {Nature microbiology},
volume = {8},
number = {7},
pages = {1199-1212},
pmid = {37264141},
issn = {2058-5276},
mesh = {Archaea ; *Petroleum/metabolism ; *Hydrothermal Vents ; Anaerobiosis ; Alkanes/metabolism ; Sulfates/metabolism ; },
abstract = {Methanogenic and methanotrophic archaea produce and consume the greenhouse gas methane, respectively, using the reversible enzyme methyl-coenzyme M reductase (Mcr). Recently, Mcr variants that can activate multicarbon alkanes have been recovered from archaeal enrichment cultures. These enzymes, called alkyl-coenzyme M reductase (Acrs), are widespread in the environment but remain poorly understood. Here we produced anoxic cultures degrading mid-chain petroleum n-alkanes between pentane (C5) and tetradecane (C14) at 70 °C using oil-rich Guaymas Basin sediments. In these cultures, archaea of the genus Candidatus Alkanophaga activate the alkanes with Acrs and completely oxidize the alkyl groups to CO2. Ca. Alkanophaga form a deep-branching sister clade to the methanotrophs ANME-1 and are closely related to the short-chain alkane oxidizers Ca. Syntrophoarchaeum. Incapable of sulfate reduction, Ca. Alkanophaga shuttle electrons released from alkane oxidation to the sulfate-reducing Ca. Thermodesulfobacterium syntrophicum. These syntrophic consortia are potential key players in petroleum degradation in heated oil reservoirs.},
}
@article {pmid37256053,
year = {2023},
author = {Hou, G and Wazir, ZG and Liu, J and Wang, G and Rong, F and Xu, Y and Li, M and Liu, K and Liu, A and Liu, H and Wang, F},
title = {Effects of sulfadiazine and Cu on soil potential nitrification and ammonia-oxidizing archaea and bacteria communities across different soils.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1153199},
pmid = {37256053},
issn = {1664-302X},
abstract = {INTRODUCTION: Sulfadiazine (SDZ) and copper (Cu) are frequently detected in agricultural soils, but little is known on their single or combined impact on ammonia oxidizing microbial community and function across different soils.<br><br>METHODS: In this study, a microcosm was conducted to distinguish the microbial ecotoxicity of SDZ and Cu across different soils by analyzing soil potential nitrification rate (PNR) and the amoA gene sequences.<br><br>RESULTS: The results showed that the single spiking of SDZ caused a consistent decrease of soil PNR among three tested soils, but no consistent synergistic inhibition of SDZ and Cu was observed across these soils. Moreover, across three tested soils, the distinct responses to the single or joint exposure of SDZ and Cu were found in amoA gene abundance, and diversity as well as the identified genus taxa of ammonia-oxidizing archaea (AOA) and bacteria (AOB). Meanwhile, only the specific genus taxa of AOA or AOB consistently corresponded to the variation of soil PNR across different treated soils. The further principal component analysis (PCA) exhibited that the variable influence of SDZ and Cu on ammonia oxidizing microbial community and function was greatly dependent on soil type.<br><br>DISCUSSION: Therefore, in addition to ecological functionality and the specific prokaryotic taxa, soil microbial ecotoxicity of SDZ and Cu also was dependent on edaphic factors derived from soil types. This study proposes an integrative assessment of soil properties and multiple microbial targets to soil contamination management.},
}
@article {pmid37252776,
year = {2023},
author = {Wang, BB and Bao, CX and Sun, YP and Hou, J and Cui, HL},
title = {Halobacterium wangiae sp. nov. and Halobacterium zhouii sp. nov., two extremely halophilic archaea isolated from sediment of a salt lake and saline soil of an inland saltern.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {73},
number = {5},
pages = {},
doi = {10.1099/ijsem.0.005922},
pmid = {37252776},
issn = {1466-5034},
mesh = {*Halobacterium ; RNA, Ribosomal, 16S/genetics ; Lakes/microbiology ; Fatty Acids/chemistry ; Phylogeny ; Base Composition ; Sequence Analysis, DNA ; DNA, Bacterial/genetics ; Bacterial Typing Techniques ; Glycolipids/chemistry ; China ; DNA, Archaeal/genetics ; *Halobacteriaceae ; },
abstract = {Two novel halophilic archaeal strains, Gai3-17[T] and XZYJT26[T], were isolated from the sediment of Gaize salt lake and the saline soil of Mangkang ancient solar saltern in Tibet, PR China, respectively. Strains Gai3-17[T] and XZYJT26[T] were related to each other (96.5 and 89.7% similarity, respectively) and showed 97.5-95.4 and 91.5-87.7% similarities to the current members of Halobacterium based on 16S rRNA and rpoB' genes. The phylogenomic analysis indicated that strains Gai3-17[T] and XZYJT26[T] formed two distinct clades and clustered with the Halobacterium species. The two strains can be differentiated from the type strains of the six species with validly published names based on several phenotypic characteristics. The phospholipids of the two strains were phosphatidic acid, phosphatidylglycerol and phosphatidylglycerol phosphate methyl ester. One major glycolipid, sulphated galactosyl mannosyl glucosyl diether, was detected in strain Gai3-17[T], while four glycolipids, mannosyl glucosyl diether, sulphated mannosyl glucosyl diether, disulphated mannosyl glucosyl diether and sulphated galactosyl mannosyl glucosyl diether were observed in strain XZYJT26[T]. The average nucleotide identity, digital DNA-DNA hybridization and amino acid identity values among the two strains and the members of Halobacterium were no more than 81, 25 and 77 %, respectively. These overall genome-related indices were below the threshold values for species boundary, indicating that strains Gai3-17[T] and XZYJT26[T] represent two novel species of Halobacterium. Thus, two novel species, Halobacterium wangiae sp. nov. and Halobacterium zhouii sp. nov., are proposed to accommodate strains Gai3-17[T] (=CGMCC 1.16101[T]=JCM 33551[T]) and XZYJT26[T] (=CGMCC 1.16682[T]=JCM 33556[T]), respectively.},
}
@article {pmid37237946,
year = {2023},
author = {Ávila-Román, J and Gómez-Villegas, P and de Carvalho, CCCR and Vigara, J and Motilva, V and León, R and Talero, E},
title = {Up-Regulation of the Nrf2/HO-1 Antioxidant Pathway in Macrophages by an Extract from a New Halophilic Archaea Isolated in Odiel Saltworks.},
journal = {Antioxidants (Basel, Switzerland)},
volume = {12},
number = {5},
pages = {},
pmid = {37237946},
issn = {2076-3921},
support = {US-1380844//Operative FEDER Program-Andaluc&#xed;a 2014-2020/ ; UHU-1257518//Operative FEDER Program-Andaluc&#xed;a 2014-2020/ ; PID2019-110438RB-C22 -AEI/FEDER//Spanish Agencia Estatal de Investigaci&#xf3;n/ ; 2020-PY20//the Andalusian government (I+D+i-JA-PAIDI-Retos projects/ ; },
abstract = {The production of reactive oxygen species (ROS) plays an important role in the progression of many inflammatory diseases. The search for antioxidants with the ability for scavenging free radicals from the body cells that reduce oxidative damage is essential to prevent and treat these pathologies. Haloarchaea are extremely halophilic microorganisms that inhabit hypersaline environments, such as saltworks or salt lakes, where they have to tolerate high salinity, and elevated ultraviolet (UV) and infrared radiations. To cope with these extreme conditions, haloarchaea have developed singular mechanisms to maintain an osmotic balance with the medium, and are endowed with unique compounds, not found in other species, with bioactive properties that have not been fully explored. This study aims to assess the potential of haloarchaea as a new source of natural antioxidant and anti-inflammatory agents. A carotenoid-producing haloarchaea was isolated from Odiel Saltworks (OS) and identified on the basis of its 16S rRNA coding gene sequence as a new strain belonging to the genus Haloarcula. The Haloarcula sp. OS acetone extract (HAE) obtained from the biomass contained bacterioruberin and mainly C18 fatty acids, and showed potent antioxidant capacity using ABTS assay. This study further demonstrates, for the first time, that pretreatment with HAE of lipopolysaccharide (LPS)-stimulated macrophages results in a reduction in ROS production, a decrease in the pro-inflammatory cytokines TNF-α and IL-6 levels, and up-regulation of the factor Nrf2 and its target gene heme oxygenase-1 (HO-1), supporting the potential of the HAE as a therapeutic agent in the treatment of oxidative stress-related inflammatory diseases.},
}
@article {pmid37204206,
year = {2023},
author = {Ma, X and Hu, Y and Li, XX and Tan, S and Cheng, M and Hou, J and Cui, HL},
title = {Halomicroarcula laminariae sp. nov. and Halomicroarcula marina sp. nov., extremely halophilic archaea isolated from salted brown alga Laminaria and coastal saline-alkali lands.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {73},
number = {5},
pages = {},
doi = {10.1099/ijsem.0.005889},
pmid = {37204206},
issn = {1466-5034},
mesh = {*Laminaria ; *Halobacteriaceae ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Glycolipids/chemistry ; Fatty Acids/chemistry ; Base Composition ; Sequence Analysis, DNA ; Bacterial Typing Techniques ; DNA, Bacterial/genetics ; Sodium Chloride ; *Halobacteriales ; *Haloarcula ; Comparative Genomic Hybridization ; China ; DNA, Archaeal/genetics ; },
abstract = {Four extremely halophilic archaeal strains, LYG-108[T], LYG-24, DT1[T] and YSSS71, were isolated from salted Laminaria produced in Lianyungang and saline soil from the coastal beach at Jiangsu, PR China. The four strains were found to be related to the current species of Halomicroarcula (showing 88.1-98.5% and 89.3-93.6% similarities, respectively) as revealed by phylogenetic analysis based on 16S rRNA and rpoB' genes. These phylogenies were fully supported by the phylogenomic analysis, and the overall genome-related indexes (average nucleotide identity, DNA-DNA hybridization and average amino acid identity) among these four strains and the Halomicroarcula species were 77-84 %, 23-30 % and 71-83 %, respectively, clearly below the threshold values for species demarcation. Additionally, the phylogenomic and comparative genomic analyses revealed that Halomicroarcula salina YGH18[T] is related to the current species of Haloarcula rather than those of Halomicroarcula, Haloarcula salaria Namwong et al. 2011 is a later heterotypic synonym of Haloarcula argentinensis Ihara et al. 1997, and Haloarcula quadrata Oren et al. 1999 is a later heterotypic synonym of Haloarcula marismortui Oren et al. 1990. The major polar lipids of strains LYG-108[T], LYG-24, DT1[T] and YSSS71 were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulphate, sulphated mannosyl glucosyl diether and additional glycosyl-cardiolipins. All these results showed that strains LYG-108[T] (=CGMCC 1.13607[T]=JCM 32950[T]) and LYG-24 (=CGMCC 1.13605=JCM 32949) represent a new species of the genus Halomicroarcula, for which the name Halomicroarcula laminariae sp. nov. is proposed; strains DT1[T] (=CGMCC 1.18928[T]=JCM 35414[T]) and YSSS71 (=CGMCC 1.18783=JCM 34915) also represent a new species of the genus Halomicroarcula, for which the name Halomicroarcula marina sp. nov. is proposed.},
}
@article {pmid37202434,
year = {2023},
author = {Wang, Z and Li, Y and Zheng, W and Ji, Y and Duan, M and Ma, L},
title = {Ammonia oxidizing archaea and bacteria respond to different manure application rates during organic vegetable cultivation in Northwest China.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {8064},
pmid = {37202434},
issn = {2045-2322},
mesh = {*Archaea/genetics ; *Ammonia ; Vegetables ; Manure/microbiology ; Oxidation-Reduction ; Bacteria/genetics ; China ; Nitrification ; Carbon ; Nitrogen ; Soil Microbiology ; Phylogeny ; },
abstract = {Ammonia oxidization is a critical process in nitrogen cycling that involves ammonia oxidizing archaea (AOA) and bacteria (AOB). However, the effects of different manure amounts on ammonia-oxidizing microorganisms (AOMs) over the course of organic vegetables production remains unclear. We used the amoA gene to evaluated AOMs abundance and community structure in organic vegetable fields. Quantitative PCR revealed that AOB were more abundant than AOA. Among them, the amoA copy number of AOB treated with 900 kgN ha[-1] was 21.3 times that of AOA. The potential nitrification rate was significantly correlated with AOB abundance (P < 0.0001) but not with AOA, suggesting that AOB might contribute more to nitrification than AOA. AOB sequences were classified into Nitrosomonas and Nitrosospira, and AOA into Nitrosopumilus and Nitrososphaera. Nitrosomonas and Nitrosopumilus were predominant in treatments that received manure nitrogen at ≥ 900 kg ha[-1] (52.7-56.5%) and when manure was added (72.7-99.8%), respectively, whereas Nitrosospira and Nitrososphaera occupied more than a half percentage in those that received ≤ 600 kg ha[-1] (58.4-84.9%) and no manure (59.6%). A similar manure rate resulted in more identical AOMs' community structures than greater difference manure rate. The bacterial amoA gene abundances and ratios of AOB and AOA showed significantly positive correlations with soil electrical conductivity, total carbon and nitrogen, nitrate, phosphorus, potassium, and organic carbon, indicating that these were potential key factors influencing AOMs. This study explored the AOMs' variation in organic vegetable fields in Northwest China and provided a theoretical basis and reference for the subsequent formulation of proper manure management.},
}
@article {pmid37198640,
year = {2023},
author = {Dondjou, DT and Diedhiou, AG and Mbodj, D and Mofini, MT and Pignoly, S and Ndiaye, C and Diedhiou, I and Assigbetse, K and Manneh, B and Laplaze, L and Kane, A},
title = {Rice developmental stages modulate rhizosphere bacteria and archaea co-occurrence and sensitivity to long-term inorganic fertilization in a West African Sahelian agro-ecosystem.},
journal = {Environmental microbiome},
volume = {18},
number = {1},
pages = {42},
pmid = {37198640},
issn = {2524-6372},
abstract = {BACKGROUND: Rhizosphere microbial communities are important components of the soil-plant continuum in paddy field ecosystems. These rhizosphere communities contribute to nutrient cycling and rice productivity. The use of fertilizers is a common agricultural practice in rice paddy fields. However, the long-term impact of the fertilizers usage on the rhizosphere microbial communities at different rice developmental stages remains poorly investigated. Here, we examined the effects of long-term (27 years) N and NPK-fertilization on bacterial and archaeal community inhabiting the rice rhizosphere at three developmental stages (tillering, panicle initiation and booting) in the Senegal River Delta.<br><br>RESULTS: We found that the effect of long-term inorganic fertilization on rhizosphere microbial communities varied with the rice developmental stage, and between microbial communities in their response to N and NPK-fertilization. The microbial communities inhabiting the rice rhizosphere at panicle initiation appear to be more sensitive to long-term inorganic fertilization than those at tillering and booting stages. However, the effect of developmental stage on microbial sensitivity to long-term inorganic fertilization was more pronounced for bacterial than archaeal community. Furthermore, our data reveal dynamics of bacteria and archaea co-occurrence patterns in the rice rhizosphere, with differentiated bacterial and archaeal pivotal roles in the microbial inter-kingdom networks across developmental stages.<br><br>CONCLUSIONS: Our study brings new insights on rhizosphere bacteria and archaea co-occurrence and the long-term inorganic fertilization impact on these communities across developmental stages in field-grown rice. It would help in developing strategies for the successful manipulation of microbial communities to improve rice yields.},
}
@article {pmid37196775,
year = {2023},
author = {Aparici-Carratalá, D and Esclapez, J and Bautista, V and Bonete, MJ and Camacho, M},
title = {Archaea: current and potential biotechnological applications.},
journal = {Research in microbiology},
volume = {174},
number = {7},
pages = {104080},
doi = {10.1016/j.resmic.2023.104080},
pmid = {37196775},
issn = {1769-7123},
mesh = {*Archaea/genetics/metabolism ; *Biotechnology ; },
abstract = {Archaea are microorganisms with great ability to colonize some of the most inhospitable environments in nature, managing to survive in places with extreme characteristics for most microorganisms. Its proteins and enzymes are stable and can act under extreme conditions in which other proteins and enzymes would degrade. These attributes make them ideal candidates for use in a wide range of biotechnological applications. This review describes the most important applications, both current and potential, that archaea present in Biotechnology, classifying them according to the sector to which the application is directed. It also analyzes the advantages and disadvantages of its use.},
}
@article {pmid37194083,
year = {2023},
author = {Romero, R and Gervasi, MT and DiGiulio, DB and Jung, E and Suksai, M and Miranda, J and Theis, KR and Gotsch, F and Relman, DA},
title = {Are bacteria, fungi, and archaea present in the midtrimester amniotic fluid?.},
journal = {Journal of perinatal medicine},
volume = {51},
number = {7},
pages = {886-890},
pmid = {37194083},
issn = {1619-3997},
support = {HHSN275201300006C/HD/NICHD NIH HHS/United States ; Z01 HD002400/ImNIH/Intramural NIH HHS/United States ; },
mesh = {Pregnancy ; Female ; Humans ; *Amniotic Fluid/microbiology ; Pregnancy Trimester, Second ; *Chorioamnionitis/microbiology ; Archaea ; Retrospective Studies ; Bacteria ; Inflammation ; Fungi ; },
abstract = {OBJECTIVES: This study was conducted to determine whether bacteria, fungi, or archaea are detected in the amniotic fluid of patients who underwent midtrimester amniocentesis for clinical indications.<br><br>METHODS: Amniotic fluid samples from 692 pregnancies were tested by using a combination of culture and end-point polymerase chain reaction (PCR) techniques. Intra-amniotic inflammation was defined as an interleukin-6 concentration >2,935 pg/mL.<br><br>RESULTS: Microorganisms were detected in 0.3% (2/692) of cases based on cultivation, 1.73% (12/692) based on broad-range end-point PCR, and 2% (14/692) based on the combination of both methods. However, most (13/14) of these cases did not have evidence of intra-amniotic inflammation and delivered at term. Therefore, a positive culture or end-point PCR in most patients appears to have no apparent clinical significance.<br><br>CONCLUSIONS: Amniotic fluid in the midtrimester of pregnancy generally does not contain bacteria, fungi, or archaea. Interpretation of amniotic fluid culture and molecular microbiologic results is aided by the assessment of the inflammatory state of the amniotic cavity. The presence of microorganisms, as determined by culture or a microbial signal in the absence of intra-amniotic inflammation, appears to be a benign condition.},
}
@article {pmid37192814,
year = {2023},
author = {Grünberger, F and Jüttner, M and Knüppel, R and Ferreira-Cerca, S and Grohmann, D},
title = {Nanopore-based RNA sequencing deciphers the formation, processing, and modification steps of rRNA intermediates in archaea.},
journal = {RNA (New York, N.Y.)},
volume = {29},
number = {8},
pages = {1255-1273},
pmid = {37192814},
issn = {1469-9001},
mesh = {RNA, Ribosomal/genetics ; RNA ; Archaea/genetics ; *Nanopore Sequencing ; DNA, Complementary ; *Nanopores ; Sequence Analysis, RNA ; },
abstract = {Ribosomal RNA (rRNA) maturation in archaea is a complex multistep process that requires well-defined endo- and exoribonuclease activities to generate fully mature linear rRNAs. However, technical challenges prevented detailed mapping of rRNA processing steps and a systematic analysis of rRNA maturation pathways across the tree of life. In this study, we used long-read (PCR)-cDNA and direct RNA nanopore-based sequencing to study rRNA maturation in three archaeal model organisms, namely the Euryarchaea Haloferax volcanii and Pyrococcus furiosus and the Crenarchaeon Sulfolobus acidocaldarius Compared to standard short-read protocols, nanopore sequencing facilitates simultaneous readout of 5'- and 3'-positions, which is required for the classification of rRNA processing intermediates. More specifically, we (i) accurately detect and describe rRNA maturation stages by analysis of terminal read positions of cDNA reads and thereupon (ii) explore the stage-dependent installation of the KsgA-mediated dimethylations in H. volcanii using base-calling and signal characteristics of direct RNA reads. Due to the single-molecule sequencing capacity of nanopore sequencing, we could detect hitherto unknown intermediates with high confidence, revealing details about the maturation of archaea-specific circular rRNA intermediates. Taken together, our study delineates common principles and unique features of rRNA processing in euryarchaeal and crenarchaeal representatives, thereby significantly expanding our understanding of rRNA maturation pathways in archaea.},
}
@article {pmid37171866,
year = {2023},
author = {Pallen, MJ and Rodriguez-R, LM and Alikhan, NF},
title = {Corrigendum: Naming the unnamed: over 65,000 Candidatus names for unnamed Archaea and Bacteria in the Genome Taxonomy Database.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {73},
number = {5},
pages = {},
doi = {10.1099/ijsem.0.005885},
pmid = {37171866},
issn = {1466-5034},
}
@article {pmid37154724,
year = {2023},
author = {Demey, LM and Gumerov, VM and Xing, J and Zhulin, IB and DiRita, VJ},
title = {Transmembrane Transcription Regulators Are Widespread in Bacteria and Archaea.},
journal = {Microbiology spectrum},
volume = {11},
number = {3},
pages = {e0026623},
pmid = {37154724},
issn = {2165-0497},
support = {R35 GM131760/GM/NIGMS NIH HHS/United States ; T32 GM092715/GM/NIGMS NIH HHS/United States ; },
mesh = {Humans ; *Archaea/genetics/metabolism ; *Bacteria/genetics/metabolism ; Cell Membrane/metabolism ; Signal Transduction ; Protein Domains ; Bacterial Proteins/genetics/metabolism ; },
abstract = {To adapt and proliferate, bacteria must sense and respond to the ever-changing environment. Transmembrane transcription regulators (TTRs) are a family of one-component transcription regulators that respond to extracellular information and influence gene expression from the cytoplasmic membrane. How TTRs function to modulate expression of their target genes while localized to the cytoplasmic membrane remains poorly understood. In part, this is due to a lack of knowledge regarding the prevalence of TTRs among prokaryotes. Here, we show that TTRs are highly diverse and prevalent throughout bacteria and archaea. Our work demonstrates that TTRs are more common than previously appreciated and are enriched within specific bacterial and archaeal phyla and that many TTRs have unique transmembrane region properties that can facilitate association with detergent-resistant membranes. IMPORTANCE One-component signal transduction systems are the major class of signal transduction systems among bacteria and are commonly cytoplasmic. TTRs are a group of unique one-component signal transduction systems that influence transcription from the cytoplasmic membrane. TTRs have been implicated in a wide array of biological pathways critical for both pathogens and human commensal organisms but were considered to be rare. Here, we demonstrate that TTRs are in fact highly diverse and broadly distributed in bacteria and archaea. Our findings suggest that transcription factors can access the chromosome and influence transcription from the membrane in both archaea and bacteria. This study challenges thus the commonly held notion that signal transduction systems require a cytoplasmic transcription factor and highlights the importance of the cytoplasmic membrane in directly influencing signal transduction.},
}
@article {pmid37117330,
year = {2023},
author = {Hodgskiss, LH and Melcher, M and Kerou, M and Chen, W and Ponce-Toledo, RI and Savvides, SN and Wienkoop, S and Hartl, M and Schleper, C},
title = {Correction to: Unexpected complexity of the ammonia monooxygenase in archaea.},
journal = {The ISME journal},
volume = {17},
number = {6},
pages = {947},
doi = {10.1038/s41396-023-01403-2},
pmid = {37117330},
issn = {1751-7370},
}
@article {pmid37100405,
year = {2023},
author = {Jaffe, AL and Castelle, CJ and Banfield, JF},
title = {Habitat Transition in the Evolution of Bacteria and Archaea.},
journal = {Annual review of microbiology},
volume = {77},
number = {},
pages = {193-212},
doi = {10.1146/annurev-micro-041320-032304},
pmid = {37100405},
issn = {1545-3251},
mesh = {Animals ; Archaea/genetics ; Bacteria/genetics ; *Bacteriophages ; Genomics ; *Microbiota ; },
abstract = {Related groups of microbes are widely distributed across Earth's habitats, implying numerous dispersal and adaptation events over evolutionary time. However, relatively little is known about the characteristics and mechanisms of these habitat transitions, particularly for populations that reside in animal microbiomes. Here, we review the literature concerning habitat transitions among a variety of bacterial and archaeal lineages, considering the frequency of migration events, potential environmental barriers, and mechanisms of adaptation to new physicochemical conditions, including the modification of protein inventories and other genomic characteristics. Cells dependent on microbial hosts, particularly bacteria from the Candidate Phyla Radiation, have undergone repeated habitat transitions from environmental sources into animal microbiomes. We compare their trajectories to those of both free-living cells-including the Melainabacteria, Elusimicrobia, and methanogenic archaea-and cellular endosymbionts and bacteriophages, which have made similar transitions. We conclude by highlighting major related topics that may be worthy of future study.},
}
@article {pmid37098974,
year = {2023},
author = {Chen, X and Molenda, O and Brown, CT and Toth, CRA and Guo, S and Luo, F and Howe, J and Nesbø, CL and He, C and Montabana, EA and Cate, JHD and Banfield, JF and Edwards, EA},
title = {"Candidatus Nealsonbacteria" Are Likely Biomass Recycling Ectosymbionts of Methanogenic Archaea in a Stable Benzene-Degrading Enrichment Culture.},
journal = {Applied and environmental microbiology},
volume = {89},
number = {5},
pages = {e0002523},
pmid = {37098974},
issn = {1098-5336},
support = {P01 GM051487/GM/NIGMS NIH HHS/United States ; R01 GM065050/GM/NIGMS NIH HHS/United States ; },
mesh = {*Archaea/metabolism ; Benzene/metabolism ; Phylogeny ; Biomass ; RNA, Ribosomal, 16S/genetics/metabolism ; In Situ Hybridization, Fluorescence ; Bacteria/genetics ; *Euryarchaeota/metabolism ; },
abstract = {The Candidate Phyla Radiation (CPR), also referred to as superphylum Patescibacteria, is a very large group of bacteria with no pure culture representatives discovered by 16S rRNA sequencing or genome-resolved metagenomic analyses of environmental samples. Within the CPR, candidate phylum Parcubacteria, previously referred to as OD1, is prevalent in anoxic sediments and groundwater. Previously, we had identified a specific member of the Parcubacteria (referred to as DGGOD1a) as an important member of a methanogenic benzene-degrading consortium. Phylogenetic analyses herein place DGGOD1a within the clade "Candidatus Nealsonbacteria." Because of its persistence over many years, we hypothesized that "Ca. Nealsonbacteria" DGGOD1a must play an important role in sustaining anaerobic benzene metabolism in the consortium. To try to identify its growth substrate, we amended the culture with a variety of defined compounds (pyruvate, acetate, hydrogen, DNA, and phospholipid), as well as crude culture lysate and three subfractions thereof. We observed the greatest (10-fold) increase in the absolute abundance of "Ca. Nealsonbacteria" DGGOD1a only when the consortium was amended with crude cell lysate. These results implicate "Ca. Nealsonbacteria" in biomass recycling. Fluorescence in situ hybridization and cryogenic transmission electron microscope images revealed that "Ca. Nealsonbacteria" DGGOD1a cells were attached to larger archaeal Methanothrix cells. This apparent epibiont lifestyle was supported by metabolic predictions from a manually curated complete genome. This is one of the first examples of bacterial-archaeal episymbiosis and may be a feature of other "Ca. Nealsonbacteria" found in anoxic environments. IMPORTANCE An anaerobic microbial enrichment culture was used to study members of candidate phyla that are difficult to grow in the lab. We were able to visualize tiny "Candidatus Nealsonbacteria" cells attached to a large Methanothrix cell, revealing a novel episymbiosis.},
}
@article {pmid37097839,
year = {2023},
author = {Prakash, O and Dodsworth, JA and Dong, X and Ferry, JG and L'Haridon, S and Imachi, H and Kamagata, Y and Rhee, SK and Sagar, I and Shcherbakova, V and Wagner, D and Whitman, WB},
title = {Proposed minimal standards for description of methanogenic archaea.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {73},
number = {4},
pages = {},
doi = {10.1099/ijsem.0.005500},
pmid = {37097839},
issn = {1466-5034},
mesh = {*Archaea/genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; RNA, Ribosomal, 16S/genetics ; Base Composition ; Bacterial Typing Techniques/methods ; DNA, Bacterial/genetics ; Fatty Acids/chemistry ; *Euryarchaeota/genetics ; Methane/metabolism ; },
abstract = {Methanogenic archaea are a diverse, polyphyletic group of strictly anaerobic prokaryotes capable of producing methane as their primary metabolic product. It has been over three decades since minimal standards for their taxonomic description have been proposed. In light of advancements in technology and amendments in systematic microbiology, revision of the older criteria for taxonomic description is essential. Most of the previously recommended minimum standards regarding phenotypic characterization of pure cultures are maintained. Electron microscopy and chemotaxonomic methods like whole-cell protein and lipid analysis are desirable but not required. Because of advancements in DNA sequencing technologies, obtaining a complete or draft whole genome sequence for type strains and its deposition in a public database are now mandatory. Genomic data should be used for rigorous comparison to close relatives using overall genome related indices such as average nucleotide identity and digital DNA-DNA hybridization. Phylogenetic analysis of the 16S rRNA gene is also required and can be supplemented by phylogenies of the mcrA gene and phylogenomic analysis using multiple conserved, single-copy marker genes. Additionally, it is now established that culture purity is not essential for studying prokaryotes, and description of Candidatus methanogenic taxa using single-cell or metagenomics along with other appropriate criteria is a viable alternative. The revisions to the minimal criteria proposed here by the members of the Subcommittee on the Taxonomy of Methanogenic Archaea of the International Committee on Systematics of Prokaryotes should allow for rigorous yet practical taxonomic description of these important and diverse microbes.},
}
@article {pmid37093039,
year = {2023},
author = {Dithugoe, CD and Bezuidt, OKI and Cavan, EL and Froneman, WP and Thomalla, SJ and Makhalanyane, TP},
title = {Bacteria and Archaea Regulate Particulate Organic Matter Export in Suspended and Sinking Marine Particle Fractions.},
journal = {mSphere},
volume = {8},
number = {3},
pages = {e0042022},
pmid = {37093039},
issn = {2379-5042},
support = {0182/2017//Department of Science and Technology, Republic of South Africa (DST)/ ; 110729//National Research Foundation (NRF)/ ; 148867//National Research Foundation (NRF)/ ; },
mesh = {*Archaea/genetics/metabolism ; *Seawater/microbiology ; Particulate Matter/metabolism ; Bacteria/genetics/metabolism ; Dissolved Organic Matter ; Carbon/metabolism ; },
abstract = {The biological carbon pump (BCP) in the Southern Ocean is driven by phytoplankton productivity and is a significant organic matter sink. However, the role of particle-attached (PA) and free-living (FL) prokaryotes (bacteria and archaea) and their diversity in influencing the efficiency of the BCP is still unclear. To investigate this, we analyzed the metagenomes linked to suspended and sinking marine particles from the Sub-Antarctic Southern Ocean Time Series (SOTS) by deploying a Marine Snow Catcher (MSC), obtaining suspended and sinking particulate material, determining organic carbon and nitrogen flux, and constructing metagenome-assembled genomes (MAGs). The suspended and sinking particle-pools were dominated by bacteria with the potential to degrade organic carbon. Bacterial communities associated with the sinking fraction had more genes related to the degradation of complex organic carbon than those in the suspended fraction. Archaea had the potential to drive nitrogen metabolism via nitrite and ammonia oxidation, altering organic nitrogen concentration. The data revealed several pathways for chemoautotrophy and the secretion of recalcitrant dissolved organic carbon (RDOC) from CO2, with bacteria and archaea potentially sequestering particulate organic matter (POM) via the production of RDOC. These findings provide insights into the diversity and function of prokaryotes in suspended and sinking particles and their role in organic carbon/nitrogen export in the Southern Ocean. IMPORTANCE The biological carbon pump is crucial for the export of particulate organic matter in the ocean. Recent studies on marine microbes have shown the profound influence of bacteria and archaea as regulators of particulate organic matter export. Yet, despite the importance of the Southern Ocean as a carbon sink, we lack comparable insights regarding microbial contributions. This study provides the first insights regarding prokaryotic contributions to particulate organic matter export in the Southern Ocean. We reveal evidence that prokaryotic communities in suspended and sinking particle fractions harbor widespread genomic potential for mediating particulate organic matter export. The results substantially enhance our understanding of the role played by microorganisms in regulating particulate organic matter export in suspended and sinking marine fractions in the Southern Ocean.},
}
@article {pmid37083735,
year = {2023},
author = {Roux, S and Camargo, AP and Coutinho, FH and Dabdoub, SM and Dutilh, BE and Nayfach, S and Tritt, A},
title = {iPHoP: An integrated machine learning framework to maximize host prediction for metagenome-derived viruses of archaea and bacteria.},
journal = {PLoS biology},
volume = {21},
number = {4},
pages = {e3002083},
pmid = {37083735},
issn = {1545-7885},
mesh = {*Archaea/genetics ; Metagenome/genetics ; *Viruses/genetics ; Bacteria/genetics ; Metagenomics/methods ; Machine Learning ; Genome, Viral/genetics ; },
abstract = {The extraordinary diversity of viruses infecting bacteria and archaea is now primarily studied through metagenomics. While metagenomes enable high-throughput exploration of the viral sequence space, metagenome-derived sequences lack key information compared to isolated viruses, in particular host association. Different computational approaches are available to predict the host(s) of uncultivated viruses based on their genome sequences, but thus far individual approaches are limited either in precision or in recall, i.e., for a number of viruses they yield erroneous predictions or no prediction at all. Here, we describe iPHoP, a two-step framework that integrates multiple methods to reliably predict host taxonomy at the genus rank for a broad range of viruses infecting bacteria and archaea, while retaining a low false discovery rate. Based on a large dataset of metagenome-derived virus genomes from the IMG/VR database, we illustrate how iPHoP can provide extensive host prediction and guide further characterization of uncultivated viruses.},
}
@article {pmid37082172,
year = {2023},
author = {Zhang, Z and Fusco, S},
title = {Editorial: New insights into the genetic mechanisms of thermophilic archaea.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1185784},
pmid = {37082172},
issn = {1664-302X},
}
@article {pmid37072332,
year = {2023},
author = {Nikonov, OS and Nikonova, EY and Tarabarova, AG and Mikhaylina, AO and Kravchenko, OV and Nevskaya, NA and Nikonov, SV},
title = {Recognition of γ-Subunit by β-Subunit in Translation Initiation Factor 2. Stabilization of the GTP-Bound State of I/F 2 in Archaea and Eukaryotes.},
journal = {Biochemistry. Biokhimiia},
volume = {88},
number = {2},
pages = {221-230},
doi = {10.1134/S0006297923020062},
pmid = {37072332},
issn = {1608-3040},
mesh = {Binding Sites ; *Prokaryotic Initiation Factor-2/chemistry ; *Eukaryota/genetics/metabolism ; Archaea/genetics/metabolism ; Guanosine Triphosphate ; },
abstract = {Eukaryotic and archaeal translation initiation factor 2 (e/aIF2) functions as a heterotrimeric complex. It consists of three subunits (α, β, γ). α- and β-subunits are bound to γ-subunit by hydrogen bonds and van der Waals interactions, but do not contact each other. Although main functions of the factor are performed by the γ-subunit, reliable formation of αγ and βγ complexes is necessary for its proper functioning. In this work, we introduced mutations in the recognition part of the βγ interface and showed that hydrophobic effect plays a crucial role in the recognition of subunits both in eukaryotes and archaea. Shape and properties of the groove on the surface of γ-subunit facilitates transition of the disordered recognition part of the β-subunit into an α-helix containing approximately the same number of residues in archaea and eukaryotes. In addition, based on the newly obtained data, it was concluded that in archaea and eukaryotes, transition of the γ-subunit to the active state leads to additional contact between the region of switch 1 and C-terminal part of the β-subunit, which stabilizes helical conformation of the switch.},
}
@article {pmid37066253,
year = {2023},
author = {Cerna-Vargas, JP and Gumerov, VM and Krell, T and Zhulin, IB},
title = {Amine recognizing domain in diverse receptors from bacteria and archaea evolved from the universal amino acid sensor.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {37066253},
issn = {2692-8205},
support = {R35 GM131760/GM/NIGMS NIH HHS/United States ; },
abstract = {Bacteria contain many different receptor families that sense different signals permitting an optimal adaptation to the environment. A major limitation in microbiology is the lack of information on the signal molecules that activate receptors. Due to a significant sequence divergence, the signal recognized by sensor domains is only poorly reflected in overall sequence identity. Biogenic amines are of central physiological relevance for microorganisms and serve for example as substrates for aerobic and anaerobic growth, neurotransmitters or osmoprotectants. Based on protein structural information and sequence analysis, we report here the identification of a sequence motif that is specific for amine-sensing dCache sensor domains (dCache_1AM). These domains were identified in more than 13,000 proteins from 8,000 bacterial and archaeal species. dCache_1AM containing receptors were identified in all major receptor families including sensor kinases, chemoreceptors, receptors involved in second messenger homeostasis and Ser/Thr phosphatases. The screening of compound libraries and microcalorimetric titrations of selected dCache_1AM domains confirmed their capacity to specifically bind amines. Mutants in the amine binding motif or domains that contain a single mismatch in the binding motif, had either no or a largely reduced affinity for amines, illustrating the specificity of this motif. We demonstrate that the dCache_1AM domain has evolved from the universal amino acid sensing domain, providing novel insight into receptor evolution. Our approach enables precise "wet"-lab experiments to define the function of regulatory systems and thus holds a strong promise to address an important bottleneck in microbiology: the identification of signals that stimulate numerous receptors.},
}
@article {pmid37066119,
year = {2023},
author = {Lach, J and Strapagiel, D and Matera-Witkiewicz, A and Stączek, P},
title = {Draft genomes of halophilic Archaea strains isolated from brines of the Carpathian Foreland, Poland.},
journal = {Journal of genomics},
volume = {11},
number = {},
pages = {20-25},
pmid = {37066119},
issn = {1839-9940},
abstract = {Halophilic Archaea are a unique group of microorganisms living in saline environments. They constitute a complex group whose biodiversity has not been thoroughly studied. Here, we report three draft genomes of halophilic Archaea isolated from brines, representing the genera of Halorubrum, Halopenitus, and Haloarcula. Two of these strains, Boch-26 and POP-27, were identified as members of the genera Halorubrum and Halopenitus, respectively. However, they could not be assigned to any known species because of the excessive difference in genome sequences between these strains and any other described genomes. In contrast, the third strain, Boch-26, was identified as Haloarcula hispanica. Genome lengths of these isolates ranged from 2.7 Mbp to 3.0 Mbp, and GC content was in the 63.77%-68.77% range. Moreover, functional analysis revealed biosynthetic gene clusters (BGCs) related to terpenes production in all analysed genomes and one BGC for RRE (RiPP recognition element)-dependent RiPP (post-translationally modified peptides) biosynthesis. Moreover, the obtained results enhanced the knowledge about the salt mines microbiota biodiversity as a poorly explored environment so far.},
}
@article {pmid37060102,
year = {2023},
author = {Liang, H and Song, ZM and Zhong, Z and Zhang, D and Yang, W and Zhou, L and Older, EA and Li, J and Wang, H and Zeng, Z and Li, YX},
title = {Genomic and metabolic analyses reveal antagonistic lanthipeptides in archaea.},
journal = {Microbiome},
volume = {11},
number = {1},
pages = {74},
pmid = {37060102},
issn = {2049-2618},
mesh = {*Archaea/genetics/metabolism ; *Archaeal Proteins/genetics/metabolism ; Bacteria/genetics ; Genomics ; Microbial Interactions ; },
abstract = {BACKGROUND: Microbes produce diverse secondary metabolites (SMs) such as signaling molecules and antimicrobials that mediate microbe-microbe interaction. Archaea, the third domain of life, are a large and diverse group of microbes that not only exist in extreme environments but are abundantly distributed throughout nature. However, our understanding of archaeal SMs lags far behind our knowledge of those in bacteria and eukarya.<br><br>RESULTS: Guided by genomic and metabolic analysis of archaeal SMs, we discovered two new lanthipeptides with distinct ring topologies from a halophilic archaeon of class Haloarchaea. Of these two lanthipeptides, archalan &#x3b1; exhibited anti-archaeal activities against halophilic archaea, potentially mediating the archaeal antagonistic interactions in the halophilic niche. To our best knowledge, archalan &#x3b1; represents the first lantibiotic and the first anti-archaeal SM from the archaea domain.<br><br>CONCLUSIONS: Our study investigates the biosynthetic potential of lanthipeptides in archaea, linking lanthipeptides to antagonistic interaction via genomic and metabolic analyses and bioassay. The discovery of these archaeal lanthipeptides is expected to stimulate the experimental study of poorly characterized archaeal chemical biology and highlight the potential of archaea as a new source of bioactive SMs. Video Abstract.},
}
@article {pmid37014908,
year = {2023},
author = {Cumsille, A and Durán, RE and Rodríguez-Delherbe, A and Saona-Urmeneta, V and Cámara, B and Seeger, M and Araya, M and Jara, N and Buil-Aranda, C},
title = {GenoVi, an open-source automated circular genome visualizer for bacteria and archaea.},
journal = {PLoS computational biology},
volume = {19},
number = {4},
pages = {e1010998},
pmid = {37014908},
issn = {1553-7358},
mesh = {*Archaea/genetics ; *Bacteria/genetics ; Genomics/methods ; Software ; Genome, Microbial ; },
abstract = {The increase in microbial sequenced genomes from pure cultures and metagenomic samples reflects the current attainability of whole-genome and shotgun sequencing methods. However, software for genome visualization still lacks automation, integration of different analyses, and customizable options for non-experienced users. In this study, we introduce GenoVi, a Python command-line tool able to create custom circular genome representations for the analysis and visualization of microbial genomes and sequence elements. It is designed to work with complete or draft genomes, featuring customizable options including 25 different built-in color palettes (including 5 color-blind safe palettes), text formatting options, and automatic scaling for complete genomes or sequence elements with more than one replicon/sequence. Using a Genbank format file as the input file or multiple files within a directory, GenoVi (i) visualizes genomic features from the GenBank annotation file, (ii) integrates a Cluster of Orthologs Group (COG) categories analysis using DeepNOG, (iii) automatically scales the visualization of each replicon of complete genomes or multiple sequence elements, (iv) and generates COG histograms, COG frequency heatmaps and output tables including general stats of each replicon or contig processed. GenoVi's potential was assessed by analyzing single and multiple genomes of Bacteria and Archaea. Paraburkholderia genomes were analyzed to obtain a fast classification of replicons in large multipartite genomes. GenoVi works as an easy-to-use command-line tool and provides customizable options to automatically generate genomic maps for scientific publications, educational resources, and outreach activities. GenoVi is freely available and can be downloaded from https://github.com/robotoD/GenoVi.},
}
@article {pmid37005419,
year = {2023},
author = {Tang, SK and Zhi, XY and Zhang, Y and Makarova, KS and Liu, BB and Zheng, GS and Zhang, ZP and Zheng, HJ and Wolf, YI and Zhao, YR and Jiang, SH and Chen, XM and Li, EY and Zhang, T and Chen, PR and Feng, YZ and Xiang, MX and Lin, ZQ and Shi, JH and Chang, C and Zhang, X and Li, R and Lou, K and Wang, Y and Chang, L and Yin, M and Yang, LL and Gao, HY and Zhang, ZK and Tao, TS and Guan, TW and He, FC and Lu, YH and Cui, HL and Koonin, EV and Zhao, GP and Xu, P},
title = {Cellular differentiation into hyphae and spores in halophilic archaea.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {1827},
pmid = {37005419},
issn = {2041-1723},
mesh = {Hyphae/genetics ; Proteomics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Streptomyces/genetics ; *Halobacteriaceae/genetics ; Spores ; Cell Differentiation ; Sequence Analysis, DNA ; China ; },
abstract = {Several groups of bacteria have complex life cycles involving cellular differentiation and multicellular structures. For example, actinobacteria of the genus Streptomyces form multicellular vegetative hyphae, aerial hyphae, and spores. However, similar life cycles have not yet been described for archaea. Here, we show that several haloarchaea of the family Halobacteriaceae display a life cycle resembling that of Streptomyces bacteria. Strain YIM 93972 (isolated from a salt marsh) undergoes cellular differentiation into mycelia and spores. Other closely related strains are also able to form mycelia, and comparative genomic analyses point to gene signatures (apparent gain or loss of certain genes) that are shared by members of this clade within the Halobacteriaceae. Genomic, transcriptomic and proteomic analyses of non-differentiating mutants suggest that a Cdc48-family ATPase might be involved in cellular differentiation in strain YIM 93972. Additionally, a gene encoding a putative oligopeptide transporter from YIM 93972 can restore the ability to form hyphae in a Streptomyces coelicolor mutant that carries a deletion in a homologous gene cluster (bldKA-bldKE), suggesting functional equivalence. We propose strain YIM 93972 as representative of a new species in a new genus within the family Halobacteriaceae, for which the name Actinoarchaeum halophilum gen. nov., sp. nov. is herewith proposed. Our demonstration of a complex life cycle in a group of haloarchaea adds a new dimension to our understanding of the biological diversity and environmental adaptation of archaea.},
}
@article {pmid37000350,
year = {2023},
author = {Hu, Y and Ma, X and Li, XX and Tan, S and Cheng, M and Hou, J and Cui, HL},
title = {Natrinema caseinilyticum sp. nov., Natrinema gelatinilyticum sp. nov., Natrinema marinum sp. nov., Natrinema zhouii sp. nov., extremely halophilic archaea isolated from marine environments and a salt mine.},
journal = {Extremophiles : life under extreme conditions},
volume = {27},
number = {1},
pages = {9},
pmid = {37000350},
issn = {1433-4909},
support = {32070003//National Natural Science Foundation of China/ ; },
mesh = {Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Glycolipids ; Sodium Chloride ; *Halobacteriaceae/genetics ; China ; DNA, Archaeal/genetics ; Sequence Analysis, DNA ; },
abstract = {Four extremely halophilic archaeal strains (ZJ2[T], BND6[T], DT87[T], and YPL30[T]) were isolated from marine environments and a salt mine in China. The 16S rRNA and rpoB' gene sequence similarities among strains ZJ2[T], BND6[T], DT87[T], YPL30[T] and the current species of Natrinema were 93.2-99.3% and 89.2-95.8%, respectively. Both phylogenetic and phylogenomic analyses revealed that strains ZJ2[T], BND6[T], DT87[T], and YPL30[T] cluster with the Natrinema members. The overall genome-related indexes (ANI, isDDH, and AAI) among these four strains and the current species of genus Natrinema were 70-88%, 22-43% and 75-89%, respectively, clearly below the threshold values for species boundary. Strains ZJ2[T], BND6[T], DT87[T], and YPL30[T] could be distinguished from the related species according to differential phenotypic characteristics. The major polar lipids of the four strains were phosphatidic acid (PA), phosphatidylglycerol (PG), phosphatidylglycerol phosphate methyl ester (PGP-Me), sulfated mannosyl glucosyl diether (S-DGD-1), and disulfated mannosyl glucosyl diether (S2-DGD). The phenotypic, chemotaxonomic, phylogenetic and phylogenomic features indicated that strains ZJ2[T] (= CGMCC 1.18786[ T] = JCM 34918[ T]), BND6[T] (= CGMCC 1.18777[ T] = JCM 34909[ T]), DT87[T] (= CGMCC 1.18921[ T] = JCM 35420[ T]), and YPL30[T] (= CGMCC 1.15337[ T] = JCM 31113[ T]) represent four novel species of the genus Natrinema, for which the names, Natrinema caseinilyticum sp. nov., Natrinema gelatinilyticum sp. nov., Natrinema marinum sp. nov., and Natrinema zhouii sp. nov., are proposed.},
}
@article {pmid37000227,
year = {2023},
author = {Iguchi, A and Takemura, Y and Danshita, T and Kurihara, T and Aoki, M and Hori, S and Shigematsu, T and Syutsubo, K},
title = {Isolation and physiological properties of methanogenic archaea that degrade tetramethylammonium hydroxide.},
journal = {Applied microbiology and biotechnology},
volume = {107},
number = {9},
pages = {3047-3056},
pmid = {37000227},
issn = {1432-0614},
mesh = {*Archaea/genetics/metabolism ; Wastewater ; Sewage/chemistry ; In Situ Hybridization, Fluorescence ; RNA, Ribosomal, 16S/genetics/metabolism ; Bioreactors ; *Euryarchaeota/metabolism ; Methanosarcinaceae/genetics ; Anaerobiosis ; Waste Disposal, Fluid/methods ; },
abstract = {Tetramethylammonium hydroxide (TMAH) is a known toxic chemical used in the photolithography process of semiconductor photoelectronic processes. Significant amounts of wastewater containing TMAH are discharged from electronic industries. It is therefore attractive to apply anaerobic treatment to industrial wastewater containing TMAH. In this study, a novel TMAH-degrading methanogenic archaeon was isolated from the granular sludge of a psychrophilic upflow anaerobic sludge blanket (UASB) reactor treating synthetic wastewater containing TMAH. Although the isolate (strain NY-STAYD) was phylogenetically related to Methanomethylovorans uponensis, it was the only isolated Methanomethylovorans strain capable of TMAH degradation. Strain NY-STAYD was capable of degrading methylamine compounds, similar to the previously isolated Methanomethylovorans spp. While the strain was able to grow at temperatures ranging from 15 to 37°C, the cell yield was higher at lower temperatures. The distribution of archaeal cells affiliated with the genus Methanomethylovorans in the original granular sludge was investigated by fluorescence in situ hybridization (FISH) using specific oligonucleotide probe targeting 16S rRNA. The results demonstrated that the TMAH-degrading cells associated with the genus Methanomethylovorans were not intermingled with other microorganisms but rather isolated on the granule's surface as a lone dominant archaeon. KEY POINTS: • A TMAH-degrading methanogenic Methanomethylovorans strain was isolated • This strain was the only known Methanomethylovorans isolate that can degrade TMAH • The highest cell yield of the isolate was obtained at psychrophilic conditions.},
}
@article {pmid36999249,
year = {2023},
author = {D'Alò, F and Zucconi, L and Onofri, S and Canini, F and Cannone, N and Malfasi, F and Morais, DK and Starke, R},
title = {Effects of 5-year experimental warming in the Alpine belt on soil Archaea: Multi-omics approaches and prospects.},
journal = {Environmental microbiology reports},
volume = {15},
number = {4},
pages = {291-297},
pmid = {36999249},
issn = {1758-2229},
mesh = {*Archaea/genetics ; *Soil/chemistry ; Multiomics ; Climate Change ; Italy ; Soil Microbiology ; },
abstract = {We currently lack a predictive understanding of how soil archaeal communities may respond to climate change, particularly in Alpine areas where warming is far exceeding the global average. Here, we characterized the abundance, structure, and function of total (by metagenomics) and active soil archaea (by metatranscriptomics) after 5-year experimental field warming (+1°C) in Italian Alpine grasslands and snowbeds. Our multi-omics approach unveiled an increasing abundance of Archaea during warming in snowbeds, which was negatively correlated with the abundance of fungi (by qPCR) and micronutrients (Ca and Mg), but positively correlated with soil water content. In the snowbeds transcripts, warming resulted in the enrichment of abundances of transcription and nucleotide biosynthesis. Our study provides novel insights into possible changes in soil Archaea composition and function in the climate change scenario.},
}
@article {pmid36985233,
year = {2023},
author = {Cisek, AA and Bąk, I and Cukrowska, B},
title = {Improved Quantitative Real-Time PCR Protocol for Detection and Quantification of Methanogenic Archaea in Stool Samples.},
journal = {Microorganisms},
volume = {11},
number = {3},
pages = {},
pmid = {36985233},
issn = {2076-2607},
support = {2017/25/N/NZ7/02905//National Science Center/ ; },
abstract = {Methanogenic archaea are an important component of the human and animal intestinal microbiota, and yet their presence is rarely reported in publications describing the subject. One of the methods of quantifying the prevalence of methanogens is quantitative real-time PCR (qPCR) of the methanogen-specific mcrA gene, and one of the possible reasons for detection failure is usually a methodology bias. Here, we refined the existing protocol by changing one of the primers and improving the conditions of the qPCR reaction. As a result, at the expense of a slightly lower yet acceptable PCR efficiency, the new assay was characterized by increased specificity and sensitivity and a wider linear detection range of 7 orders of magnitude. The lowest copy number of mcrA quantified at a frequency of 100% was 21 copies per reaction. The other validation parameters tested, such as reproducibility and linearity, also gave satisfactory results. Overall, we were able to minimize the negative impacts of primer dimerization and other cross-reactions on qPCR and increase the number of not only detectable but also quantifiable stool samples-or in this case, chicken droppings.},
}
@article {pmid36985129,
year = {2023},
author = {Slobodkin, AI and Ratnikova, NM and Slobodkina, GB and Klyukina, AA and Chernyh, NA and Merkel, AY},
title = {Composition and Metabolic Potential of Fe(III)-Reducing Enrichment Cultures of Methanotrophic ANME-2a Archaea and Associated Bacteria.},
journal = {Microorganisms},
volume = {11},
number = {3},
pages = {},
pmid = {36985129},
issn = {2076-2607},
support = {22-14-00011//Russian Science Foundation/ ; No number//Ministry of Science and Higher Education of the Russian Federation/ ; },
abstract = {The key microbial group involved in anaerobic methane oxidation is anaerobic methanotrophic archaea (ANME). From a terrestrial mud volcano, we enriched a microbial community containing ANME-2a, using methane as an electron donor, Fe(III) oxide (ferrihydrite) as an electron acceptor, and anthraquinone-2,6-disulfonate as an electron shuttle. Ferrihydrite reduction led to the formation of a black, highly magnetic precipitate. A significant relative abundance of ANME-2a in batch cultures was observed over five subsequent transfers. Phylogenetic analysis revealed that, in addition to ANME-2a, two bacterial taxa belonging to uncultured Desulfobulbaceae and Anaerolineaceae were constantly present in all enrichments. Metagenome-assembled genomes (MAGs) of ANME-2a contained a complete set of genes for methanogenesis and numerous genes of multiheme c-type cytochromes (MHC), indicating the capability of methanotrophs to transfer electrons to metal oxides or to a bacterial partner. One of the ANME MAGs encoded respiratory arsenate reductase (Arr), suggesting the potential for a direct coupling of methane oxidation with As(V) reduction in the single microorganism. The same MAG also encoded uptake [NiFe] hydrogenase, which is uncommon for ANME-2. The MAG of uncultured Desulfobulbaceae contained genes of dissimilatory sulfate reduction, a Wood-Ljungdahl pathway for autotrophic CO2 fixation, hydrogenases, and 43 MHC. We hypothesize that uncultured Desulfobulbaceae is a bacterial partner of ANME-2a, which mediates extracellular electron transfer to Fe(III) oxide.},
}
@article {pmid36949474,
year = {2023},
author = {Regueira-Iglesias, A and Vázquez-González, L and Balsa-Castro, C and Vila-Blanco, N and Blanco-Pintos, T and Tamames, J and Carreira, MJ and Tomás, I},
title = {In silico evaluation and selection of the best 16S rRNA gene primers for use in next-generation sequencing to detect oral bacteria and archaea.},
journal = {Microbiome},
volume = {11},
number = {1},
pages = {58},
pmid = {36949474},
issn = {2049-2618},
mesh = {Humans ; *Archaea/genetics ; RNA, Ribosomal, 16S/genetics ; Genes, rRNA ; DNA Primers/genetics ; Bacteria/genetics ; *Microbiota/genetics ; High-Throughput Nucleotide Sequencing/methods ; Phylogeny ; },
abstract = {BACKGROUND: Sequencing has been widely used to study the composition of the oral microbiome present in various health conditions. The extent of the coverage of the 16S rRNA gene primers employed for this purpose has not, however, been evaluated in silico using oral-specific databases. This paper analyses these primers using two databases containing 16S rRNA sequences from bacteria and archaea found in the human mouth and describes some of the best primers for each domain.<br><br>RESULTS: A total of 369 distinct individual primers were identified from sequencing studies of the oral microbiome and other ecosystems. These were evaluated against a database reported in the literature of 16S rRNA sequences obtained from oral bacteria, which was modified by our group, and a self-created oral archaea database. Both databases contained the genomic variants detected for each included species. Primers were evaluated at the variant and species levels, and those with a species coverage (SC) &#x2265;75.00% were selected for the pair analyses. All possible combinations of the forward and reverse primers were identified, with the resulting 4638 primer pairs also evaluated using the two databases. The best bacteria-specific pairs targeted the 3-4, 4-7, and 3-7 16S rRNA gene regions, with SC levels of 98.83-97.14%; meanwhile, the optimum archaea-specific primer pairs amplified regions 5-6, 3-6, and 3-6, with SC estimates of 95.88%. Finally, the best pairs for detecting both domains targeted regions 4-5, 3-5, and 5-9, and produced SC values of 95.71-94.54% and 99.48-96.91% for bacteria and archaea, respectively.<br><br>CONCLUSIONS: Given the three amplicon length categories (100-300, 301-600, and >600 base&#xa0;pairs), the primer pairs with the best coverage values for detecting oral bacteria were as follows: KP_F048-OP_R043 (region 3-4; primer pair position for Escherichia coli J01859.1: 342-529), KP_F051-OP_R030 (4-7; 514-1079), and KP_F048-OP_R030 (3-7; 342-1079). For detecting oral archaea, these were as follows: OP_F066-KP_R013 (5-6; 784-undefined), KP_F020-KP_R013 (3-6; 518-undefined), and OP_F114-KP_R013 (3-6; 340-undefined). Lastly, for detecting both domains jointly they were KP_F020-KP_R032 (4-5; 518-801), OP_F114-KP_R031 (3-5; 340-801), and OP_F066-OP_R121 (5-9; 784-1405). The primer pairs with the best coverage identified herein are not among those described most widely in the oral microbiome literature. Video Abstract.},
}
@article {pmid36949220,
year = {2023},
author = {Lynes, MM and Krukenberg, V and Jay, ZJ and Kohtz, AJ and Gobrogge, CA and Spietz, RL and Hatzenpichler, R},
title = {Diversity and function of methyl-coenzyme M reductase-encoding archaea in Yellowstone hot springs revealed by metagenomics and mesocosm experiments.},
journal = {ISME communications},
volume = {3},
number = {1},
pages = {22},
pmid = {36949220},
issn = {2730-6151},
support = {DBI-1736255//National Science Foundation (NSF)/ ; DBI-1736255//National Science Foundation (NSF)/ ; DBI-1736255//National Science Foundation (NSF)/ ; DBI-1736255//National Science Foundation (NSF)/ ; DBI-1736255//National Science Foundation (NSF)/ ; DBI-1736255//National Science Foundation (NSF)/ ; DBI-1736255//National Science Foundation (NSF)/ ; },
abstract = {Metagenomic studies on geothermal environments have been central in recent discoveries on the diversity of archaeal methane and alkane metabolism. Here, we investigated methanogenic populations inhabiting terrestrial geothermal features in Yellowstone National Park (YNP) by combining amplicon sequencing with metagenomics and mesocosm experiments. Detection of methyl-coenzyme M reductase subunit A (mcrA) gene amplicons demonstrated a wide diversity of Mcr-encoding archaea inhabit geothermal features with differing physicochemical regimes across YNP. From three selected hot springs we recovered twelve Mcr-encoding metagenome assembled genomes (MAGs) affiliated with lineages of cultured methanogens as well as Candidatus (Ca.) Methanomethylicia, Ca. Hadesarchaeia, and Archaeoglobi. These MAGs encoded the potential for hydrogenotrophic, aceticlastic, hydrogen-dependent methylotrophic methanogenesis, or anaerobic short-chain alkane oxidation. While Mcr-encoding archaea represent minor fractions of the microbial community of hot springs, mesocosm experiments with methanogenic precursors resulted in the stimulation of methanogenic activity and the enrichment of lineages affiliated with Methanosaeta and Methanothermobacter as well as with uncultured Mcr-encoding archaea including Ca. Korarchaeia, Ca. Nezhaarchaeia, and Archaeoglobi. We revealed that diverse Mcr-encoding archaea with the metabolic potential to produce methane from different precursors persist in the geothermal environments of YNP and can be enriched under methanogenic conditions. This study highlights the importance of combining environmental metagenomics with laboratory-based experiments to expand our understanding of uncultured Mcr-encoding archaea and their potential impact on microbial carbon transformations in geothermal environments and beyond.},
}
@article {pmid36927099,
year = {2023},
author = {Chen, J and Li, Y and Zhong, C and Xu, Z and Lu, G and Jing, H and Liu, H},
title = {Genomic Insights into Niche Partitioning across Sediment Depth among Anaerobic Methane-Oxidizing Archaea in Global Methane Seeps.},
journal = {mSystems},
volume = {8},
number = {2},
pages = {e0117922},
pmid = {36927099},
issn = {2379-5077},
mesh = {*Archaea/genetics ; Anaerobiosis ; *Methane/metabolism ; Oxidation-Reduction ; Metagenomics ; },
abstract = {Marine sediments are important methane reservoirs. Methane efflux from the seabed is significantly restricted by anaerobic methanotrophic (ANME) archaea through a process known as anaerobic oxidation of methane (AOM). Different clades of ANME archaea occupy distinct niches in methane seeps, but their underlying molecular mechanisms still need to be fully understood. To provide genetic explanations for the niche partitioning of ANME archaea, we applied comparative genomic analysis to ANME archaeal genomes retrieved from global methane seeps. Our results showed that ANME-2 archaea are more prevalent than ANME-1 archaea in shallow sediments because they carry genes that encode a significantly higher number of outer membrane multiheme c-type cytochromes and flagellar proteins. These features make ANME-2 archaea perform direct interspecies electron transfer better and benefit more from electron acceptors in AOM. Besides, ANME-2 archaea carry genes that encode extra peroxidase compared to ANME-1 archaea, which may lead to ANME-2 archaea better tolerating oxygen toxicity. In contrast, ANME-1 archaea are more competitive in deep layers than ANME-2 archaea because they carry extra genes (mtb and mtt) for methylotrophic methanogenesis and a significantly higher number of frh and mvh genes for hydrogenotrophic methanogenesis. Additionally, ANME-1 archaea carry exclusive genes (sqr, TST, and mddA) involved in sulfide detoxification compared to ANME-2 archaea, leading to stronger sulfide tolerance. Overall, this study reveals the genomic mechanisms shaping the niche partitioning among ANME archaea in global methane seeps. IMPORTANCE Anaerobic methanotrophic (ANME) archaea are important methanotrophs in marine sediment, controlling the flux of biologically generated methane, which plays an essential role in the marine carbon cycle and climate change. So far, no strain of this lineage has been isolated in pure culture, which makes metagenomics one of the fundamental approaches to reveal their metabolic potential. Although the niche partitioning of ANME archaea was frequently reported in different studies, whether this pattern was consistent in global methane seeps had yet to be verified, and little was known about the genetic mechanisms underlying it. Here, we reviewed and analyzed the community structure of ANME archaea in global methane seeps and indicated that the niche partitioning of ANME archaea was statistically supported. Our comparative genomic analysis indicated that the capabilities of interspecies electron transfer, methanogenesis, and the resistance of oxygen and hydrogen sulfide could be critical in defining the distribution of ANME archaea in methane seep sediment.},
}
@article {pmid36920214,
year = {2023},
author = {Adlung, N and Scheller, S},
title = {Application of the Fluorescence-Activating and Absorption-Shifting Tag (FAST) for Flow Cytometry in Methanogenic Archaea.},
journal = {Applied and environmental microbiology},
volume = {89},
number = {4},
pages = {e0178622},
pmid = {36920214},
issn = {1098-5336},
mesh = {*Archaea/metabolism ; Flow Cytometry ; *Methane/metabolism ; Methanosarcina/metabolism ; },
abstract = {Methane-producing archaea play a crucial role in the global carbon cycle and are used for biotechnological fuel production. Methanogenic model organisms such as Methanococcus maripaludis and Methanosarcina acetivorans have been biochemically characterized and can be genetically engineered by using a variety of existing molecular tools. The anaerobic lifestyle and autofluorescence of methanogens, however, restrict the use of common fluorescent reporter proteins (e.g., GFP and derivatives), which require oxygen for chromophore maturation. Recently, the use of a novel oxygen-independent fluorescent activation and absorption-shifting tag (FAST) was demonstrated with M. maripaludis. Similarly, we now describe the use of the tandem activation and absorption-shifting tag protein 2 (tdFAST2), which fluoresces when the cell-permeable fluorescent ligand (fluorogen) 4-hydroxy-3,5-dimethoxybenzylidene rhodanine (HBR-3,5DOM) is present. Expression of tdFAST2 in M. acetivorans and M. maripaludis is noncytotoxic and tdFAST2:HBR-3,5DOM fluorescence is clearly distinguishable from the autofluorescence. In flow cytometry experiments, mixed methanogen cultures can be distinguished, thereby allowing for the possibility of high-throughput investigations of the characteristic dynamics within single and mixed cultures. IMPORTANCE Methane-producing archaea play an essential role in the global carbon cycle and demonstrate great potential for various biotechnological applications, e.g., biofuel production, carbon dioxide capture, and electrochemical systems. Oxygen sensitivity and high autofluorescence hinder the use of common fluorescent proteins for studying methanogens. By using tdFAST2:HBR-3,5DOM fluorescence, which functions under anaerobic conditions and is distinguishable from the autofluorescence, real-time reporter studies and high-throughput investigation of the mixed culture dynamics of methanogens via flow cytometry were made possible. This will further help accelerate the sustainable exploitation of methanogens.},
}
@article {pmid36912626,
year = {2023},
author = {Li, D and Ren, Z and Zhou, Y and Jiang, L and Zheng, M and Liu, G},
title = {Comammox Nitrospira and Ammonia-Oxidizing Archaea Are Dominant Ammonia Oxidizers in Sediments of an Acid Mine Lake Containing High Ammonium Concentrations.},
journal = {Applied and environmental microbiology},
volume = {89},
number = {3},
pages = {e0004723},
pmid = {36912626},
issn = {1098-5336},
mesh = {Humans ; Archaea/metabolism ; Ammonia/metabolism ; *Ammonium Compounds/metabolism ; Lakes ; RNA, Ribosomal, 16S/genetics/metabolism ; Oxidation-Reduction ; Bacteria ; Nitrification ; Phylogeny ; *Leukemia, Myeloid, Acute ; },
abstract = {Exploring nitrifiers in extreme environments is vital to expanding our understanding of nitrogen cycle and microbial diversity. This study presents that complete ammonia oxidation (comammox) Nitrospira, together with acidophilic ammonia-oxidizing archaea (AOA), dominate in the nitrifying guild in sediments of an acid mine lake (AML). The lake water was characterized by acidic pH below 5 with a high ammonium concentration of 175 mg-N/liter, which is rare on the earth. Nitrification was active in sediments with a maximum nitrate production potential of 70.5 μg-N/(g-dry weight [dw] day) for mixed sediments. Quantitative PCR assays determined that in AML sediments, comammox Nitrospira and AOA amoA genes had relative abundances of 52% and 41%, respectively, among the total amoA genes. Further assays with 16S rRNA and amoA gene amplicon sequencing and metagenomics confirmed their dominance and revealed that the comammox Nitrospira found in sediments belonged to comammox Nitrospira clade A.2. Metagenomic binning retrieved a metagenome-assembled genome (MAG) of the comammox Nitrospira from sediments (completeness = 96.76%), and phylogenomic analysis suggested that it was a novel comammox Nitrospira. Comparative genomic investigation revealed that this comammox Nitrospira contained diverse metal resistance genes and an acidophile-affiliated F-type ATPase. Moreover, it had a more diverse genomic characteristic on nitrogen metabolism than the AOA in sediments and canonical AOB did. The results suggest that comammox Nitrospira is a versatile nitrifier that can adapt to acidic environments even with high ammonium concentrations. IMPORTANCE Ammonia-oxidizing archaea (AOA) was previously considered the sole dominant ammonia oxidizer in acidic environments. This study, however, found that complete ammonia oxidation (comammox) Nitrospira was also a dominant ammonia oxidizer in the sediments of an acidic mine lake, which had an acidic pH < 5 and a high ammonium concentration of 175 mg-N/liter. In combination with average nucleotide identity analysis, phylogenomic analysis suggested it is a novel strain of comammox Nitrospira. Moreover, the adaption of comammox Nitrospira to the acidic lake had been comprehensively investigated based on genome-centric metagenomic approaches. The outcomes of this study significantly expand our understanding of the diversity and adaptability of ammonia oxidizers in the acidic environments.},
}
@article {pmid36893867,
year = {2023},
author = {Cheng, H and Yang, Y and He, Y and Zhan, X and Liu, Y and Hu, Z and Huang, H and Yao, X and Yang, W and Jin, J and Ren, B and Liu, J and Hu, Q and Jin, Y and Shen, L},
title = {Spatio-temporal variations of activity of nitrate-driven anaerobic oxidation of methane and community structure of Candidatus Methanoperedens-like archaea in sediment of Wuxijiang river.},
journal = {Chemosphere},
volume = {324},
number = {},
pages = {138295},
doi = {10.1016/j.chemosphere.2023.138295},
pmid = {36893867},
issn = {1879-1298},
mesh = {*Archaea/genetics/metabolism ; *Nitrates/metabolism ; Ecosystem ; Rivers ; Methane/metabolism ; Anaerobiosis ; Oxidation-Reduction ; },
abstract = {Nitrate-driven anaerobic oxidation of methane (AOM), catalyzing by Candidatus Methanoperedens-like archaea, is a new addition in the global CH4 cycle. This AOM process acts as a novel pathway for CH4 emission reduction in freshwater aquatic ecosystems; however, its quantitative importance and regulatory factors in riverine ecosystems are nearly unknown. Here, we examined the spatio-temporal changes of the communities of Methanoperedens-like archaea and nitrate-driven AOM activity in sediment of Wuxijiang River, a mountainous river in China. These archaeal community composition varied significantly among reaches (upper, middle, and lower reaches) and between seasons (winter and summer), but their mcrA gene diversity showed no significant spatial or temporal variations. The copy numbers of Methanoperedens-like archaeal mcrA genes were 1.32 × 10[5]-2.47 × 10[7] copies g[-1] (dry weight), and the activity of nitrate-driven AOM was 0.25-1.73 nmol CH4 g[-1] (dry weight) d[-1], which could potentially reduce 10.3% of CH4 emissions from rivers. Significant spatio-temporal variations of mcrA gene abundance and nitrate-driven AOM activity were found. Both the gene abundance and activity increased significantly from upper to lower reaches in both seasons, and were significantly higher in sediment collected in summer than in winter. In addition, the variations of Methanoperedens-like archaeal communities and nitrate-driven AOM activity were largely impacted by the sediment temperature, NH4[+] and organic carbon contents. Taken together, both time and space scales need to be considered for better evaluating the quantitative importance of nitrate-driven AOM in reducing CH4 emissions from riverine ecosystems.},
}
@article {pmid36888658,
year = {2023},
author = {Wan, XS and Hou, L and Kao, SJ and Zhang, Y and Sheng, HX and Shen, H and Tong, S and Qin, W and Ward, BB},
title = {Pathways of N2O production by marine ammonia-oxidizing archaea determined from dual-isotope labeling.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {120},
number = {11},
pages = {e2220697120},
pmid = {36888658},
issn = {1091-6490},
mesh = {*Archaea/metabolism ; *Ammonia/metabolism ; Nitrification ; Nitrites/metabolism ; Isotope Labeling ; Oxygen/metabolism ; Oxidation-Reduction ; Nitrous Oxide/metabolism ; },
abstract = {The ocean is a net source of the greenhouse gas and ozone-depleting substance, nitrous oxide (N2O), to the atmosphere. Most of that N2O is produced as a trace side product during ammonia oxidation, primarily by ammonia-oxidizing archaea (AOA), which numerically dominate the ammonia-oxidizing community in most marine environments. The pathways to N2O production and their kinetics, however, are not completely understood. Here, we use [15]N and [18]O isotopes to determine the kinetics of N2O production and trace the source of nitrogen (N) and oxygen (O) atoms in N2O produced by a model marine AOA species, Nitrosopumilus maritimus. We find that during ammonia oxidation, the apparent half saturation constants of nitrite and N2O production are comparable, suggesting that both processes are enzymatically controlled and tightly coupled at low ammonia concentrations. The constituent atoms in N2O are derived from ammonia, nitrite, O2, and H2O via multiple pathways. Ammonia is the primary source of N atoms in N2O, but its contribution varies with ammonia to nitrite ratio. The ratio of [45]N2O to [46]N2O (i.e., single or double labeled N) varies with substrate ratio, leading to widely varying isotopic signatures in the N2O pool. O2 is the primary source for O atoms. In addition to the previously demonstrated hybrid formation pathway, we found a substantial contribution by hydroxylamine oxidation, while nitrite reduction is an insignificant source of N2O. Our study highlights the power of dual [15]N-[18]O isotope labeling to disentangle N2O production pathways in microbes, with implications for interpretation of pathways and regulation of marine N2O sources.},
}
@article {pmid36880756,
year = {2023},
author = {Taubner, RS and Baumann, LMF and Steiner, M and Pfeifer, K and Reischl, B and Korynt, K and Bauersachs, T and Mähnert, B and Clifford, EL and Peckmann, J and Schuster, B and Birgel, D and Rittmann, SKR},
title = {Lipidomics and Comparative Metabolite Excretion Analysis of Methanogenic Archaea Reveal Organism-Specific Adaptations to Varying Temperatures and Substrate Concentrations.},
journal = {mSystems},
volume = {8},
number = {2},
pages = {e0115922},
pmid = {36880756},
issn = {2379-5077},
mesh = {*Archaea/metabolism ; Temperature ; Lipidomics ; *Euryarchaeota/metabolism ; Methane ; Water/metabolism ; },
abstract = {Methanogenic archaea possess diverse metabolic characteristics and are an ecologically and biotechnologically important group of anaerobic microorganisms. Although the scientific and biotechnological value of methanogens is evident with regard to their methane-producing physiology, little is known about their amino acid excretion, and virtually nothing is known about the lipidome at different substrate concentrations and temperatures on a quantitative comparative basis. Here, we present the lipidome and a comprehensive quantitative analysis of proteinogenic amino acid excretion as well as methane, water, and biomass production of the three autotrophic, hydrogenotrophic methanogens Methanothermobacter marburgensis, Methanothermococcus okinawensis, and Methanocaldococcus villosus under varying temperatures and nutrient supplies. The patterns and rates of production of excreted amino acids and the lipidome are unique for each tested methanogen and can be modulated by varying the incubation temperature and substrate concentration, respectively. Furthermore, the temperature had a significant influence on the lipidomes of the different archaea. The water production rate was much higher, as anticipated from the rate of methane production for all studied methanogens. Our results demonstrate the need for quantitative comparative physiological studies connecting intracellular and extracellular constraints of organisms to holistically investigate microbial responses to environmental conditions. IMPORTANCE Biological methane production by methanogenic archaea has been well studied for biotechnological purposes. This study reveals that methanogenic archaea actively modulate their lipid inventory and proteinogenic amino acid excretion pattern in response to environmental changes and the possible utilization of methanogenic archaea as microbial cell factories for the targeted production of lipids and amino acids.},
}
@article {pmid36874274,
year = {2023},
author = {Mei, R and Kaneko, M and Imachi, H and Nobu, MK},
title = {The origin and evolution of methanogenesis and Archaea are intertwined.},
journal = {PNAS nexus},
volume = {2},
number = {2},
pages = {pgad023},
pmid = {36874274},
issn = {2752-6542},
abstract = {Methanogenesis has been widely accepted as an ancient metabolism, but the precise evolutionary trajectory remains hotly debated. Disparate theories exist regarding its emergence time, ancestral form, and relationship with homologous metabolisms. Here, we report the phylogenies of anabolism-involved proteins responsible for cofactor biosynthesis, providing new evidence for the antiquity of methanogenesis. Revisiting the phylogenies of key catabolism-involved proteins further suggests that the last Archaea common ancestor (LACA) was capable of versatile H2-, CO2-, and methanol-utilizing methanogenesis. Based on phylogenetic analyses of the methyl/alkyl-S-CoM reductase family, we propose that, in contrast to current paradigms, substrate-specific functions emerged through parallel evolution traced back to a nonspecific ancestor, which likely originated from protein-free reactions as predicted from autocatalytic experiments using cofactor F430. After LACA, inheritance/loss/innovation centered around methanogenic lithoautotrophy coincided with ancient lifestyle divergence, which is clearly reflected by genomically predicted physiologies of extant archaea. Thus, methanogenesis is not only a hallmark metabolism of Archaea, but the key to resolve the enigmatic lifestyle that ancestral archaea took and the transition that led to physiologies prominent today.},
}
@article {pmid36842598,
year = {2023},
author = {Zheng, P and Zhang, Q and Zou, J and Han, Q and Han, J and Wang, Q and Yao, L and Yu, G and Liang, Y},
title = {A new strategy for the enrichment of ammonia-oxidizing archaea in wastewater treatment systems: The positive role of quorum-sensing signaling molecules.},
journal = {The Science of the total environment},
volume = {873},
number = {},
pages = {162385},
doi = {10.1016/j.scitotenv.2023.162385},
pmid = {36842598},
issn = {1879-1026},
mesh = {*Archaea ; *Ammonia ; Bacteria ; Oxidation-Reduction ; Quorum Sensing ; Nitrification ; },
abstract = {Ammonia-oxidizing archaea (AOA) play an important role in natural nitrogen cycle, but are difficult to be enriched in wastewater treatment systems. In this experiment, under ambient temperature and high dissolved oxygen, different types of acyl-homoserine lactones (C6-HSL, C8-HSL, C10-HSL, C14-HSL and 3-oxo-C14-HSL) were added to five wastewater nitrification systems to achieve AOA enrichment. Results showed that AOA couldn't be detected in the blank group without the addition of signaling molecules, while the AOA could be detected in all the reactors with the addition. The enrichment effect of AOA was not obvious with added 100 or 200 nmol/L signaling molecules, while the enrichment effect was both obvious with added C8-HSL of 400 nmol/L and C10-HSL of 800 nmol/L. And relative abundance of AOA increased from undetected in the control group to 1.10 % and 0.96 %, respectively. The exogenous signaling molecules may provide new view for AOA enrichment in wastewater treatment systems.},
}
@article {pmid36835573,
year = {2023},
author = {Ngcobo, PE and Nkosi, BVZ and Chen, W and Nelson, DR and Syed, K},
title = {Evolution of Cytochrome P450 Enzymes and Their Redox Partners in Archaea.},
journal = {International journal of molecular sciences},
volume = {24},
number = {4},
pages = {},
pmid = {36835573},
issn = {1422-0067},
support = {C686//Universit of Zululand/ ; MND200527525406//National Research Foundation (NRF), South Africa/ ; },
mesh = {Humans ; *Ferredoxins/metabolism ; *Archaea/metabolism ; Phylogeny ; Oxidation-Reduction ; Cytochrome P-450 Enzyme System/metabolism ; Bacteria/metabolism ; },
abstract = {Cytochrome P450 monooxygenases (CYPs/P450s) and their redox partners, ferredoxins, are ubiquitous in organisms. P450s have been studied in biology for over six decades owing to their distinct catalytic activities, including their role in drug metabolism. Ferredoxins are ancient proteins involved in oxidation-reduction reactions, such as transferring electrons to P450s. The evolution and diversification of P450s in various organisms have received little attention and no information is available for archaea. This study is aimed at addressing this research gap. Genome-wide analysis revealed 1204 P450s belonging to 34 P450 families and 112 P450 subfamilies, where some families and subfamilies are expanded in archaea. We also identified 353 ferredoxins belonging to the four types 2Fe-2S, 3Fe-4S, 7Fe-4S and 2[4Fe-4S] in 40 archaeal species. We found that bacteria and archaea shared the CYP109, CYP147 and CYP197 families, as well as several ferredoxin subtypes, and that these genes are co-present on archaeal plasmids and chromosomes, implying the plasmid-mediated lateral transfer of these genes from bacteria to archaea. The absence of ferredoxins and ferredoxin reductases in the P450 operons suggests that the lateral transfer of these genes is independent. We present different scenarios for the evolution and diversification of P450s and ferredoxins in archaea. Based on the phylogenetic analysis and high affinity to diverged P450s, we propose that archaeal P450s could have diverged from CYP109, CYP147 and CYP197. Based on this study's results, we propose that all archaeal P450s are bacterial in origin and that the original archaea had no P450s.},
}
@article {pmid36817958,
year = {2023},
author = {Kisly, I and Tamm, T},
title = {Archaea/eukaryote-specific ribosomal proteins - guardians of a complex structure.},
journal = {Computational and structural biotechnology journal},
volume = {21},
number = {},
pages = {1249-1261},
pmid = {36817958},
issn = {2001-0370},
abstract = {In three domains of life, proteins are synthesized by large ribonucleoprotein particles called ribosomes. All ribosomes are composed of ribosomal RNAs (rRNA) and numerous ribosomal proteins (r-protein). The three-dimensional shape of ribosomes is mainly defined by a tertiary structure of rRNAs. In addition, rRNAs have a major role in decoding the information carried by messenger RNAs and catalyzing the peptide bond formation. R-proteins are essential for shaping the network of interactions that contribute to a various aspects of the protein synthesis machinery, including assembly of ribosomes and interaction of ribosomal subunits. Structural studies have revealed that many key components of ribosomes are conserved in all life domains. Besides the core structure, ribosomes contain domain-specific structural features that include additional r-proteins and extensions of rRNA and r-proteins. This review focuses specifically on those r-proteins that are found only in archaeal and eukaryotic ribosomes. The role of these archaea/eukaryote specific r-proteins in stabilizing the ribosome structure is discussed. Several examples illustrate their functions in the formation of the internal network of ribosomal subunits and interactions between the ribosomal subunits. In addition, the significance of these r-proteins in ribosome biogenesis and protein synthesis is highlighted.},
}
@article {pmid36814573,
year = {2023},
author = {Cheng, X and Xiang, X and Yun, Y and Wang, W and Wang, H and Bodelier, PLE},
title = {Archaea and their interactions with bacteria in a karst ecosystem.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1068595},
pmid = {36814573},
issn = {1664-302X},
abstract = {Karst ecosystems are widely distributed around the world, accounting for 15-20% of the global land area. However, knowledge on microbial ecology of these systems does not match with their global importance. To close this knowledge gap, we sampled three niches including weathered rock, sediment, and drip water inside the Heshang Cave and three types of soils overlying the cave (forest soil, farmland soil, and pristine karst soil). All these samples were subjected to high-throughput sequencing of V4-V5 region of 16S rRNA gene and analyzed with multivariate statistical analysis. Overall, archaeal communities were dominated by Thaumarchaeota, whereas Actinobacteria dominated bacterial communities. Thermoplasmata, Nitrosopumilaceae, Aenigmarchaeales, Crossiella, Acidothermus, and Solirubrobacter were the important predictor groups inside the Heshang Cave, which were correlated to NH4 [+] availability. In contrast, Candidatus Nitrososphaera, Candidatus Nitrocosmicus, Thaumarchaeota Group 1.1c, and Pseudonocardiaceae were the predictors outside the cave, whose distribution was correlated with pH, Ca[2+], and NO2 [-]. Tighter network structures were found in archaeal communities than those of bacteria, whereas the topological properties of bacterial networks were more similar to those of total prokaryotic networks. Both chemolithoautotrophic archaea (Candidatus Methanoperedens and Nitrosopumilaceae) and bacteria (subgroup 7 of Acidobacteria and Rokubacteriales) were the dominant keystone taxa within the co-occurrence networks, potentially playing fundamental roles in obtaining energy under oligotrophic conditions and thus maintaining the stability of the cave ecosystem. To be noted, all the keystone taxa of karst ecosystems were related to nitrogen cycling, which needs further investigation, particularly the role of archaea. The predicted ecological functions in karst soils mainly related to carbohydrate metabolism, biotin metabolism, and synthesis of fatty acid. Our results offer new insights into archaeal ecology, their potential functions, and archaeal interactions with bacteria, which enhance our understanding about the microbial dark matter in the subsurface karst ecosystems.},
}
@article {pmid36808147,
year = {2023},
author = {Gios, E and Mosley, OE and Weaver, L and Close, M and Daughney, C and Handley, KM},
title = {Ultra-small bacteria and archaea exhibit genetic flexibility towards groundwater oxygen content, and adaptations for attached or planktonic lifestyles.},
journal = {ISME communications},
volume = {3},
number = {1},
pages = {13},
pmid = {36808147},
issn = {2730-6151},
support = {UOAX1720//Ministry of Business, Innovation and Employment (MBIE)/ ; UOAX1720//Ministry of Business, Innovation and Employment (MBIE)/ ; UOAX1720//Ministry of Business, Innovation and Employment (MBIE)/ ; UOAX1720//Ministry of Business, Innovation and Employment (MBIE)/ ; UOAX1720//Ministry of Business, Innovation and Employment (MBIE)/ ; UOAX1720//Ministry of Business, Innovation and Employment (MBIE)/ ; },
abstract = {Aquifers are populated by highly diverse microbial communities, including unusually small bacteria and archaea. The recently described Patescibacteria (or Candidate Phyla Radiation) and DPANN radiation are characterized by ultra-small cell and genomes sizes, resulting in limited metabolic capacities and probable dependency on other organisms to survive. We applied a multi-omics approach to characterize the ultra-small microbial communities over a wide range of aquifer groundwater chemistries. Results expand the known global range of these unusual organisms, demonstrate the wide geographical range of over 11,000 subsurface-adapted Patescibacteria, Dependentiae and DPANN archaea, and indicate that prokaryotes with ultra-small genomes and minimalistic metabolism are a characteristic feature of the terrestrial subsurface. Community composition and metabolic activities were largely shaped by water oxygen content, while highly site-specific relative abundance profiles were driven by a combination of groundwater physicochemistries (pH, nitrate-N, dissolved organic carbon). We provide insights into the activity of ultra-small prokaryotes with evidence that they are major contributors to groundwater community transcriptional activity. Ultra-small prokaryotes exhibited genetic flexibility with respect to groundwater oxygen content, and transcriptionally distinct responses, including proportionally greater transcription invested into amino acid and lipid metabolism and signal transduction in oxic groundwater, along with differences in taxa transcriptionally active. Those associated with sediments differed from planktonic counterparts in species composition and transcriptional activity, and exhibited metabolic adaptations reflecting a surface-associated lifestyle. Finally, results showed that groups of phylogenetically diverse ultra-small organisms co-occurred strongly across sites, indicating shared preferences for groundwater conditions.},
}
@article {pmid36804975,
year = {2023},
author = {Zhang, Q and Chen, M and Leng, Y and Wang, X and Fu, Y and Wang, D and Zhao, X and Gao, W and Li, N and Chen, X and Fan, C and Li, Q},
title = {Organic substitution stimulates ammonia oxidation-driven N2O emissions by distinctively enriching keystone species of ammonia-oxidizing archaea and bacteria in tropical arable soils.},
journal = {The Science of the total environment},
volume = {872},
number = {},
pages = {162183},
doi = {10.1016/j.scitotenv.2023.162183},
pmid = {36804975},
issn = {1879-1026},
mesh = {*Archaea ; Soil/chemistry ; Ammonia ; Oxidation-Reduction ; Soil Microbiology ; Bacteria ; *Betaproteobacteria ; Nitrification ; },
abstract = {Partial organic substitution (POS) is pivotal in enhancing soil productivity and changing nitrous oxide (N2O) emissions by profoundly altering soil nitrogen (N) cycling, where ammonia oxidation is a fundamental core process. However, the regulatory mechanisms of N2O production by ammonia oxidizers at the microbial community level under POS regimes remain unclear. This study explored soil ammonia oxidation and related N2O production, further building an understanding of the correlations between ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) activity and community structure in tropical arable soils under four-year field management regimes (CK, without fertilizer N; N, with only inorganic N; M1N1, with 1/2 organic N + 1/2 inorganic N; M1N2, with 1/3 organic N + 2/3 inorganic N). AOA contributed more to potential ammonia oxidation (PAO) than AOB across all treatments. In comparison with CK, N treatment had no obvious effects on PAO and lowered related N2O emissions by decreasing soil pH and downregulating the abundance of AOA- and AOB-amoA. POS regimes significantly enhanced PAO and N2O emissions relative to N treatment by promoting the abundances and contributions of AOA and AOB. The stimulated AOA-dominated N2O production under M1N1 was correlated with promoted development of Nitrososphaera. By contrast, the increased AOB-dominated N2O production under M1N2 was linked to the enhanced development of Nitrosospira multiformis. Our study suggests organic substitutions with different proportions of inorganic and organic N distinctively regulate the development of specific species of ammonia oxidizers to increase associated N2O emissions. Accordingly, appropriate options should be adopted to reduce environmental risks under POS regimes in tropical croplands.},
}
@article {pmid36796795,
year = {2023},
author = {Diao, M and Balkema, C and Suárez-Muñoz, M and Huisman, J and Muyzer, G},
title = {Succession of bacteria and archaea involved in the nitrogen cycle of a seasonally stratified lake.},
journal = {FEMS microbiology letters},
volume = {370},
number = {},
pages = {},
pmid = {36796795},
issn = {1574-6968},
mesh = {Humans ; *Archaea/genetics ; Lakes/microbiology ; RNA, Ribosomal, 16S/genetics ; Nitrates ; Oxidation-Reduction ; Bacteria/genetics ; Nitrogen Cycle ; Ammonia ; *Ammonium Compounds ; Nitrogen ; Phylogeny ; Geologic Sediments/microbiology ; },
abstract = {Human-driven changes affect nutrient inputs, oxygen solubility, and the hydrodynamics of lakes, which affect biogeochemical cycles mediated by microbial communities. However, information on the succession of microbes involved in nitrogen cycling in seasonally stratified lakes is still incomplete. Here, we investigated the succession of nitrogen-transforming microorganisms in Lake Vechten over a period of 19 months, combining 16S rRNA gene amplicon sequencing and quantification of functional genes. Ammonia-oxidizing archaea (AOA) and bacteria (AOB) and anammox bacteria were abundant in the sediment during winter, accompanied by nitrate in the water column. Nitrogen-fixing bacteria and denitrifying bacteria emerged in the water column in spring when nitrate was gradually depleted. Denitrifying bacteria containing nirS genes were exclusively present in the anoxic hypolimnion. During summer stratification, abundances of AOA, AOB, and anammox bacteria decreased sharply in the sediment, and ammonium accumulated in hypolimnion. After lake mixing during fall turnover, abundances of AOA, AOB, and anammox bacteria increased and ammonium was oxidized to nitrate. Hence, nitrogen-transforming microorganisms in Lake Vechten displayed a pronounced seasonal succession, which was strongly determined by the seasonal stratification pattern. These results imply that changes in stratification and vertical mixing induced by global warming are likely to alter the nitrogen cycle of seasonally stratified lakes.},
}
@article {pmid36794928,
year = {2023},
author = {Akpudo, YM and Bezuidt, OK and Makhalanyane, TP},
title = {Metagenome-Assembled Genomes of Four Southern Ocean Archaea Harbor Multiple Genes Linked to Polyethylene Terephthalate and Polyhydroxybutyrate Plastic Degradation.},
journal = {Microbiology resource announcements},
volume = {12},
number = {3},
pages = {e0109822},
pmid = {36794928},
issn = {2576-098X},
support = {//National Research Foundation (NRF)/ ; //Technology Innovation Agency/ ; },
abstract = {Here, we present four archaeal metagenome-assembled genomes (MAGs) (three Thaumarchaeota MAGs and one Thermoplasmatota MAG) from a polar upwelling zone in the Southern Ocean. These archaea harbor putative genes encoding enzymes such as polyethylene terephthalate (PET) hydrolases (PETases) and polyhydroxybutyrate (PHB) depolymerases, which are associated with microbial degradation of PET and PHB plastics.},
}
@article {pmid36792581,
year = {2023},
author = {Filée, J and Becker, HF and Mellottee, L and Eddine, RZ and Li, Z and Yin, W and Lambry, JC and Liebl, U and Myllykallio, H},
title = {Bacterial origins of thymidylate metabolism in Asgard archaea and Eukarya.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {838},
pmid = {36792581},
issn = {2041-1723},
mesh = {*Archaea/metabolism ; *Eukaryota/genetics/metabolism ; Phylogeny ; Thymidylate Synthase/genetics/metabolism ; Bacteria/genetics/metabolism ; Amino Acids/metabolism ; Folic Acid/metabolism ; DNA/metabolism ; },
abstract = {Asgard archaea include the closest known archaeal relatives of eukaryotes. Here, we investigate the evolution and function of Asgard thymidylate synthases and other folate-dependent enzymes required for the biosynthesis of DNA, RNA, amino acids and vitamins, as well as syntrophic amino acid utilization. Phylogenies of Asgard folate-dependent enzymes are consistent with their horizontal transmission from various bacterial groups. We experimentally validate the functionality of thymidylate synthase ThyX of the cultured 'Candidatus Prometheoarchaeum syntrophicum'. The enzyme efficiently uses bacterial-like folates and is inhibited by mycobacterial ThyX inhibitors, even though the majority of experimentally tested archaea are known to use carbon carriers distinct from bacterial folates. Our phylogenetic analyses suggest that the eukaryotic thymidylate synthase, required for de novo DNA synthesis, is not closely related to archaeal enzymes and might have been transferred from bacteria to protoeukaryotes during eukaryogenesis. Altogether, our study suggests that the capacity of eukaryotic cells to duplicate their genetic material is a sum of archaeal (replisome) and bacterial (thymidylate synthase) characteristics. We also propose that recent prevalent lateral gene transfer from bacteria has markedly shaped the metabolism of Asgard archaea.},
}
@article {pmid36759127,
year = {2023},
author = {Wolff, P and Lechner, A and Droogmans, L and Grosjean, H and Westhof, E},
title = {Identification of U[p]47 in three thermophilic archaea, one mesophilic archaeon, and one hyperthermophilic bacterium.},
journal = {RNA (New York, N.Y.)},
volume = {29},
number = {5},
pages = {551-556},
pmid = {36759127},
issn = {1469-9001},
mesh = {*Archaea/genetics ; Bacteria/genetics ; *Sulfolobus/genetics ; },
abstract = {Analysis of the profile of the tRNA modifications in several Archaea allowed us to observe a novel modified uridine in the V-loop of several tRNAs from two species: Pyrococcus furiosus and Sulfolobus acidocaldarius Recently, Ohira and colleagues characterized 2'-phosphouridine (U[p]) at position 47 in tRNAs of thermophilic Sulfurisphaera tokodaii, as well as in several other archaea and thermophilic bacteria. From the presence of the gene arkI corresponding to the RNA kinase responsible for U[p]47 formation, they also concluded that U[p]47 should be present in tRNAs of other thermophilic Archaea Reanalysis of our earlier data confirms that the unidentified residue in tRNAs of both P. furiosus and S. acidocaldarius is indeed 2'-phosphouridine followed by m[5]C48. Moreover, we find this modification in several tRNAs of other Archaea and of the hyperthermophilic bacterium Aquifex aeolicus.},
}
@article {pmid36752722,
year = {2023},
author = {Cooper, CR and Lewis, AM and Notey, JS and Mukherjee, A and Willard, DJ and Blum, PH and Kelly, RM},
title = {Interplay between transcriptional regulators and VapBC toxin-antitoxin loci during thermal stress response in extremely thermoacidophilic archaea.},
journal = {Environmental microbiology},
volume = {25},
number = {6},
pages = {1200-1215},
pmid = {36752722},
issn = {1462-2920},
support = {R01 GM090209/GM/NIGMS NIH HHS/United States ; T32 GM008776/GM/NIGMS NIH HHS/United States ; T32 GM133366/GM/NIGMS NIH HHS/United States ; },
mesh = {*Antitoxins/genetics ; *Toxins, Biological/genetics/metabolism ; Heat-Shock Response/genetics ; *Sulfolobus solfataricus/genetics/metabolism ; Escherichia coli/genetics ; },
abstract = {Thermoacidophilic archaea lack sigma factors and the large inventory of heat shock proteins (HSPs) widespread in bacterial genomes, suggesting other strategies for handling thermal stress are involved. Heat shock transcriptomes for the thermoacidophilic archaeon Saccharolobus (f. Sulfolobus) solfataricus 98/2 revealed genes that were highly responsive to thermal stress, including transcriptional regulators YtrASs (Ssol_2420) and FadRSs (Ssol_0314), as well as type II toxin-antitoxin (TA) loci VapBC6 (Ssol_2337, Ssol_2338) and VapBC22 (Ssol_0819, Ssol_0818). The role, if any, of type II TA loci during stress response in microorganisms, such as Escherichia coli, is controversial. But, when genes encoding YtrASs , FadRSs , VapC22, VapB6, and VapC6 were systematically mutated in Sa. solfataricus 98/2, significant up-regulation of the other genes within this set was observed, implicating an interconnected regulatory network during thermal stress response. VapBC6 and VapBC22 have close homologues in other Sulfolobales, as well as in other archaea (e.g. Pyrococcus furiosus and Archaeoglobus fulgidus), and their corresponding genes were also heat shock responsive. The interplay between VapBC TA loci and heat shock regulators in Sa solfataricus 98/2 not only indicates a cellular mechanism for heat shock response that differs from bacteria but one that could have common features within the thermophilic archaea.},
}
@article {pmid36752534,
year = {2023},
author = {Dahl, MB and Kreyling, J and Petters, S and Wang, H and Mortensen, MS and Maccario, L and Sørensen, SJ and Urich, T and Weigel, R},
title = {Warmer winters result in reshaping of the European beech forest soil microbiome (bacteria, archaea and fungi)-With potential implications for ecosystem functioning.},
journal = {Environmental microbiology},
volume = {25},
number = {6},
pages = {1118-1135},
doi = {10.1111/1462-2920.16347},
pmid = {36752534},
issn = {1462-2920},
mesh = {Ecosystem ; *Fagus ; Archaea/genetics ; Soil/chemistry ; Forests ; Bacteria/genetics ; Climate Change ; *Mycorrhizae ; Seasons ; Snow ; Nitrogen ; },
abstract = {In temperate regions, climate warming alters temperature and precipitation regimes. During winter, a decline in insulating snow cover changes the soil environment, where especially frost exposure can have severe implications for soil microorganisms and subsequently for soil nutrient dynamics. Here, we investigated winter climate change responses in European beech forests soil microbiome. Nine study sites with each three treatments (snow exclusion, insolation, and ambient) were investigated. Long-term adaptation to average climate was explored by comparing across sites. Triplicated treatment plots were used to evaluate short-term (one single winter) responses. Community profiles of bacteria, archaea and fungi were created using amplicon sequencing. Correlations between the microbiome, vegetation and soil physicochemical properties were found. We identify core members of the forest-microbiome and link them to key processes, for example, mycorrhizal symbiont and specialized beech wood degraders (fungi) and nitrogen cycling (bacteria, archaea). For bacteria, the shift of the microbiome composition due to short-term soil temperature manipulations in winter was similar to the community differences observed between long-term relatively cold to warm conditions. The results suggest a strong link between the changes in the microbiomes and changes in environmental processes, for example, nitrogen dynamics, driven by variations in winter climate.},
}
@article {pmid36729913,
year = {2023},
author = {Denise, R and Babor, J and Gerlt, JA and de Crécy-Lagard, V},
title = {Pyridoxal 5'-phosphate synthesis and salvage in Bacteria and Archaea: predicting pathway variant distributions and holes.},
journal = {Microbial genomics},
volume = {9},
number = {2},
pages = {},
pmid = {36729913},
issn = {2057-5858},
support = {R01 GM129793/GM/NIGMS NIH HHS/United States ; },
mesh = {*Archaea/genetics/metabolism ; *Pyridoxal/metabolism ; Bacteria/genetics/metabolism ; Phosphates ; },
abstract = {Pyridoxal 5’-phosphate or PLP is a cofactor derived from B6 vitamers and essential for growth in all known organisms. PLP synthesis and salvage pathways are well characterized in a few model species even though key components, such as the vitamin B6 transporters, are still to be identified in many organisms including the model bacteria Escherichia coli or Bacillus subtilis . Using a comparative genomic approach, PLP synthesis and salvage pathways were predicted in 5840 bacterial and archaeal species with complete genomes. The distribution of the two known de novo biosynthesis pathways and previously identified cases of non-orthologous displacements were surveyed in the process. This analysis revealed that several PLP de novo pathway genes remain to be identified in many organisms, either because sequence similarity alone cannot be used to discriminate among several homologous candidates or due to non-orthologous displacements. Candidates for some of these pathway holes were identified using published TnSeq data, but many remain. We find that ~10 % of the analysed organisms rely on salvage but further analyses will be required to identify potential transporters. This work is a starting point to model the exchanges of B6 vitamers in communities, predict the sensitivity of a given organism to drugs targeting PLP synthesis enzymes, and identify numerous gaps in knowledge that will need to be tackled in the years to come.},
}
@article {pmid36724220,
year = {2023},
author = {Ngugi, DK and Salcher, MM and Andrei, AS and Ghai, R and Klotz, F and Chiriac, MC and Ionescu, D and Büsing, P and Grossart, HP and Xing, P and Priscu, JC and Alymkulov, S and Pester, M},
title = {Postglacial adaptations enabled colonization and quasi-clonal dispersal of ammonia-oxidizing archaea in modern European large lakes.},
journal = {Science advances},
volume = {9},
number = {5},
pages = {eadc9392},
pmid = {36724220},
issn = {2375-2548},
mesh = {*Archaea/genetics ; *Lakes ; Ammonia ; Ecosystem ; Oxidation-Reduction ; Phylogeny ; },
abstract = {Ammonia-oxidizing archaea (AOA) play a key role in the aquatic nitrogen cycle. Their genetic diversity is viewed as the outcome of evolutionary processes that shaped ancestral transition from terrestrial to marine habitats. However, current genome-wide insights into AOA evolution rarely consider brackish and freshwater representatives or provide their divergence timeline in lacustrine systems. An unbiased global assessment of lacustrine AOA diversity is critical for understanding their origins, dispersal mechanisms, and ecosystem roles. Here, we leveraged continental-scale metagenomics to document that AOA species diversity in freshwater systems is remarkably low compared to marine environments. We show that the uncultured freshwater AOA, "Candidatus Nitrosopumilus limneticus," is ubiquitous and genotypically static in various large European lakes where it evolved 13 million years ago. We find that extensive proteome remodeling was a key innovation for freshwater colonization of AOA. These findings reveal the genetic diversity and adaptive mechanisms of a keystone species that has survived clonally in lakes for millennia.},
}
@article {pmid36721520,
year = {2022},
author = {Beddal, A and Boutaiba, S and Laassami, A and Hamaidi, F and Enache, M},
title = {Characterization by polyphasic approach of some indigenous halophilic archaea of Djelfa's rock salt "Hadjr el Meelh", Algeria.},
journal = {Iranian journal of microbiology},
volume = {14},
number = {4},
pages = {535-544},
pmid = {36721520},
issn = {2008-3289},
abstract = {BACKGROUND AND OBJECTIVES: Hadjr El Melh of Djelfa is an example of hypersaline ecosystems, which can harbor a wide variety of microorganisms under hostile physicochemical conditions. Given the importance of the study of halophilic microorganisms present there in terms of fundamental and applied microbiology, the purpose of this study was to characterize some halophilic archaea isolated from the brines of this environment.<br><br>MATERIALS AND METHODS: Eight water samples were chosen randomly and collected for physicochemical and microbiological analyses. Isolation of halophilic archaea was carried out by membrane filter technique. Ten strains were identified by polyphasic approach and tested for enzymes production.<br><br>RESULTS: Water samples of Djelfa's rock salt were slightly acidic to neutral in pH (6.55-7.36) with salinity ranging from 258.68 g/l to 493.91 g/l. Phenotypic, biochemical, taxonomic and phylogenetic characteristics indicated that all strains were classified within the family of Halobacteiaceae. Based on the comparison of DNA sequences encoded 16S rRNA, it was determined that seven strains were affiliated to the genus Haloarcula, two strains were related to the genus Halobacterium and one strain within the genus Haloferax. Production of different enzymes such as protease, amylase, esterase, lipase, lecithinase, gelatinase and cellulase on solid medium indicated that one strain (S2-2) produced amylase, esterase, lecithinase and protease. However, no strains showed cellulolytic or lipolytic activity. Gelatinase was found in all tested strains.<br><br>CONCLUSION: This report constitutes the first preliminary study of culturable halophilic archaea recovered from the brines of Djelfa's rock salt with a promising enzymatic potential in various fields of biotechnology.},
}
@article {pmid36721060,
year = {2023},
author = {Hodgskiss, LH and Melcher, M and Kerou, M and Chen, W and Ponce-Toledo, RI and Savvides, SN and Wienkoop, S and Hartl, M and Schleper, C},
title = {Unexpected complexity of the ammonia monooxygenase in archaea.},
journal = {The ISME journal},
volume = {17},
number = {4},
pages = {588-599},
pmid = {36721060},
issn = {1751-7370},
mesh = {*Archaea/classification/enzymology ; *Oxidoreductases/chemistry/genetics/metabolism ; Nitrification ; Native Polyacrylamide Gel Electrophoresis ; Phylogeny ; Gene Expression ; },
abstract = {Ammonia oxidation, as the first step of nitrification, constitutes a critical process in the global nitrogen cycle. However, fundamental knowledge of its key enzyme, the copper-dependent ammonia monooxygenase, is lacking, in particular for the environmentally abundant ammonia-oxidizing archaea (AOA). Here the structure of the enzyme is investigated by blue-native gel electrophoresis and proteomics from native membrane complexes of two AOA. Besides the known AmoABC subunits and the earlier predicted AmoX, two new protein subunits, AmoY and AmoZ, were identified. They are unique to AOA, highly conserved and co-regulated, and their genes are linked to other AMO subunit genes in streamlined AOA genomes. Modeling and in-gel cross-link approaches support an overall protomer structure similar to the distantly related bacterial particulate methane monooxygenase but also reveals clear differences in extracellular domains of the enzyme. These data open avenues for further structure-function studies of this ecologically important nitrification complex.},
}
@article {pmid36720870,
year = {2023},
author = {Daugeron, MC and Missoury, S and Da Cunha, V and Lazar, N and Collinet, B and van Tilbeurgh, H and Basta, T},
title = {A paralog of Pcc1 is the fifth core subunit of the KEOPS tRNA-modifying complex in Archaea.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {526},
pmid = {36720870},
issn = {2041-1723},
mesh = {*Adenosine ; *Archaea/genetics ; Biological Evolution ; Eukaryota ; RNA, Transfer/genetics ; },
abstract = {In Archaea and Eukaryotes, the synthesis of a universal tRNA modification, N[6]-threonyl-carbamoyl adenosine (t[6]A), is catalyzed by the KEOPS complex composed of Kae1, Bud32, Cgi121, and Pcc1. A fifth subunit, Gon7, is found only in Fungi and Metazoa. Here, we identify and characterize a fifth KEOPS subunit in Archaea. This protein, dubbed Pcc2, is a paralog of Pcc1 and is widely conserved in Archaea. Pcc1 and Pcc2 form a heterodimer in solution, and show modest sequence conservation but very high structural similarity. The five-subunit archaeal KEOPS does not form dimers but retains robust tRNA binding and t[6]A synthetic activity. Pcc2 can substitute for Pcc1 but the resulting KEOPS complex is inactive, suggesting a distinct function for the two paralogs. Comparative sequence and structure analyses point to a possible evolutionary link between archaeal Pcc2 and eukaryotic Gon7. Our work indicates that Pcc2 regulates the oligomeric state of the KEOPS complex, a feature that seems to be conserved from Archaea to Eukaryotes.},
}
@article {pmid36715325,
year = {2023},
author = {Yang, Y and Liu, J and Fu, X and Zhou, F and Zhang, S and Zhang, X and Huang, Q and Krupovic, M and She, Q and Ni, J and Shen, Y},
title = {A novel RHH family transcription factor aCcr1 and its viral homologs dictate cell cycle progression in archaea.},
journal = {Nucleic acids research},
volume = {51},
number = {4},
pages = {1707-1723},
pmid = {36715325},
issn = {1362-4962},
mesh = {*Transcription Factors/genetics ; Archaea ; Cell Division ; *Sulfolobus/genetics ; Gene Expression Regulation ; },
abstract = {Cell cycle regulation is of paramount importance for all forms of life. Here, we report that a conserved and essential cell cycle-specific transcription factor (designated as aCcr1) and its viral homologs control cell division in Sulfolobales. We show that the transcription level of accr1 reaches peak during active cell division (D-phase) subsequent to the expression of CdvA, an archaea-specific cell division protein. Cells over-expressing the 58-aa-long RHH (ribbon-helix-helix) family cellular transcription factor as well as the homologs encoded by large spindle-shaped viruses Acidianus two-tailed virus (ATV) and Sulfolobus monocaudavirus 3 (SMV3) display significant growth retardation and cell division failure, manifesting as enlarged cells with multiple chromosomes. aCcr1 over-expression results in downregulation of 17 genes (>4-fold), including cdvA. A conserved motif, aCcr1-box, located between the TATA-binding box and the translation initiation site of 13 out of the 17 highly repressed genes, is critical for aCcr1 binding. The aCcr1-box is present in the promoters and 5' UTRs of cdvA genes across Sulfolobales, suggesting that aCcr1-mediated cdvA repression is an evolutionarily conserved mechanism by which archaeal cells dictate cytokinesis progression, whereas their viruses take advantage of this mechanism to manipulate the host cell cycle.},
}
@article {pmid36709544,
year = {2023},
author = {Umegawa, Y and Kawatake, S and Murata, M and Matsuoka, S},
title = {Combined effect of the head groups and alkyl chains of archaea lipids when interacting with bacteriorhodopsin.},
journal = {Biophysical chemistry},
volume = {294},
number = {},
pages = {106959},
doi = {10.1016/j.bpc.2023.106959},
pmid = {36709544},
issn = {1873-4200},
mesh = {*Bacteriorhodopsins/chemistry/metabolism ; Phospholipids/chemistry ; Membrane Lipids/chemistry ; Halobacterium salinarum/chemistry/metabolism ; Phosphates/metabolism ; },
abstract = {Bacteriorhodopsin (bR), a transmembrane protein with seven α-helices, is highly expressed in the purple membrane (PM) of archaea such as Halobacterium salinarum. It is well known that bR forms two-dimensional crystals with acidic lipids such as phosphatidylglycerol phosphate methyl ester (PGP-Me)-a major component of PM lipids bearing unique chemical structures-methyl-branched alkyl chains, ether linkages, and divalent anionic head groups with two phosphodiester groups. Therefore, we aimed to determine which functional groups of PGP-Me are essential for the boundary lipids of bR and how these functionalities interact with bR. To this end, we compared various well-known phospholipids (PLs) that carry one of the structural features of PGP-Me, and evaluated the affinity of PLs to bR using the centerband-only analysis of rotor-unsynchronized spin echo (COARSE) method in solid-state NMR measurements and thermal shift assays. The results clearly showed that the branched methyl groups of alkyl chains and double negative charges in the head groups are important for PL interactions with bR. We then examined the effect of phospholipids on the monomer-trimer exchange of bR using circular dichroism (CD) spectra. The results indicated that the divalent negative charge in a head group stabilizes the trimer structure, while the branched methyl chains significantly enhance the PLs' affinity for bR, thus dispersing bR trimers in the PM even at high concentrations. Finally, we investigated the effects of PL on the proton-pumping activity of bR based on the decay rate constant of the M intermediate of a bR photocycle. The findings showed that bR activities decreased to 20% in 1,2-dimyristoyl-sn-glycero-3-phosphate (DMPA), and in 1,2-diphytanoyl-sn-glycero-3-phosphocholine (DPhPC) bilayers as compared to that in PM. Meanwhile, 1,2-Diphytanoyl-sn-glycero-3-phosphate (DPhPA) bilayers bearing both negative charges and branched methyl groups preserved over 80% of the activity. These results strongly suggest that the head groups and alkyl chains of phospholipids are essential for boundary lipids and greatly influence the biological function of bR.},
}
@article {pmid36694212,
year = {2023},
author = {Jaffe, AL and Bardot, C and Le Jeune, AH and Liu, J and Colombet, J and Perrière, F and Billard, H and Castelle, CJ and Lehours, AC and Banfield, JF},
title = {Variable impact of geochemical gradients on the functional potential of bacteria, archaea, and phages from the permanently stratified Lac Pavin.},
journal = {Microbiome},
volume = {11},
number = {1},
pages = {14},
pmid = {36694212},
issn = {2049-2618},
support = {S10 OD018174/OD/NIH HHS/United States ; },
mesh = {*Archaea/genetics/metabolism ; *Bacteriophages/metabolism ; Bacteria/genetics/metabolism ; Lakes/microbiology ; Oxygen/metabolism ; Water ; Methane/metabolism ; Phylogeny ; Geologic Sediments/microbiology ; },
abstract = {BACKGROUND: Permanently stratified lakes contain diverse microbial communities that vary with depth and so serve as useful models for studying the relationships between microbial community structure and geochemistry. Recent work has shown that these lakes can also harbor numerous bacteria and archaea from novel lineages, including those from the Candidate Phyla Radiation (CPR). However, the extent to which geochemical stratification differentially impacts carbon metabolism and overall genetic potential in CPR bacteria compared to other organisms is not well defined.<br><br>RESULTS: Here, we determine the distribution of microbial lineages along an oxygen gradient in Lac Pavin, a deep, stratified lake in central France, and examine the influence of this gradient on their metabolism. Genome-based analyses revealed an enrichment of distinct C1 and CO2 fixation pathways in the oxic lake interface and anoxic zone/sediments, suggesting that oxygen likely plays a role in structuring metabolic strategies in non-CPR bacteria and archaea. Notably, we find that the oxidation of methane and its byproducts is largely spatially separated from methane production, which is mediated by diverse communities of sediment methanogens that vary on the centimeter scale. In contrast, we detected evidence for RuBisCO throughout the water column and sediments, including form II/III and form III-related enzymes encoded by CPR bacteria in the water column and DPANN archaea in the sediments. On the whole, though, CPR bacteria and phages did not show strong signals of gene content differentiation by depth, despite the fact that distinct species groups populate different lake and sediment compartments.<br><br>CONCLUSIONS: Overall, our analyses suggest that environmental gradients in Lac Pavin select for capacities of CPR bacteria and phages to a lesser extent than for other bacteria and archaea. This may be due to the fact that selection in the former groups is indirect and depends primarily on host characteristics. Video Abstract.},
}
@article {pmid36690779,
year = {2023},
author = {Yu, Y and Wang, P and Cao, HY and Teng, ZJ and Zhu, Y and Wang, M and McMinn, A and Chen, Y and Xiang, H and Zhang, YZ and Chen, XL and Zhang, YQ},
title = {Novel D-glutamate catabolic pathway in marine Proteobacteria and halophilic archaea.},
journal = {The ISME journal},
volume = {17},
number = {4},
pages = {537-548},
pmid = {36690779},
issn = {1751-7370},
mesh = {*Glutamic Acid/metabolism ; *Proteobacteria ; Ecosystem ; Bacteria ; Archaea/genetics/metabolism ; },
abstract = {D-glutamate (D-Glu) is an essential component of bacterial peptidoglycans, representing an important, yet overlooked, pool of organic matter in global oceans. However, little is known on D-Glu catabolism by marine microorganisms. Here, a novel catabolic pathway for D-Glu was identified using the marine bacterium Pseudoalteromonas sp. CF6-2 as the model. Two novel enzymes (DgcN, DgcA), together with a transcriptional regulator DgcR, are crucial for D-Glu catabolism in strain CF6-2. Genetic and biochemical data confirm that DgcN is a N-acetyltransferase which catalyzes the formation of N-acetyl-D-Glu from D-Glu. DgcA is a racemase that converts N-acetyl-D-Glu to N-acetyl-L-Glu, which is further hydrolyzed to L-Glu. DgcR positively regulates the transcription of dgcN and dgcA. Structural and biochemical analyses suggested that DgcN and its homologs, which use D-Glu as the acyl receptor, represent a new group of the general control non-repressible 5 (GCN5)-related N-acetyltransferases (GNAT) superfamily. DgcA and DgcN occur widely in marine bacteria (particularly Rhodobacterales) and halophilic archaea (Halobacteria) and are abundant in marine and hypersaline metagenome datasets. Thus, this study reveals a novel D-Glu catabolic pathway in ecologically important marine bacteria and halophilic archaea and helps better understand the catabolism and recycling of D-Glu in these ecosystems.},
}
@article {pmid36687602,
year = {2022},
author = {Corona Ramírez, A and Cailleau, G and Fatton, M and Dorador, C and Junier, P},
title = {Diversity of Lysis-Resistant Bacteria and Archaea in the Polyextreme Environment of Salar de Huasco.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {826117},
pmid = {36687602},
issn = {1664-302X},
abstract = {The production of specialized resting cells is a remarkable strategy developed by several organisms to survive unfavorable environmental conditions. Spores are specialized resting cells that are characterized by low to absent metabolic activity and higher resistance. Spore-like cells are known from multiple groups of bacteria, which can form spores under suboptimal growth conditions (e.g., starvation). In contrast, little is known about the production of specialized resting cells in archaea. In this study, we applied a culture-independent method that uses physical and chemical lysis, to assess the diversity of lysis-resistant bacteria and archaea and compare it to the overall prokaryotic diversity (direct DNA extraction). The diversity of lysis-resistant cells was studied in the polyextreme environment of the Salar de Huasco. The Salar de Huasco is a high-altitude athalassohaline wetland in the Chilean Altiplano. Previous studies have shown a high diversity of bacteria and archaea in the Salar de Huasco, but the diversity of lysis-resistant microorganisms has never been investigated. The underlying hypothesis was that the combination of extreme abiotic conditions might favor the production of specialized resting cells. Samples were collected from sediment cores along a saline gradient and microbial mats were collected in small surrounding ponds. A significantly different diversity and composition were found in the sediment cores or microbial mats. Furthermore, our results show a high diversity of lysis-resistant cells not only in bacteria but also in archaea. The bacterial lysis-resistant fraction was distinct in comparison to the overall community. Also, the ability to survive the lysis-resistant treatment was restricted to a few groups, including known spore-forming phyla such as Firmicutes and Actinobacteria. In contrast to bacteria, lysis resistance was widely spread in archaea, hinting at a generalized resistance to lysis, which is at least comparable to the resistance of dormant cells in bacteria. The enrichment of Natrinema and Halarchaeum in the lysis-resistant fraction could hint at the production of cyst-like cells or other resistant cells. These results can guide future studies aiming to isolate and broaden the characterization of lysis-resistant archaea.},
}
@article {pmid36683362,
year = {2022},
author = {Tandon, K and Ricci, F and Costa, J and Medina, M and Kühl, M and Blackall, LL and Verbruggen, H},
title = {Genomic view of the diversity and functional role of archaea and bacteria in the skeleton of the reef-building corals Porites lutea and Isopora palifera.},
journal = {GigaScience},
volume = {12},
number = {},
pages = {},
pmid = {36683362},
issn = {2047-217X},
support = {DP200101613//Australian Research Council/ ; //University of Melbourne/ ; GBMF9206//Gordon and Betty Moore Foundation/ ; },
mesh = {Animals ; *Anthozoa/genetics ; Archaea/genetics ; Coral Reefs ; Bacteria/genetics ; Metagenome ; Genomics ; },
abstract = {At present, our knowledge on the compartmentalization of coral holobiont microbiomes is highly skewed toward the millimeter-thin coral tissue, leaving the diverse coral skeleton microbiome underexplored. Here, we present a genome-centric view of the skeleton of the reef-building corals Porites lutea and Isopora palifera, through a compendium of ∼400 high-quality bacterial and archaeal metagenome-assembled genomes (MAGs), spanning 34 phyla and 57 classes. Skeletal microbiomes harbored a diverse array of stress response genes, including dimethylsulfoniopropionate synthesis (dsyB) and metabolism (DMSP lyase). Furthermore, skeletal MAGs encoded an average of 22 ± 15 genes in P. lutea and 28 ± 23 in I. palifera with eukaryotic-like motifs thought to be involved in maintaining host association. We provide comprehensive insights into the putative functional role of the skeletal microbiome on key metabolic processes such as nitrogen fixation, dissimilatory and assimilatory nitrate, and sulfate reduction. Our study provides critical genomic resources for a better understanding of the coral skeletal microbiome and its role in holobiont functioning.},
}
@article {pmid36674956,
year = {2023},
author = {Baehren, C and Pembaur, A and Weil, PP and Wewers, N and Schult, F and Wirth, S and Postberg, J and Aydin, M},
title = {The Overlooked Microbiome-Considering Archaea and Eukaryotes Using Multiplex Nanopore-16S-/18S-rDNA-Sequencing: A Technical Report Focusing on Nasopharyngeal Microbiomes.},
journal = {International journal of molecular sciences},
volume = {24},
number = {2},
pages = {},
pmid = {36674956},
issn = {1422-0067},
support = {IFF 2021-02//Witten/Herdecke University/ ; 2021-0246//Helios Kliniken/ ; },
mesh = {Humans ; Archaea/genetics ; Eukaryota/genetics ; Phylogeny ; DNA, Ribosomal ; *Nanopores ; Pilot Projects ; *Microbiota/genetics ; Bacteria ; Nasopharynx ; RNA, Ribosomal, 16S/genetics ; },
abstract = {In contrast to bacteria, microbiome analyses often neglect archaea, but also eukaryotes. This is partly because they are difficult to culture due to their demanding growth requirements, or some even have to be classified as uncultured microorganisms. Consequently, little is known about the relevance of archaea in human health and diseases. Contemporary broad availability and spread of next generation sequencing techniques now enable a stronger focus on such microorganisms, whose cultivation is difficult. However, due to the enormous evolutionary distances between bacteria, archaea and eukaryotes, the implementation of sequencing strategies for smaller laboratory scales needs to be refined to achieve as a holistic view on the microbiome as possible. Here, we present a technical approach that enables simultaneous analyses of archaeal, bacterial and eukaryotic microbial communities to study their roles in development and courses of respiratory disorders. We thus applied combinatorial 16S-/18S-rDNA sequencing strategies for sequencing-library preparation. Considering the lower total microbiota density of airway surfaces, when compared with gut microbiota, we optimized the DNA purification workflow from nasopharyngeal swab specimens. As a result, we provide a protocol that allows the efficient combination of bacterial, archaeal, and eukaryotic libraries for nanopore-sequencing using Oxford Nanopore Technologies MinION devices and subsequent phylogenetic analyses. In a pilot study, this workflow allowed the identification of some environmental archaea, which were not correlated with airway microbial communities before. Moreover, we assessed the protocol's broader applicability using a set of human stool samples. We conclude that the proposed protocol provides a versatile and adaptable tool for combinatorial studies on bacterial, archaeal, and eukaryotic microbiomes on a small laboratory scale.},
}
@article {pmid36671499,
year = {2023},
author = {De Lise, F and Iacono, R and Moracci, M and Strazzulli, A and Cobucci-Ponzano, B},
title = {Archaea as a Model System for Molecular Biology and Biotechnology.},
journal = {Biomolecules},
volume = {13},
number = {1},
pages = {},
pmid = {36671499},
issn = {2218-273X},
support = {2019-3-U.O.//Agenzia Spaziale Italiana/ ; },
mesh = {*Archaea/metabolism ; Bacteria/genetics ; *Euryarchaeota/genetics/metabolism ; Biotechnology ; Molecular Biology ; },
abstract = {Archaea represents the third domain of life, displaying a closer relationship with eukaryotes than bacteria. These microorganisms are valuable model systems for molecular biology and biotechnology. In fact, nowadays, methanogens, halophiles, thermophilic euryarchaeota, and crenarchaeota are the four groups of archaea for which genetic systems have been well established, making them suitable as model systems and allowing for the increasing study of archaeal genes' functions. Furthermore, thermophiles are used to explore several aspects of archaeal biology, such as stress responses, DNA replication and repair, transcription, translation and its regulation mechanisms, CRISPR systems, and carbon and energy metabolism. Extremophilic archaea also represent a valuable source of new biomolecules for biological and biotechnological applications, and there is growing interest in the development of engineered strains. In this review, we report on some of the most important aspects of the use of archaea as a model system for genetic evolution, the development of genetic tools, and their application for the elucidation of the basal molecular mechanisms in this domain of life. Furthermore, an overview on the discovery of new enzymes of biotechnological interest from archaea thriving in extreme environments is reported.},
}
@article {pmid36660825,
year = {2023},
author = {Nissley, AJ and Penev, PI and Watson, ZL and Banfield, JF and Cate, JHD},
title = {Rare ribosomal RNA sequences from archaea stabilize the bacterial ribosome.},
journal = {Nucleic acids research},
volume = {51},
number = {4},
pages = {1880-1894},
pmid = {36660825},
issn = {1362-4962},
support = {T32 GM066698/GM/NIGMS NIH HHS/United States ; },
mesh = {*RNA, Ribosomal/metabolism ; *Peptidyl Transferases/metabolism ; Escherichia coli/genetics ; Archaea/genetics ; Base Sequence ; Ribosomes/metabolism ; Bacteria/genetics ; Binding Sites ; Uridine/metabolism ; Cytidine/metabolism ; RNA, Ribosomal, 23S/metabolism ; RNA, Bacterial/metabolism ; },
abstract = {The ribosome serves as the universally conserved translator of the genetic code into proteins and supports life across diverse temperatures ranging from below freezing to above 120°C. Ribosomes are capable of functioning across this wide range of temperatures even though the catalytic site for peptide bond formation, the peptidyl transferase center, is nearly universally conserved. Here we find that Thermoproteota, a phylum of thermophilic Archaea, substitute cytidine for uridine at large subunit rRNA positions 2554 and 2555 (Escherichia coli numbering) in the A loop, immediately adjacent to the binding site for the 3'-end of A-site tRNA. We show by cryo-EM that E. coli ribosomes with uridine to cytidine mutations at these positions retain the proper fold and post-transcriptional modification of the A loop. Additionally, these mutations do not affect cellular growth, protect the large ribosomal subunit from thermal denaturation, and increase the mutational robustness of nucleotides in the peptidyl transferase center. This work identifies sequence variation across archaeal ribosomes in the peptidyl transferase center that likely confers stabilization of the ribosome at high temperatures and develops a stable mutant bacterial ribosome that can act as a scaffold for future ribosome engineering efforts.},
}
@article {pmid36658397,
year = {2023},
author = {Laso-Pérez, R and Wu, F and Crémière, A and Speth, DR and Magyar, JS and Zhao, K and Krupovic, M and Orphan, VJ},
title = {Evolutionary diversification of methanotrophic ANME-1 archaea and their expansive virome.},
journal = {Nature microbiology},
volume = {8},
number = {2},
pages = {231-245},
pmid = {36658397},
issn = {2058-5276},
mesh = {*Archaea ; *Ecosystem ; Phylogeny ; Virome ; Geologic Sediments ; Anaerobiosis ; Methane/metabolism ; Alkanes/metabolism ; },
abstract = {'Candidatus Methanophagales' (ANME-1) is an order-level clade of archaea responsible for anaerobic methane oxidation in deep-sea sediments. The diversity, ecology and evolution of ANME-1 remain poorly understood. In this study, we use metagenomics on deep-sea hydrothermal samples to expand ANME-1 diversity and uncover the effect of virus-host dynamics. Phylogenetic analyses reveal a deep-branching, thermophilic family, 'Candidatus Methanospirareceae', closely related to short-chain alkane oxidizers. Global phylogeny and near-complete genomes show that hydrogen metabolism within ANME-1 is an ancient trait that was vertically inherited but differentially lost during lineage diversification. Metagenomics also uncovered 16 undescribed virus families so far exclusively targeting ANME-1 archaea, showing unique structural and replicative signatures. The expansive ANME-1 virome contains a metabolic gene repertoire that can influence host ecology and evolution through virus-mediated gene displacement. Our results suggest an evolutionary continuum between anaerobic methane and short-chain alkane oxidizers and underscore the effects of viruses on the dynamics and evolution of methane-driven ecosystems.},
}
@article {pmid36639538,
year = {2023},
author = {Zhang, CJ and Liu, YR and Cha, G and Liu, Y and Zhou, XQ and Lu, Z and Pan, J and Cai, M and Li, M},
title = {Potential for mercury methylation by Asgard archaea in mangrove sediments.},
journal = {The ISME journal},
volume = {17},
number = {3},
pages = {478-485},
pmid = {36639538},
issn = {1751-7370},
mesh = {*Mercury/metabolism ; Archaea/genetics/metabolism ; Ecosystem ; Methylation ; Phylogeny ; *Methylmercury Compounds/metabolism ; Geologic Sediments/microbiology ; },
abstract = {Methylmercury (MeHg) is a potent neurotoxin that bioaccumulates along food chains. The conversion of MeHg from mercury (Hg) is mediated by a variety of anaerobic microorganisms carrying hgcAB genes. Mangrove sediments are potential hotspots of microbial Hg methylation; however, the microorganisms responsible for Hg methylation are poorly understood. Here, we conducted metagenomic and metatranscriptomic analyses to investigate the diversity and distribution of putative microbial Hg-methylators in mangrove ecosystems. The highest hgcA abundance and expression occurred in surface sediments in Shenzhen, where the highest MeHg concentration was also observed. We reconstructed 157 metagenome-assembled genomes (MAGs) carrying hgcA and identified several putative novel Hg-methylators, including one Asgard archaea (Lokiarchaeota). Further analysis of MAGs revealed that Deltaproteobacteria, Euryarchaeota, Bacteroidetes, Chloroflexi, and Lokiarchaeota were the most abundant and active Hg-methylating groups, implying their crucial role in MeHg production. By screening publicly available MAGs, 104 additional Asgard MAGs carrying hgcA genes were identified from a wide range of coast, marine, permafrost, and lake sediments. Protein homology modelling predicts that Lokiarchaeota HgcAB proteins contained the highly conserved amino acid sequences and folding structures required for Hg methylation. Phylogenetic tree revealed that hgcA genes from Asgard clustered with fused hgcAB genes, indicating a transitional stage of Asgard hgcA genes. Our findings thus suggest that Asgard archaea are potential novel Hg-methylating microorganisms and play an important role in hgcA evolution.},
}
@article {pmid36622233,
year = {2023},
author = {Jia, Y and Lahm, M and Chen, Q and Powers, L and Gonsior, M and Chen, F},
title = {The Predominance of Ammonia-Oxidizing Archaea in an Oceanic Microbial Community Amended with Cyanobacterial Lysate.},
journal = {Microbiology spectrum},
volume = {11},
number = {1},
pages = {e0240522},
pmid = {36622233},
issn = {2165-0497},
mesh = {Archaea ; Ammonia ; Dissolved Organic Matter ; Oceans and Seas ; *Ammonium Compounds ; Oxidation-Reduction ; *Microbiota ; *Synechococcus ; Carbon ; Phylogeny ; },
abstract = {When the oligotrophic microbial community was amended with Synechococcus-derived dissolved organic matter (SDOM) and incubated under the dark condition, archaea relative abundance was initially very low but made up more than 60% of the prokaryotic community on day 60, and remained dominant for at least 9 months. The archaeal sequences were dominated by Candidatus Nitrosopumilus, the Group I.1a Thaumarchaeota. The increase of Thaumarchaeota in the dark incubation corresponded to the period of delayed ammonium oxidation upon an initially steady increase in ammonia, supporting the remarkable competency of Thaumarchaeota in energy utilization and fixation of inorganic carbon in the ocean. IMPORTANCE Thaumarchaeota, which are ammonia-oxidizing archaea (AOA), are mainly chemolithoautotrophs that can fix inorganic carbon to produce organic matter in the dark. Their distinctive physiological traits and high abundance in the water column indicate the significant ecological roles they play in the open ocean. In our study, we found predominant Thaumarchaeota in the microbial community amended with cyanobacteria-derived lysate under the dark condition. Furthermore, Thaumarchaeota remained dominant in the microbial community even after 1 year of incubation. Through the ammonification process, dissolved organic matter (DOM) from cyanobacterial lysate was converted to ammonium which was used as an energy source for Thaumarchaeota to fix inorganic carbon into biomass. Our study further advocates the important roles of Thaumarchaeota in the ocean's biogeochemical cycle.},
}
@article {pmid36584837,
year = {2023},
author = {Yang, WT and Shen, LD and Bai, YN},
title = {Role and regulation of anaerobic methane oxidation catalyzed by NC10 bacteria and ANME-2d archaea in various ecosystems.},
journal = {Environmental research},
volume = {219},
number = {},
pages = {115174},
doi = {10.1016/j.envres.2022.115174},
pmid = {36584837},
issn = {1096-0953},
mesh = {*Archaea ; *Ecosystem ; Nitrites ; Methane ; Anaerobiosis ; Bacteria ; Oxidation-Reduction ; Catalysis ; Geologic Sediments ; Phylogeny ; },
abstract = {Freshwater wetlands, paddy fields, inland aquatic ecosystems and coastal wetlands are recognized as important sources of atmospheric methane (CH4). Currently, increasing evidence shows the potential importance of the anaerobic oxidation of methane (AOM) mediated by NC10 bacteria and a novel cluster of anaerobic methanotrophic archaea (ANME)-ANME-2d in mitigating CH4 emissions from different ecosystems. To better understand the role of NC10 bacteria and ANME-2d archaea in CH4 emission reduction, the current review systematically summarizes different AOM processes and the functional microorganisms involved in freshwater wetlands, paddy fields, inland aquatic ecosystems and coastal wetlands. NC10 bacteria are widely present in these ecosystems, and the nitrite-dependent AOM is identified as an important CH4 sink and induces nitrogen loss. Nitrite- and nitrate-dependent AOM co-occur in the environment, and they are mainly affected by soil/sediment inorganic nitrogen and organic carbon contents. Furthermore, salinity is another key factor regulating the two AOM processes in coastal wetlands. In addition, ANME-2d archaea have the great potential to couple AOM to the reduction of iron (III), manganese (IV), sulfate, and even humics in different ecosystems. However, the study on the environmental distribution of ANME-2d archaea and their role in CH4 mitigation in environments is insufficient. In this study, we propose several directions for future research on the different AOM processes and respective functional microorganisms.},
}
@article {pmid36573238,
year = {2022},
author = {Moll, J and Hoppe, B},
title = {Evaluation of primers for the detection of deadwood-inhabiting archaea via amplicon sequencing.},
journal = {PeerJ},
volume = {10},
number = {},
pages = {e14567},
pmid = {36573238},
issn = {2167-8359},
mesh = {*Archaea/genetics ; Ecosystem ; Bacteria/genetics ; *Euryarchaeota ; Wood/microbiology ; Trees/microbiology ; },
abstract = {Archaea have been reported from deadwood of a few different tree species in temperate and boreal forest ecosystems in the past. However, while one of their functions is well linked to methane production any additional contribution to wood decomposition is not understood and underexplored which may be also attributed to lacking investigations on their diversity in this substrate. With this current work, we aim at encouraging further investigations by providing aid in primer choice for DNA metabarcoding using Illumina amplicon sequencing. We tested 16S primer pairs on genomic DNA extracted from woody tissue of four temperate deciduous tree species. Three primer pairs were specific to archaea and one prokaryotic primer pair theoretically amplifies both, bacterial and archaeal DNA. Methanobacteriales and Methanomassiliicoccales have been consistently identified as dominant orders across all datasets but significant variability in ASV richness was observed using different primer combinations. Nitrososphaerales have only been identified when using archaea-specific primer sets. In addition, the most commonly applied primer combination targeting prokaryotes in general yielded the lowest relative proportion of archaeal sequences per sample, which underlines the fact, that using target specific primers unraveled a yet unknown diversity of archaea in deadwood. Hence, archaea seem to be an important group of the deadwood-inhabiting community and further research is needed to explore their role during the decomposition process.},
}
@article {pmid36567186,
year = {2023},
author = {Zhang, X and Zhang, C and Liu, Y and Zhang, R and Li, M},
title = {Non-negligible roles of archaea in coastal carbon biogeochemical cycling.},
journal = {Trends in microbiology},
volume = {31},
number = {6},
pages = {586-600},
doi = {10.1016/j.tim.2022.11.008},
pmid = {36567186},
issn = {1878-4380},
mesh = {*Archaea/genetics/metabolism ; Ecosystem ; *Microbiota ; Methane/metabolism ; Carbon/metabolism ; },
abstract = {Coastal zones are among the world's most productive ecosystems. They store vast amounts of organic carbon, as 'blue carbon' reservoirs, and impact global climate change. Archaeal communities are integral components of coastal microbiomes but their ecological roles are often overlooked. However, archaeal diversity, metabolism, evolution, and interactions, revealed by recent studies using rapidly developing cutting-edge technologies, place archaea as important players in coastal carbon biogeochemical cycling. We here summarize the latest advances in the understanding of archaeal carbon cycling processes in coastal ecosystems, specifically, archaeal involvement in CO2 fixation, organic biopolymer transformation, and methane metabolism. We also showcase the potential to use of archaeal communities to increase carbon sequestration and reduce methane production, with implications for mitigating climate change.},
}
@article {pmid36552364,
year = {2022},
author = {Li, Q and Wang, N and Han, W and Zhang, B and Zang, J and Qin, Y and Wang, L and Liu, J and Zhang, T},
title = {Soil Geochemical Properties Influencing the Diversity of Bacteria and Archaea in Soils of the Kitezh Lake Area, Antarctica.},
journal = {Biology},
volume = {11},
number = {12},
pages = {},
pmid = {36552364},
issn = {2079-7737},
support = {No.ZR2020KC036//Natural Science Foundation of Shandong Province/ ; No.GY0219Q10//Basic Scientific Fund for National Public Research Institutes of China/ ; No.41776198//National Natural Science Foundation of China/ ; },
abstract = {It is believed that polar regions are influenced by global warming more significantly, and because polar regions are less affected by human activities, they have certain reference values for future predictions. This study aimed to investigate the effects of climate warming on soil microbial communities in lake areas, taking Kitezh Lake, Antarctica as the research area. Below-peak soil, intertidal soil, and sediment were taken at the sampling sites, and we hypothesized that the diversity and composition of the bacterial and archaeal communities were different among the three sampling sites. Through 16S rDNA sequencing and analysis, bacteria and archaea with high abundance were obtained. Based on canonical correspondence analysis and redundancy analysis, pH and phosphate had a great influence on the bacterial community whereas pH and nitrite had a great influence on the archaeal community. Weighted gene coexpression network analysis was used to find the hub bacteria and archaea related to geochemical factors. The results showed that in addition to pH, phosphate, and nitrite, moisture content, ammonium, nitrate, and total carbon content also play important roles in microbial diversity and structure at different sites by changing the abundance of some key microbiota.},
}
@article {pmid36544005,
year = {2023},
author = {Löwe, J},
title = {Mysterious Asgard archaea microbes reveal their inner secrets.},
journal = {Nature},
volume = {613},
number = {7943},
pages = {246-248},
pmid = {36544005},
issn = {1476-4687},
mesh = {*Archaea/genetics ; Phylogeny ; *Eukaryotic Cells ; Eukaryota/genetics ; Genome, Archaeal ; },
}
@article {pmid36543797,
year = {2022},
author = {Zhao, W and Zhong, B and Zheng, L and Tan, P and Wang, Y and Leng, H and de Souza, N and Liu, Z and Hong, L and Xiao, X},
title = {Proteome-wide 3D structure prediction provides insights into the ancestral metabolism of ancient archaea and bacteria.},
journal = {Nature communications},
volume = {13},
number = {1},
pages = {7861},
pmid = {36543797},
issn = {2041-1723},
mesh = {*Archaea/genetics/metabolism ; *Proteome/metabolism ; Phylogeny ; Evolution, Molecular ; Bacteria/genetics/metabolism ; },
abstract = {Ancestral metabolism has remained controversial due to a lack of evidence beyond sequence-based reconstructions. Although prebiotic chemists have provided hints that metabolism might originate from non-enzymatic protometabolic pathways, gaps between ancestral reconstruction and prebiotic processes mean there is much that is still unknown. Here, we apply proteome-wide 3D structure predictions and comparisons to investigate ancestorial metabolism of ancient bacteria and archaea, to provide information beyond sequence as a bridge to the prebiotic processes. We compare representative bacterial and archaeal strains, which reveal surprisingly similar physiological and metabolic characteristics via microbiological and biophysical experiments. Pairwise comparison of protein structures identify the conserved metabolic modules in bacteria and archaea, despite interference from overly variable sequences. The conserved modules (for example, middle of glycolysis, partial TCA, proton/sulfur respiration, building block biosynthesis) constitute the basic functions that possibly existed in the archaeal-bacterial common ancestor, which are remarkably consistent with the experimentally confirmed protometabolic pathways. These structure-based findings provide a new perspective to reconstructing the ancestral metabolism and understanding its origin, which suggests high-throughput protein 3D structure prediction is a promising approach, deserving broader application in future ancestral exploration.},
}
@article {pmid36541769,
year = {2023},
author = {Bai, T and Pu, X and Guo, X and Liu, J and Zhao, L and Zhang, X and Zhang, S and Cheng, L},
title = {Effects of Dietary Nonfibrous Carbohydrate/Neutral Detergent Fiber Ratio on Methanogenic Archaea and Cellulose-Degrading Bacteria in the Rumen of Karakul Sheep: a 16S rRNA Gene Sequencing Study.},
journal = {Applied and environmental microbiology},
volume = {89},
number = {1},
pages = {e0129122},
pmid = {36541769},
issn = {1098-5336},
mesh = {Animals ; *Archaea/metabolism ; *Bacteria/metabolism ; Cellulose/metabolism ; Diet/veterinary ; *Dietary Carbohydrates/metabolism ; *Dietary Fiber/metabolism ; Methane/metabolism ; RNA, Ribosomal, 16S/genetics/metabolism ; *Rumen/metabolism/microbiology ; Sheep, Domestic ; },
abstract = {The study was conducted to investigate the effects of dietary nonfibrous carbohydrate (NFC)/neutral detergent fiber (NDF) ratio on methanogenic archaea and cellulose-degrading bacteria in Karakul sheep by 16S rRNA gene sequencing. Twelve Karakul sheep were randomly divided into four groups, each group with three replicates, and they were fed with four dietary NFC/NDF ratios at 0.54, 0.96, 1.37, and 1.90 as groups 1, 2, 3, and 4, respectively. The experiment lasted for four periods: I (1 to 18 days), II (19 to 36 days), III (37 to 54 days), and IV (55 to 72 days); during each period, rumen contents were collected before morning feeding to investigate on methanogenic archaea and cellulose-degrading bacteria. The results showed that with an increase in dietary NFC/NDF ratio, the number of rumen archaea operational taxonomic units and the diversity of archaea decrease. The most dominant methanogens did not change with dietary NFC/NDF ratio and prolongation of experimental periods. Methanobrevibacter was the most dominant genus. At the species level, the relative abundance of Methanobrevibacter ruminantium first increased and then decreased when the NFC/NDF ratio increased. When the dietary NFC/NDF ratio was 0.96, the structure of archaea was largely changed, and the relative abundance of Fibrobacter sp. strain UWCM, Ruminococcus flavefaciens, and Ruminococcus albus were the highest. When the dietary NFC/NDF ratio was 1.37, the relative abundance of Butyrivibrio fibrisolvens was higher than for other groups. Based on all the data, we concluded that a dietary NFC/NDF ratio of ca. 0.96 to 1.37 was a suitable ratio to support optimal sheep production. IMPORTANCE CH4 produced by ruminants aggravates the greenhouse effect and cause wastage of feed energy, and CH4 emissions are related to methanogens. According to the current literature, there is a symbiotic relationship between methanogens and cellulolytic bacteria, so reducing methane will inevitably affect the degradation of fiber materials. This experiment used 16S rRNA gene high-throughput sequencing technology to explore the balance relationship between methanogens and cellulolytic bacteria for the first time through a long-term feeding period. The findings provide fundamental data, supporting for the diet structures with potential to reduce CH4 emission.},
}
@article {pmid36529166,
year = {2023},
author = {Jiang, Z and Tang, S and Liao, Y and Li, S and Wang, S and Zhu, X and Ji, G},
title = {Effect of low temperature on contributions of ammonia oxidizing archaea and bacteria to nitrous oxide in constructed wetlands.},
journal = {Chemosphere},
volume = {313},
number = {},
pages = {137585},
doi = {10.1016/j.chemosphere.2022.137585},
pmid = {36529166},
issn = {1879-1298},
mesh = {*Archaea/genetics ; *Nitrous Oxide ; Ammonia ; Wetlands ; Temperature ; Nitrification ; Oxidation-Reduction ; Soil Microbiology ; Bacteria/genetics ; Phylogeny ; },
abstract = {Constructed wetlands (CWs) have been widely used for ecological remediation of micro-polluted source water. Nitrous oxide (N2O) from CWs has caused great concern as a greenhouse gas. However, the contribution of ammonia oxidation driven by ammonia oxidizing archaea (AOA) and ammonia oxidizing bacteria (AOB) to N2O emission, especially at low temperature, was unknown. This study aimed to quantify the contributions of AOA and AOB to N2O through lab-scale subsurface CWs. The N2O emission flux of CW at 8 °C was 1.23 mg m[-2]·h[-1], significantly lower than that at 25 °C (1.92 mg m[-2]·h[-1]). The contribution of ammonia oxidation to N2O at 8 °C (33.04%) was significantly higher than that at 25 °C (24.17%). The N2O production from AOA increased from 1.91 ng N·g[-1] at 25 °C to 4.11 ng N·g[-1] soil at 8 °C and its contribution increased from 23.38% to 30.18% (P < 0.05). Low temperature impaired functional gene groups and inhibited the activity of AOB, resulting in its declined contribution. Based on the transcriptional analysis, AOA was less affected by low temperature, thus stably contributing to N2O. Moreover, community diversity and relationships of AOA were enhanced at 8 °C, while AOB declined. The results confirmed the significant contribution of AOA and demonstrated molecular mechanisms (higher activity and community stability) of the increased contribution of AOA to N2O at low temperature.},
}
@article {pmid38818484,
year = {2022},
author = {Zhou, Z and Liu, Y and Anantharaman, K and Li, M},
title = {The expanding Asgard archaea invoke novel insights into Tree of Life and eukaryogenesis.},
journal = {mLife},
volume = {1},
number = {4},
pages = {374-381},
pmid = {38818484},
issn = {2770-100X},
abstract = {The division of organisms on the Tree of Life into either a three-domain (3D) tree or a two-domain (2D) tree has been disputed for a long time. Ever since the discovery of Archaea by Carl Woese in 1977 using 16S ribosomal RNA sequence as the evolutionary marker, there has been a great advance in our knowledge of not only the growing diversity of Archaea but also the evolutionary relationships between different lineages of living organisms. Here, we present this perspective to summarize the progress of archaeal diversity and changing notion of the Tree of Life. Meanwhile, we provide the latest progress in genomics/physiology-based discovery of Asgard archaeal lineages as the closest relative of Eukaryotes. Furthermore, we propose three major directions for future research on exploring the "next one" closest Eukaryote relative, deciphering the function of archaeal eukaryotic signature proteins and eukaryogenesis from both genomic and physiological aspects, and understanding the roles of horizontal gene transfer, viruses, and mobile elements in eukaryogenesis.},
}
@article {pmid36519377,
year = {2023},
author = {Kucukyildirim, S and Ozdemirel, HO and Lynch, M},
title = {Similar mutation rates but different mutation spectra in moderate and extremely halophilic archaea.},
journal = {G3 (Bethesda, Md.)},
volume = {13},
number = {3},
pages = {},
pmid = {36519377},
issn = {2160-1836},
support = {R35 GM122566/GM/NIGMS NIH HHS/United States ; },
mesh = {Mutation Rate ; *Haloferax volcanii/genetics/metabolism ; Mutation ; DNA Repair ; *Archaeal Proteins/genetics/metabolism ; Archaea/genetics ; },
abstract = {Archaea are a major part of Earth's microbiota and extremely diverse. Yet, we know very little about the process of mutation that drives such diversification. To expand beyond previous work with the moderate halophilic archaeal species Haloferax volcanii, we performed a mutation-accumulation experiment followed by whole-genome sequencing in the extremely halophilic archaeon Halobacterium salinarum. Although Hfx. volcanii and Hbt. salinarum have different salt requirements, both species have highly polyploid genomes and similar GC content. We accumulated mutations for an average of 1250 generations in 67 mutation accumulation lines of Hbt. salinarum, and revealed 84 single-base substitutions and 10 insertion-deletion mutations. The estimated base-substitution mutation rate of 3.99 × 10-10 per site per generation or 1.0 × 10-3 per genome per generation in Hbt. salinarum is similar to that reported for Hfx. volcanii (1.2 × 10-3 per genome per generation), but the genome-wide insertion-deletion rate and spectrum of mutations are somewhat dissimilar in these archaeal species. The spectra of spontaneous mutations were AT biased in both archaea, but they differed in significant ways that may be related to differences in the fidelity of DNA replication/repair mechanisms or a simple result of the different salt concentrations.},
}
@article {pmid36512566,
year = {2022},
author = {, },
title = {Expression of Concern: A Versatile Medium for Cultivating Methanogenic Archaea.},
journal = {PloS one},
volume = {17},
number = {12},
pages = {e0278740},
pmid = {36512566},
issn = {1932-6203},
}
@article {pmid36499474,
year = {2022},
author = {Ginsbach, LF and Gonzalez, JM},
title = {Understanding Life at High Temperatures: Relationships of Molecular Channels in Enzymes of Methanogenic Archaea and Their Growth Temperatures.},
journal = {International journal of molecular sciences},
volume = {23},
number = {23},
pages = {},
pmid = {36499474},
issn = {1422-0067},
support = {EQC2019-005634-P//Ministerio de Ciencia e Innovaci&#xf3;n/ ; EQC2019-005634-P//Feder/ ; PID2020-119373GB-I00//Ministerio de Ciencia e Innovaci&#xf3;n/ ; Laura Ginsbach//German Academic Exchange Service/ ; },
mesh = {*Archaea/metabolism ; Phylogeny ; *Methane/metabolism ; Temperature ; Hot Temperature ; },
abstract = {Analyses of protein structures have shown the existence of molecular channels in enzymes from Prokaryotes. Those molecular channels suggest a critical role of spatial voids in proteins, above all, in those enzymes functioning under high temperature. It is expected that these spaces within the protein structure are required to access the active site and to maximize availability and thermal stability of their substrates and cofactors. Interestingly, numerous substrates and cofactors have been reported to be highly temperature-sensitive biomolecules. Methanogens represent a singular phylogenetic group of Archaea that performs anaerobic respiration producing methane during growth. Methanogens inhabit a variety of environments including the full range of temperatures for the known living forms. Herein, we carry out a dimensional analysis of molecular tunnels in key enzymes of the methanogenic pathway from methanogenic Archaea growing optimally over a broad temperature range. We aim to determine whether the dimensions of the molecular tunnels are critical for those enzymes from thermophiles. Results showed that at increasing growth temperature the dimensions of molecular tunnels in the enzymes methyl-coenzyme M reductase and heterodisulfide reductase become increasingly restrictive and present strict limits at the highest growth temperatures, i.e., for hyperthermophilic methanogens. However, growth at lower temperature allows a wide dimensional range for the molecular spaces in these enzymes. This is in agreement with previous suggestions on a potential major role of molecular tunnels to maintain biomolecule stability and activity of some enzymes in microorganisms growing at high temperatures. These results contribute to better understand archaeal growth at high temperatures. Furthermore, an optimization of the dimensions of molecular tunnels would represent an important adaptation required to maintain the activity of key enzymes of the methanogenic pathway for those methanogens growing optimally at high temperatures.},
}
@article {pmid36461738,
year = {2023},
author = {Ponlachantra, K and Suginta, W and Robinson, RC and Kitaoku, Y},
title = {AlphaFold2: A versatile tool to predict the appearance of functional adaptations in evolution: Profilin interactions in uncultured Asgard archaea: Profilin interactions in uncultured Asgard archaea.},
journal = {BioEssays : news and reviews in molecular, cellular and developmental biology},
volume = {45},
number = {2},
pages = {e2200119},
doi = {10.1002/bies.202200119},
pmid = {36461738},
issn = {1521-1878},
support = {JPMJCR19S5//JST CREST/ ; //Moore-Simons Project/ ; GBMF9743//Origin of the Eukaryotic Cell/ ; //Vidyasirimedhi Institute of Science and Technology (VISTEC)/ ; },
mesh = {*Archaea/metabolism ; *Profilins/genetics/metabolism ; Actins ; Phylogeny ; Furylfuramide/metabolism ; Eukaryota/metabolism ; },
abstract = {The release of AlphaFold2 (AF2), a deep-learning-aided, open-source protein structure prediction program, from DeepMind, opened a new era of molecular biology. The astonishing improvement in the accuracy of the structure predictions provides the opportunity to characterize protein systems from uncultured Asgard archaea, key organisms in evolutionary biology. Despite the accumulation in metagenomics-derived Asgard archaea eukaryotic-like protein sequences, limited structural and biochemical information have restricted the insight in their potential functions. In this review, we focus on profilin, an actin-dynamics regulating protein, which in eukaryotes, modulates actin polymerization through (1) direct actin interaction, (2) polyproline binding, and (3) phospholipid binding. We assess AF2-predicted profilin structures in their potential abilities to participate in these activities. We demonstrate that AF2 is a powerful new tool for understanding the emergence of biological functional traits in evolution.},
}
@article {pmid36445127,
year = {2022},
author = {Woo, Y and Cruz, MC and Wuertz, S},
title = {Selective Enrichment of Nitrososphaera viennensis-Like Ammonia-Oxidizing Archaea over Ammonia-Oxidizing Bacteria from Drinking Water Biofilms.},
journal = {Microbiology spectrum},
volume = {10},
number = {6},
pages = {e0184522},
pmid = {36445127},
issn = {2165-0497},
mesh = {*Archaea ; *Drinking Water ; Ammonia ; Nitrites ; Oxidation-Reduction ; Soil Microbiology ; Bacteria/genetics ; Biofilms ; Pyruvates ; Phylogeny ; },
abstract = {Ammonia-oxidizing archaea (AOA) can oxidize ammonia to nitrite for energy gain. They have been detected in chloraminated drinking water distribution systems (DWDS) along with the more common ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB). To date, no members of the AOA have been isolated or enriched from drinking water environments. To begin the investigation of the role of AOA in chloraminated DWDS, we developed a selective approach using biofilm samples from a full-scale operational network as inoculum. A Nitrososphaera viennensis-like AOA taxon was enriched from a mixed community that also included Nitrosomonas-like AOB while gradually scaling up the culture volume. Dimethylthiourea (DMTU) and pyruvate at 100 μM were added to promote the growth of AOA while inhibiting AOB. This resulted in the eventual washout of AOB, while NOB were absent after 2 or 3 rounds of amendment with 24 μM sodium azide. The relative abundance of AOA in the enrichment increased from 0.2% to 39.5% after adding DMTU and pyruvate, and further to 51.6% after filtration through a 0.45-μm pore size membrane, within a period of approximately 6 months. IMPORTANCE Chloramination has been known to increase the risk of nitrification episodes in DWDS due to the presence of ammonia-oxidizing microorganisms. Among them, AOB are more frequently detected than AOA. All publicly available cultures of AOA have been isolated from soil, marine or surface water environments, meaning they are allochthonous to DWDS. Hence, monochloramine exposure studies involving these strains may not accurately reflect their role in DWDS. The described method allows for the rapid enrichment of autochthonous AOA from drinking water nitrifying communities. The high relative abundance of AOA in the resulting enrichment culture reduces any confounding effects of co-existing heterotrophic bacteria when investigating the response of AOA to varied levels of monochloramine in drinking water.},
}
@article {pmid36444822,
year = {2023},
author = {Hagagy, N and Abdel-Mawgoud, M and Akhtar, N and Selim, S and AbdElgawad, H},
title = {The new isolated Archaea strain improved grain yield, metabolism and quality of wheat plants under Co stress conditions.},
journal = {Journal of plant physiology},
volume = {280},
number = {},
pages = {153876},
doi = {10.1016/j.jplph.2022.153876},
pmid = {36444822},
issn = {1618-1328},
mesh = {*Triticum/metabolism ; *Edible Grain ; Soil/chemistry ; Cobalt/metabolism ; Sugars/metabolism ; },
abstract = {Heavy metal (e.g. cobalt) pollution causes a serious of environmental and agricultural problems. On the other hand, plant growth-promoting microorganisms enhance plant growth and mitigate heavy metal stress. Herein, we isolated and identified the unclassified species strain NARS9, belong to Haloferax,. Cobalt (Co, 200 mg/kg soil) stress mitigating impact of the identified on wheat grains yield, primary and secondary metabolism and grain quality was investigated. Co alone significantly induced Co accumulation in wheat grain (260%), and consequently reduced wheat yield (130%) and quality. Haloferax NARS9 alone significantly enhanced grain chemicals composition (i.e., total sugars (89%) and organic acids (e.g., oxalic and isobutyric acids), essential amino acids (e.g., threonine, lysine, and histidine) and unsaturated fatty acids (e.g. eicosenoic, erucic and tetracosenoic acids). Interestingly, Co stress induced wheat grain yield, reduction were significantly mitigated by Haloferax NARS9 treatment by 26% compared to Co stress alone. Under Co stress, Haloferax NARS9 significantly increased sugar metabolism including sucrose and starch levels and their metabolic enzymes (i.e. invertases, sucrose synthase, starch synthase). This in turn increased organic acid (e.g. oxalic (70%) and malic acids (60%)) and amino acids. levels and biosynthetic enzymes, e.g. glutamine synthetase and threonine synthase. Increased sugars levels by Haloferax NARS9 under Co treatment also provided a route for the biosynthesis of saturated fatty acids, particularly palmitic and stearic acids. Furthermore, Haloferax NARS9 treatment supported the wheat nutritive value through increasing minerals (Ca, Fe, Mn, Zn) and antioxidants i.e., polyphenol, flavonoids, ASC and GSH and total polyamines by 50%, 110%, 400%, 30%, and 90% respectively). These in parallel with the increase in the activity of (phenylalanine ammonia-lyase (110%) in phenolic metabolism). Overall, this study demonstrates the potentiality of Haloferax NARS9 in harnessing carbon and nitrogen metabolism differentially in wheat plants to cope with Co toxicity. Our results also suggested that the use of Haloferax NARS9 in agricultural fields can improve growth and nutritional value of wheat grains.},
}
@article {pmid36434094,
year = {2022},
author = {Sato, T and Utashima, SH and Yoshii, Y and Hirata, K and Kanda, S and Onoda, Y and Jin, JQ and Xiao, S and Minami, R and Fukushima, H and Noguchi, A and Manabe, Y and Fukase, K and Atomi, H},
title = {A non-carboxylating pentose bisphosphate pathway in halophilic archaea.},
journal = {Communications biology},
volume = {5},
number = {1},
pages = {1290},
pmid = {36434094},
issn = {2399-3642},
mesh = {*Ribulose-Bisphosphate Carboxylase/genetics/metabolism ; *Ribose/metabolism ; Pentoses/metabolism ; Archaea/genetics/metabolism ; Guanosine/metabolism ; Phosphates ; },
abstract = {Bacteria and Eucarya utilize the non-oxidative pentose phosphate pathway to direct the ribose moieties of nucleosides to central carbon metabolism. Many archaea do not possess this pathway, and instead, Thermococcales utilize a pentose bisphosphate pathway involving ribose-1,5-bisphosphate (R15P) isomerase and ribulose-1,5-bisphosphate (RuBP) carboxylase/oxygenase (Rubisco). Intriguingly, multiple genomes from halophilic archaea seem only to harbor R15P isomerase, and do not harbor Rubisco. In this study, we identify a previously unrecognized nucleoside degradation pathway in halophilic archaea, composed of guanosine phosphorylase, ATP-dependent ribose-1-phosphate kinase, R15P isomerase, RuBP phosphatase, ribulose-1-phosphate aldolase, and glycolaldehyde reductase. The pathway converts the ribose moiety of guanosine to dihydroxyacetone phosphate and ethylene glycol. Although the metabolic route from guanosine to RuBP via R15P is similar to that of the pentose bisphosphate pathway in Thermococcales, the downstream route does not utilize Rubisco and is unique to halophilic archaea.},
}
@article {pmid36414709,
year = {2023},
author = {Lee, S and Sieradzki, ET and Nicol, GW and Hazard, C},
title = {Propagation of viral genomes by replicating ammonia-oxidising archaea during soil nitrification.},
journal = {The ISME journal},
volume = {17},
number = {2},
pages = {309-314},
pmid = {36414709},
issn = {1751-7370},
mesh = {*Archaea/metabolism ; *Soil/chemistry ; Nitrification ; Bacteria/genetics ; Ammonia/metabolism ; Soil Microbiology ; Oxidation-Reduction ; Genome, Viral ; Phylogeny ; },
abstract = {Ammonia-oxidising archaea (AOA) are a ubiquitous component of microbial communities and dominate the first stage of nitrification in some soils. While we are beginning to understand soil virus dynamics, we have no knowledge of the composition or activity of those infecting nitrifiers or their potential to influence processes. This study aimed to characterise viruses having infected autotrophic AOA in two nitrifying soils of contrasting pH by following transfer of assimilated CO2-derived [13]C from host to virus via DNA stable-isotope probing and metagenomic analysis. Incorporation of [13]C into low GC mol% AOA and virus genomes increased DNA buoyant density in CsCl gradients but resulted in co-migration with dominant non-enriched high GC mol% genomes, reducing sequencing depth and contig assembly. We therefore developed a hybrid approach where AOA and virus genomes were assembled from low buoyant density DNA with subsequent mapping of [13]C isotopically enriched high buoyant density DNA reads to identify activity of AOA. Metagenome-assembled genomes were different between the two soils and represented a broad diversity of active populations. Sixty-four AOA-infecting viral operational taxonomic units (vOTUs) were identified with no clear relatedness to previously characterised prokaryote viruses. These vOTUs were also distinct between soils, with 42% enriched in [13]C derived from hosts. The majority were predicted as capable of lysogeny and auxiliary metabolic genes included an AOA-specific multicopper oxidase suggesting infection may augment copper uptake essential for central metabolic functioning. These findings indicate virus infection of AOA may be a frequent process during nitrification with potential to influence host physiology and activity.},
}
@article {pmid36413802,
year = {2023},
author = {Matse, DT and Jeyakumar, P and Bishop, P and Anderson, CWN},
title = {Copper induces nitrification by ammonia-oxidizing bacteria and archaea in pastoral soils.},
journal = {Journal of environmental quality},
volume = {52},
number = {1},
pages = {49-63},
doi = {10.1002/jeq2.20440},
pmid = {36413802},
issn = {1537-2537},
mesh = {*Archaea/genetics ; *Soil ; Bacteria/genetics ; Nitrification ; Ammonia ; Copper ; Oxidation-Reduction ; Soil Microbiology ; Phylogeny ; },
abstract = {Copper (Cu) is the main co-factor in the functioning of the ammonia monooxygenase (AMO) enzyme, which is responsible for the first step of ammonia oxidation. We report a greenhouse-based pot experiment that examines the response of ammonia-oxidizing bacteria and archaea (AOB and AOA) to different bioavailable Cu concentrations in three pastoral soils (Recent, Pallic, and Pumice soils) planted with ryegrass (Lolium perenne L.). Five treatments were used: control (no urine and Cu), urine only at 300 mg N kg[-1] soil (Cu0), urine + 1 mg Cu kg[-1] soil (Cu1), urine + 10 mg Cu kg[-1] soil (Cu10), and urine + 100 mg Cu kg[-1] soil (Cu100). Pots were destructively sampled at Day 0, 1, 7, 15, and 25 after urine application. The AOB/AOA amoA gene abundance was analyzed by real-time quantitative polymerase chain reaction at Days 1 and 15. The AOB amoA gene abundance increased 10.0- and 22.6-fold in the Recent soil and 2.1- and 2.5-fold in the Pallic soil for the Cu10 compared with Cu0 on Days 1 and 15, respectively. In contrast, the Cu100 was associated with a reduction in AOB amoA gene abundance in the Recent and Pallic soils but not in the Pumice soil. This may be due to the influence of soil cation exchange capacity differences on the bioavailable Cu. Bioavailable Cu in the Recent and Pallic soils influenced nitrification and AOB amoA gene abundance, as evidenced by the strong positive correlation between bioavailable Cu, nitrification, and AOB amoA. However, bioavailable Cu did not influence the nitrification and AOA amoA gene abundance increase.},
}
@article {pmid36406397,
year = {2022},
author = {Yuan, H and Zhang, W and Yin, H and Zhang, R and Wang, J},
title = {Taxonomic dependency of beta diversity for bacteria, archaea, and fungi in a semi-arid lake.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {998496},
pmid = {36406397},
issn = {1664-302X},
abstract = {Microbial beta diversity has been recently studied along the water depth in aquatic ecosystems, however its turnover and nestedness components remain elusive especially for multiple taxonomic groups. Based on the beta diversity partitioning developed by Baselga and Local Contributions to Beta Diversity (LCBD) partitioning by Legendre, we examined the water-depth variations in beta diversity components of bacteria, archaea and fungi in surface sediments of Hulun Lake, a semi-arid lake in northern China, and further explored the relative importance of environmental drivers underlying their patterns. We found that the relative abundances of Proteobacteria, Chloroflexi, Euryarchaeota, and Rozellomycota increased toward deep water, while Acidobacteria, Parvarchaeota, and Chytridiomycota decreased. For bacteria and archaea, there were significant (p < 0.05) decreasing water-depth patterns for LCBD and LCBDRepl (i.e., species replacement), while increasing patterns for total beta diversity and turnover, implying that total beta diversity and LCBD were dominated by species turnover or LCBDRepl. Further, bacteria showed a strong correlation with archaea regarding LCBD, total beta diversity and turnover. Such parallel patterns among bacteria and archaea were underpinned by similar ecological processes like environmental selection. Total beta diversity and turnover were largely affected by sediment total nitrogen, while LCBD and LCBDRepl were mainly constrained by water NO2 [-]-N and NO3 [-]-N. For fungal community variation, no significant patterns were observed, which may be due to different drivers like water nitrogen or phosphorus. Taken together, our findings provide compelling evidences for disentangling the underlying mechanisms of community variation in multiple aquatic microbial taxonomic groups.},
}
@article {pmid36402873,
year = {2022},
author = {Hu, L and Dong, Z and Wang, Z and Xiao, L and Zhu, B},
title = {The contributions of ammonia oxidizing bacteria and archaea to nitrification-dependent N2O emission in alkaline and neutral purple soils.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {19928},
pmid = {36402873},
issn = {2045-2322},
support = {U20A20107//the Key Project of National Science Foundation of China/ ; 41301266//National Natural Science Foundation of China/ ; },
mesh = {*Archaea/genetics ; Nitrification ; Soil/chemistry ; Ammonia ; Soil Microbiology ; Bacteria/genetics ; Oxidation-Reduction ; *Betaproteobacteria/genetics ; },
abstract = {Nitrification is believed to be one of the primary processes of N2O emission in the agroecological system, which is controlled by soil microbes and mainly regulated by soil pH, oxygen content and NH4[+] availability. Previous studies have proved that the relative contributions of ammonia oxidizing bacteria (AOB) and archaea (AOA) to N2O production were varied with soil pH, however, there is still no consensus on the regulating mechanism of nitrification-derived N2O production by soil pH. In this study, 1-octyne (a selective inhibitor of AOB) and acetylene (an inhibitor of AOB and AOA) were used in a microcosm incubation experiment to differentiate the relative contribution of AOA and AOB to N2O emissions in a neutral (pH = 6.75) and an alkaline (pH = 8.35) soils. We found that the amendment of ammonium (NH4[+]) observably stimulated the production of both AOA and AOB-related N2O and increased the ammonia monooxygenase (AMO) gene abundances of AOA and AOB in the two test soils. Among which, AOB dominated the process of ammonia oxidation in the alkaline soil, contributing 70.8% of N2O production derived from nitrification. By contrast, the contribution of AOA and AOB accounted for about one-third of nitrification-related N2O in acidic soil, respectively. The results indicated that pH was a key factor to change abundance and activity of AOA and AOB, which led to the differentiation of derivation of N2O production in purple soils. We speculate that both NH4[+] content and soil pH mediated specialization of ammonia-oxidizing microorganisms together; and both specialization results and N2O yield led to the different N2O emission characteristics in purple soils. These results may help inform the development of N2O reduction strategies in the future.},
}
@article {pmid36400771,
year = {2022},
author = {Schoelmerich, MC and Ouboter, HT and Sachdeva, R and Penev, PI and Amano, Y and West-Roberts, J and Welte, CU and Banfield, JF},
title = {A widespread group of large plasmids in methanotrophic Methanoperedens archaea.},
journal = {Nature communications},
volume = {13},
number = {1},
pages = {7085},
pmid = {36400771},
issn = {2041-1723},
mesh = {*Archaea/metabolism ; Anaerobiosis ; *Methane/metabolism ; Oxidation-Reduction ; Plasmids/genetics ; },
abstract = {Anaerobic methanotrophic (ANME) archaea obtain energy from the breakdown of methane, yet their extrachromosomal genetic elements are little understood. Here we describe large plasmids associated with ANME archaea of the Methanoperedens genus in enrichment cultures and other natural anoxic environments. By manual curation we show that two of the plasmids are large (155,605 bp and 191,912 bp), circular, and may replicate bidirectionally. The plasmids occur in the same copy number as the main chromosome, and plasmid genes are actively transcribed. One of the plasmids encodes three tRNAs, ribosomal protein uL16 and elongation factor eEF2; these genes appear to be missing in the host Methanoperedens genome, suggesting an obligate interdependence between plasmid and host. Our work opens the way for the development of genetic vectors to shed light on the physiology and biochemistry of Methanoperedens, and potentially genetically edit them to enhance growth and accelerate methane oxidation rates.},
}
@article {pmid36385454,
year = {2023},
author = {Zhou, Y and Zhou, L and Yan, S and Chen, L and Krupovic, M and Wang, Y},
title = {Diverse viruses of marine archaea discovered using metagenomics.},
journal = {Environmental microbiology},
volume = {25},
number = {2},
pages = {367-382},
doi = {10.1111/1462-2920.16287},
pmid = {36385454},
issn = {1462-2920},
mesh = {*Archaea/genetics/virology ; *Archaeal Viruses/genetics ; Genome, Viral ; Metagenomics/methods ; Phylogeny ; Viral Proteins/genetics ; },
abstract = {During the past decade, metagenomics became a method of choice for the discovery of novel viruses. However, host assignment for uncultured viruses remains challenging, especially for archaeal viruses, which are grossly undersampled compared to viruses of bacteria and eukaryotes. Here, we assessed the utility of CRISPR spacer targeting, tRNA gene matching and homology searches for viral signature proteins, such as major capsid proteins, for the assignment of archaeal hosts and validated these approaches on metaviromes from Yangshan Harbor (YSH). We report 35 new genomes of viruses which could be confidently assigned to hosts representing diverse lineages of marine archaea. We show that the archaeal YSH virome is highly diverse, with some viruses enriching the previously described virus groups, such as magroviruses of Marine Group II Archaea (Poseidoniales), and others representing novel groups of marine archaeal viruses. Metagenomic recruitment of Tara Oceans datasets on the YSH viral genomes demonstrated the presence of YSH Poseidoniales and Nitrososphaeria viruses in the global oceans, but also revealed the endemic YSH-specific viral lineages. Furthermore, our results highlight the relationship between the soil and marine thaumarchaeal viruses. We propose three new families within the class Caudoviricetes for the classification of the five complete viral genomes predicted to replicate in marine Poseidoniales and Nitrososphaeria, two ecologically important and widespread archaeal groups. This study illustrates the utility of viral metagenomics in exploring the archaeal virome and provides new insights into the diversity, distribution and evolution of marine archaeal viruses.},
}
@article {pmid36383678,
year = {2022},
author = {Ghaly, TM and Tetu, SG and Penesyan, A and Qi, Q and Rajabal, V and Gillings, MR},
title = {Discovery of integrons in Archaea: Platforms for cross-domain gene transfer.},
journal = {Science advances},
volume = {8},
number = {46},
pages = {eabq6376},
pmid = {36383678},
issn = {2375-2548},
abstract = {Horizontal gene transfer between different domains of life is increasingly being recognized as an important evolutionary driver, with the potential to increase the pace of biochemical innovation and environmental adaptation. However, the mechanisms underlying the recruitment of exogenous genes from foreign domains are mostly unknown. Integrons are a family of genetic elements that facilitate this process within Bacteria. However, they have not been reported outside Bacteria, and thus their potential role in cross-domain gene transfer has not been investigated. Here, we discover that integrons are also present in 75 archaeal metagenome-assembled genomes from nine phyla, and are particularly enriched among Asgard archaea. Furthermore, we provide experimental evidence that integrons can facilitate the recruitment of archaeal genes by bacteria. Our findings establish a previously unknown mechanism of cross-domain gene transfer whereby bacteria can incorporate archaeal genes from their surrounding environment via integron activity. These findings have important implications for prokaryotic ecology and evolution.},
}
@article {pmid36372432,
year = {2022},
author = {Kuroda, K and Kubota, K and Kagemasa, S and Nakai, R and Hirakata, Y and Yamamoto, K and Nobu, MK and Narihiro, T},
title = {Novel Cross-domain Symbiosis between Candidatus Patescibacteria and Hydrogenotrophic Methanogenic Archaea Methanospirillum Discovered in a Methanogenic Ecosystem.},
journal = {Microbes and environments},
volume = {37},
number = {4},
pages = {},
pmid = {36372432},
issn = {1347-4405},
mesh = {*Archaea/genetics ; Methanospirillum/genetics ; Symbiosis ; Ecosystem ; In Situ Hybridization, Fluorescence ; Phylogeny ; *Euryarchaeota ; Bacteria/genetics ; RNA, Ribosomal, 16S/genetics ; },
abstract = {To identify novel cross-domain symbiosis between Candidatus Patescibacteria and Archaea, we performed fluorescence in situ hybridization (FISH) on enrichment cultures derived from methanogenic bioreactor sludge with the newly designed 32-520-1066 probe targeting the family-level uncultured clade 32-520/UBA5633 lineage in the class Ca. Paceibacteria. All FISH-detectable 32-520/UBA5633 cells were attached to Methanospirillum, indicating high host specificity. Transmission electron microscopy observations revealed 32-520/UBA5633-like cells that were specifically adherent to the plug structure of Methanospirillum-like rod-shaped cells. The metagenome-assembled genomes of 32-520/UBA5633 encoded unique gene clusters comprising pilin signal peptides and type IV pilins. These results provide novel insights into unseen symbiosis between Ca. Patescibacteria and Archaea.},
}
@article {pmid36367391,
year = {2023},
author = {Boyd, ES and Spietz, RL and Kour, M and Colman, DR},
title = {A naturalist perspective of microbiology: Examples from methanogenic archaea.},
journal = {Environmental microbiology},
volume = {25},
number = {1},
pages = {184-198},
doi = {10.1111/1462-2920.16285},
pmid = {36367391},
issn = {1462-2920},
mesh = {Humans ; *Archaea/genetics ; *Euryarchaeota ; },
abstract = {Storytelling has been the primary means of knowledge transfer over human history. The effectiveness and reach of stories are improved when the message is appropriate for the target audience. Oftentimes, the stories that are most well received and recounted are those that have a clear purpose and that are told from a variety of perspectives that touch on the varied interests of the target audience. Whether scientists realize or not, they are accustomed to telling stories of their own scientific discoveries through the preparation of manuscripts, presentations, and lectures. Perhaps less frequently, scientists prepare review articles or book chapters that summarize a body of knowledge on a given subject matter, meant to be more holistic recounts of a body of literature. Yet, by necessity, such summaries are often still narrow in their scope and are told from the perspective of a particular discipline. In other words, interdisciplinary reviews or book chapters tend to be the rarity rather than the norm. Here, we advocate for and highlight the benefits of interdisciplinary perspectives on microbiological subjects.},
}
@article {pmid36358054,
year = {2022},
author = {Gu, S and Wang, R and Xing, H and Yu, M and Shen, S and Zhao, L and Sun, J and Li, Y},
title = {Effects of different low temperature conditions on anaerobic digestion efficiency of pig manure and composition of archaea community.},
journal = {Water science and technology : a journal of the International Association on Water Pollution Research},
volume = {86},
number = {5},
pages = {1181-1192},
doi = {10.2166/wst.2022.267},
pmid = {36358054},
issn = {0273-1223},
mesh = {Swine ; Animals ; *Manure ; *Archaea/metabolism ; Anaerobiosis ; Temperature ; Fatty Acids, Volatile/metabolism ; Bioreactors ; Methane/metabolism ; },
abstract = {To explore the effect of low temperature on the anaerobic digestion of pig manure, the anaerobic digestion experiment was carried out under the conditions of inoculum concentration of 30% and TS of 8%. Five low-temperature gradients of 4, 8, 12, 16 and 20 °C were set to study the activities of gas production, pH, solluted chemical oxygen demand (SCOD), volatile fatty acids (VFAs), coenzymes F420 and archaea community composition in the digestion process. The results were demonstrated: as the temperature decreased, the more unstable the gas production became, the less gas production produced, and the later the gas peak occurred. There were no significant peaks at either 4 °C or 8 °C, and the SCOD was unstable over time. From 12 °C, the SCOD increased over time, and the higher the temperature, the faster the growth trend. The pH was always greater than 7.6. 8, 12, 16, 20 °C had different degrees of VFAs accumulation at the late digestion stage. The higher the temperature, the greater the amount of volatile acid accumulation. When the VFAs of each reactor reached the maximum, the proportion of acetic acid also reached the highest. The digestion system of the five treatment groups was dominated by hydrogen-nutrient methanogenic pathway. The results could provide a further reference for the mechanism of anaerobic digestion of pig manure at low temperatures.},
}
@article {pmid36350548,
year = {2023},
author = {Hepowit, NL and Maupin-Furlow, JA},
title = {Application of Archaea in Deubiquitinase-Like Enzyme Discovery and Activity Assay.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2591},
number = {},
pages = {151-169},
pmid = {36350548},
issn = {1940-6029},
support = {R01 GM057498/GM/NIGMS NIH HHS/United States ; },
mesh = {*Ubiquitins/metabolism ; *Archaea/metabolism ; Ubiquitin/metabolism ; Eukaryotic Cells/metabolism ; Deubiquitinating Enzymes ; },
abstract = {Archaea can be used as microbial platforms to discover new types of deubiquitinase-like (DUB-like) enzymes and to produce ubiquitin/ubiquitin-like (Ub/Ubl) protein conjugates as substrates for DUB/DUB-like activity assays. Here we outline how to use archaea to synthesize, purify, and assay the activity of DUB-like enzymes with unusual properties, including catalytic activity in hypersaline conditions, organic solvents, and high temperatures. We also outline the application of archaea in forming Ub/Ubl isopeptide linkages that include the covalent attachments of diverse archaeal and eukaryotic Ub/Ubls to target proteins. Archaea form these Ub/Ubl-linked protein conjugates in vivo, and the resulting products are found to serve as useful DUB substrates for in vitro assays.},
}
@article {pmid36332026,
year = {2022},
author = {Adam, PS and Kolyfetis, GE and Bornemann, TLV and Vorgias, CE and Probst, AJ},
title = {Genomic remnants of ancestral methanogenesis and hydrogenotrophy in Archaea drive anaerobic carbon cycling.},
journal = {Science advances},
volume = {8},
number = {44},
pages = {eabm9651},
pmid = {36332026},
issn = {2375-2548},
abstract = {Anaerobic methane metabolism is among the hallmarks of Archaea, originating very early in their evolution. Here, we show that the ancestor of methane metabolizers was an autotrophic CO2-reducing hydrogenotrophic methanogen that possessed the two main complexes, methyl-CoM reductase (Mcr) and tetrahydromethanopterin-CoM methyltransferase (Mtr), the anaplerotic hydrogenases Eha and Ehb, and a set of other genes collectively called "methanogenesis markers" but could not oxidize alkanes. Overturning recent inferences, we demonstrate that methyl-dependent hydrogenotrophic methanogenesis has emerged multiple times independently, either due to a loss of Mtr while Mcr is inherited vertically or from an ancient lateral acquisition of Mcr. Even if Mcr is lost, Mtr, Eha, Ehb, and the markers can persist, resulting in mixotrophic metabolisms centered around the Wood-Ljungdahl pathway. Through their methanogenesis remnants, Thorarchaeia and two newly reconstructed order-level lineages in Archaeoglobi and Bathyarchaeia act as metabolically versatile players in carbon cycling of anoxic environments across the globe.},
}
@article {pmid36332013,
year = {2022},
author = {Verma, A and Åberg-Zingmark, E and Sparrman, T and Mushtaq, AU and Rogne, P and Grundström, C and Berntsson, R and Sauer, UH and Backman, L and Nam, K and Sauer-Eriksson, E and Wolf-Watz, M},
title = {Insights into the evolution of enzymatic specificity and catalysis: From Asgard archaea to human adenylate kinases.},
journal = {Science advances},
volume = {8},
number = {44},
pages = {eabm4089},
pmid = {36332013},
issn = {2375-2548},
mesh = {Humans ; *Archaea/genetics ; *Adenylate Kinase/chemistry ; Catalysis ; Catalytic Domain ; },
abstract = {Enzymatic catalysis is critically dependent on selectivity, active site architecture, and dynamics. To contribute insights into the interplay of these properties, we established an approach with NMR, crystallography, and MD simulations focused on the ubiquitous phosphotransferase adenylate kinase (AK) isolated from Odinarchaeota (OdinAK). Odinarchaeota belongs to the Asgard archaeal phylum that is believed to be the closest known ancestor to eukaryotes. We show that OdinAK is a hyperthermophilic trimer that, contrary to other AK family members, can use all NTPs for its phosphorylation reaction. Crystallographic structures of OdinAK-NTP complexes revealed a universal NTP-binding motif, while [19]F NMR experiments uncovered a conserved and rate-limiting dynamic signature. As a consequence of trimerization, the active site of OdinAK was found to be lacking a critical catalytic residue and is therefore considered to be "atypical." On the basis of discovered relationships with human monomeric homologs, our findings are discussed in terms of evolution of enzymatic substrate specificity and cold adaptation.},
}
@article {pmid36316034,
year = {2023},
author = {Peiter, N and Rother, M},
title = {In vivo probing of SECIS-dependent selenocysteine translation in Archaea.},
journal = {Life science alliance},
volume = {6},
number = {1},
pages = {},
pmid = {36316034},
issn = {2575-1077},
mesh = {*Selenocysteine/genetics ; Archaea/genetics ; *Selenium ; 3' Untranslated Regions ; Base Sequence ; Selenoproteins/genetics ; },
abstract = {Cotranslational insertion of selenocysteine (Sec) proceeds by recoding UGA to a sense codon. This recoding is governed by the Sec insertion sequence (SECIS) element, an RNA structure on the mRNA, but size, location, structure determinants, and mechanism differ for Bacteria, Eukarya, and Archaea. For Archaea, the structure-function relation of the SECIS is poorly understood, as only rather laborious experimental approaches are established. Furthermore, these methods do not allow for quantitative probing of Sec insertion. In order to overcome these limitations, we engineered bacterial β-lactamase into an archaeal selenoprotein, thereby establishing a reporter system, which correlates enzyme activity to Sec insertion. Using this system, in vivo Sec insertion depending on the availability of selenium and the presence of a SECIS element was assessed in Methanococcus maripaludis Furthermore, a minimal SECIS element required for Sec insertion in M. maripaludis was defined and a conserved structural motif shown to be essential for function. Besides developing a convenient tool for selenium research, converting a bacterial enzyme into an archaeal selenoprotein provides proof of concept that novel selenoproteins can be engineered in Archaea.},
}
@article {pmid36314867,
year = {2022},
author = {Cha, G and Liu, Y and Yang, Q and Bai, L and Cheng, L and Fan, W},
title = {Comparative Genomic Insights into Chemoreceptor Diversity and Habitat Adaptation of Archaea.},
journal = {Applied and environmental microbiology},
volume = {88},
number = {22},
pages = {e0157422},
pmid = {36314867},
issn = {1098-5336},
mesh = {*Archaea ; Phylogeny ; Ligands ; *Genomics ; Ecosystem ; },
abstract = {Diverse archaea, including many unknown species and phylogenetically deeply rooted taxa, survive in extreme environments. They play crucial roles in the global carbon cycle and element fluxes in many terrestrial, marine, saline, host-associated, hot-spring, and oilfield environments. There is little knowledge of the diversity of chemoreceptors that are presumably involved in their habitat adaptation. Thus, we have explored this diversity through phylogenetic and comparative genomic analyses of complete archaeal genomes. The results show that chemoreceptors are significantly richer in archaea of mild environments than in those of extreme environments, that specific ligand-binding domains of the chemoreceptors are strongly associated with specific habitats, and that the number of chemoreceptors correlates with genome size. The results indicate that the successful adaptation of archaea to specific habitats has been associated with the acquisition and maintenance of chemoreceptors, which may be crucial for their survival in these environments. IMPORTANCE Archaea are capable of sensing and responding to environmental changes by several signal transduction systems with different mechanisms. Much attention is paid to model organisms with complex signaling networks to understand their composition and function, but general principles regarding how an archaeal species organizes its chemoreceptor diversity and habitat adaptation are poorly understood. Here, we have explored this diversity through phylogenetic and comparative genomic analyses of complete archaeal genomes. Signaling sensing and adaptation processes are tightly related to the ligand-binding domain, and it is clear that evolution and natural selection in specialized niches under constant conditions have selected for smaller genome sizes. Taken together, our results extend the understanding of archaeal adaptations to different environments and emphasize the importance of ecological constraints in shaping their evolution.},
}
@article {pmid36301308,
year = {2023},
author = {Khan, F and Kaza, S},
title = {Crystal structure of an L-type lectin domain from archaea.},
journal = {Proteins},
volume = {91},
number = {4},
pages = {456-465},
doi = {10.1002/prot.26440},
pmid = {36301308},
issn = {1097-0134},
mesh = {Animals ; *Lectins/chemistry ; *Archaea/genetics/metabolism ; Phylogeny ; Plant Lectins ; Binding Sites ; Crystallography, X-Ray ; },
abstract = {The crystal structures of an L-type lectin domain from Methanocaldococcus jannaschii in apo and mannose-bound forms have been determined. A thorough investigation of L-type lectin domains from several organisms provides insight into the differences in these domains from different kingdoms of life. While the overall fold of the L-type lectin domain is conserved, differences in the lengths of the carbohydrate-binding loops and significant variations in the Mn[2+] -binding site compared to the Ca[2+] -binding site are observed. Furthermore, the sequence and phylogenetic analyses suggest that the archaeal L-type lectin domain is evolutionarily closer to the plant legume lectins than to its bacterial or animal counterparts. This is the first report of the biochemical, structural, sequence, and phylogenetic analyses of an L-type lectin domain from archaea and serves to enhance our understanding of the species-specific differences and evolution of L-type lectin domains.},
}
@article {pmid36280648,
year = {2022},
author = {Baati, H and Siala, M and Azri, C and Ammar, E and Trigui, M},
title = {Hydrolytic enzyme screening and carotenoid production evaluation of halophilic archaea isolated from highly heavy metal-enriched solar saltern sediments.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {53},
number = {4},
pages = {1893-1906},
pmid = {36280648},
issn = {1678-4405},
mesh = {RNA, Ribosomal, 16S/genetics ; *Carotenoids ; Antioxidants ; Archaea/genetics ; *Metals, Heavy ; },
abstract = {This paper aimed to screen the enzymatic activities and evaluate the carotenoid production level of twenty-two halophilic archaea isolated from Sfax solar saltern sediments. The molecular identification performed by sequencing the 16S rRNA genes showed that all strains have a high similarity degree (99.7-100%) with Halobacterium salinarum NRC-1. The strains were screened for the presence of eight hydrolase activities using agar plate-based assays. The most detected enzyme was gelatinase (77.27% of total strains), followed by protease (63.63%) and amylase activities (50%). The carotenoid production yields of the strains ranged between 2.027 and 14.880 mg/l. The UV-Visible spectroscopy of pigments revealed that it was a bacterioruberin type. When evaluated and compared to the standard β-carotene, the antioxidant capacities of these pigments showed a scavenging activity of more than 75% at a concentration of 5 μg/ml for three strains (AS16, AS17, and AS18). Then a sequence of one-step optimization processes was performed, using the one-factor-at-a-time approach, to define the optimum conditions for growth and carotenoid production of the highest carotenoid producing strain (AS17). Different environmental factors and nutritional conditions were tested. Variations in these factors were found to deeply influence growth and carotenoid production. A maximum carotenoid production (16.490 mg/l), higher than that of the control (14.880 mg/l), was observed at 37 °C, pH 7, 250 g/l of salinity, with 80% air phase in the flask at 110 rpm, in presence of light and in culture media containing (g/l) 10, yeast extract; 7.5, casamino acid; 20, MgSO4; 4, KCl; and 3, trisodium citrate.},
}
@article {pmid36270146,
year = {2022},
author = {Yan, G and Sun, X and Dong, Y and Gao, W and Gao, P and Li, B and Yan, W and Zhang, H and Soleimani, M and Yan, B and Häggblom, MM and Sun, W},
title = {Vanadate reducing bacteria and archaea may use different mechanisms to reduce vanadate in vanadium contaminated riverine ecosystems as revealed by the combination of DNA-SIP and metagenomic-binning.},
journal = {Water research},
volume = {226},
number = {},
pages = {119247},
doi = {10.1016/j.watres.2022.119247},
pmid = {36270146},
issn = {1879-2448},
mesh = {Humans ; *Archaea/genetics/metabolism ; *Metagenome ; Vanadates/metabolism ; Vanadium/metabolism ; Ecosystem ; Anaerobiosis ; Bacteria/genetics/metabolism ; Methane/metabolism ; Methanosarcina/genetics ; Oxidation-Reduction ; Isotopes ; DNA/metabolism ; },
abstract = {Vanadium (V) is a transitional metal that poses health risks to exposed humans. Microorganisms play an important role in remediating V contamination by reducing more toxic and mobile vanadate (V(V)) to less toxic and mobile V(IV). In this study, DNA-stable isotope probing (SIP) coupled with metagenomic-binning was used to identify microorganisms responsible for V(V) reduction and determine potential metabolic mechanisms in cultures inoculated with a V-contaminated river sediment. Anaeromyxobacter and Geobacter spp. were identified as putative V(V)-reducing bacteria, while Methanosarcina spp. were identified as putative V(V)-reducing archaea. The bacteria may use the two nitrate reductases NarG and NapA for respiratory V(V) reduction, as has been demonstrated previously for other species. It is proposed that Methanosarcina spp. may reduce V(V) via anaerobic methane oxidation pathways (AOM-V) rather than via respiratory V(V) reduction performed by their bacterial counterparts, as indicated by the presence of genes associated with anaerobic methane oxidation coupled with metal reduction in the metagenome assembled genome (MAG) of Methanosarcina. Briefly, methane may be oxidized through the "reverse methanogenesis" pathway to produce electrons, which may be further captured by V(V) to promote V(V) reduction. More specially, V(V) reduction by members of Methanosarcina may be driven by electron transport (CoMS-SCoB heterodisulfide reductase (HdrDE), F420H2 dehydrogenases (Fpo), and multi-heme c-type cytochrome (MHC)). The identification of putative V(V)-reducing bacteria and archaea and the prediction of their different pathways for V(V) reduction expand current knowledge regarding the potential fate of V(V) in contaminated sites.},
}
@article {pmid36266535,
year = {2022},
author = {Shao, N and Fan, Y and Chou, CW and Yavari, S and Williams, RV and Amster, IJ and Brown, SM and Drake, IJ and Duin, EC and Whitman, WB and Liu, Y},
title = {Expression of divergent methyl/alkyl coenzyme M reductases from uncultured archaea.},
journal = {Communications biology},
volume = {5},
number = {1},
pages = {1113},
pmid = {36266535},
issn = {2399-3642},
support = {S10 OD025118/OD/NIH HHS/United States ; S10 RR028859/RR/NCRR NIH HHS/United States ; },
mesh = {*Archaea/genetics/metabolism ; *Mesna/metabolism ; Oxidoreductases/metabolism ; Methane/metabolism ; },
abstract = {Methanogens and anaerobic methane-oxidizing archaea (ANME) are important players in the global carbon cycle. Methyl-coenzyme M reductase (MCR) is a key enzyme in methane metabolism, catalyzing the last step in methanogenesis and the first step in anaerobic methane oxidation. Divergent mcr and mcr-like genes have recently been identified in uncultured archaeal lineages. However, the assembly and biochemistry of MCRs from uncultured archaea remain largely unknown. Here we present an approach to study MCRs from uncultured archaea by heterologous expression in a methanogen, Methanococcus maripaludis. Promoter, operon structure, and temperature were important determinants for MCR production. Both recombinant methanococcal and ANME-2 MCR assembled with the host MCR forming hybrid complexes, whereas tested ANME-1 MCR and ethyl-coenzyme M reductase only formed homogenous complexes. Together with structural modeling, this suggests that ANME-2 and methanogen MCRs are structurally similar and their reaction directions are likely regulated by thermodynamics rather than intrinsic structural differences.},
}
@article {pmid36266339,
year = {2022},
author = {Hocher, A and Borrel, G and Fadhlaoui, K and Brugère, JF and Gribaldo, S and Warnecke, T},
title = {Growth temperature and chromatinization in archaea.},
journal = {Nature microbiology},
volume = {7},
number = {11},
pages = {1932-1942},
pmid = {36266339},
issn = {2058-5276},
support = {MC_UP_1102/7/MRC_/Medical Research Council/United Kingdom ; MC-A658-5TY40/MRC_/Medical Research Council/United Kingdom ; },
mesh = {*Archaea/genetics ; Chromatin/genetics ; *Proteomics ; Temperature ; },
abstract = {DNA in cells is associated with proteins that constrain its structure and affect DNA-templated processes including transcription and replication. HU and histones are the main constituents of chromatin in bacteria and eukaryotes, respectively, with few exceptions. Archaea, in contrast, have diverse repertoires of nucleoid-associated proteins (NAPs). To analyse the evolutionary and ecological drivers of this diversity, we combined a phylogenomic survey of known and predicted NAPs with quantitative proteomic data. We identify the Diaforarchaea as a hotbed of NAP gain and loss, and experimentally validate candidate NAPs in two members of this clade, Thermoplasma volcanium and Methanomassiliicoccus luminyensis. Proteomic analysis across a diverse sample of 19 archaea revealed that NAP investment varies from <0.03% to >5% of total protein. This variation is predicted by growth temperature. We propose that high levels of chromatinization have evolved as a mechanism to prevent uncontrolled helix denaturation at higher temperatures, with implications for the origin of chromatin in both archaea and eukaryotes.},
}
@article {pmid36256551,
year = {2022},
author = {Xin, YJ and Bao, CX and Tan, S and Hou, J and Cui, HL},
title = {Haladaptatus halobius sp. nov. and Haladaptatus salinisoli sp. nov., two extremely halophilic archaea isolated from Gobi saline soil.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {72},
number = {10},
pages = {},
doi = {10.1099/ijsem.0.005543},
pmid = {36256551},
issn = {1466-5034},
mesh = {RNA, Ribosomal, 16S/genetics ; Phylogeny ; *Soil ; DNA, Archaeal/genetics ; Base Composition ; Sequence Analysis, DNA ; Fatty Acids/chemistry ; DNA, Bacterial/genetics ; Bacterial Typing Techniques ; *Halobacteriaceae ; Glycolipids/chemistry ; Sulfates ; Phosphatidylglycerols/analysis ; Nucleotides ; Amino Acids ; Phosphatidic Acids/analysis ; Esters ; },
abstract = {Two extremely halophilic archaeal strains, PSR5[T] and PSR8[T], were isolated from a saline soil sample collected from the Tarim Basin, Xinjiang, PR China. Both strains had two copies of the 16S rRNA genes rrn1 and rrn2, showing 2.6 and 3.9% divergence, respectively. The rrn1 gene of PSR5[T] showed 98.4 and 95.3% similarity to the rrn1 and rrn2 genes of strain PSR8[T]; the rrn2 gene of PSR5[T] displayed 97.4 and 96.7% similarity to those of strain PSR8[T], respectively. Phylogenetic analyses based on the 16S rRNA and rpoB' genes revealed that strains PSR5[T] and PSR8[T] formed a single cluster, and then tightly clustered with the current four Haladaptatus species (93.5-97.1% similarities for the 16S rRNA gene and 89.3-90.9% similarities for the rpoB' gene, respectively). Several phenotypic characteristics differentiate strains PSR5[T] and PSR8[T] from current Haladaptatus members. The polar lipids of the two strains are phosphatidic acid, phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester phosphatidylglycerol sulphate and three glycolipids. One of the glycolipids is sulphated mannosyl glucosyl diether, and the remaining two glycolipids are unidentified. The average nucleotide identity, in silico DNA-DNA hybridization, amino acid identity and percentage of conserved proteins values between the two strains were 88.5, 39.1, 89.3 and 72.8 %, respectively, much lower than the threshold values proposed as a species boundary. These values among the two strains and Haladaptatus members were 77.9-79.2, 22.0-23.5, 75.1-78.2 and 56.8-69.9 %, respectively, much lower than the recommended threshold values for species delimitation. These results suggested that strains PSR5[T] and PSR8[T] represent two novel species of Haladaptatus. Based on phenotypic, chemotaxonomic, genomic and phylogenetic properties, strains PSR5[T] (=CGMCC 1.16851[T]=JCM 34141[T]) and PSR8[T] (=CGMCC 1.17025[T]=JCM 34142[T]) represent two novel species of the genus Haladaptatus, for which the names Haladaptatus halobius sp. nov. and Haladaptatus salinisoli sp. nov. are proposed.},
}
@article {pmid36253512,
year = {2022},
author = {van Wolferen, M and Pulschen, AA and Baum, B and Gribaldo, S and Albers, SV},
title = {The cell biology of archaea.},
journal = {Nature microbiology},
volume = {7},
number = {11},
pages = {1744-1755},
pmid = {36253512},
issn = {2058-5276},
support = {203276/WT_/Wellcome Trust/United Kingdom ; BB/P001440/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; MC_UP_1201/27/MRC_/Medical Research Council/United Kingdom ; 203276/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Humans ; *Archaea ; Phylogeny ; *Biological Evolution ; Eukaryota ; Ecology ; },
abstract = {The past decade has revealed the diversity and ubiquity of archaea in nature, with a growing number of studies highlighting their importance in ecology, biotechnology and even human health. Myriad lineages have been discovered, which expanded the phylogenetic breadth of archaea and revealed their central role in the evolutionary origins of eukaryotes. These discoveries, coupled with advances that enable the culturing and live imaging of archaeal cells under extreme environments, have underpinned a better understanding of their biology. In this Review we focus on the shape, internal organization and surface structures that are characteristic of archaeal cells as well as membrane remodelling, cell growth and division. We also highlight some of the technical challenges faced and discuss how new and improved technologies will help address many of the key unanswered questions.},
}
@article {pmid36251741,
year = {2022},
author = {Hofmann, M and Norris, PR and Malik, L and Schippers, A and Schmidt, G and Wolf, J and Neumann-Schaal, M and Hedrich, S},
title = {Metallosphaera javensis sp. nov., a novel species of thermoacidophilic archaea, isolated from a volcanic area.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {72},
number = {10},
pages = {},
doi = {10.1099/ijsem.0.005536},
pmid = {36251741},
issn = {1466-5034},
mesh = {*Archaea/genetics ; Bacterial Typing Techniques ; Base Composition ; DNA, Bacterial/genetics ; Fatty Acids/chemistry ; Iron ; Nucleotides ; Phylogeny ; Quinones ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sugars ; Sulfides ; *Sulfolobaceae ; Sulfur ; Sulfur Compounds ; },
abstract = {A novel thermoacidophilic archeaon, strain J1[T] (=DSM 112778[T],=JCM 34702[T]), was isolated from a hot pool in a volcanic area of Java, Indonesia. Cells of the strain were irregular, motile cocci of 1.0-1.2 µm diameter. Aerobic, organoheterotrophic growth with casamino acids was observed at an optimum temperature of 70 °C in a range of 55-78 °C and at an optimum pH of 3 in a range of 1.5 to 5. Various organic compounds were utilized, including a greater variety of sugars than has been reported for growth of other species of the genus. Chemolithoautotrophic growth was observed with reduced sulphur compounds, including mineral sulphides. Ferric iron was reduced during anaerobic growth with elemental sulphur. Cellular lipids were calditoglycerocaldarchaeol and caldarchaeol with some derivates. The organism contained the respiratory quinone caldariellaquinone. On the basis of phylogenetic and chemotaxonomic comparison with its closest relatives, it was concluded that strain J1[T] represents a novel species, for which the name Metallosphaera javensis is proposed. Low DNA-DNA relatedness values (16S rRNA gene <98.4%, average nucleotide identity (ANI) <80.1%) distinguished J1[T] from other species of the genus Metallosphaera and the DNA G+C content of 47.3% is the highest among the known species of the genus.},
}
@article {pmid36239851,
year = {2022},
author = {Zheng, XW and Wu, ZP and Sun, YP and Wang, BB and Hou, J and Cui, HL},
title = {Halorussus vallis sp. nov., Halorussus aquaticus sp. nov., Halorussus gelatinilyticus sp. nov., Halorussus limi sp. nov., Halorussus salilacus sp. nov., Halorussus salinisoli sp. nov.: six extremely halophilic archaea isolated from solar saltern, salt lake and saline soil.},
journal = {Extremophiles : life under extreme conditions},
volume = {26},
number = {3},
pages = {32},
pmid = {36239851},
issn = {1433-4909},
support = {32070003//National Natural Science Foundation of China/ ; },
mesh = {Base Composition ; China ; DNA, Archaeal/genetics ; Esters ; Glycolipids ; *Halobacteriaceae ; *Lakes ; Nucleotides ; Phosphatidylglycerols ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Soil ; Sulfates ; },
abstract = {Six novel halophilic archaeal strains of XZYJT10[T], XZYJ18[T], XZYJT40[T], XZYJT49[T], YCN54[T] and LT46[T] were isolated from a solar saltern in Tibet, a salt lake in Shanxi, and a saline soil in Xinjiang, China. Sequence similarities of 16S rRNA and rpoB' genes among strains XZYJT10[T], XZYJ18[T], XZYJT40[T], XZYJT49[T], YCN54[T], LT46[T] and current members of Halorussus were 90.6-97.8% and 87.8-96.4%, respectively. The average nucleotide identity and in silico DNA-DNA hybridization values among these six strains and current Halorussus members were in the range of 76.5-87.5% and 21.0-33.8%, respectively. These values were all below the species boundary threshold values. The phylogenomic tree based on 122 conserved archaeal protein marker genes revealed that the six novel strains formed individual distinct branches and clustered tightly with Halorussus members. Several phenotypic characteristics distinguished the six strains from current Halorussus members. Polar lipid analysis showed that the six novel strains contained phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulfate and two to three glycolipids. Phenotypic, chemotaxonomic and phylogenetic properties showed that the six strains represented six novel species within the genus Halorussus, for which the names Halorussus vallis sp. nov., Halorussus aquaticus sp. nov., Halorussus gelatinilyticus sp. nov., Halorussus limi sp. nov., Halorussus salilacus sp. nov., and Halorussus salinisoli sp. nov. are proposed.},
}
@article {pmid36232866,
year = {2022},
author = {Uzelac, M and Li, Y and Chakladar, J and Li, WT and Ongkeko, WM},
title = {Archaea Microbiome Dysregulated Genes and Pathways as Molecular Targets for Lung Adenocarcinoma and Squamous Cell Carcinoma.},
journal = {International journal of molecular sciences},
volume = {23},
number = {19},
pages = {},
pmid = {36232866},
issn = {1422-0067},
mesh = {*Adenocarcinoma of Lung/pathology ; Archaea/genetics ; *Carcinoma, Non-Small-Cell Lung/genetics ; *Carcinoma, Squamous Cell/pathology ; Female ; Humans ; *Lung Neoplasms/pathology ; Male ; *Microbiota/genetics ; },
abstract = {The human microbiome is a vast collection of microbial species that exist throughout the human body and regulate various bodily functions and phenomena. Of the microbial species that exist in the human microbiome, those within the archaea domain have not been characterized to the extent of those in more common domains, despite their potential for unique metabolic interaction with host cells. Research has correlated tumoral presence of bacterial microbial species to the development and progression of lung cancer; however, the impacts and influences of archaea in the microbiome remain heavily unexplored. Within the United States lung cancer remains highly fatal, responsible for over 100,000 deaths every year with a 5-year survival rate of roughly 22.9%. This project attempts to investigate specific archaeal species' correlation to lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC) incidence, patient staging, death rates across individuals of varying ages, races, genders, and smoking-statuses, and potential molecular targets associated with archaea microbiome. Archaeal species abundance was assessed across lung tissue samples of 527 LUAD patients, 479 LUSC patients, and 99 healthy individuals. Nine archaeal species were found to be of significantly altered abundance in cancerous samples as compared to normal counterparts, 6 of which are common to both LUAD and LUSC subgroups. Several of these species are of the taxonomic class Thermoprotei or the phylum Euryarchaeota, both known to contain metabolic processes distinct from most bacterial species. Host-microbe metabolic interactions may be responsible for the observed correlation of these species' abundance with cancer incidence. Significant microbes were correlated to patient gene expression to reveal genes of altered abundance with respect to high and low archaeal presence. With these genes, cellular oncogenic signaling pathways were analyzed for enrichment across cancer and normal samples. In comparing gene expression between LUAD and adjacent normal samples, 2 gene sets were found to be significantly enriched in cancers. In LUSC comparison, 6 sets were significantly enriched in cancer, and 34 were enriched in normals. Microbial counts across healthy and cancerous patients were then used to develop a machine-learning based predictive algorithm, capable of distinguishing lung cancer patients from healthy normal with 99% accuracy.},
}
@article {pmid36229494,
year = {2022},
author = {Jeter, VL and Schwarzwalder, AH and Rayment, I and Escalante-Semerena, JC},
title = {Structural studies of the phosphoribosyltransferase involved in cobamide biosynthesis in methanogenic archaea and cyanobacteria.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {17175},
pmid = {36229494},
issn = {2045-2322},
support = {R35 GM130399/GM/NIGMS NIH HHS/United States ; },
mesh = {Adenosine Monophosphate ; Archaea/metabolism ; Aspartic Acid ; Cobamides/metabolism ; Crystallography, X-Ray ; *Cyanobacteria/metabolism ; *Euryarchaeota/metabolism ; Glutamates ; Ligands ; Pentosyltransferases/genetics/metabolism ; Phosphates/metabolism ; },
abstract = {Cobamides (Cbas) are coenzymes used by cells across all domains of life, but de novo synthesis is only found in some bacteria and archaea. Five enzymes assemble the nucleotide loop in the alpha phase of the corrin ring. Condensation of the activated ring and nucleobase yields adenosyl-Cba 5'-phosphate, which upon dephosphorylation yields the biologically active coenzyme (AdoCba). Base activation is catalyzed by a phosphoribosyltransferase (PRTase). The structure of the Salmonella enterica PRTase enzyme (i.e., SeCobT) is well-characterized, but archaeal PRTases are not. To gain insights into the mechanism of base activation by the PRTase from Methanocaldococcus jannaschii (MjCobT), we solved crystal structures of the enzyme in complex with substrate and products. We determined several structures: (i) a 2.2 Å structure of MjCobT in the absence of ligand (apo), (ii) structures of MjCobT bound to nicotinate mononucleotide (NaMN) and α-ribazole 5'-phosphate (α-RP) or α-adenylyl-5'-phosphate (α-AMP) at 2.3 and 1.4 Å, respectively. In MjCobT the general base that triggers the reaction is an aspartate residue (Asp 52) rather than a glutamate residue (E317) as in SeCobT. Notably, the dimer interface in MjCobT is completely different from that observed in SeCobT. Finally, entry PDB 3L0Z does not reflect the correct structure of MjCobT.},
}
@article {pmid36212815,
year = {2022},
author = {Benito Merino, D and Zehnle, H and Teske, A and Wegener, G},
title = {Deep-branching ANME-1c archaea grow at the upper temperature limit of anaerobic oxidation of methane.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {988871},
pmid = {36212815},
issn = {1664-302X},
abstract = {In seafloor sediments, the anaerobic oxidation of methane (AOM) consumes most of the methane formed in anoxic layers, preventing this greenhouse gas from reaching the water column and finally the atmosphere. AOM is performed by syntrophic consortia of specific anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria (SRB). Cultures with diverse AOM partners exist at temperatures between 12°C and 60°C. Here, from hydrothermally heated sediments of the Guaymas Basin, we cultured deep-branching ANME-1c that grow in syntrophic consortia with Thermodesulfobacteria at 70°C. Like all ANME, ANME-1c oxidize methane using the methanogenesis pathway in reverse. As an uncommon feature, ANME-1c encode a nickel-iron hydrogenase. This hydrogenase has low expression during AOM and the partner Thermodesulfobacteria lack hydrogen-consuming hydrogenases. Therefore, it is unlikely that the partners exchange hydrogen during AOM. ANME-1c also does not consume hydrogen for methane formation, disputing a recent hypothesis on facultative methanogenesis. We hypothesize that the ANME-1c hydrogenase might have been present in the common ancestor of ANME-1 but lost its central metabolic function in ANME-1c archaea. For potential direct interspecies electron transfer (DIET), both partners encode and express genes coding for extracellular appendages and multiheme cytochromes. Thermodesulfobacteria encode and express an extracellular pentaheme cytochrome with high similarity to cytochromes of other syntrophic sulfate-reducing partner bacteria. ANME-1c might associate specifically to Thermodesulfobacteria, but their co-occurrence is so far only documented for heated sediments of the Gulf of California. However, in the deep seafloor, sulfate-methane interphases appear at temperatures up to 80°C, suggesting these as potential habitats for the partnership of ANME-1c and Thermodesulfobacteria.},
}
@article {pmid36203131,
year = {2022},
author = {Somee, MR and Amoozegar, MA and Dastgheib, SMM and Shavandi, M and Maman, LG and Bertilsson, S and Mehrshad, M},
title = {Genome-resolved analyses show an extensive diversification in key aerobic hydrocarbon-degrading enzymes across bacteria and archaea.},
journal = {BMC genomics},
volume = {23},
number = {1},
pages = {690},
pmid = {36203131},
issn = {1471-2164},
mesh = {*Archaea ; Bacteria ; Biodegradation, Environmental ; Carbon/metabolism ; Hydrocarbons/metabolism ; Hydrogen/metabolism ; *Petroleum/metabolism ; Phylogeny ; },
abstract = {BACKGROUND: Hydrocarbons (HCs) are organic compounds composed solely of carbon and hydrogen that are mainly accumulated in oil reservoirs. As the introduction of all classes of hydrocarbons including crude oil and oil products into the environment has increased significantly, oil pollution has become a global ecological problem. However, our perception of pathways for biotic degradation of major HCs and key enzymes in these bioconversion processes has mainly been based on cultured microbes and is biased by uneven taxonomic representation. Here we used Annotree to provide a gene-centric view of the aerobic degradation ability of aliphatic and aromatic HCs in 23,446 genomes from 123 bacterial and 14 archaeal phyla. RESULTS: Apart from the widespread genetic potential for HC degradation in Proteobacteria, Actinobacteriota, Bacteroidota, and Firmicutes, genomes from an additional 18 bacterial and 3 archaeal phyla also hosted key HC degrading enzymes. Among these, such degradation potential has not been previously reported for representatives in the phyla UBA8248, Tectomicrobia, SAR324, and Eremiobacterota. Genomes containing whole pathways for complete degradation of HCs were only detected in Proteobacteria and Actinobacteriota. Except for several members of Crenarchaeota, Halobacterota, and Nanoarchaeota that have tmoA, ladA, and alkB/M key genes, respectively, representatives of archaeal genomes made a small contribution to HC degradation. None of the screened archaeal genomes coded for complete HC degradation pathways studied here; however, they contribute significantly to peripheral routes of HC degradation with bacteria.<br><br>CONCLUSION: Phylogeny reconstruction showed that the reservoir of key aerobic hydrocarbon-degrading enzymes in Bacteria and Archaea undergoes extensive diversification via gene duplication and horizontal gene transfer. This diversification could potentially enable microbes to rapidly adapt to novel and manufactured HCs that reach the environment.},
}
@article {pmid36181435,
year = {2022},
author = {Zhang, X and Huang, Y and Liu, Y and Xu, W and Pan, J and Zheng, X and Du, H and Zhang, C and Lu, Z and Zou, D and Liu, Z and Cai, M and Xiong, J and Zhu, Y and Dong, Z and Jiang, H and Dong, H and Jiang, J and Luo, Z and Huang, L and Li, M},
title = {An Ancient Respiratory System in the Widespread Sedimentary Archaea Thermoprofundales.},
journal = {Molecular biology and evolution},
volume = {39},
number = {10},
pages = {},
pmid = {36181435},
issn = {1537-1719},
mesh = {*Archaea/genetics/metabolism ; *Hydrogenase/chemistry/genetics/metabolism ; Sodium Chloride/metabolism ; Phylogeny ; Respiratory System/metabolism ; Amino Acids/genetics ; Antiporters/genetics/metabolism ; },
abstract = {Thermoprofundales, formerly Marine Benthic Group D (MBG-D), is a ubiquitous archaeal lineage found in sedimentary environments worldwide. However, its taxonomic classification, metabolic pathways, and evolutionary history are largely unexplored because of its uncultivability and limited number of sequenced genomes. In this study, phylogenomic analysis and average amino acid identity values of a collection of 146 Thermoprofundales genomes revealed five Thermoprofundales subgroups (A-E) with distinct habitat preferences. Most of the microorganisms from Subgroups B and D were thermophiles inhabiting hydrothermal vents and hot spring sediments, whereas those from Subgroup E were adapted to surface environments where sunlight is available. H2 production may be featured in Thermoprofundales as evidenced by a gene cluster encoding the ancient membrane-bound hydrogenase (MBH) complex. Interestingly, a unique structure separating the MBH gene cluster into two modular units was observed exclusively in the genomes of Subgroup E, which included a peripheral arm encoding the [NiFe] hydrogenase domain and a membrane arm encoding the Na+/H+ antiporter domain. These two modular structures were confirmed to function independently by detecting the H2-evolving activity in vitro and salt tolerance to 0.2 M NaCl in vivo, respectively. The peripheral arm of Subgroup E resembles the proposed common ancestral respiratory complex of modern respiratory systems, which plays a key role in the early evolution of life. In addition, molecular dating analysis revealed that Thermoprofundales is an early emerging archaeal lineage among the extant MBH-containing microorganisms, indicating new insights into the evolution of this ubiquitous archaea lineage.},
}
@article {pmid36160229,
year = {2022},
author = {Meng, K and Chung, CZ and Söll, D and Krahn, N},
title = {Unconventional genetic code systems in archaea.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {1007832},
pmid = {36160229},
issn = {1664-302X},
support = {R35 GM122560/GM/NIGMS NIH HHS/United States ; },
abstract = {Archaea constitute the third domain of life, distinct from bacteria and eukaryotes given their ability to tolerate extreme environments. To survive these harsh conditions, certain archaeal lineages possess unique genetic code systems to encode either selenocysteine or pyrrolysine, rare amino acids not found in all organisms. Furthermore, archaea utilize alternate tRNA-dependent pathways to biosynthesize and incorporate members of the 20 canonical amino acids. Recent discoveries of new archaeal species have revealed the co-occurrence of these genetic code systems within a single lineage. This review discusses the diverse genetic code systems of archaea, while detailing the associated biochemical elements and molecular mechanisms.},
}
@article {pmid36152750,
year = {2022},
author = {Guo, LT and Amikura, K and Jiang, HK and Mukai, T and Fu, X and Wang, YS and O'Donoghue, P and Söll, D and Tharp, JM},
title = {Ancestral archaea expanded the genetic code with pyrrolysine.},
journal = {The Journal of biological chemistry},
volume = {298},
number = {11},
pages = {102521},
pmid = {36152750},
issn = {1083-351X},
support = {K99 GM141320/GM/NIGMS NIH HHS/United States ; R35 GM122560/GM/NIGMS NIH HHS/United States ; 165985//CIHR/Canada ; },
mesh = {*Amino Acyl-tRNA Synthetases/metabolism ; *Archaea/enzymology/genetics ; *Genetic Code ; *Lysine/analogs &amp; derivatives/genetics ; Methanosarcina ; RNA, Transfer/genetics ; },
abstract = {The pyrrolysyl-tRNA synthetase (PylRS) facilitates the cotranslational installation of the 22nd amino acid pyrrolysine. Owing to its tolerance for diverse amino acid substrates, and its orthogonality in multiple organisms, PylRS has emerged as a major route to install noncanonical amino acids into proteins in living cells. Recently, a novel class of PylRS enzymes was identified in a subset of methanogenic archaea. Enzymes within this class (ΔPylSn) lack the N-terminal tRNA-binding domain that is widely conserved amongst PylRS enzymes, yet remain active and orthogonal in bacteria and eukaryotes. In this study, we use biochemical and in vivo UAG-readthrough assays to characterize the aminoacylation efficiency and substrate spectrum of a ΔPylSn class PylRS from the archaeon Candidatus Methanomethylophilus alvus. We show that, compared with the full-length enzyme from Methanosarcina mazei, the Ca. M. alvus PylRS displays reduced aminoacylation efficiency but an expanded amino acid substrate spectrum. To gain insight into the evolution of ΔPylSn enzymes, we performed molecular phylogeny using 156 PylRS and 105 pyrrolysine tRNA (tRNA[Pyl]) sequences from diverse archaea and bacteria. This analysis suggests that the PylRS•tRNA[Pyl] pair diverged before the evolution of the three domains of life, placing an early limit on the evolution of the Pyl-decoding trait. Furthermore, our results document the coevolutionary history of PylRS and tRNA[Pyl] and reveal the emergence of tRNA[Pyl] sequences with unique A73 and U73 discriminator bases. The orthogonality of these tRNA[Pyl] species with the more common G73-containing tRNA[Pyl] will enable future efforts to engineer PylRS systems for further genetic code expansion.},
}
@article {pmid36150484,
year = {2022},
author = {Guo, Z and Jalalah, M and Alsareii, SA and Harraz, FA and Thakur, N and Salama, ES},
title = {Biochar addition augmented the microbial community and aided the digestion of high-loading slaughterhouse waste: Active enzymes of bacteria and archaea.},
journal = {Chemosphere},
volume = {309},
number = {Pt 1},
pages = {136535},
doi = {10.1016/j.chemosphere.2022.136535},
pmid = {36150484},
issn = {1879-1298},
mesh = {Archaea/metabolism ; Biofuels ; Anaerobiosis ; Bioreactors ; Abattoirs ; Methane/metabolism ; *Hydrogenase/metabolism ; Bacteria/metabolism ; *Microbiota ; Fatty Acids, Volatile/metabolism ; *Lyases/metabolism ; Transaminases ; Digestion ; },
abstract = {The biogas production (BP), volatile fatty acids (VFAs), microbial communities, and microbes' active enzymes were studied upon the addition of biochar (0-1.5%) at 6% and 8% slaughterhouse waste (SHW) loadings. The 0.5% biochar enhanced BP by 1.5- and 1.6-folds in 6% and 8% SHW-loaded reactors, respectively. Increasing the biochar up to 1.5% caused a reduction in BP at 6% SHW. However, the BP from 8% of SHW was enhanced by 1.4-folds at 1.5% biochar. The VFAs production in all 0.5% biochar amended reactors was highly significant compared to control (p-value < 0.05). The biochar addition increased the bacterial and archaeal diversity at both 6% and 8% SHW loadings. The highest number of OTUs at 0.5% biochar were 567 and 525 in 6% and 8% SHW, respectively. Biochar prompted the Clostridium abundance and increased the lyases and transaminases involved in the degradation of lipids and protein, respectively. Biochar addition improved the Methanosaeta and Methanosphaera abundance in which the major enzymes were reductase and hydrogenase. The archaeal enzymes showed mixed acetoclastic and hydrogenotrophic methanogenesis.},
}
@article {pmid36144426,
year = {2022},
author = {Pilotto, S and Werner, F},
title = {How to Shut Down Transcription in Archaea during Virus Infection.},
journal = {Microorganisms},
volume = {10},
number = {9},
pages = {},
pmid = {36144426},
issn = {2076-2607},
support = {206166/Z/17/Z/WT_/Wellcome Trust/United Kingdom ; WT 207446/Z/17/Z//Wellcome Investigator Award in Science/ ; /WT_/Wellcome Trust/United Kingdom ; 207446/Z/17/Z/WT_/Wellcome Trust/United Kingdom ; 202679/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; },
abstract = {Multisubunit RNA polymerases (RNAPs) carry out transcription in all domains of life; during virus infection, RNAPs are targeted by transcription factors encoded by either the cell or the virus, resulting in the global repression of transcription with distinct outcomes for different host-virus combinations. These repressors serve as versatile molecular probes to study RNAP mechanisms, as well as aid the exploration of druggable sites for the development of new antibiotics. Here, we review the mechanisms and structural basis of RNAP inhibition by the viral repressor RIP and the crenarchaeal negative regulator TFS4, which follow distinct strategies. RIP operates by occluding the DNA-binding channel and mimicking the initiation factor TFB/TFIIB. RIP binds tightly to the clamp and locks it into one fixed position, thereby preventing conformational oscillations that are critical for RNAP function as it progresses through the transcription cycle. TFS4 engages with RNAP in a similar manner to transcript cleavage factors such as TFS/TFIIS through the NTP-entry channel; TFS4 interferes with the trigger loop and bridge helix within the active site by occlusion and allosteric mechanisms, respectively. The conformational changes in RNAP described above are universally conserved and are also seen in inactive dimers of eukaryotic RNAPI and several inhibited RNAP complexes of both bacterial and eukaryotic RNA polymerases, including inactive states that precede transcription termination. A comparison of target sites and inhibitory mechanisms reveals that proteinaceous repressors and RNAP-specific antibiotics use surprisingly common ways to inhibit RNAP function.},
}
@article {pmid36135934,
year = {2022},
author = {Groult, B and Bredin, P and Lazar, CS},
title = {Ecological processes differ in community assembly of Archaea, Bacteria and Eukaryotes in a biogeographical survey of groundwater habitats in the Quebec region (Canada).},
journal = {Environmental microbiology},
volume = {24},
number = {12},
pages = {5898-5910},
doi = {10.1111/1462-2920.16219},
pmid = {36135934},
issn = {1462-2920},
mesh = {Archaea/genetics ; Eukaryota ; Quebec ; RNA, Ribosomal, 16S ; Bacteria/genetics ; *Groundwater/microbiology ; *Microbiota ; },
abstract = {Aquifers are inhabited by microorganisms from the three major domains of life: Archaea, Eukaryotes and Bacteria. Although interest in the processes that govern the assembly of these microbial communities is growing, their study is almost systematically limited to one of the three domains of life. Archaea, Bacteria and Eukaryotes are however interconnected and essential to understand the functioning of their living ecosystems. We, therefore, conducted a spatial study of the distribution of microorganisms by sampling 35 wells spread over an area of 10,000 km[2] in the Quebec region (Canada). The obtained data allowed us to define the impact of geographic distance and geochemical water composition on the microbial communities. A null model approach was used to infer the relative influence of stochastic and determinist ecological processes on the assembly of the microbial community from all three domains. We found that the organisms from these three groups are mainly governed by stochastic mechanisms. However, this apparent similarity does not reflect the differences in the processes that govern the phyla assembly. The results obtained highlight the importance of considering all the microorganisms without neglecting their individual specificities.},
}
@article {pmid36125864,
year = {2022},
author = {Pallen, MJ and Rodriguez-R, LM and Alikhan, NF},
title = {Naming the unnamed: over 65,000 Candidatus names for unnamed Archaea and Bacteria in the Genome Taxonomy Database.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {72},
number = {9},
pages = {},
doi = {10.1099/ijsem.0.005482},
pmid = {36125864},
issn = {1466-5034},
support = {MR/L015080/1/MRC_/Medical Research Council/United Kingdom ; MR/T030062/1/MRC_/Medical Research Council/United Kingdom ; },
mesh = {*Archaea/genetics ; Bacteria/genetics ; Bacterial Typing Techniques ; Base Composition ; DNA, Bacterial/genetics ; *Fatty Acids/chemistry ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; },
abstract = {Thousands of new bacterial and archaeal species and higher-level taxa are discovered each year through the analysis of genomes and metagenomes. The Genome Taxonomy Database (GTDB) provides hierarchical sequence-based descriptions and classifications for new and as-yet-unnamed taxa. However, bacterial nomenclature, as currently configured, cannot keep up with the need for new well-formed names. Instead, microbiologists have been forced to use hard-to-remember alphanumeric placeholder labels. Here, we exploit an approach to the generation of well-formed arbitrary Latinate names at a scale sufficient to name tens of thousands of unnamed taxa within GTDB. These newly created names represent an important resource for the microbiology community, facilitating communication between bioinformaticians, microbiologists and taxonomists, while populating the emerging landscape of microbial taxonomic and functional discovery with accessible and memorable linguistic labels.},
}
@article {pmid36125771,
year = {2022},
author = {Adam, PS and Bornemann, TLV and Probst, AJ},
title = {Progress and Challenges in Studying the Ecophysiology of Archaea.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2522},
number = {},
pages = {469-486},
pmid = {36125771},
issn = {1940-6029},
mesh = {Alkanes ; *Archaea/genetics ; *Genome, Archaeal ; Methane ; Phylogeny ; },
abstract = {It has been less than two decades since the study of archaeal ecophysiology has become unshackled from the limitations of cultivation and amplicon sequencing through the advent of metagenomics. As a primer to the guide on producing archaeal genomes from metagenomes, we briefly summarize here how different meta'omics, imaging, and wet lab methods have contributed to progress in understanding the ecophysiology of Archaea. We then peer into the history of how our knowledge on two particularly important lineages was assembled: the anaerobic methane and alkane oxidizers, encountered primarily among Euryarchaeota, and the nanosized, mainly parasitic, members of the DPANN superphylum.},
}
@article {pmid36125745,
year = {2022},
author = {Thomsen, J and Weidenbach, K and Metcalf, WW and Schmitz, RA},
title = {Genetic Methods and Construction of Chromosomal Mutations in Methanogenic Archaea.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2522},
number = {},
pages = {105-117},
pmid = {36125745},
issn = {1940-6029},
mesh = {*Archaea ; *Hypoxanthine Phosphoribosyltransferase/genetics ; Mutation ; Purines ; },
abstract = {Genetic manipulation through markerless exchange enables the modification of several genomic regions without leaving a selection marker in the genome. Here, a method using hpt coding for hypoxanthine phosphoribosyltransferase as a counter selectable marker is described. For Methanosarcina species a chromosomal deletion of the hpt gene is firstly generated, which confers resistance to the purine analogue 8-aza-2,6-diaminopurine (8-ADP). In a second step, the reintroduction of the hpt gene on a plasmid leads to a selectable loss of 8-ADP resistance after a homologous recombination event (pop-in). A subsequent pop-out event restores the 8-ADP resistance and can generate chromosomal mutants with frequencies of about 50%.},
}
@article {pmid36125740,
year = {2022},
author = {Forterre, P},
title = {Archaea: A Goldmine for Molecular Biologists and Evolutionists.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2522},
number = {},
pages = {1-21},
pmid = {36125740},
issn = {1940-6029},
mesh = {*Archaea/genetics ; Bacteria/genetics ; *Biological Evolution ; Eukaryota/genetics ; Genome, Archaeal ; RNA, Ribosomal, 16S ; },
abstract = {The rebuttal of the prokaryote-eukaryote dichotomy and the elaboration of the three domains concept by Carl Woese and colleagues has been a breakthrough in biology. With the methodologies available at this time, they have shown that a single molecule, the 16S ribosomal RNA, could reveal the global organization of the living world. Later on, mining archaeal genomes led to major discoveries in archaeal molecular biology, providing a third model for comparative molecular biology. These analyses revealed the strong eukaryal flavor of the basic molecular fabric of Archaea and support rooting the universal tree between Bacteria and Arcarya (the clade grouping Archaea and Eukarya). However, in contradiction with this conclusion, it remains to understand why the archaeal and bacterial mobilomes are so similar and so different from the eukaryal one. These last years, the number of recognized archaea lineages (phyla?) has exploded. The archaeal nomenclature is now in turmoil and debates about the nature of the last universal common ancestor, the last archaeal common ancestor, and the topology of the tree of life are still going on. Interestingly, the expansion of the archaeal eukaryome, especially in the Asgard archaea, has provided new opportunities to study eukaryogenesis. In recent years, the application to Archaea of the new methodologies described in the various chapters of this book have opened exciting avenues to study the molecular biology and the physiology of these fascinating microorganisms.},
}
@article {pmid36125558,
year = {2022},
author = {Chow, C and Padda, KP and Puri, A and Chanway, CP},
title = {An Archaic Approach to a Modern Issue: Endophytic Archaea for Sustainable Agriculture.},
journal = {Current microbiology},
volume = {79},
number = {11},
pages = {322},
pmid = {36125558},
issn = {1432-0991},
support = {GR006717//Natural Sciences and Engineering Research Council of Canada/ ; },
mesh = {Agriculture/methods ; Amino Acids/metabolism ; *Archaea/genetics ; *Coffee/metabolism ; Endophytes/genetics/metabolism ; Plant Growth Regulators/metabolism ; Plants ; },
abstract = {Archaea have existed for over 3.5 billion years, yet they were detected in the plant endosphere only in the recent past and still, not much is known about them. Archaeal endophytes may be important microorganisms for sustainable agriculture, particularly in the face of climate change and increasing food demand due to population growth. Recent advances in culture-independent methods of research have revealed a diverse abundance of archaea from the phyla Euryarchaeota, Crenarchaeaota, and Thaumarchaeota globally that are associated with significant crops such as maize, rice, coffee, and olive. Novel insights into the plant microbiome have revealed specific genes in archaea that may be involved in numerous plant metabolic functions including amino acid production and phytohormone modulation. This is the first review article to address what is known about archaea as endophytes, including their patterns of colonization and abundance in various parts of different crop plants grown under diverse environmental conditions. This review aims to facilitate mainstream discussions and encourage future research regarding the occurrence and role of endophytic archaea in plants, particularly in relation to agricultural applications.},
}
@article {pmid36111740,
year = {2022},
author = {Yue, Y and Wang, F and Pan, J and Chen, XP and Tang, Y and Yang, Z and Ma, J and Li, M and Yang, M},
title = {Spatiotemporal dynamics, community assembly and functional potential of sedimentary archaea in reservoirs: coaction of stochasticity and nutrient load.},
journal = {FEMS microbiology ecology},
volume = {98},
number = {11},
pages = {},
doi = {10.1093/femsec/fiac109},
pmid = {36111740},
issn = {1574-6941},
mesh = {*Archaea/genetics ; RNA, Ribosomal, 16S/genetics ; *Ecosystem ; Geologic Sediments/chemistry ; Nutrients ; China ; Phylogeny ; DNA, Archaeal/genetics ; },
abstract = {Archaea participate in biogeochemical cycles in aquatic ecosystems, and deciphering their community dynamics and assembly mechanisms is key to understanding their ecological functions. Here, sediments from 12 selected reservoirs from the Wujiang and Pearl River basins in southwest China were investigated using 16S rRNA Illumina sequencing and quantitative PCR for archaeal abundance and richness in all seasons. Generally, archaeal abundance and α-diversity were significantly correlated with temperature; however, β-diversity analysis showed that community structures varied greatly among locations rather than seasons, indicating a distance-decay pattern with geographical variation. The null model revealed the major contribution of stochasticity to archaeal community assembly, which was further confirmed by the neutral community model that could explain 71.7% and 90.2% of the variance in archaeal assembly in the Wujiang and Pearl River basins, respectively. Moreover, sediment total nitrogen and organic carbon levels were significantly correlated with archaeal abundance and α-diversity. Interestingly, these nutrient levels were positively and negatively correlated, respectively, with the abundance of methanogenic and ammonia-oxidized archaea: the dominant sedimentary archaea in these reservoirs. Taken together, this work systematically characterized archaeal community profiles in reservoir sediments and demonstrated the combined action of stochastic processes and nutrient load in shaping archaeal communities in reservoir ecosystems.},
}
@article {pmid36083447,
year = {2022},
author = {Zhu, Q and Mirarab, S},
title = {Assembling a Reference Phylogenomic Tree of Bacteria and Archaea by Summarizing Many Gene Phylogenies.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2569},
number = {},
pages = {137-165},
pmid = {36083447},
issn = {1940-6029},
mesh = {*Archaea/genetics ; *Bacteria/genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; Phylogeny ; Software ; },
abstract = {Phylogenomics is the inference of phylogenetic trees based on multiple marker genes sampled in the genomes of interest. An important challenge in phylogenomics is the potential incongruence among the evolutionary histories of individual genes, which can be widespread in microorganisms due to the prevalence of horizontal gene transfer. This protocol introduces the procedures for building a phylogenetic tree of a large number of microbial genomes using a broad sampling of marker genes that are representative of whole-genome evolution. The protocol highlights the use of a gene tree summary method, which can effectively reconstruct the species tree while accounting for the topological conflicts among individual gene trees. The pipeline described in this protocol is scalable to tens of thousands of genomes while retaining high accuracy. We discussed multiple software tools, libraries, and scripts to enable convenient adoption of the protocol. The protocol is suitable for microbiology and microbiome studies based on public genomes and metagenomic data.},
}
@article {pmid36050385,
year = {2022},
author = {Hoegenauer, C and Hammer, HF and Mahnert, A and Moissl-Eichinger, C},
title = {Methanogenic archaea in the human gastrointestinal tract.},
journal = {Nature reviews. Gastroenterology &amp; hepatology},
volume = {19},
number = {12},
pages = {805-813},
pmid = {36050385},
issn = {1759-5053},
support = {P 32697/FWF_/Austrian Science Fund FWF/Austria ; },
mesh = {Humans ; *Archaea/physiology ; *Euryarchaeota ; Gastrointestinal Tract/microbiology ; Methane ; Bacteria ; },
abstract = {The human microbiome is strongly interwoven with human health and disease. Besides bacteria, viruses and eukaryotes, numerous archaea are located in the human gastrointestinal tract and are responsible for methane production, which can be measured in clinical methane breath analyses. Methane is an important readout for various diseases, including intestinal methanogen overgrowth. Notably, the archaea responsible for methane production are largely overlooked in human microbiome studies due to their non-bacterial biology and resulting detection issues. As such, their importance for health and disease remains largely unclear to date, in particular as not a single archaeal representative has been deemed to be pathogenic. In this Perspective, we discuss the current knowledge on the clinical relevance of methanogenic archaea. We explain the archaeal unique response to antibiotics and their negative and positive effects on human physiology, and present the current understanding of the use of methane as a diagnostic marker.},
}
@article {pmid36043790,
year = {2022},
author = {Kuroda, K and Yamamoto, K and Nakai, R and Hirakata, Y and Kubota, K and Nobu, MK and Narihiro, T},
title = {Symbiosis between Candidatus Patescibacteria and Archaea Discovered in Wastewater-Treating Bioreactors.},
journal = {mBio},
volume = {13},
number = {5},
pages = {e0171122},
pmid = {36043790},
issn = {2150-7511},
mesh = {*Archaea/metabolism ; Symbiosis/genetics ; Wastewater ; Phylogeny ; In Situ Hybridization, Fluorescence ; Sewage ; Bacteria/genetics ; *Euryarchaeota ; Bioreactors ; Protein Sorting Signals/genetics ; },
abstract = {Each prokaryotic domain, Bacteria and Archaea, contains a large and diverse group of organisms characterized by their ultrasmall cell size and symbiotic lifestyles (potentially commensal, mutualistic, and parasitic relationships), namely, Candidatus Patescibacteria (also known as the Candidate Phyla Radiation/CPR superphylum) and DPANN archaea, respectively. Cultivation-based approaches have revealed that Ca. Patescibacteria and DPANN symbiotically interact with bacterial and archaeal partners and hosts, respectively, but that cross-domain symbiosis and parasitism have never been observed. By amending wastewater treatment sludge samples with methanogenic archaea, we observed increased abundances of Ca. Patescibacteria (Ca. Yanofskybacteria/UBA5738) and, using fluorescence in situ hybridization (FISH), discovered that nearly all of the Ca. Yanofskybacteria/UBA5738 cells were attached to Methanothrix (95.7 ± 2.1%) and that none of the cells were attached to other lineages, implying high host dependency and specificity. Methanothrix filaments (multicellular) with Ca. Yanofskybacteria/UBA5738 attached had significantly more cells with no or low detectable ribosomal activity (based on FISH fluorescence) and often showed deformations at the sites of attachment (based on transmission electron microscopy), suggesting that the interaction is parasitic. Metagenome-assisted metabolic reconstruction showed that Ca. Yanofskybacteria/UBA5738 lacks most of the biosynthetic pathways necessary for cell growth and universally conserves three unique gene arrays that contain multiple genes with signal peptides in the metagenome-assembled genomes of the Ca. Yanofskybacteria/UBA5738 lineage. The results shed light on a novel cross-domain symbiosis and inspire potential strategies for culturing CPR and DPANN. IMPORTANCE One highly diverse phylogenetic group of Bacteria, Ca. Patescibacteria, remains poorly understood, but, from the few cultured representatives and metagenomic investigations, they are thought to live symbiotically or parasitically with other bacteria or even with eukarya. We explored the possibility of symbiotic interactions with Archaea by amending wastewater treatment sludge samples that were rich in Ca. Patescibacteria and Archaea with an isolate archaeon that is closely related to a methanogen population abundant in situ (Methanothrix). This strategic cultivation successfully established enrichment cultures that were mainly comprised of Ca. Patescibacteria (family level lineage Ca. Yanofskybacteria/UBA5738) and Methanothrix, in which we found highly specific physical interactions between the two organisms. Microscopic observations based on transmission electron microscopy, target-specific fluorescence in situ hybridization, and metagenomic analyses showed evidence that the interaction is likely parasitic. The results show a novel cross-domain parasitism between Bacteria and Archaea and suggest that the amendment of host Archaea may be an effective approach in culturing novel Ca. Patescibacteria.},
}
@article {pmid36030953,
year = {2022},
author = {Gou, Y and Song, Y and Yang, S and Yang, Y and Cheng, Y and Li, J and Zhang, T and Cheng, Y and Wang, H},
title = {Polycyclic aromatic hydrocarbon removal from subsurface soil mediated by bacteria and archaea under methanogenic conditions: Performance and mechanisms.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {313},
number = {},
pages = {120023},
doi = {10.1016/j.envpol.2022.120023},
pmid = {36030953},
issn = {1873-6424},
mesh = {Archaea/metabolism ; Bacteria/metabolism ; Biodegradation, Environmental ; Carbon Dioxide/metabolism ; *Polycyclic Aromatic Hydrocarbons/analysis ; Soil ; Soil Microbiology ; *Soil Pollutants/analysis ; },
abstract = {In situ anoxic bioremediation is an easy-to-use technology to remediate polycyclic aromatic hydrocarbon (PAH)-contaminated soil. Degradation of PAHs mediated by soil bacteria and archaea using CO2 as the electron acceptor is an important process for eliminating PAHs under methanogenic conditions; however, knowledge of the performance and mechanisms involved is poorly unveiled. In this study, the effectiveness and efficiency of NaHCO3 (CO2) as an electron acceptor to stimulate the degradation of PAHs by bacteria and archaea in highly contaminated soil were investigated. The results showed that CO2 addition (EC2000) promoted PAH degradation compared to soil without added CO2 (EC0), with 4.18%, 9.01%-8.05%, and 6.19%-12.45% increases for 2-, 3- and 4-ring PAHs after 250 days of incubation, respectively. Soil bacterial abundances increased with increasing incubation time, especially for EC2000 (2.90 × 10[8] g[-1] soil higher than EC0, p < 0.05). Different succession patterns of the soil bacterial and archaeal communities during PAH degradation were observed. According to the PCoA and ANOSIM results, the soil bacterial communities were greatly (ANOSIM: R = 0.7232, P = 0.001) impacted by electron acceptors, whereas significant differences in the archaeal communities were not observed (ANOSIM: R = 0.553, P = 0.001). Soil bacterial and archaeal co-occurrence network analyses showed that positive correlations outnumbered the negative correlations throughout the incubation period for both treatments (e.g., EC0 and EC2000), suggesting the prevalence of coexistence/cooperation within and between these two domains rather than competition. The higher complexity, connectance, edge, and node numbers in EC2000 revealed stronger linkage and a more stable co-occurrence network compared to EC0. The results of this study could improve the knowledge on the removal of PAHs and the responses of soil bacteria and archaea to CO2 application, as well as a scientific basis for the in situ anoxic bioremediation of PAH-contaminated industrial sites.},
}
@article {pmid36029340,
year = {2022},
author = {Amores, GR and Zepeda-Ramos, G and García-Fajardo, LV and Hernández, E and Guillén-Navarro, K},
title = {The gut microbiome analysis of Anastrepha obliqua reveals inter-kingdom diversity: bacteria, fungi, and archaea.},
journal = {Archives of microbiology},
volume = {204},
number = {9},
pages = {579},
pmid = {36029340},
issn = {1432-072X},
support = {CB-2008-01-101389//Consejo Nacional de Ciencia y Tecnolog&#xed;a/ ; Fellowship 17171//Consejo Nacional de Ciencia y Tecnolog&#xed;a/ ; },
mesh = {Animals ; Archaea ; Bacteria ; Fungi ; *Gastrointestinal Microbiome ; Male ; *Tephritidae ; },
abstract = {The fruit fly Anastrepha obliqua is an economically important pest. The sterile insect technique to control it involves mass production and release of sterile flies to reduce the reproduction of the wild population. As noted in different Tephritidae, the performance of sterile males may be affected by the assimilation of nutrients under mass-rearing conditions. In the wild, the fly's life cycle suggests the acquisition of different organisms that could modulate its fitness and physiology. For A. obliqua, there is no information regarding microorganisms other than bacteria. This study analyzed bacteria, fungal, and archaea communities in the A. obliqua gut through denaturing gradient gel electrophoresis (DGGE) profiles of 16S (using a different set of primers for bacteria and archaea) and 18S ribosomal DNA markers. We found that wild flies presented higher microbial diversity related to fructose assimilation than laboratory species, suggesting that microorganisms have led to a specialized metabolism to process nutrients associated with an artificial diet. We identified species that have not been previously described in this fruit fly, especially actinobacteria and archaea, by employing different primer sets aimed at the same molecular marker but targeting diverse hypervariable regions of 16S rDNA. The possibility that Archaea affect fly fitness should not be ignored. This report on the intestinal microbial (bacteria, archaea, and fungi) composition of A. obliqua contributes to our understanding of the role of microorganisms in the development and physiology of the flies.},
}
@article {pmid36009875,
year = {2022},
author = {Alharbi, F and Knura, T and Siebers, B and Ma, K},
title = {Thermostable and O2-Insensitive Pyruvate Decarboxylases from Thermoacidophilic Archaea Catalyzing the Production of Acetaldehyde.},
journal = {Biology},
volume = {11},
number = {8},
pages = {},
pmid = {36009875},
issn = {2079-7737},
support = {NA//Natural Sciences and Engineering Research Council (Canada)/ ; 031L0078A//HotSysAPP project within the e:bio initiative by the Federal Ministry of Education and Research (BMBF)/ ; },
abstract = {Pyruvate decarboxylase (PDC) is a key enzyme involved in ethanol fermentation, and it catalyzes the decarboxylation of pyruvate to acetaldehyde and CO2. Bifunctional PORs/PDCs that also have additional pyruvate:ferredoxin oxidoreductase (POR) activity are found in hyperthermophiles, and they are mostly oxygen-sensitive and CoA-dependent. Thermostable and oxygen-stable PDC activity is highly desirable for biotechnological applications. The enzymes from the thermoacidophiles Saccharolobus (formerly Sulfolobus) solfataricus (Ss, Topt = 80 °C) and Sulfolobus acidocaldarius (Sa, Topt = 80 °C) were purified and characterized, and their biophysical and biochemical properties were determined comparatively. Both enzymes were shown to be heterodimeric, and their two subunits were determined by SDS-PAGE to be 37 ± 3 kDa and 65 ± 2 kDa, respectively. The purified enzymes from S. solfataricus and S. acidocaldarius showed both PDC and POR activities which were CoA-dependent, and they were thermostable with half-life times of 2.9 ± 1 and 1.1 ± 1 h at 80 °C, respectively. There was no loss of activity in the presence of oxygen. Optimal pH values for their PDC and POR activity were determined to be 7.9 and 8.6, respectively. In conclusion, both thermostable SsPOR/PDC and SaPOR/PDC catalyze the CoA-dependent production of acetaldehyde from pyruvate in the presence of oxygen.},
}
@article {pmid36005527,
year = {2022},
author = {Grivard, A and Goubet, I and Duarte Filho, LMS and Thiéry, V and Chevalier, S and de Oliveira-Junior, RG and El Aouad, N and Guedes da Silva Almeida, JR and Sitarek, P and Quintans-Junior, LJ and Grougnet, R and Agogué, H and Picot, L},
title = {Archaea Carotenoids: Natural Pigments with Unexplored Innovative Potential.},
journal = {Marine drugs},
volume = {20},
number = {8},
pages = {},
pmid = {36005527},
issn = {1660-3397},
support = {2022 Pr Val&#xe9;rie THIERY//Ligue Nationale contre le Cancer/ ; },
mesh = {*Archaea/metabolism ; Biotechnology ; *Carotenoids/metabolism ; Pigmentation ; },
abstract = {For more than 40 years, marine microorganisms have raised great interest because of their major ecological function and their numerous applications for biotechnology and pharmacology. Particularly, Archaea represent a resource of great potential for the identification of new metabolites because of their adaptation to extreme environmental conditions and their original metabolic pathways, allowing the synthesis of unique biomolecules. Studies on archaeal carotenoids are still relatively scarce and only a few works have focused on their industrial scale production and their biotechnological and pharmacological properties, while the societal demand for these bioactive pigments is growing. This article aims to provide a comprehensive review of the current knowledge on carotenoid metabolism in Archaea and the potential applications of these pigments in biotechnology and medicine. After reviewing the ecology and classification of these microorganisms, as well as their unique cellular and biochemical characteristics, this paper highlights the most recent data concerning carotenoid metabolism in Archaea, the biological properties of these pigments, and biotechnological considerations for their production at industrial scale.},
}
@article {pmid35992648,
year = {2022},
author = {Yoshinaga, M and Nakayama, T and Inagaki, Y},
title = {A novel structural maintenance of chromosomes (SMC)-related protein family specific to Archaea.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {913088},
pmid = {35992648},
issn = {1664-302X},
abstract = {The ATPases belonging to the structural maintenance of chromosomes (SMC) superfamily are involved in the maintenance of chromosome organization and dynamics, as well as DNA repair. The major proteins in this superfamily recognized to date are either conserved among the three domains of Life (i.e., SMC and Rad50) or specific to Bacteria (i.e., RecF, RecN, and MukB). In Archaea, no protein related to SMC (SMC-related protein) with a broad taxonomic distribution has been reported. Nevertheless, two SMC-related proteins, namely coalescin and Sph, have been identified in crenarchaea Sulfolobus spp. and the euryarchaeon Halobacterium salinarum, respectively, hinting that the diversity of SMC-related proteins has been overlooked in Archaea. In this study, we report a novel SMC-related protein that is distributed among broad archaeal lineages and termed "Archaea-specific SMC-related proteins" or "ASRPs." We further demonstrate that the ASRP family encloses both coalescin and Sph but the two proteins represent only a tip of the diversity of this family.},
}
@article {pmid35985606,
year = {2022},
author = {Mafra, D and Ribeiro, M and Fonseca, L and Regis, B and Cardozo, LFMF and Fragoso Dos Santos, H and Emiliano de Jesus, H and Schultz, J and Shiels, PG and Stenvinkel, P and Rosado, A},
title = {Archaea from the gut microbiota of humans: Could be linked to chronic diseases?.},
journal = {Anaerobe},
volume = {77},
number = {},
pages = {102629},
doi = {10.1016/j.anaerobe.2022.102629},
pmid = {35985606},
issn = {1095-8274},
mesh = {Humans ; Archaea/genetics ; *Gastrointestinal Microbiome ; Methanobrevibacter/genetics ; *Euryarchaeota ; Methane ; Chronic Disease ; },
abstract = {Archaea comprise a unique domain of organisms with distinct biochemical and genetic differences from bacteria. Methane-forming archaea, methanogens, constitute the predominant group of archaea in the human gut microbiota, with Methanobrevibacter smithii being the most prevalent. However, the effect of methanogenic archaea and their methane production on chronic disease remains controversial. As perturbation of the microbiota is a feature of chronic conditions, such as cardiovascular disease, neurodegenerative diseases and chronic kidney disease, assessing the influence of archaea could provide a new clue to mitigating adverse effects associated with dysbiosis. In this review, we will discuss the putative role of archaea in the gut microbiota in humans and the possible link to chronic diseases.},
}
@article {pmid35968005,
year = {2022},
author = {Peng, Y and Xie, T and Wu, Z and Zheng, W and Zhang, T and Howe, S and Chai, J and Deng, F and Li, Y and Zhao, J},
title = {Archaea: An under-estimated kingdom in livestock animals.},
journal = {Frontiers in veterinary science},
volume = {9},
number = {},
pages = {973508},
pmid = {35968005},
issn = {2297-1769},
abstract = {Archaea are considered an essential group of gut microorganisms in both humans and animals. However, they have been neglected in previous studies, especially those involving non-ruminants. In this study, we re-analyzed published metagenomic and metatranscriptomic data sequenced from matched samples to explore the composition and the expression activity of gut archaea in ruminants (cattle and sheep) and monogastric animals (pig and chicken). Our results showed that the alpha and beta diversity of each host species, especially cattle and chickens, calculated from metagenomic and metatranscriptomic data were significantly different, suggesting that metatranscriptomic data better represent the functional status of archaea. We detected that the relative abundance of 17 (cattle), 7 (sheep), 20 (pig), and 2 (chicken) archaeal species were identified in the top 100 archaeal taxa when analyzing the metagenomic datasets, and these species were classified as the "active archaeal species" for each host species by comparison with corresponding metatranscriptomic data. For example, The expressive abundance in metatranscriptomic dataset of Methanosphaera cuniculi and Methanosphaera stadtmanae were 30- and 27-fold higher than that in metagenomic abundance, indicating their potentially important function in the pig gut. Here we aim to show the potential importance of archaea in the livestock digestive tract and encourage future research in this area, especially on the gut archaea of monogastric animals.},
}
@article {pmid35965098,
year = {2022},
author = {Zhao, H and Zhang, L},
title = {Metagenome-assembled Genomes of Six Novel Ammonia-oxidizing Archaea (AOA) from Agricultural Upland Soil.},
journal = {Microbes and environments},
volume = {37},
number = {3},
pages = {},
pmid = {35965098},
issn = {1347-4405},
mesh = {*Ammonia/metabolism ; *Archaea ; Bacteria ; Metagenome ; Nitrites/metabolism ; Oxidation-Reduction ; Soil ; Soil Microbiology ; },
abstract = {Ammonia-oxidizing archaea (AOA), key players in agricultural upland soil nitrification, convert soil ammonium to nitrite. The microbial oxidation of ammonia to nitrite is an important part of the global biogeochemical nitrogen cycle. In the present study, we recovered six novel AOA metagenome-assembled genomes (MAGs) containing genes for carbon (C) fixation and nitrogen (N) metabolism by using a deep shotgun metagenomic sequencing strategy. We also found that these AOA MAGs possessed cobalamin synthesis genes, suggesting that AOA are vitamin suppliers in agricultural upland soil. Collectively, the present results deepen our understanding of the metabolic potential and phylogeny of AOA in agroecosystems.},
}
@article {pmid35922624,
year = {2022},
author = {Ledesma, L and Hernandez-Guerrero, R and Perez-Rueda, E},
title = {Prediction of DNA-Binding Transcription Factors in Bacteria and Archaea Genomes.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2516},
number = {},
pages = {103-112},
pmid = {35922624},
issn = {1940-6029},
mesh = {Archaea/metabolism ; Bacteria/metabolism ; DNA/metabolism ; *Genome, Archaeal/genetics ; Genome, Bacterial ; Humans ; *Transcription Factors/metabolism ; },
abstract = {DNA-binding transcription factors (TFs) play a central role in the gene expression of all organisms, from viruses to humans, including bacteria and archaea. The role of these proteins is the fate of gene expression in the context of environmental challenges. Because thousands of genomes have been sequenced to date, predictions of the encoded proteins are validated through the use of bioinformatics tools to obtain the necessary experimental, posterior knowledge. In this chapter, we describe three approaches to identify TFs in protein sequences. The first approach integrates the results of sequence comparisons and PFAM assignments, using as reference a manually curated collection of TFs. The second approach considers the prediction of DNA-binding structures, such as the classical helix-turn-helix (HTH); and the third approach considers a deep learning model. We suggest that all approaches must be considered together to increase the possibility of identifying new TFs in bacterial and archaeal genomes.},
}
@article {pmid35922623,
year = {2022},
author = {Sybers, D and Charlier, D and Peeters, E},
title = {In Vitro Transcription Assay for Archaea Belonging to Sulfolobales.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2516},
number = {},
pages = {81-102},
pmid = {35922623},
issn = {1940-6029},
mesh = {*Archaea/genetics/metabolism ; *Archaeal Proteins/chemistry ; DNA-Binding Proteins/metabolism ; DNA-Directed RNA Polymerases/genetics/metabolism ; Sulfolobales/genetics/metabolism ; Transcription Factors/metabolism ; Transcription, Genetic ; },
abstract = {Archaeal transcription and its regulation are characterized by a mosaic of eukaryotic and bacterial features. Molecular analysis of the functioning of the archaeal RNA polymerase, basal transcription factors, and specific promoter-containing DNA templates allows to unravel the mechanisms of transcription regulation in archaea. In vitro transcription is a technique that allows the study of this process in a simplified and controlled environment less complex than the archaeal cell. In this chapter, we present an in vitro transcription methodology for the study of transcription in Sulfolobales. It is described how to purify the RNA polymerase and the basal transcription factors TATA-binding protein and transcription factor B of Saccharolobus solfataricus and how to perform in vitro transcription reactions and transcript detection. Application of this protocol for other archaeal species could require minor modifications to protein overexpression and purification conditions.},
}
@article {pmid35922619,
year = {2022},
author = {Maruyama, H},
title = {Micrococcal Nuclease Digestion Assays for the Analysis of Chromosome Structure in Archaea.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2516},
number = {},
pages = {29-38},
pmid = {35922619},
issn = {1940-6029},
mesh = {*Archaea/genetics/metabolism ; Chromatin/genetics ; DNA/genetics ; Digestion ; *Micrococcal Nuclease/metabolism ; Nucleosomes ; },
abstract = {The digestion of chromosomes using micrococcal nuclease (MNase) enables the analysis of their fundamental structural units. For example, the digestion of eukaryotic chromatin using MNase results in laddered DNA fragments (~150 bp increment), which reflects the length of the DNA wrapped around regularly spaced nucleosomes. Here, we describe the application of MNase to examine the chromosome structure in Archaea. We used Thermococcus kodakarensis, a hyperthermophilic euryarchaeon that encodes proteins homologous to eukaryotic histones. Methods for chromosome extraction and agarose gel electrophoresis of MNase-digested DNA including small fragments (~30 bp) are also described.},
}
@article {pmid35922618,
year = {2022},
author = {Rashid, FM and Detmar, L and Dame, RT},
title = {Chromosome Conformation Capture in Bacteria and Archaea.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2516},
number = {},
pages = {1-28},
pmid = {35922618},
issn = {1940-6029},
mesh = {*Archaea/genetics ; Bacteria/genetics ; Chromatin/genetics ; *Chromosomes/genetics ; High-Throughput Nucleotide Sequencing/methods ; Nucleic Acid Conformation ; },
abstract = {The three-dimensional structure of the chromosome is encoded within its sequence and regulates activities such as replication and transcription. This necessitates the study of the spatial organization of the chromosome in relation to the underlying sequence. Chromosome conformation capture (3C) techniques are proximity ligation-based approaches that simplify the three-dimensional architecture of the chromosome into a one-dimensional library of hybrid ligation junctions. Deciphering the information contained in these libraries resolves chromosome architecture in a sequence-specific manner. This chapter describes the preparation of 3C libraries for bacteria and archaea. It details how the three-dimensional architecture of local chromatin can be extracted from the 3C library using qPCR (3C-qPCR), and it summarizes the processing of 3C libraries for next-generation sequencing (3C-Seq) for a study of global chromosome organization.},
}
@article {pmid35922580,
year = {2022},
author = {Wang, BB and Sun, YP and Wu, ZP and Zheng, XW and Hou, J and Cui, HL},
title = {Halorientalis salina sp. nov., Halorientalis marina sp. nov., Halorientalis litorea sp. nov.: three extremely halophilic archaea isolated from a salt lake and coarse sea salt.},
journal = {Extremophiles : life under extreme conditions},
volume = {26},
number = {3},
pages = {26},
pmid = {35922580},
issn = {1433-4909},
support = {32070003//National Natural Science Foundation of China/ ; },
mesh = {Base Composition ; China ; DNA, Archaeal/genetics ; Glycolipids/metabolism ; *Halobacteriaceae ; *Lakes ; Phosphatidic Acids/metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; },
abstract = {Three halophilic archaeal strains, NEN8[T], GDY88[T] and ZY14[T], were isolated from a salt lake in Tibet and coarse sea salt samples from Guangdong and Hebei, China, respectively. These strains formed three separate clades (showing 94.4-95.8% and 87.1-89.4% similarities, respectively) and then clustered with the current Halorientalis members (showing 90.7-97.6% and 87.0-91.2% similarities, respectively), as revealed by phylogenetic analyses based on 16S rRNA and rpoB' genes. The overall genome-related index, average nucleotide identity (ANI), in silico DNA-DNA hybridization (DDH), average amino acid identity (AAI) and the percentage of conserved proteins (POCP) values, among the three strains and members of the genus Halorientalis were 76.0-88.0%, 21.3-37.2%, 69.0-88.3% and 57.7-78.1%, clearly below the threshold values for species demarcation. Strains NEN8[T], GDY88[T] and ZY14[T] could be distinguished from current Halorientalis species according to differential phenotypic characteristics. The major polar lipids of the three strains were phosphatidylglycerol (PG), phosphatidylglycerol phosphate methyl ester (PGP-Me), sulfated mannosyl glucosyl diether (S-DGD-1) and disulfated mannosyl glucosyl diether (S2-DGD). In addition, mannosyl glucosyl diether (DGD-1) was detected in strain NEN8[T] and phosphatidic acid (PA), posssulfated galactosyl mannosyl glucosyl diether (S-TGD-1) and sulfated mannosyl glucosyl diether-phosphatidic acid (S-DGD-PA) were observed in strain ZY14[T]. These results revealed that strains NEN8[T] (= CGMCC 1.17213[T] = JCM 34155[T]), GDY88[T] (= CGMCC 1.18548[T] = JCM 34481[T]) and ZY14[T] (= CGMCC 1.17178[T] = JCM 34154[T]) represent three novel species of the genus Halorientalis, for which the names Halorientalis salina sp. nov., Halorientalis marina sp. nov. and Halorientalis litorea sp. nov. are proposed.},
}
@article {pmid35917471,
year = {2022},
author = {Wegener, G and Laso-Pérez, R and Orphan, VJ and Boetius, A},
title = {Anaerobic Degradation of Alkanes by Marine Archaea.},
journal = {Annual review of microbiology},
volume = {76},
number = {},
pages = {553-577},
doi = {10.1146/annurev-micro-111021-045911},
pmid = {35917471},
issn = {1545-3251},
mesh = {*Alkanes/metabolism ; Anaerobiosis ; *Archaea ; Methane/metabolism ; Oxidation-Reduction ; Phylogeny ; },
abstract = {Alkanes are saturated apolar hydrocarbons that range from their simplest form, methane, to high-molecular-weight compounds. Although alkanes were once considered biologically recalcitrant under anaerobic conditions, microbiological investigations have now identified several microbial taxa that can anaerobically degrade alkanes. Here we review recent discoveries in the anaerobic oxidation of alkanes with a specific focus on archaea that use specific methyl coenzyme M reductases to activate their substrates. Our understanding of the diversity of uncultured alkane-oxidizing archaea has expanded through the use of environmental metagenomics and enrichment cultures of syntrophic methane-, ethane-, propane-, and butane-oxidizing marine archaea with sulfate-reducing bacteria. A recently cultured group of archaea directly couples long-chain alkane degradation with methane formation, expanding the range of substrates used for methanogenesis. This article summarizes the rapidly growing knowledge of the diversity, physiology, and habitat distribution of alkane-degrading archaea.},
}
@article {pmid35905325,
year = {2022},
author = {Rattanasriampaipong, R and Zhang, YG and Pearson, A and Hedlund, BP and Zhang, S},
title = {Archaeal lipids trace ecology and evolution of marine ammonia-oxidizing archaea.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {119},
number = {31},
pages = {e2123193119},
pmid = {35905325},
issn = {1091-6490},
mesh = {*Ammonia/metabolism ; *Archaea/genetics ; *Diglycerides ; *Evolution, Molecular ; *Membrane Lipids ; Oxidation-Reduction ; Phylogeny ; Water ; },
abstract = {Archaeal membrane lipids are widely used for paleotemperature reconstructions, yet these molecular fossils also bear rich information about ecology and evolution of marine ammonia-oxidizing archaea (AOA). Here we identified thermal and nonthermal behaviors of archaeal glycerol dialkyl glycerol tetraethers (GDGTs) by comparing the GDGT-based temperature index (TEX86) to the ratio of GDGTs with two and three cyclopentane rings (GDGT-2/GDGT-3). Thermal-dependent biosynthesis should increase TEX86 and decrease GDGT-2/GDGT-3 when the ambient temperature increases. This presumed temperature-dependent (PTD) trend is observed in GDGTs derived from cultures of thermophilic and mesophilic AOA. The distribution of GDGTs in suspended particulate matter (SPM) and sediments collected from above the pycnocline-shallow water samples-also follows the PTD trend. These similar GDGT distributions between AOA cultures and shallow water environmental samples reflect shallow ecotypes of marine AOA. While there are currently no cultures of deep AOA clades, GDGTs derived from deep water SPM and marine sediment samples exhibit nonthermal behavior deviating from the PTD trend. The presence of deep AOA increases the GDGT-2/GDGT-3 ratio and distorts the temperature-controlled correlation between GDGT-2/GDGT-3 and TEX86. We then used Gaussian mixture models to statistically characterize these diagnostic patterns of modern AOA ecology from paleo-GDGT records to infer the evolution of marine AOA from the Mid-Mesozoic to the present. Long-term GDGT-2/GDGT-3 trends suggest a suppression of today's deep water marine AOA during the Mesozoic-early Cenozoic greenhouse climates. Our analysis provides invaluable insights into the evolutionary timeline and the expansion of AOA niches associated with major oceanographic and climate changes.},
}
@article {pmid35886964,
year = {2022},
author = {Chong, PL and Chang, A and Yu, A and Mammedova, A},
title = {Vesicular and Planar Membranes of Archaea Lipids: Unusual Physical Properties and Biomedical Applications.},
journal = {International journal of molecular sciences},
volume = {23},
number = {14},
pages = {},
pmid = {35886964},
issn = {1422-0067},
mesh = {*Archaea ; Lipids ; *Liposomes ; Membranes ; Protons ; },
abstract = {Liposomes and planar membranes made of archaea or archaea-like lipids exhibit many unusual physical properties compared to model membranes composed of conventional diester lipids. Here, we review several recent findings in this research area, which include (1) thermosensitive archaeosomes with the capability to drastically change the membrane surface charge, (2) MthK channel's capability to insert into tightly packed tetraether black lipid membranes and exhibit channel activity with surprisingly high calcium sensitivity, and (3) the intercalation of apolar squalane into the midplane space of diether bilayers to impede proton permeation. We also review the usage of tetraether archaeosomes as nanocarriers of therapeutics and vaccine adjuvants, as well as the biomedical applications of planar archaea lipid membranes. The discussion on archaeosomal therapeutics is focused on partially purified tetraether lipid fractions such as the polar lipid fraction E (PLFE) and glyceryl caldityl tetraether (GCTE), which are the main components of PLFE with the sugar and phosphate removed.},
}
@article {pmid35880875,
year = {2022},
author = {Boswinkle, K and McKinney, J and Allen, KD},
title = {Highlighting the Unique Roles of Radical S-Adenosylmethionine Enzymes in Methanogenic Archaea.},
journal = {Journal of bacteriology},
volume = {204},
number = {8},
pages = {e0019722},
pmid = {35880875},
issn = {1098-5530},
support = {CHE-2105598//National Science Foundation (NSF)/ ; },
mesh = {Archaea/genetics/metabolism ; Catalysis ; *Greenhouse Gases/metabolism ; *Iron-Sulfur Proteins/metabolism ; S-Adenosylmethionine/chemistry/metabolism ; },
abstract = {Radical S-adenosylmethionine (SAM) enzymes catalyze an impressive variety of difficult biochemical reactions in various pathways across all domains of life. These metalloenzymes employ a reduced [4Fe-4S] cluster and SAM to generate a highly reactive 5'-deoxyadenosyl radical that is capable of initiating catalysis on otherwise unreactive substrates. Interestingly, the genomes of methanogenic archaea encode many unique radical SAM enzymes with underexplored or completely unknown functions. These organisms are responsible for the yearly production of nearly 1 billion tons of methane, a potent greenhouse gas as well as a valuable energy source. Thus, understanding the details of methanogenic metabolism and elucidating the functions of essential enzymes in these organisms can provide insights into strategies to decrease greenhouse gas emissions as well as inform advances in bioenergy production processes. This minireview provides an overview of the current state of the field regarding the functions of radical SAM enzymes in methanogens and discusses gaps in knowledge that should be addressed.},
}
@article {pmid35852729,
year = {2023},
author = {Flusche, T and Rajan, R},
title = {Molecular Details of DNA Integration by CRISPR-Associated Proteins During Adaptation in Bacteria and Archaea.},
journal = {Advances in experimental medicine and biology},
volume = {1414},
number = {},
pages = {27-43},
pmid = {35852729},
issn = {0065-2598},
support = {P20 GM103640/GM/NIGMS NIH HHS/United States ; },
mesh = {*Archaea/genetics ; Bacteria/genetics ; Acclimatization ; Biotechnology ; RNA ; *CRISPR-Associated Proteins/genetics ; },
abstract = {Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) proteins constitute an adaptive immune system in bacteria and archaea, where immunological memory is retained in the CRISPR locus as short pieces of the intruding nucleic acid, termed spacers. The adaptation to new infections occurs through the integration of a new spacer into the CRISPR array. For immune protection, spacers are transcribed into CRISPR RNAs (crRNA) that are used to guide the effector nuclease of the system in sequence-dependent target cleavage. Spacers originate as a prespacer from either DNA or RNA depending on the CRISPR-Cas system being observed, and the nearly universal Cas proteins, Cas1 and Cas2, insert the prespacer into the CRISPR locus during adaptation in all systems that contain them. The mechanism of site-specific prespacer integration varies across CRISPR classes and types, and distinct differences can even be found within the same subtype. In this review, the current knowledge on the mechanisms of prespacer integration in type II-A CRISPR-Cas systems will be described. Comparisons of the currently characterized type II-A systems show that distinct mechanisms exist within different members of this subtype and are correlated to sequence-specific interactions of Cas proteins and the DNA elements present in the CRISPR array. These observations indicate that nature has fine-tuned the mechanistic details while performing the basic step of DNA integration by Cas proteins, which offers unique advantages to develop Cas1-Cas2-based biotechnology.},
}
@article {pmid35811376,
year = {2022},
author = {Villain, P and Catchpole, R and Forterre, P and Oberto, J and da Cunha, V and Basta, T},
title = {Expanded Dataset Reveals the Emergence and Evolution of DNA Gyrase in Archaea.},
journal = {Molecular biology and evolution},
volume = {39},
number = {8},
pages = {},
pmid = {35811376},
issn = {1537-1719},
mesh = {*Archaea/genetics/metabolism ; Bacteria/genetics ; *DNA Gyrase/genetics ; DNA Topoisomerases, Type I/genetics ; Gene Transfer, Horizontal ; },
abstract = {DNA gyrase is a type II topoisomerase with the unique capacity to introduce negative supercoiling in DNA. In bacteria, DNA gyrase has an essential role in the homeostatic regulation of supercoiling. While ubiquitous in bacteria, DNA gyrase was previously reported to have a patchy distribution in Archaea but its emergent function and evolutionary history in this domain of life remains elusive. In this study, we used phylogenomic approaches and an up-to date sequence dataset to establish global and archaea-specific phylogenies of DNA gyrases. The most parsimonious evolutionary scenario infers that DNA gyrase was introduced into the lineage leading to Euryarchaeal group II via a single horizontal gene transfer from a bacterial donor which we identified as an ancestor of Gracilicutes and/or Terrabacteria. The archaea-focused trees indicate that DNA gyrase spread from Euryarchaeal group II to some DPANN and Asgard lineages via rare horizontal gene transfers. The analysis of successful recent transfers suggests a requirement for syntropic or symbiotic/parasitic relationship between donor and recipient organisms. We further show that the ubiquitous archaeal Topoisomerase VI may have co-evolved with DNA gyrase to allow the division of labor in the management of topological constraints. Collectively, our study reveals the evolutionary history of DNA gyrase in Archaea and provides testable hypotheses to understand the prerequisites for successful establishment of DNA gyrase in a naive archaeon and the associated adaptations in the management of topological constraints.},
}
@article {pmid35810262,
year = {2022},
author = {Ou, YF and Dong, HP and McIlroy, SJ and Crowe, SA and Hallam, SJ and Han, P and Kallmeyer, J and Simister, RL and Vuillemin, A and Leu, AO and Liu, Z and Zheng, YL and Sun, QL and Liu, M and Tyson, GW and Hou, LJ},
title = {Expanding the phylogenetic distribution of cytochrome b-containing methanogenic archaea sheds light on the evolution of methanogenesis.},
journal = {The ISME journal},
volume = {16},
number = {10},
pages = {2373-2387},
pmid = {35810262},
issn = {1751-7370},
support = {41725002//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42030411//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {Archaea/genetics/metabolism ; Cytochromes/genetics ; Cytochromes b/genetics/metabolism ; *Euryarchaeota/metabolism ; *Hydrogenase/metabolism ; Methane/metabolism ; Phylogeny ; },
abstract = {Methane produced by methanogenic archaea has an important influence on Earth's changing climate. Methanogenic archaea are phylogenetically diverse and widespread in anoxic environments. These microorganisms can be divided into two subgroups based on whether or not they use b-type cytochromes for energy conservation. Methanogens with b-type cytochromes have a wider substrate range and higher growth yields than those without them. To date, methanogens with b-type cytochromes were found exclusively in the phylum "Ca. Halobacteriota" (formerly part of the phylum Euryarchaeota). Here, we present the discovery of metagenome-assembled genomes harboring methyl-coenzyme M reductase genes reconstructed from mesophilic anoxic sediments, together with the previously reported thermophilic "Ca. Methylarchaeum tengchongensis", representing a novel archaeal order, designated the "Ca. Methylarchaeales", of the phylum Thermoproteota (formerly the TACK superphylum). These microorganisms contain genes required for methyl-reducing methanogenesis and the Wood-Ljundahl pathway. Importantly, the genus "Ca. Methanotowutia" of the "Ca. Methylarchaeales" encode a cytochrome b-containing heterodisulfide reductase (HdrDE) and methanophenazine-reducing hydrogenase complex that have similar gene arrangements to those found in methanogenic Methanosarcinales. Our results indicate that members of the "Ca. Methylarchaeales" are methanogens with cytochromes and can conserve energy via membrane-bound electron transport chains. Phylogenetic and amalgamated likelihood estimation analyses indicate that methanogens with cytochrome b-containing electron transfer complexes likely evolved before diversification of Thermoproteota or "Ca. Halobacteriota" in the early Archean Eon. Surveys of public sequence databases suggest that members of the lineage are globally distributed in anoxic sediments and may be important players in the methane cycle.},
}
@article {pmid35796992,
year = {2022},
author = {Kern, M and Ferreira-Cerca, S},
title = {Differential Translation Activity Analysis Using Bioorthogonal Noncanonical Amino Acid Tagging (BONCAT) in Archaea.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2533},
number = {},
pages = {229-246},
pmid = {35796992},
issn = {1940-6029},
mesh = {Alkynes/chemistry ; *Amino Acids/metabolism ; Archaea/metabolism ; *Azides/chemistry ; Click Chemistry/methods ; Proteins/chemistry ; Proteomics/methods ; },
abstract = {The study of protein production and degradation in a quantitative and time-dependent manner is a major challenge to better understand cellular physiological response. Among available technologies bioorthogonal noncanonical amino acid tagging (BONCAT) is an efficient approach allowing for time-dependent labeling of proteins through the incorporation of chemically reactive noncanonical amino acids like L-azidohomoalanine (L-AHA). The azide-containing amino-acid derivative enables a highly efficient and specific reaction termed click chemistry, whereby the azide group of the L-AHA reacts with a reactive alkyne derivate, like dibenzocyclooctyne (DBCO) derivatives, using strain-promoted alkyne-azide cycloaddition (SPAAC). Moreover, available DBCO containing reagents are versatile and can be coupled to fluorophore (e.g., Cy7) or affinity tag (e.g., biotin) derivatives, for easy visualization and affinity purification, respectively.Here, we describe a step-by-step BONCAT protocol optimized for the model archaeon Haloferax volcanii , but which is also suitable to harness other biological systems. Finally, we also describe examples of downstream visualization, affinity purification of L-AHA-labeled proteins and differential expression analysis.In conclusion, the following BONCAT protocol expands the available toolkit to explore proteostasis using time-resolved semiquantitative proteomic analysis in archaea .},
}
@article {pmid35773279,
year = {2022},
author = {Buessecker, S and Palmer, M and Lai, D and Dimapilis, J and Mayali, X and Mosier, D and Jiao, JY and Colman, DR and Keller, LM and St John, E and Miranda, M and Gonzalez, C and Gonzalez, L and Sam, C and Villa, C and Zhuo, M and Bodman, N and Robles, F and Boyd, ES and Cox, AD and St Clair, B and Hua, ZS and Li, WJ and Reysenbach, AL and Stott, MB and Weber, PK and Pett-Ridge, J and Dekas, AE and Hedlund, BP and Dodsworth, JA},
title = {An essential role for tungsten in the ecology and evolution of a previously uncultivated lineage of anaerobic, thermophilic Archaea.},
journal = {Nature communications},
volume = {13},
number = {1},
pages = {3773},
pmid = {35773279},
issn = {2041-1723},
mesh = {Anaerobiosis ; *Archaea/metabolism ; Metagenome ; Phylogeny ; *Tungsten ; },
abstract = {Trace metals have been an important ingredient for life throughout Earth's history. Here, we describe the genome-guided cultivation of a member of the elusive archaeal lineage Caldarchaeales (syn. Aigarchaeota), Wolframiiraptor gerlachensis, and its growth dependence on tungsten. A metagenome-assembled genome (MAG) of W. gerlachensis encodes putative tungsten membrane transport systems, as well as pathways for anaerobic oxidation of sugars probably mediated by tungsten-dependent ferredoxin oxidoreductases that are expressed during growth. Catalyzed reporter deposition-fluorescence in-situ hybridization (CARD-FISH) and nanoscale secondary ion mass spectrometry (nanoSIMS) show that W. gerlachensis preferentially assimilates xylose. Phylogenetic analyses of 78 high-quality Wolframiiraptoraceae MAGs from terrestrial and marine hydrothermal systems suggest that tungsten-associated enzymes were present in the last common ancestor of extant Wolframiiraptoraceae. Our observations imply a crucial role for tungsten-dependent metabolism in the origin and evolution of this lineage, and hint at a relic metabolic dependence on this trace metal in early anaerobic thermophiles.},
}
@article {pmid35770746,
year = {2022},
author = {Cai, M and Tang, X},
title = {Human Archaea and Associated Metabolites in Health and Disease.},
journal = {Biochemistry},
volume = {61},
number = {24},
pages = {2835-2840},
doi = {10.1021/acs.biochem.2c00232},
pmid = {35770746},
issn = {1520-4995},
mesh = {Humans ; *Archaea/metabolism ; Bacteria/metabolism ; Fungi ; *Euryarchaeota ; },
abstract = {Trillions of microorganisms, including bacteria, archaea, fungi, and viruses, live in or on the human body. Microbe-microbe and microbe-host interactions are often influenced by diffusible and microbe-associated small molecules. Over the past few years, it has become evident that these interactions have a substantial impact on human health and disease. In this Perspective, we summarize the research involving the discovery of methanogenic and non-methanogenic archaea associated with the human body. In particular, we emphasize the importance of some archaeal metabolites in mediating intra- and interspecies interactions in the ecological environment of the human body. A deep understanding of the archaeal metabolites as well as their biological functions may reveal in more detail whether and how archaea are involved in maintaining human health and/or causing certain diseases.},
}
@article {pmid35765181,
year = {2022},
author = {Kropp, C and Lipp, J and Schmidt, AL and Seisenberger, C and Linde, M and Hinrichs, KU and Babinger, P},
title = {Identification of acetylated diether lipids in halophilic Archaea.},
journal = {MicrobiologyOpen},
volume = {11},
number = {3},
pages = {e1299},
pmid = {35765181},
issn = {2045-8827},
mesh = {*Archaea/metabolism ; *Bacillales ; Ethers/chemistry/metabolism ; Mass Spectrometry ; Terpenes/metabolism ; },
abstract = {As a hallmark of Archaea, their cell membranes are comprised of ether lipids. However, Archaea-type ether lipids have recently been identified in Bacteria as well, with a somewhat different composition: In Bacillales, sn-glycerol 1-phosphate is etherified with one C35 isoprenoid chain, which is longer than the typical C20 chain in Archaea, and instead of a second isoprenoid chain, the product heptaprenylglyceryl phosphate becomes dephosphorylated and afterward diacetylated by the O-acetyltransferase YvoF. Interestingly, database searches have revealed YvoF homologs in Halobacteria (Archaea), too. Here, we demonstrate that YvoF from Haloferax volcanii can acetylate geranylgeranylglycerol in vitro. Additionally, we present the first-time identification of acetylated diether lipids in H. volcanii and Halobacterium salinarum by mass spectrometry. A variety of different acetylated lipids, namely acetylated archaeol, and acetylated archaetidylglycerol, were found, suggesting that halobacterial YvoF has a broad substrate range. We suppose that the acetyl group might serve to modify the polarity of the lipid headgroup, with still unknown biological effects.},
}
@article {pmid37938729,
year = {2022},
author = {Wang, L and Wang, Y and Huang, X and Ma, R and Li, J and Wang, F and Jiao, N and Zhang, R},
title = {Potential metabolic and genetic interaction among viruses, methanogen and methanotrophic archaea, and their syntrophic partners.},
journal = {ISME communications},
volume = {2},
number = {1},
pages = {50},
pmid = {37938729},
issn = {2730-6151},
support = {91951209//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42006097//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2020M671942//China Postdoctoral Science Foundation/ ; },
abstract = {The metabolism of methane in anoxic ecosystems is mainly mediated by methanogens and methane-oxidizing archaea (MMA), key players in global carbon cycling. Viruses are vital in regulating their host fate and ecological function. However, our knowledge about the distribution and diversity of MMA viruses and their interactions with hosts is rather limited. Here, by searching metagenomes containing mcrA (the gene coding for the α-subunit of methyl-coenzyme M reductase) from a wide variety of environments, 140 viral operational taxonomic units (vOTUs) that potentially infect methanogens or methane-oxidizing archaea were retrieved. Four MMA vOTUs (three infecting the order Methanobacteriales and one infecting the order Methanococcales) were predicted to cross-domain infect sulfate-reducing bacteria. By facilitating assimilatory sulfur reduction, MMA viruses may increase the fitness of their hosts in sulfate-depleted anoxic ecosystems and benefit from synthesis of the sulfur-containing amino acid cysteine. Moreover, cell-cell aggregation promoted by MMA viruses may be beneficial for both the viruses and their hosts by improving infectivity and environmental stress resistance, respectively. Our results suggest a potential role of viruses in the ecological and environmental adaptation of methanogens and methane-oxidizing archaea.},
}
@article {pmid35761090,
year = {2022},
author = {Banciu, HL and Gridan, IM and Zety, AV and Baricz, A},
title = {Asgard archaea in saline environments.},
journal = {Extremophiles : life under extreme conditions},
volume = {26},
number = {2},
pages = {21},
pmid = {35761090},
issn = {1433-4909},
support = {PN-III-P4-ID-PCE-2020-1559//Ministry of Research, Innovation and Digitization, CNCS/CCCDI - UEFISCDI/ ; },
mesh = {*Archaea ; Eukaryotic Cells/metabolism ; *Genome, Archaeal ; Metagenome ; Phylogeny ; },
abstract = {Members of candidate Asgardarchaeota superphylum appear to share numerous eukaryotic-like attributes thus being broadly explored for their relevance to eukaryogenesis. On the contrast, the ecological roles of Asgard archaea remains understudied. Asgard archaea have been frequently associated to low-oxygen aquatic sedimentary environments worldwide spanning a broad but not extreme salinity range. To date, the available information on diversity and potential biogeochemical roles of Asgardarchaeota mostly sourced from marine habitats and to a much lesser extend from true saline environments (i.e., > 3% w/v total salinity). Here, we provide an overview on diversity and ecological implications of Asgard archaea distributed across saline environments and briefly explore their metagenome-resolved potential for osmoadaptation. Loki-, Thor- and Heimdallarchaeota are the dominant Asgard clades in saline habitats where they might employ anaerobic/microaerophilic organic matter degradation and autotrophic carbon fixation. Homologs of primary solute uptake ABC transporters seemingly prevail in Thorarchaeota, whereas those putatively involved in trehalose and ectoine biosynthesis were mostly inferred in Lokiarchaeota. We speculate that Asgardarchaeota might adopt compatible solute-accumulating ('salt-out') strategy as response to salt stress. Our current understanding on the distribution, ecology and salt-adaptive strategies of Asgardarchaeota in saline environments are, however, limited by insufficient sampling and incompleteness of the available metagenome-assembled genomes. Extensive sampling combined with 'omics'- and cultivation-based approaches seem, therefore, crucial to gain deeper knowledge on this particularly intriguing archaeal lineage.},
}
@article {pmid35760837,
year = {2022},
author = {Rambo, IM and Langwig, MV and Leão, P and De Anda, V and Baker, BJ},
title = {Genomes of six viruses that infect Asgard archaea from deep-sea sediments.},
journal = {Nature microbiology},
volume = {7},
number = {7},
pages = {953-961},
pmid = {35760837},
issn = {2058-5276},
mesh = {*Archaea/genetics/metabolism ; Eukaryota/genetics ; Genome, Archaeal ; Metagenome ; Phylogeny ; *Viruses/genetics ; },
abstract = {Asgard archaea are globally distributed prokaryotic microorganisms related to eukaryotes; however, viruses that infect these organisms have not been described. Here, using metagenome sequences recovered from deep-sea hydrothermal sediments, we characterize six relatively large (up to 117 kb) double-stranded DNA (dsDNA) viral genomes that infected two Asgard archaeal phyla, Lokiarchaeota and Helarchaeota. These viruses encode Caudovirales-like structural proteins, as well as proteins distinct from those described in known archaeal viruses. Their genomes contain around 1-5% of genes associated with eukaryotic nucleocytoplasmic large DNA viruses (NCLDVs) and appear to be capable of semi-autonomous genome replication, repair, epigenetic modifications and transcriptional regulation. Moreover, Helarchaeota viruses may hijack host ubiquitin systems similar to eukaryotic viruses. Genomic analysis of these Asgard viruses reveals that they contain features of both prokaryotic and eukaryotic viruses, and provides insights into their potential infection and host interaction mechanisms.},
}
@article {pmid35759872,
year = {2022},
author = {Garcia, PS and Gribaldo, S and Borrel, G},
title = {Diversity and Evolution of Methane-Related Pathways in Archaea.},
journal = {Annual review of microbiology},
volume = {76},
number = {},
pages = {727-755},
doi = {10.1146/annurev-micro-041020-024935},
pmid = {35759872},
issn = {1545-3251},
mesh = {*Archaea ; *Methane/metabolism ; Oxidation-Reduction ; Phylogeny ; },
abstract = {Methane is one of the most important greenhouse gases on Earth and holds an important place in the global carbon cycle. Archaea are the only organisms that use methanogenesis to produce energy and rely on the methyl-coenzyme M reductase complex (Mcr). Over the last decade, new results have significantly reshaped our view of the diversity of methane-related pathways in the Archaea. Many new lineages that synthesize or use methane have been identified across the whole archaeal tree, leading to a greatly expanded diversity of substrates and mechanisms. In this review, we present the state of the art of these advances and how they challenge established scenarios of the origin and evolution of methanogenesis, and we discuss the potential trajectories that may have led to this strikingly wide range of metabolisms.},
}
@article {pmid35751084,
year = {2022},
author = {Xiong, X and Rao, Y and Tu, X and Wang, Z and Gong, J and Yang, Y and Wu, H and Liu, X},
title = {Gut archaea associated with bacteria colonization and succession during piglet weaning transitions.},
journal = {BMC veterinary research},
volume = {18},
number = {1},
pages = {243},
pmid = {35751084},
issn = {1746-6148},
mesh = {Animals ; Archaea/genetics ; Bacteria/genetics ; *Mucorales ; *Physical Conditioning, Animal ; Swine ; Weaning ; },
abstract = {BACKGROUND: Host-associated gut microbial communities are key players in shaping the fitness and health of animals. However, most current studies have focused on the gut bacteria, neglecting important gut fungal and archaeal components of these communities. Here, we investigated the gut fungi and archaea community composition in Large White piglets using shotgun metagenomic sequencing, and systematically evaluated how community composition association with gut microbiome, functional capacity, and serum metabolites varied across three weaning periods.<br><br>RESULTS: We found that Mucoromycota, Ascomycota and Basidiomycota were the most common fungi phyla and Euryarchaeota was the most common archaea phyla across individuals. We identified that Methanosarcina siciliae was the most significantly different archaea species among three weaning periods, while Parasitella parasitica, the only differential fungi species, was significantly and positively correlated with Methanosarcina siciliae enriched in day 28 group. The random forest analysis also identified Methanosarcina siciliae and Parasitella parasitica as weaning-biased archaea and fungi at the species level. Additionally, Methanosarcina siciliae was significantly correlated with P. copri and the shifts of functional capacities of the gut microbiome and several CAZymes in day 28 group. Furthermore, characteristic successional alterations in gut archaea, fungi, bacteria, and serum metabolites with each weaning step revealed a weaning transition coexpression network, e.g., Methanosarcina siciliae and P. copri were positively and significantly correlated with 15-HEPE, 8-O-Methyloblongine, and Troxilin B3.<br><br>CONCLUSION: Our findings provide a deep insight into the interactions among gut archaea, fungi, bacteria, and serum metabolites and will present a theoretical framework for understanding gut bacterial colonization and succession association with archaea during piglet weaning transitions.},
}
@article {pmid35743947,
year = {2022},
author = {Doytchinov, VV and Dimov, SG},
title = {Microbial Community Composition of the Antarctic Ecosystems: Review of the Bacteria, Fungi, and Archaea Identified through an NGS-Based Metagenomics Approach.},
journal = {Life (Basel, Switzerland)},
volume = {12},
number = {6},
pages = {},
pmid = {35743947},
issn = {2075-1729},
support = {70-25-72 from 03.08.2021//NATIONAL CENTER FOR POLAR STUDIES - SOFIA UNIVERSITY "ST. KLIMENT OHRIDSKI"/ ; },
abstract = {Antarctica represents a unique environment, both due to the extreme meteorological and geological conditions that govern it and the relative isolation from human influences that have kept its environment largely undisturbed. However, recent trends in climate change dictate an unavoidable change in the global biodiversity as a whole, and pristine environments, such as Antarctica, allow us to study and monitor more closely the effects of the human impact. Additionally, due to its inaccessibility, Antarctica contains a plethora of yet uncultured and unidentified microorganisms with great potential for useful biological activities and production of metabolites, such as novel antibiotics, proteins, pigments, etc. In recent years, amplicon-based next-generation sequencing (NGS) has allowed for a fast and thorough examination of microbial communities to accelerate the efforts of unknown species identification. For these reasons, in this review, we present an overview of the archaea, bacteria, and fungi present on the Antarctic continent and the surrounding area (maritime Antarctica, sub-Antarctica, Southern Sea, etc.) that have recently been identified using amplicon-based NGS methods.},
}
@article {pmid35741701,
year = {2022},
author = {Ding, R and Yang, N and Liu, J},
title = {The Osmoprotectant Switch of Potassium to Compatible Solutes in an Extremely Halophilic Archaea Halorubrum kocurii 2020YC7.},
journal = {Genes},
volume = {13},
number = {6},
pages = {},
pmid = {35741701},
issn = {2073-4425},
mesh = {Betaine/metabolism ; *Halobacteriales ; *Halorubrum ; Potassium/metabolism ; Sodium Chloride/metabolism ; Trehalose ; },
abstract = {The main osmoadaptive mechanisms of extremely halophilic archaea include the "salt-in" strategy and the "compatible solutes" strategy. Here we report the osmoadaptive mechanism of an extremely halophilic archaea H. kocurii 2020YC7, isolated from a high salt environment sample. Genomic data revealed that strain 2020YC7 harbors genes trkA, trkH, kch for K[+] uptake, kefB for K[+] output, treS for trehalose production from polysaccharide, and betaine/carnitine/choline transporter family gene for glycine betaine uptake. Strain 2020YC7 could accumulate 8.17 to 28.67 μmol/mg protein K[+] in a defined medium, with its content increasing along with the increasing salinity from 100 to 200 g/L. When exogenous glycine betaine was added, glycine betaine functioned as the primary osmotic solute between 200 and 250 g/L NaCl, which was accumulated up to 15.27 mg/mg protein in 2020YC7 cells. RT-qPCR results completely confirmed these results. Notably, the concentrations of intracellular trehalose decreased from 5.26 to 2.61 mg/mg protein as the NaCl increased from 50 to 250 g/L. In combination with this result, the transcript level of gene treS, which catalyzes the production of trehalose from polysaccharide, was significantly up-regulated at 50-100 g/L NaCl. Therefore, trehalose does not act as an osmotic solute at high NaCl concentrations (more than 100 g/L) but at relatively low NaCl concentrations (50-100 g/L). And we propose that the degradation of cell wall polysaccharide, as a source of trehalose in a low-salt environment, may be one of the reasons for the obligate halophilic characteristics of strain 2020YC7.},
}
@article {pmid35720372,
year = {2022},
author = {Krawczyk, KT and Locht, C and Kowalewicz-Kulbat, M},
title = {Halophilic Archaea Halorhabdus Rudnickae and Natrinema Salaciae Activate Human Dendritic Cells and Orient T Helper Cell Responses.},
journal = {Frontiers in immunology},
volume = {13},
number = {},
pages = {833635},
pmid = {35720372},
issn = {1664-3224},
mesh = {Cytokines ; Dendritic Cells ; *Halobacteriaceae ; Humans ; *Interleukin-13/pharmacology ; T-Lymphocytes, Helper-Inducer ; },
abstract = {Halophilic archaea are procaryotic organisms distinct from bacteria, known to thrive in hypersaline environments, including salt lakes, salterns, brines and salty food. They have also been identified in the human microbiome. The biological significance of halophiles for human health has rarely been examined. The interactions between halophilic archaea and human dendritic cells (DCs) and T cells have not been identified so far. Here, we show for the first time that the halophilic archaea Halorhabdus rudnickae and Natrinema salaciae activate human monocyte-derived DCs, induce DC maturation, cytokine production and autologous T cell activation. In vitro both strains induced DC up-regulation of the cell-surface receptors CD86, CD80 and CD83, and cytokine production, including IL-12p40, IL-10 and TNF-α, but not IL-23 and IL-12p70. Furthermore, autologous CD4[+] T cells produced significantly higher amounts of IFN-γ and IL-13, but not IL-17A when co-cultured with halophile-stimulated DCs in comparison to T cells co-cultured with unstimulated DCs. IFN-γ was almost exclusively produced by naïve T cells, while IL-13 was produced by both naïve and memory CD4[+] T cells. Our findings thus show that halophilic archaea are recognized by human DCs and are able to induce a balanced cytokine response. The immunomodulatory functions of halophilic archaea and their potential ability to re-establish the immune balance may perhaps participate in the beneficial effects of halotherapies.},
}
@article {pmid35706137,
year = {2022},
author = {Hu, W and Hou, Q and Delgado-Baquerizo, M and Stegen, JC and Du, Q and Dong, L and Ji, M and Sun, Y and Yao, S and Gong, H and Xiong, J and Xia, R and Liu, J and Aqeel, M and Akram, MA and Ran, J and Deng, J},
title = {Continental-scale niche differentiation of dominant topsoil archaea in drylands.},
journal = {Environmental microbiology},
volume = {24},
number = {11},
pages = {5483-5497},
doi = {10.1111/1462-2920.16099},
pmid = {35706137},
issn = {1462-2920},
mesh = {*Archaea/genetics ; *Ecosystem ; Soil Microbiology ; Ammonia ; Soil ; Oxidation-Reduction ; Nitrification ; Phylogeny ; },
abstract = {Archaea represent a diverse group of microorganisms often associated with extreme environments. However, an integrated understanding of biogeographical patterns of the specialist Haloarchaea and the potential generalist ammonia-oxidizing archaea (AOA) across large-scale environmental gradients remains limited. We hypothesize that niche differentiation determines their distinct distributions along environmental gradients. To test the hypothesis, we use a continental-scale research network including 173 dryland sites across northern China. Our results demonstrate that Haloarchaea and AOA dominate topsoil archaeal communities. As hypothesized, Haloarchaea and AOA show strong niche differentiation associated with two ecosystem types mainly found in China's drylands (i.e. deserts vs. grasslands), and they differ in the degree of habitat specialization. The relative abundance and richness of Haloarchaea are higher in deserts due to specialization to relatively high soil salinity and extreme climates, while those of AOA are greater in grassland soils. Our results further indicate a divergence in ecological processes underlying the segregated distributions of Haloarchaea and AOA. Haloarchaea are governed primarily by environmental-based processes while the more generalist AOA are assembled mostly via spatial-based processes. Our findings add to existing knowledge of large-scale biogeography of topsoil archaea, advancing our predictive understanding on changes in topsoil archaeal communities in a drier world.},
}
@article {pmid35697693,
year = {2022},
author = {Hatano, T and Palani, S and Papatziamou, D and Salzer, R and Souza, DP and Tamarit, D and Makwana, M and Potter, A and Haig, A and Xu, W and Townsend, D and Rochester, D and Bellini, D and Hussain, HMA and Ettema, TJG and Löwe, J and Baum, B and Robinson, NP and Balasubramanian, M},
title = {Asgard archaea shed light on the evolutionary origins of the eukaryotic ubiquitin-ESCRT machinery.},
journal = {Nature communications},
volume = {13},
number = {1},
pages = {3398},
pmid = {35697693},
issn = {2041-1723},
support = {MC_U105184326/MRC_/Medical Research Council/United Kingdom ; MC_UP_1201/27/MRC_/Medical Research Council/United Kingdom ; 203276/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; WT101885MA/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Archaea/genetics/metabolism ; *Endosomal Sorting Complexes Required for Transport/metabolism ; *Eukaryota/genetics/metabolism ; Eukaryotic Cells/metabolism ; Ubiquitin/genetics ; },
abstract = {The ESCRT machinery, comprising of multiple proteins and subcomplexes, is crucial for membrane remodelling in eukaryotic cells, in processes that include ubiquitin-mediated multivesicular body formation, membrane repair, cytokinetic abscission, and virus exit from host cells. This ESCRT system appears to have simpler, ancient origins, since many archaeal species possess homologues of ESCRT-III and Vps4, the components that execute the final membrane scission reaction, where they have been shown to play roles in cytokinesis, extracellular vesicle formation and viral egress. Remarkably, metagenome assemblies of Asgard archaea, the closest known living relatives of eukaryotes, were recently shown to encode homologues of the entire cascade involved in ubiquitin-mediated membrane remodelling, including ubiquitin itself, components of the ESCRT-I and ESCRT-II subcomplexes, and ESCRT-III and Vps4. Here, we explore the phylogeny, structure, and biochemistry of Asgard homologues of the ESCRT machinery and the associated ubiquitylation system. We provide evidence for the ESCRT-I and ESCRT-II subcomplexes being involved in ubiquitin-directed recruitment of ESCRT-III, as it is in eukaryotes. Taken together, our analyses suggest a pre-eukaryotic origin for the ubiquitin-coupled ESCRT system and a likely path of ESCRT evolution via a series of gene duplication and diversification events.},
}
@article {pmid35695998,
year = {2022},
author = {Verma, D and Kumar, V and Satyanarayana, T},
title = {Genomic attributes of thermophilic and hyperthermophilic bacteria and archaea.},
journal = {World journal of microbiology &amp; biotechnology},
volume = {38},
number = {8},
pages = {135},
pmid = {35695998},
issn = {1573-0972},
mesh = {*Archaea/genetics ; *Bacteria/genetics ; Genes, Archaeal ; Genomics ; Metagenome ; Phylogeny ; },
abstract = {Thermophiles and hyperthermophiles are immensely useful in understanding the evolution of life, besides their utility in environmental and industrial biotechnology. Advancements in sequencing technologies have revolutionized the field of microbial genomics. The massive generation of data enhances the sequencing coverage multi-fold and allows to analyse the entire genomic features of microbes efficiently and accurately. The mandate of a pure isolate can also be bypassed where whole metagenome-assembled genomes and single cell-based sequencing have fulfilled the majority of the criteria to decode various attributes of microbial genomes. A boom has, therefore, been seen in analysing the extremophilic bacteria and archaea using sequence-based approaches. Due to extensive sequence analysis, it becomes easier to understand the gene flow and their evolution among the members of bacteria and archaea. For instance, sequencing unveiled that Thermotoga maritima shares around 24% of genes of archaeal origin. Comparative and functional genomics provide an analytical view to understanding the microbial diversity of thermophilic bacteria and archaea, their interactions with other microbes, their adaptations, gene flow, and evolution over time. In this review, the genomic features of thermophilic bacteria and archaea are dealt with comprehensively.},
}
@article {pmid35667126,
year = {2022},
author = {Gophna, U and Altman-Price, N},
title = {Horizontal Gene Transfer in Archaea-From Mechanisms to Genome Evolution.},
journal = {Annual review of microbiology},
volume = {76},
number = {},
pages = {481-502},
doi = {10.1146/annurev-micro-040820-124627},
pmid = {35667126},
issn = {1545-3251},
mesh = {*Archaea/genetics ; Bacteria/genetics ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Phylogeny ; },
abstract = {Archaea remains the least-studied and least-characterized domain of life despite its significance not just to the ecology of our planet but also to the evolution of eukaryotes. It is therefore unsurprising that research into horizontal gene transfer (HGT) in archaea has lagged behind that of bacteria. Indeed, several archaeal lineages may owe their very existence to large-scale HGT events, and thus understanding both the molecular mechanisms and the evolutionary impact of HGT in archaea is highly important. Furthermore, some mechanisms of gene exchange, such as plasmids that transmit themselves via membrane vesicles and the formation of cytoplasmic bridges that allows transfer of both chromosomal and plasmid DNA, may be archaea-specific. This review summarizes what we know about HGT in archaea, and the barriers that restrict it, highlighting exciting recent discoveries and pointing out opportunities for future research.},
}
@article {pmid35665142,
year = {2022},
author = {Selim, S and Akhtar, N and Hagagy, N and Alanazi, A and Warrad, M and El Azab, E and Elamir, MYM and Al-Sanea, MM and Jaouni, SKA and Abdel-Mawgoud, M and Shah, AA and Abdelgawad, H},
title = {Selection of Newly Identified Growth-Promoting Archaea Haloferax Species With a Potential Action on Cobalt Resistance in Maize Plants.},
journal = {Frontiers in plant science},
volume = {13},
number = {},
pages = {872654},
pmid = {35665142},
issn = {1664-462X},
abstract = {Soil contamination with cobalt (Co) negatively impacts plant growth and production. To combat Co toxicity, plant growth-promoting microorganisms for improving plant growth are effectively applied. To this end, unclassified haloarchaeal species strain NRS_31 (OL912833), belonging to Haloferax genus, was isolated, identified for the first time, and applied to mitigate the Co phytotoxic effects on maize plants. This study found that high Co levels in soil lead to Co accumulation in maize leaves. Co accumulation in the leaves inhibited maize growth and photosynthetic efficiency, inducing oxidative damage in the tissue. Interestingly, pre-inoculation with haloarchaeal species significantly reduced Co uptake and mitigated the Co toxicity. Induced photosynthesis improved sugar metabolism, allocating more carbon to defend against Co stress. Concomitantly, the biosynthetic key enzymes involved in sucrose (sucrose-P-synthase and invertases) and proline (pyrroline-5- carboxylate synthetase (P5CS), pyrroline-5-carboxylate reductase (P5CR)) biosynthesis significantly increased to maintain plant osmotic potential. In addition to their osmoregulation potential, soluble sugars and proline can contribute to maintaining ROS hemostasis. Maize leaves managed their oxidative homeostasis by increasing the production of antioxidant metabolites (such as phenolics and tocopherols) and increasing the activity of ROS-scavenging enzymes (such as POX, CAT, SOD, and enzymes involved in the AsA/GSH cycle). Inside the plant tissue, to overcome heavy Co toxicity, maize plants increased the synthesis of heavy metal-binding ligands (metallothionein, phytochelatins) and the metal detoxifying enzymes (glutathione S transferase). Overall, the improved ROS homeostasis, osmoregulation, and Co detoxification systems were the basis underlying Co oxidative stress, mitigating haloarchaeal treatment's impact.},
}
@article {pmid35660788,
year = {2022},
author = {Lim, JK and Yang, JI and Kim, YJ and Park, YJ and Kim, YH},
title = {Bioconversion of CO to formate by artificially designed carbon monoxide:formate oxidoreductase in hyperthermophilic archaea.},
journal = {Communications biology},
volume = {5},
number = {1},
pages = {539},
pmid = {35660788},
issn = {2399-3642},
mesh = {*Carbon Monoxide/metabolism ; Formate Dehydrogenases/genetics/metabolism ; Formates/metabolism ; Hydrogen/metabolism ; *Thermococcus/genetics/metabolism ; },
abstract = {Ferredoxin-dependent metabolic engineering of electron transfer circuits has been developed to enhance redox efficiency in the field of synthetic biology, e.g., for hydrogen production and for reduction of flavoproteins or NAD(P)[+]. Here, we present the bioconversion of carbon monoxide (CO) gas to formate via a synthetic CO:formate oxidoreductase (CFOR), designed as an enzyme complex for direct electron transfer between non-interacting CO dehydrogenase and formate dehydrogenase using an electron-transferring Fe-S fusion protein. The CFOR-introduced Thermococcus onnurineus mutant strains showed CO-dependent formate production in vivo and in vitro. The maximum formate production rate from purified CFOR complex and specific formate productivity from the bioreactor were 2.2 ± 0.2 μmol/mg/min and 73.1 ± 29.0 mmol/g-cells/h, respectively. The CO-dependent CO2 reduction/formate production activity of synthetic CFOR was confirmed, indicating that direct electron transfer between two unrelated dehydrogenases was feasible via mediation of the FeS-FeS fusion protein.},
}
@article {pmid35651488,
year = {2022},
author = {Zhong, L and Qing, J and Liu, M and Cai, X and Li, G and Li, FY and Chen, G and Xu, X and Xue, K and Wang, Y},
title = {Fungi and Archaea Control Soil N2O Production Potential in Chinese Grasslands Rather Than Bacteria.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {844663},
pmid = {35651488},
issn = {1664-302X},
abstract = {Nitrous oxide (N2O) is a powerful greenhouse gas and the predominant stratospheric ozone-depleting substance. Soil is a major source of N2O but remains largely uncertain due to the complicated processes of nitrification and denitrification performed by various groups of microbes such as bacteria, fungi, and archaea. We used incubation experiments to measure the total fungal, archaeal, and bacterial N2O production potential and the microbial functional genes in soils along 3,000 km Chinese grassland transect, including meadow steppe, typical steppe, desert steppe, alpine meadow, and alpine steppe. The results indicated that fungi, archaea, and bacteria contributed 25, 34, and 19% to nitrification and 46, 29, and 15% to denitrification, respectively. The AOA and AOB genes were notably correlated with the total nitrification enzyme activity (TNEA), whereas both narG and nirK genes were significantly correlated with total denitrification enzyme activity (TDEA) at p < 0.01. The correlations between AOA and ANEA (archaeal nitrification enzyme activity), AOB and BNEA (bacterial nitrification enzyme activity), and narG, nirK, and BDEA (bacterial denitrification enzyme activity) showed higher coefficients than those between the functional genes and TNEA/TDEA. The structural equation modeling (SEM) results showed that fungi are dominant in N2O production processes, followed by archaea in the northern Chinese grasslands. Our findings indicate that the microbial functional genes are powerful predictors of the N2O production potential, after distinguishing bacterial, fungal, and archaeal processes. The key variables of N2O production and the nitrogen (N) cycle depend on the dominant microbial functional groups in the N-cycle in soils.},
}
@article {pmid38817676,
year = {2022},
author = {Liu, Y and Li, M},
title = {The unstable evolutionary position of Korarchaeota and its relationship with other TACK and Asgard archaea.},
journal = {mLife},
volume = {1},
number = {2},
pages = {218-222},
pmid = {38817676},
issn = {2770-100X},
abstract = {The applications of marker gene concatenation have been advanced to resolve the key questions in the Tree of Life. However, the interphylum evolutionary relationship between Korarchaeota of TACK (Thaumarchaeota, Aigarchaeota, Crenarchaeota, Korarchaeota) and Asgard archaea remains uncertain. We applied a marker gene ranking procedure to examine their evolutionary history. Our updated trees showed confident placements of (1) Korarchaeota as the basal branch to other TACK archaea and as a sister group to Asgard archaea; (2) Njordarchaeota at basal branch to Korarchaeota instead of within Asgard archaea. They highlight the importance of evaluating marker genes for phylogeny inference of the Archaea domain.},
}
@article {pmid35639688,
year = {2022},
author = {Thevasundaram, K and Gallagher, JJ and Cherng, F and Chang, MCY},
title = {Engineering nonphotosynthetic carbon fixation for production of bioplastics by methanogenic archaea.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {119},
number = {23},
pages = {e2118638119},
pmid = {35639688},
issn = {1091-6490},
support = {T32 GM066698/GM/NIGMS NIH HHS/United States ; },
mesh = {*Archaea/metabolism ; Carbon Cycle ; Carbon Dioxide/metabolism ; Chemoautotrophic Growth ; *Euryarchaeota/metabolism ; },
abstract = {The conversion of CO2 to value-added products allows both capture and recycling of greenhouse gas emissions. While plants and other photosynthetic organisms play a key role in closing the global carbon cycle, their dependence on light to drive carbon fixation can be limiting for industrial chemical synthesis. Methanogenic archaea provide an alternative platform as an autotrophic microbial species capable of non-photosynthetic CO2 fixation, providing a potential route to engineered microbial fermentation to synthesize chemicals from CO2 without the need for light irradiation. One major challenge in this goal is to connect upstream carbon-fixation pathways with downstream biosynthetic pathways, given the distinct differences in metabolism between archaea and typical heterotrophs. We engineered the model methanogen, Methanococcus maripaludis, to divert acetyl-coenzyme A toward biosynthesis of value-added chemicals, including the bioplastic polyhydroxybutyrate (PHB). A number of studies implicated limitations in the redox pool, with NAD(P)(H) pools in M. maripaludis measured to be <15% of that of Escherichia coli, likely since methanogenic archaea utilize F420 and ferredoxins instead. Multiple engineering strategies were used to precisely target and increase the cofactor pool, including heterologous expression of a synthetic nicotinamide salvage pathway as well as an NAD+-dependent formate dehydrogenase from Candida boidinii. Engineered strains of M. maripaludis with improved NADH pools produced up to 171 ± 4 mg/L PHB and 24.0 ± 1.9% of dry cell weight. The metabolic engineering strategies presented in this study broaden the utility of M. maripaludis for sustainable chemical synthesis using CO2 and may be transferable to related archaeal species.},
}
@article {pmid35633707,
year = {2022},
author = {Zheng, J and Tao, L and Dini-Andreote, F and Luan, L and Kong, P and Xue, J and Zhu, G and Xu, Q and Jiang, Y},
title = {Dynamic Responses of Ammonia-Oxidizing Archaea and Bacteria Populations to Organic Material Amendments Affect Soil Nitrification and Nitrogen Use Efficiency.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {911799},
pmid = {35633707},
issn = {1664-302X},
abstract = {Organic material amendments have been proposed as an effective strategy to promote soil health by enhancing soil fertility and promoting nitrogen (N) cycling and N use efficiency (NUE). Thus, it is important to investigate the extent to which the structure and function of ammonia-oxidizing archaea (AOA) and bacteria (AOB) differentially respond to the organic material amendments in field settings. Here, we conducted a 9-year field experiment to track the responses of AOA and AOB populations to the organic material amendments and measured the potential nitrification activity (PNA), plant productivity, and NUE in the plant rhizosphere interface. Our results revealed that the organic material amendments significantly enhanced the abundance and diversity of AOA and AOB populations. Further, significant differences were observed in the composition and co-occurrence network of AOA and AOB. A higher occurrence of potential competitive interactions between taxa and enumerated potential keystone taxa was observed in the AOA-AOB network. Moreover, we found that AOA was more important than AOB for PNA under the organic material amendments. Structural equation modeling suggested that the diversity of AOA and AOB populations induced by the potential competitive interactions with keystone taxa dynamically accelerated the rate of PNA, and positively affected plant productivity and NUE under the organic material amendments. Collectively, our study offers new insights into the ecology and functioning of ammonia oxidizers and highlights the positive effects of organic material amendments on nitrogen cycling dynamics.},
}
@article {pmid35630397,
year = {2022},
author = {Liu, H and Zhou, P and Cheung, S and Lu, Y and Liu, H and Jing, H},
title = {Distribution and Oxidation Rates of Ammonia-Oxidizing Archaea Influenced by the Coastal Upwelling off Eastern Hainan Island.},
journal = {Microorganisms},
volume = {10},
number = {5},
pages = {},
pmid = {35630397},
issn = {2076-2607},
support = {41776147//the National Natural Science Foundation of China/ ; 91751116//the Training Program of the Major Research Plan of the National Natural Science Foundation of China/ ; 2016YFC0304905//the National Key Research and Development Program of China/ ; 420RC677//the Hainan Provincial Natural Science Foundation of China for High-level Talents/ ; },
abstract = {Coastal upwelling causes variations in temperature, salinity and inorganic nutrients in the water column, consequently leading to the shift of microbial populations and their metabolic activities. Impacts of the eastern Hainan upwelling (EHU) on the ammonia-oxidizing archaea (AOA) were investigated based on the amoA gene using pyrosequencing and quantitative PCR at both DNA and cDNA levels, together with the determination of the ammonia oxidation (AO) rate measured with [15]N-labelled ammonium. By comparing stations with and without upwelling influence, we found that coastal upwelling correlated with an increase in amoA gene abundance, the dominance of distinct clades for AOA communities at the respective gene and transcript levels, and a large increase in the proportion of the SCM1-like (Nitrosopumilus maritimus-like) cluster as well. The AO rates were generally higher in the deeper water (~25 m), which was in significant positive correlation with the proportion of cluster Water Column A (WCA) at the transcript level, indicating the potential contribution of this cluster to in situ ammonia oxidization. Our study demonstrated that coastal upwelling had a significant impact on the AOA community and ammonia oxidization rate; therefore, this physical forcing should be considered in the future assessment of the global nitrogen budgets and biogeochemical nitrogen cycles.},
}
@article {pmid35625610,
year = {2022},
author = {Pastor, MM and Sakrikar, S and Rodriguez, DN and Schmid, AK},
title = {Comparative Analysis of rRNA Removal Methods for RNA-Seq Differential Expression in Halophilic Archaea.},
journal = {Biomolecules},
volume = {12},
number = {5},
pages = {},
pmid = {35625610},
issn = {2218-273X},
support = {T32 GM136627/GM/NIGMS NIH HHS/United States ; },
mesh = {*Archaea/genetics/metabolism ; RNA, Messenger/genetics ; *RNA, Ribosomal/genetics/metabolism ; RNA-Seq ; Sequence Analysis, RNA/methods ; },
abstract = {Despite intense recent research interest in archaea, the scientific community has experienced a bottleneck in the study of genome-scale gene expression experiments by RNA-seq due to the lack of commercial and specifically designed rRNA depletion kits. The high rRNA:mRNA ratio (80-90%: ~10%) in prokaryotes hampers global transcriptomic analysis. Insufficient ribodepletion results in low sequence coverage of mRNA, and therefore, requires a substantially higher number of replicate samples and/or sequencing reads to achieve statistically reliable conclusions regarding the significance of differential gene expression between case and control samples. Here, we show that after the discontinuation of the previous version of RiboZero (Illumina, San Diego, CA, USA) that was useful in partially or completely depleting rRNA from archaea, archaeal transcriptomics studies have experienced a slowdown. To overcome this limitation, here, we analyze the efficiency for four different hybridization-based kits from three different commercial suppliers, each with two sets of sequence-specific probes to remove rRNA from four different species of halophilic archaea. We conclude that the key for transcriptomic success with the currently available tools is the probe-specificity for the rRNA sequence hybridization. With this paper, we provide insights into the archaeal community for selecting certain reagents and strategies over others depending on the archaeal species of interest. These methods yield improved RNA-seq sensitivity and enhanced detection of low abundance transcripts.},
}
@article {pmid35623507,
year = {2022},
author = {Fonseca de Souza, L and Alvarez, DO and Domeignoz-Horta, LA and Gomes, FV and de Souza Almeida, C and Merloti, LF and Mendes, LW and Andreote, FD and Bohannan, BJM and Mazza Rodrigues, JL and Nüsslein, K and Tsai, SM},
title = {Maintaining grass coverage increases methane uptake in Amazonian pastures, with a reduction of methanogenic archaea in the rhizosphere.},
journal = {The Science of the total environment},
volume = {838},
number = {Pt 2},
pages = {156225},
doi = {10.1016/j.scitotenv.2022.156225},
pmid = {35623507},
issn = {1879-1026},
mesh = {Animals ; *Archaea ; Cattle ; *Methane ; Poaceae/genetics ; RNA, Ribosomal, 16S/genetics ; Rhizosphere ; Soil/chemistry ; Soil Microbiology ; },
abstract = {Cattle ranching is the largest driver of deforestation in the Brazilian Amazon. The rainforest-to-pasture conversion affects the methane cycle in upland soils, changing it from sink to source of atmospheric methane. However, it remains unknown if management practices could reduce the impact of land-use on methane cycling. In this work, we evaluated how pasture management can regulate the soil methane cycle either by maintaining continuous grass coverage on pasture soils, or by liming the soil to amend acidity. Methane fluxes from forest and pasture soils were evaluated in moisture-controlled greenhouse experiments with and without grass cover (Urochloa brizantha cv. Marandu) or liming. We also assessed changes in the soil microbial community structure of both bare (bulk) and rhizospheric pasture soils through high throughput sequencing of the 16S rRNA gene, and quantified the methane cycling microbiota by their respective marker genes related to methane generation (mcrA) or oxidation (pmoA). The experiments used soils from eastern and western Amazonia, and concurrent field studies allowed us to confirm greenhouse data. The presence of a grass cover not only increased methane uptake by up to 35% in pasture soils, but also reduced the abundance of the methane-producing community. In the grass rhizosphere this reduction was up to 10-fold. Methane-producing archaea belonged to the genera Methanosarcina sp., Methanocella sp., Methanobacterium sp., and Rice Cluster I. Further, we showed that soil liming to increasing pH compromised the capacity of forest and pasture soils to be a sink for methane, and instead converted formerly methane-consuming forest soils to become methane sources in only 40-80 days. Liming reduced the relative abundance of Beijerinckiacea family in forest soils, which account for many known methanotrophs. Our results demonstrate that pasture management that maintains grass coverage can mitigate soil methane emissions, compared to bare (bulk) pasture soil.},
}
@article {pmid35618771,
year = {2022},
author = {Badel, C and Samson, RY and Bell, SD},
title = {Chromosome organization affects genome evolution in Sulfolobus archaea.},
journal = {Nature microbiology},
volume = {7},
number = {6},
pages = {820-830},
pmid = {35618771},
issn = {2058-5276},
support = {R01 GM135178/GM/NIGMS NIH HHS/United States ; },
mesh = {Archaea/genetics ; Chromosomes ; Evolution, Molecular ; Replication Origin ; *Sulfolobus/genetics ; },
abstract = {In all organisms, the DNA sequence and the structural organization of chromosomes affect gene expression. The extremely thermophilic crenarchaeon Sulfolobus has one circular chromosome with three origins of replication. We previously revealed that this chromosome has defined A and B compartments that have high and low gene expression, respectively. As well as higher levels of gene expression, the A compartment contains the origins of replication. To evaluate the impact of three-dimensional organization on genome evolution, we characterized the effect of replication origins and compartmentalization on primary sequence evolution in eleven Sulfolobus species. Using single-nucleotide polymorphism analyses, we found that distance from an origin of replication was associated with increased mutation rates in the B but not in the A compartment. The enhanced polymorphisms distal to replication origins suggest that replication termination may have a causal role in their generation. Further mutational analyses revealed that the sequences in the A compartment are less likely to be mutated, and that there is stronger purifying selection than in the B compartment. Finally, we applied the Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) to show that the B compartment is less accessible than the A compartment. Taken together, our data suggest that compartmentalization of chromosomal DNA can influence chromosome evolution in Sulfolobus. We propose that the A compartment serves as a haven for stable maintenance of gene sequences, while sequences in the B compartment can be diversified.},
}
@article {pmid35616996,
year = {2022},
author = {Bao, CX and Li, SY and Xin, YJ and Hou, J and Cui, HL},
title = {Natrinema halophilum sp. nov., Natrinema salinisoli sp. nov., Natrinema amylolyticum sp. nov. and Haloterrigena alkaliphila sp. nov., four extremely halophilic archaea isolated from salt mine, saline soil and salt lake.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {72},
number = {5},
pages = {},
doi = {10.1099/ijsem.0.005385},
pmid = {35616996},
issn = {1466-5034},
mesh = {Bacterial Typing Techniques ; Base Composition ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; Fatty Acids/chemistry ; Glycolipids/chemistry ; *Halobacteriaceae ; *Lakes ; Phosphatidic Acids ; Phosphatidylglycerols ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Soil ; },
abstract = {Four halophilic archaeal strains, YPL8[T], SLN56[T], LT61[T] and KZCA68[T], were isolated from a salt mine, saline soil and a salt lake located in different regions of China. Sequence similarities of 16S rRNA and rpoB' genes among strains YPL8[T], SLN56[T], LT61[T] and the current members of Natrinema were 94.1-98.2 % and 89.3-95.1 %, respectively, while these values among strain KZCA68[T] and the current members of Haloterrigena were 97.2-97.4 % and 91.7-91.9 %, respectively. The average nucleotide identity, in silico DNA-DNA hybridization and average amino acid identity values among these four strains and their closely related species were all lower than the threshold values for species boundary. All four strains were unable to hydrolyse casein, gelatin, or Tween 80. Strain YPL8[T] contained phosphatidic acid (PA), phosphatidylglycerol (PG), phosphatidylglycerol phosphate methyl ester (PGP-Me), sulfated mannosyl glucosyl diether (S-DGD-1), disulfated mannosyl glucosyl diether (S2-DGD) and sulfated mannosyl glucosyl diether-phosphatidic acid (S-DGD-PA). Strain SLN56[T] contained PA, PG, phosphatidylglycerol sulphate (PGS), PGP-Me, S-DGD-1, S2-DGD and S-DGD-PA. Strain LT61[T] contained PA, PG, PGS, PGP-Me, S-DGD-1 and S2-DGD. The phospholipids of strain KZCA68[T] were PA, PG and PGP-Me. These results showed that strains YPL8[T] (=CGMCC 1.13883[T]=JCM 31181[T]), SLN56[T] (=CGMCC 1.14945[T]=JCM 30832[T]) and LT61[T] (=CGMCC 1.14942[T]=JCM 30668[T]) represent novel species of the genus Natrinema, for which the names, Natrinema halophilum sp. nov., Natrinema salinisoli sp. nov. and Natrinema amylolyticum sp. nov. are proposed. Strain KZCA68[T] (=CGMCC 1.17211[T]=JCM 34158[T]) represents a novel species of Haloterrigena, for which the name Haloterrigena alkaliphila sp. nov. is proposed.},
}
@article {pmid35615789,
year = {2022},
author = {Dyksma, S and Gallert, C},
title = {Effect of magnetite addition on transcriptional profiles of syntrophic Bacteria and Archaea during anaerobic digestion of propionate in wastewater sludge.},
journal = {Environmental microbiology reports},
volume = {14},
number = {4},
pages = {664-678},
doi = {10.1111/1758-2229.13080},
pmid = {35615789},
issn = {1758-2229},
mesh = {Anaerobiosis ; *Archaea/genetics ; Bacteria/genetics ; *Euryarchaeota/genetics ; Ferrosoferric Oxide/pharmacology ; Formates/pharmacology ; Methane ; Propionates ; Sewage ; Wastewater ; },
abstract = {Anaerobic digestion (AD) is an important technology for the effective conversion of waste and wastewater to methane. Here, syntrophic bacteria transfer molecular hydrogen (H2), formate, or directly supply electrons (direct interspecies electron transfer, DIET) to the methanogens. Evidence is accumulating that the methanation of short-chain fatty acids can be enhanced by the addition of conductive material to the anaerobic digester, which has often been attributed to the stimulation of DIET. Since little is known about the transcriptional response of a complex AD microbial community to the addition of conductive material, we added magnetite to propionate-fed laboratory-scale reactors that were inoculated with wastewater sludge. Compared to the control reactors, the magnetite-amended reactors showed improved methanation of propionate. A genome-centric metatranscriptomics approach identified the active SCFA-oxidizing bacteria that affiliated with Firmicutes, Desulfobacterota and Cloacimonadota. The transcriptional profiles revealed that the syntrophic bacteria transferred acetate, H2 and formate to acetoclastic and hydrogenotrophic methanogens, whereas transcription of potential determinants for DIET such as conductive pili and outer-membrane cytochromes did not significantly change with magnetite addition. Overall, changes in the transcriptional profiles of syntrophic Bacteria and Archaea in propionate-fed lab-scale reactors amended with magnetite refute a major role of DIET in the studied system.},
}
@article {pmid35610383,
year = {2023},
author = {Pierangeli, GMF and Domingues, MR and Choueri, RB and Hanisch, WS and Gregoracci, GB and Benassi, RF},
title = {Spatial Variation and Environmental Parameters Affecting the Abundant and Rare Communities of Bacteria and Archaea in the Sediments of Tropical Urban Reservoirs.},
journal = {Microbial ecology},
volume = {86},
number = {1},
pages = {297-310},
pmid = {35610383},
issn = {1432-184X},
mesh = {*Archaea/genetics ; *Geologic Sediments/microbiology ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; Water Quality ; },
abstract = {Microbial communities in freshwater sediments play an important role in organic matter remineralization, contributing to biogeochemical cycles, nutrient release, and greenhouse gases emissions. Bacterial and archaeal communities might show spatial or seasonal patterns and were shown to be influenced by distinct environmental parameters and anthropogenic activities, including pollution and damming. Here, we determined the spatial variation and the environmental variables influencing the abundant and rare bacterial and archaeal communities in the sediments of eutrophic-hypereutrophic reservoirs from a tropical urban area in Brazil. The most abundant microbes included mainly Anaerolineae and Deltaproteobacteria genera from the Bacteria domain, and Methanomicrobia genera from the Archaea domain. Microbial communities differed spatially in each reservoir, reflecting the establishment of specific environmental conditions. Locations with better or worst water quality, or close to a dam, showed more distinct microbial communities. Besides the water column depth, microbial communities were affected by some pollution indicators, including total phosphorus, orthophosphate, electrical conductivity, and biochemical oxygen demand. Distinct proportions of variation were explained by spatial and environmental parameters for each microbial community. Furthermore, spatial variations in environmental parameters affecting these communities, especially the most distinct ones, contributed to microbial variations mediated by spatial and environmental properties together. Finally, our study showed that different pressures in each reservoir affected the sediment microbiota, promoting different responses and possible adaptations of abundant and rare bacterial and archaeal communities.},
}
@article {pmid35607968,
year = {2022},
author = {Semler, AC and Fortney, JL and Fulweiler, RW and Dekas, AE},
title = {Cold Seeps on the Passive Northern U.S. Atlantic Margin Host Globally Representative Members of the Seep Microbiome with Locally Dominant Strains of Archaea.},
journal = {Applied and environmental microbiology},
volume = {88},
number = {11},
pages = {e0046822},
pmid = {35607968},
issn = {1098-5336},
mesh = {*Archaea/metabolism ; Geologic Sediments/microbiology ; Methane/metabolism ; Methanosarcinales/genetics ; *Microbiota ; Oxidation-Reduction ; Phylogeny ; RNA, Ribosomal, 16S/genetics/metabolism ; Seawater/microbiology ; },
abstract = {Marine cold seeps are natural sites of methane emission and harbor distinct microbial communities capable of oxidizing methane. The majority of known cold seeps are on tectonically active continental margins, but recent discoveries have revealed abundant seeps on passive margins as well, including on the U.S. Atlantic Margin (USAM). We sampled in and around four USAM seeps and combined pore water geochemistry measurements with amplicon sequencing of 16S rRNA and mcrA (DNA and RNA) to investigate the microbial communities present, their assembly processes, and how they compare to communities at previously studied sites. We found that the USAM seeps contained communities consistent with the canonical seep microbiome at the class and order levels but differed markedly at the sequence variant level, especially within the anaerobic methanotrophic (ANME) archaea. The ANME populations were highly uneven, with just a few dominant mcrA sequence variants at each seep. Interestingly, the USAM seeps did not form a distinct phylogenetic cluster when compared with other previously described seeps around the world. Consistent with this, we found only a very weak (though statistically significant) distance-decay trend in seep community similarity across a global data set. Ecological assembly indices suggest that the USAM seep communities were assembled primarily deterministically, in contrast to the surrounding nonseep sediments, where stochastic processes dominated. Together, our results suggest that the primary driver of seep microbial community composition is local geochemistry-specifically methane, sulfide, nitrate, acetate, and ammonium concentrations-rather than the geologic context, the composition of nearby seeps, or random events of dispersal. IMPORTANCE Cold seeps are now known to be widespread features of passive continental margins, including the northern U.S. Atlantic Margin (USAM). Methane seepage is expected to intensify at these relatively shallow seeps as bottom waters warm and underlying methane hydrates dissociate. While methanotrophic microbial communities might reduce or prevent methane release, microbial communities on passive margins have rarely been characterized. In this study, we investigated the Bacteria and Archaea at four cold seeps on the northern USAM and found that despite being colocated on the same continental slope, the communities significantly differ by site at the sequence variant level, particularly methane-cycling community members. Differentiation by site was not observed in similarly spaced background sediments, raising interesting questions about the dispersal pathways of cold seep microorganisms. Understanding the genetic makeup of these discrete seafloor ecosystems and how their microbial communities develop will be increasingly important as the climate changes.},
}
@article {pmid35605022,
year = {2022},
author = {Martinez-Gutierrez, CA and Aylward, FO},
title = {Genome size distributions in bacteria and archaea are strongly linked to evolutionary history at broad phylogenetic scales.},
journal = {PLoS genetics},
volume = {18},
number = {5},
pages = {e1010220},
pmid = {35605022},
issn = {1553-7404},
mesh = {*Archaea/genetics ; Bacteria/genetics ; *Evolution, Molecular ; Genome Size ; Phylogeny ; },
abstract = {The evolutionary forces that determine genome size in bacteria and archaea have been the subject of intense debate over the last few decades. Although the preferential loss of genes observed in prokaryotes is explained through the deletional bias, factors promoting and preventing the fixation of such gene losses often remain unclear. Importantly, statistical analyses on this topic typically do not consider the potential bias introduced by the shared ancestry of many lineages, which is critical when using species as data points because of the potential dependence on residuals. In this study, we investigated the genome size distributions across a broad diversity of bacteria and archaea to evaluate if this trait is phylogenetically conserved at broad phylogenetic scales. After model fit, Pagel's lambda indicated a strong phylogenetic signal in genome size data, suggesting that the diversification of this trait is influenced by shared evolutionary histories. We used a phylogenetic generalized least-squares analysis (PGLS) to test whether phylogeny influences the predictability of genome size from dN/dS ratios and 16S copy number, two variables that have been previously linked to genome size. These results confirm that failure to account for evolutionary history can lead to biased interpretations of genome size predictors. Overall, our results indicate that although bacteria and archaea can rapidly gain and lose genetic material through gene transfers and deletions, respectively, phylogenetic signal for genome size distributions can still be recovered at broad phylogenetic scales that should be taken into account when inferring the drivers of genome size evolution.},
}
@article {pmid35604119,
year = {2022},
author = {Popp, PF and Gumerov, VM and Andrianova, EP and Bewersdorf, L and Mascher, T and Zhulin, IB and Wolf, D},
title = {Phyletic Distribution and Diversification of the Phage Shock Protein Stress Response System in Bacteria and Archaea.},
journal = {mSystems},
volume = {7},
number = {3},
pages = {e0134821},
pmid = {35604119},
issn = {2379-5077},
support = {R35 GM131760/GM/NIGMS NIH HHS/United States ; },
mesh = {*Bacterial Proteins/genetics ; Archaea/genetics ; Heat-Shock Proteins/genetics ; Escherichia coli/genetics ; *Bacteriophages/metabolism ; },
abstract = {Maintaining cell envelope integrity is of vital importance for all microorganisms. Not surprisingly, evolution has shaped conserved protein protection networks that connect stress perception, transmembrane signal transduction, and mediation of cellular responses upon cell envelope stress. The phage shock protein (Psp) stress response is one such conserved protection network. Most knowledge about the Psp response derives from studies in the Gram-negative model bacterium Escherichia coli, where the Psp system consists of several well-defined protein components. Homologous systems were identified in representatives of the Proteobacteria, Actinobacteria, and Firmicutes. However, the Psp system distribution in the microbial world remains largely unknown. By carrying out a large-scale, unbiased comparative genomics analysis, we found components of the Psp system in many bacterial and archaeal phyla and describe that the predicted Psp systems deviate dramatically from the known prototypes. The core proteins PspA and PspC have been integrated into various (often phylum-specifically) conserved protein networks during evolution. Based on protein domain-based and gene neighborhood analyses of pspA and pspC homologs, we built a natural classification system for Psp networks in bacteria and archaea. We validate our approach by performing a comprehensive in vivo protein interaction study of Psp domains identified in the Gram-positive model organism Bacillus subtilis and found a strong interconnected protein network. Our study highlights the diversity of Psp domain organizations and potentially diverse functions across the plethora of the microbial landscape, thus laying the ground for studies beyond known Psp functions in underrepresented organisms. IMPORTANCE The PspA protein domain is found in all domains of life, highlighting its central role in Psp networks. To date, all insights into the core functions of Psp responses derive mainly from protein network blueprints representing only three bacterial phyla. Despite large overlaps in function and regulation, the evolutionary diversity of Psp networks remains largely elusive. Here, we present an unbiased protein domain- and genomic context-centered approach that describes and classifies Psp systems. Our results suggest so-far-unknown Psp-associated roles with other protein networks giving rise to new functions. We demonstrate the applicability of our approach by dissecting the Psp protein network present in Bacillus subtilis and demonstrate Psp domains working in concert with other cell envelope stress response systems. We find that the Psp-like protein universe reflects a surprising diversity within the bacterial and archaeal microbial world.},
}
@article {pmid35602962,
year = {2022},
author = {Wu, J and Hong, Y and He, X and Liu, X and Ye, J and Jiao, L and Li, Y and Wang, Y and Ye, F and Yang, Y and Du, J},
title = {Niche differentiation of ammonia-oxidizing archaea and related autotrophic carbon fixation potential in the water column of the South China Sea.},
journal = {iScience},
volume = {25},
number = {5},
pages = {104333},
pmid = {35602962},
issn = {2589-0042},
abstract = {The significant primary production by ammonia-oxidizing archaea (AOA) in the ocean was reported, but the carbon fixation process of AOA and its community composition along the water depth remain unclear. Here, we investigated the abundance, community composition, and potential carbon fixation of AOA in water columns of the South China Sea. Higher abundances of the amoA and accA genes of AOA were found below the euphotic zone. Similarly, higher carbon fixation potential of AOA, evaluated by the ratios of amoA to accA gene, was also observed below euphotic zone and the ratios increased with increasing water depth. The vertical niche differentiation of AOA was further evidenced, with the dominant genus shifting from Nitrosopelagicus in the epipelagic zone to uncultured genus in the meso- and bathypelagic zones. Our findings highlight the higher carbon fixation potential of AOA in deep water and the significance of AOA to the ocean carbon budget.},
}
@article {pmid35544775,
year = {2022},
author = {Tunçkanat, T and Gendron, A and Sadler, Z and Neitz, A and Byquist, S and Lie, TJ and Allen, KD},
title = {Lysine 2,3-Aminomutase and a Newly Discovered Glutamate 2,3-Aminomutase Produce β-Amino Acids Involved in Salt Tolerance in Methanogenic Archaea.},
journal = {Biochemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.biochem.2c00014},
pmid = {35544775},
issn = {1520-4995},
abstract = {Many methanogenic archaea synthesize β-amino acids as osmolytes that allow survival in high salinity environments. Here, we investigated the radical S-adenosylmethionine (SAM) aminomutases involved in the biosynthesis of N[ε]-acetyl-β-lysine and β-glutamate in Methanococcus maripaludis C7. Lysine 2,3-aminomutase (KAM), encoded by MmarC7_0106, was overexpressed and purified from Escherichia coli, followed by biochemical characterization. In the presence of l-lysine, SAM, and dithionite, this archaeal KAM had a kcat = 14.3 s[-1] and a Km = 19.2 mM. The product was shown to be 3(S)-β-lysine, which is like the well-characterized Clostridium KAM as opposed to the E. coli KAM that produces 3(R)-β-lysine. We further describe the function of MmarC7_1783, a putative radical SAM aminomutase with a ∼160 amino acid extension at its N-terminus. Bioinformatic analysis of the possible substrate-binding residues suggested a function as glutamate 2,3-aminomutase, which was confirmed here through heterologous expression in a methanogen followed by detection of β-glutamate in cell extracts. β-Glutamate has been known to serve as an osmolyte in select methanogens for a long time, but its biosynthetic origin remained unknown until now. Thus, this study defines the biosynthetic routes for β-lysine and β-glutamate in M. maripaludis and expands the importance and diversity of radical SAM enzymes in all domains of life.},
}
@article {pmid35508560,
year = {2022},
author = {Fisk, LM and Barton, L and Maccarone, LD and Jenkins, SN and Murphy, DV},
title = {Seasonal dynamics of ammonia-oxidizing bacteria but not archaea influence soil nitrogen cycling in a semi-arid agricultural soil.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {7299},
pmid = {35508560},
issn = {2045-2322},
mesh = {Ammonia/metabolism ; *Archaea/genetics/metabolism ; Bacteria/genetics/metabolism ; *Betaproteobacteria/metabolism ; Nitrification ; Nitrogen/metabolism ; Oxidation-Reduction ; Phylogeny ; Seasons ; Soil/chemistry ; Soil Microbiology ; Water/metabolism ; },
abstract = {Nitrification, a key pathway of nitrogen (N) loss from agricultural soils, is performed by ammonia-oxidizing bacteria (AOB) and archaea (AOA). We examined the seasonal dynamics (2 years) of ammonia oxidizer gene abundances across a gradient of soil carbon (C) and N in a semi-arid soil after 8 years of tillage and crop residue treatments. AOB was more dominant than AOA in the surface soil, as AOA were undetected in 96% of samples. Seasonal variation in AOB abundance was related to substrate availability; AOB gene copy numbers increased at the end of the growing season (during summer fallow) following higher concentrations in dissolved organic matter soil water. This suggests increased co-location between AOB and substrate resources in pores still filled with water as the soils dried. AOB was however not statistically related to soil ammonium concentrations, soil water content, rainfall or temperature. Organic matter inputs enhanced AOB abundance independent of seasonal variation. AOB abundance was greatest in autumn and immediately preceding the start of the growing season, and coincided with elevated soil nitrate concentrations. The growth of the AOB population is likely to contribute to increased risk of N loss through leaching and/or denitrification at the start of the crop growing season following summer fallow.},
}
@article {pmid35500274,
year = {2022},
author = {Lemaire, ON and Wagner, T},
title = {A Structural View of Alkyl-Coenzyme M Reductases, the First Step of Alkane Anaerobic Oxidation Catalyzed by Archaea.},
journal = {Biochemistry},
volume = {61},
number = {10},
pages = {805-821},
pmid = {35500274},
issn = {1520-4995},
mesh = {*Alkanes/metabolism ; Anaerobiosis ; *Archaea/chemistry ; Catalysis ; Mesna/metabolism ; Methane/metabolism ; Oxidation-Reduction ; Oxidoreductases/metabolism ; Phylogeny ; },
abstract = {Microbial anaerobic oxidation of alkanes intrigues the scientific community by way of its impact on the global carbon cycle, and its biotechnological applications. Archaea are proposed to degrade short- and long-chain alkanes to CO2 by reversing methanogenesis, a theoretically reversible process. The pathway would start with alkane activation, an endergonic step catalyzed by methyl-coenzyme M reductase (MCR) homologues that would generate alkyl-thiols carried by coenzyme M. While the methane-generating MCR found in methanogens has been well characterized, the enzymatic activity of the putative alkane-fixing counterparts has not been validated so far. Such an absence of biochemical investigations contrasts with the current explosion of metagenomics data, which draws new potential alkane-oxidizing pathways in various archaeal phyla. Therefore, validating the physiological function of these putative alkane-fixing machines and investigating how their structures, catalytic mechanisms, and cofactors vary depending on the targeted alkane have become urgent needs. The first structural insights into the methane- and ethane-capturing MCRs highlighted unsuspected differences and proposed some explanations for their substrate specificity. This Perspective reviews the current physiological, biochemical, and structural knowledge of alkyl-CoM reductases and offers fresh ideas about the expected mechanistic and chemical differences among members of this broad family. We conclude with the challenges of the investigation of these particular enzymes, which might one day generate biofuels for our modern society.},
}
@article {pmid35489791,
year = {2022},
author = {Glodowska, M and Welte, CU and Kurth, JM},
title = {Metabolic potential of anaerobic methane oxidizing archaea for a broad spectrum of electron acceptors.},
journal = {Advances in microbial physiology},
volume = {80},
number = {},
pages = {157-201},
doi = {10.1016/bs.ampbs.2022.01.003},
pmid = {35489791},
issn = {2162-5468},
mesh = {Anaerobiosis ; *Archaea/metabolism ; Electrons ; Ferric Compounds/metabolism ; Methane/metabolism ; *Microbiota ; Oxidation-Reduction ; },
abstract = {Methane (CH4) is a potent greenhouse gas significantly contributing to the climate warming we are currently facing. Microorganisms play an important role in the global CH4 cycle that is controlled by the balance between anaerobic production via methanogenesis and CH4 removal via methanotrophic oxidation. Research in recent decades advanced our understanding of CH4 oxidation, which until 1976 was believed to be a strictly aerobic process. Anaerobic oxidation of methane (AOM) coupled to sulfate reduction is now known to be an important sink of CH4 in marine ecosystems. Furthermore, in 2006 it was discovered that anaerobic CH4 oxidation can also be coupled to nitrate reduction (N-DAMO), demonstrating that AOM may be much more versatile than previously thought and linked to other electron acceptors. In consequence, an increasing number of studies in recent years showed or suggested that alternative electron acceptors can be used in the AOM process including Fe[III], Mn[IV], As[V], Cr[VI], Se[VI], Sb[V], V[V], and Br[V]. In addition, humic substances as well as biochar and perchlorate (ClO4[-]) were suggested to mediate AOM. Anaerobic methanotrophic archaea, the so-called ANME archaea, are key players in the AOM process, yet we are still lacking deeper understanding of their metabolism, electron acceptor preferences and their interaction with other microbial community members. It is still not clear whether ANME archaea can oxidize CH4 and reduce metallic electron acceptors independently or via electron transfer to syntrophic partners, interspecies electron transfer, nanowires or conductive pili. Therefore, the aim of this review is to summarize and discuss the current state of knowledge about ANME archaea, focusing on their physiology, metabolic flexibility and potential to use various electron acceptors.},
}
@article {pmid35437913,
year = {2022},
author = {Campbell, BC and Greenfield, P and Gong, S and Barnhart, EP and Midgley, DJ and Paulsen, IT and George, SC},
title = {Methanogenic archaea in subsurface coal seams are biogeographically distinct: an analysis of metagenomically-derived mcrA sequences.},
journal = {Environmental microbiology},
volume = {24},
number = {9},
pages = {4065-4078},
pmid = {35437913},
issn = {1462-2920},
mesh = {Animals ; Archaea/metabolism ; Coal/microbiology ; *Euryarchaeota/genetics ; *Greenhouse Gases/metabolism ; Methane/metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics/metabolism ; Soil ; },
abstract = {The production of methane as an end-product of organic matter degradation in the absence of other terminal electron acceptors is common, and has often been studied in environments such as animal guts, soils and wetlands due to its potency as a greenhouse gas. To date, however, the study of the biogeographic distribution of methanogens across coal seam environments has been minimal. Here, we show that coal seams are host to a diverse range of methanogens, which are distinctive to each geological basin. Based on comparisons to close relatives from other methanogenic environments, the dominant methanogenic pathway in these basins is hydrogenotrophic, with acetoclastic being a second major pathway in the Surat Basin. Finally, mcrA and 16S rRNA gene primer biases were predominantly seen to affect the detection of Methanocellales, Methanomicrobiales and Methanosarcinales taxa in this study. Subsurface coal methanogenic community distributions and pathways presented here provide insights into important metabolites and bacterial partners for in situ coal biodegradation.},
}
@article {pmid35422794,
year = {2022},
author = {Kamruzzaman, M and Yan, A and Castro-Escarpulli, G},
title = {Editorial: CRISPR-Cas Systems in Bacteria and Archaea.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {887778},
pmid = {35422794},
issn = {1664-302X},
}
@article {pmid35420474,
year = {2022},
author = {He, W and Gao, H and Wu, D and Jiang, S and Huang, W and Chen, C and Deng, Z and Xiong, L and Wu, G and Wang, L},
title = {Structural and Functional Analysis of DndE Involved in DNA Phosphorothioation in the Haloalkaliphilic Archaea Natronorubrum bangense JCM10635.},
journal = {mBio},
volume = {13},
number = {3},
pages = {e0071622},
pmid = {35420474},
issn = {2150-7511},
mesh = {DNA/metabolism ; DNA, Bacterial/metabolism ; *DNA, Superhelical/metabolism ; Escherichia coli/genetics/metabolism ; *Halobacteriaceae/genetics/metabolism ; Oxygen/metabolism ; Sulfur/metabolism ; },
abstract = {Phosphorothioate (PT) modification, a sequence-specific modification that replaces the nonbridging oxygen atom with sulfur in a DNA phosphodiester through the gene products of dndABCDE or sspABCD, is widely distributed in prokaryotes. DNA PT modification functions together with gene products encoded by dndFGH, pbeABCD, or sspE to form defense systems that can protect against invasion by exogenous DNA particles. While the functions of the multiple enzymes in the PT system have been elucidated, the exact role of DndE in the PT process is still obscure. Here, we solved the crystal structure of DndE from the haloalkaliphilic archaeal strain Natronorubrum bangense JCM10635 at a resolution of 2.31 Å. Unlike the tetrameric conformation of DndE in Escherichia coli B7A, DndE from N. bangense JCM10635 exists in a monomeric conformation and can catalyze the conversion of supercoiled DNA to nicked or linearized products. Moreover, DndE exhibits preferential binding affinity to nicked DNA by virtue of the R19- and K23-containing positively charged surface. This work provides insight into how DndE functions in PT modification and the potential sulfur incorporation mechanism of DNA PT modification. IMPORTANCE DndABCDE proteins have been demonstrated to catalyze DNA PT modification with the nonbridging oxygen in the DNA sugar-phosphate backbone replaced by sulfur. In the PT modification pathway, DndA exerts cysteine desulfurase activity capable of catalyzing the mobilization of sulfur from l-cysteine, which involves the ion-sulfur cluster assembly of DndC. This is regarded as the initial step of the DNA PT modification. Moreover, DndD has ATPase activity in vitro, which is believed to provide energy for the oxygen-sulfur swap, while the function of DndE is unknown. However, the exact function of the key enzyme DndE remains to be elucidated. By determining the structure of DndE from the haloalkaliphilic strain Natronorubrum bangense JCM10635, we showed that the archaeal DndE adopts a monomer conformation. Notably, DndE can introduce nicks to supercoiled DNA and exhibits a binding preference for nicked DNA; the nicking is believed to be the initial step for DNA to facilitate the sulfur incorporation.},
}
@article {pmid35408816,
year = {2022},
author = {Huang, C and Liu, X and Chen, Y and Zhou, J and Li, W and Ding, N and Huang, L and Chen, J and Zhang, Z},
title = {A Novel Family of Winged-Helix Single-Stranded DNA-Binding Proteins from Archaea.},
journal = {International journal of molecular sciences},
volume = {23},
number = {7},
pages = {},
pmid = {35408816},
issn = {1422-0067},
support = {2020YFA0906800//National Key R&amp;D Program of China/ ; 32170050//National Natural Science Foundation of China/ ; 92051109//National Natural Science Foundation of China/ ; },
mesh = {Archaea/metabolism ; DNA/chemistry ; DNA, Single-Stranded ; *DNA-Binding Proteins/metabolism ; *Sulfolobus/genetics ; },
abstract = {The winged helix superfamily comprises a large number of structurally related nucleic acid-binding proteins. While these proteins are often shown to bind dsDNA, few are known to bind ssDNA. Here, we report the identification and characterization of Sul7s, a novel winged-helix single-stranded DNA binding protein family highly conserved in Sulfolobaceae. Sul7s from Sulfolobus islandicus binds ssDNA with an affinity approximately 15-fold higher than that for dsDNA in vitro. It prefers binding oligo(dT)30 over oligo(dC)30 or a dG-rich 30-nt oligonucleotide, and barely binds oligo(dA)30. Further, binding by Sul7s inhibits DNA strand annealing, but shows little effect on the melting temperature of DNA duplexes. The solution structure of Sul7s determined by NMR shows a winged helix-turn-helix fold, consisting of three α-helices, three β-strands, and two short wings. It interacts with ssDNA via a large positively charged binding surface, presumably resulting in ssDNA deformation. Our results shed significant light on not only non-OB fold single-stranded DNA binding proteins in Archaea, but also the divergence of the winged-helix proteins in both function and structure during evolution.},
}
@article {pmid35405221,
year = {2022},
author = {Yang, P and Tang, KW and Tong, C and Lai, DYF and Wu, L and Yang, H and Zhang, L and Tang, C and Hong, Y and Zhao, G},
title = {Changes in sediment methanogenic archaea community structure and methane production potential following conversion of coastal marsh to aquaculture ponds.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {305},
number = {},
pages = {119276},
doi = {10.1016/j.envpol.2022.119276},
pmid = {35405221},
issn = {1873-6424},
mesh = {Aquaculture ; Archaea ; Ecosystem ; Methane ; *Ponds ; *Wetlands ; },
abstract = {Widespread conversion of coastal wetlands into aquaculture ponds in coastal region often results in degradation of the wetland ecosystems, but its effects on sediment's potential to produce greenhouse gases remain unclear. Using field sampling, incubation experiments and molecular analysis, we studied the sediment CH4 production potential and the relevant microbial communities in a brackish marsh and the nearby aquaculture ponds in the Min River Estuary in southeastern China. Sediment CH4 production potential was higher in the summer and autumn months than in spring and winter months, and it was significantly correlated with sediment carbon content among all environmental variables. The mean sediment CH4 production potential in the aquaculture ponds (20.1 ng g[-1] d[-1]) was significantly lower than that in the marsh (45.2 ng g[-1] d[-1]). While Methanobacterium dominated in both habitats (41-59%), the overall composition of sediment methanogenic archaea communities differed significantly between the two habitats (p < 0.05) and methanogenic archaea alpha diversity was lower in the aquaculture ponds (p < 0.01). Network analysis revealed that interactions between sediment methanogenic archaea were much weaker in the ponds than in the marsh. Overall, these findings suggest that conversion of marsh land to aquaculture ponds significantly altered the sediment methanogenic archaea community structure and diversity and lowered the sediment's capacity to produce CH4.},
}
@article {pmid35402889,
year = {2022},
author = {Al-Ajeel, S and Spasov, E and Sauder, LA and McKnight, MM and Neufeld, JD},
title = {Ammonia-oxidizing archaea and complete ammonia-oxidizing Nitrospira in water treatment systems.},
journal = {Water research X},
volume = {15},
number = {},
pages = {100131},
pmid = {35402889},
issn = {2589-9147},
abstract = {Nitrification, the oxidation of ammonia to nitrate via nitrite, is important for many engineered water treatment systems. The sequential steps of this respiratory process are carried out by distinct microbial guilds, including ammonia-oxidizing bacteria (AOB) and archaea (AOA), nitrite-oxidizing bacteria (NOB), and newly discovered members of the genus Nitrospira that conduct complete ammonia oxidation (comammox). Even though all of these nitrifiers have been identified within water treatment systems, their relative contributions to nitrogen cycling are poorly understood. Although AOA contribute to nitrification in many wastewater treatment plants, they are generally outnumbered by AOB. In contrast, AOA and comammox Nitrospira typically dominate relatively low ammonia environments such as drinking water treatment, tertiary wastewater treatment systems, and aquaculture/aquarium filtration. Studies that focus on the abundance of ammonia oxidizers may misconstrue the actual role that distinct nitrifying guilds play in a system. Understanding which ammonia oxidizers are active is useful for further optimization of engineered systems that rely on nitrifiers for ammonia removal. This review highlights known distributions of AOA and comammox Nitrospira in engineered water treatment systems and suggests future research directions that will help assess their contributions to nitrification and identify factors that influence their distributions and activity.},
}
@article {pmid35384236,
year = {2022},
author = {Vuong, P and Moreira-Grez, B and Wise, MJ and Whiteley, AS and Kumaresan, D and Kaur, P},
title = {From rags to enriched: metagenomic insights into ammonia-oxidizing archaea following ammonia enrichment of a denuded oligotrophic soil ecosystem.},
journal = {Environmental microbiology},
volume = {24},
number = {7},
pages = {3097-3110},
pmid = {35384236},
issn = {1462-2920},
mesh = {*Ammonia/metabolism ; *Archaea/metabolism ; Bacteria ; Ecosystem ; Metagenome ; Nitrification ; Nitrogen/metabolism ; Oxidation-Reduction ; Soil ; Soil Microbiology ; },
abstract = {Stored topsoil acts as a microbial inoculant for ecological restoration of land after disturbance, but the altered circumstances frequently create unfavourable conditions for microbial survival. Nitrogen cycling is a critical indicator for ecological success and this study aimed to investigate the cornerstone taxa driving the process. Previous in silico studies investigating stored topsoil discovered persistent archaeal taxa with the potential for re-establishing ecological activity. Ammonia oxidization is the limiting step in nitrification and as such, ammonia-oxidizing archaea (AOA) can be considered one of the gatekeepers for the re-establishment of the nitrogen cycle in disturbed soils. Semi-arid soil samples were enriched with ammonium sulfate to promote the selective enrichment of ammonia oxidizers for targeted genomic recovery, and to investigate the microbial response of the microcosm to nitrogen input. Ammonia addition produced an increase in AOA population, particularly within the genus Candidatus Nitrosotalea, from which metagenome-assembled genomes (MAGs) were successfully recovered. The Ca. Nitrosotalea archaeon candidates' ability to survive in extreme conditions and rapidly respond to ammonia input makes it a potential bioprospecting target for application in ecological restoration of semi-arid soils and the recovered MAGs provide a metabolic blueprint for developing potential strategies towards isolation of these acclimated candidates.},
}
@article {pmid35380107,
year = {2022},
author = {Gupta, D and Shalvarjian, KE and Nayak, DD},
title = {An Archaea-specific c-type cytochrome maturation machinery is crucial for methanogenesis in Methanosarcina acetivorans.},
journal = {eLife},
volume = {11},
number = {},
pages = {},
pmid = {35380107},
issn = {2050-084X},
mesh = {*Archaea/metabolism ; Cytochromes/metabolism ; Electron Transport/genetics ; Methane/metabolism ; *Methanosarcina/genetics ; },
abstract = {c-Type cytochromes (cyt c) are proteins that undergo post-translational modification to covalently bind heme, which allows them to facilitate redox reactions in electron transport chains across all domains of life. Genomic evidence suggests that cyt c are involved in electron transfer processes among the Archaea, especially in members that produce or consume the potent greenhouse gas methane. However, neither the maturation machinery for cyt c in Archaea nor their role in methane metabolism has ever been functionally characterized. Here, we have used CRISPR-Cas9 genome editing tools to map a distinct pathway for cyt c biogenesis in the model methanogenic archaeon Methanosarcina acetivorans, and have also identified substrate-specific functional roles for cyt c during methanogenesis. Although the cyt c maturation machinery from M. acetivorans is universally conserved in the Archaea, our evolutionary analyses indicate that different clades of Archaea acquired this machinery through multiple independent horizontal gene transfer events from different groups of Bacteria. Overall, we demonstrate the convergent evolution of a novel Archaea-specific cyt c maturation machinery and its physiological role during methanogenesis, a process which contributes substantially to global methane emissions.},
}
@article {pmid35369442,
year = {2022},
author = {Thirumalaisamy, G and Malik, PK and Trivedi, S and Kolte, AP and Bhatta, R},
title = {Effect of Long-Term Supplementation With Silkworm Pupae Oil on the Methane Yield, Ruminal Protozoa, and Archaea Community in Sheep.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {780073},
pmid = {35369442},
issn = {1664-302X},
abstract = {Supplementation with lipids and oils is one of the most efficient strategies for reducing enteric methane emission. However, high costs and adverse impacts on fiber degradation restrict the use of conventional oils. Silkworm pupae, a non-conventional oil source rarely used for human consumption in India, could be one of the cheaper alternatives for methane mitigation. The objective of this study was to investigate the effect on sheep of long-term supplementation (180 days) of silkworm pupae oil (SWPO) with two distinct supplementation regimes (daily and biweekly) on daily enteric methane emission, methane yield, nutrient digestibility, rumen fermentation, ruminal archaea community composition, and protozoal population. The effect of the discontinuation of oil supplementation on enteric methane emission was also investigated. Eighteen adult male sheep, randomly divided into three groups (n = 6), were provisioned with a mixed diet consisting of 10.1% crude protein (CP) and 11.7 MJ/kg metabolizable energy formulated using finger millet straw and concentrate in a 55:45 ratio. SWPO was supplemented at 2% of dry matter intake (DMI) in test groups either daily (CON) or biweekly (INT), while no oil was supplemented in the control group (CTR). DMI (p = 0.15) and CP (p = 0.16) in the CON and INT groups were similar to that of the CTR group; however, the energy intake (MJ/kg) in the supplemented groups (CON and INT) was higher (p < 0.001) than in CTR. In the CON group, body weight gain (kg, p = 0.02) and average daily gain (g, p = 0.02) were both higher than in the CTR. The daily methane emission in the CON (17.5 g/day) and INT (18.0 g/day) groups was lower (p = 0.01) than the CTR group (23.6 g/day), indicating a reduction of 23-25% due to SWPO supplementation. Similarly, compared with the CTR group, methane yields (g/kg DMI) in test groups were also significantly lower (p < 0.01). The transient nature of the anti-methanogenic effect of SWPO was demonstrated in the oil discontinuation study, where daily methane emission reverted to pre-supplementation levels after a short period. The recorded methanogens were affiliated to the families Methanobacteriaceae, Methanomassilliicoccaceae, and Methanosarcinaceae. The long-term supplementation of oil did not induce any significant change in the rumen archaeal community, whereas minor species such as Group3b exhibited differing abundance among the groups. Methanobrevibacter, irrespective of treatment, was the largest genus, while Methanobrevibacter gottschalkii was the dominant species. Oil supplementation in CON and INT compared with CTR decreased (p < 0.01) the numbers of total protozoa (× 10[7] cells/ml), Entodiniomorphs (× 10[7] cells/ml), and Holotrichs (× 10[6] cells/ml). SWPO continuous supplementation (CON group) resulted in the largest reduction in enteric methane emission and relatively higher body weight gain (p = 0.02) in sheep.},
}
@article {pmid38818328,
year = {2022},
author = {Wang, Y and Xie, R and Hou, J and Lv, Z and Li, L and Hu, Y and Huang, H and Wang, F},
title = {The late Archaean to early Proterozoic origin and evolution of anaerobic methane-oxidizing archaea.},
journal = {mLife},
volume = {1},
number = {1},
pages = {96-100},
pmid = {38818328},
issn = {2770-100X},
abstract = {Microorganisms, called anaerobic methane-oxidizing archaea (ANME), can reduce a large amount of greenhouse gas methane and therefore have the potential to cool the Earth. We collected nearly all ANMEs genomes in public databases and performed a comprehensive comparative genomic analysis and molecular dating. Our results show that ANMEs originated in the late Archaean to early Proterozoic eon. During this period of time, our planet Earth was experiencing the Great Oxygenation Event and Huronian Glaciation, a dramatic drop in the Earth's surface temperature. This suggests that the emergence of ANMEs may contribute to the reduction of methane at that time, which is an unappreciated potential cause that led to the Huronian Glaciation.},
}
@article {pmid35347497,
year = {2022},
author = {Yuan, B and Wu, W and Yue, S and Zou, P and Yang, R and Zhou, X},
title = {Community structure, distribution pattern, and influencing factors of soil Archaea in the construction area of a large-scale photovoltaic power station.},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {25},
number = {3},
pages = {571-586},
pmid = {35347497},
issn = {1618-1905},
support = {51979222//National Natural Science Foundation of China/ ; },
mesh = {*Archaea/genetics ; Humans ; *Microbiota ; RNA, Ribosomal, 16S ; Soil/chemistry ; Soil Microbiology ; },
abstract = {The photovoltaic power station in Qinghai has been built for 8 years; however, its impact on the regional soil ecological environment has not been studied in depth. To reveal the structure and distribution pattern of archaeal communities in desert soil under the influence of a large photovoltaic power station, a comparative study was carried out between the soil affected by photovoltaic panels and the bare land samples outside the photovoltaic station in Gonghe, Qinghai Province. The abundance, community structure, diversity, and distribution characteristics of archaea were analyzed by quantitative PCR and Illumina-MiSeq high-throughput sequencing, and the main environmental factors affecting the variation in soil archaeal community were identified by RDA. The contribution rate of environmental factors and human factors to microbial community diversity was quantitatively evaluated by VPA. The results showed that there was no significant difference in soil nutrients and other physicochemical factors between the photovoltaic power station and bare land. Thaumarchaeota was the dominant archaeal phylum in the area, accounting for more than 99% of archaeal phylum, while at the level of genus, Nitrososphaera was the dominant archaeal genera. There was no significant difference in archaeal community structure between and under different types of PV panels. The analysis has shown that the construction of a photovoltaic station has little effect on the community structure of soil archaea in a desert area, and it was speculated that the selection of niche played a leading role in the distribution pattern of soil archaeal community. This study provides the basis for a scientific understanding of the characteristics and distribution patterns of soil archaeal communities affected by the construction of a photovoltaic power station.},
}
@article {pmid35340443,
year = {2022},
author = {Schiller, H and Young, C and Schulze, S and Tripepi, M and Pohlschroder, M},
title = {A Twist to the Kirby-Bauer Disk Diffusion Susceptibility Test: an Accessible Laboratory Experiment Comparing Haloferax volcanii and Escherichia coli Antibiotic Susceptibility to Highlight the Unique Cell Biology of Archaea.},
journal = {Journal of microbiology &amp; biology education},
volume = {23},
number = {1},
pages = {},
pmid = {35340443},
issn = {1935-7877},
abstract = {Archaea, once thought to only live in extreme environments, are present in many ecosystems, including the human microbiome, and they play important roles ranging from nutrient cycling to bioremediation. Yet this domain is often overlooked in microbiology classes and rarely included in laboratory exercises. Excluding archaea from high school and undergraduate curricula prevents students from learning the uniqueness and importance of this domain. Here, we have modified a familiar and popular microbiology experiment-the Kirby-Bauer disk diffusion antibiotic susceptibility test-to include, together with the model bacterium Escherichia coli, the model archaeon Haloferax volcanii. Students will learn the differences and similarities between archaea and bacteria by using antibiotics that target, for example, the bacterial peptidoglycan cell wall or the ribosome. Furthermore, the experiment provides a platform to reiterate basic cellular biology concepts that students may have previously discussed. We have developed two versions of this experiment, one designed for an undergraduate laboratory curriculum and the second, limited to H. volcanii, that high school students can perform in their classrooms. This nonpathogenic halophile can be cultured aerobically at ambient temperature in high-salt media, preventing contamination, making the experiment low-cost and safe for use in the high school setting.},
}
@article {pmid35336099,
year = {2022},
author = {Cisek, AA and Bąk, I and Stefańska, I and Binek, M},
title = {Selection and Optimization of High-Yielding DNA Isolation Protocol for Quantitative Analyses of Methanogenic Archaea.},
journal = {Microorganisms},
volume = {10},
number = {3},
pages = {},
pmid = {35336099},
issn = {2076-2607},
support = {2017/25/N/NZ7/02905//National Science Center/ ; },
abstract = {Methanogenic archaea are a functionally important component of the intestinal microbiota of humans and animals, participating in the utilization of detrimental hydrogen produced during gut fermentation. Despite this, archaeal DNA has rarely been found in intestinal microbiome analyses, which prompts the need to optimize detecting procedures of these microorganisms, including the DNA isolation step. Three commercially available kits for DNA isolation and one extra purification kit that removes PCR inhibitors were evaluated on chicken droppings. In addition, different variants of mechanical lysis and a double elution were tested to ensure the maximum efficiency of DNA isolation from archaea as well as bacteria. A quantitative real-time PCR was used to monitor the optimization progress. As a result, the combination of the selected Genomic Mini AX Bacteria+ kit with a 2-min-long sonication by ultrasonic probe and enzymatic pretreatment gave excellent extraction efficiency rates for DNA of methanogenic archaea (an approximate 50-fold increase compared to the standard enzymatic lysis described by the producer) and, at the same time, provided optimal protection of DNA extracted from bacteria susceptible to enzymatic lysis. The presented results indicate that the optimized protocol allows for highly efficient extraction of total DNA, which is well-suited for quantitative microbial analyses by real-time PCR.},
}
@article {pmid35323924,
year = {2022},
author = {Klein, T and Poghosyan, L and Barclay, JE and Murrell, JC and Hutchings, MI and Lehtovirta-Morley, LE},
title = {Cultivation of ammonia-oxidising archaea on solid medium.},
journal = {FEMS microbiology letters},
volume = {369},
number = {1},
pages = {},
pmid = {35323924},
issn = {1574-6968},
support = {BBS/E/J/000PR9790/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Agar ; *Ammonia ; *Archaea/genetics ; Culture Media ; Nitrification ; Oxidation-Reduction ; Phylogeny ; Soil Microbiology ; },
abstract = {Ammonia-oxidising archaea (AOA) are environmentally important microorganisms involved in the biogeochemical cycling of nitrogen. Routine cultivation of AOA is exclusively performed in liquid cultures and reports on their growth on solid medium are scarce. The ability to grow AOA on solid medium would be beneficial for not only the purification of enrichment cultures but also for developing genetic tools. The aim of this study was to develop a reliable method for growing individual colonies from AOA cultures on solid medium. Three phylogenetically distinct AOA strains were tested: 'Candidatus Nitrosocosmicus franklandus C13', Nitrososphaera viennensis EN76 and 'Candidatus Nitrosotalea sinensis Nd2'. Of the gelling agents tested, agar and Bacto-agar severely inhibited growth of all three strains. In contrast, both 'Ca. N. franklandus C13' and N. viennensis EN76 tolerated Phytagel™ while the acidophilic 'Ca. N. sinensis Nd2' was completely inhibited. Based on these observations, we developed a Liquid-Solid (LS) method that involves immobilising cells in Phytagel™ and overlaying with liquid medium. This approach resulted in the development of visible distinct colonies from 'Ca. N. franklandus C13' and N. viennensis EN76 cultures and lays the groundwork for the genetic manipulation of this group of microorganisms.},
}
@article {pmid38818326,
year = {2022},
author = {Da Cunha, V and Gaïa, M and Forterre, P},
title = {The expanding Asgard archaea and their elusive relationships with Eukarya.},
journal = {mLife},
volume = {1},
number = {1},
pages = {3-12},
pmid = {38818326},
issn = {2770-100X},
abstract = {The discovery of Asgard archaea and the exploration of their diversity over the last 6 years have deeply impacted the scientific community working on eukaryogenesis, rejuvenating an intense debate on the topology of the universal tree of life (uTol). Here, we discuss how this debate is impacted by two recent publications that expand the number of Asgard lineages and eukaryotic signature proteins (ESPs). We discuss some of the main difficulties that can impair the phylogenetic reconstructions of the uTol and suggest that the debate about its topology is not settled. We notably hypothesize the existence of horizontal gene transfers between ancestral Asgards and proto-eukaryotes that could result in the observed abnormal behaviors of some Asgard ESPs and universal marker proteins. This hypothesis is relevant regardless of the scenario considered regarding eukaryogenesis. It implies that the Asgards were already diversified before the last eukaryotic common ancestor and shared the same biotopes with proto-eukaryotes. We suggest that some Asgards might be still living in symbiosis today with modern Eukarya.},
}
@article {pmid35276174,
year = {2022},
author = {Wang, JT and Zhang, YB and Xiao, Q and Zhang, LM},
title = {Archaea is more important than bacteria in driving soil stoichiometry in phosphorus deficient habitats.},
journal = {The Science of the total environment},
volume = {827},
number = {},
pages = {154417},
doi = {10.1016/j.scitotenv.2022.154417},
pmid = {35276174},
issn = {1879-1026},
mesh = {*Archaea ; Bacteria ; Forests ; *Microbiota ; Nitrogen/analysis ; Phosphorus/analysis ; Soil/chemistry ; Soil Microbiology ; },
abstract = {Phosphorus deficiency is a critical limit on the cycling of carbon (C), nitrogen (N) and phosphorus (P) in forest ecosystems. Despite the pivotal roles of microbes in driving the biogeochemical cycling of C/N/P, our knowledge on the relationships of soil bacteria and archaea to P deficiency in forest ecosystems remains scarce. Here, we studied 110 acidic soils (average pH 4.5) collected across 700-km subtropical forests with a gradient of available phosphorus (AP) ranging from 0.21 to 17.6 mg/kg. We analyzed the soil C/N/P stoichiometry and studied soil bacterial and archaeal diversity/abundance via high throughput sequencing and qPCR approaches. Our results show that soil P decoupled with N or C when below 3 mg/kg but coupled with C and N when above 3 mg/kg. Archaeal diversity and abundance were significantly higher in low AP (< 3 mg/kg) soils than in high AP (>3 mg/kg) soils, while bacterial were less changed. Compared with bacteria, archaea are more strongly related with soil stoichiometry (C:N, C:P, N:P), especially when AP was less than 3 mg/kg. Taxonomic and functional composition analysis further confirmed that archaeal rather than bacterial taxonomic composition was significantly related with functional composition of microbial communities. Taken together, our results show that archaea are more important than bacteria in driving soil stoichiometry in phosphorus deficient habitats and suggest a niche differentiation of soil bacteria and archaea in regulating the soil C/N/P cycling in subtropical forests.},
}
@article {pmid35270425,
year = {2022},
author = {Xu, A and Li, L and Xie, J and Gopalakrishnan, S and Zhang, R and Luo, Z and Cai, L and Liu, C and Wang, L and Anwar, S and Jiang, Y},
title = {Changes in Ammonia-Oxidizing Archaea and Bacterial Communities and Soil Nitrogen Dynamics in Response to Long-Term Nitrogen Fertilization.},
journal = {International journal of environmental research and public health},
volume = {19},
number = {5},
pages = {},
pmid = {35270425},
issn = {1660-4601},
mesh = {*Ammonia/metabolism ; *Archaea/genetics/metabolism ; Bacteria/genetics/metabolism ; Fertilization ; Fertilizers ; Nitrogen/metabolism ; Oxidation-Reduction ; Phylogeny ; Soil/chemistry ; Soil Microbiology ; },
abstract = {Ammonia oxidizing archaea (AOA) and bacteria (AOB) mediate a crucial step in nitrogen (N) metabolism. The effect of N fertilizer rates on AOA and AOB communities is less studied in the wheat-fallow system from semi-arid areas. Based on a 17-year wheat field experiment, we explored the effect of five N fertilizer rates (0, 52.5, 105, 157.5, and 210 kg ha[-1] yr[-1]) on the AOA and AOB community composition. This study showed that the grain yield of wheat reached the maximum at 105 kg N ha[-1] (49% higher than control), and no further significant increase was observed at higher N rates. With the increase of N, AOA abundance decreased in a regular trend from 4.88 × 10[7] to 1.05 × 10[7] copies g[-1] dry soil, while AOB abundance increased from 3.63 × 10[7] up to a maximum of 8.24 × 10[7] copies g[-1] dry soil with the N105 treatment (105 kg N ha[-1] yr[-1]). Application rates of N fertilizer had a more significant impact on the AOB diversity than on AOA diversity, and the highest AOB diversity was found under the N105 treatment in this weak alkaline soil. The predominant phyla of AOA and AOB were Thaumarchaeota and Proteobacteria, respectively, and higher N treatment (N210) resulted in a significant decrease in the relative abundance of genus Nitrosospira. In addition, AOA and AOB communities were significantly associated with grain yield of wheat, soil potential nitrification activity (PNA), and some soil physicochemical parameters such as pH, NH4-N, and NO3-N. Among them, soil moisture was the most influential edaphic factor for structuring the AOA community and NH4-N for the AOB community. Overall, 105 kg N ha[-1] yr[-1] was optimum for the AOB community and wheat yield in the semi-arid area.},
}
@article {pmid35260828,
year = {2022},
author = {Klotz, F and Kitzinger, K and Ngugi, DK and Büsing, P and Littmann, S and Kuypers, MMM and Schink, B and Pester, M},
title = {Quantification of archaea-driven freshwater nitrification from single cell to ecosystem levels.},
journal = {The ISME journal},
volume = {16},
number = {6},
pages = {1647-1656},
pmid = {35260828},
issn = {1751-7370},
support = {GRK 2272/1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; },
mesh = {Ammonia/metabolism ; *Archaea/genetics/metabolism ; Ecosystem ; Lakes ; *Nitrification ; Oxidation-Reduction ; Phylogeny ; },
abstract = {Deep oligotrophic lakes sustain large populations of the class Nitrososphaeria (Thaumarchaeota) in their hypolimnion. They are thought to be the key ammonia oxidizers in this habitat, but their impact on N-cycling in lakes has rarely been quantified. We followed this archaeal population in one of Europe's largest lakes, Lake Constance, for two consecutive years using metagenomics and metatranscriptomics combined with stable isotope-based activity measurements. An abundant (8-39% of picoplankton) and transcriptionally active archaeal ecotype dominated the nitrifying community. It represented a freshwater-specific species present in major inland water bodies, for which we propose the name "Candidatus Nitrosopumilus limneticus". Its biomass corresponded to 12% of carbon stored in phytoplankton over the year´s cycle. Ca. N. limneticus populations incorporated significantly more ammonium than most other microorganisms in the hypolimnion and were driving potential ammonia oxidation rates of 6.0 ± 0.9 nmol l[‒1] d[‒1], corresponding to potential cell-specific rates of 0.21 ± 0.11 fmol cell[-1] d[-1]. At the ecosystem level, this translates to a maximum capacity of archaea-driven nitrification of 1.76 × 10[9] g N-ammonia per year or 11% of N-biomass produced annually by phytoplankton. We show that ammonia-oxidizing archaea play an equally important role in the nitrogen cycle of deep oligotrophic lakes as their counterparts in marine ecosystems.},
}
@article {pmid35246355,
year = {2022},
author = {Ithurbide, S and Gribaldo, S and Albers, SV and Pende, N},
title = {Spotlight on FtsZ-based cell division in Archaea.},
journal = {Trends in microbiology},
volume = {30},
number = {7},
pages = {665-678},
doi = {10.1016/j.tim.2022.01.005},
pmid = {35246355},
issn = {1878-4380},
mesh = {*Archaea/metabolism ; *Bacteria/metabolism ; Bacterial Proteins/genetics/metabolism ; Cell Division ; Eukaryota/metabolism ; },
abstract = {Compared with the extensive knowledge on cell division in model eukaryotes and bacteria, little is known about how archaea divide. Interestingly, both endosomal sorting complex required for transport (ESCRT)-based and FtsZ-based cell division systems are found in members of the Archaea. In the past couple of years, several studies have started to shed light on FtsZ-based cell division processes in members of the Euryarchaeota. In this review we highlight recent findings in this emerging field of research. We present current knowledge of the cell division machinery of halophiles which relies on two FtsZ proteins, and we compare it with that of methanobacteria, which relies on only one FtsZ. Finally, we discuss how these differences relate to the distinct cell envelopes of these two archaeal model systems.},
}
@article {pmid35221208,
year = {2023},
author = {Stevens, KM and Warnecke, T},
title = {Histone variants in archaea - An undiscovered country.},
journal = {Seminars in cell &amp; developmental biology},
volume = {135},
number = {},
pages = {50-58},
doi = {10.1016/j.semcdb.2022.02.016},
pmid = {35221208},
issn = {1096-3634},
support = {MC_UP_1102/7/MRC_/Medical Research Council/United Kingdom ; },
mesh = {Humans ; *Histones/genetics ; *Archaea/genetics/chemistry ; Nucleosomes/genetics ; Chromatin ; Eukaryotic Cells ; },
abstract = {Exchanging core histones in the nucleosome for paralogous variants can have important functional ramifications. Many of these variants, and their physiological roles, have been characterized in exquisite detail in model eukaryotes, including humans. In comparison, our knowledge of histone biology in archaea remains rudimentary. This is true in particular for our knowledge of histone variants. Many archaea encode several histone genes that differ in sequence, but do these paralogs make distinct, adaptive contributions to genome organization and regulation in a manner comparable to eukaryotes? Below, we review what we know about histone variants in archaea at the level of structure, regulation, and evolution. In all areas, our knowledge pales when compared to the wealth of insight that has been gathered for eukaryotes. Recent findings, however, provide tantalizing glimpses into a rich and largely undiscovered country that is at times familiar and eukaryote-like and at times strange and uniquely archaeal. We sketch a preliminary roadmap for further exploration of this country; an undertaking that may ultimately shed light not only on chromatin biology in archaea but also on the origin of histone-based chromatin in eukaryotes.},
}
@article {pmid35220398,
year = {2022},
author = {Yin, X and Zhou, G and Cai, M and Zhu, QZ and Richter-Heitmann, T and Aromokeye, DA and Liu, Y and Nimzyk, R and Zheng, Q and Tang, X and Elvert, M and Li, M and Friedrich, MW},
title = {Catabolic protein degradation in marine sediments confined to distinct archaea.},
journal = {The ISME journal},
volume = {16},
number = {6},
pages = {1617-1626},
pmid = {35220398},
issn = {1751-7370},
support = {project-ID 49926684//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; project-ID 390741601//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; No. 2018M633111//China Postdoctoral Science Foundation/ ; No. 91851105, 31622002, 31600093, and 31700430//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Archaea/genetics/metabolism ; Carbon/metabolism ; *Geologic Sediments ; Peptide Hydrolases/metabolism ; Phylogeny ; Proteolysis ; RNA, Ribosomal, 16S/metabolism ; },
abstract = {Metagenomic analysis has facilitated prediction of a variety of carbon utilization potentials by uncultivated archaea including degradation of protein, which is a wide-spread carbon polymer in marine sediments. However, the activity of detrital catabolic protein degradation is mostly unknown for the vast majority of archaea. Here, we show actively executed protein catabolism in three archaeal phyla (uncultivated Thermoplasmata, SG8-5; Bathyarchaeota subgroup 15; Lokiarchaeota subgroup 2c) by RNA- and lipid-stable isotope probing in incubations with different marine sediments. However, highly abundant potential protein degraders Thermoprofundales (MBG-D) and Lokiarchaeota subgroup 3 were not incorporating [13]C-label from protein during incubations. Nonetheless, we found that the pathway for protein utilization was present in metagenome associated genomes (MAGs) of active and inactive archaea. This finding was supported by screening extracellular peptidases in 180 archaeal MAGs, which appeared to be widespread but not correlated to organisms actively executing this process in our incubations. Thus, our results have important implications: (i) multiple low-abundant archaeal groups are actually catabolic protein degraders; (ii) the functional role of widespread extracellular peptidases is not an optimal tool to identify protein catabolism, and (iii) catabolic degradation of sedimentary protein is not a common feature of the abundant archaeal community in temperate and permanently cold marine sediments.},
}
@article {pmid35189237,
year = {2022},
author = {Li, M and He, H and Mi, T and Zhen, Y},
title = {Spatiotemporal dynamics of ammonia-oxidizing archaea and bacteria contributing to nitrification in sediments from Bohai Sea and South Yellow Sea, China.},
journal = {The Science of the total environment},
volume = {825},
number = {},
pages = {153972},
doi = {10.1016/j.scitotenv.2022.153972},
pmid = {35189237},
issn = {1879-1026},
mesh = {*Ammonia ; *Archaea/genetics ; Bacteria/genetics ; China ; Geologic Sediments/microbiology ; Nitrification ; Oxidation-Reduction ; Phylogeny ; Soil Microbiology ; },
abstract = {Nitrification is a central process in nitrogen cycle in the ocean. Ammonia-oxidizing archaea (AOA) and bacteria (AOB) play significant roles in ammonia oxidation which is the first and rate-limiting step in nitrification, and their differential contribution to nitrification is an important issue, attracting extensive attention. In this study, based on the quantification of archaeal and bacterial amoA gene and the measurement of potential nitrification rate (PNR), we investigated the spatiotemporal dynamics of PNRs and the amoA gene abundance and transcript abundance of aerobic ammonia oxidizers in surface sediments collected in summer and spring across ~900 km of the Bohai Sea and Yellow Sea in China. The results revealed that the contribution of AOA to nitrification was greater than that of AOB in coastal sediments, probably due to salinity and ammonia concentration. Besides, seasons had significant effect on amoA gene abundance and transcript abundance, especially for AOA, while both seasons and sea areas had significant influence on PNR of AOA and AOB. Further analysis showed complex relationships among amoA gene abundances, transcript abundances and PNRs. More importantly, both spatial (geographic distance) and environmental factors were vital in explaining the variations of ammonia-oxidizing microorganism abundances and the PNRs.},
}
@article {pmid35181078,
year = {2022},
author = {Wei, W and Hu, X and Yang, S and Wang, K and Zeng, C and Hou, Z and Cui, H and Liu, S and Zhu, L},
title = {Denitrifying halophilic archaea derived from salt dominate the degradation of nitrite in salted radish during pickling.},
journal = {Food research international (Ottawa, Ont.)},
volume = {152},
number = {},
pages = {110906},
doi = {10.1016/j.foodres.2021.110906},
pmid = {35181078},
issn = {1873-7145},
mesh = {China ; Nitrates ; *Nitrites/metabolism ; Nitrogen/metabolism ; *Raphanus/chemistry ; },
abstract = {Salted radish is a popular high-salinity table food in China, and nitrite is always generated during the associated pickling process. However, this nitrite can be naturally degraded, and the underlying mechanism is unknown. Here, we identified the microbial groups that dominate the natural degradation of nitrite in salted radish and clarified the related metabolic mechanism. Based on dynamic monitoring of pH and the concentrations of nitrogen compounds as well as high-throughput sequencing analysis of the structural succession of microbial communities in the tested salted radish, we determined that the halophilic archaea derived from pickling salt dominate the natural degradation of nitrite via denitrification. Based on isolation, identification, nitrite reduction assays, and genome annotation, we further determined that Haloarcula, Halolamina, and Halobacterium were the key genera. These halophilic archaea might cope with high salt stress through the "salt-in" mechanism with the assistance of the accumulation of potassium ions, obtain electrons necessary for "truncated denitrification" from the metabolism of extracellular glucose absorbed from salted radish, and efficiently reduce nitrite to nitrogen, bypassing nitrite generation from nitrate reduction. The present study provides important information for the prevention and control of nitrite hazards in salted vegetables with high salinity, such as salted radish.},
}
@article {pmid35165305,
year = {2022},
author = {Xu, B and Li, F and Cai, L and Zhang, R and Fan, L and Zhang, C},
title = {A holistic genome dataset of bacteria, archaea and viruses of the Pearl River estuary.},
journal = {Scientific data},
volume = {9},
number = {1},
pages = {49},
pmid = {35165305},
issn = {2052-4463},
support = {91951120//National Natural Science Foundation of China (National Science Foundation of China)/ ; 91851210//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Archaea/genetics ; *Bacteria/genetics ; Estuaries ; Genome ; *Microbiota/genetics ; Rivers ; *Viruses/genetics ; },
abstract = {Estuaries are one of the most important coastal ecosystems. While microbiomes and viromes have been separately investigated in some estuaries, few studies holistically deciphered the genomes and connections of viruses and their microbial hosts along an estuarine salinity gradient. Here we applied deep metagenomic sequencing on microbial and viral communities in surface waters of the Pearl River estuary, one of China's largest estuaries with strong anthropogenic impacts. Overall, 1,205 non-redundant prokaryotic genomes with ≥50% completeness and ≤10% contamination, and 78,502 non-redundant viral-like genomes were generated from samples of three size fractions and five salinity levels. Phylogenomic analysis and taxonomy classification show that majority of these estuarine prokaryotic and viral genomes are novel at species level according to public databases. Potential connections between the microbial and viral populations were further investigated by host-virus matching. These combined microbial and viral genomes provide an important complement of global marine genome datasets and should greatly facilitate our understanding of microbe-virus interactions, evolution and their implications in estuarine ecosystems.},
}
@article {pmid35165204,
year = {2022},
author = {Schorn, S and Ahmerkamp, S and Bullock, E and Weber, M and Lott, C and Liebeke, M and Lavik, G and Kuypers, MMM and Graf, JS and Milucka, J},
title = {Diverse methylotrophic methanogenic archaea cause high methane emissions from seagrass meadows.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {119},
number = {9},
pages = {},
pmid = {35165204},
issn = {1091-6490},
mesh = {Aerobiosis ; Alismatales/*metabolism ; Anaerobiosis ; Euryarchaeota/classification/*metabolism ; Geologic Sediments ; Mediterranean Sea ; Methane/*metabolism ; Microbiota ; Oxidation-Reduction ; Phylogeny ; Species Specificity ; },
abstract = {Marine coastlines colonized by seagrasses are a net source of methane to the atmosphere. However, methane emissions from these environments are still poorly constrained, and the underlying processes and responsible microorganisms remain largely unknown. Here, we investigated methane turnover in seagrass meadows of Posidonia oceanica in the Mediterranean Sea. The underlying sediments exhibited median net fluxes of methane into the water column of ca. 106 µmol CH4 ⋅ m[-2] ⋅ d[-1] Our data show that this methane production was sustained by methylated compounds produced by the plant, rather than by fermentation of buried organic carbon. Interestingly, methane production was maintained long after the living plant died off, likely due to the persistence of methylated compounds, such as choline, betaines, and dimethylsulfoniopropionate, in detached plant leaves and rhizomes. We recovered multiple mcrA gene sequences, encoding for methyl-coenzyme M reductase (Mcr), the key methanogenic enzyme, from the seagrass sediments. Most retrieved mcrA gene sequences were affiliated with a clade of divergent Mcr and belonged to the uncultured Candidatus Helarchaeota of the Asgard superphylum, suggesting a possible involvement of these divergent Mcr in methane metabolism. Taken together, our findings identify the mechanisms controlling methane emissions from these important blue carbon ecosystems.},
}
@article {pmid35145493,
year = {2021},
author = {Chen, S and Tao, J and Chen, Y and Wang, W and Fan, L and Zhang, C},
title = {Interactions Between Marine Group II Archaea and Phytoplankton Revealed by Population Correlations in the Northern Coast of South China Sea.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {785532},
pmid = {35145493},
issn = {1664-302X},
abstract = {Marine Group II (MGII) archaea (Poseidoniales) are the most abundant surface marine planktonic archaea and are widely distributed in both coastal and pelagic waters. The factors affecting their distribution and activity are poorly understood. MGII archaea have the metabolic potential to utilize algae-derived organic matter and are frequently observed in high abundance during or following phytoplankton blooms, suggesting that they are key players of the marine food web. In this study, we studied interactions between MGII archaea and the diverse taxa of phytoplankton in the northern coast of South China Sea. Non-metric multidimensional scaling and cluster analyses demonstrated distinct MGII community patterns in the Pearl River plume (PRP) and the open regions of the northern South China Sea (ONSCS), with MGIIb dominating the former and MGIIa and MGIIb showing remarkable variations in the latter for the same sampling season. Nevertheless, positive correlations (Pearson correlation: R > 0.8 and P < 0.01) in absolute abundances of ribosomal RNA (rRNA)-derived complementary DNA and rRNA genes from network analyses were found between MGII archaea and phytoplankton (cyanobacteria, haptophytes, and stramenopiles in both PRP and ONSCS) among different particle size fractions, indicating their intrinsic relationships under changing environmental conditions. The results of this study may shed light on the multiple interactions between co-existing species in the micro-niches of different oceanic regions.},
}
@article {pmid35142133,
year = {2022},
author = {Cui, L and Fan, X and Zheng, Y},
title = {[Enhanced heterologous expression of the cytochrome c from uncultured anaerobic methanotrophic archaea].},
journal = {Sheng wu gong cheng xue bao = Chinese journal of biotechnology},
volume = {38},
number = {1},
pages = {226-237},
doi = {10.13345/j.cjb.210193},
pmid = {35142133},
issn = {1872-2075},
mesh = {Anaerobiosis ; Archaea/metabolism ; *Cytochromes c/genetics/metabolism ; *Escherichia coli/genetics/metabolism ; Heme/metabolism ; },
abstract = {Cytochrome c is a type of heme proteins that are widely distributed in living organisms. It consists of heme and apocytochrome c, and has potential applications in bioelectronics, biomedicine and pollutant degradation. However, heterologous overexpression of cytochrome c is still challenging. To date, expression of the cytochrome c from uncultured anaerobic methanotrophic archaea has not been reported, and nothing is known about the function of this cytochrome c. A his tagged cytochrome c was successfully expressed in E. coli by introducing a thrombin at the N-terminus of CytC4 and co-expressing CcmABCDEFGH, which is responsible for the maturation of cytochrome c. Shewanella oneidensis, which naturally has enzymes for cytochrome c maturation, was then used as a host to further increase the expression of CytC4. Indeed, a significantly higher expression of CytC4 was achieved in S. oneidensis when compared with in E. coli. The successful heterologous overexpression of CytC4 will facilitate the exploitation of its physiological functions and biotechnological applications.},
}
@article {pmid35126338,
year = {2021},
author = {Hedlund, BP and Zhang, C and Wang, F and Rinke, C and Martin, WF},
title = {Editorial: Ecology, Metabolism and Evolution of Archaea-Perspectives From Proceedings of the International Workshop on Geo-Omics of Archaea.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {827229},
pmid = {35126338},
issn = {1664-302X},
}
@article {pmid35101434,
year = {2022},
author = {Liu, BB and Govindan, R and Muthuchamy, M and Cheng, S and Li, X and Ye, L and Wang, LY and Guo, SX and Li, WJ and Alharbi, NS and M Khaled, J and Kadaikunnan, S},
title = {Halophilic archaea and their extracellular polymeric compounds in the treatment of high salt wastewater containing phenol.},
journal = {Chemosphere},
volume = {294},
number = {},
pages = {133732},
doi = {10.1016/j.chemosphere.2022.133732},
pmid = {35101434},
issn = {1879-1298},
mesh = {Archaea/metabolism ; Extracellular Polymeric Substance Matrix/metabolism ; *Phenol/metabolism ; Phenols ; *Wastewater ; },
abstract = {Phenol is one of the major organic pollutants in high salt industrial wastewaters. The biological treatment of such waste using microorganisms is considered to be a cost-effective and eco-friendly method. However, in this process, salt tolerance of microorganisms is one of the main limiting factors. Halophilic microorganisms, especially halophilic archaea are thought to be appropriate for such treatment. To develop a novel effective biological method for high salt phenol wastewater treatment, the influence of phenol in high salt phenol wastewater on halophilic archaea and their extracellular polymeric substances (EPS) should be investigated. In the present study, using phenol enrichment method, 75 halophilic archaeal strains were isolated from Wuyongbulake salt lake sediment sample. The majority of the identified strains were phenol-tolerant. Six strains with high phenol tolerance were chosen, and the phenol scavenging effect was observed in the microbial suspension, supernatant, and EPS. It was noticed that the phenol degradation rate of suspensions of both strains 869-1, and 121-1 in salt water exhibited the highest rates of 83.7%, while the supernatant of strain 869-1 reached the highest rate of 78.2%. When combined with the comprehensive analysis of the artificial wastewater simulation experiment, it was discovered that in the artificial wastewater containing phenol, the phenol degradation rate of suspension of strain A387 exhibited the highest rates of 55.74% both, and supernatant of strain 630-3 reached the highest rate of 62.3%. The EPS produced by strains A00135, 558-1, 869-1, 121-1 and A387 removed 100% phenol within 96 h, and the phenol removal efficiency of EPS produced by 869-1 reached 56.1% under an artificial wastewater simulation experiment with high salt (15%NaCl) condition. The present study suggests that halophilic archaea and their EPS play an important role in phenol degradation. This approach could be potentially used for industrial high-salt wastewater treatment.},
}
@article {pmid35098330,
year = {2023},
author = {Shen, LD and Geng, CY and Ren, BJ and Jin, JH and Huang, HC and Liu, X and Yang, WT and Yang, YL and Liu, JQ and Tian, MH},
title = {Detection and Quantification of Candidatus Methanoperedens-Like Archaea in Freshwater Wetland Soils.},
journal = {Microbial ecology},
volume = {85},
number = {2},
pages = {441-453},
pmid = {35098330},
issn = {1432-184X},
support = {41977037//National Natural Science Foundation of China/ ; BK20190092//Natural Science Foundation of Jiangsu Province/ ; },
mesh = {*Archaea/genetics ; *Wetlands ; Nitrates ; Soil ; Phylogeny ; Oxidation-Reduction ; Fresh Water ; Methane ; Water ; Iron ; Anaerobiosis ; },
abstract = {Candidatus Methanoperedens-like archaea, which can use multiple electron acceptors (nitrate, iron, manganese, and sulfate) for anaerobic methane oxidation, could play an important role in reducing methane emissions from freshwater wetlands. Currently, very little is known about the distribution and community composition of Methanoperedens-like archaea in freshwater wetlands, particularly based on their alpha subunit of methyl-coenzyme M reductase (mcrA) genes. Here, the community composition, diversity, and abundance of Methanoperedens-like archaea were investigated in a freshwater wetland through high-throughput sequencing and quantitative PCR on their mcrA genes. A large number of Methanoperedens-like mcrA gene sequences (119,250) were recovered, and a total of 31 operational taxonomic units (OTUs) were generated based on 95% sequence similarity cut-off. The majority of Methanoperedens-like sequences can be grouped into three distinct clusters that were closely associated with the known Methanoperedens species which can couple anaerobic methane oxidation to nitrate or iron reduction. The community composition of Methanoperedens-like archaea differed significantly among different sampling sites, and their mcrA gene abundance was 1.49 × 10[6] ~ 4.62 × 10[6] copies g[-1] dry soil in the examined wetland. In addition, the community composition of Methanoperedens-like archaea was significantly affected by the soil water content, and the archaeal abundance was significantly positively correlated with the water content. Our results suggest that the mcrA gene is a good biomarker for detection and quantification of Methanoperedens-like archaea, and provide new insights into the distribution and environmental regulation of these archaea in freshwater wetlands.},
}
@article {pmid35076275,
year = {2022},
author = {Rasmussen, AN and Francis, CA},
title = {Genome-Resolved Metagenomic Insights into Massive Seasonal Ammonia-Oxidizing Archaea Blooms in San Francisco Bay.},
journal = {mSystems},
volume = {7},
number = {1},
pages = {e0127021},
pmid = {35076275},
issn = {2379-5077},
mesh = {*Archaea ; *Ammonia ; Metagenomics ; Bays ; Metagenome ; San Francisco ; RNA, Ribosomal, 16S ; Seasons ; Nitrites ; Urease/genetics ; Oxidation-Reduction ; Geologic Sediments/microbiology ; Water ; Nitrogen ; },
abstract = {Ammonia-oxidizing archaea (AOA) are key for the transformation of ammonia to oxidized forms of nitrogen in aquatic environments around the globe, including nutrient-rich coastal and estuarine waters such as San Francisco Bay (SFB). Using metagenomics and 16S rRNA gene amplicon libraries, we found that AOA are more abundant than ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB), except in the freshwater stations in SFB. In South SFB, we observed recurrent AOA blooms of "Candidatus Nitrosomarinus catalina" SPOT01-like organisms, which account for over 20% of 16S rRNA gene amplicons in both surface and bottom waters and co-occur with weeks of high nitrite concentrations (>10 μM) in the oxic water column. We observed pronounced nitrite peaks occurring in the autumn for 7 of the last 9 years (2012 to 2020), suggesting that seasonal AOA blooms are common in South SFB. We recovered two high-quality AOA metagenome-assembled genomes (MAGs), including a Nitrosomarinus-like genome from the South SFB bloom and another Nitrosopumilus genome originating from Suisun Bay in North SFB. Both MAGs cluster with genomes from other estuarine/coastal sites. Analysis of Nitrosomarinus-like genomes show that they are streamlined, with low GC content and high coding density, and harbor urease genes. Our findings support the unique niche of Nitrosomarinus-like organisms which dominate coastal/estuarine waters and provide insights into recurring AOA blooms in SFB. IMPORTANCE Ammonia-oxidizing archaea (AOA) carry out key transformations of ammonia in estuarine systems such as San Francisco Bay (SFB)-the largest estuary on the west coast of North America-and play a significant role in both local and global nitrogen cycling. Using metagenomics and 16S rRNA gene amplicon libraries, we document a massive, recurrent AOA bloom in South SFB that co-occurs with months of high nitrite concentrations in the oxic water column. Our study is the first to generate metagenome-assembled genomes (MAGs) from SFB, and through this process we recovered two high-quality AOA MAGs, one of which originated from bloom samples. These AOA MAGs yield new insight into the Nitrosopumilus and Nitrosomarinus-like lineages and their potential niches in coastal and estuarine systems. Nitrosomarinus-like AOA are abundant in coastal regions around the globe, and we highlight the common occurrence of urease genes, low GC content, and range of salinity tolerances within this lineage.},
}
@article {pmid35069467,
year = {2021},
author = {Rodríguez-Gijón, A and Nuy, JK and Mehrshad, M and Buck, M and Schulz, F and Woyke, T and Garcia, SL},
title = {A Genomic Perspective Across Earth's Microbiomes Reveals That Genome Size in Archaea and Bacteria Is Linked to Ecosystem Type and Trophic Strategy.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {761869},
pmid = {35069467},
issn = {1664-302X},
abstract = {Our view of genome size in Archaea and Bacteria has remained skewed as the data has been dominated by genomes of microorganisms that have been cultivated under laboratory settings. However, the continuous effort to catalog Earth's microbiomes, specifically propelled by recent extensive work on uncultivated microorganisms, provides an opportunity to revise our perspective on genome size distribution. We present a meta-analysis that includes 26,101 representative genomes from 3 published genomic databases; metagenomic assembled genomes (MAGs) from GEMs and stratfreshDB, and isolates from GTDB. Aquatic and host-associated microbial genomes present on average the smallest estimated genome sizes (3.1 and 3.0 Mbp, respectively). These are followed by terrestrial microbial genomes (average 3.7 Mbp), and genomes from isolated microorganisms (average 4.3 Mbp). On the one hand, aquatic and host-associated ecosystems present smaller genomes sizes in genera of phyla with genome sizes above 3 Mbp. On the other hand, estimated genome size in phyla with genomes under 3 Mbp showed no difference between ecosystems. Moreover, we observed that when using 95% average nucleotide identity (ANI) as an estimator for genetic units, only 3% of MAGs cluster together with genomes from isolated microorganisms. Although there are potential methodological limitations when assembling and binning MAGs, we found that in genome clusters containing both environmental MAGs and isolate genomes, MAGs were estimated only an average 3.7% smaller than isolate genomes. Even when assembly and binning methods introduce biases, estimated genome size of MAGs and isolates are very similar. Finally, to better understand the ecological drivers of genome size, we discuss on the known and the overlooked factors that influence genome size in different ecosystems, phylogenetic groups, and trophic strategies.},
}
@article {pmid35052563,
year = {2021},
author = {Neira, G and Vergara, E and Cortez, D and Holmes, DS},
title = {A Large-Scale Multiple Genome Comparison of Acidophilic Archaea (pH ≤ 5.0) Extends Our Understanding of Oxidative Stress Responses in Polyextreme Environments.},
journal = {Antioxidants (Basel, Switzerland)},
volume = {11},
number = {1},
pages = {},
pmid = {35052563},
issn = {2076-3921},
support = {1181717//Fondecyt/ ; FB210008//Centro Ciencia &amp; Vida, Financiamiento Basal para Centros Cient&#xed;ficos y Tecnol&#xf3;gicos de Excelencia de ANID/ ; },
abstract = {Acidophilic archaea thrive in anaerobic and aerobic low pH environments (pH < 5) rich in dissolved heavy metals that exacerbate stress caused by the production of reactive oxygen species (ROS) such as hydrogen peroxide (H2O2), hydroxyl radical (·OH) and superoxide (O2[-]). ROS react with lipids, proteins and nucleic acids causing oxidative stress and damage that can lead to cell death. Herein, genes and mechanisms potentially involved in ROS mitigation are predicted in over 200 genomes of acidophilic archaea with sequenced genomes. These organisms are often be subjected to simultaneous multiple stresses such as high temperature, high salinity, low pH and high heavy metal loads. Some of the topics addressed include: (1) the phylogenomic distribution of these genes and what this can tell us about the evolution of these mechanisms in acidophilic archaea; (2) key differences in genes and mechanisms used by acidophilic versus non-acidophilic archaea and between acidophilic archaea and acidophilic bacteria and (3) how comparative genomic analysis predicts novel genes or pathways involved in oxidative stress responses in archaea and likely horizontal gene transfer (HGT) events.},
}
@article {pmid35049347,
year = {2022},
author = {McMahon, FT and Lonergan, CM and Gilmore, BF and Megaw, J},
title = {Draft Genome Sequences of Halobacterium sp. Strains KA-4 and KA-6, Two Extremely Halophilic Archaea Isolated from a Triassic Salt Deposit in Northern Ireland.},
journal = {Microbiology resource announcements},
volume = {11},
number = {1},
pages = {e0116521},
pmid = {35049347},
issn = {2576-098X},
abstract = {Here, we report the draft genome sequences of Halobacterium sp. strains KA-4 and KA-6. These extremely halophilic archaea were isolated from a Triassic halite deposit in Northern Ireland. Based on 16S sequence identity, they were deemed to be closely related strains of Halobacterium noricense but with some notable phenotypic differences.},
}
@article {pmid37938653,
year = {2022},
author = {Vigneron, A and Cruaud, P and Lovejoy, C and Vincent, WF},
title = {Genomic evidence of functional diversity in DPANN archaea, from oxic species to anoxic vampiristic consortia.},
journal = {ISME communications},
volume = {2},
number = {1},
pages = {4},
pmid = {37938653},
issn = {2730-6151},
abstract = {DPANN archaea account for half of the archaeal diversity of the biosphere, but with few cultivated representatives, their metabolic potential and environmental functions are poorly understood. The extreme geochemical and environmental conditions in meromictic ice-capped Lake A, in the Canadian High Arctic, provided an isolated, stratified model ecosystem to resolve the distribution and metabolism of uncultured aquatic DPANN archaea living across extreme redox and salinity gradients, from freshwater oxygenated conditions, to saline, anoxic, sulfidic waters. We recovered 28 metagenome-assembled genomes (MAGs) of DPANN archaea that provided genetic insights into their ecological function. Thiosulfate oxidation potential was detected in aerobic Woesearchaeota, whereas diverse metabolic functions were identified in anaerobic DPANN archaea, including degradation and fermentation of cellular compounds, and sulfide and polysulfide reduction. We also found evidence for "vampiristic" metabolism in several MAGs, with genes coding for pore-forming toxins, peptidoglycan degradation, and RNA scavenging. The vampiristic MAGs co-occurred with other DPANNs having complementary metabolic capacities, leading to the possibility that DPANN form interspecific consortia that recycle microbial carbon, nutrients and complex molecules through a DPANN archaeal shunt, adding hidden novel complexity to anaerobic microbial food webs.},
}
@article {pmid35040218,
year = {2022},
author = {Papenfort, K and Woodson, SA and Schmitz, RA and Winkler, WC},
title = {Special Issue: Regulating with RNA in Microbes: In conjunction with the 6th Meeting on Regulating with RNA in Bacteria and Archaea.},
journal = {Molecular microbiology},
volume = {117},
number = {1},
pages = {1-3},
doi = {10.1111/mmi.14867},
pmid = {35040218},
issn = {1365-2958},
support = {R13 AI147570/AI/NIAID NIH HHS/United States ; R13 AI154714/AI/NIAID NIH HHS/United States ; },
mesh = {Archaea/*genetics/physiology ; Bacteria/*genetics ; Bacterial Physiological Phenomena ; Evolution, Molecular ; *RNA Processing, Post-Transcriptional ; RNA, Archaeal/genetics ; RNA, Bacterial/genetics ; RNA, Untranslated/*genetics ; RNA-Binding Proteins/genetics/*metabolism ; },
}
@article {pmid35027677,
year = {2022},
author = {Wu, F and Speth, DR and Philosof, A and Crémière, A and Narayanan, A and Barco, RA and Connon, SA and Amend, JP and Antoshechkin, IA and Orphan, VJ},
title = {Unique mobile elements and scalable gene flow at the prokaryote-eukaryote boundary revealed by circularized Asgard archaea genomes.},
journal = {Nature microbiology},
volume = {7},
number = {2},
pages = {200-212},
pmid = {35027677},
issn = {2058-5276},
mesh = {Archaea/*genetics ; Archaeal Proteins/genetics ; Bacteria/genetics ; Eukaryota/*genetics ; *Evolution, Molecular ; *Gene Flow ; *Genome, Archaeal ; Metagenomics ; Phylogeny ; Prokaryotic Cells/*metabolism ; },
abstract = {Eukaryotic genomes are known to have garnered innovations from both archaeal and bacterial domains but the sequence of events that led to the complex gene repertoire of eukaryotes is largely unresolved. Here, through the enrichment of hydrothermal vent microorganisms, we recovered two circularized genomes of Heimdallarchaeum species that belong to an Asgard archaea clade phylogenetically closest to eukaryotes. These genomes reveal diverse mobile elements, including an integrative viral genome that bidirectionally replicates in a circular form and aloposons, transposons that encode the 5,000 amino acid-sized proteins Otus and Ephialtes. Heimdallaechaeal mobile elements have garnered various genes from bacteria and bacteriophages, likely playing a role in shuffling functions across domains. The number of archaea- and bacteria-related genes follow strikingly different scaling laws in Asgard archaea, exhibiting a genome size-dependent ratio and a functional division resembling the bacteria- and archaea-derived gene repertoire across eukaryotes. Bacterial gene import has thus likely been a continuous process unaltered by eukaryogenesis and scaled up through genome expansion. Our data further highlight the importance of viewing eukaryogenesis in a pan-Asgard context, which led to the proposal of a conceptual framework, that is, the Heimdall nucleation-decentralized innovation-hierarchical import model that accounts for the emergence of eukaryotic complexity.},
}
@article {pmid35022241,
year = {2022},
author = {Sakai, HD and Nur, N and Kato, S and Yuki, M and Shimizu, M and Itoh, T and Ohkuma, M and Suwanto, A and Kurosawa, N},
title = {Insight into the symbiotic lifestyle of DPANN archaea revealed by cultivation and genome analyses.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {119},
number = {3},
pages = {},
pmid = {35022241},
issn = {1091-6490},
mesh = {Archaea/classification/cytology/*genetics/*physiology ; Coculture Techniques ; Evolution, Molecular ; Gene Transfer, Horizontal ; *Genome, Archaeal ; Genomics ; Nanoarchaeota ; Phylogeny ; Symbiosis/*genetics/*physiology ; },
abstract = {Decades of culture-independent analyses have resulted in proposals of many tentative archaeal phyla with no cultivable representative. Members of DPANN (an acronym of the names of the first included phyla Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanohaloarchaeota, and Nanoarchaeota), an archaeal superphylum composed of at least 10 of these tentative phyla, are generally considered obligate symbionts dependent on other microorganisms. While many draft/complete genome sequences of DPANN archaea are available and their biological functions have been considerably predicted, only a few examples of their successful laboratory cultivation have been reported, limiting our knowledge of their symbiotic lifestyles. Here, we investigated physiology, morphology, and host specificity of an archaeon of the phylum "Candidatus Micrarchaeota" (ARM-1) belonging to the DPANN superphylum by cultivation. We constructed a stable coculture system composed of ARM-1 and its original host Metallosphaera sp. AS-7 belonging to the order Sulfolobales Further host-switching experiments confirmed that ARM-1 grew on five different archaeal species from three genera-Metallosphaera, Acidianus, and Saccharolobus-originating from geologically distinct hot, acidic environments. The results suggested the existence of DPANN archaea that can grow by relying on a range of hosts. Genomic analyses showed inferred metabolic capabilities, common/unique genetic contents of ARM-1 among cultivated micrarchaeal representatives, and the possibility of horizontal gene transfer between ARM-1 and members of the order Sulfolobales Our report sheds light on the symbiotic lifestyles of DPANN archaea and will contribute to the elucidation of their biological/ecological functions.},
}
@article {pmid35021862,
year = {2022},
author = {Salter, TL and Magee, BA and Waite, JH and Sephton, MA},
title = {Mass Spectrometric Fingerprints of Bacteria and Archaea for Life Detection on Icy Moons.},
journal = {Astrobiology},
volume = {22},
number = {2},
pages = {143-157},
doi = {10.1089/ast.2020.2394},
pmid = {35021862},
issn = {1557-8070},
mesh = {Archaea ; Bacteria ; *Exobiology/methods ; Extraterrestrial Environment/chemistry ; Mass Spectrometry ; *Moon ; },
abstract = {The icy moons of the outer Solar System display evidence of subsurface liquid water and, therefore, potential habitability for life. Flybys of Saturn's moon Enceladus by the Cassini spacecraft have provided measurements of material from plumes that suggest hydrothermal activity and the presence of organic matter. Jupiter's moon Europa may have similar plumes and is the target for the forthcoming Europa Clipper mission that carries a high mass resolution and high sensitivity mass spectrometer, called the MAss Spectrometer for Planetary EXploration (MASPEX), with the capability for providing detailed characterization of any organic materials encountered. We have performed a series of experiments using pyrolysis-gas chromatography-mass spectrometry to characterize the mass spectrometric fingerprints of microbial life. A range of extremophile Archaea and Bacteria have been analyzed and the laboratory data converted to MASPEX-type signals. Molecular characteristics of protein, carbohydrate, and lipid structures were detected, and the characteristic fragmentation patterns corresponding to these different biological structures were identified. Protein pyrolysis fragments included phenols, nitrogen heterocycles, and cyclic dipeptides. Oxygen heterocycles, such as furans, were detected from carbohydrates. Our data reveal how mass spectrometry on Europa Clipper can aid in the identification of the presence of life, by looking for characteristic bacterial fingerprints that are similar to those from simple Earthly organisms.},
}
@article {pmid38716123,
year = {2022},
author = {Kanno, N and Kato, S and Itoh, T and Ohkuma, M and Shigeto, S},
title = {Resonance Raman analysis of intracellular vitamin B12 analogs in methanogenic archaea.},
journal = {Analytical science advances},
volume = {3},
number = {5-6},
pages = {165-173},
pmid = {38716123},
issn = {2628-5452},
abstract = {Methanogenic archaea (methanogens) are microorganisms that can synthesize methane. They are found in diverse environments ranging from paddy fields to animal digestive tracts to deep-sea hydrothermal vents. Investigating their distribution and physiological activity is crucial for the detailed analysis of the dynamics of greenhouse gas generation and the search for the environmental limits of life. In methanogens, cobamide cofactors (vitamin B12 analogs) play a key role in methane synthesis and carbon fixation, thus serving as a marker compound that metabolically characterizes them. Here, we report on resonance Raman detection of cobamides in methanogenic cells without destroying cells and provide structural insights into those cobamides. We succeeded in detecting cobamides in four representative methanogens Methanosarcina mazei, Methanosarcina barkeri, Methanopyrus kandleri, and Methanocaldococcus jannaschii. The former two are mesophilic, cytochrome-containing methanogens, whereas the latter two are hyperthermophilic, non-cytochrome-containing methanogens. The 532 nm-excited Raman spectra of single or multiple cells of the four species all showed resonance Raman bands of cobamides arising mainly from the corrin ring, with the most intense one at ∼1500 cm[-1]. We envision that resonance Raman microspectroscopy could be useful for in situ, nondestructive identification of methanogenic cells that produce high levels of cobamides.},
}
@article {pmid34987183,
year = {2022},
author = {Diamond, S and Lavy, A and Crits-Christoph, A and Matheus Carnevali, PB and Sharrar, A and Williams, KH and Banfield, JF},
title = {Soils and sediments host Thermoplasmata archaea encoding novel copper membrane monooxygenases (CuMMOs).},
journal = {The ISME journal},
volume = {16},
number = {5},
pages = {1348-1362},
pmid = {34987183},
issn = {1751-7370},
mesh = {Ammonia/metabolism ; *Archaea/metabolism ; Carbon/metabolism ; Copper/metabolism ; *Euryarchaeota/metabolism ; Mixed Function Oxygenases/genetics ; Phylogeny ; Soil ; },
abstract = {Copper membrane monooxygenases (CuMMOs) play critical roles in the global carbon and nitrogen cycles. Organisms harboring these enzymes perform the first, and rate limiting, step in aerobic oxidation of ammonia, methane, or other simple hydrocarbons. Within archaea, only organisms in the order Nitrososphaerales (Thaumarchaeota) encode CuMMOs, which function exclusively as ammonia monooxygenases. From grassland and hillslope soils and aquifer sediments, we identified 20 genomes from distinct archaeal species encoding divergent CuMMO sequences. These archaea are phylogenetically clustered in a previously unnamed Thermoplasmatota order, herein named the Ca. Angelarchaeales. The CuMMO proteins in Ca. Angelarchaeales are more similar in structure to those in Nitrososphaerales than those of bacteria, and contain all functional residues required for general monooxygenase activity. Ca. Angelarchaeales genomes are significantly enriched in blue copper proteins (BCPs) relative to sibling lineages, including plastocyanin-like electron carriers and divergent nitrite reductase-like (nirK) 2-domain cupredoxin proteins co-located with electron transport machinery. Ca. Angelarchaeales also encode significant capacity for peptide/amino acid uptake and degradation and share numerous electron transport mechanisms with the Nitrososphaerales. Ca. Angelarchaeales are detected at high relative abundance in some of the environments where their genomes originated from. While the exact substrate specificities of the novel CuMMOs identified here have yet to be determined, activity on ammonia is possible given their metabolic and ecological context. The identification of an archaeal CuMMO outside of the Nitrososphaerales significantly expands the known diversity of CuMMO enzymes in archaea and suggests previously unaccounted organisms contribute to critical global nitrogen and/or carbon cycling functions.},
}
@article {pmid34986784,
year = {2022},
author = {Aouad, M and Flandrois, JP and Jauffrit, F and Gouy, M and Gribaldo, S and Brochier-Armanet, C},
title = {A divide-and-conquer phylogenomic approach based on character supermatrices resolves early steps in the evolution of the Archaea.},
journal = {BMC ecology and evolution},
volume = {22},
number = {1},
pages = {1},
pmid = {34986784},
issn = {2730-7182},
mesh = {*Archaea/genetics ; *Eukaryota ; Phylogeny ; },
abstract = {BACKGROUND: The recent rise in cultivation-independent genome sequencing has provided key material to explore uncharted branches of the Tree of Life. This has been particularly spectacular concerning the Archaea, projecting them at the center stage as prominently relevant to understand early stages in evolution and the emergence of fundamental metabolisms as well as the origin of eukaryotes. Yet, resolving deep divergences remains a challenging task due to well-known tree-reconstruction artefacts and biases in extracting robust ancient phylogenetic signal, notably when analyzing data sets including the three Domains of Life. Among the various strategies aimed at mitigating these problems, divide-and-conquer approaches remain poorly explored, and have been primarily based on reconciliation among single gene trees which however notoriously lack ancient phylogenetic signal.<br><br>RESULTS: We analyzed sub-sets of full supermatrices&#xa0;covering the whole Tree of Life with specific taxonomic sampling to robustly resolve different parts of the archaeal phylogeny in light of their current diversity. Our results strongly support the existence and early emergence of two main clades, Cluster I and Cluster II, which we name Ouranosarchaea and Gaiarchaea, and we clarify the placement of important novel archaeal lineages within these two clades. However, the monophyly and branching of the fast evolving nanosized DPANN members remains unclear and worth of further study.<br><br>CONCLUSIONS: We inferred a well resolved rooted phylogeny of the Archaea that includes all recently described phyla of high taxonomic rank. This phylogeny represents a valuable reference to study the evolutionary events associated to the early steps of the diversification of the archaeal domain. Beyond the specifics of archaeal phylogeny, our results demonstrate the power of divide-and-conquer approaches to resolve deep phylogenetic relationships, which should be applied to progressively resolve the entire Tree of Life.},
}
@article {pmid34986141,
year = {2022},
author = {Chadwick, GL and Skennerton, CT and Laso-Pérez, R and Leu, AO and Speth, DR and Yu, H and Morgan-Lang, C and Hatzenpichler, R and Goudeau, D and Malmstrom, R and Brazelton, WJ and Woyke, T and Hallam, SJ and Tyson, GW and Wegener, G and Boetius, A and Orphan, VJ},
title = {Comparative genomics reveals electron transfer and syntrophic mechanisms differentiating methanotrophic and methanogenic archaea.},
journal = {PLoS biology},
volume = {20},
number = {1},
pages = {e3001508},
pmid = {34986141},
issn = {1545-7885},
mesh = {Anaerobiosis ; *Archaea/genetics/metabolism ; *Electrons ; Genomics ; Geologic Sediments/microbiology ; Methane/metabolism ; Oxidation-Reduction ; Phylogeny ; Sulfates/metabolism ; },
abstract = {The anaerobic oxidation of methane coupled to sulfate reduction is a microbially mediated process requiring a syntrophic partnership between anaerobic methanotrophic (ANME) archaea and sulfate-reducing bacteria (SRB). Based on genome taxonomy, ANME lineages are polyphyletic within the phylum Halobacterota, none of which have been isolated in pure culture. Here, we reconstruct 28 ANME genomes from environmental metagenomes and flow sorted syntrophic consortia. Together with a reanalysis of previously published datasets, these genomes enable a comparative analysis of all marine ANME clades. We review the genomic features that separate ANME from their methanogenic relatives and identify what differentiates ANME clades. Large multiheme cytochromes and bioenergetic complexes predicted to be involved in novel electron bifurcation reactions are well distributed and conserved in the ANME archaea, while significant variations in the anabolic C1 pathways exists between clades. Our analysis raises the possibility that methylotrophic methanogenesis may have evolved from a methanotrophic ancestor.},
}
@article {pmid34984789,
year = {2022},
author = {Chazan, A and Rozenberg, A and Mannen, K and Nagata, T and Tahan, R and Yaish, S and Larom, S and Inoue, K and Béjà, O and Pushkarev, A},
title = {Diverse heliorhodopsins detected via functional metagenomics in freshwater Actinobacteria, Chloroflexi and Archaea.},
journal = {Environmental microbiology},
volume = {24},
number = {1},
pages = {110-121},
doi = {10.1111/1462-2920.15890},
pmid = {34984789},
issn = {1462-2920},
mesh = {*Actinobacteria/genetics ; Archaea/genetics ; *Chloroflexi ; Fresh Water ; Metagenomics ; Rhodopsins, Microbial ; },
abstract = {The recently discovered rhodopsin family of heliorhodopsins (HeRs) is abundant in diverse microbial environments. So far, the functional and biological roles of HeRs remain unknown. To tackle this issue, we combined experimental and computational screens to gain some novel insights. Here, 10 readily expressed HeR genes were found using functional metagenomics on samples from two freshwater environments. These HeRs originated from diverse prokaryotic groups: Actinobacteria, Chloroflexi and Archaea. Heterologously expressed HeRs absorbed light in the green and yellow wavelengths (543-562 nm) and their photocycles exhibited diverse kinetic characteristics. To approach the physiological function of the HeRs, we used our environmental clones along with thousands of microbial genomes to analyze genes neighbouring HeRs. The strongest association was found with the DegV family involved in activation of fatty acids, which allowed us to hypothesize that HeRs might be involved in light-induced membrane lipid modifications.},
}
@article {pmid34962596,
year = {2021},
author = {Li, SY and Xin, YJ and Bao, CX and Hou, J and Cui, HL},
title = {Haloprofundus salilacus sp. nov., Haloprofundus halobius sp. nov. and Haloprofundus salinisoli sp. nov.: three extremely halophilic archaea isolated from salt lake and saline soil.},
journal = {Extremophiles : life under extreme conditions},
volume = {26},
number = {1},
pages = {6},
pmid = {34962596},
issn = {1433-4909},
support = {31770005//National Natural Science Foundation of China/ ; },
mesh = {Base Composition ; China ; DNA, Archaeal ; Glycolipids ; *Halobacteriaceae/genetics ; *Lakes ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Soil ; },
abstract = {Three halophilic archaeal strains, Gai1-5[T], SEDH52[T] and SQT7-1[T] were isolated from Gaize salt lake and Xiadi salt lake in Tibet, and saline soil from Xinjiang, respectively. Phylogenetic analysis based on 16S rRNA gene and rpoB' gene sequences showed that these three strains formed different branches separating them from Haloprofundus halophilus NK23[T] (97.7-98.3% similarities for 16S rRNA gene and 94.7-94.8% similarities for rpoB' gene, respectively) and Haloprofundus marisrubri SB9[T] (94.7-96.4% similarities for 16S rRNA gene and 92.3-93.2% similarities for rpoB' gene, respectively). Several phenotypic characteristics distinguish the strains Gai1-5[ T], SEDH52[T] and SQT7-1[T] from Haloprofundus halophilus NK23[T] and Haloprofundus marisrubri SB9[T]. The average nucleotide identity (ANI) and in silico DNA-DNA hybridization (isDDH) values among the three strains and current Haloprofundus members were in the range of 83.3-88.3% and 27.2-35.7%, respectively, far below the species boundary threshold values. The major polar lipids of three strains were phosphatidic acid (PA), phosphatidylglycerol (PG), phosphatidylglycerol sulphate (PGS), phosphatidylglycerol phosphate methyl ester (PGP-Me), sulfated mannosyl glucosyl diether (S-DGD-1), mannosyl glucosyl diether-phosphatidic acid (DGD-PA) and sulfated mannosyl glucosyl diether-phosphatidic acid (S-DGD-PA). These results showed that strains Gai1-5[T] (= CGMCC 1.16079[T] = JCM 33561[T]), SQT7-1[T] (= CGMCC 1.16063[T] = JCM 33553[ T]) and SEDH52[T] (= CGMCC 1.17434[T]) represented three novel species in the genus Haloprofundus, for which the names Haloprofundus salilacus sp. nov., Haloprofundus salinisoli sp. nov., and Haloprofundus halobius sp. nov. are proposed.},
}
@article {pmid34948099,
year = {2021},
author = {De Falco, M and De Felice, M},
title = {Take a Break to Repair: A Dip in the World of Double-Strand Break Repair Mechanisms Pointing the Gaze on Archaea.},
journal = {International journal of molecular sciences},
volume = {22},
number = {24},
pages = {},
pmid = {34948099},
issn = {1422-0067},
support = {FOE-2019, DSB.AD004.271//CNR project NUTR-AGE/ ; F/200050/01-03/X45//NUTRABEST/ ; },
mesh = {*Archaea/genetics/metabolism ; *DNA Breaks, Double-Stranded ; *DNA Repair ; *DNA, Archaeal/genetics/metabolism ; *Genomic Instability ; Humans ; },
abstract = {All organisms have evolved many DNA repair pathways to counteract the different types of DNA damages. The detection of DNA damage leads to distinct cellular responses that bring about cell cycle arrest and the induction of DNA repair mechanisms. In particular, DNA double-strand breaks (DSBs) are extremely toxic for cell survival, that is why cells use specific mechanisms of DNA repair in order to maintain genome stability. The choice among the repair pathways is mainly linked to the cell cycle phases. Indeed, if it occurs in an inappropriate cellular context, it may cause genome rearrangements, giving rise to many types of human diseases, from developmental disorders to cancer. Here, we analyze the most recent remarks about the main pathways of DSB repair with the focus on homologous recombination. A thorough knowledge in DNA repair mechanisms is pivotal for identifying the most accurate treatments in human diseases.},
}
@article {pmid34927901,
year = {2021},
author = {Otzen, DE and Dueholm, MS and Najarzadeh, Z and Knowles, TPJ and Ruggeri, FS},
title = {In situ Sub-Cellular Identification of Functional Amyloids in Bacteria and Archaea by Infrared Nanospectroscopy.},
journal = {Small methods},
volume = {5},
number = {6},
pages = {e2001002},
doi = {10.1002/smtd.202001002},
pmid = {34927901},
issn = {2366-9608},
support = {8021-00208B//Independent Research Foundation Denmark | Natural Sciences/ ; 6111-00241B//Independent Research Foundation Denmark | Technology and Production/ ; 13351//Villum Foundation/ ; },
mesh = {Amyloid/chemistry/*isolation &amp; purification/*metabolism ; Amyloidogenic Proteins/chemistry/isolation &amp; purification/*metabolism ; Archaea/*metabolism ; Bacteria/*metabolism ; Bacterial Outer Membrane ; Biofilms ; Escherichia coli/metabolism ; Escherichia coli Proteins ; Humans ; Protein Structure, Secondary ; Pseudomonas/metabolism ; },
abstract = {Formation of amyloid structures is originally linked to human disease. However, amyloid materials are found extensively in the animal and bacterial world where they stabilize intra- and extra-cellular environments like biofilms or cell envelopes. To date, functional amyloids have largely been studied using optical microscopy techniques in vivo, or after removal from their biological context for higher-resolution studies in vitro. Furthermore, conventional microscopies only indirectly identify amyloids based on morphology or unspecific amyloid dyes. Here, the high chemical and spatial (≈20 nm) resolution of Infrared Nanospectroscopy (AFM-IR) to investigate functional amyloid from Escherichia coli (curli), Pseudomonas (Fap), and the Archaea Methanosaeta (MspA) in situ is exploited. It is demonstrated that AFM-IR identifies amyloid protein within single intact cells through their cross β-sheet secondary structure, which has a unique spectroscopic signature in the amide I band of protein. Using this approach, nanoscale-resolved chemical images and spectra of purified curli and Methanosaeta cell wall sheaths are provided. The results highlight significant differences in secondary structure between E. coli cells with and without curli. Taken together, these results suggest that AFM-IR is a new and powerful label-free tool for in situ investigations of the biophysical state of functional amyloid and biomolecules in general.},
}
@article {pmid34917055,
year = {2021},
author = {Lu, S and Liu, X and Liu, C and Cheng, G and Zhou, R and Li, Y},
title = {A Review of Ammonia-Oxidizing Archaea and Anaerobic Ammonia-Oxidizing Bacteria in the Aquaculture Pond Environment in China.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {775794},
pmid = {34917055},
issn = {1664-302X},
abstract = {The excessive ammonia produced in pond aquaculture processes cannot be ignored. In this review, we present the distribution and diversity of ammonia-oxidizing archaea (AOA) and anaerobic ammonia-oxidizing bacteria (AnAOB) in the pond environment. Combined with environmental conditions, we analyze the advantages of AOA and AnAOB in aquaculture water treatment and discuss the current situation of pond water treatment engineering involving these microbes. AOA and AnAOB play an important role in the nitrogen removal process of aquaculture pond water, especially in seasonal low temperatures and anoxic sediment layers. Finally, we prospect the application of bioreactors to purify pond aquaculture water using AOA and AnAOB, in autotrophic nitrogen removal, which can reduce the production of greenhouse gases (such as nitrous oxide) and is conducive to the development of environmentally sustainable pond aquaculture.},
}
@article {pmid34910467,
year = {2021},
author = {Wang, Y and Xu, J and Cui, D and Kong, L and Chen, S and Xie, W and Zhang, C},
title = {Classification and Identification of Archaea Using Single-Cell Raman Ejection and Artificial Intelligence: Implications for Investigating Uncultivated Microorganisms.},
journal = {Analytical chemistry},
volume = {93},
number = {51},
pages = {17012-17019},
doi = {10.1021/acs.analchem.1c03495},
pmid = {34910467},
issn = {1520-6882},
mesh = {*Artificial Intelligence ; In Situ Hybridization, Fluorescence ; *Lipids ; Phylogeny ; RNA, Ribosomal, 16S ; },
abstract = {Archaea can produce special cellular components such as polyhydroxyalkanoates, carotenoids, rhodopsin, and ether lipids, which have valuable applications in medicine and green energy production. Most of the archaeal species are uncultivated, posing challenges to investigating their biomarker components and biochemical properties. In this study, we applied Raman spectroscopy to examine the biological characteristics of nine archaeal isolates, including halophilic archaea (Haloferax larsenii, Haloarcula argentinensis, Haloferax mediterranei, Halomicrobium mukohataei, Halomicrobium salinus, Halorussus sp., Natrinema gari), thermophilic archaea (Sulfolobus acidocaldarius), and marine group I (MGI) archaea (Nitrosopumilus maritimus). Linear discriminant analysis of the Raman spectra allowed visualization of significant separations among the nine archaeal isolates. Machine-learning classification models based on support vector machine achieved accuracies of 88-100% when classifying the nine archaeal species. The predicted results were validated by DNA sequencing analysis of cells isolated from the mixture by Raman-activated cell sorting. Raman spectra of uncultured archaea (MGII) were also obtained based on Raman spectroscopy and fluorescence in situ hybridization. The results combining multiple Raman-based techniques indicated that MGII may have the ability to produce lipids distinct from other archaeal species. Our study provides a valuable approach for investigating and classifying archaea, especially uncultured species, at the single-cell level.},
}
@article {pmid34894218,
year = {2022},
author = {Stevens, KM and Hocher, A and Warnecke, T},
title = {Deep Conservation of Histone Variants in Thermococcales Archaea.},
journal = {Genome biology and evolution},
volume = {14},
number = {1},
pages = {},
pmid = {34894218},
issn = {1759-6653},
support = {MC_UP_1102/7/MRC_/Medical Research Council/United Kingdom ; MC-A658-5TY40/MRC_/Medical Research Council/United Kingdom ; },
mesh = {Archaea/genetics/metabolism ; Chromatin ; *Histones/genetics ; Nucleosomes/genetics ; Phylogeny ; *Thermococcales/genetics/metabolism ; },
abstract = {Histones are ubiquitous in eukaryotes where they assemble into nucleosomes, binding and wrapping DNA to form chromatin. One process to modify chromatin and regulate DNA accessibility is the replacement of histones in the nucleosome with paralogous variants. Histones are also present in archaea but whether and how histone variants contribute to the generation of different physiologically relevant chromatin states in these organisms remains largely unknown. Conservation of paralogs with distinct properties can provide prima facie evidence for defined functional roles. We recently revealed deep conservation of histone paralogs with different properties in the Methanobacteriales, but little is known experimentally about these histones. In contrast, the two histones of the model archaeon Thermococcus kodakarensis, HTkA and HTkB, have been examined in some depth, both in vitro and in vivo. HTkA and HTkB exhibit distinct DNA-binding behaviors and elicit unique transcriptional responses when deleted. Here, we consider the evolution of HTkA/B and their orthologs across the order Thermococcales. We find histones with signature HTkA- and HTkB-like properties to be present in almost all Thermococcales genomes. Phylogenetic analysis indicates the presence of one HTkA- and one HTkB-like histone in the ancestor of Thermococcales and long-term maintenance of these two paralogs throughout Thermococcales diversification. Our results support the notion that archaea and eukaryotes have convergently evolved histone variants that carry out distinct adaptive functions. Intriguingly, we also detect more highly diverged histone-fold proteins, related to those found in some bacteria, in several Thermococcales genomes. The functions of these bacteria-type histones remain unknown, but structural modeling suggests that they can form heterodimers with HTkA/B-like histones.},
}
@article {pmid34871608,
year = {2022},
author = {Liu, Y and Wang, Q and Pan, Q and Zhou, X and Peng, Z and Jahng, D and Yang, B and Pan, X},
title = {Ventilation induced evolution pattern of archaea, fungi, bacteria and their potential roles during co-bioevaporation treatment of concentrated landfill leachate and food waste.},
journal = {Chemosphere},
volume = {289},
number = {},
pages = {133122},
doi = {10.1016/j.chemosphere.2021.133122},
pmid = {34871608},
issn = {1879-1298},
mesh = {Archaea/genetics ; Bacteria/genetics ; Bioreactors ; Food ; Fungi/genetics ; *Refuse Disposal ; Waste Disposal Facilities ; *Water Pollutants, Chemical/analysis ; },
abstract = {To obtain a favorable aeration type in co-bioevaporation treatment of concentrated landfill leachate and food waste, and to deeply understand the co-bioevaporation mechanisms, the temporal evolution differences of archaea, fungi and bacteria as well as the related microbial metabolism genes and functional enzymes under intermittent ventilation (IV) and continuous ventilation (CV) were investigated. Results through metagenomics analysis showed that the less sufficient oxygen and longer thermophilic phase in IV stimulated the vigorous growth of archaea, while CV was beneficial for fungal growth. Even genes of carbohydrates and lipids metabolism and ATP-associated enzymes (enzyme 2.7.13.3 and 3.6.4.12), as well as peptidoglycan biosynthesis enzyme (enzyme 3.4.16.4), were more abundant in CV, IV hold better DNA repair ability, higher microbial viability, and less dehydrogenase sensitivity to temperatures due to the critical contribution of Pseudomonas (3.1-45.9%). Furthermore, IV consumed a similar amount of heat for water evaporation with nearly half of the ventilation of CV and was a favorable aeration type in the practical application of co-bioevaporation.},
}
@article {pmid34850144,
year = {2021},
author = {Yen, CY and Lin, MG and Chen, BW and Ng, IW and Read, N and Kabli, AF and Wu, CT and Shen, YY and Chen, CH and Barillà, D and Sun, YJ and Hsiao, CD},
title = {Chromosome segregation in Archaea: SegA- and SegB-DNA complex structures provide insights into segrosome assembly.},
journal = {Nucleic acids research},
volume = {49},
number = {22},
pages = {13150-13164},
pmid = {34850144},
issn = {1362-4962},
support = {BB/M007839/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/R006369/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Adenosine Diphosphate/metabolism ; Adenosine Triphosphatases/chemistry/genetics/metabolism ; Adenosine Triphosphate/metabolism ; Archaeal Proteins/chemistry/*genetics/metabolism ; Chromatin/genetics/metabolism/ultrastructure ; *Chromosome Segregation ; Chromosomes, Archaeal/*genetics ; Crystallography, X-Ray ; DNA, Archaeal/chemistry/*genetics/metabolism ; DNA-Binding Proteins/chemistry/genetics/metabolism ; Microscopy, Electron ; Models, Molecular ; Multiprotein Complexes/chemistry/metabolism/ultrastructure ; Mutation ; Nucleic Acid Conformation ; Protein Binding ; Protein Conformation ; Sulfolobus solfataricus/*genetics/metabolism ; },
abstract = {Genome segregation is a vital process in all organisms. Chromosome partitioning remains obscure in Archaea, the third domain of life. Here, we investigated the SegAB system from Sulfolobus solfataricus. SegA is a ParA Walker-type ATPase and SegB is a site-specific DNA-binding protein. We determined the structures of both proteins and those of SegA-DNA and SegB-DNA complexes. The SegA structure revealed an atypical, novel non-sandwich dimer that binds DNA either in the presence or in the absence of ATP. The SegB structure disclosed a ribbon-helix-helix motif through which the protein binds DNA site specifically. The association of multiple interacting SegB dimers with the DNA results in a higher order chromatin-like structure. The unstructured SegB N-terminus plays an essential catalytic role in stimulating SegA ATPase activity and an architectural regulatory role in segrosome (SegA-SegB-DNA) formation. Electron microscopy results also provide a compact ring-like segrosome structure related to chromosome organization. These findings contribute a novel mechanistic perspective on archaeal chromosome segregation.},
}
@article {pmid34846953,
year = {2022},
author = {Vavilin, VA and Lokshina, LY and Rytov, SV},
title = {Anaerobic oxidation of methane coupled with sulphate reduction: high concentration of methanotrophic archaea might be responsible for low stable isotope fractionation factors in methane.},
journal = {Isotopes in environmental and health studies},
volume = {58},
number = {1},
pages = {44-59},
doi = {10.1080/10256016.2021.2000405},
pmid = {34846953},
issn = {1477-2639},
mesh = {Anaerobiosis ; *Archaea ; Factor VII ; Geologic Sediments ; Isotopes ; *Methane ; Oxidation-Reduction ; Sulfates ; },
abstract = {The changes in δ[13]CH4 and δ[12]C[1]H3[2]H during sulphate-dependent anaerobic oxidation of methane (AOM) were described using dynamic modelling. The batch sulphate-dependent AOM at the nearly linear dynamics of methane oxidation with different enriched cultures originating from three marine sediments was simulated. The traditional Rayleigh equation for carbon and hydrogen stable isotopes in methane was derived from the basic dynamic isotope equation. The general and reduced models, taking into account the reaction stoichiometry and based on balances of chemical elements and their isotopes, describes a redistribution of stable isotope values in the sulphate-dependent AOM process. It was shown that AOM is the first and rate-limiting step in the whole AOM + SR (sulphate reduction) process. The different fractionation factors of carbon and hydrogen isotopes in methane were obtained for three marine sediments. It was concluded that during incubation the highest concentration of methanotrophic archaea might be responsible for the lowest fractionation factors of stable isotopes of carbon and hydrogen in methane. The interpretation of this phenomenon was suggested. Different concentrations of methanotrophic archaea can lead to variations of isotope fractionation factors.},
}
@article {pmid34841354,
year = {2021},
author = {Tan, RSG and Zhou, M and Li, F and Guan, LL},
title = {Identifying active rumen epithelial associated bacteria and archaea in beef cattle divergent in feed efficiency using total RNA-seq.},
journal = {Current research in microbial sciences},
volume = {2},
number = {},
pages = {100064},
pmid = {34841354},
issn = {2666-5174},
abstract = {To date, the role of ruminal epithelial attached microbiota in cattle feed efficiency is undefined. In this study, we aimed to characterize transcriptionally active bacteria and archaea attached to the rumen epithelial wall and to determine whether they differ in cattle with varied feed efficiency. RNA-sequencing was performed to obtain the rumen epithelial transcriptomes from 9 of the most efficient (low RFI) and 9 of the most inefficient (high RFI) animals. The bacteria and archaea 16S rRNA transcripts were identified using an in-house developed pipeline, enriched from filtered reads that did not map to the bovine genome. Archaea from unclassified genera belonging to the Euryarchaeota phylum showed the most activity on the rumen epithelium of low RFI (81.3 ± 1.9%) and high RFI (76.4 ± 3.0%) steers. Bacteria from the Succinivibrionaceae family showed the greatest activity of bacteria on the low RFI (28.7 ± 9.0%) and high RFI (33.9± 8.8%) epithelium. Of the bacterial families, Campylobacteraceae and Neisseriaceae had significantly greater activity on the low RFI epithelium (p < 0.05) and are known to play a role in oxygen scavenging. Greater activity of rumen epithelial attached oxygen scavenging bacteria may provide more optimal feed fermentation conditions, which contributes to high fermentation efficiency in the rumen.},
}
@article {pmid34827555,
year = {2021},
author = {Amin, K and Tranchimand, S and Benvegnu, T and Abdel-Razzak, Z and Chamieh, H},
title = {Glycoside Hydrolases and Glycosyltransferases from Hyperthermophilic Archaea: Insights on Their Characteristics and Applications in Biotechnology.},
journal = {Biomolecules},
volume = {11},
number = {11},
pages = {},
pmid = {34827555},
issn = {2218-273X},
mesh = {*Archaea/enzymology/genetics ; *Glycoside Hydrolases/genetics/metabolism/chemistry ; *Biotechnology ; *Glycosyltransferases/metabolism/genetics/chemistry ; Archaeal Proteins/metabolism/genetics/chemistry ; },
abstract = {Hyperthermophilic Archaea colonizing unnatural habitats of extremes conditions such as volcanoes and deep-sea hydrothermal vents represent an unmeasurable bioresource for enzymes used in various industrial applications. Their enzymes show distinct structural and functional properties and are resistant to extreme conditions of temperature and pressure where their mesophilic homologs fail. In this review, we will outline carbohydrate-active enzymes (CAZymes) from hyperthermophilic Archaea with specific focus on the two largest families, glycoside hydrolases (GHs) and glycosyltransferases (GTs). We will present the latest advances on these enzymes particularly in the light of novel accumulating data from genomics and metagenomics sequencing technologies. We will discuss the contribution of these enzymes from hyperthermophilic Archaea to industrial applications and put the emphasis on newly identifed enzymes. We will highlight their common biochemical and distinct features. Finally, we will overview the areas that remain to be explored to identify novel promising hyperthermozymes.},
}
@article {pmid34825404,
year = {2022},
author = {Coker, OO},
title = {Non-bacteria microbiome (virus, fungi, and archaea) in gastrointestinal cancer.},
journal = {Journal of gastroenterology and hepatology},
volume = {37},
number = {2},
pages = {256-262},
doi = {10.1111/jgh.15738},
pmid = {34825404},
issn = {1440-1746},
mesh = {Archaea ; Fungi ; *Gastrointestinal Microbiome ; *Gastrointestinal Neoplasms/microbiology/prevention &amp; control ; Humans ; Viruses ; },
abstract = {The gastrointestinal tract houses millions of microbes collectively referred to as the gut microbiome. The gut microbes comprise of bacteria, viruses, fungi, archaea, and microscopic eukaryotes, which co-evolved or colonize the gut forming complex symbiotic and mutualistic relationships. A state of homeostasis is required between host and gut microbiome relationship to maintain several host beneficial processes. Alterations in the taxonomic and functional composition of the gut microbes are associated with several human diseases including gastrointestinal cancers. Owed to their overwhelming abundance and ease of characterization, several studies focus on the role of bacteria in gastrointestinal cancers. There is however growing evidence that non-bacteria gut microbes are associated with the pathogenesis of gastrointestinal cancers. This review details the association of non-bacteria gut microbes including fungi, viruses, and archaea and their potential manipulation in the prevention and treatment of human gastrointestinal cancers.},
}
@article {pmid34808316,
year = {2022},
author = {Fan, Q and Fan, X and Fu, P and Li, Y and Zhao, Y and Hua, D},
title = {Anaerobic digestion of wood vinegar wastewater using domesticated sludge: Focusing on the relationship between organic degradation and microbial communities (archaea, bacteria, and fungi).},
journal = {Bioresource technology},
volume = {347},
number = {},
pages = {126384},
doi = {10.1016/j.biortech.2021.126384},
pmid = {34808316},
issn = {1873-2976},
mesh = {Acetic Acid ; Anaerobiosis ; Archaea ; Bacteria ; Bioreactors ; Fungi ; Methane ; Methanol ; *Microbiota ; *Sewage ; Wastewater ; },
abstract = {Thermochemical process of biomass is one of the promising renewable energy technologies; however, the by-product (wood vinegar wastewater) is rich in refractory organics, which is harmful to the environment and inhibits the conversion efficiency of microorganisms. Consequently, the dominant functional microbial communities corresponding to the various substrate were obtained through the continuous domestication, and the relationship between the dominant functional communities and the degradation of organic compounds was comprehensively analyzed. The bacterial community was absolutely dominant (approximately 85%), while archaea and fungi had similar relative abundance. The diversity showed that glucose was not conducive to the development of microbial diversity, while the substrate containing wood vinegar wastewater showed the opposite trend. The functional analysis revealed that the enrichment of bacteria associated with the hydrolysis and acidification of organics increased in the domestication process. Glucose facilitated hydrogen-trophic methanogenesis as the main methanogenic pathway in the methanogenic stage.},
}
@article {pmid34803972,
year = {2021},
author = {Durán-Viseras, A and Sánchez-Porro, C and Ventosa, A},
title = {Genomic Insights Into New Species of the Genus Halomicroarcula Reveals Potential for New Osmoadaptative Strategies in Halophilic Archaea.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {751746},
pmid = {34803972},
issn = {1664-302X},
abstract = {Metagenomic studies on prokaryotic diversity of hypersaline soils from the Odiel saltmarshes, South-west Spain, revealed a high proportion of genomic sequences not related to previously cultivated taxa, that might be related to haloarchaea with a high environmental and nutritional flexibility. In this study, we used a culturomics approach in order to isolate new haloarchaeal microorganisms from these hypersaline soils. Four haloarchaeal strains, designated strains F24A[T], F28, F27[T], and F13[T], phylogenetically related to the genus Halomicroarcula, were isolated and characterized in detail. The phylogenomic tree based on the 100 orthologous single-copy genes present in the genomes of these four strains as well as those of the type strains of the species Halomicroarcula pellucida CECT 7537[T], Halomicroarcula salina JCM 18369[T] and Halomicroarcula limicola JCM 18640[T], that were determined in this study, revealed that these four new isolates clustered on three groups, with strains F24A[T] and F28 within a single cluster, and altogether with the species of Halomicroarcula. Additionally, Orthologous Average Nucleotide Identity (OrthoANI), digital DNA-DNA hybridization (dDDH) and Average Amino-acid Identity (AAI) values, likewise phenotypic characteristics, including their polar lipids profiles, permitted to determine that they represent three new species, for which we propose the names Halomicroarcula rubra sp. nov. (type strain F13[T]), Halomicroarcula nitratireducens sp. nov. (type strain F27[T]) and Halomicroarcula salinisoli sp. nov. (type strain F24A[T]). An in deep comparative genomic analysis of species of the genus Halomicroarcula, including their metabolism, their capability to biosynthesize secondary metabolites and their osmoregulatory adaptation mechanisms was carried out. Although they use a salt-in strategy, the identification of the complete pathways for the biosynthesis of the compatible solutes trehalose and glycine betaine, not identified before in any other haloarchaea, might suggest alternative osmoadaptation strategies for this group. This alternative osmoregulatory mechanism would allow this group of haloarchaea to be versatile and eco-physiologically successful in hypersaline environments and would justify the capability of the species of this genus to grow not only on environments with high salt concentrations [up to 30% (w/v) salts], but also under intermediate to low salinities.},
}
@article {pmid34796612,
year = {2022},
author = {Saghaï, A and Banjeree, S and Degrune, F and Edlinger, A and García-Palacios, P and Garland, G and van der Heijden, MGA and Herzog, C and Maestre, FT and Pescador, DS and Philippot, L and Rillig, MC and Romdhane, S and Hallin, S},
title = {Diversity of archaea and niche preferences among putative ammonia-oxidizing Nitrososphaeria dominating across European arable soils.},
journal = {Environmental microbiology},
volume = {24},
number = {1},
pages = {341-356},
doi = {10.1111/1462-2920.15830},
pmid = {34796612},
issn = {1462-2920},
mesh = {*Ammonia ; *Archaea ; Nitrification ; Oxidation-Reduction ; Phylogeny ; Soil ; Soil Microbiology ; },
abstract = {Archaeal communities in arable soils are dominated by Nitrososphaeria, a class within Thaumarchaeota comprising all known ammonia-oxidizing archaea (AOA). AOA are key players in the nitrogen cycle and defining their niche specialization can help predicting effects of environmental change on these communities. However, hierarchical effects of environmental filters on AOA and the delineation of niche preferences of nitrososphaerial lineages remain poorly understood. We used phylogenetic information at fine scale and machine learning approaches to identify climatic, edaphic and geomorphological drivers of Nitrososphaeria and other archaea along a 3000 km European gradient. Only limited insights into the ecology of the low-abundant archaeal classes could be inferred, but our analyses underlined the multifactorial nature of niche differentiation within Nitrososphaeria. Mean annual temperature, C:N ratio and pH were the best predictors of their diversity, evenness and distribution. Thresholds in the predictions could be defined for C:N ratio and cation exchange capacity. Furthermore, multiple, independent and recent specializations to soil pH were detected in the Nitrososphaeria phylogeny. The coexistence of widespread ecophysiological differences between closely related soil Nitrososphaeria highlights that their ecology is best studied at fine phylogenetic scale.},
}
@article {pmid34790173,
year = {2021},
author = {Trouche, B and Brandt, MI and Belser, C and Orejas, C and Pesant, S and Poulain, J and Wincker, P and Auguet, JC and Arnaud-Haond, S and Maignien, L},
title = {Diversity and Biogeography of Bathyal and Abyssal Seafloor Bacteria and Archaea Along a Mediterranean-Atlantic Gradient.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {702016},
pmid = {34790173},
issn = {1664-302X},
abstract = {Seafloor sediments cover the majority of planet Earth and microorganisms inhabiting these environments play a central role in marine biogeochemical cycles. Yet, description of the biogeography and distribution of sedimentary microbial life is still too sparse to evaluate the relative contribution of processes driving this distribution, such as the levels of drift, connectivity, and specialization. To address this question, we analyzed 210 archaeal and bacterial metabarcoding libraries from a standardized and horizon-resolved collection of sediment samples from 18 stations along a longitudinal gradient from the eastern Mediterranean to the western Atlantic. Overall, we found that biogeographic patterns depended on the scale considered: while at local scale the selective influence of contemporary environmental conditions appeared strongest, the heritage of historic processes through dispersal limitation and drift became more apparent at regional scale, and ended up superseding contemporary influences at inter-regional scale. When looking at environmental factors, the structure of microbial communities was correlated primarily with water depth, with a clear transition between 800 and 1,200 meters below sea level. Oceanic basin, water temperature, and sediment depth were other important explanatory parameters of community structure. Finally, we propose increasing dispersal limitation and ecological drift with sediment depth as a probable factor for the enhanced divergence of deeper horizons communities.},
}
@article {pmid34777272,
year = {2021},
author = {Satari, L and Guillén, A and Latorre-Pérez, A and Porcar, M},
title = {Beyond Archaea: The Table Salt Bacteriome.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {714110},
pmid = {34777272},
issn = {1664-302X},
abstract = {Commercial table salt is a condiment with food preservative properties by decreasing water activity and increasing osmotic pressure. Salt is also a source of halophilic bacteria and archaea. In the present research, the diversity of halotolerant and halophilic microorganisms was studied in six commercial table salts by culture-dependent and culture-independent techniques. Three table salts were obtained from marine origins: Atlantic Ocean, Mediterranean (Ibiza Island), and Odiel marshes (supermarket marine salt). Other salts supplemented with mineral and nutritional ingredients were also used: Himalayan pink, Hawaiian black, and one with dried vegetables known as Viking salt. The results of 16S rRNA gene sequencing reveal that the salts from marine origins display a similar archaeal taxonomy, but with significant variations among genera. Archaeal taxa Halorubrum, Halobacterium, Hallobellus, Natronomonas, Haloplanus, Halonotius, Halomarina, and Haloarcula were prevalent in those three marine salts. Furthermore, the most abundant archaeal genera present in all salts were Natronomonas, Halolamina, Halonotius, Halapricum, Halobacterium, Haloarcula, and uncultured Halobacterales. Sulfitobacter sp. was the most frequent bacteria, represented almost in all salts. Other genera such as Bacillus, Enterococcus, and Flavobacterium were the most frequent taxa in the Viking, Himalayan pink, and black salts, respectively. Interestingly, the genus Salinibacter was detected only in marine-originated salts. A collection of 76 halotolerant and halophilic bacterial and haloarchaeal species was set by culturing on different media with a broad range of salinity and nutrient composition. Comparing the results of 16S rRNA gene metataxonomic and culturomics revealed that culturable bacteria Acinetobacter, Aquibacillus, Bacillus, Brevundimonas, Fictibacillus, Gracilibacillus, Halobacillus, Micrococcus, Oceanobacillus, Salibacterium, Salinibacter, Terribacillus, Thalassobacillus, and also Archaea Haloarcula, Halobacterium, and Halorubrum were identified at least in one sample by both methods. Our results show that salts from marine origins are dominated by Archaea, whereas salts from other sources or salt supplemented with ingredients are dominated by bacteria.},
}
@article {pmid34740642,
year = {2022},
author = {Zou, W and Lang, M and Zhang, L and Liu, B and Chen, X},
title = {Ammonia-oxidizing bacteria rather than ammonia-oxidizing archaea dominate nitrification in a nitrogen-fertilized calcareous soil.},
journal = {The Science of the total environment},
volume = {811},
number = {},
pages = {151402},
doi = {10.1016/j.scitotenv.2021.151402},
pmid = {34740642},
issn = {1879-1026},
mesh = {Ammonia ; *Archaea/genetics ; *Betaproteobacteria ; Ecosystem ; Fertilization ; Nitrification ; Nitrogen ; Oxidation-Reduction ; Phylogeny ; Soil ; Soil Microbiology ; },
abstract = {Microbe-driven nitrification is a key process that affects nitrogen (N) utilization by plants and N loss to the environment in agro-ecosystems. Ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) are important microorganisms that dominate the ammonia oxidation process (the first and rate-limiting step of nitrification). Calcareous soils are widely distributed, accounting for more than 30% of the Earth's land. However, the effects of long-term N fertilization on the potential nitrification rate (PNR) and on AOA and AOB in calcareous soils are poorly understood. In this study, we comprehensively assessed the effects of N application (applied at five rates as urea with 0, 73.5, 105, 136.5 and 250 kg N ha[-1] for 12 years) on soil chemical characteristics, PNR, N use efficiency (NUE) and the community characteristics of AOB and AOA in a calcareous soil. N application rate affected AOB beta diversity more than that of AOA. Compared to no N control, N application significantly decreased the relative abundance of Group I.1b clade A of AOA and Nitrosospira cluster 3a.2 of AOB, but increased Nitrosomonas cluster 7 of AOB. The relative abundance of Nitrosospira cluster 3a.2 of AOB was negatively correlated with PNR. A structural equation model showed a direct effect of N application rate on the content of soil organic matter and nitrate, the alpha and beta diversity of AOA and AOB. Nitrate and AOB beta diversity were the key factors affecting PNR. Overall, the alpha, beta diversity and community composition of AOB contribute more to PNR than AOA in calcareous soils with high organic matter content. Understanding the relationship between the characteristics of AOA and AOB in calcareous soils and PNR will help to improve NUE.},
}
@article {pmid34737728,
year = {2021},
author = {Vázquez-Campos, X and Kinsela, AS and Bligh, MW and Payne, TE and Wilkins, MR and Waite, TD},
title = {Genomic Insights Into the Archaea Inhabiting an Australian Radioactive Legacy Site.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {732575},
pmid = {34737728},
issn = {1664-302X},
abstract = {During the 1960s, small quantities of radioactive materials were co-disposed with chemical waste at the Little Forest Legacy Site (LFLS, Sydney, Australia). The microbial function and population dynamics in a waste trench during a rainfall event have been previously investigated revealing a broad abundance of candidate and potentially undescribed taxa in this iron-rich, radionuclide-contaminated environment. Applying genome-based metagenomic methods, we recovered 37 refined archaeal MAGs, mainly from undescribed DPANN Archaea lineages without standing in nomenclature and 'Candidatus Methanoperedenaceae' (ANME-2D). Within the undescribed DPANN, the newly proposed orders 'Ca. Gugararchaeales', 'Ca. Burarchaeales' and 'Ca. Anstonellales', constitute distinct lineages with a more comprehensive central metabolism and anabolic capabilities within the 'Ca. Micrarchaeota' phylum compared to most other DPANN. The analysis of new and extant 'Ca. Methanoperedens spp.' MAGs suggests metal ions as the ancestral electron acceptors during the anaerobic oxidation of methane while the respiration of nitrate/nitrite via molybdopterin oxidoreductases would have been a secondary acquisition. The presence of genes for the biosynthesis of polyhydroxyalkanoates in most 'Ca. Methanoperedens' also appears to be a widespread characteristic of the genus for carbon accumulation. This work expands our knowledge about the roles of the Archaea at the LFLS, especially, DPANN Archaea and 'Ca. Methanoperedens', while exploring their diversity, uniqueness, potential role in elemental cycling, and evolutionary history.},
}
@article {pmid34725736,
year = {2021},
author = {Sutter, JM and Johnsen, U and Reinhardt, A and Schönheit, P},
title = {Correction to: Pentose degradation in archaea: Halorhabdus species degrade D-xylose, L-arabinose and D-ribose via bacterial-type pathways.},
journal = {Extremophiles : life under extreme conditions},
volume = {25},
number = {5-6},
pages = {527},
doi = {10.1007/s00792-021-01248-7},
pmid = {34725736},
issn = {1433-4909},
}
@article {pmid34721370,
year = {2021},
author = {Liu, LJ and Jiang, Z and Wang, P and Qin, YL and Xu, W and Wang, Y and Liu, SJ and Jiang, CY},
title = {Physiology, Taxonomy, and Sulfur Metabolism of the Sulfolobales, an Order of Thermoacidophilic Archaea.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {768283},
pmid = {34721370},
issn = {1664-302X},
abstract = {The order Sulfolobales (phylum Crenarchaeota) is a group of thermoacidophilic archaea. The first member of the Sulfolobales was discovered in 1972, and current 23 species are validly named under the International Code of Nomenclature of Prokaryotes. The majority of members of the Sulfolobales is obligately or facultatively chemolithoautotrophic. When they grow autotrophically, elemental sulfur or reduced inorganic sulfur compounds are their energy sources. Therefore, sulfur metabolism is the most important physiological characteristic of the Sulfolobales. The functions of some enzymes and proteins involved in sulfur reduction, sulfur oxidation, sulfide oxidation, thiosulfate oxidation, sulfite oxidation, tetrathionate hydrolysis, and sulfur trafficking have been determined. In this review, we describe current knowledge about the physiology, taxonomy, and sulfur metabolism of the Sulfolobales, and note future challenges in this field.},
}
@article {pmid34691003,
year = {2021},
author = {Anchal, and Kaushik, V and Goel, M},
title = {Distribution of Peptidyl-Prolyl Isomerase (PPIase) in the Archaea.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {751049},
pmid = {34691003},
issn = {1664-302X},
abstract = {Cis-trans isomerization of the peptide bond prior to proline is an intrinsically slow process but plays an essential role in protein folding. In vivo cis-trans isomerization reaction is catalyzed by Peptidyl-prolyl isomerase (PPIases), a category of proteins widely distributed among all the three domains of life. The present study is majorly focused on the distribution of different types of PPIases in the archaeal domain. All the three hitherto known families of PPIases (namely FKBP, Cyclophilin and parvulin) were studied to identify the evolutionary conservation across the phylum archaea. The basic function of cyclophilin, FKBP and parvulin has been conserved whereas the sequence alignment suggested variations in each clade. The conserved residues within the predicted motif of each family are unique. The available protein structures of different PPIase across various domains were aligned to ascertain the structural variation in the catalytic site. The structural alignment of native PPIase proteins among various groups suggested that the apo-protein may have variable conformations but when bound to their specific inhibitors, they attain similar active site configuration. This is the first study of its kind which explores the distribution of archaeal PPIases, along with detailed structural and functional analysis of each type of PPIase found in archaea.},
}
@article {pmid34688753,
year = {2022},
author = {Wunderer, M and Markt, R and Lackner, N and Wagner, AO},
title = {The glutamyl tail length of the cofactor F420 in the methanogenic Archaea Methanosarcina thermophila and Methanoculleus thermophilus.},
journal = {The Science of the total environment},
volume = {809},
number = {},
pages = {151112},
doi = {10.1016/j.scitotenv.2021.151112},
pmid = {34688753},
issn = {1879-1026},
mesh = {Methane ; *Methanomicrobiaceae/enzymology ; Methanosarcina/*enzymology ; Riboflavin/analogs &amp; derivatives ; },
abstract = {The cofactor F420 is synthesized by many different organisms and as a redox cofactor, it plays a crucial role in the redox reactions of catabolic and biosynthetic metabolic pathways. It consists of a deazaflavin structure, which is linked via lactate to an oligoglutamate chain, that can vary in length. In the present study, the methanogenic Archaea Methanosarcina thermophila and Methanoculleus thermophilus were cultivated on different carbon sources and their coenzyme F420 composition has been assayed by reversed-phase ion-pair high-performance liquid chromatography with fluorometric detection regarding both, overall cofactor F420 production and distribution of F420 glutamyl tail length. In Methanosarcina thermophila cultivated on methanol, acetate, and a mixture of acetate and methanol, the most abundant cofactors were F420-5 and F420-4, whereby the last digit refers to the number of expressed glutamyl rests. By contrast, in the obligate CO2 reducing Methanoculleus thermophilus the most abundant cofactors were F420-3 and F420-4. In Methanosarcina thermophila, the relative proportions of the expressed F420 tail length changed during batch growth on all three carbon sources. Over time F420-3 and F420-4 decreased while F420-5 and F420-6 increased in their relative proportion in comparison to total F420 content. In contrast, in Methanoculleus thermophilus the relative abundance of the different F420 cofactors remained stable. It was also possible to differentiate the two methanogenic Archaea based on the glutamyl tail length of the cofactor F420. The cofactor F420-5 in concentrations >2% could only be assigned to Methanosarcina thermophila. In all four variants a trend for a positive correlation between the DNA concentration and the total concentration of the cofactor could be shown. Except for the variant Methanosarcinathermophila with acetate as sole carbon source the same could be shown between the concentration of the mcrA gene copy number and the total concentration of the cofactor.},
}
@article {pmid36697601,
year = {2021},
author = {Sumi, T and Harada, K},
title = {Kinetics of the ancestral carbon metabolism pathways in deep-branching bacteria and archaea.},
journal = {Communications chemistry},
volume = {4},
number = {1},
pages = {149},
pmid = {36697601},
issn = {2399-3669},
support = {JP20K05431//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; },
abstract = {The origin of life is believed to be chemoautotrophic, deriving all biomass components from carbon dioxide, and all energy from inorganic redox couples in the environment. The reductive tricarboxylic acid cycle (rTCA) and the Wood-Ljungdahl pathway (WL) have been recognized as the most ancient carbon fixation pathways. The rTCA of the chemolithotrophic Thermosulfidibacter takaii, which was recently demonstrated to take place via an unexpected reverse reaction of citrate synthase, was reproduced using a kinetic network model, and a competition between reductive and oxidative fluxes on rTCA due to an acetyl coenzyme A (ACOA) influx upon acetate uptake was revealed. Avoiding ACOA direct influx into rTCA from WL is, therefore, raised as a kinetically necessary condition to maintain a complete rTCA. This hypothesis was confirmed for deep-branching bacteria and archaea, and explains the kinetic factors governing elementary processes in carbon metabolism evolution from the last universal common ancestor.},
}
@article {pmid34666825,
year = {2021},
author = {Wang, B and Liu, N and Yang, M and Wang, L and Liang, X and Liu, CQ},
title = {Co-occurrence of planktonic bacteria and archaea affects their biogeographic patterns in China's coastal wetlands.},
journal = {Environmental microbiome},
volume = {16},
number = {1},
pages = {19},
pmid = {34666825},
issn = {2524-6372},
support = {U1612441//national natural science foundation of china/ ; 2016YFA0601001//key technologies research and development program/ ; },
abstract = {Planktonic bacteria and archaea play a key role in maintaining ecological functions in aquatic ecosystems; however, their biogeographic patterns and underlying mechanisms have not been well known in coastal wetlands including multiple types and at a large space scale. Therefore, planktonic bacteria and archaea and related environmental factors were investigated in twenty-one wetlands along China's coast to understand the above concerns. The results indicated that planktonic bacteria had different biogeographic pattern from planktonic archaea, and both patterns were not dependent on the wetland's types. Deterministic selection shapes the former's community structure, whereas stochastic processes regulate the latter's, being consistent with the fact that planktonic archaea have a larger niche breadth than planktonic bacteria. Planktonic bacteria and archaea co-occur, and their co-occurrence rather than salinity is more important in shaping their community structure although salinity is found to be a main environmental deterministic factor in the coastal wetland waters. This study highlights the role of planktonic bacteria-archaea co-occurrence on their biogeographic patterns, and thus provides a new insight into studying underlying mechanisms of microbial biogeography in coastal wetlands.},
}
@article {pmid34665251,
year = {2021},
author = {Westoby, M and Nielsen, DA and Gillings, MR and Gumerov, VM and Madin, JS and Paulsen, IT and Tetu, SG},
title = {Strategic traits of bacteria and archaea vary widely within substrate-use groups.},
journal = {FEMS microbiology ecology},
volume = {97},
number = {11},
pages = {},
doi = {10.1093/femsec/fiab142},
pmid = {34665251},
issn = {1574-6941},
mesh = {*Archaea/genetics ; *Bacteria/genetics ; Genome Size ; Phenotype ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Quantitative traits such as maximum growth rate and cell radial diameter are one facet of ecological strategy variation across bacteria and archaea. Another facet is substrate-use pathways, such as iron reduction or methylotrophy. Here, we ask how these two facets intersect, using a large compilation of data for culturable species and examining seven quantitative traits (genome size, signal transduction protein count, histidine kinase count, growth temperature, temperature-adjusted maximum growth rate, cell radial diameter and 16S rRNA operon copy number). Overall, quantitative trait variation within groups of organisms possessing a particular substrate-use pathway was very broad, outweighing differences between substrate-use groups. Although some substrate-use groups had significantly different means for some quantitative traits, standard deviation of quantitative trait values within each substrate-use pathway mostly averaged between 1.6 and 1.8 times larger than standard deviation across group means. Most likely, this wide variation reflects ecological strategy: for example, fast maximum growth rate is likely to express an early successional or copiotrophic strategy, and maximum growth varies widely within most substrate-use pathways. In general, it appears that these quantitative traits express different and complementary information about ecological strategy, compared with substrate use.},
}
@article {pmid34661841,
year = {2022},
author = {Ye, H and Tang, C and Cao, Y and Li, X and Huang, P},
title = {Contribution of ammonia-oxidizing archaea and bacteria to nitrification under different biogeochemical factors in acidic soils.},
journal = {Environmental science and pollution research international},
volume = {29},
number = {12},
pages = {17209-17222},
pmid = {34661841},
issn = {1614-7499},
support = {No. 2017B020236001//Applied Science and Technology Research and Development Project of Guangdong Province, China/ ; No.41877470//General Program of the National Natural Science Foundation of China/ ; No.42077154//General Program of the National Natural Science Foundation of China/ ; },
mesh = {Ammonia/chemistry ; *Archaea/genetics ; Bacteria/genetics ; Ecosystem ; *Nitrification ; Oxidation-Reduction ; Phylogeny ; Soil/chemistry ; Soil Microbiology ; },
abstract = {Nitrification in soils is an essential process that involves archaeal and bacterial ammonia-oxidizers. Despite its importance, the relative contributions of soil factors to the abundance of ammonia-oxidizing archaea (AOA) and bacteria (AOB) and their nitrification performances are seldom discussed. The aim of this study was to determine the effects of AOA and AOB abundance and different environmental conditions (pH, TC, TN, moisture, and temperature) on nitrification performance. The soils of the long-term fertilized tea orchards and forests were sampled in the field, and nitrification experiments were conducted in the laboratory. The acid soils were collected from the field and used in laboratory incubation experiments to calculate the nitrification rate, including the net nitrification rate (NN rate), nitrification potential (NP), and nitrification kinetics. The basic parameters, different forms of nitrogen content, and AOA and AOB amoA gene copies were also analyzed. Compared with the forest soil, the tea orchard soil had a lower pH and higher nitrogen content (p < 0.05). The AOA and AOB abundance in the soils of the forests and tea orchards were pH-dependent. The NN rate and NP had good relationships with AOA or AOB in the forest soil; however, poor relationships were observed in the tea orchard soil. When pH < 4, the performances of AOA and AOB were restricted by pH and the environment, especially in long-term fertilized farmlands. Long-term fertilization can cause soil acidification, which regulates the abundance of AOA and AOB and their nitrifying ability. The soil environment rather than AOA or AOB could control nitrification in long-term fertilized farmlands with a pH below 4. These findings could improve fertilization efficiency and control nutrient runoff in hilly agricultural ecosystems.},
}
@article {pmid34655277,
year = {2022},
author = {Chouhan, BPS and Gade, M and Martinez, D and Toledo-Patino, S and Laurino, P},
title = {Implications of divergence of methionine adenosyltransferase in archaea.},
journal = {FEBS open bio},
volume = {12},
number = {1},
pages = {130-145},
pmid = {34655277},
issn = {2211-5463},
mesh = {*Archaea/genetics/metabolism ; Catalytic Domain ; Methionine ; *Methionine Adenosyltransferase/chemistry/genetics/metabolism ; S-Adenosylmethionine/chemistry ; },
abstract = {Methionine adenosyltransferase (MAT) catalyzes the biosynthesis of S-adenosyl methionine from l-methionine and ATP. MAT enzymes are ancient, believed to share a common ancestor, and are highly conserved in all three domains of life. However, the sequences of archaeal MATs show considerable divergence compared with their bacterial and eukaryotic counterparts. Furthermore, the structural significance and functional significance of this sequence divergence are not well understood. In the present study, we employed structural analysis and ancestral sequence reconstruction to investigate archaeal MAT divergence. We observed that the dimer interface containing the active site (which is usually well conserved) diverged considerably between the bacterial/eukaryotic MATs and archaeal MAT. A detailed investigation of the available structures supports the sequence analysis outcome: The protein domains and subdomains of bacterial and eukaryotic MAT are more similar than those of archaea. Finally, we resurrected archaeal MAT ancestors. Interestingly, archaeal MAT ancestors show substrate specificity, which is lost during evolution. This observation supports the hypothesis of a common MAT ancestor for the three domains of life. In conclusion, we have demonstrated that archaeal MAT is an ideal system for studying an enzyme family that evolved differently in one domain compared with others while maintaining the same catalytic activity.},
}
@article {pmid34650523,
year = {2021},
author = {Bhattarai, B and Bhattacharjee, AS and Coutinho, FH and Goel, RK},
title = {Viruses and Their Interactions With Bacteria and Archaea of Hypersaline Great Salt Lake.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {701414},
pmid = {34650523},
issn = {1664-302X},
abstract = {Viruses play vital biogeochemical and ecological roles by (a) expressing auxiliary metabolic genes during infection, (b) enhancing the lateral transfer of host genes, and (c) inducing host mortality. Even in harsh and extreme environments, viruses are major players in carbon and nutrient recycling from organic matter. However, there is much that we do not yet understand about viruses and the processes mediated by them in the extreme environments such as hypersaline habitats. The Great Salt Lake (GSL) in Utah, United States is a hypersaline ecosystem where the biogeochemical role of viruses is poorly understood. This study elucidates the diversity of viruses and describes virus-host interactions in GSL sediments along a salinity gradient. The GSL sediment virosphere consisted of Haloviruses (32.07 ± 19.33%) and members of families Siphoviridae (39.12 ± 19.8%), Myoviridae (13.7 ± 6.6%), and Podoviridae (5.43 ± 0.64%). Our results demonstrate that salinity alongside the concentration of organic carbon and inorganic nutrients (nitrogen and phosphorus) governs the viral, bacteria, and archaeal diversity in this habitat. Computational host predictions for the GSL viruses revealed a wide host range with a dominance of viruses that infect Proteobacteria, Actinobacteria, and Firmicutes. Identification of auxiliary metabolic genes for photosynthesis (psbA), carbon fixation (rbcL, cbbL), formaldehyde assimilation (SHMT), and nitric oxide reduction (NorQ) shed light on the roles played by GSL viruses in biogeochemical cycles of global relevance.},
}
@article {pmid34628131,
year = {2021},
author = {Castro, I and Costa, H and Turgeman-Grott, I and Allers, T and Mendo, S and Caetano, T},
title = {The lanthipeptide biosynthetic clusters of the domain Archaea.},
journal = {Microbiological research},
volume = {253},
number = {},
pages = {126884},
doi = {10.1016/j.micres.2021.126884},
pmid = {34628131},
issn = {1618-0623},
mesh = {*Archaea/genetics ; Eukaryota ; Euryarchaeota ; *Peptides/genetics ; },
abstract = {Research on Archaea's secondary metabolites is still lagging behind that of Bacteria and Eukarya. Our goal was to contribute to this knowledge gap by analyzing the lanthipeptide's clusters in Archaea. As previously proposed, Archaea encodes only class II synthetases (LanMs), which we found to be confined to the class Halobacteria (also known as haloarchaea). In total, we analyzed the phylogeny and the domains of 42 LanMs. Four types were identified, and the majority of them belong to the CCG group due to their cyclization domain, which includes LanMs of Cyanobacteria. Putative cognate peptides were predicted for most of LanMs and are a very diverse group of molecules that share a Kx(Y/F)(D/E)xx(F/Y) motif in their leader peptides. According to their homology, some of them were categorized into subfamilies, including Halolancins, Haladacins, Haloferaxcins and Halobiforcins. Many LanM genes were associated with mobile genetic elements, and their vicinities mainly encode ABC and MFS transporters, tailoring enzymes and uncharacterized proteins. Our results suggest that the biosynthesis of lanthipeptides in haloarchaea can entail distinct enzymology that must lead to the production of peptides with novel structures and unpredicted biological and ecological roles. Finally, an Haloferax mediterranei knockout, lacking its three lanM genes, was generated, and it was concluded that its antimicrobial activity is not primarily related to the production of lanthipeptides.},
}
@article {pmid34606606,
year = {2021},
author = {Payne, LJ and Todeschini, TC and Wu, Y and Perry, BJ and Ronson, CW and Fineran, PC and Nobrega, FL and Jackson, SA},
title = {Identification and classification of antiviral defence systems in bacteria and archaea with PADLOC reveals new system types.},
journal = {Nucleic acids research},
volume = {49},
number = {19},
pages = {10868-10878},
pmid = {34606606},
issn = {1362-4962},
mesh = {Adenosine Triphosphatases/genetics/metabolism ; Antibiosis/*genetics ; Archaea/classification/*genetics/metabolism/virology ; Archaeal Proteins/*genetics/metabolism ; Bacteria/classification/*genetics/metabolism/virology ; Bacterial Proteins/*genetics/metabolism ; Bacteriophages/*genetics/growth &amp; development ; CRISPR-Cas Systems ; DNA Helicases/genetics/metabolism ; DNA Modification Methylases/genetics/metabolism ; Markov Chains ; Phylogeny ; *Software ; Terminology as Topic ; },
abstract = {To provide protection against viral infection and limit the uptake of mobile genetic elements, bacteria and archaea have evolved many diverse defence systems. The discovery and application of CRISPR-Cas adaptive immune systems has spurred recent interest in the identification and classification of new types of defence systems. Many new defence systems have recently been reported but there is a lack of accessible tools available to identify homologs of these systems in different genomes. Here, we report the Prokaryotic Antiviral Defence LOCator (PADLOC), a flexible and scalable open-source tool for defence system identification. With PADLOC, defence system genes are identified using HMM-based homologue searches, followed by validation of system completeness using gene presence/absence and synteny criteria specified by customisable system classifications. We show that PADLOC identifies defence systems with high accuracy and sensitivity. Our modular approach to organising the HMMs and system classifications allows additional defence systems to be easily integrated into the PADLOC database. To demonstrate application of PADLOC to biological questions, we used PADLOC to identify six new subtypes of known defence systems and a putative novel defence system comprised of a helicase, methylase and ATPase. PADLOC is available as a standalone package (https://github.com/padlocbio/padloc) and as a webserver (https://padloc.otago.ac.nz).},
}
@article {pmid34578152,
year = {2021},
author = {Krawczyk, A and Salamon, D and Kowalska-Duplaga, K and Bogiel, T and Gosiewski, T},
title = {Association of Fungi and Archaea of the Gut Microbiota with Crohn's Disease in Pediatric Patients-Pilot Study.},
journal = {Pathogens (Basel, Switzerland)},
volume = {10},
number = {9},
pages = {},
pmid = {34578152},
issn = {2076-0817},
support = {2019/33/N/NZ5/00698//National Science Center in Poland/ ; },
abstract = {The composition of bacteria is often altered in Crohn's disease (CD), but its connection to the disease is not fully understood. Gut archaea and fungi have recently been suggested to play a role as well. In our study, the presence and number of selected species of fungi and archaea in pediatric patients with CD and healthy controls were evaluated. Stool samples were collected from children with active CD (n = 54), non-active CD (n = 37) and control subjects (n = 33). The prevalence and the number of selected microorganisms were assessed by real-time PCR. The prevalence of Candida tropicalis was significantly increased in active CD compared to non-active CD and the control group (p = 0.011 and p = 0.036, respectively). The number of Malassezia spp. cells was significantly lower in patients with active CD compared to the control group, but in non-active CD, a significant increase was observed (p = 0.005 and p = 0.020, respectively). There were no statistically significant differences in the colonization by archaea. The obtained results indicate possible correlations with the course of the CD; however, further studies of the entire archeobiome and the mycobiome are necessary in order to receive a complete picture.},
}
@article {pmid34575103,
year = {2021},
author = {Merkel, AY and Chernyh, NA and Pimenov, NV and Bonch-Osmolovskaya, EA and Slobodkin, AI},
title = {Diversity and Metabolic Potential of the Terrestrial Mud Volcano Microbial Community with a High Abundance of Archaea Mediating the Anaerobic Oxidation of Methane.},
journal = {Life (Basel, Switzerland)},
volume = {11},
number = {9},
pages = {},
pmid = {34575103},
issn = {2075-1729},
support = {. 17-74-30025//Russian Science Foundation/ ; n/a//Ministry of Science and Higher Education of the Russian Federation/ ; },
abstract = {Terrestrial mud volcanoes (TMVs) are important natural sources of methane emission. The microorganisms inhabiting these environments remain largely unknown. We studied the phylogenetic composition and metabolic potential of the prokaryotic communities of TMVs located in the Taman Peninsula, Russia, using a metagenomic approach. One of the examined sites harbored a unique community with a high abundance of anaerobic methane-oxidizing archaea belonging to ANME-3 group (39% of all 16S rRNA gene reads). The high number of ANME-3 archaea was confirmed by qPCR, while the process of anaerobic methane oxidation was demonstrated by radioisotopic experiments. We recovered metagenome-assembled genomes (MAGs) of archaeal and bacterial community members and analyzed their metabolic capabilities. The ANME-3 MAG contained a complete set of genes for methanogenesis as well as of ribosomal RNA and did not encode proteins involved in dissimilatory nitrate or sulfate reduction. The presence of multiheme c-type cytochromes suggests that ANME-3 can couple methane oxidation with the reduction of metal oxides or with the interspecies electron transfer to a bacterial partner. The bacterial members of the community were mainly represented by autotrophic, nitrate-reducing, sulfur-oxidizing bacteria, as well as by fermentative microorganisms. This study extends the current knowledge of the phylogenetic and metabolic diversity of prokaryotes in TMVs and provides a first insight into the genomic features of ANME-3 archaea.},
}
@article {pmid34543104,
year = {2022},
author = {Weidenbach, K and Gutt, M and Cassidy, L and Chibani, C and Schmitz, RA},
title = {Small Proteins in Archaea, a Mainly Unexplored World.},
journal = {Journal of bacteriology},
volume = {204},
number = {1},
pages = {e0031321},
pmid = {34543104},
issn = {1098-5530},
mesh = {Archaea/genetics/*metabolism ; Archaeal Proteins/genetics/*metabolism ; Gene Expression Regulation, Archaeal/*physiology ; Genome, Archaeal ; },
abstract = {In recent years, increasing numbers of small proteins have moved into the focus of science. Small proteins have been identified and characterized in all three domains of life, but the majority remains functionally uncharacterized, lack secondary structure, and exhibit limited evolutionary conservation. While quite a few have already been described for bacteria and eukaryotic organisms, the amount of known and functionally analyzed archaeal small proteins is still very limited. In this review, we compile the current state of research, show strategies for systematic approaches for global identification of small archaeal proteins, and address selected functionally characterized examples. Besides, we document exemplarily for one archaeon the tool development and optimization to identify small proteins using genome-wide approaches.},
}
@article {pmid34535658,
year = {2021},
author = {Blombach, F and Fouqueau, T and Matelska, D and Smollett, K and Werner, F},
title = {Promoter-proximal elongation regulates transcription in archaea.},
journal = {Nature communications},
volume = {12},
number = {1},
pages = {5524},
pmid = {34535658},
issn = {2041-1723},
support = {/WT_/Wellcome Trust/United Kingdom ; WT 207446/Z/17/Z/WT_/Wellcome Trust/United Kingdom ; },
mesh = {CRISPR-Cas Systems/genetics ; DNA/metabolism ; DNA-Directed RNA Polymerases/metabolism ; Oxidative Stress/genetics ; *Promoter Regions, Genetic ; Regression Analysis ; Sulfolobus solfataricus/*genetics/growth &amp; development ; *Transcription Elongation, Genetic ; },
abstract = {Recruitment of RNA polymerase and initiation factors to the promoter is the only known target for transcription activation and repression in archaea. Whether any of the subsequent steps towards productive transcription elongation are involved in regulation is not known. We characterised how the basal transcription machinery is distributed along genes in the archaeon Saccharolobus solfataricus. We discovered a distinct early elongation phase where RNA polymerases sequentially recruit the elongation factors Spt4/5 and Elf1 to form the transcription elongation complex (TEC) before the TEC escapes into productive transcription. TEC escape is rate-limiting for transcription output during exponential growth. Oxidative stress causes changes in TEC escape that correlate with changes in the transcriptome. Our results thus establish that TEC escape contributes to the basal promoter strength and facilitates transcription regulation. Impaired TEC escape coincides with the accumulation of initiation factors at the promoter and recruitment of termination factor aCPSF1 to the early TEC. This suggests two possible mechanisms for how TEC escape limits transcription, physically blocking upstream RNA polymerases during transcription initiation and premature termination of early TECs.},
}
@article {pmid34531846,
year = {2021},
author = {Lin, T and Zhang, L and Wu, M and Jiang, D and Li, Z and Yang, Z},
title = {Repair of Hypoxanthine in DNA Revealed by DNA Glycosylases and Endonucleases From Hyperthermophilic Archaea.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {736915},
pmid = {34531846},
issn = {1664-302X},
abstract = {Since hyperthermophilic Archaea (HA) thrive in high-temperature environments, which accelerate the rates of deamination of base in DNA, their genomic stability is facing a severe challenge. Hypoxanthine (Hx) is one of the common deaminated bases in DNA. Generally, replication of Hx in DNA before repaired causes AT → GC mutation. Biochemical data have demonstrated that 3-methyladenine DNA glycosylase II (AlkA) and Family V uracil DNA glycosylase (UDG) from HA could excise Hx from DNA, thus triggering a base excision repair (BER) process for Hx repair. Besides, three endonucleases have been reported from HA: Endonuclease V (EndoV), Endonuclease Q (EndoQ), and Endonuclease NucS (EndoNucS), capable of cleaving Hx-containing DNA, thereby providing alternative pathways for Hx repair. Both EndoV and EndoQ could cleave one DNA strand with Hx, thus forming a nick and further initiating an alternative excision repair (AER) process for the follow-up repair. By comparison, EndoNucS cleaves both strands of Hx-containing DNA in a restriction endonuclease manner, thus producing a double-stranded break (DSB). This created DSB might be repaired by homologous recombination (HR) or by a combination activity of DNA polymerase (DNA pol), flap endonuclease 1 (FEN1), and DNA ligase (DNA lig). Herein, we reviewed the most recent advances in repair of Hx in DNA triggered by DNA glycosylases and endonucleases from HA, and proposed future research directions.},
}
@article {pmid34526983,
year = {2021},
author = {Franke, JD and Fuerst, JA and Poole, AM},
title = {Editorial: Structure, Function and Evolution of Complex Cellular Organization in Bacteria and Archaea.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {751416},
pmid = {34526983},
issn = {1664-302X},
}
@article {pmid34516368,
year = {2021},
author = {Pallen, MJ},
title = {The status Candidatus for uncultured taxa of Bacteria and Archaea: SWOT analysis.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {71},
number = {9},
pages = {},
pmid = {34516368},
issn = {1466-5034},
mesh = {*Archaea/classification ; *Bacteria/classification ; Phylogeny ; Terminology as Topic ; },
abstract = {The status Candidatus was introduced to bacterial taxonomy in the 1990s to accommodate uncultured taxa defined by analyses of DNA sequences. Here I review the strengths, weaknesses, opportunities and threats (SWOT) associated with the status Candidatus in the light of a quarter century of use, twinned with recent developments in bacterial taxonomy and sequence-based taxonomic discovery. Despite ambiguities as to its scope, philosophical objections to its use and practical problems in implementation, the status Candidatus has now been applied to over 1000 taxa and has been widely adopted by journals and databases. Although lacking priority under the International Code for Nomenclature of Prokaryotes, many Candidatus names have already achieved de facto standing in the academic literature and in databases via description of a taxon in a peer-reviewed publication, alongside deposition of a genome sequence and there is a clear path to valid publication of such names on culture. Continued and increased use of Candidatus names provides an alternative to the potential upheaval that might accompany creation of a new additional code of nomenclature and provides a ready solution to the urgent challenge of naming many thousands of newly discovered but uncultured species.},
}
@article {pmid34509601,
year = {2021},
author = {Kumar, V and Singh, B and van Belkum, MJ and Diep, DB and Chikindas, ML and Ermakov, AM and Tiwari, SK},
title = {Halocins, natural antimicrobials of Archaea: Exotic or special or both?.},
journal = {Biotechnology advances},
volume = {53},
number = {},
pages = {107834},
doi = {10.1016/j.biotechadv.2021.107834},
pmid = {34509601},
issn = {1873-1899},
mesh = {Anti-Bacterial Agents ; *Anti-Infective Agents/pharmacology ; *Archaea ; Sodium Chloride ; },
abstract = {Haloarchaea are adapted to survive under extreme saline conditions by accumulating osmolytes and salts to counteract the high osmotic pressure in their habitats. As a consequence, their proteins have evolved to remain active, or even most active, at very high ionic strength. Halocins are proteinaceous antimicrobial substances that are ribosomally-synthesized by haloarchaea and they provide the producers an advantage in the competition for nutrients and ecological niches. These antimicrobials are stable at high temperature, elevated salt concentrations, and alkaline pH conditions. These properties have endowed them with great potential in diverse biotechnological applications, which involve extreme processing conditions (such as high salt concentrations, high pressure, or high temperatures). They kill target cells by inhibition of Na[+]/H[+] antiporter in the membrane or modification/disruption of the cell membrane leading to cell lysis. In general, the taxonomy of haloarchaea and their typical phenotypic and genotypic characteristics are well studied; however, information regarding their halocins, especially aspects related to genetics, biosynthetic pathways, mechanism of action, and structure-function relationship is very limited. A few studies have demonstrated the potential applications of halocins in the preservation of salted food products and brine-cured hides in leather industries, protecting the myocardium from ischemia and reperfusion injury, as well as from life-threatening diseases such as cardiac arrest and cancers. In recent years, genome mining has been an essential tool to decipher the genetic basis of halocin biosynthesis. Nevertheless, this is likely the tip of the iceberg as genome analyses have revealed many putative halocins in databases waiting for further investigation. Identification and characterization of this source of halocins may lead to antimicrobials for future therapeutics and/or food preservation. Hence, the present review analyzes different aspects of halocins such as biosynthesis, mechanism of action against target cells, and potential biotechnological applications.},
}
@article {pmid37938279,
year = {2021},
author = {Thomas, CM and Taib, N and Gribaldo, S and Borrel, G},
title = {Comparative genomic analysis of Methanimicrococcus blatticola provides insights into host adaptation in archaea and the evolution of methanogenesis.},
journal = {ISME communications},
volume = {1},
number = {1},
pages = {47},
pmid = {37938279},
issn = {2730-6151},
support = {ANR-19-CE02-0005-01//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-16-CE02-0005-01//Agence Nationale de la Recherche (French National Research Agency)/ ; },
abstract = {Other than the Methanobacteriales and Methanomassiliicoccales, the characteristics of archaea that inhabit the animal microbiome are largely unknown. Methanimicrococcus blatticola, a member of the Methanosarcinales, currently reunites two unique features within this order: it is a colonizer of the animal digestive tract and can only reduce methyl compounds with H2 for methanogenesis, a increasingly recognized metabolism in the archaea and whose origin remains debated. To understand the origin of these characteristics, we have carried out a large-scale comparative genomic analysis. We infer the loss of more than a thousand genes in M. blatticola, by far the largest genome reduction across all Methanosarcinales. These include numerous elements for sensing the environment and adapting to more stable gut conditions, as well as a significant remodeling of the cell surface components likely involved in host and gut microbiota interactions. Several of these modifications parallel those previously observed in phylogenetically distant archaea and bacteria from the animal microbiome, suggesting large-scale convergent mechanisms of adaptation to the gut. Strikingly, M. blatticola has lost almost all genes coding for the H4MPT methyl branch of the Wood-Ljungdahl pathway (to the exception of mer), a phenomenon never reported before in any member of Class I or Class II methanogens. The loss of this pathway illustrates one of the evolutionary processes that may have led to the emergence of methyl-reducing hydrogenotrophic methanogens, possibly linked to the colonization of organic-rich environments (including the animal gut) where both methyl compounds and hydrogen are abundant.},
}
@article {pmid34491083,
year = {2021},
author = {Li, L and Zhang, W and Zhang, S and Song, L and Sun, Q and Zhang, H and Xiang, H and Dong, X},
title = {Bacteria and Archaea Synergistically Convert Glycine Betaine to Biogenic Methane in the Formosa Cold Seep of the South China Sea.},
journal = {mSystems},
volume = {6},
number = {5},
pages = {e0070321},
pmid = {34491083},
issn = {2379-5077},
support = {2018YFC0310801//Ministry of Science and Technology of the People's Republic of China (MOST)/ ; },
abstract = {Cold seeps are globally widespread seafloor ecosystems that feature abundant methane production and flourishing chemotrophic benthic communities. Chemical evidence indicates that cold seep methane is largely biogenic; however, the primary methane-producing organisms and associated pathways involved in methanogenesis remain elusive. This work detected methane production when glycine betaine (GBT) or trimethylamine (TMA) was added to the sediment microcosms of the Formosa cold seep, South China Sea. The methane production was suppressed by antibiotic inhibition of bacteria, while GBT was accumulated. This suggests that the widely used osmoprotectant GBT could be converted to cold seep biogenic methane via the synergistic activity of bacteria and methanogenic archaea because archaea are not sensitive to antibiotics and no bacteria are known to produce ample methane (mM). 16S rRNA gene diversity analyses revealed that the predominant bacterial and archaeal genera in the GBT-amended methanogenic microcosms included Oceanirhabdus and Methanococcoides. Moreover, metagenomic analyses detected the presence of grdH and mtgB genes that are involved in GBT reduction and demethylation, respectively. Two novel species were obtained, including bacterium Oceanirhabdus seepicola, which reduces GBT to TMA, and a methanogenic archaeon, Methanococcoides seepicolus, which produces methane from TMA and GBT. The two strains reconstituted coculture efficiently converted GBT to methane at 18°C; however, at 4°C addition of dimethylglycine (DMG), the GBT demethylation product, was necessary. Therefore, this work demonstrated that GBT is the precursor not only of the biogenic methane but also of the cryoprotectant DMG to the microorganisms at the Formosa cold seep. IMPORTANCE Numerous cold seeps have been found in global continental margins where methane is enriched in pore waters that are forced upward from sediments. Therefore, high concerns have been focused on the methane-producing organisms and the metabolic pathways in these environments because methane is a potent greenhouse gas. In this study, GBT was identified as the main precursor for methane in the Formosa cold seep of the South China Sea. Further, synergism of bacteria and methanogenic archaea was identified in GBT conversion to methane via the GBT reduction pathway, while methanogen-mediated GBT demethylation to methane was also observed. In addition, GBT-demethylated product dimethyl glycine acted as a cryoprotectant that promoted the cold seep microorganisms at cold temperatures. GBT is an osmoprotectant that is widely used by marine organisms, and therefore, the GBT-derived methanogenic pathway reported here could be widely distributed among global cold seep environments.},
}
@article {pmid34490397,
year = {2021},
author = {Hu, D and Yang, J and Qi, Y and Li, B and Li, K and Mok, KM},
title = {Metagenomic Analysis of Fecal Archaea, Bacteria, Eukaryota, and Virus in Przewalski's Horses Following Anthelmintic Treatment.},
journal = {Frontiers in veterinary science},
volume = {8},
number = {},
pages = {708512},
pmid = {34490397},
issn = {2297-1769},
abstract = {Intestinal microbiota is involved in immune response and metabolism of the host. The frequent use of anthelmintic compounds for parasite expulsion causes disturbance to the equine intestinal microbiota. However, most studies were on the effects of such treatment on the intestinal bacterial microbes; none is on the entire microbial community including archaea and eukaryotic and viral community in equine animals. This study is the first to explore the differences of the microbial community composition and structure in Przewalski's horses prior to and following anthelmintic treatment, and to determine the corresponding changes of their functional attributes based on metagenomic sequencing. Results showed that in archaea, the methanogen of Euryarchaeota was the dominant phylum. Under this phylum, anthelmintic treatment increased the Methanobrevibacter genus and decreased the Methanocorpusculum genus and two other dominant archaea species, Methanocorpusculum labreanum and Methanocorpusculum bavaricum. In bacteria, Firmicutes and Bacteroidetes were the dominant phyla. Anthelmintic treatment increased the genera of Clostridium and Eubacterium and decreased those of Bacteroides and Prevotella and dominant bacteria species. These altered genera were associated with immunity and digestion. In eukaryota, anthelmintic treatment also changed the genera related to digestion and substantially decreased the relative abundances of identified species. In virus, anthelmintic treatment increased the genus of unclassified_d__Viruses and decreased those of unclassified_f__Siphoviridae and unclassified_f__Myoviridae. Most of the identified viral species were classified into phage, which were more sensitive to anthelmintic treatment than other viruses. Furthermore, anthelmintic treatment was found to increase the number of pathogens related to some clinical diseases in horses. The COG and KEGG function analysis showed that the intestinal microbiota of Przewalski's horse mainly participated in the carbohydrate and amino acid metabolism. The anthelmintic treatment did not change their overall function; however, it displaced the population of the functional microbes involved in each function or pathway. These results provide a complete view on the changes caused by anthelmintic treatment in the intestinal microbiota of the Przewalski's horses.},
}
@article {pmid34489912,
year = {2021},
author = {Makarova, KS and Wolf, YI and Karamycheva, S and Koonin, EV},
title = {A Unique Gene Module in Thermococcales Archaea Centered on a Hypervariable Protein Containing Immunoglobulin Domains.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {721392},
pmid = {34489912},
issn = {1664-302X},
abstract = {Molecular mechanisms involved in biological conflicts and self vs nonself recognition in archaea remain poorly characterized. We apply phylogenomic analysis to identify a hypervariable gene module that is widespread among Thermococcales. These loci consist of an upstream gene coding for a large protein containing several immunoglobulin (Ig) domains and unique combinations of downstream genes, some of which also contain Ig domains. In the large Ig domain containing protein, the C-terminal Ig domain sequence is hypervariable, apparently, as a result of recombination between genes from different Thermococcales. To reflect the hypervariability, we denote this gene module VARTIG (VARiable Thermococcales IG). The overall organization of the VARTIG modules is similar to the organization of Polymorphic Toxin Systems (PTS). Archaeal genomes outside Thermococcales encode a variety of Ig domain proteins, but no counterparts to VARTIG and no Ig domains with comparable levels of variability. The specific functions of VARTIG remain unknown but the identified features of this system imply three testable hypotheses: (i) involvement in inter-microbial conflicts analogous to PTS, (ii) role in innate immunity analogous to the vertebrate complement system, and (iii) function in self vs nonself discrimination analogous to the vertebrate Major Histocompatibility Complex. The latter two hypotheses seem to be of particular interest given the apparent analogy to the vertebrate immunity.},
}
@article {pmid34487604,
year = {2022},
author = {Haiming, T and Chao, L and Kaikai, C and Lihong, S and Li, W and Weiyan, L and Xiaoping, X and Ke, W},
title = {Effects of short-term soil tillage practice on activity and community structure of ammonia-oxidizing bacteria and archaea under the double-cropping rice field.},
journal = {Journal of applied microbiology},
volume = {132},
number = {2},
pages = {1307-1318},
doi = {10.1111/jam.15289},
pmid = {34487604},
issn = {1365-2672},
support = {//National Natural Science Foundation of China/ ; 2019JJ10003//Innovative Research Groups of the Natural Science Foundation of Hunan Province/ ; },
mesh = {Ammonia ; Archaea/genetics ; *Betaproteobacteria ; Nitrification ; *Oryza ; Oxidation-Reduction ; Phylogeny ; Soil ; Soil Microbiology ; },
abstract = {AIMS: The potential nitrification activity (PNA), population size and community composition of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) in paddy soil from a short-term (5 years) tillage field experiment conducted at tillering stage of late rice were investigated using the shaken slurry method and quantitative real-time polymerase chain reaction.<br><br>METHODS AND RESULTS: The experiment included four tillage treatments: conventional tillage with crop residue incorporation (CT), rotary tillage with crop residue incorporation (RT), no-tillage with crop residue returning (NT) and rotary tillage with all crop residues removed as a control (RTO). The results showed that PNA in paddy soil of CT, RT and NT treatments was higher than that of RTO treatment, and the abundance of AOA and AOB was much higher in paddy soil of CT, RT and NT treatments than RTO treatment. Meanwhile, PNA and the abundance of AOB and AOA in paddy soil were greatly enhanced by combined application of tillage and crop residue, whereas PNA and the abundance of AOB and AOA in paddy soil were decreased by combined application of no-tillage and crop residue. Moreover, PNA was closely correlated with the abundance and community structure of AOB rather than AOA. The results also showed that PNA and the population sizes of AOB and AOA in crop incorporation treatments were higher than that of crop residue removed treatment. Cluster and redundancy analyses indicated that crop residue effect played a more important role in shaping AOA community structure compared to short-term tillage management.<br><br>CONCLUSIONS: The results indicated that AOB rather than AOA functionally dominated ammonia oxidation in the double-cropping rice paddy soil, the activities of AOB and AOA were increased and the community structure was also changed under the combination of conventional tillage, rotary tillage and crop residue condition.<br><br>The activity and community structure of AOB and AOA, which were affected by the combination of tillage and crop residue managements, play an important role in cycling of nitrogen.},
}
@article {pmid34464803,
year = {2022},
author = {Cai, M and Yin, X and Tang, X and Zhang, C and Zheng, Q and Li, M},
title = {Metatranscriptomics reveals different features of methanogenic archaea among global vegetated coastal ecosystems.},
journal = {The Science of the total environment},
volume = {802},
number = {},
pages = {149848},
doi = {10.1016/j.scitotenv.2021.149848},
pmid = {34464803},
issn = {1879-1026},
mesh = {*Archaea/genetics ; *Ecosystem ; Methane ; Methanosarcinaceae ; Methanosarcinales ; Phylogeny ; },
abstract = {Vegetated coastal ecosystems (VCEs; i.e., mangroves, saltmarshes, and seagrasses) represent important sources of natural methane emission. Despite recent advances in the understanding of novel taxa and pathways associated with methanogenesis in these ecosystems, the key methanogenic players and the contribution of different substrates to methane formation remain elusive. Here, we systematically investigate the community and activity of methanogens using publicly available metatranscriptomes at a global scale together with our in-house metatranscriptomic dataset. Taxonomic profiling reveals that 13 groups of methanogenic archaea were transcribed in the investigated VCEs, and they were predominated by Methanosarcinales. Among these VCEs, methanogens exhibited all the three known methanogenic pathways in some mangrove sediments, where methylotrophic methanogens Methanosarcinales/Methanomassiliicoccales grew on diverse methyl compounds and coexisted with hydrogenotrophic (mainly Methanomicrobiales) and acetoclastic (mainly Methanothrix) methanogens. Contrastingly, the predominant methanogenic pathway in saltmarshes and seagrasses was constrained to methylotrophic methanogenesis. These findings reveal different archaeal methanogens in VCEs and suggest the potentially distinct methanogenesis contributions in these VCEs to the global warming.},
}
@article {pmid34442741,
year = {2021},
author = {Koirala, A and Brözel, VS},
title = {Phylogeny of Nitrogenase Structural and Assembly Components Reveals New Insights into the Origin and Distribution of Nitrogen Fixation across Bacteria and Archaea.},
journal = {Microorganisms},
volume = {9},
number = {8},
pages = {},
pmid = {34442741},
issn = {2076-2607},
abstract = {The phylogeny of nitrogenase has only been analyzed using the structural proteins NifHDK. As nifHDKENB has been established as the minimum number of genes necessary for in silico prediction of diazotrophy, we present an updated phylogeny of diazotrophs using both structural (NifHDK) and cofactor assembly proteins (NifENB). Annotated Nif sequences were obtained from InterPro from 963 culture-derived genomes. Nif sequences were aligned individually and concatenated to form one NifHDKENB sequence. Phylogenies obtained using PhyML, FastTree, RapidNJ, and ASTRAL from individuals and concatenated protein sequences were compared and analyzed. All six genes were found across the Actinobacteria, Aquificae, Bacteroidetes, Chlorobi, Chloroflexi, Cyanobacteria, Deferribacteres, Firmicutes, Fusobacteria, Nitrospira, Proteobacteria, PVC group, and Spirochaetes, as well as the Euryarchaeota. The phylogenies of individual Nif proteins were very similar to the overall NifHDKENB phylogeny, indicating the assembly proteins have evolved together. Our higher resolution database upheld the three cluster phylogeny, but revealed undocumented horizontal gene transfers across phyla. Only 48% of the 325 genera containing all six nif genes are currently supported by biochemical evidence of diazotrophy. In addition, this work provides reference for any inter-phyla comparison of Nif sequences and a quality database of Nif proteins that can be used for identifying new Nif sequences.},
}
@article {pmid34436605,
year = {2021},
author = {Martinez-Gutierrez, CA and Aylward, FO},
title = {Phylogenetic Signal, Congruence, and Uncertainty across Bacteria and Archaea.},
journal = {Molecular biology and evolution},
volume = {38},
number = {12},
pages = {5514-5527},
pmid = {34436605},
issn = {1537-1719},
mesh = {*Archaea/genetics ; *Bacteria/genetics ; Biological Evolution ; Phylogeny ; Uncertainty ; },
abstract = {Reconstruction of the Tree of Life is a central goal in biology. Although numerous novel phyla of bacteria and archaea have recently been discovered, inconsistent phylogenetic relationships are routinely reported, and many inter-phylum and inter-domain evolutionary relationships remain unclear. Here, we benchmark different marker genes often used in constructing multidomain phylogenetic trees of bacteria and archaea and present a set of marker genes that perform best for multidomain trees constructed from concatenated alignments. We use recently-developed Tree Certainty metrics to assess the confidence of our results and to obviate the complications of traditional bootstrap-based metrics. Given the vastly disparate number of genomes available for different phyla of bacteria and archaea, we also assessed the impact of taxon sampling on multidomain tree construction. Our results demonstrate that biases between the representation of different taxonomic groups can dramatically impact the topology of resulting trees. Inspection of our highest-quality tree supports the division of most bacteria into Terrabacteria and Gracilicutes, with Thermatogota and Synergistota branching earlier from these superphyla. This tree also supports the inclusion of the Patescibacteria within the Terrabacteria as a sister group to the Chloroflexota instead of as a basal-branching lineage. For the Archaea, our tree supports three monophyletic lineages (DPANN, Euryarchaeota, and TACK/Asgard), although we note the basal placement of the DPANN may still represent an artifact caused by biased sequence composition. Our findings provide a robust and standardized framework for multidomain phylogenetic reconstruction that can be used to evaluate inter-phylum relationships and assess uncertainty in conflicting topologies of the Tree of Life.},
}
@article {pmid34394058,
year = {2021},
author = {Kostygov, AY and Alves, JMP and Yurchenko, V},
title = {Editorial: Symbioses Between Protists and Bacteria/Archaea.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {709184},
pmid = {34394058},
issn = {1664-302X},
}
@article {pmid34391833,
year = {2021},
author = {Moghimipour, E and Abedishirehjin, S and Baghbadorani, MA and Handali, S},
title = {Bacteria and Archaea: A new era of cancer therapy.},
journal = {Journal of controlled release : official journal of the Controlled Release Society},
volume = {338},
number = {},
pages = {1-7},
doi = {10.1016/j.jconrel.2021.08.019},
pmid = {34391833},
issn = {1873-4995},
mesh = {*Antineoplastic Agents ; Archaea ; Bacteria ; Drug Delivery Systems ; Nanotechnology ; *Neoplasms/drug therapy ; },
abstract = {Cancer is one of the most important mortality in the world. The major drawbacks of chemotherapy are the poor absorption of drugs into tumor tissues and development of resistance against anti-cancer agents. To overcome these limitations, the use of microorganisms has been extensively considered in the treatment of cancer. Microorganisms (bacteria/Archaea) secrete different bioactive compounds that can efficiently inhibit cancer cells growth. Biological nanocarriers derived from microorganisms including outer membrane vesicles (OMVs), bacterial ghosts (BGs) and archaeosomes have also been considered as drug delivery systems. Conjugation of drug loaded nanocarriers to bacteria strongly kills the cancer cells after internalization through the bacteria. Merging of microbiology and nanotechnology may provide versatile microbial nano-hybrids for promising treatment of cancer. This strategy causes more amount of drug to enter into cancer cells. In this review, we present evidence that microorganism, their derivatives as well as their intervention with nanotechnology can be a powerful vehicle for eradication cancer.},
}
@article {pmid34379636,
year = {2021},
author = {Acharya, S and Dahal, A and Bhattarai, HK},
title = {Evolution and origin of sliding clamp in bacteria, archaea and eukarya.},
journal = {PloS one},
volume = {16},
number = {8},
pages = {e0241093},
pmid = {34379636},
issn = {1932-6203},
mesh = {Amino Acid Sequence ; Archaea/*genetics ; Bacteria/*genetics ; DNA/genetics ; DNA Replication/genetics ; DNA-Directed DNA Polymerase/genetics ; Eukaryota/*genetics ; Evolution, Molecular ; Firmicutes/genetics ; Phylogeny ; Proliferating Cell Nuclear Antigen/genetics ; Pyrococcus furiosus/genetics ; },
abstract = {The replication of DNA is an essential process in all domains of life. A protein often involved in replication is the sliding clamp. The sliding clamp encircles the DNA and helps replicative polymerase stay attached to the replication machinery increasing the processivity of the polymerase. In eukaryotes and archaea, the sliding clamp is called the Proliferating Cell Nuclear Antigen (PCNA) and consists of two domains. This PCNA forms a trimer encircling the DNA as a hexamer. In bacteria, the structure of the sliding clamp is highly conserved, but the protein itself, called beta clamp, contains three domains, which dimerize to form a hexamer. The bulk of literature touts a conservation of the structure of the sliding clamp, but fails to recognize the conservation of protein sequence among sliding clamps. In this paper, we have used PSI blast to the second iteration in NCBI to show a statistically significant sequence homology between Pyrococcus furiosus PCNA and Kallipyga gabonensis beta clamp. The last two domains of beta clamp align with the two domains of PCNA. This homology data demonstrates that PCNA and beta clamp arose from a common ancestor. In this paper, we have further used beta clamp and PCNA sequences from diverse bacteria, archaea and eukarya to build maximum likelihood phylogenetic tree. Most, but not all, species in different domains of life harbor one sliding clamp from vertical inheritance. Some of these species that have two or more sliding clamps have acquired them from gene duplication or horizontal gene transfer events.},
}
@article {pmid34378142,
year = {2022},
author = {Xie, R and Wang, Y and Huang, D and Hou, J and Li, L and Hu, H and Zhao, X and Wang, F},
title = {Expanding Asgard members in the domain of Archaea sheds new light on the origin of eukaryotes.},
journal = {Science China. Life sciences},
volume = {65},
number = {4},
pages = {818-829},
pmid = {34378142},
issn = {1869-1889},
mesh = {*Archaea/genetics/metabolism ; *Eukaryota/genetics ; Eukaryotic Cells/metabolism ; Phylogeny ; },
abstract = {The hypothesis that eukaryotes originated from within the domain Archaea has been strongly supported by recent phylogenomic analyses placing Heimdallarchaeota-Wukongarchaeota branch from the Asgard superphylum as the closest known archaeal sister-group to eukaryotes. However, our understanding is still limited in terms of the relationship between eukaryotes and archaea, as well as the evolution and ecological functions of the Asgard archaea. Here, we describe three previously unknown phylum-level Asgard archaeal lineages, tentatively named Sigyn-, Freyr- and Njordarchaeota. Additional members in Wukongarchaeota and Baldrarchaeota from distinct environments are also reported here, further expanding their ecological roles and metabolic capacities. Comprehensive phylogenomic analyses further supported the origin of eukaryotes within Asgard archaea and a new lineage Njordarchaeota was supposed as the known closest branch with the eukaryotic nuclear host lineage. Metabolic reconstruction suggests that Njordarchaeota may have a heterotrophic lifestyle with capability of peptides and amino acids utilization, while Sigynarchaeota and Freyrarchaeota also have the potentials to fix inorganic carbon via the Wood-Ljungdahl pathway and degrade organic matters. Additionally, the Ack/Pta pathway for homoacetogenesis and de novo anaerobic cobalamin biosynthesis pathway were found in Freyrarchaeota and Wukongrarchaeota, respectively. Some previously unidentified eukaryotic signature proteins for intracellular membrane trafficking system, and the homologue of mu/sigma subunit of adaptor protein complex, were identified in Freyrarchaeota. This study expands the Asgard superphylum, sheds new light on the evolution of eukaryotes and improves our understanding of ecological functions of the Asgard archaea.},
}
@article {pmid34367583,
year = {2021},
author = {Wu, D and Zhao, C and Bai, H and Feng, F and Sui, X and Sun, G},
title = {Characteristics and metabolic patterns of soil methanogenic archaea communities in the high-latitude natural forested wetlands of China.},
journal = {Ecology and evolution},
volume = {11},
number = {15},
pages = {10396-10408},
pmid = {34367583},
issn = {2045-7758},
abstract = {Soil methanogenic microorganisms are one of the primary methane-producing microbes in wetlands. However, we still poorly understand the community characteristic and metabolic patterns of these microorganisms according to vegetation type and seasonal changes. Therefore, to better elucidate the effects of the vegetation type and seasonal factors on the methanogenic community structure and metabolic patterns, we detected the characteristics of the soil methanogenic mcrA gene from three types of natural wetlands in different seasons in the Xiaoxing'an Mountain region, China. The results indicated that the distribution of Methanobacteriaceae (hydrogenotrophic methanogens) was higher in winter, while Methanosarcinaceae and Methanosaetaceae accounted for a higher proportion in summer. Hydrogenotrophic methanogenesis was the dominant trophic pattern in each wetland. The results of principal coordinate analysis and cluster analysis showed that the vegetation type considerably influenced the methanogenic community composition. The methanogenic community structure in the Betula platyphylla-Larix gmelinii wetland was relatively different from the structure of the other two wetland types. Indicator species analysis further demonstrated that the corresponding species of indicator operational taxonomic units from the Alnus sibirica wetland and the Betula ovalifolia wetland were similar. Network analysis showed that cooperative and competitive relationships exist both within and between the same or different trophic methanogens. The core methanogens with higher abundance in each wetland were conducive to the adaptation to environmental disturbances. This information is crucial for the assessment of metabolic patterns of soil methanogenic archaea and future fluxes in the wetlands of the Xiaoxing'an Mountain region given their vulnerability.},
}
@article {pmid34367089,
year = {2021},
author = {Londei, P and Ferreira-Cerca, S},
title = {Ribosome Biogenesis in Archaea.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {686977},
pmid = {34367089},
issn = {1664-302X},
abstract = {Making ribosomes is a major cellular process essential for the maintenance of functional ribosome homeostasis and to ensure appropriate gene expression. Strikingly, although ribosomes are universally conserved ribonucleoprotein complexes decoding the genetic information contained in messenger RNAs into proteins, their biogenesis shows an intriguing degree of variability across the tree of life. In this review, we summarize our knowledge on the least understood ribosome biogenesis pathway: the archaeal one. Furthermore, we highlight some evolutionary conserved and divergent molecular features of making ribosomes across the tree of life.},
}
@article {pmid34364295,
year = {2021},
author = {Xiao, L and Liu, G and Gong, F and Cai, Z and Li, Y},
title = {The reductive carboxylation activity of heterotetrameric pyruvate synthases from hyperthermophilic archaea.},
journal = {Biochemical and biophysical research communications},
volume = {572},
number = {},
pages = {151-156},
doi = {10.1016/j.bbrc.2021.07.091},
pmid = {34364295},
issn = {1090-2104},
mesh = {Archaea/*enzymology ; Carboxylic Acids/metabolism ; Oxidation-Reduction ; Pyruvate Synthase/*metabolism ; },
abstract = {Pyruvate synthase (pyruvate:ferredoxin oxidoreductase, PFOR) catalyzes the interconversion of acetyl-CoA and pyruvate, but the reductive carboxylation activities of heterotetrameric PFORs remain largely unknown. In this study, we cloned, expressed, and purified selected six heterotetrameric PFORs from hyperthermophilic archaea. The reductive carboxylation activities of these heterotetrameric PFORs were measured at 70 °C and the ratio of reductive carboxylation activity to oxidative decarboxylation activity (red/ox ratio) were calculated. Four out of six showed reductive decarboxylation activities. Among them, the PFORpfm from Pyrolobus fumarii showed the highest reductive carboxylation activities and the highest red/ox ratio, which were 54.32 mU/mg and 0.51, respectively. The divergence of the reductive carboxylation activities and the red/ox ratios of heterotetrameric PFORs in hyperthermophilic archaea indicate the diversity of the functions of PFOR over long-term evolution. This can help us better understand the autotrophic CO2 fixation process in thermal vent, or in other CO2-rich high temperature habitat.},
}
@article {pmid34359268,
year = {2021},
author = {Deng, F and Li, Y and Peng, Y and Wei, X and Wang, X and Howe, S and Yang, H and Xiao, Y and Li, H and Zhao, J and Li, Y},
title = {The Diversity, Composition, and Metabolic Pathways of Archaea in Pigs.},
journal = {Animals : an open access journal from MDPI},
volume = {11},
number = {7},
pages = {},
pmid = {34359268},
issn = {2076-2615},
support = {2019KSYS011//Key Laboratory of Animal Molecular Design and Precise Breeding of Guangdong Higher Educa-tion Institutes/ ; 2019B030301010//Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding/ ; },
abstract = {Archaea are an essential class of gut microorganisms in humans and animals. Despite the substantial progress in gut microbiome research in the last decade, most studies have focused on bacteria, and little is known about archaea in mammals. In this study, we investigated the composition, diversity, and functional potential of gut archaeal communities in pigs by re-analyzing a published metagenomic dataset including a total of 276 fecal samples from three countries: China (n = 76), Denmark (n = 100), and France (n = 100). For alpha diversity (Shannon Index) of the archaeal communities, Chinese pigs were less diverse than Danish and French pigs (p < 0.001). Consistently, Chinese pigs also possessed different archaeal community structures from the other two groups based on the Bray-Curtis distance matrix. Methanobrevibacter was the most dominant archaeal genus in Chinese pigs (44.94%) and French pigs (15.41%), while Candidatus methanomethylophilus was the most predominant in Danish pigs (15.71%). At the species level, the relative abundance of Candidatus methanomethylophilus alvus, Natrialbaceae archaeon XQ INN 246, and Methanobrevibacter gottschalkii were greatest in Danish, French, and Chinese pigs with a relative abundance of 14.32, 11.67, and 16.28%, respectively. In terms of metabolic potential, the top three pathways in the archaeal communities included the MetaCyc pathway related to the biosynthesis of L-valine, L-isoleucine, and isobutanol. Interestingly, the pathway related to hydrogen consumption (METHANOGENESIS-PWY) was only observed in archaeal reads, while the pathways participating in hydrogen production (FERMENTATION-PWY and PWY4LZ-257) were only detected in bacterial reads. Archaeal communities also possessed CAZyme gene families, with the top five being AA3, GH43, GT2, AA6, and CE9. In terms of antibiotic resistance genes (ARGs), the class of multidrug resistance was the most abundant ARG, accounting for 87.41% of archaeal ARG hits. Our study reveals the diverse composition and metabolic functions of archaea in pigs, suggesting that archaea might play important roles in swine nutrition and metabolism.},
}
@article {pmid34354121,
year = {2021},
author = {Clark, IM and Hughes, DJ and Fu, Q and Abadie, M and Hirsch, PR},
title = {Metagenomic approaches reveal differences in genetic diversity and relative abundance of nitrifying bacteria and archaea in contrasting soils.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {15905},
pmid = {34354121},
issn = {2045-2322},
support = {BBS/E/C/00005196/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/C/000I0310/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Ammonia/analysis ; Archaea/*genetics ; Bacteria/*genetics ; Fertilizers/analysis ; Genetic Variation/genetics ; Metagenome/genetics ; Metagenomics/methods ; Nitrification/*genetics/physiology ; Nitrites/analysis ; Oxidation-Reduction ; Phylogeny ; Soil/chemistry ; Soil Microbiology ; },
abstract = {The abundance and phylogenetic diversity of functional genes involved in nitrification were assessed in Rothamsted field plots under contrasting management regimes-permanent bare fallow, grassland, and arable (wheat) cultivation maintained for more than 50 years. Metagenome and metatranscriptome analysis indicated nitrite oxidizing bacteria (NOB) were more abundant than ammonia oxidizing archaea (AOA) and bacteria (AOB) in all soils. The most abundant AOA and AOB in the metagenomes were, respectively, Nitrososphaera and Ca. Nitrososcosmicus (family Nitrososphaeraceae) and Nitrosospira and Nitrosomonas (family Nitrosomonadaceae). The most abundant NOB were Nitrospira including the comammox species Nitrospira inopinata, Ca. N. nitrificans and Ca. N. nitrosa. Anammox bacteria were also detected. Nitrospira and the AOA Nitrososphaeraceae showed most transcriptional activity in arable soil. Similar numbers of sequences were assigned to the amoA genes of AOA and AOB, highest in the arable soil metagenome and metatranscriptome; AOB amoA reads included those from comammox Nitrospira clades A and B, in addition to Nitrosomonadaceae. Nitrification potential assessed in soil from the experimental sites (microcosms amended or not with DCD at concentrations inhibitory to AOB but not AOA), was highest in arable samples and lower in all assays containing DCD, indicating AOB were responsible for oxidizing ammonium fertilizer added to these soils.},
}
@article {pmid34350672,
year = {2021},
author = {Wakai, M and Hayashi, S and Chiba, Y and Koike, S and Nagashima, K and Kobayashi, Y},
title = {Growth and morphologic response of rumen methanogenic archaea and bacteria to cashew nut shell liquid and its alkylphenol components.},
journal = {Animal science journal = Nihon chikusan Gakkaiho},
volume = {92},
number = {1},
pages = {e13598},
doi = {10.1111/asj.13598},
pmid = {34350672},
issn = {1740-0929},
support = {JPJ009237//Cabinet Office, Government of Japan, Cross-ministerial Moonshot Agriculture, Forestry and Fisheries Research and Development Program/ ; },
mesh = {*Anacardium ; Animals ; Archaea ; Bacteria ; Methane ; Nuts ; *Rumen ; },
abstract = {The growth and morphology of rumen methanogenic archaea (15 strains of 10 species in 5 genera, including 7 strains newly isolated in the present study) and bacteria (14 species in 12 genera) were investigated using unsupplemented in vitro pure cultures and cultures supplemented with cashew nut shell liquid (CNSL) and its phenolic compound components, anti-methanogenic agents for ruminant animals. Growth of most of the methanogens tested was inhibited by CNSL and alkylphenols at different concentrations ranging from 1.56 to 12.5 μg/ml. Of the alkylphenols tested, anacardic acid exhibited the most potent growth inhibition. Three gram-negative bacterial species involved in propionate production were resistant to CNSL and alkylphenols (>50 μg/ml). All the methanogens and bacteria that were sensitive to CNSL and alkylphenols exhibited altered morphology; disruption of the cell surface was notable, possibly due to surfactant activity of the tested materials. Cells division was inhibited in some organisms, with cell elongation and unclear septum formation observed. These results indicate that CNSL and alkylphenols, particularly anacardic acid, inhibit both rumen bacteria and methanogens in a selective manner, which could help mitigate rumen methane generation.},
}
@article {pmid34347515,
year = {2021},
author = {French, E and Kozlowski, JA and Bollmann, A},
title = {Competition between Ammonia-Oxidizing Archaea and Bacteria from Freshwater Environments.},
journal = {Applied and environmental microbiology},
volume = {87},
number = {20},
pages = {e0103821},
pmid = {34347515},
issn = {1098-5336},
mesh = {Ammonia/*metabolism ; Archaea/genetics/growth &amp; development/*metabolism ; Fresh Water/*microbiology ; *Microbial Interactions ; Nitrosomonas/genetics/growth &amp; development/*metabolism ; Oxidation-Reduction ; Phylogeny ; },
abstract = {In the environment, nutrients are rarely available in a constant supply. Therefore, microorganisms require strategies to compete for limiting nutrients. In freshwater systems, ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) compete with heterotrophic bacteria, photosynthetic microorganisms, and each other for ammonium, which AOA and AOB utilize as their sole source of energy and nitrogen. We investigated the competition between highly enriched cultures of AOA (AOA-AC1) and AOB (AOB-G5-7) for ammonium. Based on the amoA gene, the newly enriched archaeal ammonia oxidizer in AOA-AC1 was closely related to Nitrosotenuis spp., and the bacterial ammonia oxidizer in AOB-G5-7, Nitrosomonas sp. strain Is79, belonged to the Nitrosomonas oligotropha group (Nitrosomonas cluster 6a). Growth experiments in batch cultures showed that AOB-G5-7 had higher growth rates than AOA-AC1 at higher ammonium concentrations. During chemostat competition experiments under ammonium-limiting conditions, AOA-AC1 dominated the cultures, while AOB-G5-7 decreased in abundance. In batch cultures, the outcome of the competition between AOA and AOB was determined by the initial ammonium concentrations. AOA-AC1 was the dominant ammonia oxidizer at an initial ammonium concentration of 50 μM, and AOB-G5-7 was dominant at 500 μM. These findings indicate that during direct competition, AOA-AC1 was able to use ammonium that was unavailable to AOB-G5-7, while AOB-G5-7 dominated at higher ammonium concentrations. The results are in strong accordance with environmental survey data suggesting that AOA are mainly responsible for ammonia oxidation under more oligotrophic conditions, whereas AOB dominate under eutrophic conditions. IMPORTANCE Nitrification is an important process in the global nitrogen cycle. The first step, ammonia oxidation to nitrite, can be carried out by ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). In many natural environments, these ammonia oxidizers coexist. Therefore, it is important to understand the population dynamics in response to increasing ammonium concentrations. Here, we study the competition between AOA and AOB enriched from freshwater systems. The results demonstrate that AOA are more abundant in systems with low ammonium availabilities and that AOB are more abundant when the ammonium availability increases. These results will help to predict potential shifts in the community composition of ammonia oxidizers in the environment due to changes in ammonium availability.},
}
@article {pmid34346295,
year = {2023},
author = {Santos, MVD and Goes, RHTB and Takiya, CS and Cabral, LDS and Mombach, MA and Oliveira, RT and Silva, NGD and Anschau, DG and Freitas Júnior, JE and de Araújo, MLGML and Gandra, JR},
title = {Effect of increasing doses of chitosan to grazing beef steers on the relative population and transcript abundance of Archaea and cellulolytic and amylolytic bacterias.},
journal = {Animal biotechnology},
volume = {34},
number = {2},
pages = {246-252},
doi = {10.1080/10495398.2021.1954936},
pmid = {34346295},
issn = {1532-2378},
mesh = {Cattle ; Animals ; *Diet/veterinary ; Archaea ; *Chitosan/pharmacology ; Animal Feed/analysis ; Bacteria ; },
abstract = {This paper aims to investigate the influence of increasing chitosan doses on the relative proportion and abundance of cellulotytic, amylolytic bacteria, and Archaea transcripts for grazing cattle. Five rumen cannulated crossbread steers [3.6 months and 300 ± 25 kg body LW (live weight), mean ± standard deviation] were used in a 5 × 5 latin square design, randomly assigned to treatment sequence containing chitosan added to 0, 400, 800, 1200, or 1600 mg/kg concentrate. There was the effect of chitosan on the population of Fibrobacter succinogenes, Ruminococcus albus, and Archaea. The lowest population of these bacteria of 576.60 mg/kg DM (dry matter), 1010.40 mg/kg DM, and 634.80 mg/kg DM were noted when chitosan was added at levels of 3.87, 4.16, and 3.52. Except for Ruminococcus albus, which was not affected by increasing chitosan doses, supplementation of this additive in the concentrate quadratically increased the relative abundance of Fibrobacter succinogenes and Archaea Supplemental 740 mg CHI/kg concentrate for grazing steers receiving concentrate at 150 grams/100 kg LW is recommended to promote minimal effect on the relative population and abundance of cellulolytics and amylomatics and to restrict Archaea growth.},
}
@article {pmid34343555,
year = {2022},
author = {Zhu, J and Yan, X and Zhou, L and Li, N and Liao, C and Wang, X},
title = {Insight of bacteria and archaea in Feammox community enriched from different soils.},
journal = {Environmental research},
volume = {203},
number = {},
pages = {111802},
doi = {10.1016/j.envres.2021.111802},
pmid = {34343555},
issn = {1096-0953},
mesh = {*Ammonium Compounds ; Archaea ; Bacteria ; Ferric Compounds ; Nitrogen/analysis ; Oxidation-Reduction ; *Soil ; Soil Microbiology ; },
abstract = {Anaerobic ammonium oxidation coupled to Fe(III) reduction, known as Feammox, is a newly discovered nitrogen-cycling process, which serves an important role in the pathways of nitrogen loss in the environment. However, the specific types of microorganisms involved in Feammox currently remain unclear. In this study, we selected two groups of soil samples (paddy and mine), from considerably different habitats in South China, to acclimate Feammox colonies. The Paddy Group had a shorter lag period than the Mine Group, while the ammonium transformation rate was nearly equal in both groups in the mature period. The emergence of the Feammox activity was found to be associated with the increased abundance of iron-reducing bacteria, especially Clostridium_sensu_stricto_12, Desulfitobacterium, Thermoanaerobaculum, Anaeromyxobacter and Geobacter. Ammonium oxidizing archaea and methanogens were dominant among the known archaea. These findings extend our knowledge of the microbial community composition of the potential Feammox microbes from soils under different environmental conditions, which broadens our understanding of this important Fe/N transformation process.},
}
@article {pmid34327792,
year = {2021},
author = {Li, C and Hambright, KD and Bowen, HG and Trammell, MA and Grossart, HP and Burford, MA and Hamilton, DP and Jiang, H and Latour, D and Meyer, EI and Padisák, J and Zamor, RM and Krumholz, LR},
title = {Global co-occurrence of methanogenic archaea and methanotrophic bacteria in Microcystis aggregates.},
journal = {Environmental microbiology},
volume = {23},
number = {11},
pages = {6503-6519},
doi = {10.1111/1462-2920.15691},
pmid = {34327792},
issn = {1462-2920},
mesh = {Archaea/genetics ; *Euryarchaeota/genetics ; Eutrophication ; Lakes/microbiology ; Methane ; *Microcystis/genetics ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Global warming and eutrophication contribute to the worldwide increase in cyanobacterial blooms, and the level of cyanobacterial biomass is strongly associated with rises in methane emissions from surface lake waters. Hence, methane-metabolizing microorganisms may be important for modulating carbon flow in cyanobacterial blooms. Here, we surveyed methanogenic and methanotrophic communities associated with floating Microcystis aggregates in 10 lakes spanning four continents, through sequencing of 16S rRNA and functional marker genes. Methanogenic archaea (mainly Methanoregula and Methanosaeta) were detectable in 5 of the 10 lakes and constituted the majority (~50%-90%) of the archaeal community in these lakes. Three of the 10 lakes contained relatively more abundant methanotrophs than the other seven lakes, with the methanotrophic genera Methyloparacoccus, Crenothrix, and an uncultured species related to Methylobacter dominating and nearly exclusively found in each of those three lakes. These three are among the five lakes in which methanogens were observed. Operational taxonomic unit (OTU) richness and abundance of methanotrophs were strongly positively correlated with those of methanogens, suggesting that their activities may be coupled. These Microcystis-aggregate-associated methanotrophs may be responsible for a hitherto overlooked sink for methane in surface freshwaters, and their co-occurrence with methanogens sheds light on the methane cycle in cyanobacterial aggregates.},
}
@article {pmid34316016,
year = {2022},
author = {Jung, MY and Sedlacek, CJ and Kits, KD and Mueller, AJ and Rhee, SK and Hink, L and Nicol, GW and Bayer, B and Lehtovirta-Morley, L and Wright, C and de la Torre, JR and Herbold, CW and Pjevac, P and Daims, H and Wagner, M},
title = {Ammonia-oxidizing archaea possess a wide range of cellular ammonia affinities.},
journal = {The ISME journal},
volume = {16},
number = {1},
pages = {272-283},
pmid = {34316016},
issn = {1751-7370},
mesh = {*Ammonia/metabolism ; *Archaea/genetics/metabolism ; Bacteria/genetics/metabolism ; Nitrification ; Oxidation-Reduction ; Phylogeny ; Soil Microbiology ; },
abstract = {Nitrification, the oxidation of ammonia to nitrate, is an essential process in the biogeochemical nitrogen cycle. The first step of nitrification, ammonia oxidation, is performed by three, often co-occurring guilds of chemolithoautotrophs: ammonia-oxidizing bacteria (AOB), archaea (AOA), and complete ammonia oxidizers (comammox). Substrate kinetics are considered to be a major niche-differentiating factor between these guilds, but few AOA strains have been kinetically characterized. Here, the ammonia oxidation kinetic properties of 12 AOA representing all major cultivated phylogenetic lineages were determined using microrespirometry. Members of the genus Nitrosocosmicus have the lowest affinity for both ammonia and total ammonium of any characterized AOA, and these values are similar to previously determined ammonia and total ammonium affinities of AOB. This contrasts previous assumptions that all AOA possess much higher substrate affinities than their comammox or AOB counterparts. The substrate affinity of ammonia oxidizers correlated with their cell surface area to volume ratios. In addition, kinetic measurements across a range of pH values supports the hypothesis that-like for AOB-ammonia and not ammonium is the substrate for the ammonia monooxygenase enzyme of AOA and comammox. Together, these data will facilitate predictions and interpretation of ammonia oxidizer community structures and provide a robust basis for establishing testable hypotheses on competition between AOB, AOA, and comammox.},
}
@article {pmid34286299,
year = {2021},
author = {Coutinho, FH and Zaragoza-Solas, A and López-Pérez, M and Barylski, J and Zielezinski, A and Dutilh, BE and Edwards, R and Rodriguez-Valera, F},
title = {RaFAH: Host prediction for viruses of Bacteria and Archaea based on protein content.},
journal = {Patterns (New York, N.Y.)},
volume = {2},
number = {7},
pages = {100274},
pmid = {34286299},
issn = {2666-3899},
support = {RC2 DK116713/DK/NIDDK NIH HHS/United States ; },
abstract = {Culture-independent approaches have recently shed light on the genomic diversity of viruses of prokaryotes. One fundamental question when trying to understand their ecological roles is: which host do they infect? To tackle this issue we developed a machine-learning approach named Random Forest Assignment of Hosts (RaFAH), that uses scores to 43,644 protein clusters to assign hosts to complete or fragmented genomes of viruses of Archaea and Bacteria. RaFAH displayed performance comparable with that of other methods for virus-host prediction in three different benchmarks encompassing viruses from RefSeq, single amplified genomes, and metagenomes. RaFAH was applied to assembled metagenomic datasets of uncultured viruses from eight different biomes of medical, biotechnological, and environmental relevance. Our analyses led to the identification of 537 sequences of archaeal viruses representing unknown lineages, whose genomes encode novel auxiliary metabolic genes, shedding light on how these viruses interfere with the host molecular machinery. RaFAH is available at https://sourceforge.net/projects/rafah/.},
}
@article {pmid34285362,
year = {2022},
author = {Yu, H and Skennerton, CT and Chadwick, GL and Leu, AO and Aoki, M and Tyson, GW and Orphan, VJ},
title = {Sulfate differentially stimulates but is not respired by diverse anaerobic methanotrophic archaea.},
journal = {The ISME journal},
volume = {16},
number = {1},
pages = {168-177},
pmid = {34285362},
issn = {1751-7370},
mesh = {Anaerobiosis ; *Archaea/metabolism ; Geologic Sediments/microbiology ; Humans ; Methane/metabolism ; Oxidation-Reduction ; Phylogeny ; *Sulfates/metabolism ; },
abstract = {Sulfate-coupled anaerobic oxidation of methane (AOM) is a major methane sink in marine sediments. Multiple lineages of anaerobic methanotrophic archaea (ANME) often coexist in sediments and catalyze this process syntrophically with sulfate-reducing bacteria (SRB), but the potential differences in ANME ecophysiology and mechanisms of syntrophy remain unresolved. A humic acid analog, anthraquinone 2,6-disulfonate (AQDS), could decouple archaeal methanotrophy from bacterial sulfate reduction and serve as the terminal electron acceptor for AOM (AQDS-coupled AOM). Here in sediment microcosm experiments, we examined variations in physiological response between two co-occurring ANME-2 families (ANME-2a and ANME-2c) and tested the hypothesis of sulfate respiration by ANME-2. Sulfate concentrations as low as 100 µM increased AQDS-coupled AOM nearly 2-fold matching the rates of sulfate-coupled AOM. However, the SRB partners remained inactive in microcosms with sulfate and AQDS and neither ANME-2 families respired sulfate, as shown by their cellular sulfur contents and anabolic activities measured using nanoscale secondary ion mass spectrometry. ANME-2a anabolic activity was significantly higher than ANME-2c, suggesting that ANME-2a was primarily responsible for the observed sulfate stimulation of AQDS-coupled AOM. Comparative transcriptomics showed significant upregulation of ANME-2a transcripts linked to multiple ABC transporters and downregulation of central carbon metabolism during AQDS-coupled AOM compared to sulfate-coupled AOM. Surprisingly, genes involved in sulfur anabolism were not differentially expressed during AQDS-coupled AOM with and without sulfate amendment. Collectively, this data indicates that ANME-2 archaea are incapable of respiring sulfate, but sulfate availability differentially stimulates the growth and AOM activity of different ANME lineages.},
}
@article {pmid34282942,
year = {2021},
author = {Umbach, AK and Stegelmeier, AA and Neufeld, JD},
title = {Archaea Are Rare and Uncommon Members of the Mammalian Skin Microbiome.},
journal = {mSystems},
volume = {6},
number = {4},
pages = {e0064221},
pmid = {34282942},
issn = {2379-5077},
support = {NA//Gouvernement du Canada | Natural Sciences and Engineering Research Council of Canada (NSERC)/ ; },
abstract = {Although previous research demonstrates that skin-associated archaea are rarely detected within human skin microbiome data, exist at relatively low abundance, and are primarily affiliated with the Methanobacteriota and Halobacteriota phyla, other studies suggest that archaea are consistently detected and relatively abundant on human skin, with skin "archaeomes" dominated by putative ammonia oxidizers of the Nitrososphaeria class (Thermoproteota phylum, formerly Thaumarchaeota). Here, we evaluated new and existing 16S rRNA gene sequence data sourced from mammalian skin and skin-associated surfaces and generated with two commonly used universal prokaryotic primer sets to assess archaeal prevalence, relative abundance, and taxonomic distribution. Archaeal 16S rRNA gene sequences were detected in only 17.5% of 1,688 samples by high-throughput sequence data, with most of the archaeon-positive samples associated with nonhuman mammalian skin. Only 5.9% of human-associated skin sample data sets contained sequences affiliated with archaeal 16S rRNA genes. When detected, the relative abundance of sequences affiliated with archaeal amplicon sequence variants (ASVs) was less than 1% for most mammalian skin samples and did not exceed 2% for any samples. Although several computer keyboard microbial profiles were dominated by Nitrososphaeria sequences, all other skin microbiome data sets tested were primarily composed of sequences affiliated with Methanobacteriota and Halobacteriota phyla. Our findings revise downward recent estimates of human skin archaeal distributions and relative abundances, especially those affiliated with the Nitrososphaeria, reflecting a limited and infrequent archaeal presence within the mammalian skin microbiome. IMPORTANCE The current state of research on mammalian skin-associated archaea is limited, with the few papers focusing on potential skin archaeal communities often in disagreement with each other. As such, there is no consensus on the prevalence or taxonomic composition of archaea on mammalian skin. Mammalian skin health is in part influenced by its complex microbiota and consortium of bacteria and potential archaea. Without a clear foundational analysis and characterization of the mammalian skin archaeome, it will be difficult for future research to explore the potential impact of skin-associated archaea on skin health and function. The current work provides a much-needed analysis of the mammalian skin archaeome and contributes to building a foundation from which further discussion and exploration of the skin archaeome might continue.},
}
@article {pmid34276623,
year = {2021},
author = {Dong, Y and Shan, Y and Xia, K and Shi, L},
title = {The Proposed Molecular Mechanisms Used by Archaea for Fe(III) Reduction and Fe(II) Oxidation.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {690918},
pmid = {34276623},
issn = {1664-302X},
abstract = {Iron (Fe) is the fourth most abundant element in the Earth's crust where ferrous Fe [Fe(II)] and ferric Fe [Fe(III)] can be used by archaea for energy conservation. In these archaea-Fe interactions, Fe(III) serves as terminal electron acceptor for anaerobic respiration by a variety of archaea, while Fe(II) serves as electron donor and/or energy sources for archaeal growth. As no Fe is incorporated into the archaeal cells, these redox reactions are referred to as dissimilatory Fe(III) reduction and Fe(II) oxidation, respectively. Dissimilatory Fe(III)-reducing archaea (FeRA) and Fe(II)-oxidizing archaea (FeOA) are widespread on Earth where they play crucial roles in biogeochemical cycling of not only Fe, but also carbon and sulfur. To reduce extracellular Fe(III) (oxyhydr)oxides, some FeRA transfer electrons directly to the Fe(III) (oxyhydr)oxides most likely via multiheme c-type cytochromes (c-Cyts). These multiheme c-Cyts may form the pathways similar to those found in bacteria for transferring electrons from the quinone/quinol pool in the cytoplasmic membrane to the Fe(III) (oxyhydr)oxides external to the archaeal cells. Use of multiheme c-Cyts for extracellular Fe(III) reduction by both Domains of Archaea and Bacteria emphasizes an ancient mechanism of extracellular electron transfer, which is well conserved. Other FeRA, however, reduce Fe(III) (oxyhydr)oxides indirectly via electron shuttles. Similarly, it is proposed that FeOA use pathways to oxidize Fe(II) on the surface of the cytoplasmic membrane and then to transfer the released electrons across the cytoplasmic membrane inward to the O2 and NAD[+] in the cytoplasm. In this review, we focus on the latest understandings of the molecular mechanisms used by FeRA and FeOA for Fe(III) reduction and Fe(II) oxidation, respectively.},
}
@article {pmid34267287,
year = {2021},
author = {Wang, L and Huang, D},
title = {Soil ammonia-oxidizing archaea in a paddy field with different irrigation and fertilization managements.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {14563},
pmid = {34267287},
issn = {2045-2322},
mesh = {Agricultural Irrigation/*methods ; Ammonia/*metabolism ; Archaea/*metabolism ; China ; Crenarchaeota/metabolism ; *Fertilizers ; Hydrogen-Ion Concentration ; Oryza/growth &amp; development ; Oxidation-Reduction ; Soil/chemistry ; *Soil Microbiology ; },
abstract = {Because ammonia-oxidizing archaea (AOA) are ubiquitous and highly abundant in almost all terrestrial soils, they play an important role in soil nitrification. However, the changes in the structure and function of AOA communities and their edaphic drivers in paddy soils under different fertilization and irrigation regimes remain unclear. In this study, we investigated AOA abundance, diversity and activity in acid paddy soils by a field experiment. Results indicated that the highest potential ammonia oxidation (PAO) (0.011 μg NO 2 [-] -N g[-1] d.w.day[-1]) was found in T2 (optimal irrigation and fertilization)-treated soils, whereas the lowest PAO (0.004 μg NO 2 [-] -N g[-1] d.w.day[-1]) in T0 (traditional irrigation)- treated soils. Compared with the T0-treated soil, the T2 treatment significantly (P < 0.05) increased AOA abundances. Furthermore, the abundance of AOA was significantly (P < 0.01) positively correlated with pH, soil organic carbon (SOC), and PAO. Meanwhile, pH and SOC content were significantly (P < 0.05) higher in the T2-treated soil than those in the T1 (traditional irrigation and fertilization)- treated soil. In addition, these two edaphic factors further influenced the AOA community composition. The AOA phylum Crenarchaeota was mainly found in the T2-treated soils. Phylogenetic analysis revealed that most of the identified OTUs of AOA were mainly affiliated with Crenarchaeota. Furthermore, the T2 treatment had higher rice yield than the T0 and T1 treatments. Together, our findings confirm that T2 might ameliorate soil chemical properties, regulate the AOA community structure, increase the AOA abundance, enhance PAO and consequently maintain rice yields in the present study.},
}
@article {pmid34253852,
year = {2022},
author = {Jørgensen, BB},
title = {Do methanogenic archaea cause reductive pyrite dissolution in subsurface sediments?.},
journal = {The ISME journal},
volume = {16},
number = {1},
pages = {1-2},
pmid = {34253852},
issn = {1751-7370},
mesh = {*Archaea/genetics ; *Euryarchaeota ; Iron ; Solubility ; Sulfides ; },
}
@article {pmid34248899,
year = {2021},
author = {Christakis, CA and Barkay, T and Boyd, ES},
title = {Expanded Diversity and Phylogeny of mer Genes Broadens Mercury Resistance Paradigms and Reveals an Origin for MerA Among Thermophilic Archaea.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {682605},
pmid = {34248899},
issn = {1664-302X},
support = {R01 ES030940/ES/NIEHS NIH HHS/United States ; },
abstract = {Mercury (Hg) is a highly toxic element due to its high affinity for protein sulfhydryl groups, which upon binding, can destabilize protein structure and decrease enzyme activity. Prokaryotes have evolved enzymatic mechanisms to detoxify inorganic Hg and organic Hg (e.g., MeHg) through the activities of mercuric reductase (MerA) and organomercury lyase (MerB), respectively. Here, the taxonomic distribution and evolution of MerAB was examined in 84,032 archaeal and bacterial genomes, metagenome assembled genomes, and single-cell genomes. Homologs of MerA and MerB were identified in 7.8 and 2.1% percent of genomes, respectively. MerA was identified in the genomes of 10 archaeal and 28 bacterial phyla previously unknown to code for this functionality. Likewise, MerB was identified in 2 archaeal and 11 bacterial phyla previously unknown to encode this functionality. Surprisingly, homologs of MerB were identified in a number of genomes (∼50% of all MerB-encoding genomes) that did not encode MerA, suggesting alternative mechanisms to detoxify Hg(II) once it is generated in the cytoplasm. Phylogenetic reconstruction of MerA place its origin in thermophilic Thermoprotei (Crenarchaeota), consistent with high levels of Hg(II) in geothermal environments, the natural habitat of this archaeal class. MerB appears to have been recruited to the mer operon relatively recently and likely among a mesophilic ancestor of Euryarchaeota and Thaumarchaeota. This is consistent with the functional dependence of MerB on MerA and the widespread distribution of mesophilic microorganisms that methylate Hg(II) at lower temperature. Collectively, these results expand the taxonomic and ecological distribution of mer-encoded functionalities, and suggest that selection for Hg(II) and MeHg detoxification is dependent not only on the availability and type of mercury compounds in the environment but also the physiological potential of the microbes who inhabit these environments. The expanded diversity and environmental distribution of MerAB identify new targets to prioritize for future research.},
}
@article {pmid34245190,
year = {2022},
author = {Wang, S and Narsing Rao, MP and Wei, D and Sun, L and Fang, BZ and Li, WQ and Yu, LH and Li, WJ},
title = {Complete genome sequencing and comparative genome analysis of the extremely halophilic archaea, Haloterrigena daqingensis.},
journal = {Biotechnology and applied biochemistry},
volume = {69},
number = {4},
pages = {1482-1488},
doi = {10.1002/bab.2220},
pmid = {34245190},
issn = {1470-8744},
mesh = {DNA, Archaeal/genetics ; *Halobacteriaceae/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Whole Genome Sequencing ; },
abstract = {In the present study, we report the complete genome sequencing of Haloterrigena daqingensis species. The genome of H. daqingensis JX313[T] consisted of a circular chromosome with three plasmids. The genome size and G+C content were estimated to be 3835796 bp and 61.7%, respectively. A total of 4158 genes were predicted with six rRNAs and 45 tRNAs. Metabolic pathway analysis suggests that H. daqingensis JX313[T] codes for all the necessary genes responsible to sustain its life at saline environment. The pan-genome analysis suggests that the number of singleton-gene between H. daqingensis and other Haloterrigena species varied. The study not only helps us understand H. daqingensis strategy for dealing with high stress, but it also provides an overview of its genomic makeup.},
}
@article {pmid34217274,
year = {2021},
author = {Kakuk, B and Wirth, R and Maróti, G and Szuhaj, M and Rakhely, G and Laczi, K and Kovács, KL and Bagi, Z},
title = {Early response of methanogenic archaea to H2 as evaluated by metagenomics and metatranscriptomics.},
journal = {Microbial cell factories},
volume = {20},
number = {1},
pages = {127},
pmid = {34217274},
issn = {1475-2859},
support = {FK123902//Nemzeti Kutat&#xe1;si Fejleszt&#xe9;si &#xe9;s Innov&#xe1;ci&#xf3;s Hivatal/ ; PD132145//Nemzeti Kutat&#xe1;si Fejleszt&#xe9;si &#xe9;s Innov&#xe1;ci&#xf3;s Hivatal/ ; FK123899//Nemzeti Kutat&#xe1;si Fejleszt&#xe9;si &#xe9;s Innov&#xe1;ci&#xf3;s Hivatal/ ; GINOP- 2.2.1-15-2017-00081//Nemzeti Kutat&#xe1;si &#xe9;s Technol&#xf3;giai Hivatal/ ; EFOP- 3.6.2-16-2017-00010//Nemzeti Kutat&#xe1;si &#xe9;s Technol&#xf3;giai Hivatal/ ; 2020-1.1.2-PIACI-KFI-2020-00117//Nemzeti Kutat&#xe1;si &#xe9;s Technol&#xf3;giai Hivatal/ ; LP2020-5/2020//Magyar Tudom&#xe1;nyos Akad&#xe9;mia/ ; 2020-3.1.2.-ZFR-KVG-2020-00009//nemzeti kutat&#xe1;si &#xe9;s technol&#xf3;giai hivatal/ ; },
mesh = {Anaerobiosis ; Bacteria/genetics/metabolism ; Carbon Dioxide/metabolism ; Fermentation ; Gene Expression Regulation, Archaeal ; Genome, Archaeal ; Hydrogen/*metabolism ; Metagenome ; Metagenomics ; Methane/*biosynthesis ; Methanomicrobiaceae/genetics/*metabolism ; Methanosarcina/genetics/*metabolism ; Microbiota ; *Transcriptome ; },
abstract = {BACKGROUND: The molecular machinery of the complex microbiological cell factory of biomethane production is not fully understood. One of the process control elements is the regulatory role of hydrogen (H2). Reduction of carbon dioxide (CO2) by H2 is rate limiting factor in methanogenesis, but the community intends to keep H2 concentration low in order to maintain the redox balance of the overall system. H2 metabolism in methanogens becomes increasingly important in the Power-to-Gas renewable energy conversion and storage technologies.<br><br>RESULTS: The early response of the mixed mesophilic microbial community to H2 gas injection was investigated with the goal of uncovering the first responses of the microbial community in the CH4 formation and CO2 mitigation Power-to-Gas process. The overall microbial composition changes, following a 10&#xa0;min excessive bubbling of H2 through the reactor, was investigated via metagenome and metatranscriptome sequencing. The overall composition and taxonomic abundance of the biogas producing anaerobic community did not change appreciably 2 hours after the H2 treatment, indicating that this time period was too short to display differences in the proliferation of the members of the microbial community. There was, however, a substantial increase in the expression of genes related to hydrogenotrophic methanogenesis of certain groups of Archaea. As an early response to H2 exposure the activity of the hydrogenotrophic methanogenesis in the genus Methanoculleus was upregulated but the hydrogenotrophic pathway in genus Methanosarcina was downregulated. The RT-qPCR data corroborated the metatranscriptomic RESULTS: H2 injection also altered the metabolism of a number of microbes belonging in the kingdom Bacteria. Many Bacteria possess the enzyme sets for the Wood-Ljungdahl pathway. These and the homoacetogens are partners for syntrophic community interactions between the distinct kingdoms of Archaea and Bacteria.<br><br>CONCLUSIONS: External H2 regulates the functional activity of certain Bacteria and Archaea. The syntrophic cross-kingdom interactions in H2 metabolism are important for the efficient operation of the Power-to-Gas process. Therefore, mixed communities are recommended for the large scale Power-to-Gas process rather than single hydrogenotrophic methanogen strains. Fast and reproducible response from the microbial community can be exploited in turn-off and turn-on of the Power-to-Gas microbial cell factories.},
}
@article {pmid34213183,
year = {2020},
author = {Wang, X and He, Z and Li, X and Song, Q and Zou, X and Song, X and Feng, L},
title = {[Comparison of pretreatment methods in lipid analysis and ultra-performance liquid chromatography-mass spectrometry analysis of archaea].},
journal = {Se pu = Chinese journal of chromatography},
volume = {38},
number = {8},
pages = {914-922},
doi = {10.3724/SP.J.1123.2019.12009},
pmid = {34213183},
issn = {1872-2059},
mesh = {*Archaea/chemistry ; Chromatography, High Pressure Liquid ; *Lipidomics ; Lipids/*analysis ; Mass Spectrometry ; Pyrococcus/chemistry ; Reproducibility of Results ; },
abstract = {Archaea are single-cell microorganisms, structurally and biochemically similar to bacteria and fungi. Most of them live in extreme environments, such as high salt, extremely acidic, extremely hot, and anaerobicenvironments. The membrane structure and related metabolic pathways of archaea are different from those of other microorganisms. Therefore, studying the lipid metabolism of archaea is of great significance for exploring the life activities in extreme environments. As the first step in lipidomic analysis, lipid extraction and pretreatment methods play an important role, as they influence the accuracy and reliability of the final results. We harnessed ultra-performance liquid chromatography coupled with high-resolution mass spectrometry (UPLC-HRMS) to detect the total normal lipids. The hyperthermophilic archaeon Pyrococcus yayanosii was selected as the model. The Bligh-Dyer acidic method, Folch method, methyl tert-butyl ether (MTBE) method, and solid-phase extraction (SPE) method were compared by multi-component analysis in terms of extraction efficiency, reproducibility, and extraction discrimination. Comprehensive analysis revealed that the SPE and MTBE methods showed the best extraction repeatability and extraction efficiency, and were suitable for high-throughput microbial lipid extraction. Finally, normal lipid components of P. yayanosii were comprehensively analyzed by SPE coupled with UPLC-HRMS. A total of 1402 lipid components were identified. This article aims to provide a reference for non-targeted lipidomic analysis of archaea and other microorganisms towards understanding their lipid metabolism.},
}
@article {pmid34207561,
year = {2021},
author = {Abellan-Schneyder, I and Siebert, A and Hofmann, K and Wenning, M and Neuhaus, K},
title = {Full-Length SSU rRNA Gene Sequencing Allows Species-Level Detection of Bacteria, Archaea, and Yeasts Present in Milk.},
journal = {Microorganisms},
volume = {9},
number = {6},
pages = {},
pmid = {34207561},
issn = {2076-2607},
support = {n/a (grant for a scientist//Research Foundation of Dairy Science at the Technical University of Munich (VFMF)/ ; n/a (grant for a doctorate position)//ZIEL-Institute for Food &amp; Health at the Technical University of Munich/ ; 281A105616//Federal Ministry of Food and Agriculture (BMEL)/ ; AiF 20027N//IGF Project of the FEI via AiF/ ; },
abstract = {Full-length SSU rRNA gene sequencing allows species-level identification of the microorganisms present in milk samples. Here, we used bulk-tank raw milk samples of two German dairies and detected, using this method, a great diversity of bacteria, archaea, and yeasts within the samples. Moreover, the species-level classification was improved in comparison to short amplicon sequencing. Therefore, we anticipate that this approach might be useful for the detection of possible mastitis-causing species, as well as for the control of spoilage-associated microorganisms. In a proof of concept, we showed that we were able to identify several putative mastitis-causing or mastitis-associated species such as Streptococcusuberis, Streptococcusagalactiae, Streptococcusdysgalactiae, Escherichiacoli and Staphylococcusaureus, as well as several Candida species. Overall, the presented full-length approach for the sequencing of SSU rRNA is easy to conduct, able to be standardized, and allows the screening of microorganisms in labs with Illumina sequencing machines.},
}
@article {pmid34202810,
year = {2021},
author = {Pfeiffer, F and Dyall-Smith, M},
title = {Open Issues for Protein Function Assignment in Haloferax volcanii and Other Halophilic Archaea.},
journal = {Genes},
volume = {12},
number = {7},
pages = {},
pmid = {34202810},
issn = {2073-4425},
mesh = {Archaeal Proteins/classification/*genetics ; Halobacteriales/classification/*genetics ; Haloferax volcanii/*genetics ; Molecular Sequence Annotation ; },
abstract = {BACKGROUND: Annotation ambiguities and annotation errors are a general challenge in genomics. While a reliable protein function assignment can be obtained by experimental characterization, this is expensive and time-consuming, and the number of such Gold Standard Proteins (GSP) with experimental support remains very low compared to proteins annotated by sequence homology, usually through automated pipelines. Even a GSP may give a misleading assignment when used as a reference: the homolog may be close enough to support isofunctionality, but the substrate of the GSP is absent from the species being annotated. In such cases, the enzymes cannot be isofunctional. Here, we examined a variety of such issues in halophilic archaea (class Halobacteria), with a strong focus on the model haloarchaeon Haloferax volcanii.<br><br>RESULTS: Annotated proteins of Hfx. volcanii were identified for which public databases tend to assign a function that is probably incorrect. In some cases, an alternative, probably correct, function can be predicted or inferred from the available evidence, but this has not been adopted by public databases because experimental validation is lacking. In other cases, a probably invalid specific function is predicted by homology, and while there is evidence that this assigned function is unlikely, the true function remains elusive. We listed 50 of those cases, each with detailed background information, so that a conclusion about the most likely biological function can be drawn. For reasons of brevity and comprehension, only the key aspects are listed in the main text, with detailed information being provided in a corresponding section of the Supplementary Materials.<br><br>CONCLUSIONS: Compiling, describing and summarizing these open annotation issues and functional predictions will benefit the scientific community in the general effort to improve the evaluation of protein function assignments and more thoroughly detail them. By highlighting the gaps and likely annotation errors currently in the databases, we hope this study will provide a framework for experimentalists to systematically confirm (or disprove) our function predictions or to uncover yet more unexpected functions.},
}
@article {pmid34190386,
year = {2022},
author = {Tamisier, M and Schmidt, M and Vogt, C and Kümmel, S and Stryhanyuk, H and Musat, N and Richnow, HH and Musat, F},
title = {Iron corrosion by methanogenic archaea characterized by stable isotope effects and crust mineralogy.},
journal = {Environmental microbiology},
volume = {24},
number = {2},
pages = {583-595},
doi = {10.1111/1462-2920.15658},
pmid = {34190386},
issn = {1462-2920},
mesh = {*Archaea ; Carbon Isotopes/analysis ; Corrosion ; *Euryarchaeota ; Iron ; Isotopes ; Methane ; },
abstract = {Carbon and hydrogen stable isotope effects associated with methane formation by the corrosive archaeon Methanobacterium strain IM1 were determined during growth with hydrogen and iron. Isotope analyses were complemented by structural, elemental and molecular composition analyses of corrosion crusts. During growth with H2 , strain IM1 formed methane with average δ[13] C of -43.5‰ and δ[2] H of -370‰. Corrosive growth led to methane more depleted in [13] C, with average δ[13] C ranging from -56‰ to -64‰ during the early and the late growth phase respectively. The corresponding δ[2] H were less impacted by the growth phase, with average values ranging from -316 to -329‰. The stable isotope fractionation factors, α 13 C CO 2 / CH 4 , were 1.026 and 1.042 for hydrogenotrophic and corrosive growth respectively. Corrosion crusts formed by strain IM1 have a domed structure, appeared electrically conductive and were composed of siderite, calcite and iron sulfide, the latter formed by precipitation of sulfide (from culture medium) with ferrous iron generated during corrosion. Strain IM1 cells were found attached to crust surfaces and encrusted deep inside crust domes. Our results may assist to diagnose methanogens-induced corrosion in the field and suggest that intrusion of sulfide in anoxic settings may stimulate corrosion by methanogenic archaea via formation of semiconductive crusts.},
}
@article {pmid34158628,
year = {2021},
author = {Zhao, R and Mogollón, JM and Roerdink, DL and Thorseth, IH and Økland, I and Jørgensen, SL},
title = {Ammonia-oxidizing archaea have similar power requirements in diverse marine oxic sediments.},
journal = {The ISME journal},
volume = {15},
number = {12},
pages = {3657-3667},
pmid = {34158628},
issn = {1751-7370},
mesh = {*Ammonia ; *Archaea/genetics ; Bacteria ; Geologic Sediments ; Nitrification ; Oxidation-Reduction ; Phylogeny ; },
abstract = {Energy/power availability is regarded as one of the ultimate controlling factors of microbial abundance in the deep biosphere, where fewer cells are found in habitats of lower energy availability. A critical assumption driving the proportional relationship between total cell abundance and power availability is that the cell-specific power requirement keeps constant or varies over smaller ranges than other variables, which has yet to be validated. Here we present a quantitative framework to determine the cell-specific power requirement of the omnipresent ammonia-oxidizing archaea (AOA) in eight sediment cores with 3-4 orders of magnitude variations of organic matter flux and oxygen penetration depth. Our results show that despite the six orders of magnitude variations in the rates and power supply of nitrification and AOA abundances across these eight cores, the cell-specific power requirement of AOA from different cores and depths overlaps within the narrow range of 10[-19]-10[-17] W cell[-1], where the lower end may represent the basal power requirement of microorganisms persisting in subseafloor sediments. In individual cores, AOA also exhibit similar cell-specific power requirements, regardless of the AOA population size or sediment depth/age. Such quantitative insights establish a relationship between the power supply and the total abundance of AOA, and therefore lay a foundation for a first-order estimate of the standing stock of AOA in global marine oxic sediments.},
}
@article {pmid34153824,
year = {2021},
author = {Chen, Z and Liu, WS and Zhong, X and Zheng, M and Fei, YH and He, H and Ding, K and Chao, Y and Tang, YT and Wang, S and Qiu, R},
title = {Genome- and community-level interaction insights into the ecological role of archaea in rare earth element mine drainage in South China.},
journal = {Water research},
volume = {201},
number = {},
pages = {117331},
doi = {10.1016/j.watres.2021.117331},
pmid = {34153824},
issn = {1879-2448},
mesh = {*Archaea/genetics ; China ; Genome, Archaeal ; Metagenome ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S ; },
abstract = {Microbial communities play crucial roles in mine drainage generation and remediation. Despite the wide distribution of archaea in the mine ecosystem, their diversity and ecological roles remain less understood than bacteria. Here, we retrieved 56 archaeal metagenome-assembled genomes from a river impacted by rare earth element (REE) mining activities in South China. Genomic analysis showed that archaea represented four distinct lineages, including phyla of Thaumarchaeota, Micrarchaeota, Nanoarchaeota and Thermoplasmata. These archaea represented a considerable fraction (up to 40%) of the total prokaryote community, which might contribute to nitrogen and sulfur cycling in the REE mine drainage. Reconstructed metabolic potential among diverse archaea taxa revealed that archaea were involved in the network of ammonia oxidation, denitrification, sulfate redox reaction, and required substrates supplied by other community members. As the dominant driver of ammonia oxidation, Thaumarchaeota might provide substrates to support the survival of two nano-sized archaea belonging to Micrarchaeota and Nanoarchaeota. Despite the absence of biosynthesis pathways for amino acids and nucleotides, the potential capacity for nitrite reduction (nirD) was observed in Micrarchaeota, indicating that these nano-sized archaea encompassed diverse metabolisms. Moreover, Thermoplasmata, as keystone taxa in community, might be the main genetic donor for the other three archaeal phyla, transferring many environmental resistance related genes (e.g., V/A-type ATPase and Vitamin B12-transporting ATPase). The genetic interactions within archaeal community through horizontal gene transfer might be the key to the formation of archaeal resistance and functional partitioning. This study provides putative metabolic and genetic insights into the diverse archaea taxa from community-level perspectives, and highlights the ecological roles of archaea in REE contaminated aquatic environment.},
}
@article {pmid34151666,
year = {2021},
author = {Ziegler, CA and Freddolino, PL},
title = {The leucine-responsive regulatory proteins/feast-famine regulatory proteins: an ancient and complex class of transcriptional regulators in bacteria and archaea.},
journal = {Critical reviews in biochemistry and molecular biology},
volume = {56},
number = {4},
pages = {373-400},
pmid = {34151666},
issn = {1549-7798},
support = {R35 GM128637/GM/NIGMS NIH HHS/United States ; T32 GM007544/GM/NIGMS NIH HHS/United States ; },
mesh = {Archaea/genetics/*metabolism ; Archaeal Proteins/genetics/*metabolism ; Escherichia coli/genetics/*metabolism ; Escherichia coli Proteins/genetics/*metabolism ; Leucine-Responsive Regulatory Protein/genetics/*metabolism ; },
abstract = {Since the discovery of the Escherichia coli leucine-responsive regulatory protein (Lrp) almost 50 years ago, hundreds of Lrp homologs have been discovered, occurring in 45% of sequenced bacteria and almost all sequenced archaea. Lrp-like proteins are often referred to as the feast/famine regulatory proteins (FFRPs), reflecting their common regulatory roles. Acting as either global or local transcriptional regulators, FFRPs detect the environmental nutritional status by sensing small effector molecules (usually amino acids) and regulate the expression of genes involved in metabolism, virulence, motility, nutrient transport, stress tolerance, and antibiotic resistance to implement appropriate behaviors for the specific ecological niche of each organism. Despite FFRPs' complexity, a significant role in gene regulation, and prevalence throughout prokaryotes, the last comprehensive review on this family of proteins was published about a decade ago. In this review, we integrate recent notable findings regarding E. coli Lrp and other FFRPs across bacteria and archaea with previous observations to synthesize a more complete view on the mechanistic details and biological roles of this ancient class of transcription factors.},
}
@article {pmid34149676,
year = {2021},
author = {De Lise, F and Strazzulli, A and Iacono, R and Curci, N and Di Fenza, M and Maurelli, L and Moracci, M and Cobucci-Ponzano, B},
title = {Programmed Deviations of Ribosomes From Standard Decoding in Archaea.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {688061},
pmid = {34149676},
issn = {1664-302X},
abstract = {Genetic code decoding, initially considered to be universal and immutable, is now known to be flexible. In fact, in specific genes, ribosomes deviate from the standard translational rules in a programmed way, a phenomenon globally termed recoding. Translational recoding, which has been found in all domains of life, includes a group of events occurring during gene translation, namely stop codon readthrough, programmed ± 1 frameshifting, and ribosome bypassing. These events regulate protein expression at translational level and their mechanisms are well known and characterized in viruses, bacteria and eukaryotes. In this review we summarize the current state-of-the-art of recoding in the third domain of life. In Archaea, it was demonstrated and extensively studied that translational recoding regulates the decoding of the 21st and the 22nd amino acids selenocysteine and pyrrolysine, respectively, and only one case of programmed -1 frameshifting has been reported so far in Saccharolobus solfataricus P2. However, further putative events of translational recoding have been hypothesized in other archaeal species, but not extensively studied and confirmed yet. Although this phenomenon could have some implication for the physiology and adaptation of life in extreme environments, this field is still underexplored and genes whose expression could be regulated by recoding are still poorly characterized. The study of these recoding episodes in Archaea is urgently needed.},
}
@article {pmid34145392,
year = {2021},
author = {Kurth, JM and Nobu, MK and Tamaki, H and de Jonge, N and Berger, S and Jetten, MSM and Yamamoto, K and Mayumi, D and Sakata, S and Bai, L and Cheng, L and Nielsen, JL and Kamagata, Y and Wagner, T and Welte, CU},
title = {Methanogenic archaea use a bacteria-like methyltransferase system to demethoxylate aromatic compounds.},
journal = {The ISME journal},
volume = {15},
number = {12},
pages = {3549-3565},
pmid = {34145392},
issn = {1751-7370},
mesh = {*Euryarchaeota/enzymology/genetics ; Methane/*metabolism ; *Methyltransferases/genetics ; },
abstract = {Methane-generating archaea drive the final step in anaerobic organic compound mineralization and dictate the carbon flow of Earth's diverse anoxic ecosystems in the absence of inorganic electron acceptors. Although such Archaea were presumed to be restricted to life on simple compounds like hydrogen (H2), acetate or methanol, an archaeon, Methermicoccus shengliensis, was recently found to convert methoxylated aromatic compounds to methane. Methoxylated aromatic compounds are important components of lignin and coal, and are present in most subsurface sediments. Despite the novelty of such a methoxydotrophic archaeon its metabolism has not yet been explored. In this study, transcriptomics and proteomics reveal that under methoxydotrophic growth M. shengliensis expresses an O-demethylation/methyltransferase system related to the one used by acetogenic bacteria. Enzymatic assays provide evidence for a two step-mechanisms in which the methyl-group from the methoxy compound is (1) transferred on cobalamin and (2) further transferred on the C1-carrier tetrahydromethanopterin, a mechanism distinct from conventional methanogenic methyl-transfer systems which use coenzyme M as final acceptor. We further hypothesize that this likely leads to an atypical use of the methanogenesis pathway that derives cellular energy from methyl transfer (Mtr) rather than electron transfer (F420H2 re-oxidation) as found for methylotrophic methanogenesis.},
}
@article {pmid34145390,
year = {2021},
author = {Murali, R and Gennis, RB and Hemp, J},
title = {Evolution of the cytochrome bd oxygen reductase superfamily and the function of CydAA' in Archaea.},
journal = {The ISME journal},
volume = {15},
number = {12},
pages = {3534-3548},
pmid = {34145390},
issn = {1751-7370},
support = {R01 AI148160/AI/NIAID NIH HHS/United States ; },
mesh = {Archaea/enzymology/*genetics ; Archaeal Proteins/*genetics ; Cytochrome b Group/*genetics ; Electron Transport Chain Complex Proteins/*genetics ; Evolution, Molecular ; Oxidation-Reduction ; *Oxidoreductases/genetics ; Oxygen ; },
abstract = {Cytochrome bd-type oxygen reductases (cytbd) belong to one of three enzyme superfamilies that catalyze oxygen reduction to water. They are widely distributed in Bacteria and Archaea, but the full extent of their biochemical diversity is unknown. Here we used phylogenomics to identify three families and several subfamilies within the cytbd superfamily. The core architecture shared by all members of the superfamily consists of four transmembrane helices that bind two active site hemes, which are responsible for oxygen reduction. While previously characterized cytochrome bd-type oxygen reductases use quinol as an electron donor to reduce oxygen, sequence analysis shows that only one of the identified families has a conserved quinol binding site. The other families are missing this feature, suggesting that they use an alternative electron donor. Multiple gene duplication events were identified within the superfamily, resulting in significant evolutionary and structural diversity. The CydAA' cytbd, found exclusively in Archaea, is formed by the co-association of two superfamily paralogs. We heterologously expressed CydAA' from Caldivirga maquilingensis and demonstrated that it performs oxygen reduction with quinol as an electron donor. Strikingly, CydAA' is the first isoform of cytbd containing only b-type hemes shown to be active when isolated from membranes, demonstrating that oxygen reductase activity in this superfamily is not dependent on heme d.},
}
@article {pmid34142100,
year = {2021},
author = {Takemata, N and Bell, SD},
title = {Chromosome conformation capture assay combined with biotin enrichment for hyperthermophilic archaea.},
journal = {STAR protocols},
volume = {2},
number = {2},
pages = {100576},
pmid = {34142100},
issn = {2666-1667},
support = {R01 GM135178/GM/NIGMS NIH HHS/United States ; },
mesh = {Biotin/*metabolism ; *Chromosomes, Archaeal ; Genes, Archaeal ; Sequence Analysis, DNA/methods ; Sulfolobus acidocaldarius/genetics/*metabolism ; },
abstract = {Chromosome organization in archaea has long been enigmatic due, in part, to the typically small cell size of archaea and the extremophilic nature of many of the model archaeal species studies, rendering live-cell imaging technically challenging. To circumvent these problems, we recently applied chromosome conformation capture combined with biotin enrichment and deep sequencing (Hi-C) to members of hyperthermophilic archaeal genus Sulfolobus. Our optimized Hi-C protocol described here permits delineation of how Sulfolobus species organize their chromosomes. For complete details on the use and execution of this protocol, please refer to Takemata et al. (2019).},
}
@article {pmid34140936,
year = {2021},
author = {Castelle, CJ and Méheust, R and Jaffe, AL and Seitz, K and Gong, X and Baker, BJ and Banfield, JF},
title = {Protein Family Content Uncovers Lineage Relationships and Bacterial Pathway Maintenance Mechanisms in DPANN Archaea.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {660052},
pmid = {34140936},
issn = {1664-302X},
abstract = {DPANN are small-celled archaea that are generally predicted to be symbionts, and in some cases are known episymbionts of other archaea. As the monophyly of the DPANN remains uncertain, we hypothesized that proteome content could reveal relationships among DPANN lineages, constrain genetic overlap with bacteria, and illustrate how organisms with hybrid bacterial and archaeal protein sets might function. We tested this hypothesis using protein family content that was defined in part using 3,197 genomes including 569 newly reconstructed genomes. Protein family content clearly separates the final set of 390 DPANN genomes from other archaea, paralleling the separation of Candidate Phyla Radiation (CPR) bacteria from all other bacteria. This separation is partly driven by hypothetical proteins, some of which may be symbiosis-related. Pacearchaeota with the most limited predicted metabolic capacities have Form II/III and III-like Rubisco, suggesting metabolisms based on scavenged nucleotides. Intriguingly, the Pacearchaeota and Woesearchaeota with the smallest genomes also tend to encode large extracellular murein-like lytic transglycosylase domain proteins that may bind and degrade components of bacterial cell walls, indicating that some might be episymbionts of bacteria. The pathway for biosynthesis of bacterial isoprenoids is widespread in Woesearchaeota genomes and is encoded in proximity to genes involved in bacterial fatty acids synthesis. Surprisingly, in some DPANN genomes we identified a pathway for synthesis of queuosine, an unusual nucleotide in tRNAs of bacteria. Other bacterial systems are predicted to be involved in protein refolding. For example, many DPANN have the complete bacterial DnaK-DnaJ-GrpE system and many Woesearchaeota and Pacearchaeota possess bacterial group I chaperones. Thus, many DPANN appear to have mechanisms to ensure efficient protein folding of both archaeal and laterally acquired bacterial proteins.},
}
@article {pmid34138841,
year = {2021},
author = {Schulze, S and Pfeiffer, F and Garcia, BA and Pohlschroder, M},
title = {Comprehensive glycoproteomics shines new light on the complexity and extent of glycosylation in archaea.},
journal = {PLoS biology},
volume = {19},
number = {6},
pages = {e3001277},
pmid = {34138841},
issn = {1545-7885},
support = {P01 CA196539/CA/NCI NIH HHS/United States ; R01 AI118891/AI/NIAID NIH HHS/United States ; },
mesh = {Amino Acid Sequence ; Archaeal Proteins/chemistry/*metabolism ; Biological Assay ; Cell Shape/drug effects ; Databases, Protein ; Glycopeptides/chemistry/*metabolism ; Glycoproteins/chemistry/*metabolism ; Glycosylation/drug effects ; Haloferax volcanii/drug effects/*metabolism ; Mutation/genetics ; Phenotype ; Phylogeny ; Proteomics ; Sodium Chloride/pharmacology ; },
abstract = {Glycosylation is one of the most complex posttranslational protein modifications. Its importance has been established not only for eukaryotes but also for a variety of prokaryotic cellular processes, such as biofilm formation, motility, and mating. However, comprehensive glycoproteomic analyses are largely missing in prokaryotes. Here, we extend the phenotypic characterization of N-glycosylation pathway mutants in Haloferax volcanii and provide a detailed glycoproteome for this model archaeon through the mass spectrometric analysis of intact glycopeptides. Using in-depth glycoproteomic datasets generated for the wild-type (WT) and mutant strains as well as a reanalysis of datasets within the Archaeal Proteome Project (ArcPP), we identify the largest archaeal glycoproteome described so far. We further show that different N-glycosylation pathways can modify the same glycosites under the same culture conditions. The extent and complexity of the Hfx. volcanii N-glycoproteome revealed here provide new insights into the roles of N-glycosylation in archaeal cell biology.},
}
@article {pmid34119867,
year = {2021},
author = {Shen, LD and Yang, YL and Liu, JQ and Hu, ZH and Liu, X and Tian, MH and Yang, WT and Jin, JH and Wang, HY and Wang, YY and Wu, HS},
title = {Different responses of ammonia-oxidizing archaea and bacteria in paddy soils to elevated CO2 concentration.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {286},
number = {},
pages = {117558},
doi = {10.1016/j.envpol.2021.117558},
pmid = {34119867},
issn = {1873-6424},
mesh = {*Ammonia ; *Archaea/genetics ; Bacteria/genetics ; Carbon Dioxide ; Ecosystem ; Nitrification ; Oxidation-Reduction ; Phylogeny ; Soil ; Soil Microbiology ; },
abstract = {The elevated atmospheric CO2 concentration is well known to have an important effect on soil nutrient cycling. Ammonia oxidation, mediated by ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB), is the rate-limiting step in soil nitrification, which controls the availability of two key soil nutrients (ammonium and nitrate) for crops. Until now, how the AOA and AOB communities in paddy soils respond to elevated CO2 remains largely unknown. Here, we examined the communities of AOA and AOB and nitrification potential at both surface (0-5 cm) and subsurface (5-10 cm) soil layers of paddy fields under three different CO2 treatments, including CK (ambient CO2 concentration), LT (CK + 160 ppm of CO2) and HT (CK + 200 ppm of CO2). The elevated CO2 was found to have a greater impact on the community structure of AOB than that of AOA in surface soils as revealed by high-throughput sequencing of their amoA genes. However, no obvious variation of AOA or AOB communities was observed in subsurface soils among different CO2 treatments. The abundance of AOA and AOB, and nitrification potential were significantly increased in surface soils under elevated CO2. The variation of AOB abundance correlated well with the variation of nitrification potential. The soil water content and dissolved organic carbon content had important impacts on the dynamic of AOB communities and nitrification potential. Overall, our results showed different responses of AOA and AOB communities to elevated CO2 in paddy ecosystems, and AOB were more sensitive to the rising CO2 concentration.},
}
@article {pmid34113850,
year = {2021},
author = {Takemata, N and Bell, SD},
title = {High-resolution analysis of chromosome conformation in hyperthermophilic archaea.},
journal = {STAR protocols},
volume = {2},
number = {2},
pages = {100562},
pmid = {34113850},
issn = {2666-1667},
support = {R01 GM135178/GM/NIGMS NIH HHS/United States ; },
mesh = {*Chromosomes ; DNA, Archaeal/genetics ; High-Throughput Nucleotide Sequencing/methods ; Polymerase Chain Reaction/methods ; Sulfolobus/*genetics ; },
abstract = {Chromosome conformation capture (3C) techniques are emerging as promising approaches to study genome organization in Archaea, the least understood domain of life in terms of chromosome biology. Here, we describe a 3C technique combined with deep sequencing for the hyperthermophilic archaeal genus Sulfolobus. Instead of using restriction enzymes compatible with fill-in labeling, this protocol uses the 4-bp blunt cutter AluI to generate high-resolution (up to 2 kb) contact maps from Sulfolobus species. For complete details on the use and execution of this protocol, please refer to Takemata and Bell (2021).},
}
@article {pmid34113328,
year = {2021},
author = {Garnier, F and Couturier, M and Débat, H and Nadal, M},
title = {Archaea: A Gold Mine for Topoisomerase Diversity.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {661411},
pmid = {34113328},
issn = {1664-302X},
abstract = {The control of DNA topology is a prerequisite for all the DNA transactions such as DNA replication, repair, recombination, and transcription. This global control is carried out by essential enzymes, named DNA-topoisomerases, that are mandatory for the genome stability. Since many decades, the Archaea provide a significant panel of new types of topoisomerases such as the reverse gyrase, the type IIB or the type IC. These more or less recent discoveries largely contributed to change the understanding of the role of the DNA topoisomerases in all the living world. Despite their very different life styles, Archaea share a quasi-homogeneous set of DNA-topoisomerases, except thermophilic organisms that possess at least one reverse gyrase that is considered a marker of the thermophily. Here, we discuss the effect of the life style of Archaea on DNA structure and topology and then we review the content of these essential enzymes within all the archaeal diversity based on complete sequenced genomes available. Finally, we discuss their roles, in particular in the processes involved in both the archaeal adaptation and the preservation of the genome stability.},
}
@article {pmid34112969,
year = {2021},
author = {Payne, D and Spietz, RL and Boyd, ES},
title = {Reductive dissolution of pyrite by methanogenic archaea.},
journal = {The ISME journal},
volume = {15},
number = {12},
pages = {3498-3507},
pmid = {34112969},
issn = {1751-7370},
mesh = {*Archaea/genetics ; Iron ; Solubility ; *Sulfides ; },
abstract = {The formation and fate of pyrite (FeS2) modulates global iron, sulfur, carbon, and oxygen biogeochemical cycles and has done so since early in Earth's geological history. A longstanding paradigm is that FeS2 is stable at low temperature and is unavailable to microorganisms in the absence of oxygen and oxidative weathering. Here, we show that methanogens can catalyze the reductive dissolution of FeS2 at low temperature (≤38 °C) and utilize dissolution products to meet cellular iron and sulfur demands associated with the biosynthesis of simple and complex co-factors. Direct access to FeS2 is required to catalyze its reduction and/or to assimilate iron monosulfide that likely forms through coupled reductive dissolution and precipitation, consistent with close associations observed between cells and FeS2. These findings demonstrate that FeS2 is bioavailable to anaerobic methanogens and can be mobilized in low temperature anoxic environments. Given that methanogens evolved at least 3.46 Gya, these data indicate that the microbial contribution to the iron and sulfur cycles in ancient and contemporary anoxic environments may be more complex and robust than previously recognized, with impacts on the sources and sinks of iron and sulfur and other bio-essential and thiophilic elements such as nickel and cobalt.},
}
@article {pmid37223257,
year = {2021},
author = {Liu, J and Soler, N and Gorlas, A and Cvirkaite-Krupovic, V and Krupovic, M and Forterre, P},
title = {Extracellular membrane vesicles and nanotubes in Archaea.},
journal = {microLife},
volume = {2},
number = {},
pages = {uqab007},
pmid = {37223257},
issn = {2633-6693},
abstract = {Membrane-bound extracellular vesicles (EVs) are secreted by cells from all three domains of life and their implication in various biological processes is increasingly recognized. In this review, we summarize the current knowledge on archaeal EVs and nanotubes, and emphasize their biological significance. In archaea, the EVs and nanotubes have been largely studied in representative species from the phyla Crenarchaeota and Euryarchaeota. The archaeal EVs have been linked to several physiological processes such as detoxification, biomineralization and transport of biological molecules, including chromosomal, viral or plasmid DNA, thereby taking part in genome evolution and adaptation through horizontal gene transfer. The biological significance of archaeal nanotubes is yet to be demonstrated, although they could participate in EV biogenesis or exchange of cellular contents. We also discuss the biological mechanisms leading to EV/nanotube biogenesis in Archaea. It has been recently demonstrated that, similar to eukaryotes, EV budding in crenarchaea depends on the ESCRT machinery, whereas the mechanism of EV budding in euryarchaeal lineages, which lack the ESCRT-III homologues, remains unknown.},
}
@article {pmid34099860,
year = {2021},
author = {Watanabe, S and Murase, Y and Watanabe, Y and Sakurai, Y and Tajima, K},
title = {Crystal structures of aconitase X enzymes from bacteria and archaea provide insights into the molecular evolution of the aconitase superfamily.},
journal = {Communications biology},
volume = {4},
number = {1},
pages = {687},
pmid = {34099860},
issn = {2399-3642},
mesh = {Aconitate Hydratase/*chemistry ; Agrobacterium tumefaciens/chemistry/*enzymology ; Catalytic Domain ; Crystallography, X-Ray ; Evolution, Molecular ; Models, Molecular ; Protein Conformation ; Thermococcus/chemistry/*enzymology ; },
abstract = {Aconitase superfamily members catalyze the homologous isomerization of specific substrates by sequential dehydration and hydration and contain a [4Fe-4S] cluster. However, monomeric and heterodimeric types of function unknown aconitase X (AcnX) have recently been characterized as a cis-3-hydroxy-L-proline dehydratase (AcnXType-I) and mevalonate 5-phosphate dehydratase (AcnXType-II), respectively. We herein elucidated the crystal structures of AcnXType-I from Agrobacterium tumefaciens (AtAcnX) and AcnXType-II from Thermococcus kodakarensis (TkAcnX) without a ligand and in complex with substrates. AtAcnX and TkAcnX contained the [2Fe-2S] and [3Fe-4S] clusters, respectively, conforming to UV and EPR spectroscopy analyses. The binding sites of the [Fe-S] cluster and substrate were clearlydifferent from those that were completely conserved in other aconitase enzymes; however, theoverall structural frameworks and locations of active sites were partially similar to each other.These results provide novel insights into the evolutionary scenario of the aconitase superfamilybased on the recruitment hypothesis.},
}
@article {pmid34088904,
year = {2021},
author = {Pende, N and Sogues, A and Megrian, D and Sartori-Rupp, A and England, P and Palabikyan, H and Rittmann, SKR and Graña, M and Wehenkel, AM and Alzari, PM and Gribaldo, S},
title = {SepF is the FtsZ anchor in archaea, with features of an ancestral cell division system.},
journal = {Nature communications},
volume = {12},
number = {1},
pages = {3214},
pmid = {34088904},
issn = {2041-1723},
mesh = {Archaeal Proteins/chemistry/genetics/*metabolism ; Bacterial Proteins/chemistry/genetics/metabolism ; Cell Cycle ; Cell Division/genetics/*physiology ; Conserved Sequence ; Crystallography, X-Ray ; Evolution, Molecular ; Methanobrevibacter/genetics/*metabolism/ultrastructure ; Microscopy, Electron, Transmission ; Models, Molecular ; Phylogeny ; Protein Binding ; Protein Interaction Domains and Motifs ; Protein Structure, Quaternary ; Recombinant Proteins/genetics/metabolism/ultrastructure ; },
abstract = {Most archaea divide by binary fission using an FtsZ-based system similar to that of bacteria, but they lack many of the divisome components described in model bacterial organisms. Notably, among the multiple factors that tether FtsZ to the membrane during bacterial cell constriction, archaea only possess SepF-like homologs. Here, we combine structural, cellular, and evolutionary analyses to demonstrate that SepF is the FtsZ anchor in the human-associated archaeon Methanobrevibacter smithii. 3D super-resolution microscopy and quantitative analysis of immunolabeled cells show that SepF transiently co-localizes with FtsZ at the septum and possibly primes the future division plane. M. smithii SepF binds to membranes and to FtsZ, inducing filament bundling. High-resolution crystal structures of archaeal SepF alone and in complex with the FtsZ C-terminal domain (FtsZCTD) reveal that SepF forms a dimer with a homodimerization interface driving a binding mode that is different from that previously reported in bacteria. Phylogenetic analyses of SepF and FtsZ from bacteria and archaea indicate that the two proteins may date back to the Last Universal Common Ancestor (LUCA), and we speculate that the archaeal mode of SepF/FtsZ interaction might reflect an ancestral feature. Our results provide insights into the mechanisms of archaeal cell division and pave the way for a better understanding of the processes underlying the divide between the two prokaryotic domains.},
}
@article {pmid34065163,
year = {2021},
author = {Vázquez-Madrigal, AS and Barbachano-Torres, A and Arellano-Plaza, M and Kirchmayr, MR and Finore, I and Poli, A and Nicolaus, B and De la Torre Zavala, S and Camacho-Ruiz, RM},
title = {Effect of Carbon Sources in Carotenoid Production from Haloarcula sp. M1, Halolamina sp. M3 and Halorubrum sp. M5, Halophilic Archaea Isolated from Sonora Saltern, Mexico.},
journal = {Microorganisms},
volume = {9},
number = {5},
pages = {},
pmid = {34065163},
issn = {2076-2607},
abstract = {The isolation and molecular and chemo-taxonomic identification of seventeen halophilic archaea from the Santa Bárbara saltern, Sonora, México, were performed. Eight strains were selected based on pigmentation. Molecular identification revealed that the strains belonged to the Haloarcula, Halolamina and Halorubrum genera. Neutral lipids (quinones) were identified in all strains. Glycolipid S-DGD was found only in Halolamina sp. strain M3; polar phospholipids 2,3-O-phytanyl-sn-glycerol-1-phosphoryl-3-sn-glycerol (PG), 2,3-di-O-phytanyl-sn-glycero-1-phospho-3'-sn-glycerol-1'-methyl phosphate (PGP-Me) and sodium salt 1-(3-sn-phosphatidyl)-rac-glycerol were found in all the strains; and one unidentified glyco-phospholipid in strains M1, M3 and M4. Strains M1, M3 and M5 were selected for further studies based on carotenoid production. The effect of glucose and succinic and glutamic acid on carotenoid production was assessed. In particular, carotenoid production and growth significantly improved in the presence of glucose in strains Haloarcula sp. M1 and Halorubrum sp. M5 but not in Halolamina sp. M3. Glutamic and succinic acid had no effect on carotenoid production, and even was negative for Halorubrum sp. M5. Growth was increased by glutamic and succinic acid on Haloarcula sp. M1 but not in the other strains. This work describes for first time the presence of halophilic archaea in the Santa Bárbara saltern and highlights the differences in the effect of carbon sources on the growth and carotenoid production of haloarchaea.},
}
@article {pmid34060911,
year = {2021},
author = {McNichol, J and Berube, PM and Biller, SJ and Fuhrman, JA},
title = {Evaluating and Improving Small Subunit rRNA PCR Primer Coverage for Bacteria, Archaea, and Eukaryotes Using Metagenomes from Global Ocean Surveys.},
journal = {mSystems},
volume = {6},
number = {3},
pages = {e0056521},
pmid = {34060911},
issn = {2379-5077},
support = {3779//Gordon and Betty Moore Foundation (GBMF)/ ; OCE-1737409//National Science Foundation (NSF)/ ; 549943//Simons Foundation (SF)/ ; },
abstract = {Small subunit rRNA (SSU rRNA) amplicon sequencing can quantitatively and comprehensively profile natural microbiomes, representing a critically important tool for studying diverse global ecosystems. However, results will only be accurate if PCR primers perfectly match the rRNA of all organisms present. To evaluate how well marine microorganisms across all 3 domains are detected by this method, we compared commonly used primers with >300 million rRNA gene sequences retrieved from globally distributed marine metagenomes. The best-performing primers compared to 16S rRNA of bacteria and archaea were 515Y/926R and 515Y/806RB, which perfectly matched over 96% of all sequences. Considering cyanobacterial and chloroplast 16S rRNA, 515Y/926R had the highest coverage (99%), making this set ideal for quantifying marine primary producers. For eukaryotic 18S rRNA sequences, 515Y/926R also performed best (88%), followed by V4R/V4RB (18S rRNA specific; 82%)-demonstrating that the 515Y/926R combination performs best overall for all 3 domains. Using Atlantic and Pacific Ocean samples, we demonstrate high correspondence between 515Y/926R amplicon abundances (generated for this study) and metagenomic 16S rRNA (median R[2] = 0.98, n = 272), indicating amplicons can produce equally accurate community composition data compared with shotgun metagenomics. Our analysis also revealed that expected performance of all primer sets could be improved with minor modifications, pointing toward a nearly completely universal primer set that could accurately quantify biogeochemically important taxa in ecosystems ranging from the deep sea to the surface. In addition, our reproducible bioinformatic workflow can guide microbiome researchers studying different ecosystems or human health to similarly improve existing primers and generate more accurate quantitative amplicon data. IMPORTANCE PCR amplification and sequencing of marker genes is a low-cost technique for monitoring prokaryotic and eukaryotic microbial communities across space and time but will work optimally only if environmental organisms match PCR primer sequences exactly. In this study, we evaluated how well primers match globally distributed short-read oceanic metagenomes. Our results demonstrate that primer sets vary widely in performance, and that at least for marine systems, rRNA amplicon data from some primers lack significant biases compared to metagenomes. We also show that it is theoretically possible to create a nearly universal primer set for diverse saline environments by defining a specific mixture of a few dozen oligonucleotides, and present a software pipeline that can guide rational design of primers for any environment with available meta'omic data.},
}
@article {pmid37938645,
year = {2021},
author = {Huang, L and Chakrabarti, S and Cooper, J and Perez, A and John, SM and Daroub, SH and Martens-Habbena, W},
title = {Ammonia-oxidizing archaea are integral to nitrogen cycling in a highly fertile agricultural soil.},
journal = {ISME communications},
volume = {1},
number = {1},
pages = {19},
pmid = {37938645},
issn = {2730-6151},
abstract = {Nitrification is a central process in the global nitrogen cycle, carried out by a complex network of ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), complete ammonia-oxidizing (comammox) bacteria, and nitrite-oxidizing bacteria (NOB). Nitrification is responsible for significant nitrogen leaching and N2O emissions and thought to impede plant nitrogen use efficiency in agricultural systems. However, the actual contribution of each nitrifier group to net rates and N2O emissions remain poorly understood. We hypothesized that highly fertile agricultural soils with high organic matter mineralization rates could allow a detailed characterization of N cycling in these soils. Using a combination of molecular and activity measurements, we show that in a mixed AOA, AOB, and comammox community, AOA outnumbered low diversity assemblages of AOB and comammox 50- to 430-fold, and strongly dominated net nitrification activities with low N2O yields between 0.18 and 0.41 ng N2O-N per µg NOx-N in cropped, fallow, as well as native soil. Nitrification rates were not significantly different in plant-covered and fallow plots. Mass balance calculations indicated that plants relied heavily on nitrate, and not ammonium as primary nitrogen source in these soils. Together, these results imply AOA as integral part of the nitrogen cycle in a highly fertile agricultural soil.},
}
@article {pmid34027477,
year = {2021},
author = {Cockram, C and Thierry, A and Koszul, R},
title = {Generation of gene-level resolution chromosome contact maps in bacteria and archaea.},
journal = {STAR protocols},
volume = {2},
number = {2},
pages = {100512},
pmid = {34027477},
issn = {2666-1667},
mesh = {Archaea/*genetics ; Bacteria/*genetics ; *Chromosome Mapping ; Chromosomes, Archaeal/*genetics ; Chromosomes, Bacterial/*genetics ; Genome, Archaeal ; Genome, Bacterial ; },
abstract = {Chromosome conformation capture (Hi-C) has become a routine method for probing the 3D organization of genomes. However, when applied to bacteria and archaea, current protocols are expensive and limited in their resolution. By dissecting the different steps of published eukaryotic and prokaryotic Hi-C protocols, we have developed a cost- and time-effective approach to generate high-resolution (down to 500 bp - 1 kb) contact matrices of both bacteria and archaea genomes. For complete details on the use and execution of this protocol, please refer to Cockram et al. (2020).},
}
@article {pmid34027378,
year = {2021},
author = {Inkinen, J and Siponen, S and Jayaprakash, B and Tiwari, A and Hokajärvi, AM and Pursiainen, A and Ikonen, J and Kauppinen, A and Miettinen, IT and Paananen, J and Torvinen, E and Kolehmainen, M and Pitkänen, T},
title = {Diverse and active archaea communities occur in non-disinfected drinking water systems-Less activity revealed in disinfected and hot water systems.},
journal = {Water research X},
volume = {12},
number = {},
pages = {100101},
pmid = {34027378},
issn = {2589-9147},
abstract = {The knowledge about the members of active archaea communities in DWDS is limited. The current understanding is based on high-throughput 16S ribosomal RNA gene (DNA-based) amplicon sequencing that reveals the diversity of active, dormant, and dead members of the prokaryote (bacteria, archaea) communities. The sequencing primers optimized for bacteria community analysis may underestimate the share of the archaea community. This study characterized archaea communities at five full-scale drinking water distribution systems (DWDS), representing a variety of drinking water production units (A-E); A&amp;B use artificially recharged non-disinfected groundwater (ARG), the other DWDS's supplied water disinfected by using ultraviolet (UV) light and chlorine compounds, C&amp;D were surface waterworks and E was a ground waterworks. For the first time for archaea community analyses, this study employed the archaea-specific high-throughput sequencing primers for 16S ribosomal RNA (rRNA) as a target (reverse-transcribed cDNA; an RNA-based approach) in addition to the previously used 16S rRNA gene target (rDNA; a DNA-based approach) to reveal the active fraction of the archaea present in DWDS. The archaea community structure in varying environmental conditions in the water and biofilm of the five DWDSs were investigated by taking into consideration the system properties (cold or hot water system) and water age (distance from the treatment plants) in samples from each season of one year. The RNA-based archaea amplicon reads were obtained mostly from cold water samples from DWDSs (A-B) distributing water without disinfection where the DNA-based and RNA-based analysis created separate clusters in a weighted beta-diversity analysis. The season and location in DWDS A further affected the diversity of these archaea communities as was seen by different clusters in beta-diversity plots. The recovery of archaea reads was not adequate for analysis in any of the disinfected samples in DWDSs C-E or non-disinfected hot water in DWDSs A-B when utilizing RNA-based template. The metabolically active archaea community of DWDSs thus seemed to be effectively controlled by disinfection of water and in the hot water systems by the temperature. All biofilms regardless of DWDS showed lower species richness values (mainly Nitrososphaeria class) than non-disinfected water from DWDSs A-B where several archaea classes occurred (e.g. Woesearchaeia, Nitrososphaeria, Micrarchaeia, Methanomicrobia, Iairchaeia, Bathyarchaeia) indicating only part of the archaea members were able to survive in biofilms. Thus, Archaea has been shown as a significant part of normal DWDS biota, and their role especially in non-disinfected DWDS may be more important than previously considered.},
}
@article {pmid34026962,
year = {2020},
author = {Bomberg, M and Miettinen, H},
title = {Data on the optimization of an archaea-specific probe-based qPCR assay.},
journal = {Data in brief},
volume = {33},
number = {},
pages = {106610},
pmid = {34026962},
issn = {2352-3409},
abstract = {Estimation of archaeal numbers by use of fluorescent DNA binding dyes is challenging, because primers targeting the archaeal 16SrRNA genes readily also bind to bacterial 16S rRNA gene sequences, especially when the relative abundance of bacteria is greater than that of archaea. In order to increase specificity, we optimized a fluorescent probe-based assay using previously published archaeal primers and probe. The assay was tested on genomic DNA of pure bacterial and archaeal cultures and optimized using PCR amplicons of the archaeal pure cultures. The used bacterial strains showed slight amplification using the fluorescent dye assay, whereas all archaeal strains could be amplified with the archaea primers used. Due to differences in genome size and number of 16S rRNA gene copies between the tested archaeal strains, the amplification level varied greatly between the strains. Therefore, we also tested the amplification using PCR amplified fragments of the archaeal 16S rRNA genes. The tests with the archaeal 16S rRNA gene amplicons showed good amplification, although the amplification efficiency still varied between archaeal strains. The qPCR assay was used to estimate the archaeal numbers in process water of a multi-metal mine's metallurgical plant [1] and will be used in similar future microbiological analysis included in the H2020 ITERAMS project (Grant agreement# 730480).},
}
@article {pmid34026831,
year = {2021},
author = {Lei, L and Burton, ZF},
title = {Early Evolution of Transcription Systems and Divergence of Archaea and Bacteria.},
journal = {Frontiers in molecular biosciences},
volume = {8},
number = {},
pages = {651134},
pmid = {34026831},
issn = {2296-889X},
abstract = {DNA template-dependent multi-subunit RNA polymerases (RNAPs) found in all three domains of life and some viruses are of the two-double-Ψ-β-barrel (DPBB) type. The 2-DPBB protein format is also found in some RNA template-dependent RNAPs and a major replicative DNA template-dependent DNA polymerase (DNAP) from Archaea (PolD). The 2-DPBB family of RNAPs and DNAPs probably evolved prior to the last universal common cellular ancestor (LUCA). Archaeal Transcription Factor B (TFB) and bacterial σ factors include homologous strings of helix-turn-helix units. The consequences of TFB-σ homology are discussed in terms of the evolution of archaeal and bacterial core promoters. Domain-specific DPBB loop inserts functionally connect general transcription factors to the RNAP active site. Archaea appear to be more similar to LUCA than Bacteria. Evolution of bacterial σ factors from TFB appears to have driven divergence of Bacteria from Archaea, splitting the prokaryotic domains.},
}
@article {pmid34019119,
year = {2021},
author = {Naitam, MG and Kaushik, R},
title = {Archaea: An Agro-Ecological Perspective.},
journal = {Current microbiology},
volume = {78},
number = {7},
pages = {2510-2521},
pmid = {34019119},
issn = {1432-0991},
support = {BT/PR6540/BCE/8/917/2012//Department of Biotechnology , Ministry of Science and Technology/ ; },
mesh = {*Archaea/genetics ; Bacteria/genetics ; Fungi/genetics ; Rhizosphere ; Soil ; *Soil Microbiology ; },
abstract = {Microorganisms inhabiting bulk soil and rhizosphere play an important role in soil biogeochemical cycles leading to enhanced plant growth and productivity. In this context, the role of bacteria is well established, however, not much reports are available about the role archaea plays in this regard. Literature suggests that archaea also play a greater role in nutrient cycling of carbon, nitrogen, sulfur, and other minerals, possess various plant growth promoting attributes, and can impart tolerance to various abiotic stresses (especially osmotic and oxidative) in areas of high salinity, low and high temperatures and hydrogen ion concentrations. Thermoacidophilic archaea have been found to potentially involve in bioleaching of mineral ores and bioremediation of chemical pollutants and aromatic compounds. Looking at immense potential of archaea in promoting plant growth, alleviating abiotic stresses, and remediating contaminated sites, detailed studies are required to establish their role in different ecological processes, and their interactions in rhizosphere with plant and other microflora (bacteria and fungi) in different ecosystems. In this review, a brief discussion on archaea from the agro-ecological point of view is presented.},
}
@article {pmid34017110,
year = {2021},
author = {Graham, F},
title = {Daily briefing: Enigmatic archaea might be key to complex life.},
journal = {Nature},
volume = {},
number = {},
pages = {},
doi = {10.1038/d41586-021-01366-4},
pmid = {34017110},
issn = {1476-4687},
}
@article {pmid33997611,
year = {2021},
author = {Clemmons, BA and Schneider, LG and Melchior, EA and Lindholm-Perry, AK and Hales, KE and Wells, JE and Freetly, HC and Hansen, SL and Drewnoski, ME and Hartman, SJ and Myer, PR},
title = {The effects of feeding ferric citrate on ruminal bacteria, methanogenic archaea and methane production in growing beef steers.},
journal = {Access microbiology},
volume = {3},
number = {1},
pages = {acmi000180},
pmid = {33997611},
issn = {2516-8290},
abstract = {Methane produced by cattle is one of the contributors of anthropogenic greenhouse gas. Methods to lessen methane emissions from cattle have been met with varying success; thus establishing consistent methods for decreasing methane production are imperative. Ferric iron may possibly act to decrease methane by acting as an alternative electron acceptor. The objective of this study was to assess the effect of ferric citrate on the rumen bacterial and archaeal communities and its impact on methane production. In this study, eight steers were used in a repeated Latin square design with 0, 250, 500 or 750 mg Fe/kg DM of ferric iron (as ferric citrate) in four different periods. Each period consisted of a 16 day adaptation period and 5 day sampling period. During each sampling period, methane production was measured, and rumen content was collected for bacterial and archaeal community analyses. Normally distributed data were analysed using a mixed model ANOVA using the GLIMMIX procedure of SAS, and non-normally distributed data were analysed in the same manner following ranking. Ferric citrate did not have any effect on bacterial community composition, methanogenic archaea nor methane production (P>0.05). Ferric citrate may not be a viable option to observe a ruminal response for decreases in enteric methane production.},
}
@article {pmid33995325,
year = {2021},
author = {Weixlbaumer, A and Grünberger, F and Werner, F and Grohmann, D},
title = {Coupling of Transcription and Translation in Archaea: Cues From the Bacterial World.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {661827},
pmid = {33995325},
issn = {1664-302X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {The lack of a nucleus is the defining cellular feature of bacteria and archaea. Consequently, transcription and translation are occurring in the same compartment, proceed simultaneously and likely in a coupled fashion. Recent cryo-electron microscopy (cryo-EM) and tomography data, also combined with crosslinking-mass spectrometry experiments, have uncovered detailed structural features of the coupling between a transcribing bacterial RNA polymerase (RNAP) and the trailing translating ribosome in Escherichia coli and Mycoplasma pneumoniae. Formation of this supercomplex, called expressome, is mediated by physical interactions between the RNAP-bound transcription elongation factors NusG and/or NusA and the ribosomal proteins including uS10. Based on the structural conservation of the RNAP core enzyme, the ribosome, and the universally conserved elongation factors Spt5 (NusG) and NusA, we discuss requirements and functional implications of transcription-translation coupling in archaea. We furthermore consider additional RNA-mediated and co-transcriptional processes that potentially influence expressome formation in archaea.},
}
@article {pmid33993308,
year = {2021},
author = {Yang, Y and Zhang, C and Lenton, TM and Yan, X and Zhu, M and Zhou, M and Tao, J and Phelps, TJ and Cao, Z},
title = {The Evolution Pathway of Ammonia-Oxidizing Archaea Shaped by Major Geological Events.},
journal = {Molecular biology and evolution},
volume = {38},
number = {9},
pages = {3637-3648},
pmid = {33993308},
issn = {1537-1719},
mesh = {*Ammonia/metabolism ; *Archaea/genetics/metabolism ; Bacteria/genetics ; Oxidation-Reduction ; Soil Microbiology ; },
abstract = {Primordial nitrification processes have been studied extensively using geochemical approaches, but the biological origination of nitrification remains unclear. Ammonia-oxidizing archaea (AOA) are widely distributed nitrifiers and implement the rate-limiting step in nitrification. They are hypothesized to have been important players in the global nitrogen cycle in Earth's early history. We performed systematic phylogenomic and marker gene analyses to elucidate the diversification timeline of AOA evolution. Our results suggested that the AOA ancestor experienced terrestrial geothermal environments at ∼1,165 Ma (1,928-880 Ma), and gradually evolved into mesophilic soil at ∼652 Ma (767-554 Ma) before diversifying into marine settings at ∼509 Ma (629-412 Ma) and later into shallow and deep oceans, respectively. Corroborated by geochemical evidence and modeling, the timing of key diversification nodes can be linked to the global magmatism and glaciation associated with the assembly and breakup of the supercontinent Rodinia, and the later oxygenation of the deep ocean. Results of this integrated study shed light on the geological forces that may have shaped the evolutionary pathways of the AOA, which played an important role in the ancient global nitrogen cycle.},
}
@article {pmid33976787,
year = {2021},
author = {Westoby, M and Nielsen, DA and Gillings, MR and Litchman, E and Madin, JS and Paulsen, IT and Tetu, SG},
title = {Cell size, genome size, and maximum growth rate are near-independent dimensions of ecological variation across bacteria and archaea.},
journal = {Ecology and evolution},
volume = {11},
number = {9},
pages = {3956-3976},
pmid = {33976787},
issn = {2045-7758},
abstract = {Among bacteria and archaea, maximum relative growth rate, cell diameter, and genome size are widely regarded as important influences on ecological strategy. Via the most extensive data compilation so far for these traits across all clades and habitats, we ask whether they are correlated and if so how. Overall, we found little correlation among them, indicating they should be considered as independent dimensions of ecological variation. Nor was correlation evident within particular habitat types. A weak nonlinearity (6% of variance) was found whereby high maximum growth rates (temperature-adjusted) tended to occur in the midrange of cell diameters. Species identified in the literature as oligotrophs or copiotrophs were clearly separated on the dimension of maximum growth rate, but not on the dimensions of genome size or cell diameter.},
}
@article {pmid33941062,
year = {2021},
author = {Mikhaylina, AO and Nikonova, EY and Kostareva, OS and Piendl, W and Erlacher, M and Tishchenko, SV},
title = {Characterization of Regulatory Elements of L11 and L1 Operons in Thermophilic Bacteria and Archaea.},
journal = {Biochemistry. Biokhimiia},
volume = {86},
number = {4},
pages = {397-408},
doi = {10.1134/S0006297921040027},
pmid = {33941062},
issn = {1608-3040},
support = {P 30486/FWF_/Austrian Science Fund FWF/Austria ; },
mesh = {Gene Expression Regulation, Archaeal ; Gene Expression Regulation, Bacterial ; Haloarcula marismortui/*genetics/metabolism ; Hot Temperature ; Operon/*genetics ; *Regulatory Sequences, Nucleic Acid ; Ribosomal Proteins/*genetics ; Thermotoga maritima/*genetics/metabolism ; Thermus thermophilus/*genetics/metabolism ; },
abstract = {Ribosomal protein L1 is a conserved two-domain protein that is involved in formation of the L1 stalk of the large ribosomal subunit. When there are no free binding sites available on the ribosomal 23S RNA, the protein binds to the specific site on the mRNA of its own operon (L11 operon in bacteria and L1 operon in archaea) preventing translation. Here we show that the regulatory properties of the r-protein L1 and its domain I are conserved in the thermophilic bacteria Thermus and Thermotoga and in the halophilic archaeon Haloarcula marismortui. At the same time the revealed features of the operon regulation in thermophilic bacteria suggest presence of two regulatory regions.},
}
@article {pmid33935987,
year = {2021},
author = {Schnakenberg, A and Aromokeye, DA and Kulkarni, A and Maier, L and Wunder, LC and Richter-Heitmann, T and Pape, T and Ristova, PP and Bühring, SI and Dohrmann, I and Bohrmann, G and Kasten, S and Friedrich, MW},
title = {Electron Acceptor Availability Shapes Anaerobically Methane Oxidizing Archaea (ANME) Communities in South Georgia Sediments.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {617280},
pmid = {33935987},
issn = {1664-302X},
abstract = {Anaerobic methane oxidizing archaea (ANME) mediate anaerobic oxidation of methane (AOM) in marine sediments and are therefore important for controlling atmospheric methane concentrations in the water column and ultimately the atmosphere. Numerous previous studies have revealed that AOM is coupled to the reduction of different electron acceptors such as sulfate, nitrate/nitrite or Fe(III)/Mn(IV). However, the influence of electron acceptor availability on the in situ ANME community composition in sediments remains largely unknown. Here, we investigated the electron acceptor availability and compared the microbial in situ communities of three methane-rich locations offshore the sub-Antarctic island South Georgia, by Illumina sequencing and qPCR of mcrA genes. The methanic zone (MZ) sediments of Royal Trough and Church Trough comprised high sulfide concentrations of up to 4 and 19 mM, respectively. In contrast, those of the Cumberland Bay fjord accounted for relatively high concentrations of dissolved iron (up to 186 μM). Whereas the ANME community in the sulfidic sites Church Trough and Royal Trough mainly comprised members of the ANME-1 clade, the order-level clade "ANME-1-related" (Lever and Teske, 2015) was most abundant in the iron-rich site in Cumberland Bay fjord, indicating that the availability of electron acceptors has a strong selective effect on the ANME community. This study shows that potential electron acceptors for methane oxidation may serve as environmental filters to select for the ANME community composition and adds to a better understanding of the global importance of AOM.},
}
@article {pmid33911286,
year = {2021},
author = {Liu, Y and Makarova, KS and Huang, WC and Wolf, YI and Nikolskaya, AN and Zhang, X and Cai, M and Zhang, CJ and Xu, W and Luo, Z and Cheng, L and Koonin, EV and Li, M},
title = {Expanded diversity of Asgard archaea and their relationships with eukaryotes.},
journal = {Nature},
volume = {593},
number = {7860},
pages = {553-557},
pmid = {33911286},
issn = {1476-4687},
support = {ZIA LM000073/ImNIH/Intramural NIH HHS/United States ; },
mesh = {Archaea/*classification ; Biological Evolution ; Eukaryota ; *Genome, Archaeal ; Metagenomics ; *Phylogeny ; },
abstract = {Asgard is a recently discovered superphylum of archaea that appears to include the closest archaeal relatives of eukaryotes[1-5]. Debate continues as to whether the archaeal ancestor of eukaryotes belongs within the Asgard superphylum or whether this ancestor is a sister group to all other archaea (that is, a two-domain versus a three-domain tree of life)[6-8]. Here we present a comparative analysis of 162 complete or nearly complete genomes of Asgard archaea, including 75 metagenome-assembled genomes that-to our knowledge-have not previously been reported. Our results substantially expand the phylogenetic diversity of Asgard and lead us to propose six additional phyla that include a deep branch that we have provisionally named Wukongarchaeota. Our phylogenomic analysis does not resolve unequivocally the evolutionary relationship between eukaryotes and Asgard archaea, but instead-depending on the choice of species and conserved genes used to build the phylogeny-supports either the origin of eukaryotes from within Asgard (as a sister group to the expanded Heimdallarchaeota-Wukongarchaeota branch) or a deeper branch for the eukaryote ancestor within archaea. Our comprehensive protein domain analysis using the 162 Asgard genomes results in a major expansion of the set of eukaryotic signature proteins. The Asgard eukaryotic signature proteins show variable phyletic distributions and domain architectures, which is suggestive of dynamic evolution through horizontal gene transfer, gene loss, gene duplication and domain shuffling. The phylogenomics of the Asgard archaea points to the accumulation of the components of the mobile archaeal 'eukaryome' in the archaeal ancestor of eukaryotes (within or outside Asgard) through extensive horizontal gene transfer.},
}
@article {pmid33907062,
year = {2021},
author = {Kitamura, R and Kozaki, T and Ishii, K and Iigo, M and Kurokura, T and Yamane, K and Maeda, I and Iwabuchi, K and Saito, T},
title = {Utilizing Cattle Manure Compost Increases Ammonia Monooxygenase A Gene Expression and Ammonia-oxidizing Activity of Both Bacteria and Archaea in Biofiltration Media for Ammonia Deodorization.},
journal = {Microbes and environments},
volume = {36},
number = {2},
pages = {},
pmid = {33907062},
issn = {1347-4405},
mesh = {Ammonia/metabolism ; Animals ; Archaea/classification/*enzymology/genetics/metabolism ; Archaeal Proteins/genetics/*metabolism ; Bacteria/classification/*enzymology/genetics/metabolism ; Bacterial Proteins/genetics/*metabolism ; Cattle ; Composting ; Filtration ; Manure/analysis/*microbiology ; Oxidation-Reduction ; Oxidoreductases/genetics/*metabolism ; Phylogeny ; },
abstract = {Malodorous emissions are a crucial and inevitable issue during the decomposition of biological waste and contain a high concentration of ammonia. Biofiltration technology is a feasible, low-cost, energy-saving method that reduces and eliminates malodors without environmental impact. In the present study, we evaluated the effectiveness of compost from cattle manure and food waste as deodorizing media based on their removal of ammonia and the expression of ammonia-oxidizing genes, and identified the bacterial and archaeal communities in these media. Ammonia was removed by cattle manure compost, but not by food waste compost. The next-generation sequencing of 16S ribosomal RNA obtained from cattle manure compost revealed the presence of ammonia-oxidizing bacteria (AOB), including Cytophagia, Alphaproteobacteria, and Gammaproteobacteria, and ammonia-oxidizing archaea (AOA), such as Thaumarchaeota. In cattle manure compost, the bacterial and archaeal ammonia monooxygenase A (amoA) genes were both up-regulated after exposure to ammonia (fold ratio of 14.2±11.8 after/before), and the bacterial and archaeal communities were more homologous after than before exposure to ammonia, which indicates the adaptation of these communities to ammonia. These results suggest the potential of cattle manure compost as an efficient biological deodorization medium due to the activation of ammonia-oxidizing microbes, such as AOB and AOA, and the up-regulation of their amoA genes.},
}
@article {pmid33901216,
year = {2021},
author = {Płaza, G and Jałowiecki, &#x141; and Głowacka, D and Hubeny, J and Harnisz, M and Korzeniewska, E},
title = {Insights into the microbial diversity and structure in a full-scale municipal wastewater treatment plant with particular regard to Archaea.},
journal = {PloS one},
volume = {16},
number = {4},
pages = {e0250514},
pmid = {33901216},
issn = {1932-6203},
mesh = {Archaea/*isolation &amp; purification ; Bacteria/isolation &amp; purification ; *Biodiversity ; Cities ; *Microbiota ; Phylogeny ; Principal Component Analysis ; *Water Purification ; },
abstract = {Due to limited description of the role and diversity of archaea in WWTPs, the aim of the study was to analyze microbial community structures and diversities with particular regard to Archaea in the samples taken from different stages of the full-scale municipal wastewater treatment plant and effluent receiving water (upstream and downstream discharge point). Our study was focused on showing how the treatment processes influenced the Eubacteria and Archaea composition. Alpha and Beta diversity were used to evaluate the microbial diversity changes in the collected samples. Proteobacteria was the largest fraction ranging from 28% to 67% with 56% relative abundance across all samples. Archaea were present in all stages of WWTP ranged from 1 to 8%. Among the Archaea, two groups of methanogens, acetoclastic (Methanosarcina, Methanosaeta) and hydrogenotrophic methanogens (Methanospirillium, Methanoculleus, Methanobrevibacter) were dominant in the technological stages. The obtained results indicate that the treated wastewater did not significantly affect eubacterial and archaeal composition in receiving water. However, differences in richness, diversity and microbial composition of Eubacteria and Archaea between the wastewater samples taken from the primary and secondary treatment were observed.},
}
@article {pmid33896087,
year = {2021},
author = {Westoby, M and Gillings, MR and Madin, JS and Nielsen, DA and Paulsen, IT and Tetu, SG},
title = {Trait dimensions in bacteria and archaea compared to vascular plants.},
journal = {Ecology letters},
volume = {24},
number = {7},
pages = {1487-1504},
doi = {10.1111/ele.13742},
pmid = {33896087},
issn = {1461-0248},
support = {//Macquarie U/ ; //Australian Research Council/ ; },
mesh = {*Archaea/genetics ; Bacteria/genetics ; *Ecology ; Phenotype ; Plants ; },
abstract = {Bacteria and archaea have very different ecology compared to plants. One similarity, though, is that much discussion of their ecological strategies has invoked concepts such as oligotrophy or stress tolerance. For plants, so-called 'trait ecology'-strategy description reframed along measurable trait dimensions-has made global syntheses possible. Among widely measured trait dimensions for bacteria and archaea three main axes are evident. Maximum growth rate in association with rRNA operon copy number expresses a rate-yield trade-off that is analogous to the acquisitive-conservative spectrum in plants, though underpinned by different trade-offs. Genome size in association with signal transduction expresses versatility. Cell size has influence on diffusive uptake and on relative wall costs. These trait dimensions, and potentially others, offer promise for interpreting ecology. At the same time, there are very substantial differences from plant trait ecology. Traits and their underpinning trade-offs are different. Also, bacteria and archaea use a variety of different substrates. Bacterial strategies can be viewed both through the facet of substrate-use pathways, and also through the facet of quantitative traits such as maximum growth rate. Preliminary evidence shows the quantitative traits vary widely within substrate-use pathways. This indicates they convey information complementary to substrate use.},
}
@article {pmid33892429,
year = {2021},
author = {Thema, M and Weidlich, T and Kaul, A and Böllmann, A and Huber, H and Bellack, A and Karl, J and Sterner, M},
title = {Optimized biological CO2-methanation with a pure culture of thermophilic methanogenic archaea in a trickle-bed reactor.},
journal = {Bioresource technology},
volume = {333},
number = {},
pages = {125135},
doi = {10.1016/j.biortech.2021.125135},
pmid = {33892429},
issn = {1873-2976},
mesh = {Bioreactors ; *Carbon Dioxide ; *Euryarchaeota ; Hydrogen ; Methane ; },
abstract = {In this study, a fully automated process converting hydrogen and carbon dioxide to methane in a high temperature trickle-bed reactor was developed from lab scale to field test level. The reactor design and system performance was optimized to yield high methane content in the product gas for direct feed-in to the gas grid. The reaction was catalyzed by a pure culture of Methanothermobacter thermoautotrophicus IM5, which formed a biofilm on ceramic packing elements. During 600 h in continuous and semi-continuous operation in countercurrent flow, the 0.05 m[3] reactor produced up to95.3 % of methane at a methane production rate of 0.35 [Formula: see text] . Adding nitrogen as carrier gas during startup, foam control and dosing of ammonium and sodium sulfide as nitrogen and sulfur source were important factors for process automation.},
}
@article {pmid33851978,
year = {2021},
author = {Grinter, R and Greening, C},
title = {Cofactor F420: an expanded view of its distribution, biosynthesis and roles in bacteria and archaea.},
journal = {FEMS microbiology reviews},
volume = {45},
number = {5},
pages = {},
pmid = {33851978},
issn = {1574-6976},
support = {APP1178715//NHMRC/ ; },
mesh = {*Archaea/genetics/metabolism ; Bacteria/genetics/metabolism ; Biosynthetic Pathways ; *Euryarchaeota/metabolism ; Humans ; Riboflavin/metabolism ; },
abstract = {Many bacteria and archaea produce the redox cofactor F420. F420 is structurally similar to the cofactors FAD and FMN but is catalytically more similar to NAD and NADP. These properties allow F420 to catalyze challenging redox reactions, including key steps in methanogenesis, antibiotic biosynthesis and xenobiotic biodegradation. In the last 5 years, there has been much progress in understanding its distribution, biosynthesis, role and applications. Whereas F420 was previously thought to be confined to Actinobacteria and Euryarchaeota, new evidence indicates it is synthesized across the bacterial and archaeal domains, as a result of extensive horizontal and vertical biosynthetic gene transfer. F420 was thought to be synthesized through one biosynthetic pathway; however, recent advances have revealed variants of this pathway and have resolved their key biosynthetic steps. In parallel, new F420-dependent biosynthetic and metabolic processes have been discovered. These advances have enabled the heterologous production of F420 and identified enantioselective F420H2-dependent reductases for biocatalysis. New research has also helped resolve how microorganisms use F420 to influence human and environmental health, providing opportunities for tuberculosis treatment and methane mitigation. A total of 50 years since its discovery, multiple paradigms associated with F420 have shifted, and new F420-dependent organisms and processes continue to be discovered.},
}
@article {pmid33847950,
year = {2021},
author = {Taib, N and Gribaldo, S and MacNeill, SA},
title = {Single-Stranded DNA-Binding Proteins in the Archaea.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2281},
number = {},
pages = {23-47},
pmid = {33847950},
issn = {1940-6029},
mesh = {Archaea/classification/genetics/*metabolism ; Archaeal Proteins/chemistry/metabolism ; DNA Repair ; DNA Replication ; DNA, Archaeal/metabolism ; DNA, Single-Stranded/chemistry/*metabolism ; DNA-Binding Proteins/*chemistry/*metabolism ; Models, Molecular ; Phylogeny ; Protein Binding ; Protein Domains ; Species Specificity ; },
abstract = {Single-stranded (ss) DNA-binding proteins are found in all three domains of life where they play vital roles in nearly all aspects of DNA metabolism by binding to and stabilizing exposed ssDNA and acting as platforms onto which DNA-processing activities can assemble. The ssDNA-binding factors SSB and RPA are extremely well conserved across bacteria and eukaryotes, respectively, and comprise one or more OB-fold ssDNA-binding domains. In the third domain of life, the archaea, multiple types of ssDNA-binding protein are found with a variety of domain architectures and subunit compositions, with OB-fold ssDNA-binding domains being a characteristic of most, but not all. This chapter summarizes current knowledge of the distribution, structure, and biological function of the archaeal ssDNA-binding factors, highlighting key features shared between clades and those that distinguish the proteins of different clades from one another. The likely cellular functions of the proteins are discussed and gaps in current knowledge identified.},
}
@article {pmid33828536,
year = {2021},
author = {Gao, K and Lu, Y},
title = {Putative Extracellular Electron Transfer in Methanogenic Archaea.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {611739},
pmid = {33828536},
issn = {1664-302X},
abstract = {It has been suggested that a few methanogens are capable of extracellular electron transfers. For instance, Methanosarcina barkeri can directly capture electrons from the coexisting microbial cells of other species. Methanothrix harundinacea and Methanosarcina horonobensis retrieve electrons from Geobacter metallireducens via direct interspecies electron transfer (DIET). Recently, Methanobacterium, designated strain YSL, has been found to grow via DIET in the co-culture with Geobacter metallireducens. Methanosarcina acetivorans can perform anaerobic methane oxidation and respiratory growth relying on Fe(III) reduction through the extracellular electron transfer. Methanosarcina mazei is capable of electromethanogenesis under the conditions where electron-transfer mediators like H2 or formate are limited. The membrane-bound multiheme c-type cytochromes (MHC) and electrically-conductive cellular appendages have been assumed to mediate the extracellular electron transfer in bacteria like Geobacter and Shewanella species. These molecules or structures are rare but have been recently identified in a few methanogens. Here, we review the current state of knowledge for the putative extracellular electron transfers in methanogens and highlight the opportunities and challenges for future research.},
}
@article {pmid37334237,
year = {2021},
author = {Jarrell, KF and Albers, SV and Machado, JNS},
title = {A comprehensive history of motility and Archaellation in Archaea.},
journal = {FEMS microbes},
volume = {2},
number = {},
pages = {xtab002},
pmid = {37334237},
issn = {2633-6685},
abstract = {Each of the three Domains of life, Eukarya, Bacteria and Archaea, have swimming structures that were all originally called flagella, despite the fact that none were evolutionarily related to either of the other two. Surprisingly, this was true even in the two prokaryotic Domains of Bacteria and Archaea. Beginning in the 1980s, evidence gradually accumulated that convincingly demonstrated that the motility organelle in Archaea was unrelated to that found in Bacteria, but surprisingly shared significant similarities to type IV pili. This information culminated in the proposal, in 2012, that the 'archaeal flagellum' be assigned a new name, the archaellum. In this review, we provide a historical overview on archaella and motility research in Archaea, beginning with the first simple observations of motile extreme halophilic archaea a century ago up to state-of-the-art cryo-tomography of the archaellum motor complex and filament observed today. In addition to structural and biochemical data which revealed the archaellum to be a type IV pilus-like structure repurposed as a rotating nanomachine (Beeby et al. 2020), we also review the initial discoveries and subsequent advances using a wide variety of approaches to reveal: complex regulatory events that lead to the assembly of the archaellum filaments (archaellation); the roles of the various archaellum proteins; key post-translational modifications of the archaellum structural subunits; evolutionary relationships; functions of archaella other than motility and the biotechnological potential of this fascinating structure. The progress made in understanding the structure and assembly of the archaellum is highlighted by comparing early models to what is known today.},
}
@article {pmid33821466,
year = {2021},
author = {Chuphal, N and Singha, KP and Sardar, P and Sahu, NP and Shamna, N and Kumar, V},
title = {Scope of Archaea in Fish Feed: a New Chapter in Aquafeed Probiotics?.},
journal = {Probiotics and antimicrobial proteins},
volume = {13},
number = {6},
pages = {1668-1695},
pmid = {33821466},
issn = {1867-1314},
mesh = {Animal Feed/*microbiology ; *Archaea/genetics ; *Probiotics ; },
abstract = {The outbreak of diseases leading to substantial loss is a major bottleneck in aquaculture. Over the last decades, the concept of using feed probiotics was more in focus to address the growth and health of cultivable aquatic organisms. The objective of this review is to provide an overview of the distinct functionality of archaea from conventional probiotics in nutrient utilization, specific caloric contribution, evading immune response and processing thermal resistance. The prime limitation of conventional probiotics is the viability of desired microbes under harsh feed processing conditions. To overcome the constraints of commercial probiotics pertaining to incompatibility towards industrial processing procedure, a super microbe, archaea, appears to be a potential alternative approach in aquaculture. The peculiarity of the archaeal cell wall provides them with heat stability and rigidity under industrial processing conditions. Besides, archaea being one of the gut microbial communities participates in various health-oriented biological functions in animals. Thus, the current review devoted that administration of archaea in aquafeed could be a promising strategy in aquaculture. Archaea may be used as a potential probiotic with the possible modes of functions and advantages over conventional probiotics in aquafeed preparation. The present review also provides the challenges associated with the use of archaea for aquaculture and a brief outline of the patents on archaea to highlight the various use of archaea in different sectors.},
}
@article {pmid33807612,
year = {2021},
author = {Gonzalez-Bosquet, J and Pedra-Nobre, S and Devor, EJ and Thiel, KW and Goodheart, MJ and Bender, DP and Leslie, KK},
title = {Bacterial, Archaea, and Viral Transcripts (BAVT) Expression in Gynecological Cancers and Correlation with Regulatory Regions of the Genome.},
journal = {Cancers},
volume = {13},
number = {5},
pages = {},
pmid = {33807612},
issn = {2072-6694},
support = {2018 Bridge Funding Award//American Association of Obstetricians and Gynecologists Foundation (AAOGF) Bridge Funding Award/ ; R01 CA99908/NH/NIH HHS/United States ; R01 CA184101/NH/NIH HHS/United States ; },
abstract = {Bacteria, archaea, and viruses are associated with numerous human cancers. To date, microbiome variations in transcription have not been evaluated relative to upper female genital tract cancer risk. Our aim was to assess differences in bacterial, archaea, and viral transcript (BAVT) expression between different gynecological cancers and normal fallopian tubes. In this case-control study we performed RNA sequencing on 12 normal tubes, 112 serous ovarian cancers (HGSC) and 62 endometrioid endometrial cancers (EEC). We used the centrifuge algorithm to classify resultant transcripts into four indexes: bacterial, archaea, viral, and human genomes. We then compared BAVT expression from normal samples, HGSC and EEC. T-test was used for univariate comparisons (correcting for multiple comparison) and lasso for multivariate modelling. For validation we performed DNA sequencing of normal tubes in comparison to HGSC and EEC BAVTs in the TCGA database. Pathway analyses were carried out to evaluate the function of significant BAVTs. Our results show that BAVT expression levels vary between different gynecological cancers. Finally, we mapped some of these BAVTs to the human genome. Numerous map locations were close to regulatory genes and long non-coding RNAs based on the pathway enrichment analysis. BAVTs may affect gynecological cancer risk and may be part of potential targets for cancer therapy.},
}
@article {pmid33798878,
year = {2021},
author = {Fan, C and Zhang, W and Chen, X and Li, N and Li, W and Wang, Q and Duan, P and Chen, M},
title = {Residual effects of four-year amendments of organic material on N2O production driven by ammonia-oxidizing archaea and bacteria in a tropical vegetable soil.},
journal = {The Science of the total environment},
volume = {781},
number = {},
pages = {146746},
doi = {10.1016/j.scitotenv.2021.146746},
pmid = {33798878},
issn = {1879-1026},
mesh = {*Ammonia ; *Archaea ; Bacteria ; Ecosystem ; Fertilizers/analysis ; Nitrification ; Oxidation-Reduction ; Soil ; Soil Microbiology ; Vegetables ; },
abstract = {Organic material (OM) applied to cropland not only enhances soil fertility but also profoundly affects soil nitrogen cycling. However, little is known about the relative contributions of soil ammonia-oxidizing archaea (AOA) and bacteria (AOB) to nitrous oxide (N2O) production during ammonia oxidation in response to the additions of diverse types of OMs in the tropical soil for vegetable production. Herein, the soils were sampled from a tropical vegetable field subjected to 4-year consecutive amendments of straw or manure. All the soils were amended with ammonium sulfate ((NH4)2SO4, applied at a dose of 150 mg N kg[-1]) and incubated aerobically for four weeks under 50% water holding capacity. 1-octyne or acetylene inhibition technique was used to differentiate the relative contributions of AOA and AOB to N2O production. Results showed that AOA dominated N2O production in soil managements of unfertilized control (CK), chemical fertilization (NPK), and NPK with straw (NPKS), whereas AOB contributed more in soil under NPK with manure (NPKM). Straw addition stimulated AOA-dependent N2O production by 94.8% despite the decreased AOA-amoA abundance. Moreover, manure incorporation triggered both AOA- and AOB-dependent N2O production by 147.2% and 233.7%, respectively, accompanied with increased AOA and AOB abundances. Those stimulating effects were stronger for AOB, owing to its sensitivity to the alleviated soil acidification and decreased soil C/N ratio. Our findings highlight the stimulated N2O emissions during ammonia oxidation by historical OM amendments in tropical vegetable soil, with the magnitude of those priming effects dependent on the types of OM, and appropriate measures need to be taken to counter this challenge in tropical agriculture ecosystems.},
}
@article {pmid33782110,
year = {2021},
author = {Liu, J and Cvirkaite-Krupovic, V and Baquero, DP and Yang, Y and Zhang, Q and Shen, Y and Krupovic, M},
title = {Virus-induced cell gigantism and asymmetric cell division in archaea.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {118},
number = {15},
pages = {},
pmid = {33782110},
issn = {1091-6490},
mesh = {Archaeal Proteins/metabolism ; Archaeal Viruses/*pathogenicity ; *Asymmetric Cell Division ; CRISPR-Cas Systems ; Endosomal Sorting Complexes Required for Transport/metabolism ; Giant Cells/*metabolism/virology ; Sulfolobales/genetics/physiology/*virology ; },
abstract = {Archaeal viruses represent one of the most mysterious parts of the global virosphere, with many virus groups sharing no evolutionary relationship to viruses of bacteria or eukaryotes. How these viruses interact with their hosts remains largely unexplored. Here we show that nonlytic lemon-shaped virus STSV2 interferes with the cell cycle control of its host, hyperthermophilic and acidophilic archaeon Sulfolobus islandicus, arresting the cell cycle in the S phase. STSV2 infection leads to transcriptional repression of the cell division machinery, which is homologous to the eukaryotic endosomal sorting complexes required for transport (ESCRT) system. The infected cells grow up to 20-fold larger in size, have 8,000-fold larger volume compared to noninfected cells, and accumulate massive amounts of viral and cellular DNA. Whereas noninfected Sulfolobus cells divide symmetrically by binary fission, the STSV2-infected cells undergo asymmetric division, whereby giant cells release normal-sized cells by budding, resembling the division of budding yeast. Reinfection of the normal-sized cells produces a new generation of giant cells. If the CRISPR-Cas system is present, the giant cells acquire virus-derived spacers and terminate the virus spread, whereas in its absence, the cycle continues, suggesting that CRISPR-Cas is the primary defense system in Sulfolobus against STSV2. Collectively, our results show how an archaeal virus manipulates the cell cycle, transforming the cell into a giant virion-producing factory.},
}
@article {pmid33776986,
year = {2021},
author = {Teske, A and Amils, R and Ramírez, GA and Reysenbach, AL},
title = {Editorial: Archaea in the Environment: Views on Archaeal Distribution, Activity, and Biogeography.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {667596},
pmid = {33776986},
issn = {1664-302X},
}
@article {pmid33776984,
year = {2021},
author = {Czekay, DP and Kothe, U},
title = {H/ACA Small Ribonucleoproteins: Structural and Functional Comparison Between Archaea and Eukaryotes.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {654370},
pmid = {33776984},
issn = {1664-302X},
abstract = {During ribosome synthesis, ribosomal RNA is modified through the formation of many pseudouridines and methylations which contribute to ribosome function across all domains of life. In archaea and eukaryotes, pseudouridylation of rRNA is catalyzed by H/ACA small ribonucleoproteins (sRNPs) utilizing different H/ACA guide RNAs to identify target uridines for modification. H/ACA sRNPs are conserved in archaea and eukaryotes, as they share a common general architecture and function, but there are also several notable differences between archaeal and eukaryotic H/ACA sRNPs. Due to the higher protein stability in archaea, we have more information on the structure of archaeal H/ACA sRNPs compared to eukaryotic counterparts. However, based on the long history of yeast genetic and other cellular studies, the biological role of H/ACA sRNPs during ribosome biogenesis is better understood in eukaryotes than archaea. Therefore, this review provides an overview of the current knowledge on H/ACA sRNPs from archaea, in particular their structure and function, and relates it to our understanding of the roles of eukaryotic H/ACA sRNP during eukaryotic ribosome synthesis and beyond. Based on this comparison of our current insights into archaeal and eukaryotic H/ACA sRNPs, we discuss what role archaeal H/ACA sRNPs may play in the formation of ribosomes.},
}
@article {pmid33771626,
year = {2021},
author = {Orona-Navar, A and Aguilar-Hernández, I and Nigam, KDP and Cerdán-Pasarán, A and Ornelas-Soto, N},
title = {Alternative sources of natural pigments for dye-sensitized solar cells: Algae, cyanobacteria, bacteria, archaea and fungi.},
journal = {Journal of biotechnology},
volume = {332},
number = {},
pages = {29-53},
doi = {10.1016/j.jbiotec.2021.03.013},
pmid = {33771626},
issn = {1873-4863},
mesh = {*Archaea ; Carotenoids ; *Cyanobacteria ; Fungi ; Plants ; },
abstract = {Dye-sensitized solar cells have been of great interest in photovoltaic technology due to their capacity to convert energy at a low cost. The use of natural pigments means replacing expensive chemical synthesis processes by easily extractable pigments that are non-toxic and environmentally friendly. Although most of the pigments used for this purpose are obtained from higher plants, there are potential alternative sources that have been underexploited and have shown encouraging results, since pigments can also be obtained from organisms like bacteria, cyanobacteria, microalgae, yeast, and molds, which have the potential of being cultivated in bioreactors or optimized by biotechnological processes. The aforementioned organisms are sources of diverse sensitizers like photosynthetic pigments, accessory pigments, and secondary metabolites such as chlorophylls, bacteriochlorophylls, carotenoids, and phycobiliproteins. Moreover, retinal proteins, photosystems, and reaction centers from these organisms can also act as sensitizers. In this review, the use of natural sensitizers extracted from algae, cyanobacteria, bacteria, archaea, and fungi is assessed. The reported photoconversion efficiencies vary from 0.001 % to 4.6 % for sensitizers extracted from algae and microalgae, 0.004 to 1.67 % for bacterial sensitizers, 0.07-0.23 % for cyanobacteria, 0.09 to 0.049 % for archaea and 0.26-2.3 % for pigments from fungi.},
}
@article {pmid37938628,
year = {2021},
author = {Shafiee, RT and Diver, PJ and Snow, JT and Zhang, Q and Rickaby, REM},
title = {Marine ammonia-oxidising archaea and bacteria occupy distinct iron and copper niches.},
journal = {ISME communications},
volume = {1},
number = {1},
pages = {1},
pmid = {37938628},
issn = {2730-6151},
abstract = {Ammonia oxidation by archaea and bacteria (AOA and AOB), is the first step of nitrification in the oceans. As AOA have an ammonium affinity 200-fold higher than AOB isolates, the chemical niche allowing AOB to persist in the oligotrophic ocean remains unclear. Here we show that marine isolates, Nitrosopumilus maritimus strain SCM1 (AOA) and Nitrosococcus oceani strain C-107 (AOB) have contrasting physiologies in response to the trace metals iron (Fe) and copper (Cu), holding potential implications for their niche separation in the oceans. A greater affinity for unchelated Fe may allow AOB to inhabit shallower, euphotic waters where ammonium supply is high, but competition for Fe is rife. In contrast to AOB, AOA isolates have a greater affinity and toxicity threshold for unchelated Cu providing additional explanation to the greater success of AOA in the marine environment where Cu availability can be highly variable. Using comparative genomics, we predict that the proteomic and metal transport basis giving rise to contrasting physiologies in isolates is widespread across phylogenetically diverse marine AOA and AOB that are not yet available in pure culture. Our results develop the testable hypothesis that ammonia oxidation may be limited by Cu in large tracts of the open ocean and suggest a relatively earlier emergence of AOB than AOA when considered in the context of evolving trace metal availabilities over geologic time.},
}
@article {pmid33753464,
year = {2021},
author = {Galperin, MY and Wolf, YI and Garushyants, SK and Vera Alvarez, R and Koonin, EV},
title = {Non-essential ribosomal proteins in bacteria and archaea identified using COGs.},
journal = {Journal of bacteriology},
volume = {203},
number = {11},
pages = {},
pmid = {33753464},
issn = {1098-5530},
abstract = {Ribosomal proteins (RPs) are highly conserved across the bacterial and archaeal domains. Although many RPs are essential for survival, genome analysis demonstrates the absence of some RP genes in many bacterial and archaeal genomes. Furthermore, global transposon mutagenesis and/or targeted deletion showed that elimination of some RP genes had only a moderate effect on the bacterial growth rate. Here, we systematically analyze the evolutionary conservation of RPs in prokaryotes by compiling the list of the ribosomal genes that are missing from one or more genomes in the recently updated version of the Clusters of Orthologous Genes (COG) database. Some of these absences occurred because the respective genes carried frameshifts, presumably, resulting from sequencing errors, while others were overlooked and not translated during genome annotation. Apart from these annotation errors, we identified multiple genuine losses of RP genes in a variety of bacteria and archaea. Some of these losses are clade-specific, whereas others occur in symbionts and parasites with dramatically reduced genomes. The lists of computationally and experimentally defined non-essential ribosomal genes show a substantial overlap, revealing a common trend in prokaryote ribosome evolution that could be linked to the architecture and assembly of the ribosomes. Thus, RPs that are located at the surface of the ribosome and/or are incorporated at a late stage of ribosome assembly are more likely to be non-essential and to be lost during microbial evolution, particularly, in the course of genome compaction.IMPORTANCEIn many prokaryote genomes, one or more ribosomal protein (RP) genes are missing. Analysis of 1,309 prokaryote genomes included in the COG database shows that only about half of the RPs are universally conserved in bacteria and archaea. In contrast, up to 16 other RPs are missing in some genomes, primarily, tiny (<1 Mb) genomes of host-associated bacteria and archaea. Ten universal and nine archaea-specific ribosomal proteins show clear patterns of lineage-specific gene loss. Most of the RPs that are frequently lost from bacterial genomes are located on the ribosome periphery and are non-essential in Escherichia coli and Bacillus subtilis These results reveal general trends and common constraints in the architecture and evolution of ribosomes in prokaryotes.},
}
@article {pmid33726663,
year = {2021},
author = {Bize, A and Midoux, C and Mariadassou, M and Schbath, S and Forterre, P and Da Cunha, V},
title = {Exploring short k-mer profiles in cells and mobile elements from Archaea highlights the major influence of both the ecological niche and evolutionary history.},
journal = {BMC genomics},
volume = {22},
number = {1},
pages = {186},
pmid = {33726663},
issn = {1471-2164},
support = {ANR-17-CE05-0011-01//Agence Nationale de la Recherche/ ; 340440/ERC_/European Research Council/International ; },
mesh = {*Archaea/genetics ; Ecosystem ; Phylogeny ; Plasmids ; *Viruses/genetics ; },
abstract = {BACKGROUND: K-mer-based methods have greatly advanced in recent years, largely driven by the realization of their biological significance and by the advent of next-generation sequencing. Their speed and their independence from the annotation process are major advantages. Their utility in the study of the mobilome has recently emerged and they seem a priori adapted to the patchy gene distribution and the lack of universal marker genes of viruses and plasmids. To provide a framework for the interpretation of results from k-mer based methods applied to archaea or their mobilome, we analyzed the 5-mer DNA profiles of close to 600 archaeal cells, viruses and plasmids. Archaea is one of the three domains of life. Archaea seem enriched in extremophiles and are associated with a high diversity of viral and plasmid families, many of which are specific to this domain. We explored the dataset structure by multivariate and statistical analyses, seeking to identify the underlying factors.<br><br>RESULTS: For cells, the 5-mer profiles were inconsistent with the phylogeny of archaea. At a finer taxonomic level, the influence of the taxonomy and the environmental constraints on 5-mer profiles was very strong. These two factors were interdependent to a significant extent, and the respective weights of their contributions varied according to the clade. A convergent adaptation was observed for the class Halobacteria, for which a strong 5-mer signature was identified. For mobile elements, coevolution with the host had a clear influence on their 5-mer profile. This enabled us to identify one previously known and one new case of recent host transfer based on the atypical composition of the mobile elements involved. Beyond the effect of coevolution, extrachromosomal elements strikingly retain the specific imprint of their own viral or plasmid taxonomic family in their 5-mer profile.<br><br>CONCLUSION: This specific imprint confirms that the evolution of extrachromosomal elements is driven by multiple parameters and is not restricted to host adaptation. In addition, we detected only recent host transfer events, suggesting the fast evolution of short k-mer profiles. This calls for caution when using k-mers for host prediction, metagenomic binning or phylogenetic reconstruction.},
}
@article {pmid33720296,
year = {2021},
author = {Zhang, C and Meckenstock, RU and Weng, S and Wei, G and Hubert, CRJ and Wang, JH and Dong, X},
title = {Marine sediments harbor diverse archaea and bacteria with the potential for anaerobic hydrocarbon degradation via fumarate addition.},
journal = {FEMS microbiology ecology},
volume = {97},
number = {5},
pages = {},
doi = {10.1093/femsec/fiab045},
pmid = {33720296},
issn = {1574-6941},
mesh = {Anaerobiosis ; *Archaea/genetics ; Bacteria/genetics ; *Fumarates ; Geologic Sediments ; Hydrocarbons ; Phylogeny ; },
abstract = {Marine sediments can contain large amounts of alkanes and methylated aromatic hydrocarbons that are introduced by natural processes or anthropogenic activities. These compounds can be biodegraded by anaerobic microorganisms via enzymatic addition of fumarate. However, the identity and ecological roles of a significant fraction of hydrocarbon degraders containing fumarate-adding enzymes (FAE) in various marine sediments remains unknown. By combining phylogenetic reconstructions, protein homolog modelling, and functional profiling of publicly available metagenomes and genomes, 61 draft bacterial and archaeal genomes encoding anaerobic hydrocarbon degradation via fumarate addition were obtained. Besides Desulfobacterota (previously known as Deltaproteobacteria) that are well-known to catalyze these reactions, Chloroflexi are dominant FAE-encoding bacteria in hydrocarbon-impacted sediments, potentially coupling sulfate reduction or fermentation to anaerobic hydrocarbon degradation. Among Archaea, besides Archaeoglobi previously shown to have this capability, genomes of Heimdallarchaeota, Lokiarchaeota, Thorarchaeota and Thermoplasmata also suggest fermentative hydrocarbon degradation using archaea-type FAE. These bacterial and archaeal hydrocarbon degraders occur in a wide range of marine sediments, including high abundances of FAE-encoding Asgard archaea associated with natural seeps and subseafloor ecosystems. Our results expand the knowledge of diverse archaeal and bacterial lineages engaged in anaerobic degradation of alkanes and methylated aromatic hydrocarbons.},
}
@article {pmid33694023,
year = {2021},
author = {Jain, A and Krishnan, KP},
title = {Marine Group-II archaea dominate particle-attached as well as free-living archaeal assemblages in the surface waters of Kongsfjorden, Svalbard, Arctic Ocean.},
journal = {Antonie van Leeuwenhoek},
volume = {114},
number = {5},
pages = {633-647},
pmid = {33694023},
issn = {1572-9699},
support = {Indian Arctic Programme//Ministry of Earth Sciences/ ; },
mesh = {*Archaea/genetics ; Ecosystem ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Seawater ; Svalbard ; },
abstract = {Marine archaea are a significant component of the global oceanic ecosystems, including the polar oceans. However, only a few attempts have been made to study archaea in the high Arctic fjords. Given the importance of Archaea in carbon and nitrogen cycling, it is imperative to explore their diversity and community composition in the high Arctic fjords, such as Kongsfjorden (Svalbard). In the present study, we evaluated archaeal diversity and community composition in the size-fractionated microbial population, viz-a-viz free-living (FL; 0.2-3 μm) and particle-attached (PA; > 3 μm) using archaeal V3-V4 16S rRNA gene amplicon sequencing. Our results indicate that the overall archaeal community in the surface water of Kongsfjorden was dominated by the members of the marine group-II (MGII) archaea, followed by the MGI group members, including Nitrosopumilaceae and Nitrososphaeraceae. Although a clear niche partitioning between PA and FL archaeal communities was not observed, 2 OTUs among 682 OTUs, and 3 ASVs out of 1932 ASVs were differentially abundant among the fractions. OTU001/ASV0002, classified as MGIIa, was differentially abundant in the PA fraction. OTU006/ASV0006/ASV0010 affiliated with MGIIb were differentially abundant in the FL fraction. Particulate organic nitrogen and C:N ratio were the most significant variables (P < 0.05) explaining the observed variation in the FL and PA archaeal communities, respectively. These results indicate an exchange between archaeal communities or a generalist lifestyle switching between FL and PA fractions. Besides, the particles' elemental composition (carbon and nitrogen) seems to play an essential role in shaping the PA archaeal communities in the surface waters of Kongsfjorden.},
}
@article {pmid33674723,
year = {2021},
author = {Mauerhofer, LM and Zwirtmayr, S and Pappenreiter, P and Bernacchi, S and Seifert, AH and Reischl, B and Schmider, T and Taubner, RS and Paulik, C and Rittmann, SKR},
title = {Hyperthermophilic methanogenic archaea act as high-pressure CH4 cell factories.},
journal = {Communications biology},
volume = {4},
number = {1},
pages = {289},
pmid = {33674723},
issn = {2399-3642},
mesh = {Amino Acid Motifs ; High-Throughput Screening Assays ; *Industrial Microbiology ; Kinetics ; Membrane Glycoproteins/metabolism ; Methane/*metabolism ; Methanocaldococcaceae/growth &amp; development/*metabolism ; Methanocaldococcus/growth &amp; development/*metabolism ; Oxidoreductases/metabolism ; Pressure ; Renewable Energy ; },
abstract = {Bioprocesses converting carbon dioxide with molecular hydrogen to methane (CH4) are currently being developed to enable a transition to a renewable energy production system. In this study, we present a comprehensive physiological and biotechnological examination of 80 methanogenic archaea (methanogens) quantifying growth and CH4 production kinetics at hyperbaric pressures up to 50 bar with regard to media, macro-, and micro-nutrient supply, specific genomic features, and cell envelope architecture. Our analysis aimed to systematically prioritize high-pressure and high-performance methanogens. We found that the hyperthermophilic methanococci Methanotorris igneus and Methanocaldococcoccus jannaschii are high-pressure CH4 cell factories. Furthermore, our analysis revealed that high-performance methanogens are covered with an S-layer, and that they harbour the amino acid motif Tyr[α444] Gly[α445] Tyr[α446] in the alpha subunit of the methyl-coenzyme M reductase. Thus, high-pressure biological CH4 production in pure culture could provide a purposeful route for the transition to a carbon-neutral bioenergy sector.},
}
@article {pmid37073339,
year = {2021},
author = {Hu, H and Natarajan, VP and Wang, F},
title = {Towards enriching and isolation of uncultivated archaea from marine sediments using a refined combination of conventional microbial cultivation methods.},
journal = {Marine life science &amp; technology},
volume = {3},
number = {2},
pages = {231-242},
pmid = {37073339},
issn = {2662-1746},
abstract = {UNLABELLED: The archaea that can be readily cultivated in the laboratory are only a small fraction of the total diversity that exists in nature. Although molecular ecology methods, such as metagenomic sequencing, can provide valuable information independent of cell cultivation, it is only through cultivation-based experiments that they may be fully characterized, both for their physiological and ecological properties. Here, we report our efforts towards enriching and isolation of uncultivated archaea from marine sediments using a refined combination of conventional microbial cultivation methods. Initially, cells were retrieved from the sediment samples through a cell extraction procedure and the sediment-free mixed cells were then divided into different size-range fractions by successive filtration through 0.8 µm, 0.6 µm and 0.2 µm membranes. Archaeal 16S rRNA gene analyses indicated noticeable retention of different archaeal groups in different fractions. For each fraction, supplementation with a variety of defined substrates (e.g., methane, sulfate, and lignin) and stepwise dilutions led to highly active enrichment cultures of several archaeal groups with Bathyarchaeota most prominently enriched. Finally, using a roll-bottle technique, three co-cultures consisting of Bathyarchaeota (subgroup-8) and a bacterial species affiliated with either Pseudomonas or Glutamicibacter were obtained. Our results demonstrate that a combination of cell extraction, size fractionation, and roll-bottle isolation methods could be a useful protocol for the successful enrichment and isolation of numerous slow-growing archaeal groups from marine sediments.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42995-021-00092-0.},
}
@article {pmid33637253,
year = {2021},
author = {Zheng, M and He, S and Feng, Y and Wang, M and Liu, YX and Dang, C and Wang, J},
title = {Active ammonia-oxidizing bacteria and archaea in wastewater treatment systems.},
journal = {Journal of environmental sciences (China)},
volume = {102},
number = {},
pages = {273-282},
doi = {10.1016/j.jes.2020.09.039},
pmid = {33637253},
issn = {1001-0742},
mesh = {Ammonia ; *Archaea/genetics ; Nitrification ; Oxidation-Reduction ; Phylogeny ; Soil Microbiology ; *Water Purification ; },
abstract = {Ammonia-oxidizing bacteria (AOB) and archaea (AOA) are two microbial groups mediating nitrification, yet little is presently known about their abundances and community structures at the transcriptional level in wastewater treatment systems (WWTSs). This is a significant issue, as the numerical abundance of AOA or AOB at the gene level may not necessarily represent their functional role in ammonia oxidation. Using amoA genes as molecular markers, this study investigated the transcriptional abundance and community structure of active AOA and AOB in 14 WWTSs. Quantitative PCR results indicated that the transcriptional abundances of AOB amoA (averaged: 1.6 × 10[8] copies g[-1] dry sludge) were higher than those of AOA (averaged: 3.4 × 10[7] copies g[-1] dry sludge) in all WWTSs despite several higher abundances of AOA amoA at the gene level. Moreover, phylogenetic analysis demonstrated that Nitrosomonas europaea and unknown clusters accounted for 37.66% and 49.96% of the total AOB amoA transcripts, respectively, suggesting their dominant role in driving ammonia oxidation. Meanwhile, AOA amoA transcripts were only successfully retrieved from 3 samples, and the Nitrosospaera sister cluster dominated, accounting for 83.46%. Finally, the substrate utilization kinetics of different AOA and AOB species might play a fundamental role in shaping their niche differentiation, community composition, and functional activity. This study provides a basis for evaluating the relative contributions of ammonia-oxidizing microorganisms (AOMs) to nitrogen conversions in WWTSs.},
}
@article {pmid33624267,
year = {2021},
author = {Kim, JG and Gazi, KS and Awala, SI and Jung, MY and Rhee, SK},
title = {Ammonia-oxidizing archaea in biological interactions.},
journal = {Journal of microbiology (Seoul, Korea)},
volume = {59},
number = {3},
pages = {298-310},
pmid = {33624267},
issn = {1976-3794},
mesh = {Ammonia/*metabolism ; Archaea/classification/genetics/isolation &amp; purification/*metabolism ; Ecosystem ; Nitrification ; Oxidation-Reduction ; Phylogeny ; },
abstract = {The third domain Archaea was known to thrive in extreme or anoxic environments based on cultivation studies. Recent metagenomics-based approaches revealed a widespread abundance of archaea, including ammonia-oxidizing archaea (AOA) of Thaumarchaeota in non-extreme and oxic environments. AOA alter nitrogen species availability by mediating the first step of chemolithoautotrophic nitrification, ammonia oxidation to nitrite, and are important primary producers in ecosystems, which affects the distribution and activity of other organisms in ecosystems. Thus, information on the interactions of AOA with other cohabiting organisms is a crucial element in understanding nitrogen and carbon cycles in ecosystems as well as the functioning of whole ecosystems. AOA are self-nourishing, and thus interactions of AOA with other organisms can often be indirect and broad. Besides, there are possibilities of specific and obligate interactions. Mechanisms of interaction are often not clearly identified but only inferred due to limited knowledge on the interaction factors analyzed by current technologies. Here, we overviewed different types of AOA interactions with other cohabiting organisms, which contribute to understanding AOA functions in ecosystems.},
}
@article {pmid33620581,
year = {2021},
author = {Sorokin, DY and Roman, P and Kolganova, TV},
title = {Halo(natrono)archaea from hypersaline lakes can utilize sulfoxides other than DMSO as electron acceptors for anaerobic respiration.},
journal = {Extremophiles : life under extreme conditions},
volume = {25},
number = {2},
pages = {173-180},
pmid = {33620581},
issn = {1433-4909},
support = {19-04-00401//Russuan Foundation for Basic Research/ ; },
mesh = {Anaerobiosis ; *Dimethyl Sulfoxide ; Electrons ; *Lakes ; Phylogeny ; RNA, Ribosomal, 16S ; Respiration ; Russia ; Siberia ; },
abstract = {Dimethylsulfoxide (DMSO) has long been known to support anaerobic respiration in a few species of basically aerobic extremely halophilic euryarchaea living in hypersaline lakes. Recently, it has also been shown to be utilized as an additional electron acceptor in basically anaerobic sulfur-reducing haloarchaea. Here we investigated whether haloarchaea would be capable of anaerobic respiration with other two sulfoxides, methionine sulfoxide (MSO) and tetramethylene sulfoxide (TMSO). For this, anaerobic enrichment cultures were inoculated with sediments from hypersaline salt and soda lakes in southwestern Siberia and southern Russia. Positive enrichments were obtained for both MSO and TMSO with yeast extract but not with formate or acetate as the electron donor. Two pure cultures obtained from salt lakes, either with MSO or TMSO, were obligate anaerobes closely related to sulfur-reducing Halanaeroarchaeum sulfurireducens, although the type strain of this genus was unable to utilize any sulfoxides. Two pure cultures isolated from soda lakes were facultatively anaerobic alkaliphilic haloarchaea using O2, sulfur and sulfoxides as the electron acceptors. One isolate was identical to the previously described sulfur-reducing Natrarchaeobaculum sulfurireducens, while another one, enriched at lower alkalinity, is forming a new species in the genus Halobiforma. Since all isolates enriched with either MSO or TMSO were able to respire all three sulfoxides including DMSO and the corresponding activities were cross-induced, it suggest that a single enzyme of the DMSO-reductase family with a broad substrate specificity is responsible for various sulfoxide-dependent respiration in haloarchaea.},
}
@article {pmid33608296,
year = {2021},
author = {Cai, R and Zhang, J and Liu, R and Sun, C},
title = {Metagenomic Insights into the Metabolic and Ecological Functions of Abundant Deep-Sea Hydrothermal Vent DPANN Archaea.},
journal = {Applied and environmental microbiology},
volume = {87},
number = {9},
pages = {},
pmid = {33608296},
issn = {1098-5336},
mesh = {Amino Acids/biosynthesis ; Archaea/*genetics/metabolism ; Genome, Archaeal ; Glucose/metabolism ; Hydrothermal Vents/*microbiology ; Metagenome ; Nucleotides/biosynthesis ; Phylogeny ; },
abstract = {Due to their unique metabolism and important ecological roles, deep-sea hydrothermal archaea have attracted great scientific interest. Among these archaea, DPANN superphylum archaea are widely distributed in hydrothermal vent environments. However, DPANN metabolism and ecology remain largely unknown. In this study, we assembled 20 DPANN genomes among 43 reconstructed genomes obtained from deep-sea hydrothermal vent sediments. Phylogenetic analysis suggests 6 phyla, comprised of Aenigmarchaeota, Diapherotrites, Nanoarchaeota, Pacearchaeota, Woesearchaeota, and a new candidate phylum we have designated Kexuearchaeota These are included in the 20 DPANN archaeal members, indicating their broad diversity in this special environment. Analyses of their metabolism reveal deficiencies due to their reduced genome size, including gluconeogenesis and de novo nucleotide and amino acid biosynthesis. However, DPANN archaea possess alternate strategies to address these deficiencies. DPANN archaea also have the potential to assimilate nitrogen and sulfur compounds, indicating an important ecological role in the hydrothermal vent system.IMPORTANCE DPANN archaea show high distribution in the hydrothermal system, although they display small genome size and some incomplete biological processes. Exploring their metabolism is helpful to understand how such small forms of life adapt to this unique environment and what ecological roles they play. In this study, we obtained 20 high-quality metagenome-assembled genomes (MAGs) corresponding to 6 phyla of the DPANN group (Aenigmarchaeota, Diapherotrites, Nanoarchaeota, Pacearchaeota, Woesearchaeota, and a new candidate phylum designated Kexuearchaeota). Further metagenomic analyses provided insights on the metabolism and ecological functions of DPANN archaea to adapt to deep-sea hydrothermal environments. Our study contributes to a deeper understanding of their special lifestyles and should provide clues to cultivate this important archaeal group in the future.},
}
@article {pmid33584634,
year = {2021},
author = {Distaso, MA and Bargiela, R and Brailsford, FL and Williams, GB and Wright, S and Lunev, EA and Toshchakov, SV and Yakimov, MM and Jones, DL and Golyshin, PN and Golyshina, OV},
title = {Corrigendum: High Representation of Archaea Across All Depths in Oxic and Low-pH Sediment Layers Underlying an Acidic Stream.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {633015},
doi = {10.3389/fmicb.2021.633015},
pmid = {33584634},
issn = {1664-302X},
abstract = {[This corrects the article DOI: 10.3389/fmicb.2020.576520.].},
}
@article {pmid33582288,
year = {2021},
author = {Starke, R and Siles, JA and Fernandes, MLP and Schallert, K and Benndorf, D and Plaza, C and Jehmlich, N and Delgado-Baquerizo, M and Bastida, F},
title = {The structure and function of soil archaea across biomes.},
journal = {Journal of proteomics},
volume = {237},
number = {},
pages = {104147},
doi = {10.1016/j.jprot.2021.104147},
pmid = {33582288},
issn = {1876-7737},
mesh = {*Archaea/genetics ; Ecosystem ; RNA, Ribosomal, 16S ; *Soil ; Soil Microbiology ; },
abstract = {We lack a predictive understanding of the environmental drivers determining the structure and function of archaeal communities as well as the proteome associated with these important soil organisms. Here, we characterized the structure (by 16S rRNA gene sequencing) and function (by metaproteomics) of archaea from 32 soil samples across terrestrial ecosystems with contrasting climate and vegetation types. Our multi-"omics" approach unveiled that genes from Nitrosophaerales and Thermoplasmata dominated soils collected from four continents, and that archaea comprise 2.3 ± 0.3% of microbial proteins in these soils. Aridity positively correlated with the proportion of Nitrosophaerales genes and the number of archaeal proteins. The interaction of climate x vegetation shaped the functional profile of the archaeal community. Our study provides novel insights into the structure and function of soil archaea across climates, and highlights that these communities may be influenced by increasing global aridity.},
}
@article {pmid33561735,
year = {2021},
author = {Shalvarjian, KE and Nayak, DD},
title = {Transcriptional regulation of methanogenic metabolism in archaea.},
journal = {Current opinion in microbiology},
volume = {60},
number = {},
pages = {8-15},
doi = {10.1016/j.mib.2021.01.005},
pmid = {33561735},
issn = {1879-0364},
mesh = {*Archaea/genetics ; Gene Expression Regulation, Archaeal ; *Methane ; Methanococcus/genetics ; Methanosarcina/genetics ; },
abstract = {Methanogenesis is a widespread metabolism of evolutionary and environmental importance that is likely to have originated on early Earth. Microorganisms that perform methanogenesis, termed methanogens, belong exclusively to the domain Archaea. Despite maintaining eukaryotic transcription machinery and homologs of bacterial regulators, archaeal transcription and gene regulation appear to be distinct from either domain. While genes involved in methanogenic metabolism have been identified and characterized, their regulation in response to both extracellular and intracellular signals is less understood. Here, we review recent reports on transcriptional regulation of methanogenesis using two model methanogens, Methanococcus maripaludis and Methanosarcina acetivorans, and highlight directions for future research in this nascent field.},
}
@article {pmid33558390,
year = {2021},
author = {Kuprat, T and Ortjohann, M and Johnsen, U and Schönheit, P},
title = {Glucose Metabolism and Acetate Switch in Archaea: the Enzymes in Haloferax volcanii.},
journal = {Journal of bacteriology},
volume = {203},
number = {8},
pages = {},
pmid = {33558390},
issn = {1098-5530},
mesh = {Acetate-CoA Ligase/genetics/metabolism ; Acetates/*metabolism ; Acetyl Coenzyme A/metabolism ; Archaeal Proteins/genetics/metabolism ; Glucose/*metabolism ; Haloferax volcanii/*enzymology/genetics/growth &amp; development/metabolism ; Phosphoenolpyruvate Carboxylase/genetics/metabolism ; Phosphoglycerate Mutase/genetics/metabolism ; Phosphopyruvate Hydratase/genetics/metabolism ; Pyruvic Acid/metabolism ; },
abstract = {The halophilic archaeon Haloferax volcanii has been proposed to degrade glucose via the semiphosphorylative Entner-Doudoroff (spED) pathway. Following our previous studies on key enzymes of this pathway, we now focus on the characterization of enzymes involved in 3-phosphoglycerate conversion to pyruvate, in anaplerosis, and in acetyl coenzyme A (acetyl-CoA) formation from pyruvate. These enzymes include phosphoglycerate mutase, enolase, pyruvate kinase, phosphoenolpyruvate carboxylase, and pyruvate-ferredoxin oxidoreductase. The essential function of these enzymes were shown by transcript analyses and growth experiments with respective deletion mutants. Furthermore, we show that H. volcanii-during aerobic growth on glucose-excreted significant amounts of acetate, which was consumed in the stationary phase (acetate switch). The enzyme catalyzing the conversion of acetyl-CoA to acetate as part of the acetate overflow mechanism, an ADP-forming acetyl-CoA synthetase (ACD), was characterized. The functional involvement of ACD in acetate formation and of AMP-forming acetyl-CoA synthetases (ACSs) in activation of excreted acetate was proven by using respective deletion mutants. Together, the data provide a comprehensive analysis of enzymes of the spED pathway and of anaplerosis and report the first genetic evidence of the functional involvement of enzymes of the acetate switch in archaea.IMPORTANCE In this work, we provide a comprehensive analysis of glucose degradation via the semiphosphorylative Entner-Doudoroff pathway in the haloarchaeal model organism Haloferax volcanii The study includes transcriptional analyses, growth experiments with deletion mutants. and characterization of all enzymes involved in the conversion of 3-phosphoglycerate to acetyl coenzyme A (acetyl-CoA) and in anaplerosis. Phylogenetic analyses of several enzymes indicate various lateral gene transfer events from bacteria to haloarchaea. Furthermore, we analyzed the key players involved in the acetate switch, i.e., in the formation (overflow) and subsequent consumption of acetate during aerobic growth on glucose. Together, the data provide novel aspects of glucose degradation, anaplerosis, and acetate switch in H. volcanii and thus expand our understanding of the unusual sugar metabolism in archaea.},
}
@article {pmid33556662,
year = {2021},
author = {Du, H and Sun, T and Liu, Y and An, S and Xie, H and Wang, D and Igarashi, Y and Imanaka, T and Luo, F and Ma, M},
title = {Bacteria and archaea involved in anaerobic mercury methylation and methane oxidation in anaerobic sulfate-rich reactors.},
journal = {Chemosphere},
volume = {274},
number = {},
pages = {129773},
doi = {10.1016/j.chemosphere.2021.129773},
pmid = {33556662},
issn = {1879-1298},
mesh = {Anaerobiosis ; Animals ; *Archaea/genetics ; Bacteria/genetics ; *Mercury ; Methane ; Methylation ; Oxidation-Reduction ; Phylogeny ; Sulfates ; Swine ; },
abstract = {The identification of dominant microbes in anaerobic mercury (Hg) methylation, methylmercury (MeHg) demethylation, and methane oxidation as sulfate-reducing bacteria, methanogens or, probably, anaerobic methanotrophic archaea (ANMEs) is of great interest. To date, however, the interrelationship of bacteria and archaea involved in these processes remains unclear. Here, we demonstrated the dynamics of microorganisms participating in these processes. Anaerobic fixed-bed reactors were operated with swine manure and sludge to produce methane stably, and then, sulfate (reactor C), sulfate and Hg(II) (reactor H), and sulfate and MeHg (reactor M) were added, and the reactors were operated for 120 d, divided equally into four periods, P1-P4. The bacterial compositions changed nonsignificantly, whereas Methanosaeta in reactors H and M decreased significantly, revealing that it was irrelevant for Hg transformation. The abundances of Syntrophomonadaceae, Methanoculleus, Candidatus Methanogranum and Candidatus Methanoplasma increased continuously with time; these species probably functioned in these processes, but further evidence is needed. Desulfocella and Desulfobacterium dominated first but eventually almost vanished, while the dominant archaeal genera Methanogenium, Methanoculleus and Methanocorpusculum were closely related to ANME-1 and ANME-2. PLS-DA results indicated that both bacteria and archaea in different periods in the three reactors were clustered separately, implying that the microbial compositions in the same periods were similar and changed markedly with time.},
}
@article {pmid33555973,
year = {2020},
author = {Makarova, KS and Wolf, YI and Shmakov, SA and Liu, Y and Li, M and Koonin, EV},
title = {Unprecedented Diversity of Unique CRISPR-Cas-Related Systems and Cas1 Homologs in Asgard Archaea.},
journal = {The CRISPR journal},
volume = {3},
number = {3},
pages = {156-163},
pmid = {33555973},
issn = {2573-1602},
mesh = {Archaea/classification/*genetics/metabolism ; Archaeal Proteins/genetics/metabolism ; *CRISPR-Cas Systems ; *Clustered Regularly Interspaced Short Palindromic Repeats ; Endonucleases/genetics ; Genome, Archaeal ; Metagenome ; Phylogeny ; },
abstract = {The principal function of archaeal and bacterial CRISPR-Cas systems is antivirus adaptive immunity. However, recent genome analyses identified a variety of derived CRISPR-Cas variants at least some of which appear to perform different functions. Here, we describe a unique repertoire of CRISPR-Cas-related systems that we discovered by searching archaeal metagenome-assemble genomes of the Asgard superphylum. Several of these variants contain extremely diverged homologs of Cas1, the integrase involved in CRISPR adaptation as well as casposon transposition. Strikingly, the diversity of Cas1 in Asgard archaea alone is greater than that detected so far among the rest of archaea and bacteria. The Asgard CRISPR-Cas derivatives also encode distinct forms of Cas4, Cas5, and Cas7 proteins, and/or additional nucleases. Some of these systems are predicted to perform defense functions, but possibly not programmable ones, whereas others are likely to represent previously unknown mobile genetic elements.},
}
@article {pmid33554274,
year = {2021},
author = {Zhu, D and Shen, G and Wang, Z and Han, R and Long, Q and Gao, X and Xing, J and Li, Y and Wang, R},
title = {Distinctive distributions of halophilic Archaea across hypersaline environments within the Qaidam Basin of China.},
journal = {Archives of microbiology},
volume = {203},
number = {5},
pages = {2029-2042},
pmid = {33554274},
issn = {1432-072X},
support = {31760034//National Natural Science Foundation of China/ ; 31860030//National Natural Science Foundation of China/ ; 21967018//National Natural Science Foundation of China/ ; 2019SF121//Key Research Foundation of Development and Transformation of Qinghai Province/ ; 2018ZJ778//Applied Basic Research Program of Qinghai Province/ ; 2018ZJ930Q//Applied Basic Research Program of Qinghai Province/ ; 2020ZJ767//Applied Basic Research Program of Qinghai Province/ ; },
mesh = {China ; *Ecosystem ; *Environmental Microbiology ; Euryarchaeota/*classification/genetics ; RNA, Ribosomal, 16S/genetics ; Salinity ; Seawater/microbiology ; },
abstract = {Halophilic Archaea are widely distributed globally in hypersaline environments. However, little is known of how dominant halophilic archaeal genera are distributed across environments and how they may co-associate across ecosystems. Here, the archaeal community composition and diversity from hypersaline environments (> 300 g/L salinity; total of 33 samples) in the Qaidam Basin of China were investigated using high-throughput Illumina sequencing of 16S rRNA genes. The archaeal communities (total of 3,419 OTUs) were dominated by the class Halobacteria (31.7-99.6% relative abundances) within the phylum Euryarchaeota (90.8-99.9%). Five predominant taxa, including Halorubrum, Halobacterium, Halopenitus, Methanothrix, and Halomicrobium, were observed across most samples. However, several distinct genera were associated with individual samples and were inconsistently distributed across samples, which contrast with previous studies of hypersaline archaeal communities. Additionally, co-occurrence network analysis indicated that five network clusters were present and potentially reflective of interspecies interactions among the environments, including three clusters (clusters II, III, and IV) comprising halophilic archaeal taxa within the Halobacteriaceae and Haloferacaceae families. In addition, two other clusters (clusters I and V) were identified that comprised methanogens. Finally, salinity comprising ionic concentrations (in the order of Na[+] > Ca[2+] > Mg[2+]) and pH were most correlated with taxonomic distributions across sample sites.},
}
@article {pmid33545473,
year = {2021},
author = {Wei, H and Lin, X},
title = {Shifts in the relative abundance and potential rates of sediment ammonia-oxidizing archaea and bacteria along environmental gradients of an urban river-estuary-adjacent sea continuum.},
journal = {The Science of the total environment},
volume = {771},
number = {},
pages = {144824},
doi = {10.1016/j.scitotenv.2020.144824},
pmid = {33545473},
issn = {1879-1026},
mesh = {*Ammonia ; *Archaea/genetics ; Bacteria/genetics ; China ; Estuaries ; Humans ; Oxidation-Reduction ; Phylogeny ; Rivers ; Soil Microbiology ; },
abstract = {Ammonia-oxidizing archaea (AOA) and bacteria (AOB) play important roles in N cycling in sediments globally. However, little is known about their ammonia oxidation rates along a river-estuary-sea continuum. In this study, we investigated how the potential ammonia oxidation rates (PARs) of AOA and AOB changed spatially along a continuum comprising three habitats: the Shanghai urban river network, the Yangtze Estuary, and the adjacent East China Sea, in summer and winter. The AOA and AOB PARs (0.53 ± 0.49 and 0.72 ± 0.69 μg N g[-1] d[-1], mean ± SD, respectively) and their amoA gene abundance (0.47 ± 0.85 × 10[6] and 2.4 ± 3.54 × 10[6] copies g[-1], respectively) decreased along the continuum, particularly from the urban river to the estuary, driven by decreasing sediment total organic C and N and other correlated inorganic nutrients (e.g., NH4[+]) along the gradient of anthropogenic influences. These spatial patterns were consistent between the seasons. The urban river network, where the anthropogenic influences were strongest, saw the largest seasonal differences, as both AOA and AOB had higher PARs and abundance in summer than in winter. The ratios between AOA and AOB PARs (~0.87 ± 0.51) and gene abundances (~0.25 ± 0.24), however, were predominantly <1, indicating an AOB-dominated community. Comparing the different NH4[+] consumption pathways, total aerobic oxidation accounted for 12-26% of the total consumption, with the largest proportion in the estuary, where the system was well oxygenated, and the lowest in the adjacent sea, where inorganic N was highly depleted. This study revealed the spatiotemporal patterns of AOA and AOB potential rates and gene abundance along gradients of human influences and identified organic matter and nutrients as key environmental factors that shaped the variation of AOA and AOB along the continuum.},
}
@article {pmid33539079,
year = {2021},
author = {Wang, Y and Qin, W and Jiang, X and Ju, F and Mao, Y and Zhang, A and Stahl, DA and Zhang, T},
title = {Seasonal Prevalence of Ammonia-Oxidizing Archaea in a Full-Scale Municipal Wastewater Treatment Plant Treating Saline Wastewater Revealed by a 6-Year Time-Series Analysis.},
journal = {Environmental science &amp; technology},
volume = {55},
number = {4},
pages = {2662-2673},
doi = {10.1021/acs.est.0c07703},
pmid = {33539079},
issn = {1520-5851},
mesh = {Ammonia ; *Archaea/genetics ; Bacteria/genetics ; Extracellular Polymeric Substance Matrix ; Hong Kong ; Oxidation-Reduction ; Phylogeny ; Prevalence ; RNA, Ribosomal, 16S/genetics ; Seasons ; Wastewater ; *Water Purification ; },
abstract = {Although several molecular-based studies have demonstrated the involvement of ammonia-oxidizing archaea (AOA) in ammonia oxidation in wastewater treatment plants (WWTPs), factors affecting the persistence and growth of AOA in these engineered systems have not been resolved. Here, we show a seasonal prevalence of AOA in a full-scale WWTP (Shatin, Hong Kong SAR) over a 6-year period of observation, even outnumbering ammonia-oxidizing bacteria in the seasonal peaks in 3 years, which may be due to the high bioavailable copper concentrations. Comparative analysis of three metagenome-assembled genomes of group I.1a AOA obtained from the activated sludge and 16S rRNA gene sequences recovered from marine sediments suggested that the seawater used for toilet flushing was the primary source of the WWTP AOA. A rare AOA population in the estuarine source water became transiently abundant in the WWTP with a metagenome-based relative abundance of up to 1.3% over three seasons of observation. Correlation-based network analysis revealed a robust co-occurrence relationship between these AOA and organisms potentially active in nitrite oxidation. Moreover, a strong correlation between the dominant AOA and an abundant proteobacterial organism suggested that capacity for extracellular polymeric substance production by the proteobacterium could provide a niche for AOA within bioaggregates. Together, the study highlights the importance of long-term observation in identifying biotic and abiotic factors governing population dynamics in open systems such as full-scale WWTPs.},
}
@article {pmid33538376,
year = {2021},
author = {Sorokin, DY and Messina, E and Smedile, F and La Cono, V and Hallsworth, JE and Yakimov, MM},
title = {Carbohydrate-dependent sulfur respiration in halo(alkali)philic archaea.},
journal = {Environmental microbiology},
volume = {23},
number = {7},
pages = {3789-3808},
doi = {10.1111/1462-2920.15421},
pmid = {33538376},
issn = {1462-2920},
mesh = {*Alkalies ; *Archaea ; Carbohydrates ; Phylogeny ; Respiration ; Sulfur ; },
abstract = {Archaea are environmentally ubiquitous on Earth, and their extremophilic and metabolically versatile phenotypes make them useful as model systems for astrobiology. Here, we reveal a new functional group of halo(natrono)archaea able to utilize alpha-d-glucans (amylopectin, amylose and glycogen), sugars, and glycerol as electron donors and carbon sources for sulfur respiration. They are facultative anaerobes enriched from hypersaline sediments with either amylopectin, glucose or glycerol as electron/carbon sources and elemental sulfur as the terminal electron acceptor. They include 10 strains of neutrophilic haloarchaea from circum pH-neutral lakes and one natronoarchaeon from soda-lake sediments. The neutrophilic isolates can grow by fermentation, although addition of S[0] or dimethyl sulfoxide increased growth rate and biomass yield (with a concomitant decrease in H2). Natronoarchaeal isolate AArc-S grew only by respiration, either anaerobically with S[0] or thiosulfate as the terminal electron acceptor, or aerobically. Through genome analysis of five representative strains, we detected the full set of enzymes required for the observed catabolic and respiratory phenotypes. These findings provide evidence that sulfur-respiring haloarchaea partake in biogeochemical sulfur cycling, linked to terminal anaerobic carbon mineralization in hypersaline anoxic habitats. We discuss the implications for life detection in analogue environments such as the polar subglacial brine-lakes of Mars.},
}
@article {pmid33527146,
year = {2021},
author = {Ali, MM and Khanom, A and Nahar, K and Ali, MY and Azad, MAK and Rahman, MM},
title = {Effect of Manure Application on Net Nitrification Rates, Heavy Metal Concentrations and Nitrifying Archaea/Bacteria in Soils.},
journal = {Bulletin of environmental contamination and toxicology},
volume = {106},
number = {4},
pages = {707-713},
pmid = {33527146},
issn = {1432-0800},
mesh = {Ammonia ; *Archaea ; Bacteria/genetics ; Manure ; *Metals, Heavy ; Nitrification ; Oxidation-Reduction ; Phylogeny ; Soil ; Soil Microbiology ; },
abstract = {In this study, we determined the effect of manure application on net nitrification rates (NNRs), heavy metal concentrations (HMCs), and abundance of ammonia-oxidizing archaea (AOA)/bacteria (AOB), and nitrite-oxidizing bacteria (NOB) in soil. HMCs were measured by atomic absorption spectroscopy. Abundance of AOA, AOB, and NOB was enumerated by q-PCR. NNRs ranged from 2.8 to 14.7 mg kg[-1] h[-1] and were significantly (p < 0.05) increased in manure soils as compared to control soils. NNRs were affected by pH 7 and temperature 30°C. Cd, Fe and Pb concentrations were classified as excessively polluted, moderate contamination and slight pollution, respectively, in the manure soils. NNRs and concentrations of Fe and Pb were significantly (p < 0.00) positive correlated, but Cu and Cd were significantly (p < 0.00) negative correlated with NNRs. Application of manure significantly (p < 0.05) increased HMCs (Fe, Cu, and Pb), which have indirect and direct effects on NNRs and nitrifying bacteria.},
}
@article {pmid33519774,
year = {2020},
author = {DeLong, EF},
title = {Exploring Marine Planktonic Archaea: Then and Now.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {616086},
pmid = {33519774},
issn = {1664-302X},
abstract = {In 1977, Woese and Fox leveraged molecular phylogenetic analyses of ribosomal RNAs and identified a new microbial domain of life on Earth, the Archaebacteria (now known as Archaea). At the time of their discovery, only one archaebacterial group, the strictly anaerobic methanogens, was known. But soon, other phenotypically unrelated microbial isolates were shown to belong to the Archaea, many originating from extreme habitats, including extreme halophiles, extreme thermophiles, and thermoacidophiles. Since most Archaea seemed to inhabit extreme or strictly anoxic habitats, it came as a surprise in 1992 when two new lineages of archaea were reported to be abundant in oxygen rich, temperate marine coastal waters and the deep ocean. Since that time, studies of marine planktonic archaea have revealed many more surprises, including their unexpected ubiquity, unusual symbiotic associations, unpredicted physiologies and biogeochemistry, and global abundance. In this Perspective, early work conducted on marine planktonic Archaea by my lab group and others is discussed in terms of the relevant historical context, some of the original research motivations, and surprises and discoveries encountered along the way.},
}
@article {pmid33501490,
year = {2021},
author = {Mueller, RC and Peach, JT and Skorupa, DJ and Copié, V and Bothner, B and Peyton, BM},
title = {An emerging view of the diversity, ecology and function of Archaea in alkaline hydrothermal environments.},
journal = {FEMS microbiology ecology},
volume = {97},
number = {2},
pages = {},
doi = {10.1093/femsec/fiaa246},
pmid = {33501490},
issn = {1574-6941},
mesh = {*Archaea/genetics ; Bacteria ; Ecology ; Ecosystem ; *Hot Springs ; Phylogeny ; },
abstract = {The described diversity within the domain Archaea has recently expanded due to advances in sequencing technologies, but many habitats that likely harbor novel lineages of archaea remain understudied. Knowledge of archaea within natural and engineered hydrothermal systems, such as hot springs and engineered subsurface habitats, has been steadily increasing, but the majority of the work has focused on archaea living in acidic or circumneutral environments. The environmental pressures exerted by the combination of high temperatures and high pH likely select for divergent communities and distinct metabolic pathways from those observed in acidic or circumneutral systems. In this review, we examine what is currently known about the archaea found in thermoalkaline environments, focusing on the detection of novel lineages and knowledge of the ecology, metabolic pathways and functions of these populations and communities. We also discuss the potential of emerging multi-omics approaches, including proteomics and metabolomics, to enhance our understanding of archaea within extreme thermoalkaline systems.},
}
@article {pmid33499367,
year = {2021},
author = {Tittes, C and Schwarzer, S and Quax, TEF},
title = {Viral Hijack of Filamentous Surface Structures in Archaea and Bacteria.},
journal = {Viruses},
volume = {13},
number = {2},
pages = {},
pmid = {33499367},
issn = {1999-4915},
mesh = {Archaea/*virology ; Archaeal Viruses/*physiology ; Bacteria/*virology ; Bacteriophages/*physiology ; Cytoskeleton/*virology ; Fimbriae Proteins ; Fimbriae, Bacterial/virology ; Flagella/virology ; },
abstract = {The bacterial and archaeal cell surface is decorated with filamentous surface structures that are used for different functions, such as motility, DNA exchange and biofilm formation. Viruses hijack these structures and use them to ride to the cell surface for successful entry. In this review, we describe currently known mechanisms for viral attachment, translocation, and entry via filamentous surface structures. We describe the different mechanisms used to exploit various surface structures bacterial and archaeal viruses. This overview highlights the importance of filamentous structures at the cell surface for entry of prokaryotic viruses.},
}
@article {pmid33495623,
year = {2021},
author = {He, C and Keren, R and Whittaker, ML and Farag, IF and Doudna, JA and Cate, JHD and Banfield, JF},
title = {Genome-resolved metagenomics reveals site-specific diversity of episymbiotic CPR bacteria and DPANN archaea in groundwater ecosystems.},
journal = {Nature microbiology},
volume = {6},
number = {3},
pages = {354-365},
pmid = {33495623},
issn = {2058-5276},
support = {/HHMI/Howard Hughes Medical Institute/United States ; },
mesh = {Agriculture ; Archaea/classification/*physiology/ultrastructure ; Bacteria/classification/ultrastructure ; *Bacterial Physiological Phenomena ; Cell Adhesion ; Cell Proliferation ; *Ecosystem ; Groundwater/chemistry/*microbiology ; Humans ; Metagenome ; Metagenomics/*methods ; Microbiota ; Phylogeny ; Symbiosis ; },
abstract = {Candidate phyla radiation (CPR) bacteria and DPANN archaea are unisolated, small-celled symbionts that are often detected in groundwater. The effects of groundwater geochemistry on the abundance, distribution, taxonomic diversity and host association of CPR bacteria and DPANN archaea has not been studied. Here, we performed genome-resolved metagenomic analysis of one agricultural and seven pristine groundwater microbial communities and recovered 746 CPR and DPANN genomes in total. The pristine sites, which serve as local sources of drinking water, contained up to 31% CPR bacteria and 4% DPANN archaea. We observed little species-level overlap of metagenome-assembled genomes (MAGs) across the groundwater sites, indicating that CPR and DPANN communities may be differentiated according to physicochemical conditions and host populations. Cryogenic transmission electron microscopy imaging and genomic analyses enabled us to identify CPR and DPANN lineages that reproducibly attach to host cells and showed that the growth of CPR bacteria seems to be stimulated by attachment to host-cell surfaces. Our analysis reveals site-specific diversity of CPR bacteria and DPANN archaea that coexist with diverse hosts in groundwater aquifers. Given that CPR and DPANN organisms have been identified in human microbiomes and their presence is correlated with diseases such as periodontitis, our findings are relevant to considerations of drinking water quality and human health.},
}
@article {pmid33476388,
year = {2021},
author = {Lewis, AM and Recalde, A and Bräsen, C and Counts, JA and Nussbaum, P and Bost, J and Schocke, L and Shen, L and Willard, DJ and Quax, TEF and Peeters, E and Siebers, B and Albers, SV and Kelly, RM},
title = {The biology of thermoacidophilic archaea from the order Sulfolobales.},
journal = {FEMS microbiology reviews},
volume = {45},
number = {4},
pages = {},
pmid = {33476388},
issn = {1574-6976},
support = {GM008776-16/NH/NIH HHS/United States ; Pr-2013-0010//MERCUR/ ; T32 GM008776/GM/NIGMS NIH HHS/United States ; T32 GM133366/GM/NIGMS NIH HHS/United States ; CBET-1802939//National Science Foundation/ ; //Mercator Foundation/ ; 031L0078A//Federal Ministry of Education and Research/ ; FA9550-17-1-0268//AFOSR/ ; T32 AI007392/AI/NIAID NIH HHS/United States ; 411069969//Deutsche Forschungsgemeinschaft/ ; },
mesh = {*Archaea/genetics ; Biology ; Iron ; *Sulfolobales ; },
abstract = {Thermoacidophilic archaea belonging to the order Sulfolobales thrive in extreme biotopes, such as sulfuric hot springs and ore deposits. These microorganisms have been model systems for understanding life in extreme environments, as well as for probing the evolution of both molecular genetic processes and central metabolic pathways. Thermoacidophiles, such as the Sulfolobales, use typical microbial responses to persist in hot acid (e.g. motility, stress response, biofilm formation), albeit with some unusual twists. They also exhibit unique physiological features, including iron and sulfur chemolithoautotrophy, that differentiate them from much of the microbial world. Although first discovered >50 years ago, it was not until recently that genome sequence data and facile genetic tools have been developed for species in the Sulfolobales. These advances have not only opened up ways to further probe novel features of these microbes but also paved the way for their potential biotechnological applications. Discussed here are the nuances of the thermoacidophilic lifestyle of the Sulfolobales, including their evolutionary placement, cell biology, survival strategies, genetic tools, metabolic processes and physiological attributes together with how these characteristics make thermoacidophiles ideal platforms for specialized industrial processes.},
}
@article {pmid33469805,
year = {2021},
author = {Lyu, Z},
title = {Back to the Source: Molecular Identification of Methanogenic Archaea as Markers of Colonic Methane Production.},
journal = {Digestive diseases and sciences},
volume = {66},
number = {11},
pages = {3661-3664},
pmid = {33469805},
issn = {1573-2568},
mesh = {*Archaea/genetics ; *Euryarchaeota ; Humans ; Methane ; },
}
@article {pmid33462984,
year = {2021},
author = {Kevorkian, RT and Callahan, S and Winstead, R and Lloyd, KG},
title = {ANME-1 archaea may drive methane accumulation and removal in estuarine sediments.},
journal = {Environmental microbiology reports},
volume = {13},
number = {2},
pages = {185-194},
doi = {10.1111/1758-2229.12926},
pmid = {33462984},
issn = {1758-2229},
mesh = {Anaerobiosis ; *Archaea ; Geologic Sediments/microbiology ; *Methane/metabolism ; Oxidation-Reduction ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; },
abstract = {ANME-1 archaea subsist on the very low energy of anaerobic oxidation of methane (AOM). Most marine sediments shift from net AOM in the sulfate methane transition zone (SMTZ) to methanogenesis in the methane zone (MZ) below it. In White Oak River estuarine sediments, ANME-1 comprised 99.5% of 16S rRNA genes from amplicons and 100% of 16S rRNA genes from metagenomes of the Methanomicrobia in the SMTZ and 99.9% and 98.3%, respectively, in the MZ. Each of the 16 ANME-1 OTUs (97% similarity) had peaks in the SMTZ that coincided with peaks of putative sulfate-reducing bacteria Desulfatiglans sp. and SEEP-SRB1. In the MZ, ANME-1, but none of the putative sulfate-reducing bacteria or cultured methanogens, increased with depth. Our meta-analysis of public data showed only ANME-1 expressed methanogenic genes during both net AOM and net methanogenesis in an enrichment culture. We conclude that ANME-1 perform AOM in the SMTZ and methanogenesis in the MZ of White Oak River sediments. This metabolic flexibility may expand habitable zones in extraterrestrial environments, since it enables greater energy yields in a fluctuating energetic landscape.},
}
@article {pmid33462601,
year = {2021},
author = {Garg, SG and Kapust, N and Lin, W and Knopp, M and Tria, FDK and Nelson-Sathi, S and Gould, SB and Fan, L and Zhu, R and Zhang, C and Martin, WF},
title = {Anomalous Phylogenetic Behavior of Ribosomal Proteins in Metagenome-Assembled Asgard Archaea.},
journal = {Genome biology and evolution},
volume = {13},
number = {1},
pages = {},
pmid = {33462601},
issn = {1759-6653},
mesh = {Archaea/*genetics ; Ecosystem ; Eukaryota/genetics ; Eukaryotic Cells ; Evolution, Molecular ; *Genome, Archaeal ; Genomics ; *Metagenome ; Metagenomics ; *Phylogeny ; Ribosomal Proteins/*classification/*genetics ; },
abstract = {Metagenomic studies permit the exploration of microbial diversity in a defined habitat, and binning procedures enable phylogenomic analyses, taxon description, and even phenotypic characterizations in the absence of morphological evidence. Such lineages include asgard archaea, which were initially reported to represent archaea with eukaryotic cell complexity, although the first images of such an archaeon show simple cells with prokaryotic characteristics. However, these metagenome-assembled genomes (MAGs) might suffer from data quality problems not encountered in sequences from cultured organisms due to two common analytical procedures of bioinformatics: assembly of metagenomic sequences and binning of assembled sequences on the basis of innate sequence properties and abundance across samples. Consequently, genomic sequences of distantly related taxa, or domains, can in principle be assigned to the same MAG and result in chimeric sequences. The impacts of low-quality or chimeric MAGs on phylogenomic and metabolic prediction remain unknown. Debates that asgard archaeal data are contaminated with eukaryotic sequences are overshadowed by the lack of evidence indicating that individual asgard MAGs stem from the same chromosome. Here, we show that universal proteins including ribosomal proteins of asgard archaeal MAGs fail to meet the basic phylogenetic criterion fulfilled by genome sequences of cultured archaea investigated to date: These proteins do not share common evolutionary histories to the same extent as pure culture genomes do, pointing to a chimeric nature of asgard archaeal MAGs. Our analysis suggests that some asgard archaeal MAGs represent unnatural constructs, genome-like patchworks of genes resulting from assembly and/or the binning process.},
}
@article {pmid33453701,
year = {2021},
author = {Tao, R and Li, J and Hu, B and Chu, G},
title = {Mitigating N2O emission by synthetic inhibitors mixed with urea and cattle manure application via inhibiting ammonia-oxidizing bacteria, but not archaea, in a calcareous soil.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {273},
number = {},
pages = {116478},
doi = {10.1016/j.envpol.2021.116478},
pmid = {33453701},
issn = {1873-6424},
abstract = {Synthetic inhibitors and organic amendment have been proposed for mitigating greenhouse gas N2O emissions. However, their combined effect on the N2O emissions and ammonia-oxidizer (ammonia-oxidizing bacteria and archaea, AOB and AOA) communities remains unclear in calcareous soils under climate warming. We conducted two incubation experiments (25 and 35 °C) to examine how N2O emissions and AOA and AOB communities responded to organic amendment (urea plus cattle manure, UCM), and in combination with urease (N-(n-butyl) thiophosphoric triamide, NBPT) and nitrification inhibitor (nitrapyrin). The treatments of UCM + nitrapyrin and UCM + nitrapyrin + NBPT significantly lowered total N2O emissions by average 64.5 and 71.05% at 25 and 35 °C, respectively, compared with UCM treatment. AOB gene abundance and α-diversity (Chao1 and Shannon indices) were significantly increased by the application of urea and manure (P < 0.05). However, relative to UCM treatment, nitrapyrin addition treatments decreased AOB gene abundance and Chao 1 index by average 115.4 and 30.4% at 25 and 35 °C, respectively. PCA analysis showed that UCM or UCM plus nitrapyrin notably shifted AOB structure at both temperatures. However, fertilization had little effects on AOA community (P > 0.05). Potential nitrification rate (PNR) was greatly decreased by nitrapyrin addition, and PNR significantly positively correlated with AOB gene abundance (P = 0.0179 at 25 °C and P = 0.0029 at 35 °C) rather than AOA (P > 0.05). Structural equation model analysis showed that temperature directly increased AOA abundance but decrease AOB abundance, while fertilization indirectly influenced AOB community by altering soil NH4[+], pH and SOC. In conclusion, the combined application of organic amendment, NBPT and nitrapyrin significantly lowered N2O emissions via reducing AOB community in calcareous soil even at high temperature. Our findings provide a solid theoretical basis in mitigating N2O emissions from calcareous soil under climate warming.},
}
@article {pmid33452484,
year = {2021},
author = {Zhang, JW and Dong, HP and Hou, LJ and Liu, Y and Ou, YF and Zheng, YL and Han, P and Liang, X and Yin, GY and Wu, DM and Liu, M and Li, M},
title = {Newly discovered Asgard archaea Hermodarchaeota potentially degrade alkanes and aromatics via alkyl/benzyl-succinate synthase and benzoyl-CoA pathway.},
journal = {The ISME journal},
volume = {15},
number = {6},
pages = {1826-1843},
pmid = {33452484},
issn = {1751-7370},
mesh = {Acyl Coenzyme A ; *Alkanes ; *Archaea/genetics ; Geologic Sediments ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Succinic Acid ; },
abstract = {Asgard archaea are widely distributed in anaerobic environments. Previous studies revealed the potential capability of Asgard archaea to utilize various organic substrates including proteins, carbohydrates, fatty acids, amino acids and hydrocarbons, suggesting that Asgard archaea play an important role in sediment carbon cycling. Here, we describe a previously unrecognized archaeal phylum, Hermodarchaeota, affiliated with the Asgard superphylum. The genomes of these archaea were recovered from metagenomes generated from mangrove sediments, and were found to encode alkyl/benzyl-succinate synthases and their activating enzymes that are similar to those identified in alkane-degrading sulfate-reducing bacteria. Hermodarchaeota also encode enzymes potentially involved in alkyl-coenzyme A and benzoyl-coenzyme A oxidation, the Wood-Ljungdahl pathway and nitrate reduction. These results indicate that members of this phylum have the potential to strictly anaerobically degrade alkanes and aromatic compounds, coupling the reduction of nitrate. By screening Sequence Read Archive, additional genes encoding 16S rRNA and alkyl/benzyl-succinate synthases analogous to those in Hermodarchaeota were identified in metagenomic datasets from a wide range of marine and freshwater sediments. These findings suggest that Asgard archaea capable of degrading alkanes and aromatics via formation of alkyl/benzyl-substituted succinates are ubiquitous in sediments.},
}
@article {pmid33452028,
year = {2021},
author = {Aldridge, J and Carr, S and Weber, KA and Buan, NR},
title = {Anaerobic Production of Isoprene by Engineered Methanosarcina Species Archaea.},
journal = {Applied and environmental microbiology},
volume = {87},
number = {6},
pages = {},
pmid = {33452028},
issn = {1098-5336},
mesh = {Anaerobiosis ; Butadienes ; Hemiterpenes/*biosynthesis ; Methanol/metabolism ; Methanosarcina/genetics/*metabolism ; Mevalonic Acid ; Microorganisms, Genetically-Modified/metabolism ; },
abstract = {Isoprene is a valuable petrochemical used for a wide variety of consumer goods, such as adhesives and synthetic rubber. We were able to achieve a high yield of renewable isoprene by taking advantage of the naturally high-flux mevalonate lipid synthesis pathway in anaerobic methane-producing archaea (methanogens). Our study illustrates that by genetically manipulating Methanosarcina species methanogens, it is possible to create organisms that grow by producing the hemiterpene isoprene. Mass balance measurements show that engineered methanogens direct up to 4% of total carbon flux to isoprene, demonstrating that methanogens produce higher isoprene yields than engineered yeast, bacteria, or cyanobacteria, and from inexpensive feedstocks. Expression of isoprene synthase resulted in increased biomass and changes in gene expression that indicate that isoprene synthesis depletes membrane precursors and redirects electron flux, enabling isoprene to be a major metabolic product. Our results demonstrate that methanogens are a promising engineering chassis for renewable isoprene synthesis.IMPORTANCE A significant barrier to implementing renewable chemical technologies is high production costs relative to those for petroleum-derived products. Existing technologies using engineered organisms have difficulty competing with petroleum-derived chemicals due to the cost of feedstocks (such as glucose), product extraction, and purification. The hemiterpene monomer isoprene is one such chemical that cannot currently be produced using cost-competitive renewable biotechnologies. To reduce the cost of renewable isoprene, we have engineered methanogens to synthesize it from inexpensive feedstocks such as methane, methanol, acetate, and carbon dioxide. The "isoprenogen" strains we developed have potential to be used for industrial production of inexpensive renewable isoprene.},
}
@article {pmid33444853,
year = {2021},
author = {Yang, Y and Herbold, CW and Jung, MY and Qin, W and Cai, M and Du, H and Lin, JG and Li, X and Li, M and Gu, JD},
title = {Survival strategies of ammonia-oxidizing archaea (AOA) in a full-scale WWTP treating mixed landfill leachate containing copper ions and operating at low-intensity of aeration.},
journal = {Water research},
volume = {191},
number = {},
pages = {116798},
doi = {10.1016/j.watres.2020.116798},
pmid = {33444853},
issn = {1879-2448},
mesh = {Ammonia ; *Archaea/genetics ; Bacteria ; Copper ; Ions ; Nitrification ; Oxidation-Reduction ; Phylogeny ; Soil Microbiology ; *Water Pollutants, Chemical ; },
abstract = {Recent studies indicate that ammonia-oxidizing archaea (AOA) may play an important role in nitrogen removal by wastewater treatment plants (WWTPs). However, our knowledge of the mechanisms employed by AOA for growth and survival in full-scale WWTPs is still limited. Here, metagenomic and metatranscriptomic analyses combined with a laboratory cultivation experiment revealed that three active AOAs (WS9, WS192, and WS208) belonging to family Nitrososphaeraceae were active in the deep oxidation ditch (DOD) of a full-scale WWTP treating landfill leachate, which is configured with three continuous aerobic-anoxic (OA) modules with low-intensity aeration (≤ 1.5 mg/L). AOA coexisted with AOB and complete ammonia oxidizers (Comammox), while the ammonia-oxidizing microbial (AOM) community was unexpectedly dominated by the novel AOA strain WS9. The low aeration, long retention time, and relatively high inputs of ammonium and copper might be responsible for the survival of AOA over AOB and Comammox, while the dominance of WS9, specifically may be enhanced by substrate preference and uniquely encoded retention strategies. The urease-negative WS9 is specifically adapted for ammonia acquisition as evidenced by the high expression of an ammonium transporter, whereas two metabolically versatile urease-positive AOA strains (WS192 and WS208) can likely supplement ammonia needs with urea. This study provides important information for the survival and application of the eutrophic Nitrososphaeraceae AOA and advances our understanding of archaea-dominated ammonia oxidation in a full-scale wastewater treatment system.},
}
@article {pmid33434266,
year = {2021},
author = {Knüppel, R and Trahan, C and Kern, M and Wagner, A and Grünberger, F and Hausner, W and Quax, TEF and Albers, SV and Oeffinger, M and Ferreira-Cerca, S},
title = {Insights into synthesis and function of KsgA/Dim1-dependent rRNA modifications in archaea.},
journal = {Nucleic acids research},
volume = {49},
number = {3},
pages = {1662-1687},
pmid = {33434266},
issn = {1362-4962},
support = {PJT 386315//CIHR/Canada ; },
mesh = {Archaea/*enzymology/genetics ; Cell Movement ; Crenarchaeota/enzymology ; Euryarchaeota/enzymology ; Haloferax volcanii/enzymology ; Methyltransferases/*metabolism/physiology ; Protein Biosynthesis ; RNA, Archaeal/chemistry/*metabolism ; RNA, Ribosomal/chemistry/*metabolism ; Ribosome Subunits, Small, Archaeal/enzymology ; },
abstract = {Ribosomes are intricate molecular machines ensuring proper protein synthesis in every cell. Ribosome biogenesis is a complex process which has been intensively analyzed in bacteria and eukaryotes. In contrast, our understanding of the in vivo archaeal ribosome biogenesis pathway remains less characterized. Here, we have analyzed the in vivo role of the almost universally conserved ribosomal RNA dimethyltransferase KsgA/Dim1 homolog in archaea. Our study reveals that KsgA/Dim1-dependent 16S rRNA dimethylation is dispensable for the cellular growth of phylogenetically distant archaea. However, proteomics and functional analyses suggest that archaeal KsgA/Dim1 and its rRNA modification activity (i) influence the expression of a subset of proteins and (ii) contribute to archaeal cellular fitness and adaptation. In addition, our study reveals an unexpected KsgA/Dim1-dependent variability of rRNA modifications within the archaeal phylum. Combining structure-based functional studies across evolutionary divergent organisms, we provide evidence on how rRNA structure sequence variability (re-)shapes the KsgA/Dim1-dependent rRNA modification status. Finally, our results suggest an uncoupling between the KsgA/Dim1-dependent rRNA modification completion and its release from the nascent small ribosomal subunit. Collectively, our study provides additional understandings into principles of molecular functional adaptation, and further evolutionary and mechanistic insights into an almost universally conserved step of ribosome synthesis.},
}
@article {pmid33432457,
year = {2021},
author = {Wang, YF and Gu, JD and Dick, RP and Han, W and Yang, HX and Liao, HQ and Zhou, Y and Meng, H},
title = {Distribution of ammonia-oxidizing archaea and bacteria along an engineered coastal ecosystem in subtropical China.},
journal = {Ecotoxicology (London, England)},
volume = {30},
number = {8},
pages = {1769-1779},
pmid = {33432457},
issn = {1573-3017},
support = {2018KJCX011//Guangdong Forestry Scientific and Technological Innovation Key Program/ ; },
mesh = {*Ammonia ; *Archaea/genetics ; Bacteria/genetics ; China ; Ecosystem ; Humans ; Oxidation-Reduction ; Phylogeny ; Soil ; Soil Microbiology ; },
abstract = {Ammonia-oxidizing archaea (AOA) and bacteria (AOB) are the crucial players in nitrogen cycle. Both AOA and AOB were examined along a gradient of human activity in a coastal ecosystem from intertidal zone, grassland, and Casuarina equisetifolia forest to farmland. Results showed that the farmland soils had noticeably higher nitrate-N, available P than soils in the other three sites. Generally, AOA and AOB community structures varied across sites. The farmland mainly had Nitrosotalea-like AOA, intertidal zone was dominated by Nitrosopumilus AOA, while grassland and C. equisetifolia forest primarily harbored Nitrososphaera-like AOA. The farmland and C. equisetifolia forest owned Nitrosospira-like AOB, intertidal zone possessed Nitrosomonas-like AOB, and no AOB was detected in the grassland. AOA abundance was significantly greater than AOB in this coastal ecosystem (p < 0.05, n = 8). AOB diversity and abundance in the farmland were significantly higher than those in the other three sites (p < 0.05, n = 2). The biodiversity and abundance of AOA were not significantly correlated with any soil property (p < 0.05, n = 8). However, the diversity of AOB was significantly correlated with pH, available P and total P (p < 0.05, n = 6). The abundance of AOB was significantly correlated with pH, nitrite, available N, available P and total P (p < 0.05, n = 6). This study suggested that the community structures of AOA and AOB vary in the different parts in the bio-engineered coastal ecosystem and agricultural activity appears to influence these nitrifiers.},
}
@article {pmid37073340,
year = {2021},
author = {Cui, HL and Dyall-Smith, ML},
title = {Cultivation of halophilic archaea (class Halobacteria) from thalassohaline and athalassohaline environments.},
journal = {Marine life science &amp; technology},
volume = {3},
number = {2},
pages = {243-251},
pmid = {37073340},
issn = {2662-1746},
abstract = {UNLABELLED: As a group, the halophilic archaea (class Halobacteria) are the most salt-requiring and salt-resistant microorganisms within the domain Archaea. Halophilic archaea flourish in thalassohaline and athalassohaline environments and require over 100-150 g/L NaCl for growth and structural stability. Natural hypersaline environments vary in salt concentration, chemical composition and pH, and occur in climates ranging from tropical to polar and even under-sea. Accordingly, their resident haloarchaeal species vary enormously, as do their individual population compositions and community structures. These diverse halophilic archaeal strains are precious resources for theoretical and applied research but assessing their taxonomic and metabolic novelty and diversity in natural environments has been technically difficult up until recently. Environmental DNA-based high-throughput sequencing technology has now matured sufficiently to allow inexpensive recovery of massive amounts of sequence data, revealing the distribution and community composition of halophilic archaea in different hypersaline environments. While cultivation of haloarchaea is slow and tedious, and only recovers a fraction of the natural diversity, it is the conventional means of describing new species, and provides strains for detailed study. As of the end of May 2020, the class Halobacteria contains 71 genera and 275 species, 49.8% of which were first isolated from the marine salt environment and 50.2% from the inland salt environment, indicating that both thalassohaline and athalassohaline environments contain diverse halophilic archaea. However, there remain taxa that have not yet been isolated in pure culture, such as the nanohaloarchaea, which are widespread in the salt environment and may be one of the hot spots in the field of halophilic archaea research in the future. In this review, we focus on the cultivation strategies that have been used to isolate extremely halophilic archaea and point out some of the pitfalls and challenges.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42995-020-00087-3.},
}
@article {pmid33385817,
year = {2021},
author = {Zheng, T and Li, W and Ma, Y and Liu, J},
title = {Time-based succession existed in rural sewer biofilms: Bacterial communities, sulfate-reducing bacteria and methanogenic archaea, and sulfide and methane generation.},
journal = {The Science of the total environment},
volume = {765},
number = {},
pages = {144397},
doi = {10.1016/j.scitotenv.2020.144397},
pmid = {33385817},
issn = {1879-1026},
mesh = {*Archaea ; Bacteria ; Biofilms ; Family Characteristics ; *Methane ; Sewage ; Sulfates ; Sulfides ; },
abstract = {Rural sewers are applied widely to collect rural sewage and biofilm characteristics in rural sewers may be different with municipal sewers. The succession of bacteria communities, sulfate-reducing bacteria (SRB) and methanogenic archaea (MA) need to be studied since rural sewers have a potential risk of sulfide and methane accumulation. In this study, lab-scale rural sewer facilities were established to analyze the characteristics of sewer biofilm and the generation of sulfide and methane. The results indicate that the variation tendency of biofilm thickness in rural sewers was different with municipal sewers. Time-based bacterial succession existed in rural sewer biofilms and the predominant genus was changed from Acinetobacter (approximately 19.10%) to Pseudomonas (approximately 12.61%). SRB (mean 1.49 × 10[6]dsrA copies/cm[2]) were abundant than MA (mean 2.57 × 10[5]mcrA copies/cm[2]) while MA were eliminated gradually in rural sewer biofilms. The tendency of sulfide and methane generation was similar with the number variation of SRB and MA, indicating sulfide accumulation might be more serious trouble than methane accumulation in a long-run rural sewer. Overall, this study deeply analyzed the succession of rural sewer biofilms and found that MA and methane were automatically inhibited in rural sewers.},
}
@article {pmid33383035,
year = {2021},
author = {Laursen, SP and Bowerman, S and Luger, K},
title = {Archaea: The Final Frontier of Chromatin.},
journal = {Journal of molecular biology},
volume = {433},
number = {6},
pages = {166791},
pmid = {33383035},
issn = {1089-8638},
support = {/HHMI/Howard Hughes Medical Institute/United States ; F32 GM137496/GM/NIGMS NIH HHS/United States ; },
mesh = {Amino Acid Sequence ; Archaea/classification/*genetics/metabolism ; Archaeal Proteins/*chemistry/genetics/metabolism ; Chromatin/chemistry/metabolism/*ultrastructure ; Conserved Sequence ; DNA, Archaeal/*chemistry/genetics/metabolism ; DNA-Binding Proteins/*chemistry/genetics/metabolism ; Histones/*chemistry/genetics/metabolism ; Nucleic Acid Conformation ; Phylogeny ; Protein Binding ; Protein Conformation, alpha-Helical ; Protein Conformation, beta-Strand ; Protein Interaction Domains and Motifs ; Protein Multimerization ; },
abstract = {The three domains of life employ various strategies to organize their genomes. Archaea utilize features similar to those found in both eukaryotic and bacterial chromatin to organize their DNA. In this review, we discuss the current state of research regarding the structure-function relationships of several archaeal chromatin proteins (histones, Alba, Cren7, and Sul7d). We address individual structures as well as inferred models for higher-order chromatin formation. Each protein introduces a unique phenotype to chromatin organization, and these structures are put into the context of in vivo and in vitro data. We close by discussing the present gaps in knowledge that are preventing further studies of the organization of archaeal chromatin, on both the organismal and domain level.},
}
@article {pmid33343547,
year = {2020},
author = {Kuprat, T and Johnsen, U and Ortjohann, M and Schönheit, P},
title = {Acetate Metabolism in Archaea: Characterization of an Acetate Transporter and of Enzymes Involved in Acetate Activation and Gluconeogenesis in Haloferax volcanii.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {604926},
pmid = {33343547},
issn = {1664-302X},
abstract = {The haloarchaeon Haloferax volcanii grows on acetate as sole carbon and energy source. The genes and proteins involved in uptake and activation of acetate and in gluconeogenesis were identified and analyzed by characterization of enzymes and by growth experiments with the respective deletion mutants. (i) An acetate transporter of the sodium: solute-symporter family (SSF) was characterized by kinetic analyses of acetate uptake into H. volcanii cells. The functional involvement of the transporter was proven with a Δssf mutant. (ii) Four paralogous AMP-forming acetyl-CoA synthetases that belong to different phylogenetic clades were shown to be functionally involved in acetate activation. (iii) The essential involvement of the glyoxylate cycle as an anaplerotic sequence was concluded from growth experiments with an isocitrate lyase knock-out mutant excluding the operation of the methylaspartate cycle reported for Haloarcula species. (iv) Enzymes involved in phosphoenolpyruvate synthesis from acetate, namely two malic enzymes and a phosphoenolpyruvate synthetase, were identified and characterized. Phylogenetic analyses of haloarchaeal malic enzymes indicate a separate evolutionary line distinct from other archaeal homologs. The exclusive function of phosphoenolpyruvate synthetase in gluconeogenesis was proven by the respective knock-out mutant. Together, this is a comprehensive study of acetate metabolism in archaea.},
}
@article {pmid33329506,
year = {2020},
author = {Skretas, G and Ventura, S},
title = {Editorial: Protein Aggregation and Solubility in Microorganisms (Archaea, Bacteria and Unicellular Eukaryotes): Implications and Applications.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {620239},
pmid = {33329506},
issn = {1664-302X},
}
@article {pmid33329479,
year = {2020},
author = {Schwarz, TS and Berkemer, SJ and Bernhart, SH and Weiß, M and Ferreira-Cerca, S and Stadler, PF and Marchfelder, A},
title = {Splicing Endonuclease Is an Important Player in rRNA and tRNA Maturation in Archaea.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {594838},
pmid = {33329479},
issn = {1664-302X},
abstract = {In all three domains of life, tRNA genes contain introns that must be removed to yield functional tRNA. In archaea and eukarya, the first step of this process is catalyzed by a splicing endonuclease. The consensus structure recognized by the splicing endonuclease is a bulge-helix-bulge (BHB) motif which is also found in rRNA precursors. So far, a systematic analysis to identify all biological substrates of the splicing endonuclease has not been carried out. In this study, we employed CRISPRi to repress expression of the splicing endonuclease in the archaeon Haloferax volcanii to identify all substrates of this enzyme. Expression of the splicing endonuclease was reduced to 1% of its normal level, resulting in a significant extension of lag phase in H. volcanii growth. In the repression strain, 41 genes were down-regulated and 102 were up-regulated. As an additional approach in identifying new substrates of the splicing endonuclease, we isolated and sequenced circular RNAs, which identified excised introns removed from tRNA and rRNA precursors as well as from the 5' UTR of the gene HVO_1309. In vitro processing assays showed that the BHB sites in the 5' UTR of HVO_1309 and in a 16S rRNA-like precursor are processed by the recombinant splicing endonuclease. The splicing endonuclease is therefore an important player in RNA maturation in archaea.},
}
@article {pmid33329440,
year = {2020},
author = {Distaso, MA and Bargiela, R and Brailsford, FL and Williams, GB and Wright, S and Lunev, EA and Toshchakov, SV and Yakimov, MM and Jones, DL and Golyshin, PN and Golyshina, OV},
title = {High Representation of Archaea Across All Depths in Oxic and Low-pH Sediment Layers Underlying an Acidic Stream.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {576520},
pmid = {33329440},
issn = {1664-302X},
abstract = {Parys Mountain or Mynydd Parys (Isle of Anglesey, United Kingdom) is a mine-impacted environment, which accommodates a variety of acidophilic organisms. Our previous research of water and sediments from one of the surface acidic streams showed a high proportion of archaea in the total microbial community. To understand the spatial distribution of archaea, we sampled cores (0-20 cm) of sediment and conducted chemical analyses and taxonomic profiling of microbiomes using 16S rRNA gene amplicon sequencing in different core layers. The taxonomic affiliation of sequencing reads indicated that archaea represented between 6.2 and 54% of the microbial community at all sediment depths. Majority of archaea were associated with the order Thermoplasmatales, with the most abundant group of sequences being clustered closely with the phylotype B_DKE, followed by "E-plasma," "A-plasma," other yet uncultured Thermoplasmatales with Ferroplasma and Cuniculiplasma spp. represented in minor proportions. Thermoplasmatales were found at all depths and in the whole range of chemical conditions with their abundance correlating with sediment Fe, As, Cr, and Mn contents. The bacterial microbiome component was largely composed in all layers of sediment by members of the phyla Proteobacteria, Actinobacteria, Nitrospirae, Firmicutes, uncultured Chloroflexi (AD3 group), and Acidobacteria. This study has revealed a high abundance of Thermoplasmatales in acid mine drainage-affected sediment layers and pointed at these organisms being the main contributors to carbon, and probably to iron and sulfur cycles in this ecosystem.},
}
@article {pmid33325687,
year = {2021},
author = {Stein, LY and Klotz, MG and Lancaster, KM and Nicol, GW and Qin, W and Schleper, C and Stahl, D and Ward, BB and Yoon, S},
title = {Comment on"A Critical Review on Nitrous Oxide Production by Ammonia-Oxidizing Archaea" by Lan Wu, Xueming Chen, Wei Wei, Yiwen Liu, Dongbo Wang, and Bing-Jie Ni.},
journal = {Environmental science &amp; technology},
volume = {55},
number = {1},
pages = {797-798},
doi = {10.1021/acs.est.0c06792},
pmid = {33325687},
issn = {1520-5851},
mesh = {*Ammonia ; *Archaea ; Nitrification ; Nitrous Oxide ; Oxidation-Reduction ; },
}
@article {pmid33325686,
year = {2021},
author = {Wu, L and Wei, W and Ni, BJ},
title = {Response to Comment on "A Critical Review on Nitrous Oxide Production by Ammonia-Oxidizing Archaea".},
journal = {Environmental science &amp; technology},
volume = {55},
number = {1},
pages = {799-800},
doi = {10.1021/acs.est.0c08136},
pmid = {33325686},
issn = {1520-5851},
mesh = {*Ammonia ; *Archaea ; Nitrification ; Nitrous Oxide ; Oxidation-Reduction ; },
}
@article {pmid33320181,
year = {2021},
author = {Thomès, L and Lescure, A},
title = {Mosaic Evolution of the Phosphopantothenate Biosynthesis Pathway in Bacteria and Archaea.},
journal = {Genome biology and evolution},
volume = {13},
number = {2},
pages = {},
pmid = {33320181},
issn = {1759-6653},
mesh = {Archaea/*enzymology/genetics ; Bacteria/*enzymology/genetics ; Biosynthetic Pathways/genetics ; Coenzyme A/*biosynthesis ; *Evolution, Molecular ; Genes, Bacterial ; Symbiosis ; },
abstract = {Phosphopantothenate is a precursor to synthesis of coenzyme A, a molecule essential to many metabolic pathways. Organisms of the archaeal phyla were shown to utilize a different phosphopantothenate biosynthetic pathway from the eukaryotic and bacterial one. In this study, we report that symbiotic bacteria from the group Candidatus poribacteria present enzymes of the archaeal pathway, namely pantoate kinase and phosphopantothenate synthetase, mirroring what was demonstrated for Picrophilus torridus, an archaea partially utilizing the bacterial pathway. Our results not only support the ancient origin of the coenzyme A pathway in the three domains of life but also highlight its complex and dynamic evolution. Importantly, this study helps to improve protein annotation for this pathway in the C. poribacteria group and other related organisms.},
}
@article {pmid33316511,
year = {2021},
author = {Ding, J and Zeng, RJ},
title = {Fundamentals and potential environmental significance of denitrifying anaerobic methane oxidizing archaea.},
journal = {The Science of the total environment},
volume = {757},
number = {},
pages = {143928},
doi = {10.1016/j.scitotenv.2020.143928},
pmid = {33316511},
issn = {1879-1026},
mesh = {Anaerobiosis ; *Archaea ; Bioreactors ; Denitrification ; *Methane ; Nitrites ; Oxidation-Reduction ; },
abstract = {Many properties of denitrifying anaerobic methane oxidation (DAMO) bacteria have been explored since their first discovery, while DAMO archaea have attracted less attention. Since nitrate is more abundant than nitrite not only in wastewater but also in the natural environment, in depth investigations of the nitrate-DAMO process should be conducted to determine its environmental significance in the global carbon and nitrogen cycles. This review summarizes the status of research on DAMO archaea and the catalyzed nitrate-dependent anaerobic methane oxidation, including such aspects as laboratory enrichment, environmental distribution, and metabolic mechanism. It is shown that appropriate inocula and enrichment parameters are important for the culture enrichment and thus the subsequent DAMO activity, but there are still relatively few studies on the environmental distribution and physiological metabolism of DAMO archaea. Finally, some hypotheses and directions for future research on DAMO archaea, anaerobic methanotrophic archaea, and even anaerobically metabolizing archaea are also discussed.},
}
@article {pmid33288720,
year = {2020},
author = {Stevens, KM and Swadling, JB and Hocher, A and Bang, C and Gribaldo, S and Schmitz, RA and Warnecke, T},
title = {Histone variants in archaea and the evolution of combinatorial chromatin complexity.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {117},
number = {52},
pages = {33384-33395},
pmid = {33288720},
issn = {1091-6490},
support = {MC_UP_1102/7/MRC_/Medical Research Council/United Kingdom ; },
mesh = {Amino Acids/genetics ; Archaea/*genetics ; Chromatin/*metabolism ; DNA/metabolism ; *Evolution, Molecular ; *Genetic Variation ; Histones/chemistry/*genetics/metabolism ; Molecular Dynamics Simulation ; Mutation/genetics ; Phylogeny ; Protein Binding ; },
abstract = {Nucleosomes in eukaryotes act as platforms for the dynamic integration of epigenetic information. Posttranslational modifications are reversibly added or removed and core histones exchanged for paralogous variants, in concert with changing demands on transcription and genome accessibility. Histones are also common in archaea. Their role in genome regulation, however, and the capacity of individual paralogs to assemble into histone-DNA complexes with distinct properties remain poorly understood. Here, we combine structural modeling with phylogenetic analysis to shed light on archaeal histone paralogs, their evolutionary history, and capacity to generate combinatorial chromatin states through hetero-oligomeric assembly. Focusing on the human commensal Methanosphaera stadtmanae as a model archaeal system, we show that the heteromeric complexes that can be assembled from its seven histone paralogs vary substantially in DNA binding affinity and tetramer stability. Using molecular dynamics simulations, we go on to identify unique paralogs in M. stadtmanae and Methanobrevibacter smithii that are characterized by unstable interfaces between dimers. We propose that these paralogs act as capstones that prevent stable tetramer formation and extension into longer oligomers characteristic of model archaeal histones. Importantly, we provide evidence from phylogeny and genome architecture that these capstones, as well as other paralogs in the Methanobacteriales, have been maintained for hundreds of millions of years following ancient duplication events. Taken together, our findings indicate that at least some archaeal histone paralogs have evolved to play distinct and conserved functional roles, reminiscent of eukaryotic histone variants. We conclude that combinatorially complex histone-based chromatin is not restricted to eukaryotes and likely predates their emergence.},
}
@article {pmid33288384,
year = {2021},
author = {Pallen, MJ and Telatin, A and Oren, A},
title = {The Next Million Names for Archaea and Bacteria.},
journal = {Trends in microbiology},
volume = {29},
number = {4},
pages = {289-298},
doi = {10.1016/j.tim.2020.10.009},
pmid = {33288384},
issn = {1878-4380},
support = {BBS/E/F/000PR10355/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; MR/L015080/1/MRC_/Medical Research Council/United Kingdom ; MR/T030062/1/MRC_/Medical Research Council/United Kingdom ; },
mesh = {Archaea/*classification/*genetics ; Bacteria/*classification/*genetics ; Metagenomics ; *Phylogeny ; },
abstract = {Latin binomials, popularised in the 18th century by the Swedish naturalist Linnaeus, have stood the test of time in providing a stable, clear, and memorable system of nomenclature across biology. However, relentless and ever-deeper exploration and analysis of the microbial world has created an urgent need for huge numbers of new names for Archaea and Bacteria. Manual creation of such names remains difficult and slow and typically relies on expert-driven nomenclatural quality control. Keen to ensure that the legacy of Linnaeus lives on in the age of microbial genomics and metagenomics, we propose an automated approach, employing combinatorial concatenation of roots from Latin and Greek to create linguistically correct names for genera and species that can be used off the shelf as needed. As proof of principle, we document over a million new names for Bacteria and Archaea. We are confident that our approach provides a road map for how to create new names for decades to come.},
}
@article {pmid33276555,
year = {2020},
author = {Urbonavičius, J and Tauraitė, D},
title = {Biochemical Pathways Leading to the Formation of Wyosine Derivatives in tRNA of Archaea.},
journal = {Biomolecules},
volume = {10},
number = {12},
pages = {},
pmid = {33276555},
issn = {2218-273X},
support = {S-MIP-19-61//Lietuvos Mokslo Taryba/International ; },
mesh = {*Archaea/metabolism ; *RNA, Transfer/metabolism ; RNA, Archaeal/metabolism/genetics ; Guanosine/analogs &amp; derivatives ; Nucleosides ; },
abstract = {Tricyclic wyosine derivatives are present at position 37 in tRNA[Phe] of both eukaryotes and archaea. In eukaryotes, five different enzymes are needed to form a final product, wybutosine (yW). In archaea, 4-demethylwyosine (imG-14) is an intermediate for the formation of three different wyosine derivatives, yW-72, imG, and mimG. In this review, current knowledge regarding the archaeal enzymes involved in this process and their reaction mechanisms are summarized. The experiments aimed to elucidate missing steps in biosynthesis pathways leading to the formation of wyosine derivatives are suggested. In addition, the chemical synthesis pathways of archaeal wyosine nucleosides are discussed, and the scheme for the formation of yW-86 and yW-72 is proposed. Recent data demonstrating that wyosine derivatives are present in the other tRNA species than those specific for phenylalanine are discussed.},
}
@article {pmid33274598,
year = {2021},
author = {More, KD and Wuchter, C and Irigoien, X and Tierney, JE and Giosan, L and Grice, K and Coolen, MJL},
title = {Subseafloor Archaea reflect 139 kyrs of paleodepositional changes in the northern Red Sea.},
journal = {Geobiology},
volume = {19},
number = {2},
pages = {162-172},
doi = {10.1111/gbi.12421},
pmid = {33274598},
issn = {1472-4669},
mesh = {*Archaea/genetics ; DNA, Archaeal/genetics ; *Euryarchaeota ; Geologic Sediments ; Indian Ocean ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The vertical distribution of subseafloor archaeal communities is thought to be primarily controlled by in situ conditions in sediments such as the availability of electron acceptors and donors, although sharp community shifts have also been observed at lithological boundaries suggesting that at least a subset of vertically stratified Archaea form a long-term genetic record of coinciding environmental conditions that occurred at the time of sediment deposition. To substantiate this possibility, we performed a highly resolved 16S rRNA gene survey of vertically stratified archaeal communities paired with paleo-oceanographic proxies in a sedimentary record from the northern Red Sea spanning the last glacial-interglacial cycle (i.e., marine isotope stages 1-6; MIS1-6). Our results show a strong significant correlation between subseafloor archaeal communities and drastic paleodepositional changes associated with glacial low vs. interglacial high stands (ANOSIM; R = .73; p = .001) and only a moderately strong correlation with lithological changes. Bathyarchaeota, Lokiarchaeota, MBGA, and DHVEG-1 were the most abundant identified archaeal groups. Whether they represented ancient cell lines from the time of deposition or migrated to the specific sedimentary horizons after deposition remains speculative. However, we show that the majority of sedimentary archaeal tetraether membrane lipids were of allochthonous origin and not produced in situ. Slow post-burial growth under energy-limited conditions would explain why the downcore distribution of these dominant archaeal groups still indirectly reflect changes in the paleodepositional environment that prevailed during the analyzed marine isotope stages. In addition, archaea seeded from the overlying water column such as Thaumarchaeota and group II and III Euryarchaeota, which were likely not have been able to subsist after burial, were identified from a lower abundance of preserved sedimentary DNA signatures, and represented direct markers of paleoenvironmental changes in the Red Sea spanning the last six marine isotope stages.},
}
@article {pmid33272134,
year = {2022},
author = {Kumar, V and Behl, A and Shoaib, R and Abid, M and Shevtsov, M and Singh, S},
title = {Comparative structural insight into prefoldin subunints of archaea and eukaryotes with special emphasis on unexplored prefoldin of Plasmodium falciparum.},
journal = {Journal of biomolecular structure &amp; dynamics},
volume = {40},
number = {8},
pages = {3804-3818},
doi = {10.1080/07391102.2020.1850527},
pmid = {33272134},
issn = {1538-0254},
mesh = {*Archaea/metabolism ; Chaperonins/metabolism ; Eukaryota/metabolism ; Humans ; *Malaria ; Molecular Chaperones/chemistry ; Plasmodium falciparum/genetics/metabolism ; },
abstract = {Prefoldin (PFD) is a heterohexameric molecular chaperone which bind unfolded proteins and subsequently deliver them to a group II chaperonin for correct folding. Although there is structural and functional information available for humans and archaea PFDs, their existence and functions in malaria parasite remains uncharacterized. In the present review, we have collected the available information on prefoldin family members of archaea and humans and attempted to analyze unexplored PFD subunits of Plasmodium falciparum (Pf). Our review enhances the understanding of probable functions, structure and mechanism of substrate binding of Pf prefoldin by comparing with the available information of its homologs in archaea and H. sapiens. Three PfPFD out of six and a Pf prefoldin-like protein are reported to be essential for parasite survival that signifies their importance in malaria parasite biology. Transcriptome analyses suggest that PfPFD subunits are up-regulated at the mRNA level during asexual and sexual stages of parasite life cycle. Our in silico analysis suggested several pivotal proteins like myosin E, cytoskeletal protein (tubulin), merozoite surface protein and ring exported protein 3 as their interacting partners. Based on structural information of archaeal and H. sapiens PFDs, P. falciparum counterparts have been modelled and key interface residues were identified that are critical for oligomerization of PfPFD subunits. We collated information on PFD-substrate binding and PFD-chaperonin interaction in detail to understand the mechanism of substrate delivery in archaea and humans. Overall, our review enables readers to view the PFD family comprehensively. Communicated by Ramaswamy H. SarmaAbbreviations: HSP: Heat shock proteins; CCT: Chaperonin containing TCP-1; PFD: Prefoldin; PFLP: Prefoldin like protein; PfPFD: Plasmodium falciparum prefoldin; Pf: Plasmodium falciparum; H. sapiens: Homo sapiens; M. thermoautotrophicus: Methanobacterium thermoautotrophicus; P. horikoshii: Pyrococcus horikoshii.},
}
@article {pmid33271237,
year = {2021},
author = {Pfeifer, K and Ergal, &#x130; and Koller, M and Basen, M and Schuster, B and Rittmann, SKR},
title = {Archaea Biotechnology.},
journal = {Biotechnology advances},
volume = {47},
number = {},
pages = {107668},
doi = {10.1016/j.biotechadv.2020.107668},
pmid = {33271237},
issn = {1873-1899},
support = {P 29399/FWF_/Austrian Science Fund FWF/Austria ; },
mesh = {*Archaea/genetics ; Bacteria ; *Biotechnology ; Fungi ; *Industrial Microbiology ; Polyhydroxyalkanoates ; },
abstract = {Archaea are a domain of prokaryotic organisms with intriguing physiological characteristics and ecological importance. In Microbial Biotechnology, archaea are historically overshadowed by bacteria and eukaryotes in terms of public awareness, industrial application, and scientific studies, although their biochemical and physiological properties show a vast potential for a wide range of biotechnological applications. Today, the majority of microbial cell factories utilized for the production of value-added and high value compounds on an industrial scale are bacterial, fungal or algae based. Nevertheless, archaea are becoming ever more relevant for biotechnology as their cultivation and genetic systems improve. Some of the main advantages of archaeal cell factories are the ability to cultivate many of these often extremophilic organisms under non-sterile conditions, and to utilize inexpensive feedstocks often toxic to other microorganisms, thus drastically reducing cultivation costs. Currently, the only commercially available products of archaeal cell factories are bacterioruberin, squalene, bacteriorhodopsin and diether-/tetraether-lipids, all of which are produced utilizing halophiles. Other archaeal products, such as carotenoids and biohydrogen, as well as polyhydroxyalkanoates and methane are in early to advanced development stages, respectively. The aim of this review is to provide an overview of the current state of Archaea Biotechnology by describing the actual state of research and development as well as the industrial utilization of archaeal cell factories, their role and their potential in the future of sustainable bioprocessing, and to illustrate their physiological and biotechnological potential.},
}
@article {pmid33264986,
year = {2021},
author = {Cai, Y and Zheng, Z and Wang, X},
title = {Obstacles faced by methanogenic archaea originating from substrate-driven toxicants in anaerobic digestion.},
journal = {Journal of hazardous materials},
volume = {403},
number = {},
pages = {123938},
doi = {10.1016/j.jhazmat.2020.123938},
pmid = {33264986},
issn = {1873-3336},
mesh = {Ammonia ; Anaerobiosis ; *Archaea/genetics ; *Bioreactors ; Methane ; },
abstract = {Anaerobic digestion (AD) is used to treat waste and produce bioenergy. However, toxicants, which originate from the substrate, can inhibit or damage the digestion process. Methanogenic archaea (MA), which are the executor in the methanogenesis stage, are more sensitive than bacteria to these toxicants. This review discusses the effects of substrate-driven toxicants, namely, antibiotics, H2S and sulfate, heavy metals (HMs), long-chain fatty acids (LCFAs), and ammonia nitrogen, on the activity of MAs, methanogenic pathways, and the inter-genus succession of MAs. The adverse effects of these five toxicants on MA include effects on pH, damages to cell membranes, the prevention of protein synthesis, changes in hydrogen partial pressure, a reduction in the bioavailability of trace elements, and hindrance of mass transfer. These effects cause a reduction in MA activity and the succession of MAs and methanogenic pathways, which affect AD performance. Under the stress of these toxicants, succession occurs among HA (hydrogenotrophic methanogen), AA (acetoclastic methanogen), and MM (methylotrophic methanogen), especially HA gradually replaces AA as the dominant MA. Simultaneously, the dominant methanogenic pathway also changes from the aceticlastic pathway to other methanogenic pathways. A comprehensive understanding of the impact of toxicants on MA permits more specific targeting when developing strategies to mitigate or eliminate the effects of these toxicants.},
}
@article {pmid33264482,
year = {2021},
author = {Wilkens, D and Meusinger, R and Hein, S and Simon, J},
title = {Sequence analysis and specificity of distinct types of menaquinone methyltransferases indicate the widespread potential of methylmenaquinone production in bacteria and archaea.},
journal = {Environmental microbiology},
volume = {23},
number = {3},
pages = {1407-1421},
doi = {10.1111/1462-2920.15344},
pmid = {33264482},
issn = {1462-2920},
mesh = {*Actinobacteria ; *Archaea/enzymology ; Gammaproteobacteria ; *Methyltransferases/genetics ; Phylogeny ; Sequence Analysis ; Vitamin K 2 ; },
abstract = {Menaquinone (MK) serves as an essential membranous redox mediator in various electron transport chains of aerobic and anaerobic respiration. In addition, the composition of the quinone/quinol pool has been widely used as a biomarker in microbial taxonomy. The HemN-like class C radical SAM methyltransferases (RSMTs) MqnK, MenK and MenK2 have recently been shown to facilitate specific menaquinone methylation reactions at position C-8 (MqnK/MenK) or C-7 (MenK2) to synthesize 8-methylmenaquinone, 7-methylmenaquinone and 7,8-dimethylmenaquinone. However, the vast majority of protein sequences from the MqnK/MenK/MenK2 family belong to organisms, whose capacity to produce methylated menaquinones has not been investigated biochemically. Here, representative putative menK and menK2 genes from Collinsella tanakaei and Ferrimonas marina were individually expressed in Escherichia coli (wild-type or ubiE deletion mutant) and the corresponding cells were found to produce methylated derivatives of the endogenous MK and 2-demethylmenaquinone. Cluster and phylogenetic analyses of 828 (methyl)menaquinone methyltransferase sequences revealed signature motifs that allowed to discriminate enzymes of the MqnK/MenK/MenK2 family from other radical SAM enzymes and to identify C-7-specific menaquinone methyltransferases of the MenK2 subfamily. This study will help to predict the methylation status of the quinone/quinol pool of a microbial species (or even a microbial community) from its (meta)genome and contribute to the future design of microbial quinone/quinol pools in a Synthetic Biology approach.},
}
@article {pmid37073347,
year = {2021},
author = {Zhang, CJ and Chen, YL and Sun, YH and Pan, J and Cai, MW and Li, M},
title = {Diversity, metabolism and cultivation of archaea in mangrove ecosystems.},
journal = {Marine life science &amp; technology},
volume = {3},
number = {2},
pages = {252-262},
pmid = {37073347},
issn = {2662-1746},
abstract = {Mangroves comprise a globally significant intertidal ecosystem that contains a high diversity of microorganisms, including fungi, bacteria and archaea. Archaea is a major domain of life that plays important roles in biogeochemical cycles in these ecosystems. In this review, the potential roles of archaea in mangroves are briefly highlighted. Then, the diversity and metabolism of archaeal community of mangrove ecosystems across the world are summarized and Bathyarchaeota, Euryarchaeota, Thaumarchaeota, Woesearchaeota, and Lokiarchaeota are confirmed as the most abundant and ubiquitous archaeal groups. The metabolic potential of these archaeal groups indicates their important ecological function in carbon, nitrogen and sulfur cycling. Finally, some cultivation strategies that could be applied to uncultivated archaeal lineages from mangrove wetlands are suggested, including refinements to traditional cultivation methods based on genomic and transcriptomic information, and numerous innovative cultivation techniques such as single-cell isolation and high-throughput culturing (HTC). These cultivation strategies provide more opportunities to obtain previously uncultured archaea.},
}
@article {pmid33257309,
year = {2021},
author = {Lahme, S and Mand, J and Longwell, J and Smith, R and Enning, D},
title = {Severe Corrosion of Carbon Steel in Oil Field Produced Water Can Be Linked to Methanogenic Archaea Containing a Special Type of [NiFe] Hydrogenase.},
journal = {Applied and environmental microbiology},
volume = {87},
number = {3},
pages = {},
pmid = {33257309},
issn = {1098-5336},
mesh = {Archaea/genetics/metabolism ; Archaeal Proteins/*chemistry/genetics/metabolism ; Carbon ; Corrosion ; Hydrogenase/*chemistry/genetics/metabolism ; *Industrial Waste ; Methane/metabolism ; *Oil and Gas Fields ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Steel/*chemistry ; Wastewater/*microbiology ; },
abstract = {Methanogenic archaea have long been implicated in microbially influenced corrosion (MIC) of oil and gas infrastructure, yet a first understanding of the underlying molecular mechanisms has only recently emerged. We surveyed pipeline-associated microbiomes from geographically distinct oil field facilities and found methanogens to account for 0.2 to 9.3% of the 16S rRNA gene sequencing reads. Neither the type nor the abundance of the detected methanogens was correlated with the perceived severity of MIC in these pipelines. Using fluids from one pipeline, MIC was reproduced in the laboratory, both under stagnant conditions and in customized corrosion reactors simulating pipeline flow. High corrosion rates (up to 2.43 mm Fe[0] · yr[-1]) with macroscopic, localized corrosion features were attributed to lithotrophic, mesophilic microbial activity. Other laboratory tests with the same waters yielded negligible corrosion rates (<0.08 mm Fe[0] · yr[-1]). Recently, a novel [NiFe] hydrogenase from Methanococcus maripaludis strain OS7 was demonstrated to accelerate corrosion. We developed a specific quantitative PCR (qPCR) assay and detected the gene encoding the large subunit of this hydrogenase (labeled micH) in corrosive (>0.15 mm Fe[0] · yr[-1]) biofilms. The micH gene, on the other hand, was absent in noncorrosive biofilms, despite an abundance of methanogens. Reconstruction of a nearly complete Methanococcus maripaludis genome from a highly corrosive mixed biofilm revealed micH and associated genes in nearly identical genetic configuration to that in strain OS7, thereby supporting our hypothesis that the encoded molecular mechanism contributed to corrosion. Lastly, the proposed MIC biomarker was detected in multiple oil fields, indicating a geographically widespread involvement of this [NiFe] hydrogenase in MIC.IMPORTANCE Microorganisms can deteriorate built environments, which is particularly problematic in the case of pipelines transporting hydrocarbons to industrial end users. MIC is notoriously difficult to detect and monitor and, as a consequence, is a particularly difficult corrosion mechanism to manage. Despite the advent of molecular tools and improved microbial monitoring strategies for oil and gas operations, specific underlying MIC mechanisms in pipelines remain largely enigmatic. Emerging mechanistic understanding of methanogenic MIC derived from pure culture work allowed us to develop a qPCR assay that distinguishes technically problematic from benign methanogens in a West African oil field. Detection of the same gene in geographically diverse samples from North America hints at the widespread applicability of this assay. The research presented here offers a step toward a mechanistic understanding of biocorrosion in oil fields and introduces a binary marker for (methanogenic) MIC that can find application in corrosion management programs in industrial settings.},
}
@article {pmid33241850,
year = {2021},
author = {Kasirajan, L and Maupin-Furlow, JA},
title = {Halophilic archaea and their potential to generate renewable fuels and chemicals.},
journal = {Biotechnology and bioengineering},
volume = {118},
number = {3},
pages = {1066-1090},
pmid = {33241850},
issn = {1097-0290},
support = {R01 GM057498/GM/NIGMS NIH HHS/United States ; },
mesh = {*Biofuels ; Biological Products/*metabolism ; *Halobacteriales/genetics/growth &amp; development ; Hydrogen-Ion Concentration ; Salinity ; Sodium Chloride ; },
abstract = {Lignocellulosic biofuels and chemicals have great potential to reduce our dependence on fossil fuels and mitigate air pollution by cutting down on greenhouse gas emissions. Chemical, thermal, and enzymatic processes are used to release the sugars from the lignocellulosic biomass for conversion to biofuels. These processes often operate at extreme pH conditions, high salt concentrations, and/or high temperature. These harsh treatments add to the cost of the biofuels, as most known biocatalysts do not operate under these conditions. To increase the economic feasibility of biofuel production, microorganisms that thrive in extreme conditions are considered as ideal resources to generate biofuels and value-added products. Halophilic archaea (haloarchaea) are isolated from hypersaline ecosystems with high salt concentrations approaching saturation (1.5-5 M salt concentration) including environments with extremes in pH and/or temperature. The unique traits of haloarchaea and their enzymes that enable them to sustain catalytic activity in these environments make them attractive resources for use in bioconversion processes that must occur across a wide range of industrial conditions. Biocatalysts (enzymes) derived from haloarchaea occupy a unique niche in organic solvent, salt-based, and detergent industries. This review focuses on the use of haloarchaea and their enzymes to develop and improve biofuel production. The review also highlights how haloarchaea produce value-added products, such as antibiotics, carotenoids, and bioplastic precursors, and can do so using feedstocks considered "too salty" for most microbial processes including wastes from the olive-mill, shell fish, and biodiesel industries.},
}
@article {pmid33232349,
year = {2020},
author = {Euler, S and Jeffrey, LC and Maher, DT and Mackenzie, D and Tait, DR},
title = {Shifts in methanogenic archaea communities and methane dynamics along a subtropical estuarine land use gradient.},
journal = {PloS one},
volume = {15},
number = {11},
pages = {e0242339},
pmid = {33232349},
issn = {1932-6203},
mesh = {Agriculture ; Ammonium Compounds/metabolism ; Animal Husbandry ; Archaea/*isolation &amp; purification/metabolism ; Carbon/metabolism ; Ecosystem ; *Estuaries ; Fresh Water/analysis/microbiology ; Greenhouse Gases/analysis ; Housing ; Industry ; Methane/*metabolism ; Methanococcales/*isolation &amp; purification/metabolism ; Methylocystaceae/*isolation &amp; purification/metabolism ; *Microbiota ; Nitrates/metabolism ; Oxidation-Reduction ; Queensland ; *Saline Waters/analysis ; Salinity ; Sulfates/metabolism ; Temperature ; Thermodynamics ; *Water Microbiology ; Water Purification ; },
abstract = {In coastal aquatic ecosystems, prokaryotic communities play an important role in regulating the cycling of nutrients and greenhouse gases. In the coastal zone, estuaries are complex and delicately balanced systems containing a multitude of specific ecological niches for resident microbes. Anthropogenic influences (i.e. urban, industrial and agricultural land uses) along the estuarine continuum can invoke physical and biochemical changes that impact these niches. In this study, we investigate the relative abundance of methanogenic archaea and other prokaryotic communities, distributed along a land use gradient in the subtropical Burnett River Estuary, situated within the Great Barrier Reef catchment, Australia. Microbiological assemblages were compared to physicochemical, nutrient and greenhouse gas distributions in both pore and surface water. Pore water samples from within the most urbanised site showed a high relative abundance of methanogenic Euryarchaeota (7.8% of all detected prokaryotes), which coincided with elevated methane concentrations in the water column, ranging from 0.51 to 0.68 μM at the urban and sewage treatment plant (STP) sites, respectively. These sites also featured elevated dissolved organic carbon (DOC) concentrations (0.66 to 1.16 mM), potentially fuelling methanogenesis. At the upstream freshwater site, both methane and DOC concentrations were considerably higher (2.68 μM and 1.8 mM respectively) than at the estuarine sites (0.02 to 0.66 μM and 0.39 to 1.16 mM respectively) and corresponded to the highest relative abundance of methanotrophic bacteria. The proportion of sulfate reducing bacteria in the prokaryotic community was elevated within the urban and STP sites (relative abundances of 8.0%- 10.5%), consistent with electron acceptors with higher redox potentials (e.g. O2, NO3-) being scarce. Overall, this study showed that ecological niches in anthropogenically altered environments appear to give an advantage to specialized prokaryotes invoking a potential change in the thermodynamic landscape of the ecosystem and in turn facilitating the generation of methane-a potent greenhouse gas.},
}
@article {pmid33229086,
year = {2021},
author = {Amin, FR and Khalid, H and El-Mashad, HM and Chen, C and Liu, G and Zhang, R},
title = {Functions of bacteria and archaea participating in the bioconversion of organic waste for methane production.},
journal = {The Science of the total environment},
volume = {763},
number = {},
pages = {143007},
doi = {10.1016/j.scitotenv.2020.143007},
pmid = {33229086},
issn = {1879-1026},
mesh = {Anaerobiosis ; *Archaea ; Bacteria ; Biofuels ; *Bioreactors ; Methane ; },
abstract = {Anaerobic digestion (AD) is a widely applied technology for treating organic wastes to generate renewable energy in the form of biogas. The effectiveness of AD process depends on many factors, among which the most important is the presence of active and healthy microbial community in the anaerobic digesters, which needs to be explored. However, the deciphering of microbial populations and their functions during the AD process of different materials is still incomplete, which restricts the understanding of its long-term performance under different operational conditions. This review describes the type, morphology, functions, and specific growth conditions of commonly found hydrolytic, acidogenic, acetogenic bacteria, and archaea during the AD process. The effects of microbes on the performance and stability of the digestion process are also presented. Furthermore, the article offers a deep understanding of the AD management strategies for the enhancement of methane production and the efficiency of the energy conversion process of various organic wastes.},
}
@article {pmid33226731,
year = {2021},
author = {Diaz, PI},
title = {Subgingival fungi, Archaea, and viruses under the omics loupe.},
journal = {Periodontology 2000},
volume = {85},
number = {1},
pages = {82-89},
doi = {10.1111/prd.12352},
pmid = {33226731},
issn = {1600-0757},
mesh = {Archaea/genetics ; Bacteria/genetics ; DNA ; Fungi ; *Gingiva/microbiology ; Humans ; *Microbiota ; *Viruses ; },
abstract = {The microbial communities that inhabit the gingival crevice are responsible for the pathological processes that affect the periodontium. The changes in composition and function of subgingival bacteria as disease develops have been extensively studied. Subgingival communities, however, also contain fungi, Archaea, and viruses, which could contribute to the dysbiotic processes associated with periodontal diseases. High-throughput DNA sequencing has facilitated a better understanding of the mycobiome, archaeome, and virome. However, the number of studies available on the nonbacterial components of the subgingival microbiome remains limited in comparison with publications focusing on bacteria. Difficulties in characterizing fungal, archaeal, and viral populations arise from the small portion of the total metagenome mass they occupy and lack of comprehensive reference genome databases. In addition, specialized approaches potentially introducing bias are required to enrich for viral particles, while harsh methods of cell lysis are needed to recover nuclei acids from certain fungi. While the characterization of the subgingival diversity of fungi, Archaea and viruses is incomplete, emerging evidence suggests that they could contribute in different ways to subgingival dysbiosis. Certain fungi, such as Candida albicans are suggested to facilitate colonization of bacterial pathogens. Methanogenic Archaea are associated with periodontitis severity and are thought to partner synergistically with bacterial fermenters, while viruses may affect immune responses or shape microbial communities in ways incompletely understood. This review describes the manner in which omics approaches have improved our understanding of the diversity of fungi, Archaea, and viruses within subgingival communities. Further characterization of these understudied components of the subgingival microbiome is required, together with mechanistic studies to unravel their ecological role and potential contributions to dysbiosis.},
}
@article {pmid33223169,
year = {2021},
author = {Cai, M and Richter-Heitmann, T and Yin, X and Huang, WC and Yang, Y and Zhang, C and Duan, C and Pan, J and Liu, Y and Liu, Y and Friedrich, MW and Li, M},
title = {Ecological features and global distribution of Asgard archaea.},
journal = {The Science of the total environment},
volume = {758},
number = {},
pages = {143581},
doi = {10.1016/j.scitotenv.2020.143581},
pmid = {33223169},
issn = {1879-1026},
mesh = {*Archaea/genetics ; *Eukaryota ; Geologic Sediments ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Salinity ; },
abstract = {Asgard is a newly proposed archaeal superphylum, which has been suggested to hold the key to decipher the origin of Eukaryotes. However, their ecology remains largely unknown. Here, we conducted a meta-analysis of publicly available Asgard-associated 16S rRNA gene fragments, and found that just three previously proposed clades (Lokiarchaeota, Thorarchaeota, and Asgard clade 4) are widely distributed, whereas the other seven clades (phylum or class level) are restricted to the sediment biosphere. Asgard archaea, especially Loki- and Thorarchaeota, seem to adapt to marine sediments, and water depth (the depth of the sediment below water surface) and salinity might be crucial factors for the proportion of these microorganisms as revealed by multivariate regression analyses. However, the abundance of Asgard archaea exhibited distinct environmental drivers at the clade-level; for instance, the proportion of Asgard clade 4 was higher in less saline environments (salinity <6.35 psu), while higher for Heimdallarchaeota-AAG and Asgard clade 2 in more saline environment (salinity ≥35 psu). Furthermore, co-occurrence analysis allowed us to find a significant non-random association of different Asgard clades with other groups (e.g., Lokiarchaeota with Deltaproteobacteria and Anaerolineae; Odinarchaeota with Bathyarchaeota), suggesting different interaction potentials among these clades. Overall, these findings reveal Asgard archaea as a ubiquitous group worldwide and provide initial insights into their ecological features on a global scale.},
}
@article {pmid33202677,
year = {2020},
author = {Diene, SM and Pinault, L and Armstrong, N and Azza, S and Keshri, V and Khelaifia, S and Chabrière, E and Caetano-Anolles, G and Rolain, JM and Pontarotti, P and Raoult, D},
title = {Dual RNase and β-lactamase Activity of a Single Enzyme Encoded in Archaea.},
journal = {Life (Basel, Switzerland)},
volume = {10},
number = {11},
pages = {},
pmid = {33202677},
issn = {2075-1729},
abstract = {β-lactam antibiotics have a well-known activity which disturbs the bacterial cell wall biosynthesis and may be cleaved by β-lactamases. However, these drugs are not active on archaea microorganisms, which are naturally resistant because of the lack of β-lactam target in their cell wall. Here, we describe that annotation of genes as β-lactamases in Archaea on the basis of homologous genes is a remnant of identification of the original activities of this group of enzymes, which in fact have multiple functions, including nuclease, ribonuclease, β-lactamase, or glyoxalase, which may specialized over time. We expressed class B β-lactamase enzyme from Methanosarcina barkeri that digest penicillin G. Moreover, while weak glyoxalase activity was detected, a significant ribonuclease activity on bacterial and synthetic RNAs was demonstrated. The β-lactamase activity was inhibited by β-lactamase inhibitor (sulbactam), but its RNAse activity was not. This gene appears to have been transferred to the Flavobacteriaceae group especially the Elizabethkingia genus, in which the expressed gene shows a more specialized activity on thienamycin, but no glyoxalase activity. The expressed class C-like β-lactamase gene, from Methanosarcina sp., also shows hydrolysis activity on nitrocefin and is more closely related to DD-peptidase enzymes. Our findings highlight the need to redefine the nomenclature of β-lactamase enzymes and the specification of multipotent enzymes in different ways in Archaea and bacteria over time.},
}
@article {pmid33193193,
year = {2020},
author = {Wang, H and Bier, R and Zgleszewski, L and Peipoch, M and Omondi, E and Mukherjee, A and Chen, F and Zhang, C and Kan, J},
title = {Distinct Distribution of Archaea From Soil to Freshwater to Estuary: Implications of Archaeal Composition and Function in Different Environments.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {576661},
pmid = {33193193},
issn = {1664-302X},
abstract = {In addition to inhabiting extreme territories, Archaea are widely distributed in common environments spanning from terrestrial to aquatic environments. This study investigated and compared archaeal community structures from three different habitats (representing distinct environments): agriculture soils (from farming system trials FST, PA, United States), freshwater biofilms (from White Clay Creek, PA, United States), and estuary water (Chesapeake Bay, United States). High-throughput sequencing of 16S rRNA genes indicated that Thaumarchaeota, Euryarchaeota, Nanoarchaeota, Crenarchaeota, and Diapherotrites were the commonly found dominant phyla across these three environments. Similar to Bacteria, distinct community structure and distribution patterns for Archaea were observed in soils vs. freshwater vs. estuary. However, the abundance, richness, evenness, and diversity of archaeal communities were significantly greater in soils than it was in freshwater and estuarine environments. Indicator species (or amplicon sequence variants, ASVs) were identified from different nitrogen and carbon cycling archaeal groups in soils (Nitrososphaerales, Nitrosotaleales, Nitrosopumilales, Methanomassiliicoccales, Lainarchaeales), freshwater biofilms (Methanobacteria, Nitrososphaerales) and Chesapeake Bay (Marine Group II, Nitrosopumilales), suggesting the habitat-specificity of their biogeochemical contributions to different environments. Distinct functional aspects of Archaea were also confirmed by functional predictions (PICRUSt2 analysis). Further, co-occurrence network analysis indicated that only soil Archaea formed stable modules. Keystone species (ASVs) were identified mainly from Methanomassiliicoccales, Nitrososphaerales, Nitrosopumilales. Overall, these results indicate a strong habitat-dependent distribution of Archaea and their functional partitions within the local environments.},
}
@article {pmid33184503,
year = {2021},
author = {Murray, AE and Freudenstein, J and Gribaldo, S and Hatzenpichler, R and Hugenholtz, P and Kämpfer, P and Konstantinidis, KT and Lane, CE and Papke, RT and Parks, DH and Rossello-Mora, R and Stott, MB and Sutcliffe, IC and Thrash, JC and Venter, SN and Whitman, WB and Acinas, SG and Amann, RI and Anantharaman, K and Armengaud, J and Baker, BJ and Barco, RA and Bode, HB and Boyd, ES and Brady, CL and Carini, P and Chain, PSG and Colman, DR and DeAngelis, KM and de Los Rios, MA and Estrada-de Los Santos, P and Dunlap, CA and Eisen, JA and Emerson, D and Ettema, TJG and Eveillard, D and Girguis, PR and Hentschel, U and Hollibaugh, JT and Hug, LA and Inskeep, WP and Ivanova, EP and Klenk, HP and Li, WJ and Lloyd, KG and Löffler, FE and Makhalanyane, TP and Moser, DP and Nunoura, T and Palmer, M and Parro, V and Pedrós-Alió, C and Probst, AJ and Smits, THM and Steen, AD and Steenkamp, ET and Spang, A and Stewart, FJ and Tiedje, JM and Vandamme, P and Wagner, M and Wang, FP and Yarza, P and Hedlund, BP and Reysenbach, AL},
title = {Author Correction: Roadmap for naming uncultivated Archaea and Bacteria.},
journal = {Nature microbiology},
volume = {6},
number = {1},
pages = {136},
doi = {10.1038/s41564-020-00827-2},
pmid = {33184503},
issn = {2058-5276},
support = {DEB-1841658//National Science Foundation (NSF)/ ; },
}
@article {pmid33172134,
year = {2020},
author = {Zink, IA and Wimmer, E and Schleper, C},
title = {Heavily Armed Ancestors: CRISPR Immunity and Applications in Archaea with a Comparative Analysis of CRISPR Types in Sulfolobales.},
journal = {Biomolecules},
volume = {10},
number = {11},
pages = {},
pmid = {33172134},
issn = {2218-273X},
support = {695192/ERC_/European Research Council/International ; P29399//Austrian Science Fund/ ; DOC-fellowship//&#xd6;sterreichischen Akademie der Wissenschaften/ ; DOC completion grant//Universit&#xe4;t Wien/ ; },
mesh = {*Clustered Regularly Interspaced Short Palindromic Repeats/genetics ; *CRISPR-Cas Systems/genetics ; *Sulfolobales/genetics/immunology ; Archaea/genetics/virology/immunology ; },
abstract = {Prokaryotes are constantly coping with attacks by viruses in their natural environments and therefore have evolved an impressive array of defense systems. Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) is an adaptive immune system found in the majority of archaea and about half of bacteria which stores pieces of infecting viral DNA as spacers in genomic CRISPR arrays to reuse them for specific virus destruction upon a second wave of infection. In detail, small CRISPR RNAs (crRNAs) are transcribed from CRISPR arrays and incorporated into type-specific CRISPR effector complexes which further degrade foreign nucleic acids complementary to the crRNA. This review gives an overview of CRISPR immunity to newcomers in the field and an update on CRISPR literature in archaea by comparing the functional mechanisms and abundances of the diverse CRISPR types. A bigger fraction is dedicated to the versatile and prevalent CRISPR type III systems, as tremendous progress has been made recently using archaeal models in discerning the controlled molecular mechanisms of their unique tripartite mode of action including RNA interference, DNA interference and the unique cyclic-oligoadenylate signaling that induces promiscuous RNA shredding by CARF-domain ribonucleases. The second half of the review spotlights CRISPR in archaea outlining seminal in vivo and in vitro studies in model organisms of the euryarchaeal and crenarchaeal phyla, including the application of CRISPR-Cas for genome editing and gene silencing. In the last section, a special focus is laid on members of the crenarchaeal hyperthermophilic order Sulfolobales by presenting a thorough comparative analysis about the distribution and abundance of CRISPR-Cas systems, including arrays and spacers as well as CRISPR-accessory proteins in all 53 genomes available to date. Interestingly, we find that CRISPR type III and the DNA-degrading CRISPR type I complexes co-exist in more than two thirds of these genomes. Furthermore, we identified ring nuclease candidates in all but two genomes and found that they generally co-exist with the above-mentioned CARF domain ribonucleases Csx1/Csm6. These observations, together with published literature allowed us to draft a working model of how CRISPR-Cas systems and accessory proteins cross talk to establish native CRISPR anti-virus immunity in a Sulfolobales cell.},
}
@article {pmid33171029,
year = {2022},
author = {Dong, L and Gao, Y and Jing, X and Guo, H and Zhang, H and Lai, Q and Diao, Q},
title = {Pretreatments of Broussonetia papyrifera: in vitro assessment on gas and methane production, fermentation characteristic, and methanogenic archaea profile.},
journal = {Animal bioscience},
volume = {35},
number = {9},
pages = {1367-1378},
pmid = {33171029},
issn = {2765-0189},
support = {2017YFF0211702//National Key R&amp;D Program of China/ ; 2016YFE0109000//Key Program for International S&amp;T Cooperation Projects of China/ ; 31802085//National Natural Science Foundation of China/ ; 20A180012//National Natural Science Foundation of China/ ; Y2021GH18-2//Central Public-Interest Scientific Institution Basal Research Fund/ ; },
abstract = {OBJECTIVE: The present study was conducted to examine the gas production, fermentation characteristics, nutrient degradation, and methanogenic community composition of a rumen fluid culture with Broussonetia papyrifera (B. papyrifera) subjected to ensiling or steam explosion (SE) pretreatment.<br><br>METHODS: Fresh B. papyrifera was collected and pretreated by ensiling or SE, which was then fermented with ruminal fluids as ensiled B. papyrifera group, steam-exploded B. papyrifera group, and untreated B. papyrifera group. The gas and methane production, fermentation characteristics, nutrient degradation, and methanogenic community were determined during the fermentation.<br><br>RESULTS: Cumulative methane production was significantly improved with SE pretreatment compared with ensiled or untreated biomass accompanied with more volatile fatty acids production. After 72 h incubation, SE and ensiling pretreatments decreased the acid detergent fiber contents by 39.4% and 22.9%, and neutral detergent fiber contents by 10.6% and 47.2%, respectively. Changes of methanogenic diversity and abundance of methanogenic archaea corresponded to the variations in fermentation pattern and methane production.<br><br>CONCLUSION: Compared with ensiling pretreatment, SE can be a promising technique for the efficient utilization of B. papyrifera, which would contribute to sustainable livestock production systems.},
}
@article {pmid33161088,
year = {2021},
author = {Kajale, S and Jani, K and Sharma, A},
title = {Contribution of archaea and bacteria in sustaining climate change by oxidizing ammonia and sulfur in an Arctic Fjord.},
journal = {Genomics},
volume = {113},
number = {1 Pt 2},
pages = {1272-1276},
doi = {10.1016/j.ygeno.2020.11.005},
pmid = {33161088},
issn = {1089-8646},
mesh = {Ammonia/*metabolism ; Archaea/genetics/*metabolism ; Arctic Regions ; Bacteria/genetics/*metabolism ; *Climate Change ; Microbiota ; Oxidation-Reduction ; Sulfur/*metabolism ; },
abstract = {The present study attempts to investigate the microbial communities and their potential to oxidize ammonia and sulfur at different sites of Arctic Fjord by targeted metagenomics. The high throughput sequencing revealed archaeal Thaumarchaeota (79.3%), Crenarchaeota (10.9%), Euryarchaeota (5.4%), and Woesearchaeota (2.9%) across different depths. In contrast, the bacterial communities depict predominance of Proteobacteria (52.6%), which comprises of dominant genera viz. Sulfurovum (11.2%) and Sulfurimonas (6.3%). Characterizing the metabolic potential of microbial communities with prime focus on the ammonia and sulfur cycling revealed the presence of amoABC and narGHYZ/ nxrAB genes encoding key enzymes. The ammonia cycling coupled with an augmentation of members of Nitrosopumilus belonging to the phylum Thaumarcheaota suggests the vital role of archaeal communities. Similarly, the persistence of chemolithoautotrophic members of Sulfurovum and Sulfurimonas along with the anaerobic genera Desulfocapsa and Desulfobulbus harboring SOX (sulfur-oxidation) system indicates the modulatory role of bacterial communities in sulfur cycling.},
}
@article {pmid33157448,
year = {2021},
author = {Yang, S and Li, L and Peng, X and Song, L},
title = {Leachate microbiome profile reveals bacteria, archaea and eukaryote dynamics and methanogenic function during solid waste decomposition.},
journal = {Bioresource technology},
volume = {320},
number = {Pt A},
pages = {124359},
doi = {10.1016/j.biortech.2020.124359},
pmid = {33157448},
issn = {1873-2976},
mesh = {*Archaea/genetics ; Bacteria/genetics ; Bioreactors ; Eukaryota ; Methane ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S ; Solid Waste ; },
abstract = {Bacterial, archaeal, and eukaryotic community composition and dynamics in leachate during solid waste decomposition were investigated using Illumina MiSeq sequencing. The functional enzyme-encoding genes of methanogenic pathways were also predicted via PICRUSt. Succession of bacterial, archaeal, and eukaryotic community composition in aerobic phase (AP), anaerobic acid phase (ACP), and methanogenic phase (MP) was observed. The main representatives of microbial phyla, genera, and species significantly (p < 0.05) differed at least two phases. Protist Ciliophora occurred at ACP and was prevalent in MP, suggesting a short food chain establishment in the methanogenesis. Bacterial, archaeal, fungi and eukaryotic community structure were all pH and biochemical oxygen demand (BOD5) dependent patter. Acetoclastic and hydrogenotrophic methanogenesis pathways with associated functional genes differed during solid waste decomposition and were inhibited in ACP.},
}
@article {pmid33125862,
year = {2020},
author = {Nußbaum, P and Ithurbide, S and Walsh, JC and Patro, M and Delpech, F and Rodriguez-Franco, M and Curmi, PMG and Duggin, IG and Quax, TEF and Albers, SV},
title = {An Oscillating MinD Protein Determines the Cellular Positioning of the Motility Machinery in Archaea.},
journal = {Current biology : CB},
volume = {30},
number = {24},
pages = {4956-4972.e4},
doi = {10.1016/j.cub.2020.09.073},
pmid = {33125862},
issn = {1879-0445},
mesh = {Archaeal Proteins/genetics/*metabolism ; Cell Membrane/metabolism ; Chemotaxis/*physiology ; Haloferax volcanii/*physiology ; Intravital Microscopy ; Time-Lapse Imaging ; },
abstract = {MinD proteins are well studied in rod-shaped bacteria such as E. coli, where they display self-organized pole-to-pole oscillations that are important for correct positioning of the Z-ring at mid-cell for cell division. Archaea also encode proteins belonging to the MinD family, but their functions are unknown. MinD homologous proteins were found to be widespread in Euryarchaeota and form a sister group to the bacterial MinD family, distinct from the ParA and other related ATPase families. We aimed to identify the function of four archaeal MinD proteins in the model archaeon Haloferax volcanii. Deletion of the minD genes did not cause cell division or size defects, and the Z-ring was still correctly positioned. Instead, one of the deletions (ΔminD4) reduced swimming motility and hampered the correct formation of motility machinery at the cell poles. In ΔminD4 cells, there is reduced formation of the motility structure and chemosensory arrays, which are essential for signal transduction. In bacteria, several members of the ParA family can position the motility structure and chemosensory arrays via binding to a landmark protein, and consequently these proteins do not oscillate along the cell axis. However, GFP-MinD4 displayed pole-to-pole oscillation and formed polar patches or foci in H. volcanii. The MinD4 membrane-targeting sequence (MTS), homologous to the bacterial MinD MTS, was essential for the oscillation. Surprisingly, mutant MinD4 proteins failed to form polar patches. Thus, MinD4 from H. volcanii combines traits of different bacterial ParA/MinD proteins.},
}
@article {pmid33123879,
year = {2021},
author = {Liu, X and Shao, Y and Dong, Y and Dong, M and Xu, Z and Hu, X and Liu, A},
title = {Response of ammonia-oxidizing archaea and bacteria to sulfadiazine and copper and their interaction in black soils.},
journal = {Environmental science and pollution research international},
volume = {28},
number = {9},
pages = {11357-11368},
pmid = {33123879},
issn = {1614-7499},
support = {No.41671322//Natural Science Foundation of China/ ; No. 41877122//Natural Science Foundation of China/ ; NO. 2019GSF109058.//Shandong Skate R&amp;D Project/ ; },
mesh = {*Ammonia ; Animals ; *Archaea ; Bacteria ; Copper ; Nitrification ; Oxidation-Reduction ; Soil ; Soil Microbiology ; Sulfadiazine ; },
abstract = {The large-scale development of animal husbandry and the wide agricultural application of livestock manure lead to more and more serious co-pollution of heavy metals and antibiotics in soil. In this study, two common feed additives, copper (Cu) and sulfadiazine (SDZ), were selected as target pollutants to evaluate the toxicity and interaction of antibiotics and heavy metals on ammonia oxidizers diversity, potential nitrification rate (PNR), and enzymatic activity in black soils. The results showed that soil enzyme activity was significantly inhibited by single Cu pollution, but the toxicity could be reduced by introducing low-concentration SDZ (5 mg · kg[-1]), which showed an antagonistic effect between Cu and SDZ (5 mg · kg[-1]), while the combined toxicity of high-concentration SDZ (10 mg · kg[-1]) and Cu were strengthened compared with the single Cu contamination on soil enzymes. In contrast, soil PNR was more sensitive to single Cu pollution and its combined pollution with SDZ than the enzyme activity. Real-time fluorescence quota PCR and Illumina Hiseq/Miseq sequencing results showed that ammonia-oxidizing archaea (AOA) was decreased in C2 (200 mg · kg[-1] Cu treatment) and ammonia-oxidizing bacteria (AOB) was obviously stimulated in soil contaminated in C2, while in S5 (5 mg · kg[-1] SDZ treatment), AOB was decreased; both AOA and AOB were significantly decreased at gene level in soils with combined pollutants (C2S5, 200 mg · kg[-1] Cu combined with 5 mg · kg[-1] SDZ). So, it can be concluded that combined pollution can cause more serious toxicity on the enzymatic activity, PNR, and ammonia-oxidizing microorganisms in soil through the synergistic effect between heavy metals and antibiotics pollutants.},
}
@article {pmid33093799,
year = {2020},
author = {Jha, P and Singh, J and Vidyarthi, AS and Prasad, R},
title = {Unveiling the Biodiversity of Hyperthermophilic Archaea in Jharia Coal Mines: Potential Threat to Methanogenesis?.},
journal = {Current genomics},
volume = {21},
number = {5},
pages = {363-371},
pmid = {33093799},
issn = {1389-2029},
abstract = {AIM: To examine the biodiversity of archaeal sulfate reducers and methanogens present in the underground coal mines of Jharia using metagenomics and pyrosequencing.<br><br>OBJECTIVES: 1) Bioinformatical analysis of the metagenomic data related to a taxonomic analysis obtained from the coal to investigate complete archaeal taxonomic features of the coal bed methane (CBM) microbiome. 2) Bioinformatical analysis of the metagenomic data related to a functional analysis obtained from the coal to investigate functional features relating to taxonomic diversity of the CBM microbiome. 3) The functional attributes have been examined specifically for ORFs related to sulfite reduction and methanogenesis.The taxonomic and functional biodiversity related to euryarchaeota will help in a better understanding of the obstacles associated with methane production imposed by the sulfate reducers.<br><br>BACKGROUND: The microbial methanogenesis in the coal microbiome is a resultant of substrate utilization by primarily fermentative bacteria and methanogens. The present work reveals the biodiversity of archaeal sulfate reducers and methanogens present in the underground coal mines of Jharia using metagenomics and pyrosequencing.<br><br>METHODOLOGY: Bioinformatical analysis for structural and functional attributes was accomplished using MG-RAST. The structural analysis was accomplished using RefSeq database, whereas the functional analysis was done via CoG database with a cut off value, a sequence percent identity, and sequence alignment length cut off of 1e[-5], 60% and 45, respectively.<br><br>RESULTS: Attained communities revealed the dominance of hyperthermophilic archaea Pyrococcus furiosus along with Thermococcus kodakarensis in the coal metagenome.The obtained results also suggest the presence of dissimilatory sulfite reductase and formylmethanofuran dehydrogenase, formylmethanofuran: tetrahydromethanopterin formyltransferase involved in sulfite reduction and methanogenesis, respectively, in the microbiome.<br><br>CONCLUSION: This report is the first attempt to showcase the existence of specific euryarchaeal diversity and their related functional attributes from Jharia coal mines through high throughput sequencing. The study helps in developing a better understanding of the presence of indigenous microbes (archaea) and their functions in the coal microbiome, which can be utilized further to resolve the energy crisis.},
}
@article {pmid33077635,
year = {2020},
author = {Chávez, J and Devos, DP and Merino, E},
title = {Complementary Tendencies in the Use of Regulatory Elements (Transcription Factors, Sigma Factors, and Riboswitches) in Bacteria and Archaea.},
journal = {Journal of bacteriology},
volume = {203},
number = {2},
pages = {},
pmid = {33077635},
issn = {1098-5530},
mesh = {Archaea/classification/genetics/*physiology ; Bacteria/classification/*genetics ; Genome, Archaeal/physiology ; Genome, Bacterial/physiology ; Phylogeny ; Riboswitch/*physiology ; Sigma Factor/*physiology ; Transcription Factors/*physiology ; },
abstract = {In prokaryotes, the key players in transcription initiation are sigma factors and transcription factors that bind to DNA to modulate the process, while premature transcription termination at the 5' end of the genes is regulated by attenuation and, in particular, by attenuation associated with riboswitches. In this study, we describe the distribution of these regulators across phylogenetic groups of bacteria and archaea and find that their abundance not only depends on the genome size, as previously described, but also varies according to the phylogeny of the organism. Furthermore, we observed a tendency for organisms to compensate for the low frequencies of a particular type of regulatory element (i.e., transcription factors) with a high frequency of other types of regulatory elements (i.e., sigma factors). This study provides a comprehensive description of the more abundant COG, KEGG, and Rfam families of transcriptional regulators present in prokaryotic genomes.IMPORTANCE In this study, we analyzed the relationship between the relative frequencies of the primary regulatory elements in bacteria and archaea, namely, transcription factors, sigma factors, and riboswitches. In bacteria, we reveal a compensatory behavior for transcription factors and sigma factors, meaning that in phylogenetic groups in which the relative number of transcription factors was low, we found a tendency for the number of sigma factors to be high and vice versa. For most of the phylogenetic groups analyzed here, except for Firmicutes and Tenericutes, a clear relationship with other mechanisms was not detected for transcriptional riboswitches, suggesting that their low frequency in most genomes does not constitute a significant impact on the global variety of transcriptional regulatory elements in prokaryotic organisms.},
}
@article {pmid33068423,
year = {2020},
author = {L Bräuer, S and Basiliko, N and M P Siljanen, H and H Zinder, S},
title = {Methanogenic archaea in peatlands.},
journal = {FEMS microbiology letters},
volume = {367},
number = {20},
pages = {},
doi = {10.1093/femsle/fnaa172},
pmid = {33068423},
issn = {1574-6968},
mesh = {Archaea/*classification ; Methane/metabolism ; Microbiota/physiology ; *Soil ; *Soil Microbiology ; *Wetlands ; },
abstract = {Methane emission feedbacks in wetlands are predicted to influence global climate under climate change and other anthropogenic stressors. Herein, we review the taxonomy and physiological ecology of the microorganisms responsible for methane production in peatlands. Common in peat soils are five of the eight described orders of methanogens spanning three phyla (Euryarchaeota, Halobacterota and Thermoplasmatota). The phylogenetic affiliation of sequences found in peat suggest that members of the thus-far-uncultivated group Candidatus Bathyarchaeota (representing a fourth phylum) may be involved in methane cycling, either anaerobic oxidation of methane and/or methanogenesis, as at least a few organisms within this group contain the essential gene, mcrA, according to metagenomic data. Methanogens in peatlands are notoriously challenging to enrich and isolate; thus, much remains unknown about their physiology and how methanogen communities will respond to environmental changes. Consistent patterns of changes in methanogen communities have been reported across studies in permafrost peatland thaw where the resulting degraded feature is thermokarst. However much remains to be understood regarding methanogen community feedbacks to altered hydrology and warming in other contexts, enhanced atmospheric pollution (N, S and metals) loading and direct anthropogenic disturbances to peatlands like drainage, horticultural peat extraction, forestry and agriculture, as well as post-disturbance reclamation.},
}
@article {pmid33051370,
year = {2020},
author = {Abby, SS and Kerou, M and Schleper, C},
title = {Ancestral Reconstructions Decipher Major Adaptations of Ammonia-Oxidizing Archaea upon Radiation into Moderate Terrestrial and Marine Environments.},
journal = {mBio},
volume = {11},
number = {5},
pages = {},
pmid = {33051370},
issn = {2150-7511},
mesh = {Adaptation, Physiological/*genetics ; Ammonia/*metabolism ; Aquatic Organisms/*genetics ; Archaea/*genetics/metabolism ; Carbon Cycle ; Evolution, Molecular ; *Genome, Archaeal ; Oxidation-Reduction ; *Soil Microbiology ; },
abstract = {Unlike all other archaeal lineages, ammonia-oxidizing archaea (AOA) of the phylum Thaumarchaeota are widespread and abundant in all moderate and oxic environments on Earth. The evolutionary adaptations that led to such unprecedented ecological success of a microbial clade characterized by highly conserved energy and carbon metabolisms have, however, remained underexplored. Here, we reconstructed the genomic content and growth temperature of the ancestor of all AOA, as well as the ancestors of the marine and soil lineages, based on 39 available complete or nearly complete genomes of AOA. Our evolutionary scenario depicts an extremely thermophilic, autotrophic, aerobic ancestor from which three independent lineages of a marine and two terrestrial groups radiated into moderate environments. Their emergence was paralleled by (i) a continuous acquisition of an extensive collection of stress tolerance genes mostly involved in redox maintenance and oxygen detoxification, (ii) an expansion of regulatory capacities in transcription and central metabolic functions, and (iii) an extended repertoire of cell appendages and modifications related to adherence and interactions with the environment. Our analysis provides insights into the evolutionary transitions and key processes that enabled the conquest of the diverse environments in which contemporary AOA are found.},
}
@article {pmid33045546,
year = {2021},
author = {Park, JG and Lee, B and Heo, TY and Cheon, AI and Jun, HB},
title = {Metagenomics approach and canonical correspondence analysis of novel nitrifiers and ammonia-oxidizing archaea in full scale anaerobic-anoxic-oxic (A2/O) and oxidation ditch processes.},
journal = {Bioresource technology},
volume = {319},
number = {},
pages = {124205},
doi = {10.1016/j.biortech.2020.124205},
pmid = {33045546},
issn = {1873-2976},
mesh = {*Ammonia ; Anaerobiosis ; *Archaea/genetics ; Metagenomics ; Nitrification ; Nitrites ; Oxidation-Reduction ; Phylogeny ; },
abstract = {Various microorganisms are involved in nitrogen removal, and their group compositions depend closely on operating parameters. The structures and functions of nitrification microorganisms in full-scale anaerobic-anoxic-oxic (A2/O) and oxidation ditch processes were analyzed using metagenomics and canonical correspondence analysis. The community structure of ammonia-oxidizing archaea in the oxidation ditch was 3.8 (winter) - 6.3 (summer) times higher than in A2/O, and the complete ammonia oxidizer was only found in the oxidation ditch process. The canonical correspondence analysis of various environmental variables showed that Nitrosomonadales, Crenarchaeota, and Nitrospira inopinata correlate highly with nitrification, and Nitrospira was involved in NO2[-]-N oxidation rather than Nitrobacter. The longer solid and hydraulic retention times in the oxidation ditch were more effective in achieving a wider range of novel nitrification than A2/O. This result indicates that microbial communities of novel nitrifiers and ammonia-oxidizing archaea improved in the oxidation ditch process, significantly contributing to stable nitrogen removal.},
}
@article {pmid33040791,
year = {2020},
author = {Song, W and Sun, C},
title = {Diversity and distribution of bacteria and archaea in Tuosu Lake in Qaidam Basin.},
journal = {Cellular and molecular biology (Noisy-le-Grand, France)},
volume = {66},
number = {6},
pages = {86-92},
pmid = {33040791},
issn = {1165-158X},
mesh = {Archaea/*genetics ; Bacteria/*genetics ; Biodiversity ; Lakes ; Microbiota/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Salinity ; },
abstract = {Microbes in plateau lakes are important participants of material circulation and energy flow in plateau ecosystems. Knowledge of the microbiota, such as bacteria and archaea, community distribution and diversity in plateau lakes is the basis to understand the species succession, adaptation, maintenance and metabolic mechanisms of specific environmental microbial ecosystems. This work aimed to reveal the diversity and# succession of the microbiota in Tuosu Lake to provide a biological basis for the exploration and development of microbial resources in the plateau lakes. The distribution and diversity of microflora in Tuosu Lake, hypoxia, high altitude, alkaline, closed plateau lake with fresh water supply, was investigated. The total DNA was extracted from six samples with different salinity from different geographical locations of Tuosu Lake. The 16S rRNA gene of bacteria and archaea were determined by using high-throughput sequencing-based on an Illumina Miseq sequencing platform. The microbiota in Tuosu Lake has a high diversity and complexity and there are a large number of unclassified microbial species. The bacterial communities in Tuosu Lake are dominated by Proteobacteria (44.3%) and Actbacteria (17.2%). Among them, β-Proteobacteria is the dominant genus in the low-salt sample, while γ-Proteobacteria is more advantageous in the samples with higher salinity. The archaeal communities are dominated by Euryarchaeota (50%) and Woesearchaeota__DHVEG-6 (42.6%). The vast majority of the methanogenic archaea in Tuosu Lake samples belong to Methanomicrobia, and the methanogens in low-salinity samples are significantly more abundant than those in high-salt samples. Diversity and distribution appear to be highly influenced by water salinity and pH.},
}
@article {pmid33025566,
year = {2021},
author = {Takamura, E and Taki, S and Sakamoto, H and Satomura, T and Sakuraba, H and Ohshima, T and Suye, SI},
title = {Site-Directed Mutagenesis of Multicopper Oxidase from Hyperthermophilic Archaea for High-Voltage Biofuel Cells.},
journal = {Applied biochemistry and biotechnology},
volume = {193},
number = {2},
pages = {492-501},
pmid = {33025566},
issn = {1559-0291},
mesh = {Amino Acid Substitution ; *Archaeal Proteins/chemistry/genetics ; *Bioelectric Energy Sources ; *Mutagenesis, Site-Directed ; *Mutation, Missense ; *Oxidoreductases/chemistry/genetics ; *Pyrobaculum/enzymology/genetics ; },
abstract = {Enzymes from hyperthermophilic archaea are potential candidates for industrial use because of their superior pH, thermal, and long-term stability, and are expected to improve the long-term stability of biofuel cells (BFCs). However, the reported multicopper oxidase (MCO) from hyperthermophilic archaea has lower redox potential than MCOs from other organisms, which leads to a decrease in the cell voltage of BFCs. In this study, we attempted to positively shift the redox potential of the MCO from hyperthermophilic archaeon Pyrobaculum aerophilum (McoP). Mutations (M470L and M470F) were introduced into the axial ligand of the T1 copper atom of McoP, and the enzymatic chemistry and redox potentials were compared with that of the parent (M470). The redox potentials of M470L and M470F shifted positively by about 0.07 V compared with that of M470. In addition, the catalytic activity of the mutants towards 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulphonic acid) (ABTS) increased 1.2-1.3-fold. The thermal stability of the mutants and the electrocatalytic performance for O2 reduction of M470F was slightly reduced compared with that of M470. This research provides useful enzymes for application as biocathode catalysts for high-voltage BFCs.},
}
@article {pmid33022088,
year = {2021},
author = {Thiroux, S and Dupont, S and Nesbø, CL and Bienvenu, N and Krupovic, M and L'Haridon, S and Marie, D and Forterre, P and Godfroy, A and Geslin, C},
title = {The first head-tailed virus, MFTV1, infecting hyperthermophilic methanogenic deep-sea archaea.},
journal = {Environmental microbiology},
volume = {23},
number = {7},
pages = {3614-3626},
doi = {10.1111/1462-2920.15271},
pmid = {33022088},
issn = {1462-2920},
mesh = {Archaea/genetics ; *Archaeal Viruses/genetics ; Ecosystem ; Methanocaldococcus ; *Viruses ; },
abstract = {Deep-sea hydrothermal vents are inhabited by complex communities of microbes and their viruses. Despite the importance of viruses in controlling the diversity, adaptation and evolution of their microbial hosts, to date, only eight bacterial and two archaeal viruses isolated from abyssal ecosystems have been described. Thus, our efforts focused on gaining new insights into viruses associated with deep-sea autotrophic archaea. Here, we provide the first evidence of an infection of hyperthermophilic methanogenic archaea by a head-tailed virus, Methanocaldococcus fervens tailed virus 1 (MFTV1). MFTV1 has an isometric head of 50 nm in diameter and a 150 nm-long non-contractile tail. Virions are released continuously without causing a sudden drop in host growth. MFTV1 infects Methanocaldococcus species and is the first hyperthermophilic head-tailed virus described thus far. The viral genome is a double-stranded linear DNA of 31 kb. Interestingly, our results suggest potential strategies adopted by the plasmid pMEFER01, carried by M. fervens, to spread horizontally in hyperthermophilic methanogens. The data presented here open a new window of understanding on how the abyssal mobilome interacts with hyperthermophilic marine archaea.},
}
@article {pmid33021028,
year = {2021},
author = {Wei, D and Zeng, S and Hou, D and Zhou, R and Xing, C and Deng, X and Yu, L and Wang, H and Deng, Z and Weng, S and Huang, Z and He, J},
title = {Community diversity and abundance of ammonia-oxidizing archaea and bacteria in shrimp pond sediment at different culture stages.},
journal = {Journal of applied microbiology},
volume = {130},
number = {5},
pages = {1442-1455},
doi = {10.1111/jam.14846},
pmid = {33021028},
issn = {1365-2672},
support = {CARS-48//China Agriculture Research System/ ; //China-ASEAN Maritime Cooperation Fund/ ; //China-ASEAN Center for Joint Research and Promotion of Marine Aquaculture Technology/ ; GDOE (2019) A21//Guangdong MEPP Fund/ ; //Guangzhou Science Technology and Innovation Commission Project/ ; 20164200042090023//Guangdong Ocean and Fishery Bureau Project/ ; },
mesh = {Ammonia/*metabolism ; Animals ; *Aquaculture ; Archaea/classification/genetics/growth &amp; development/*metabolism ; Bacteria/classification/genetics/growth &amp; development/*metabolism ; Ecosystem ; Geologic Sediments/chemistry/*microbiology ; Microbiota/*physiology ; Nitrogen Cycle ; Nitrosomonadaceae/classification/growth &amp; development/metabolism ; Oxidation-Reduction ; Penaeidae/*growth &amp; development ; Phylogeny ; Ponds/microbiology ; RNA, Ribosomal, 16S ; },
abstract = {AIMS: Ammonia oxidation is a significant process of nitrogen cycles in a lot of ecosystems sediments while there are few studies in shrimp culture pond (SCP) sediments. This paper attempted to explore the community diversity and abundance of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in SCP sediments at different culture stages.<br><br>METHODS AND RESULTS: We collected SCP sediments and analysed the community diversity and abundance of AOA and bacteria in shrimp pond sediment at different culture stages using the ammonia monooxygenase (amoA) gene with quantitative PCR (qPCR) and 16S rRNA gene sequencing. The AOB-amoA gene abundance was showed higher than AOA-amoA gene abundance in SCP sediments on Day 50 and Day 60 after shrimp larvae introducing into the pond, and the diversity of AOA in SCP sediments was higher than that of AOB. The phylogenetic tree revealed that the most of AOA were the member of Nitrosopumilus and Nitrososphaera, and the majority of AOB sequences were clustered into Nitrosospira, Nitrosomonas clusters 6a and 7. The AOA community has close relationship with total organic carbon (TOC), pH, total phosphorus (TP), nitrate reductase, urease, acid phosphatase and &#x3b2;-glucosidase. The AOB community was related to TOC, C/N and nitrate reductase.<br><br>CONCLUSIONS: AOA and AOB play the different ecological roles in SCP sediments at different culture stages.<br><br>Our results suggested that the different community diversity and abundance of AOA and AOB in SCP sediments, which may improve our ecological cognition of shrimp culture stages in SCP ecosystems.},
}
@article {pmid33013726,
year = {2020},
author = {Mani, K and Taib, N and Hugoni, M and Bronner, G and Bragança, JM and Debroas, D},
title = {Transient Dynamics of Archaea and Bacteria in Sediments and Brine Across a Salinity Gradient in a Solar Saltern of Goa, India.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {1891},
pmid = {33013726},
issn = {1664-302X},
abstract = {The microbial fluctuations along an increasing salinity gradient during two different salt production phases - initial salt harvesting (ISH) phase and peak salt harvesting (PSH) phase of Siridao solar salterns in Goa, India were examined through high-throughput sequencing of 16S rRNA genes on Illumina MiSeq platform. Elemental analysis of the brine samples showed high concentration of sodium (Na[+]) and chloride (Cl[-]) ions thereby indicating its thalassohaline nature. Comparison of relative abundance of sequences revealed that Archaea transited from sediment to brine while Bacteria transited from brine to sediment with increasing salinity. Frequency of Archaea was found to be significantly enriched even in low and moderate salinity sediments with their relative sequence abundance reaching as high as 85%. Euryarchaeota was found to be the dominant archaeal phylum containing 19 and 17 genera in sediments and brine, respectively. Phylotypes belonging to Halorubrum, Haloarcula, Halorhabdus, and Haloplanus were common in both sediments and brine. Occurence of Halobacterium and Natronomonas were exclusive to sediments while Halonotius was exclusive to brine. Among sediments, relative sequence frequency of Halorubrum, and Halorhabdus decreased while Haloarcula, Haloplanus, and Natronomonas increased with increasing salinity. Similarly, the relative abundance of Haloarcula and Halorubrum increased with increasing salinity in brine. Sediments and brine samples harbored about 20 and 17 bacterial phyla, respectively. Bacteroidetes, Proteobacteria, and Chloroflexi were the common bacterial phyla in both sediments and brine while Firmicutes were dominant albeit in sediments alone. Further, Gammaproteobacteria, Alphaproteobacteria, and Deltaproteobacteria were observed to be the abundant class within the Proteobacteria. Among the bacterial genera, phylotypes belonging to Rubricoccus and Halomonas were widely detected in both brine and sediment while Thioalkalispira, Desulfovermiculus, and Marinobacter were selectively present in sediments. This study suggests that Bacteria are more susceptible to salinity fluctuations than Archaea, with many bacterial genera being compartment and phase-specific. Our study further indicated that Archaea rather than Bacteria could withstand the wide salinity fluctuation and attain a stable community structure within a short time-frame.},
}
@article {pmid33005311,
year = {2020},
author = {Jung, J and Kim, JS and Taffner, J and Berg, G and Ryu, CM},
title = {Archaea, tiny helpers of land plants.},
journal = {Computational and structural biotechnology journal},
volume = {18},
number = {},
pages = {2494-2500},
pmid = {33005311},
issn = {2001-0370},
abstract = {Archaea are members of most microbiomes. While archaea are highly abundant in extreme environments, they are less abundant and diverse in association with eukaryotic hosts. Nevertheless, archaea are a substantial constituent of plant-associated ecosystems in the aboveground and belowground phytobiome. Only a few studies have investigated the role of archaea in plant health and its potential symbiosis in ecosystems. This review discusses recent progress in identifying how archaea contribute to plant traits such as growth, adaptation to abiotic stresses, and immune activation. We synthesized the most recent functional and molecular data on archaea, including root colonization and the volatile emission to activate plant systemic immunity. These data represent a paradigm shift in our understanding of plant-microbiota interactions.},
}
@article {pmid33002447,
year = {2021},
author = {Berger, S and Cabrera-Orefice, A and Jetten, MSM and Brandt, U and Welte, CU},
title = {Investigation of central energy metabolism-related protein complexes of ANME-2d methanotrophic archaea by complexome profiling.},
journal = {Biochimica et biophysica acta. Bioenergetics},
volume = {1862},
number = {1},
pages = {148308},
doi = {10.1016/j.bbabio.2020.148308},
pmid = {33002447},
issn = {1879-2650},
support = {339880/ERC_/European Research Council/International ; },
mesh = {Archaea/*enzymology ; Archaeal Proteins/chemistry/*metabolism ; Electron Transport ; *Energy Metabolism ; },
abstract = {The anaerobic oxidation of methane is important for mitigating emissions of this potent greenhouse gas to the atmosphere and is mediated by anaerobic methanotrophic archaea. In a 'Candidatus Methanoperedens BLZ2' enrichment culture used in this study, methane is oxidized to CO2 with nitrate being the terminal electron acceptor of an anaerobic respiratory chain. Energy conservation mechanisms of anaerobic methanotrophs have mostly been studied at metagenomic level and hardly any protein data is available at this point. To close this gap, we used complexome profiling to investigate the presence and subunit composition of protein complexes involved in energy conservation processes. All enzyme complexes and their subunit composition involved in reverse methanogenesis were identified. The membrane-bound enzymes of the respiratory chain, such as F420H2:quinone oxidoreductase, membrane-bound heterodisulfide reductase, nitrate reductases and Rieske cytochrome bc1 complex were all detected. Additional or putative subunits such as an octaheme subunit as part of the Rieske cytochrome bc1 complex were discovered that will be interesting targets for future studies. Furthermore, several soluble proteins were identified, which are potentially involved in oxidation of reduced ferredoxin produced during reverse methanogenesis leading to formation of small organic molecules. Taken together these findings provide an updated, refined picture of the energy metabolism of the environmentally important group of anaerobic methanotrophic archaea.},
}
@article {pmid32994183,
year = {2020},
author = {Wolff, P and Villette, C and Zumsteg, J and Heintz, D and Antoine, L and Chane-Woon-Ming, B and Droogmans, L and Grosjean, H and Westhof, E},
title = {Comparative patterns of modified nucleotides in individual tRNA species from a mesophilic and two thermophilic archaea.},
journal = {RNA (New York, N.Y.)},
volume = {26},
number = {12},
pages = {1957-1975},
pmid = {32994183},
issn = {1469-9001},
mesh = {Base Sequence ; Methanococcus/*genetics ; Nucleic Acid Conformation ; Nucleotides/*chemistry ; Pyrococcus furiosus/*genetics ; RNA, Archaeal/chemistry/genetics ; RNA, Transfer/*chemistry/*genetics ; Sulfolobus acidocaldarius/*genetics ; },
abstract = {To improve and complete our knowledge of archaeal tRNA modification patterns, we have identified and compared the modification pattern (type and location) in tRNAs of three very different archaeal species, Methanococcus maripaludis (a mesophilic methanogen), Pyrococcus furiosus (a hyperthermophile thermococcale), and Sulfolobus acidocaldarius (an acidophilic thermophilic sulfolobale). Most abundant isoacceptor tRNAs (79 in total) for each of the 20 amino acids were isolated by two-dimensional gel electrophoresis followed by in-gel RNase digestions. The resulting oligonucleotide fragments were separated by nanoLC and their nucleotide content analyzed by mass spectrometry (MS/MS). Analysis of total modified nucleosides obtained from complete digestion of bulk tRNAs was also performed. Distinct base- and/or ribose-methylations, cytidine acetylations, and thiolated pyrimidines were identified, some at new positions in tRNAs. Novel, some tentatively identified, modifications were also found. The least diversified modification landscape is observed in the mesophilic Methanococcus maripaludis and the most complex one in Sulfolobus acidocaldarius Notable observations are the frequent occurrence of ac[4]C nucleotides in thermophilic archaeal tRNAs, the presence of m[7]G at positions 1 and 10 in Pyrococcus furiosus tRNAs, and the use of wyosine derivatives at position 37 of tRNAs, especially those decoding U1- and C1-starting codons. These results complete those already obtained by others with sets of archaeal tRNAs from Methanocaldococcus jannaschii and Haloferax volcanii.},
}
@article {pmid32991817,
year = {2021},
author = {Chen, T and Hu, W and He, S and Zhang, X and Niu, Y},
title = {Diversity and community structure of ammonia-oxidizing archaea in rhizosphere soil of four plant groups in Ebinur Lake wetland.},
journal = {Canadian journal of microbiology},
volume = {67},
number = {4},
pages = {271-280},
doi = {10.1139/cjm-2020-0228},
pmid = {32991817},
issn = {1480-3275},
mesh = {Ammonia/*metabolism ; Archaea/classification/genetics/*isolation &amp; purification/metabolism ; Lakes ; *Microbiota ; Plants/classification ; *Rhizosphere ; Seasons ; Soil/chemistry ; *Soil Microbiology ; Wetlands ; },
abstract = {The aim of this study was to reveal the differences in the community structure of ammonia-oxidizing archaea (AOA) between rhizosphere and non-rhizosphere soil, to provide a theoretical basis for further study on the relationship between halophyte rhizosphere soil microorganisms and salt tolerance. The results of diversity and community structure showed that the diversity of the AOA community in rhizosphere soil of Reeds was higher than that in non-rhizosphere soil in spring and lower than that in non-rhizosphere soil in summer and autumn. In summer, the diversity of rhizosphere soil of Karelinia caspica was higher than that of non-rhizosphere soil and lower than that of non-rhizosphere soil in spring and autumn. The diversity of rhizosphere soil of Halocnemum strobilaceum in 3 seasons was lower than that in non-rhizosphere soil. The diversity of rhizosphere soil of Salicornia was higher than that in non-rhizosphere soil in 3 seasons. In addition, the relative abundance of AOA in rhizosphere soil of 4 plants was higher than that in non-rhizosphere soil. The AOA community in all soil samples was mainly concentrated in Crenarchaeota and Thaumarchaeota. Redundancy analysis results showed salinity, soil water moisture, pH, and soil organic matter were important factors affecting the differentiation of AOA communities.},
}
@article {pmid32983044,
year = {2020},
author = {Zou, D and Liu, H and Li, M},
title = {Community, Distribution, and Ecological Roles of Estuarine Archaea.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {2060},
pmid = {32983044},
issn = {1664-302X},
abstract = {Archaea are diverse and ubiquitous prokaryotes present in both extreme and moderate environments. Estuaries, serving as links between the land and ocean, harbor numerous microbes that are relatively highly active because of massive terrigenous input of nutrients. Archaea account for a considerable portion of the estuarine microbial community. They are diverse and play key roles in the estuarine biogeochemical cycles. Ammonia-oxidizing archaea (AOA) are an abundant aquatic archaeal group in estuaries, greatly contributing estuarine ammonia oxidation. Bathyarchaeota are abundant in sediments, and they may involve in sedimentary organic matter degradation, acetogenesis, and, potentially, methane metabolism, based on genomics. Other archaeal groups are also commonly detected in estuaries worldwide. They include Euryarchaeota, and members of the DPANN and Asgard archaea. Based on biodiversity surveys of the 16S rRNA gene and some functional genes, the distribution and abundance of estuarine archaea are driven by physicochemical factors, such as salinity and oxygen concentration. Currently, increasing amount of genomic information for estuarine archaea is becoming available because of the advances in sequencing technologies, especially for AOA and Bathyarchaeota, leading to a better understanding of their functions and environmental adaptations. Here, we summarized the current knowledge on the community composition and major archaeal groups in estuaries, focusing on AOA and Bathyarchaeota. We also highlighted the unique genomic features and potential adaptation strategies of estuarine archaea, pointing out major unknowns in the field and scope for future research.},
}
@article {pmid32967357,
year = {2020},
author = {Brázda, V and Luo, Y and Bartas, M and Kaura, P and Porubiaková, O and Šťastný, J and Pečinka, P and Verga, D and Da Cunha, V and Takahashi, TS and Forterre, P and Myllykallio, H and Fojta, M and Mergny, JL},
title = {G-Quadruplexes in the Archaea Domain.},
journal = {Biomolecules},
volume = {10},
number = {9},
pages = {},
pmid = {32967357},
issn = {2218-273X},
support = {CZ.02.1.01/0.0/0.0/15_003/0000477//ERDF/International ; 18-15548S//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/International ; },
mesh = {Archaea/classification/*genetics/metabolism ; Archaeal Proteins/genetics/metabolism ; Circular Dichroism ; DNA/*chemistry/genetics/metabolism ; DNA-Binding Proteins/genetics/metabolism ; *G-Quadruplexes ; Genome, Archaeal/*genetics ; Genomics/methods ; Nucleic Acid Conformation ; Phylogeny ; RNA/*chemistry/genetics/metabolism ; Species Specificity ; },
abstract = {The importance of unusual DNA structures in the regulation of basic cellular processes is an emerging field of research. Amongst local non-B DNA structures, G-quadruplexes (G4s) have gained in popularity during the last decade, and their presence and functional relevance at the DNA and RNA level has been demonstrated in a number of viral, bacterial, and eukaryotic genomes, including humans. Here, we performed the first systematic search of G4-forming sequences in all archaeal genomes available in the NCBI database. In this article, we investigate the presence and locations of G-quadruplex forming sequences using the G4Hunter algorithm. G-quadruplex-prone sequences were identified in all archaeal species, with highly significant differences in frequency, from 0.037 to 15.31 potential quadruplex sequences per kb. While G4 forming sequences were extremely abundant in Hadesarchaea archeon (strikingly, more than 50% of the Hadesarchaea archaeon isolate WYZ-LMO6 genome is a potential part of a G4-motif), they were very rare in the Parvarchaeota phylum. The presence of G-quadruplex forming sequences does not follow a random distribution with an over-representation in non-coding RNA, suggesting possible roles for ncRNA regulation. These data illustrate the unique and non-random localization of G-quadruplexes in Archaea.},
}
@article {pmid32955155,
year = {2020},
author = {Stahl, DA},
title = {The path leading to the discovery of the ammoniaoxidizing archaea.},
journal = {Environmental microbiology},
volume = {22},
number = {11},
pages = {4507-4519},
doi = {10.1111/1462-2920.15239},
pmid = {32955155},
issn = {1462-2920},
support = {//DOE Biological and Environmental Research/ ; //Defense Advanced Research Projects Agency/ ; /EPA/EPA/United States ; /NASA/NASA/United States ; /DE/NIDCR NIH HHS/United States ; //National Science Foundation/ ; //Office of Naval Research/ ; /EPA/EPA/United States ; /NASA/NASA/United States ; /DE/NIDCR NIH HHS/United States ; },
}
@article {pmid32936753,
year = {2020},
author = {Yin, XM and Yang, XY and Hou, J and Zhu, L and Cui, HL},
title = {Natronomonas halophila sp. nov. and Natronomonas salina sp. nov., two novel halophilic archaea.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {70},
number = {11},
pages = {5686-5692},
doi = {10.1099/ijsem.0.004463},
pmid = {32936753},
issn = {1466-5034},
mesh = {China ; DNA, Archaeal/genetics ; Fatty Acids/chemistry ; Glycolipids/chemistry ; Halobacteriaceae/*classification/isolation &amp; purification ; Lakes/*microbiology ; *Mining ; Nucleic Acid Hybridization ; Phospholipids/chemistry ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Saline Waters ; Sequence Analysis, DNA ; },
abstract = {Two halophilic archaeal strains, C90[T] and YPL13[T], were isolated from a salt lake and a salt mine in PR China. The two strains were found to form two clusters (97.5 and 89.5 % similarity between them, respectively) separating them from the three current members of the genus Natronomonas (95.4-97.0 % and 86.6-89.3 % similarity, respectively) on the basis of the 16S rRNA and rpoB' gene sequence similarities and phylogenetic analysis. Diverse phenotypic characteristics differentiate strains C90[T] and YPL13[T] from current Natronomonas members. The polar lipids of strain C90[T] were phosphatidic acid, phosphatidylglycerol (PG), phosphatidylglycerol phosphate methyl ester (PGP-Me), phosphatidylglycerol sulphate, two unidentified glycolipids, a major glycolipid and a minor glycolipid, while those of strain YPL13[T] were PG, PGP-Me, two unidentified phospholipids and a glycolipid. The average nucleotide identity (ANI) and in silico DNA-DNA hybridization (isDDH) values between the two strains were 79.8 and 27.1 %, respectively, which were much lower than the threshold values proposed as a species boundaries (ANI 95-96 % and isDDH 70 %), which revealed that the two strains represent two novel species; these values (ANI 76.6-80.0 % and isDDH 21.6-27.0 %) of the strains examined in this study and the current members of Natronomonas are much lower than the recommended threshold values, suggesting that strains C90[T] and YPL13[T] represent two genomically different species of Natronomonas. These results showed that strains C90[T] (=CGMCC 1.13738[T]=JCM 32961[T]) and YPL13[T] (=CGMCC 1.13884[T]=JCM 31111[T]) represent two novel species of Natronomonas, for which the names Natronomonas halophila sp. nov. and Natronomonas salina sp. nov. are proposed.},
}
@article {pmid32935184,
year = {2021},
author = {He, Y and Zhou, Y and Weng, R and Wang, J and Chen, J and Huang, M},
title = {Responses of Ammonia-Oxidizing Archaea and Bacteria in Malodorous River Sediments to Different Remediation Techniques.},
journal = {Microbial ecology},
volume = {81},
number = {2},
pages = {314-322},
pmid = {32935184},
issn = {1432-184X},
support = {41877477//National Natural Science Foundation of China/ ; 18DZ1203806//Shanghai Science and Technology Development Funds/ ; 2017ZX07207001//National Science and Technology Major Project for Water Pollution Control and Treatment/ ; 2018ZX07208008//National Science and Technology Major Project for Water Pollution Control and Treatment/ ; },
mesh = {Ammonia/analysis/*metabolism ; Archaea/classification/genetics/isolation &amp; purification/*metabolism ; Bacteria/classification/genetics/isolation &amp; purification/*metabolism ; Calcium Compounds/analysis ; Environmental Restoration and Remediation/*methods ; Geologic Sediments/chemistry/*microbiology ; Nitrates/analysis ; Oxidation-Reduction ; Oxygen/analysis ; Rivers/chemistry/*microbiology ; Species Specificity ; Water Pollutants, Chemical/metabolism ; },
abstract = {In this study, the joint use of high throughput sequencing, real-time quantitative PCR, and ammonia-oxidizing bacteria (AOB)-inhibiting allylthiourea was used to differentiate between the contributions of ammonia-oxidizing archaea (AOA) vs AOB to ammonia oxidation and ascertain how AOA and AOB responded to two widely used river remediation techniques (aeration and Ca(NO3)2 injection). Results showed that ammonia oxidation was largely attributed to ATU-sensitive AOB rather than AOA and Nitrosomonas was the predominant AOB-related genus (53.86%) in the malodorous river. The contribution of AOB to ammonia oxidation in the context of aeration and Ca(NO3)2 injection was 75.51 ± 2.77% and 60.19 ± 10.44%, respectively. The peak of AOB/AOA ratio and the marked increase of relative abundances of Nitrosomonas and Nitrosospira in aeration runs further demonstrated aeration favored the ammonia oxidation of AOB. Comparatively, Ca(NO3)2 injection could increase the ammonia oxidation contribution of AOA from 31.32 ± 6.06 to 39.81 ± 10.44% and was significantly correlated with Nitrosococcus of AOB (r = 0.796, p < 0.05), Candidatus_Nitrosopelagicus of AOA (r = 0.986, p < 0.01), and AOA Simpson diversity (r = - 0.791, p < 0.05). Moreover, Candidatus_Nitrosopelagicus was only present in Ca(NO3)2 runs. Taken together, Ca(NO3)2 was recognized as an important factor in mediating the growth and ecological niches of ammonia oxidizers.Graphical abstract.},
}
@article {pmid32925997,
year = {2020},
author = {Aleksandrowicz, P and Brzezińska-Błaszczyk, E and Dudko, A and Agier, J},
title = {Archaea Occurrence in the Subgingival Biofilm in Patients with Peri-implantitis and Periodontitis.},
journal = {The International journal of periodontics &amp; restorative dentistry},
volume = {40},
number = {5},
pages = {677-683},
doi = {10.11607/prd.4670},
pmid = {32925997},
issn = {1945-3388},
mesh = {Archaea ; Biofilms ; *Dental Implants ; Humans ; *Peri-Implantitis ; *Periodontitis ; RNA, Ribosomal, 16S ; },
abstract = {This study aimed to determine the prevalence and diversity of archaea and select bacteria in the subgingival biofilm of patients with peri-implantitis in comparison to patients with unaffected implants and patients with periodontitis. Samples of subgingival biofilm from oral sites were collected for DNA extraction (n = 139). A 16S rRNA gene-based polymerase chain reaction assay was used to determine the presence of archaea and select bacteria. Seven samples were selected for direct sequencing. Archaea were detected in 10% of samples from peri-implantitis sites, but not in samples from the unaffected dental implant. Archaea were present in 53% and 64% of samples from mild and moderate/advanced periodontitis sites, respectively. The main representative of the Archaea domain found in biofilm from periodontitis and peri-implantitis sites was Methanobrevibacter oralis. The present results revealed that archaea are present in diseased but not healthy implants. It was also found that archaea were more abundant in periodontitis than in peri-implantitis sites. Hence, the potential role of archaea in peri-implantitis and periodontitis should be taken into consideration.},
}
@article {pmid32919036,
year = {2020},
author = {Di Giulio, M},
title = {LUCA as well as the ancestors of archaea, bacteria and eukaryotes were progenotes: Inference from the distribution and diversity of the reading mechanism of the AUA and AUG codons in the domains of life.},
journal = {Bio Systems},
volume = {198},
number = {},
pages = {104239},
doi = {10.1016/j.biosystems.2020.104239},
pmid = {32919036},
issn = {1872-8324},
mesh = {Anticodon/genetics ; Archaea/classification/*genetics ; Bacteria/classification/*genetics ; Codon/genetics ; Eukaryota/classification/*genetics ; *Evolution, Molecular ; *Genetic Code ; Genetic Variation ; Open Reading Frames/genetics ; Origin of Life ; Phylogeny ; RNA, Transfer/genetics ; },
abstract = {Here I use the rationale assuming that if of a certain trait that exerts its function in some aspect of the genetic code or, more generally, in protein synthesis, it is possible to identify the evolutionary stage of its origin then it would imply that this evolutionary moment would be characterized by a high translational noise because this trait would originate for the first time during that evolutionary stage. That is to say, if this trait had a non-marginal role in the realization of the genetic code, or in protein synthesis, then the origin of this trait would imply that, more generally, it was the genetic code itself that was still originating. But if the genetic code were still originating - at that precise evolutionary stage - then this would imply that there was a high translational noise which in turn would imply that it was in the presence of a protocell, i.e. a progenote that was by definition characterized by high translational noise. I apply this rationale to the mechanism of modification of the base 34 of the anticodon of an isoleucine tRNA that leads to the reading of AUA and AUG codons in archaea, bacteria and eukaryotes. The phylogenetic distribution of this mechanism in these phyletic lineages indicates that this mechanism originated only after the evolutionary stage of the last universal common ancestor (LUCA), namely, during the formation of cellular domains, i.e., at the stage of ancestors of these main phyletic lineages. Furthermore, given that this mechanism of modification of the base 34 of the anticodon of the isoleucine tRNA would result to emerge at a stage of the origin of the genetic code - despite in its terminal phases - then all this would imply that the ancestors of bacteria, archaea and eukaryotes were progenotes. If so, all the more so, the LUCA would also be a progenote since it preceded these ancestors temporally. A consequence of all this reasoning might be that since these three ancestors were of the progenotes that were different from each other, if at least one of them had evolved into at least two real and different cells - basically different from each other - then the number of cellular domains would not be three but it would be greater than three.},
}
@article {pmid32892054,
year = {2021},
author = {Qi, L and Ma, Z and Chang, SX and Zhou, P and Huang, R and Wang, Y and Wang, Z and Gao, M},
title = {Biochar decreases methanogenic archaea abundance and methane emissions in a flooded paddy soil.},
journal = {The Science of the total environment},
volume = {752},
number = {},
pages = {141958},
doi = {10.1016/j.scitotenv.2020.141958},
pmid = {32892054},
issn = {1879-1026},
mesh = {Archaea/genetics ; Charcoal ; Methane ; *Oryza ; *Soil ; Soil Microbiology ; },
abstract = {Biochar addition can reduce methane (CH4) emissions from paddy soils while the mechanisms involved are not entirely clear. Here, we studied the effect of biochar addition on CH4 emissions, and the abundance and community composition of methanogens and methanotrophs over two rice cultivation seasons. The experiment had the following five treatments: control (CK), chemical fertilizer application only (BC0), and 0.5% (w/w) (BC1), 1% (BC2), and 2% of biochar applied with chemical fertilizers (BC3). The season-wide CH4 emissions were decreased (P < 0.05) by 22.2-95.7% in biochar application compared with BC0 in the two rice seasons (2017 and 2018). In 2017, biochar application decreased methanogenic archaea (mcrA) but increased methanotrophic bacteria (pmoA) abundances, and decreased the ratio of mcrA/pmoA, as compared with BC0 (P < 0.05). In 2018, the abundance of mcrA was lower in BC2 and BC3 than in BC0 (P < 0.05) but was not different between BC0 and BC1, and the abundance of pmoA was lower in BC1, BC2 and BC3 than in BC0 (P < 0.05). The CH4 emissions were positively related to abundances of the mcrA gene (P < 0.01) but not to that of the pmoA gene in two rice seasons. Rice grain yield was increased by 62.2-94.1% in biochar addition treatments compared with BC0 in the first year (P < 0.01) and by 29.9-37.6% in BC2 and BC3 compared with BC0 in the second year (P < 0.05). Biochar application decreased CH4 emissions by reducing methanogenic archaea abundance in the studied flooded paddy soil.},
}
@article {pmid32892037,
year = {2021},
author = {Niu, M and Zhou, F and Yang, Y and Sun, Y and Zhu, T and Shen, F},
title = {Abundance and composition of airborne archaea during springtime mixed dust and haze periods in Beijing, China.},
journal = {The Science of the total environment},
volume = {752},
number = {},
pages = {141641},
doi = {10.1016/j.scitotenv.2020.141641},
pmid = {32892037},
issn = {1879-1026},
mesh = {*Air Pollution ; Archaea/genetics ; Beijing ; China ; *Dust/analysis ; Humans ; Phylogeny ; },
abstract = {Archaea have an important role in the elemental biogeochemical cycle and human health. However, characteristics of airborne archaea affected by anthropogenic and natural processes are unclear. In this study, we investigated the abundance, structures, influencing factors and assembly processes of the archaeal communities in the air samples collected from Beijing in springtime using quantitative polymerase chain reaction (qPCR), high-throughput sequencing technology and statistical analysis. The concentrations of airborne archaea ranged from 10[1] to 10[3] copies m[-3] (455 ± 211 copies m[-3]), accounting for 0.67% of the total prokaryote (sum of archaea and bacteria). An increase in airborne archaea was seen when the air quality shifted from clean to slightly polluted conditions. Sandstorm dust imported a large number of archaea to the local atmosphere. Euryarchaeota, Thaumarchaeota and Crenarchaeota were the dominant phyla, revealing the primary role of soil in releasing archaea to the ambient environment. Dispersal-related neutral processes play an important role in shaping the structure of airborne archaeal assembly. Of all phyla, methanogenic Euryarchaeota were most abundant in the air parcels come from the south of Beijing. Air masses from the west of Beijing, which brought sandstorm to Beijing, carried large amounts of ammonia oxidizing archaea Nitrososphaera. The results demonstrate the importance of air mass sources and local weather conditions in shaping the local airborne archaea community.},
}
@article {pmid32889138,
year = {2020},
author = {Nikolayev, S and Cohen-Rosenzweig, C and Eichler, J},
title = {Evolutionary considerations of the oligosaccharyltransferase AglB and other aspects of N-glycosylation across Archaea.},
journal = {Molecular phylogenetics and evolution},
volume = {153},
number = {},
pages = {106951},
doi = {10.1016/j.ympev.2020.106951},
pmid = {32889138},
issn = {1095-9513},
mesh = {Archaea/*classification/*enzymology/genetics ; Archaeal Proteins/*genetics ; Glycosylation ; Hexosyltransferases/*genetics ; Membrane Proteins/*genetics ; *Phylogeny ; },
abstract = {Various biological markers in members of the TACK and Asgard archaeal super-phyla show Eukarya-like traits. These include the oligosaccharyltransferase, responsible for transferring glycans from the lipid carrier upon which they are assembled onto selected asparagine residues of target proteins during N-glycosylation. In Archaea, oligosaccharyltransferase activity is catalyzed by AglB. To gain deeper insight into AglB and N-glycosylation across archaeal phylogeny, bioinformatics approaches were employed to address variability in AglB sequence motifs involved in enzyme activity, construct a phylogenetic tree based on AglB sequences, search for archaeal homologues of non-catalytic subunits of the multimeric eukaryal oligosaccharyltransferase complex and predict the presence of aglB-based clusters of glycosylation-related genes in the Euryarchaeota and the DPANN, TACK and Asgard super-phyla. In addition, site-directed mutagenesis and mass spectrometry were employed to study the natural variability in the WWDXG motif central to oligosaccharyltransferase activity seen in archaeal AglB. The results clearly distinguish AglB from members of the DPANN super-phylum and the Euryarchaeota from the same enzyme in members of the TACK and Asgard super-phyla, which showed considerable similarity to its eukaryal homologue Stt3. The results thus support the evolutionary proximity of Eukarya and the TACK and Asgard archaea.},
}
@article {pmid32887961,
year = {2020},
author = {Parks, DH and Chuvochina, M and Chaumeil, PA and Rinke, C and Mussig, AJ and Hugenholtz, P},
title = {Author Correction: A complete domain-to-species taxonomy for Bacteria and Archaea.},
journal = {Nature biotechnology},
volume = {38},
number = {9},
pages = {1098},
doi = {10.1038/s41587-020-0539-7},
pmid = {32887961},
issn = {1546-1696},
abstract = {An amendment to this paper has been published and can be accessed via a link at the top of the paper.},
}
@article {pmid32887944,
year = {2020},
author = {Reichart, NJ and Jay, ZJ and Krukenberg, V and Parker, AE and Spietz, RL and Hatzenpichler, R},
title = {Activity-based cell sorting reveals responses of uncultured archaea and bacteria to substrate amendment.},
journal = {The ISME journal},
volume = {14},
number = {11},
pages = {2851-2861},
pmid = {32887944},
issn = {1751-7370},
support = {80NSSC19K0449/ImNASA/Intramural NASA/United States ; 80NSSC19K1633/ImNASA/Intramural NASA/United States ; },
mesh = {*Archaea/genetics ; Bacteria/genetics ; *Hot Springs ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Wyoming ; },
abstract = {Metagenomic studies have revolutionized our understanding of the metabolic potential of uncultured microorganisms in various ecosystems. However, many of these genomic predictions have yet to be experimentally tested, and the functional expression of genomic potential often remains unaddressed. In order to obtain a more thorough understanding of cell physiology, novel techniques capable of testing microbial metabolism under close to in situ conditions must be developed. Here, we provide a benchmark study to demonstrate that bioorthogonal non-canonical amino acid tagging (BONCAT) in combination with fluorescence-activated cell sorting (FACS) and 16S rRNA gene sequencing can be used to identify anabolically active members of a microbial community incubated in the presence of various growth substrates or under changing physicochemical conditions. We applied this approach to a hot spring sediment microbiome from Yellowstone National Park (Wyoming, USA) and identified several microbes that changed their activity levels in response to substrate addition, including uncultured members of the phyla Thaumarchaeota, Acidobacteria, and Fervidibacteria. Because shifts in activity in response to substrate amendment or headspace changes are indicative of microbial preferences for particular growth conditions, results from this and future BONCAT-FACS studies could inform the development of cultivation media to specifically enrich uncultured microbes. Most importantly, BONCAT-FACS is capable of providing information on the physiology of uncultured organisms at as close to in situ conditions as experimentally possible.},
}
@article {pmid32857850,
year = {2020},
author = {Yue, L and Li, J and Zhang, B and Qi, L and Li, Z and Zhao, F and Li, L and Zheng, X and Dong, X},
title = {The conserved ribonuclease aCPSF1 triggers genome-wide transcription termination of Archaea via a 3'-end cleavage mode.},
journal = {Nucleic acids research},
volume = {48},
number = {17},
pages = {9589-9605},
pmid = {32857850},
issn = {1362-4962},
mesh = {Archaeal Proteins/*genetics/metabolism ; DNA, Complementary/genetics ; DNA-Directed RNA Polymerases/genetics/metabolism ; Genome, Archaeal ; Methanococcus/*genetics ; Mutation ; Phylogeny ; Ribonucleases/*genetics/metabolism ; Transcription, Genetic ; Uridine ; },
abstract = {Transcription termination defines accurate transcript 3'-ends and ensures programmed transcriptomes, making it critical to life. However, transcription termination mechanisms remain largely unknown in Archaea. Here, we reported the physiological significance of the newly identified general transcription termination factor of Archaea, the ribonuclease aCPSF1, and elucidated its 3'-end cleavage triggered termination mechanism. The depletion of Mmp-aCPSF1 in Methanococcus maripaludis caused a genome-wide transcription termination defect and disordered transcriptome. Transcript-3'end-sequencing revealed that transcriptions primarily terminate downstream of a uridine-rich motif where Mmp-aCPSF1 performed an endoribonucleolytic cleavage, and the endoribonuclease activity was determined to be essential to the in vivo transcription termination. Co-immunoprecipitation and chromatin-immunoprecipitation detected interactions of Mmp-aCPSF1 with RNA polymerase and chromosome. Phylogenetic analysis revealed that the aCPSF1 orthologs are ubiquitously distributed among the archaeal phyla, and two aCPSF1 orthologs from Lokiarchaeota and Thaumarchaeota could replace Mmp-aCPSF1 to terminate transcription of M. maripaludis. Therefore, the aCPSF1 dependent termination mechanism could be widely employed in Archaea, including Lokiarchaeota belonging to Asgard Archaea, the postulated archaeal ancestor of Eukaryotes. Strikingly, aCPSF1-dependent archaeal transcription termination reported here exposes a similar 3'-cleavage mode as the eukaryotic RNA polymerase II termination, thus would shed lights on understanding the evolutionary linking between archaeal and eukaryotic termination machineries.},
}
@article {pmid32852144,
year = {2021},
author = {Tang, HM and Xiao, XP and Li, C and Shi, LH and Cheng, KK and Wen, L and Li, WY and Wang, K},
title = {Influences of different manure N input on soil ammonia-oxidizing archaea and bacterial activity and community structure in a double-cropping rice field.},
journal = {Journal of applied microbiology},
volume = {130},
number = {3},
pages = {937-947},
doi = {10.1111/jam.14830},
pmid = {32852144},
issn = {1365-2672},
support = {31872851//National Natural Science Foundation of China/ ; 2019JJ10003//Innovative Research Groups of the Natural Science Foundation of Hunan Province/ ; },
mesh = {Ammonia/metabolism ; Archaea/classification/genetics/isolation &amp; purification/*metabolism ; Bacteria/classification/genetics/isolation &amp; purification/*metabolism ; China ; Fertilizers/analysis ; Manure/*analysis ; *Microbiota ; Nitrogen/analysis/*metabolism ; Oryza/growth &amp; development/microbiology ; Soil/chemistry ; *Soil Microbiology ; },
abstract = {AIMS: The short-term effects of different organic manure nitrogen (N) input on soil ammonia-oxidizing archaea (AOA) and bacterial (AOB) activity and community structure at maturity stages of early rice and late rice were investigated in the present paper, in a double-cropping rice system in southern China.<br><br>METHODS AND RESULTS: A field experiment was done by applying five different organic and inorganic N input treatments: (i) 100% N of chemical fertilizer (M0), (ii) 30% N of organic manure and 70% N of chemical fertilizer (M30), (iii) 50% N of organic manure and 50% N of chemical fertilizer (M50), (iv) 100% N of organic manure (M100) and (v) without N fertilizer input as control (CK). Microbial community changes were assessed using fatty acid methyl esters, and ammonia oxidizer (AO) changes were followed using quantitative PCR. The results showed that AOA were higher than that of AOB based upon amoA gene copy at maturity stages of early rice and late rice. Also, the abundance of AOB and AOA with M30, M50 and M100 treatments was significantly higher than that of CK treatment. Manure N input treatments had significant effect on AOB and AOA abundance, and a higher correlation between AOB and manure N input was observed. AOB correlated moderately with soil organic carbon content, and AOA correlated moderately with water-filled pore space.<br><br>CONCLUSIONS: This study found that abundance of AOB and AOA was increased under the given organic N conditions, and the soil AOB and AOA community and diversity were changed by different short-term organic manure N input treatments.<br><br>Soil microbial community and specific N-utilizing microbial groups were affected by organic manure N input practices.},
}
@article {pmid32851593,
year = {2020},
author = {Cendron, F and Niero, G and Carlino, G and Penasa, M and Cassandro, M},
title = {Characterizing the fecal bacteria and archaea community of heifers and lactating cows through 16S rRNA next-generation sequencing.},
journal = {Journal of applied genetics},
volume = {61},
number = {4},
pages = {593-605},
pmid = {32851593},
issn = {2190-3883},
mesh = {Animals ; Archaea/genetics/*isolation &amp; purification ; Bacteria/genetics/*isolation &amp; purification ; Breeding ; Cattle ; Feces/microbiology ; Female ; High-Throughput Nucleotide Sequencing ; Lactation/*genetics ; Microbiota/*genetics ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The aim of this study was to describe the fecal bacteria and archaea composition of Holstein-Friesian and Simmental heifers and lactating cows, using 16S rRNA gene sequencing. Bacteria and archaea communities were characterized and compared between heifers and cows of the same breed. Two breeds from different farms were considered, just to speculate about the conservation of the microbiome differences between cows and heifers that undergo different management conditions. The two breeds were from two different herds. Firmicutes, Bacteroidetes, Actinobacteria, and Proteobacteria were the most abundant phyla in all experimental groups. Alpha- and beta-diversity metrics showed significant differences between heifers and cows within the same breed, supported by principal coordinate analysis. The analysis of Holstein-Friesian fecal microbiome composition revealed 3 different bacteria families, 2 genera, and 2 species that differed between heifers and cows; on the other hand, Simmental heifers and cows differed only for one bacteria family, one archaeal genus, and one bacteria species. Results of the present study suggest that fecal communities of heifers and cows are different, and that fecal microbiome is maintained across experimental groups.},
}
@article {pmid32849470,
year = {2020},
author = {Nagler, M and Podmirseg, SM and Mayr, M and Ascher-Jenull, J and Insam, H},
title = {Quantities of Intra- and Extracellular DNA Reveal Information About Activity and Physiological State of Methanogenic Archaea.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {1894},
pmid = {32849470},
issn = {1664-302X},
abstract = {Although being a common aim of many microbial ecology studies, measuring individual physiological conditions of a microbial group or species within a complex consortium is still a challenge. Here, we propose a novel approach that is based on the quantification of sequentially extracted extracellular (exDNA) and intracellular DNA (iDNA) and reveals information about cell lysis and activity of methanogenic archaea within a biogas-producing microbial community. We monitored the methane production rates of differently treated batch anaerobic cultures and compared the concentrations of the alpha subunit of the methyl coenzyme M reductase gene of methanogenic archaea in extracellular and intracellular DNA fractions and in the classically extracted total DNA pool. Our results showed that this fine-tuned DNA approach coupled with the interpretation of the ratio between free exDNA and iDNA considerably improved microbial activity tracking compared to the classical extraction/quantification of total DNA. Additionally, it allowed to identify and quantify methanogenic populations that are inactive and those that are strongly influenced by cell lysis. We argue that despite the need of further studies, this method represents a novel approach to gain specific physiological information from a complex environmental sample and holds the potential to be applied to other microbes of interest.},
}
@article {pmid32829441,
year = {2021},
author = {Silveira, R and Silva, MRSS and de Roure Bandeira de Mello, T and Alvim, EACC and Marques, NCS and Kruger, RH and da Cunha Bustamante, MM},
title = {Bacteria and Archaea Communities in Cerrado Natural Pond Sediments.},
journal = {Microbial ecology},
volume = {81},
number = {3},
pages = {563-578},
pmid = {32829441},
issn = {1432-184X},
support = {process number 193.000.567/2009//Funda&#xe7;&#xe3;o de Apoio &#xe0; Pesquisa do Distrito Federal/ ; },
mesh = {*Archaea/genetics ; Bacteria/genetics ; Biodiversity ; Geologic Sediments ; Phylogeny ; *Ponds ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Natural ponds in the Brazilian Cerrado harbor high biodiversity but are still poorly studied, especially their microbial assemblage. The characterization of the microbial community in aquatic environments is fundamental for understanding its functioning, particularly under the increasing pressure posed by land conversion and climate change. Here, we aim to characterize the structure (abundance, richness, and diversity) and composition of the Bacteria and Archaea in the sediment of two natural ponds belonging to different basins that primarily differ in size and depth in the Cerrado. Sediment samples were collected in the dry and rainy seasons and the transition periods between both. The structure and composition of Bacteria and Archaea were assessed by 16S rRNA gene pyrosequencing. We identified 45 bacterial and four archaeal groups. Proteobacteria and Acidobacteria dominated the bacterial community, while Euryarchaeota and Thaumarchaeota dominated the archaeal community. Seasonal fluctuations in the relative abundance of microbial taxa were observed, but pond characteristics were more determinant to community composition differences. Microbial communities are highly diverse, and local variability could partially explain the microbial structure's main differences. Functional predictions based in 16S rRNA gene accessed with Tax4Fun indicated an enriched abundance of predicted methane metabolism in the deeper pond, where higher abundance of methanogenic archaea Methanocella, Methanosaeta, and Methanomicrobiaceae was detected. Our dataset encompasses the more comprehensive survey of prokaryotic microbes in Cerrado's aquatic environments. Here, we present basic and essential information about composition and diversity, for initial insights into the ecology of Bacteria and Archaea in these environments.},
}
@article {pmid32826220,
year = {2020},
author = {Dhamad, AE and Lessner, DJ},
title = {A CRISPRi-dCas9 System for Archaea and Its Use To Examine Gene Function during Nitrogen Fixation by Methanosarcina acetivorans.},
journal = {Applied and environmental microbiology},
volume = {86},
number = {21},
pages = {},
pmid = {32826220},
issn = {1098-5336},
mesh = {Archaeal Proteins/*genetics/metabolism ; *CRISPR-Cas Systems ; Gene Expression ; Genes, Archaeal/*genetics ; Methanosarcina/*genetics/metabolism ; Nitrogen Fixation/*genetics ; },
abstract = {CRISPR-based systems are emerging as the premier method to manipulate many cellular processes. In this study, a simple and efficient CRISPR interference (CRISPRi) system for targeted gene repression in archaea was developed. The Methanosarcina acetivorans CRISPR-Cas9 system was repurposed by replacing Cas9 with the catalytically dead Cas9 (dCas9) to generate a CRISPRi-dCas9 system for targeted gene repression. To test the utility of the system, genes involved in nitrogen (N2) fixation were targeted for dCas9-mediated repression. First, the nif operon (nifHI1I2DKEN) that encodes molybdenum nitrogenase was targeted by separate guide RNAs (gRNAs), one targeting the promoter and the other targeting nifD Remarkably, growth of M. acetivorans with N2 was abolished by dCas9-mediated repression of the nif operon with each gRNA. The abundance of nif transcripts was >90% reduced in both strains expressing the gRNAs, and NifD was not detected in cell lysate. Next, we targeted NifB, which is required for nitrogenase cofactor biogenesis. Expression of a gRNA targeting the coding sequence of NifB decreased nifB transcript abundance >85% and impaired but did not abolish growth of M. acetivorans with N2 Finally, to ascertain the ability to study gene regulation using CRISPRi-dCas9, nrpR1, encoding a subunit of the repressor of the nif operon, was targeted. The nrpR1 repression strain grew normally with N2 but had increased nif operon transcript abundance, consistent with NrpR1 acting as a repressor. These results highlight the utility of the system, whereby a single gRNA when expressed with dCas9 can block transcription of targeted genes and operons in M. acetivoransIMPORTANCE Genetic tools are needed to understand and manipulate the biology of archaea, which serve critical roles in the biosphere. Methanogenic archaea (methanogens) are essential for the biological production of methane, an intermediate in the global carbon cycle, an important greenhouse gas, and a biofuel. The CRISPRi-dCas9 system in the model methanogen Methanosarcina acetivorans is, to our knowledge, the first Cas9-based CRISPR interference system in archaea. Results demonstrate that the system is remarkably efficient in targeted gene repression and provide new insight into nitrogen fixation by methanogens, the only archaea with nitrogenase. Overall, the CRISPRi-dCas9 system provides a simple, yet powerful, genetic tool to control the expression of target genes and operons in methanogens.},
}
@article {pmid32822422,
year = {2020},
author = {Flores-Bautista, E and Hernandez-Guerrero, R and Huerta-Saquero, A and Tenorio-Salgado, S and Rivera-Gomez, N and Romero, A and Ibarra, JA and Perez-Rueda, E},
title = {Deciphering the functional diversity of DNA-binding transcription factors in Bacteria and Archaea organisms.},
journal = {PloS one},
volume = {15},
number = {8},
pages = {e0237135},
pmid = {32822422},
issn = {1932-6203},
mesh = {Archaea/*genetics/pathogenicity ; Archaeal Proteins/*genetics/metabolism ; Bacterial Proteins/*genetics/metabolism ; Binding Sites ; DNA, Archaeal/metabolism ; DNA, Bacterial/metabolism ; DNA-Binding Proteins/*genetics/metabolism ; Escherichia coli K12/*genetics/pathogenicity ; Gene Expression Regulation, Archaeal ; Gene Expression Regulation, Bacterial ; Genome, Archaeal ; Genome, Bacterial ; Protein Binding ; Transcription Factors/*genetics/metabolism ; Virulence/genetics ; },
abstract = {DNA-binding Transcription Factors (TFs) play a central role in regulation of gene expression in prokaryotic organisms, and similarities at the sequence level have been reported. These proteins are predicted with different abundances as a consequence of genome size, where small organisms contain a low proportion of TFs and large genomes contain a high proportion of TFs. In this work, we analyzed a collection of 668 experimentally validated TFs across 30 different species from diverse taxonomical classes, including Escherichia coli K-12, Bacillus subtilis 168, Corynebacterium glutamicum, and Streptomyces coelicolor, among others. This collection of TFs, together with 111 hidden Markov model profiles associated with DNA-binding TFs collected from diverse databases such as PFAM and DBD, was used to identify the repertoire of proteins putatively devoted to gene regulation in 1321 representative genomes of Archaea and Bacteria. The predicted regulatory proteins were posteriorly analyzed in terms of their genomic context, allowing the prediction of functions for TFs and their neighbor genes, such as genes involved in virulence, enzymatic functions, phosphorylation mechanisms, and antibiotic resistance. The functional analysis associated with PFAM groups showed diverse functional categories were significantly enriched in the collection of TFs and the proteins encoded by the neighbor genes, in particular, small-molecule binding and amino acid transmembrane transporter activities associated with the LysR family and proteins devoted to cellular aromatic compound metabolic processes or responses to drugs, stress, or abiotic stimuli in the MarR family. We consider that with the increasing data derived from new technologies, novel TFs can be identified and help improve the predictions for this class of proteins in complete genomes. The complete collection of experimentally characterized and predicted TFs is available at http://web.pcyt.unam.mx/EntrafDB/.},
}
@article {pmid32817089,
year = {2020},
author = {Fonseca, DR and Halim, MFA and Holten, MP and Costa, KC},
title = {Type IV-Like Pili Facilitate Transformation in Naturally Competent Archaea.},
journal = {Journal of bacteriology},
volume = {202},
number = {21},
pages = {},
pmid = {32817089},
issn = {1098-5530},
mesh = {Archaeal Proteins/*metabolism ; *DNA, Archaeal ; *Gene Transfer, Horizontal ; Methanococcus/*genetics ; Methanomicrobiaceae/*genetics ; },
abstract = {Naturally competent organisms are capable of DNA uptake directly from the environment through the process of transformation. Despite the importance of transformation to microbial evolution, DNA uptake remains poorly characterized outside of the bacterial domain. Here, we identify the pilus as a necessary component of the transformation machinery in archaea. We describe two naturally competent organisms, Methanococcus maripaludis and Methanoculleus thermophilus In M. maripaludis, replicative vectors were transferred with an average efficiency of 2.4 × 10[3] transformants μg[-1] DNA. In M. thermophilus, integrative vectors were transferred with an average efficiency of 2.7 × 10[3] transformants μg[-1] DNA. Additionally, natural transformation of M. thermophilus could be used to introduce chromosomal mutations. To our knowledge, this is the first demonstration of a method to introduce targeted mutations in a member of the order Methanomicrobiales For both organisms, mutants lacking structural components of the type IV-like pilus filament were defective for DNA uptake, demonstrating the importance of pili for natural transformation. Interestingly, competence could be induced in a noncompetent strain of M. maripaludis by expressing pilin genes from a replicative vector. These results expand the known natural competence pili to include examples from the archaeal domain and highlight the importance of pili for DNA uptake in diverse microbial organisms.IMPORTANCE Microbial organisms adapt and evolve by acquiring new genetic material through horizontal gene transfer. One way that this occurs is natural transformation, the direct uptake and genomic incorporation of environmental DNA by competent organisms. Archaea represent up to a third of the biodiversity on Earth, yet little is known about transformation in these organisms. Here, we provide the first characterization of a component of the archaeal DNA uptake machinery. We show that the type IV-like pilus is essential for natural transformation in two archaeal species. This suggests that pili are important for transformation across the tree of life and further expands our understanding of gene flow in archaea.},
}
@article {pmid32812678,
year = {2020},
author = {Wang, K and Yan, H and Peng, X and Hu, H and Zhang, H and Hou, D and Chen, W and Qian, P and Liu, J and Cai, J and Chai, X and Zhang, D},
title = {Community assembly of bacteria and archaea in coastal waters governed by contrasting mechanisms: A seasonal perspective.},
journal = {Molecular ecology},
volume = {29},
number = {19},
pages = {3762-3776},
doi = {10.1111/mec.15600},
pmid = {32812678},
issn = {1365-294X},
mesh = {*Archaea/genetics ; *Bacteria/genetics ; China ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seasons ; },
abstract = {Marine planktonic bacteria and archaea commonly exhibit pronounced seasonal succession in community composition. But the existence of seasonality in their assembly processes and between-domain differences in underlying mechanism are largely unassessed. Using a high-coverage sampling strategy (including single sample for each station during four cruises in different seasons), 16S rRNA gene sequencing, and null models, we investigated seasonal patterns in the processes governing spatial turnover of bacteria and archaea in surface coastal waters across a sampling grid over ~300 km in the East China Sea. We found that archaea only bloomed in prokaryotic communities during autumn and winter cruises. Seasonality mostly overwhelmed spatial variability in the compositions of both domains. Bacterial and archaeal communities were dominantly governed by deterministic and stochastic assembly processes, respectively, in autumn cruise, probably due to the differences in niche breadths (bacteria < archaea) and relative abundance (bacteria > archaea). Stochasticity dominated assembly mechanisms of both domains but was driven by distinct processes in winter cruise. Determinism-dominated assembly mechanisms of bacteria rebounded in spring and summer cruises, reflecting seasonal variability in bacterial community assembly. This could be attributed to seasonal changes in bacterial niche breadths and habitat heterogeneity across the study area. There were seasonal changes in environmental factors mediating the determinism-stochasticity balance of bacterial community assembly, holding a probability of the existence of unmeasured mediators. Our results suggest contrasting assembly mechanisms of bacteria and archaea in terms of determinism-vs.-stochasticity pattern and its seasonality, highlighting the importance of seasonal perspective on microbial community assembly in marine ecosystems.},
}
@article {pmid32788376,
year = {2020},
author = {Darnell, CL and Zheng, J and Wilson, S and Bertoli, RM and Bisson-Filho, AW and Garner, EC and Schmid, AK},
title = {The Ribbon-Helix-Helix Domain Protein CdrS Regulates the Tubulin Homolog ftsZ2 To Control Cell Division in Archaea.},
journal = {mBio},
volume = {11},
number = {4},
pages = {},
pmid = {32788376},
issn = {2150-7511},
support = {/WT_/Wellcome Trust/United Kingdom ; DP2 AI117923/AI/NIAID NIH HHS/United States ; 203276/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Archaea/*genetics/growth &amp; development ; Archaeal Proteins/*genetics ; Cell Division/*genetics ; *Gene Expression Regulation, Archaeal ; Protein Domains ; Transcription Factors/*genetics ; Transcription, Genetic ; },
abstract = {Precise control of the cell cycle is central to the physiology of all cells. In prior work we demonstrated that archaeal cells maintain a constant size; however, the regulatory mechanisms underlying the cell cycle remain unexplored in this domain of life. Here, we use genetics, functional genomics, and quantitative imaging to identify and characterize the novel CdrSL gene regulatory network in a model species of archaea. We demonstrate the central role of these ribbon-helix-helix family transcription factors in the regulation of cell division through specific transcriptional control of the gene encoding FtsZ2, a putative tubulin homolog. Using time-lapse fluorescence microscopy in live cells cultivated in microfluidics devices, we further demonstrate that FtsZ2 is required for cell division but not elongation. The cdrS-ftsZ2 locus is highly conserved throughout the archaeal domain, and the central function of CdrS in regulating cell division is conserved across hypersaline adapted archaea. We propose that the CdrSL-FtsZ2 transcriptional network coordinates cell division timing with cell growth in archaea.IMPORTANCE Healthy cell growth and division are critical for individual organism survival and species long-term viability. However, it remains unknown how cells of the domain Archaea maintain a healthy cell cycle. Understanding the archaeal cell cycle is of paramount evolutionary importance given that an archaeal cell was the host of the endosymbiotic event that gave rise to eukaryotes. Here, we identify and characterize novel molecular players needed for regulating cell division in archaea. These molecules dictate the timing of cell septation but are dispensable for growth between divisions. Timing is accomplished through transcriptional control of the cell division ring. Our results shed light on mechanisms underlying the archaeal cell cycle, which has thus far remained elusive.},
}
@article {pmid32785681,
year = {2020},
author = {Penev, PI and Fakhretaha-Aval, S and Patel, VJ and Cannone, JJ and Gutell, RR and Petrov, AS and Williams, LD and Glass, JB},
title = {Supersized Ribosomal RNA Expansion Segments in Asgard Archaea.},
journal = {Genome biology and evolution},
volume = {12},
number = {10},
pages = {1694-1710},
pmid = {32785681},
issn = {1759-6653},
support = {80NSSC18K1139/ImNASA/Intramural NASA/United States ; },
mesh = {Archaea/*chemistry/genetics ; *Evolution, Molecular ; *Models, Molecular ; *RNA Folding ; RNA, Ribosomal/*chemistry/genetics ; },
abstract = {The ribosome's common core, comprised of ribosomal RNA (rRNA) and universal ribosomal proteins, connects all life back to a common ancestor and serves as a window to relationships among organisms. The rRNA of the common core is similar to rRNA of extant bacteria. In eukaryotes, the rRNA of the common core is decorated by expansion segments (ESs) that vastly increase its size. Supersized ESs have not been observed previously in Archaea, and the origin of eukaryotic ESs remains enigmatic. We discovered that the large ribosomal subunit (LSU) rRNA of two Asgard phyla, Lokiarchaeota and Heimdallarchaeota, considered to be the closest modern archaeal cell lineages to Eukarya, bridge the gap in size between prokaryotic and eukaryotic LSU rRNAs. The elongated LSU rRNAs in Lokiarchaeota and Heimdallarchaeota stem from two supersized ESs, called ES9 and ES39. We applied chemical footprinting experiments to study the structure of Lokiarchaeota ES39. Furthermore, we used covariation and sequence analysis to study the evolution of Asgard ES39s and ES9s. By defining the common eukaryotic ES39 signature fold, we found that Asgard ES39s have more and longer helices than eukaryotic ES39s. Although Asgard ES39s have sequences and structures distinct from eukaryotic ES39s, we found overall conservation of a three-way junction across the Asgard species that matches eukaryotic ES39 topology, a result consistent with the accretion model of ribosomal evolution.},
}
@article {pmid32783333,
year = {2020},
author = {Aigle, A and Gubry-Rangin, C and Thion, C and Estera-Molina, KY and Richmond, H and Pett-Ridge, J and Firestone, MK and Nicol, GW and Prosser, JI},
title = {Experimental testing of hypotheses for temperature- and pH-based niche specialization of ammonia oxidizing archaea and bacteria.},
journal = {Environmental microbiology},
volume = {22},
number = {9},
pages = {4032-4045},
doi = {10.1111/1462-2920.15192},
pmid = {32783333},
issn = {1462-2920},
support = {//AXA Research Fund/International ; DOE Contract DE-AC52- 07NA27344, award SCW1632//Lawrence Livermore National Laboratory/International ; NE/L006286/1//Natural Environment Research Council/International ; UF150571//Royal Society/International ; },
mesh = {Ammonia/*metabolism ; Archaea/genetics/isolation &amp; purification/*metabolism ; Bacteria/genetics/isolation &amp; purification/*metabolism ; Hydrogen-Ion Concentration ; Microbiota ; Nitrification ; Oxidation-Reduction ; Soil/*chemistry ; *Soil Microbiology ; Temperature ; },
abstract = {Investigation of niche specialization in microbial communities is important in assessing consequences of environmental change for ecosystem processes. Ammonia oxidizing bacteria (AOB) and archaea (AOA) present a convenient model for studying niche specialization. They coexist in most soils and effects of soil characteristics on their relative abundances have been studied extensively. This study integrated published information on the influence of temperature and pH on AOB and AOA into several hypotheses, generating predictions that were tested in soil microcosms. The influence of perturbations in temperature was determined in pH 4.5, 6 and 7.5 soils and perturbations in pH were investigated at 15°C, 25°C and 35°C. AO activities were determined by analysing changes in amoA gene and transcript abundances, stable isotope probing and nitrate production. Experimental data supported major predictions of the effects of temperature and pH, but with several significant discrepancies, some of which may have resulted from experimental limitations. The study also provided evidence for unpredicted activity of AOB in pH 4.5 soil. Other discrepancies highlighted important deficiencies in current knowledge, particularly lack of consideration of niche overlap and the need to consider combinations of factors when assessing the influence of environmental change on microbial communities and their activities.},
}
@article {pmid32772189,
year = {2020},
author = {Alori, ET and Emmanuel, OC and Glick, BR and Babalola, OO},
title = {Plant-archaea relationships: a potential means to improve crop production in arid and semi-arid regions.},
journal = {World journal of microbiology &amp; biotechnology},
volume = {36},
number = {9},
pages = {133},
doi = {10.1007/s11274-020-02910-6},
pmid = {32772189},
issn = {1573-0972},
mesh = {Agriculture ; Archaea/classification/*physiology ; Crop Production ; Microbiota ; *Plant Development ; Plant Roots/microbiology ; Plants/*microbiology ; Soil Microbiology ; },
abstract = {Crop production in arid and semi-arid regions of the world is limited by several abiotic factors, including water stress, temperature extremes, low soil fertility, high soil pH, low soil water-holding capacity, and low soil organic matter. Moreover, arid and semi-arid areas experience low levels of rainfall with high spatial and temporal variability. Also, the indiscriminate use of chemicals, a practice that characterizes current agricultural practice, promotes crop and soil pollution potentially resulting in serious human health and environmental hazards. A reliable and sustainable alternative to current farming practice is, therefore, a necessity. One such option includes the use of plant growth-promoting microbes that can help to ameliorate some of the adverse effects of these multiple stresses. In this regard, archaea, functional components of the plant microbiome that are found both in the rhizosphere and the endosphere may contribute to the promotion of plant growth. Archaea can survive in extreme habitats such as areas with high temperatures and hypersaline water. No cases of archaea pathogenicity towards plants have been reported. Archaea appear to have the potential to promote plant growth, improve nutrient supply and protect plants against various abiotic stresses. A better understanding of recent developments in archaea functional diversity, plant colonizing ability, and modes of action could facilitate their eventual usage as reliable components of sustainable agricultural systems. The research discussed herein, therefore, addresses the potential role of archaea to improve sustainable crop production in arid and semi-arid areas.},
}
@article {pmid32770005,
year = {2020},
author = {Yang, S and Lv, Y and Liu, X and Wang, Y and Fan, Q and Yang, Z and Boon, N and Wang, F and Xiao, X and Zhang, Y},
title = {Genomic and enzymatic evidence of acetogenesis by anaerobic methanotrophic archaea.},
journal = {Nature communications},
volume = {11},
number = {1},
pages = {3941},
pmid = {32770005},
issn = {2041-1723},
mesh = {Acetates/*metabolism ; Anaerobiosis ; Archaea/*enzymology/genetics ; Bacterial Proteins/genetics/*metabolism ; Carbon Cycle/physiology ; Coenzyme A Ligases/genetics/*metabolism ; Genome, Archaeal ; Geologic Sediments/microbiology ; Metabolic Networks and Pathways/genetics ; Methane/*metabolism ; Oxidation-Reduction ; Seawater/microbiology ; },
abstract = {Anaerobic oxidation of methane (AOM) mediated by anaerobic methanotrophic archaea (ANME) is the primary process that provides energy to cold seep ecosystems by converting methane into inorganic carbon. Notably, cold seep ecosystems are dominated by highly divergent heterotrophic microorganisms. The role of the AOM process in supporting heterotrophic population remains unknown. We investigate the acetogenic capacity of ANME-2a in a simulated cold seep ecosystem using high-pressure biotechnology, where both AOM activity and acetate production are detected. The production of acetate from methane is confirmed by isotope-labeling experiments. A complete archaeal acetogenesis pathway is identified in the ANME-2a genome, and apparent acetogenic activity of the key enzymes ADP-forming acetate-CoA ligase and acetyl-CoA synthetase is demonstrated. Here, we propose a modified model of carbon cycling in cold seeps: during AOM process, methane can be converted into organic carbon, such as acetate, which further fuels the heterotrophic community in the ecosystem.},
}
@article {pmid32761262,
year = {2020},
author = {Sutter, JM and Johnsen, U and Reinhardt, A and Schönheit, P},
title = {Pentose degradation in archaea: Halorhabdus species degrade D-xylose, L-arabinose and D-ribose via bacterial-type pathways.},
journal = {Extremophiles : life under extreme conditions},
volume = {24},
number = {5},
pages = {759-772},
pmid = {32761262},
issn = {1433-4909},
support = {SCHO 316/11-1//Deutsche Forschungsgemeinschaft/ ; },
mesh = {*Arabinose/metabolism ; Bacteria ; *Halobacteriaceae/enzymology ; Pentoses ; Ribose ; *Xylose/metabolism ; },
abstract = {The degradation of the pentoses D-xylose, L-arabinose and D-ribose in the domain of archaea, in Haloferax volcanii and in Haloarcula and Sulfolobus species, has been shown to proceed via oxidative pathways to generate α-ketoglutarate. Here, we report that the haloarchaeal Halorhabdus species utilize the bacterial-type non-oxidative degradation pathways for pentoses generating xylulose-5-phosphate. The genes of these pathways are each clustered and were constitutively expressed. Selected enzymes involved in D-xylose degradation, xylose isomerase and xylulokinase, and those involved in L-arabinose degradation, arabinose isomerase and ribulokinase, were characterized. Further, D-ribose degradation in Halorhabdus species involves ribokinase, ribose-5-phosphate isomerase and D-ribulose-5-phosphate-3-epimerase. Ribokinase of Halorhabdus tiamatea and ribose-5-phosphate isomerase of Halorhabdus utahensis were characterized. This is the first report of pentose degradation via the bacterial-type pathways in archaea, in Halorhabdus species that likely acquired these pathways from bacteria. The utilization of bacterial-type pathways of pentose degradation rather than the archaeal oxidative pathways generating α-ketoglutarate might be explained by an incomplete gluconeogenesis in Halorhabdus species preventing the utilization of α-ketoglutarate in the anabolism.},
}
@article {pmid32759221,
year = {2020},
author = {Wang, F and Baquero, DP and Beltran, LC and Su, Z and Osinski, T and Zheng, W and Prangishvili, D and Krupovic, M and Egelman, EH},
title = {Structures of filamentous viruses infecting hyperthermophilic archaea explain DNA stabilization in extreme environments.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {117},
number = {33},
pages = {19643-19652},
pmid = {32759221},
issn = {1091-6490},
support = {R35 GM122510/GM/NIGMS NIH HHS/United States ; HHSN261200800001E/CA/NCI NIH HHS/United States ; },
mesh = {Archaeal Viruses/*chemistry/classification/genetics/ultrastructure ; Biological Evolution ; Capsid/chemistry/ultrastructure ; DNA Viruses/*chemistry/classification/genetics/ultrastructure ; DNA, Viral/*chemistry/genetics ; Extreme Environments ; Genome, Viral ; Phylogeny ; Sulfolobales/*virology ; Sulfolobus/*virology ; },
abstract = {Living organisms expend metabolic energy to repair and maintain their genomes, while viruses protect their genetic material by completely passive means. We have used cryo-electron microscopy (cryo-EM) to solve the atomic structures of two filamentous double-stranded DNA viruses that infect archaeal hosts living in nearly boiling acid: Saccharolobus solfataricus rod-shaped virus 1 (SSRV1), at 2.8-Å resolution, and Sulfolobus islandicus filamentous virus (SIFV), at 4.0-Å resolution. The SIFV nucleocapsid is formed by a heterodimer of two homologous proteins and is membrane enveloped, while SSRV1 has a nucleocapsid formed by a homodimer and is not enveloped. In both, the capsid proteins wrap around the DNA and maintain it in an A-form. We suggest that the A-form is due to both a nonspecific desolvation of the DNA by the protein, and a specific coordination of the DNA phosphate groups by positively charged residues. We extend these observations by comparisons with four other archaeal filamentous viruses whose structures we have previously determined, and show that all 10 capsid proteins (from four heterodimers and two homodimers) have obvious structural homology while sequence similarity can be nonexistent. This arises from most capsid residues not being under any strong selective pressure. The inability to detect homology at the sequence level arises from the sampling of viruses in this part of the biosphere being extremely sparse. Comparative structural and genomic analyses suggest that nonenveloped archaeal viruses have evolved from enveloped viruses by shedding the membrane, indicating that this trait may be relatively easily lost during virus evolution.},
}
@article {pmid32756530,
year = {2020},
author = {Pedone, E and Fiorentino, G and Bartolucci, S and Limauro, D},
title = {Enzymatic Antioxidant Signatures in Hyperthermophilic Archaea.},
journal = {Antioxidants (Basel, Switzerland)},
volume = {9},
number = {8},
pages = {},
pmid = {32756530},
issn = {2076-3921},
support = {MIUR 2017-JTNK78.006//"FLAshMoB: FunctionalAmyloid Chimera for Marine Biosensing"; GoodbyWaste: ObtainGOOD products - exploit BY-products - reduce WASTE, MIUR 2017-JTNK78.006, Italy/ ; FFABR 2017//Fondo per il Finanziamento delleAttivita' Base di Ricerca (FFABR 2017) Ministero dell'Universit&#xe0; e della Ricerca (MIUR) Italy/ ; },
abstract = {To fight reactive oxygen species (ROS) produced by both the metabolism and strongly oxidative habitats, hyperthermophilic archaea are equipped with an array of antioxidant enzymes whose role is to protect the biological macromolecules from oxidative damage. The most common ROS, such as superoxide radical (O2[-.]) and hydrogen peroxide (H2O2), are scavenged by superoxide dismutase, peroxiredoxins, and catalase. These enzymes, together with thioredoxin, protein disulfide oxidoreductase, and thioredoxin reductase, which are involved in redox homeostasis, represent the core of the antioxidant system. In this review, we offer a panorama of progression of knowledge on the antioxidative system in aerobic or microaerobic (hyper)thermophilic archaea and possible industrial applications of these enzymes.},
}
@article {pmid32747565,
year = {2020},
author = {Akıl, C and Tran, LT and Orhant-Prioux, M and Baskaran, Y and Manser, E and Blanchoin, L and Robinson, RC},
title = {Insights into the evolution of regulated actin dynamics via characterization of primitive gelsolin/cofilin proteins from Asgard archaea.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {117},
number = {33},
pages = {19904-19913},
pmid = {32747565},
issn = {1091-6490},
mesh = {Actin Depolymerizing Factors/chemistry/genetics/*metabolism ; Actins/chemistry/genetics/*metabolism ; Amino Acid Sequence ; Archaea/chemistry/genetics/*metabolism ; Archaeal Proteins/chemistry/genetics/*metabolism ; Cytoskeleton/chemistry/genetics/metabolism ; Evolution, Molecular ; Gelsolin/chemistry/genetics/*metabolism ; Genome, Archaeal ; Polymerization ; Protein Conformation, alpha-Helical ; Sequence Alignment ; },
abstract = {Asgard archaea genomes contain potential eukaryotic-like genes that provide intriguing insight for the evolution of eukaryotes. The eukaryotic actin polymerization/depolymerization cycle is critical for providing force and structure in many processes, including membrane remodeling. In general, Asgard genomes encode two classes of actin-regulating proteins from sequence analysis, profilins and gelsolins. Asgard profilins were demonstrated to regulate actin filament nucleation. Here, we identify actin filament severing, capping, annealing and bundling, and monomer sequestration activities by gelsolin proteins from Thorarchaeota (Thor), which complete a eukaryotic-like actin depolymerization cycle, and indicate complex actin cytoskeleton regulation in Asgard organisms. Thor gelsolins have homologs in other Asgard archaea and comprise one or two copies of the prototypical gelsolin domain. This appears to be a record of an initial preeukaryotic gene duplication event, since eukaryotic gelsolins are generally comprise three to six domains. X-ray structures of these proteins in complex with mammalian actin revealed similar interactions to the first domain of human gelsolin or cofilin with actin. Asgard two-domain, but not one-domain, gelsolins contain calcium-binding sites, which is manifested in calcium-controlled activities. Expression of two-domain gelsolins in mammalian cells enhanced actin filament disassembly on ionomycin-triggered calcium release. This functional demonstration, at the cellular level, provides evidence for a calcium-controlled Asgard actin cytoskeleton, indicating that the calcium-regulated actin cytoskeleton predates eukaryotes. In eukaryotes, dynamic bundled actin filaments are responsible for shaping filopodia and microvilli. By correlation, we hypothesize that the formation of the protrusions observed from Lokiarchaeota cell bodies may involve the gelsolin-regulated actin structures.},
}
@article {pmid32714287,
year = {2020},
author = {Zhang, L and Jiang, D and Wu, M and Yang, Z and Oger, PM},
title = {New Insights Into DNA Repair Revealed by NucS Endonucleases From Hyperthermophilic Archaea.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {1263},
pmid = {32714287},
issn = {1664-302X},
abstract = {Hyperthermophilic Archaea (HA) thrive in high temperature environments and their genome is facing severe stability challenge due to the increased DNA damage levels caused by high temperature. Surprisingly, HA display spontaneous mutation frequencies similar to mesophilic microorganisms, thereby indicating that the former must possess more efficient DNA repair systems than the latter to counteract the potentially enhanced mutation rates under the harsher environment. Although a few repair proteins or enzymes from HA have been biochemically and structurally characterized, the molecular mechanisms of DNA repair of HA remain largely unknown. Genomic analyses of HA revealed that they lack MutS/MutL homologues of the mismatch repair (MMR) pathway and the recognition proteins of the nucleotide excision repair (NER) pathway. Endonucleases play an essential role in DNA repair. NucS endonuclease, a novel endonuclease recently identified in some HA and bacteria, has been shown to act on branched, mismatched, and deaminated DNA, suggesting that this endonuclease is a multifunctional enzyme involved in NER, MMR, and deaminated base repair in a non-canonical manner. However, the catalytic mechanism and the physiological function of NucS endonucleases from HA need to be further clarified to determine how they participate in the different DNA repair pathways in cells from HA. In this review, we focus on recent advances in our understanding of the function of NucS endonucleases from HA in NER, MMR, and deaminated DNA repair, and propose directions for future studies of the NucS family of endonucleases.},
}
@article {pmid32691824,
year = {2020},
author = {Charlesworth, J and Kimyon, O and Manefield, M and Beloe, CJ and Burns, BP},
title = {Archaea join the conversation: detection of AHL-like activity across a range of archaeal isolates.},
journal = {FEMS microbiology letters},
volume = {367},
number = {16},
pages = {},
doi = {10.1093/femsle/fnaa123},
pmid = {32691824},
issn = {1574-6968},
mesh = {Archaea/*physiology ; Biosensing Techniques ; Plasmids/genetics ; Quorum Sensing/*genetics ; Signal Transduction ; },
abstract = {Quorum sensing is a mechanism of genetic control allowing single cell organisms to coordinate phenotypic response(s) across a local population and is often critical for ecosystem function. Although quorum sensing has been extensively studied in bacteria comparatively less is known about this mechanism in Archaea. Given the growing significance of Archaea in both natural and anthropogenic settings, it is important to delineate how widespread this phenomenon of signaling is in this domain. Employing a plasmid-based AHL biosensor in conjunction with thin-layer chromatography (TLC), the present study screened a broad range of euryarchaeota isolates for potential signaling activity. Data indicated the presence of 11 new Archaeal isolates with AHL-like activity against the LuxR-based AHL biosensor, including for the first time putative AHL activity in a thermophile. The presence of multiple signals and distinct changes between growth phases were also shown via TLC. Multiple signal molecules were detected using TLC in Haloferax mucosum, Halorubrum kocurii, Natronococcus occultus and Halobacterium salinarium. The finding of multiple novel signal producers suggests the potential for quorum sensing to play an important role not only in the regulation of complex phenotypes within Archaea but the potential for cross-talk with bacterial systems.},
}
@article {pmid32674430,
year = {2020},
author = {Hogrel, G and Lu, Y and Alexandre, N and Bossé, A and Dulermo, R and Ishino, S and Ishino, Y and Flament, D},
title = {Role of RadA and DNA Polymerases in Recombination-Associated DNA Synthesis in Hyperthermophilic Archaea.},
journal = {Biomolecules},
volume = {10},
number = {7},
pages = {},
pmid = {32674430},
issn = {2218-273X},
support = {-//Institut Fran&#xe7;ais de Recherche pour l'Exploitation de la Mer/International ; -//LIA1211 MICROBSEA/International ; },
mesh = {Archaeal Proteins/*metabolism ; DNA Polymerase III/*metabolism ; DNA Polymerase beta/*metabolism ; DNA Replication ; DNA, Archaeal/chemistry/*metabolism ; DNA-Binding Proteins/*metabolism ; Homologous Recombination ; Nucleic Acid Conformation ; Pyrococcus abyssi/*genetics/metabolism ; },
abstract = {Among the three domains of life, the process of homologous recombination (HR) plays a central role in the repair of double-strand DNA breaks and the restart of stalled replication forks. Curiously, main protein actors involved in the HR process appear to be essential for hyperthermophilic Archaea raising interesting questions about the role of HR in replication and repair strategies of those Archaea living in extreme conditions. One key actor of this process is the recombinase RadA, which allows the homologous strand search and provides a DNA substrate required for following DNA synthesis and restoring genetic information. DNA polymerase operation after the strand exchange step is unclear in Archaea. Working with Pyrococcus abyssi proteins, here we show that both DNA polymerases, family-B polymerase (PolB) and family-D polymerase (PolD), can take charge of processing the RadA-mediated recombination intermediates. Our results also indicate that PolD is far less efficient, as compared with PolB, to extend the invaded DNA at the displacement-loop (D-loop) substrate. These observations coincide with previous genetic analyses obtained on Thermococcus species showing that PolB is mainly involved in DNA repair without being essential probably because PolD could take over combined with additional partners.},
}
@article {pmid32671380,
year = {2021},
author = {Rasmussen, M and Collin, M},
title = {Archaea in Blood Cultures: Coincidence or Coinfection?.},
journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America},
volume = {73},
number = {9},
pages = {e2580-e2581},
doi = {10.1093/cid/ciaa993},
pmid = {32671380},
issn = {1537-6591},
mesh = {Archaea ; *Bacteremia ; Blood Culture ; *Coinfection ; Humans ; *Staphylococcal Infections ; },
}
@article {pmid32657581,
year = {2020},
author = {Wu, L and Chen, X and Wei, W and Liu, Y and Wang, D and Ni, BJ},
title = {A Critical Review on Nitrous Oxide Production by Ammonia-Oxidizing Archaea.},
journal = {Environmental science &amp; technology},
volume = {54},
number = {15},
pages = {9175-9190},
doi = {10.1021/acs.est.0c03948},
pmid = {32657581},
issn = {1520-5851},
mesh = {*Ammonia ; *Archaea ; Nitrification ; Nitrous Oxide ; Oxidation-Reduction ; Soil Microbiology ; },
abstract = {The continuous increase of nitrous oxide (N2O) in the atmosphere has become a global concern because of its property as a potent greenhouse gas. Given the important role of ammonia-oxidizing archaea (AOA) in ammonia oxidation and their involvement in N2O production, a clear understanding of the knowledge on archaeal N2O production is necessary for global N2O mitigation. Compared to bacterial N2O production by ammonia-oxidizing bacteria (AOB), AOA-driven N2O production pathways are less-well elucidated. In this Critical Review, we synthesized the currently proposed AOA-driven N2O production pathways in combination with enzymology distinction, analyzed the role of AOA species involved in N2O production pathways, discussed the relative contribution of AOA to N2O production in both natural and anthropogenic environments, summarized the factors affecting archaeal N2O yield, and compared the distinctions among approaches used to differentiate ammonia oxidizer-associated N2O production. We, then, put forward perspectives for archaeal N2O production and future challenges to further improve our understanding of the production pathways, putative enzymes involved and potential approaches for identification in order to potentially achieve effective N2O mitigations.},
}
@article {pmid32655535,
year = {2020},
author = {Wang, L and Pang, Q and Peng, F and Zhang, A and Zhou, Y and Lian, J and Zhang, Y and Yang, F and Zhu, Y and Ding, C and Zhu, X and Li, Y and Cui, Y},
title = {Response Characteristics of Nitrifying Bacteria and Archaea Community Involved in Nitrogen Removal and Bioelectricity Generation in Integrated Tidal Flow Constructed Wetland-Microbial Fuel Cell.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {1385},
pmid = {32655535},
issn = {1664-302X},
abstract = {This study explores nitrogen removal performance, bioelectricity generation, and the response of microbial community in two novel tidal flow constructed wetland-microbial fuel cells (TFCW-MFCs) when treating synthetic wastewater under two different chemical oxygen demand/total nitrogen (COD/TN, or simplified as C/N) ratios (10:1 and 5:1). The results showed that they achieved high and stable COD, NH4 [+]-N, and TN removal efficiencies. Besides, TN removal rate of TFCW-MFC was increased by 5-10% compared with that of traditional CW-MFC. Molecular biological analysis revealed that during the stabilization period, a low C/N ratio remarkably promoted diversities of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in the cathode layer, whereas a high one enhanced the richness of nitrite-oxidizing bacteria (NOB) in each medium; the dominant genera in AOA, AOB, and NOB were Candidatus Nitrosotenuis, Nitrosomonas, and Nitrobacter. Moreover, a high C/N ratio facilitated the growth of Nitrosomonas, while it inhibited the growth of Candidatus Nitrosotenuis. The distribution of microbial community structures in NOB was separated by space rather than time or C/N ratio, except for Nitrobacter. This is caused by the differences of pH, dissolved oxygen (DO), and nitrogen concentration. The response of microbial community characteristics to nitrogen transformations and bioelectricity generation demonstrated that TN concentration is significantly negatively correlated with AOA-shannon, AOA-chao, 16S rRNA V4-V5-shannon, and 16S rRNA V4-V5-chao, particularly due to the crucial functions of Nitrosopumilus, Planctomyces, and Aquicella. Additionally, voltage output was primarily influenced by microorganisms in the genera of Nitrosopumilus, Nitrosospira, Altererythrobacter, Gemmata, and Aquicella. This study not only presents an applicable tool to treat high nitrogen-containing wastewater, but also provides a theoretical basis for the use of TFCW-MFC and the regulation of microbial community in nitrogen removal and electricity production.},
}
@article {pmid32636492,
year = {2020},
author = {Qin, W and Zheng, Y and Zhao, F and Wang, Y and Urakawa, H and Martens-Habbena, W and Liu, H and Huang, X and Zhang, X and Nakagawa, T and Mende, DR and Bollmann, A and Wang, B and Zhang, Y and Amin, SA and Nielsen, JL and Mori, K and Takahashi, R and Virginia Armbrust, E and Winkler, MH and DeLong, EF and Li, M and Lee, PH and Zhou, J and Zhang, C and Zhang, T and Stahl, DA and Ingalls, AE},
title = {Alternative strategies of nutrient acquisition and energy conservation map to the biogeography of marine ammonia-oxidizing archaea.},
journal = {The ISME journal},
volume = {14},
number = {10},
pages = {2595-2609},
pmid = {32636492},
issn = {1751-7370},
mesh = {*Ammonia ; *Archaea/genetics ; Nitrification ; Nutrients ; Oxidation-Reduction ; Phylogeny ; },
abstract = {Ammonia-oxidizing archaea (AOA) are among the most abundant and ubiquitous microorganisms in the ocean, exerting primary control on nitrification and nitrogen oxides emission. Although united by a common physiology of chemoautotrophic growth on ammonia, a corresponding high genomic and habitat variability suggests tremendous adaptive capacity. Here, we compared 44 diverse AOA genomes, 37 from species cultivated from samples collected across diverse geographic locations and seven assembled from metagenomic sequences from the mesopelagic to hadopelagic zones of the deep ocean. Comparative analysis identified seven major marine AOA genotypic groups having gene content correlated with their distinctive biogeographies. Phosphorus and ammonia availabilities as well as hydrostatic pressure were identified as selective forces driving marine AOA genotypic and gene content variability in different oceanic regions. Notably, AOA methylphosphonate biosynthetic genes span diverse oceanic provinces, reinforcing their importance for methane production in the ocean. Together, our combined comparative physiological, genomic, and metagenomic analyses provide a comprehensive view of the biogeography of globally abundant AOA and their adaptive radiation into a vast range of marine and terrestrial habitats.},
}
@article {pmid32634668,
year = {2020},
author = {Shi, X and Gao, G and Tian, J and Wang, XC and Jin, X and Jin, P},
title = {Symbiosis of sulfate-reducing bacteria and methanogenic archaea in sewer systems.},
journal = {Environment international},
volume = {143},
number = {},
pages = {105923},
doi = {10.1016/j.envint.2020.105923},
pmid = {32634668},
issn = {1873-6750},
mesh = {*Archaea/genetics ; Bacteria ; *Sewage ; Sulfates ; Symbiosis ; },
abstract = {Sulfide and methane emissions always simultaneously exist in natural environment and constitute a major topic of societal concern. However, the metabolic environments between sulfate-reducing bacteria (SRB) and methanogenic archaea (MA) exist a great difference, which seems to be opposite to the coexisting phenomenon. To explore this issue, the comprehensive biofilm structures, substrate consuming and metabolism pathways of SRB and MA were investigated in a case study of urban sewers. The results showed that, due to the stricter environmental requirements of MA than SRB, SRB became the preponderant microorganism which promoted the rapid generation of sulfide in the initial period of biofilm formation. According to a metagenomic analysis, the SRB appeared to be more preferential than MA in sewers, and the preponderant SRB could provide a key medium (Methyl-coenzyme M) for methane metabolism. Therefore, the diversity of MA gradually increased, and the symbiosis system formed preliminarily. In addition, via L-cysteine, methane metabolism also participated in sulfide consumption which was involved in cysteine and methionine metabolism. This phenomenon of sulfide consumption led to the forward reaction of sulfide metabolism, which could promote sulfide generation while stabilizing the pH value (H[+] concentration) and S[2-] concentrations which should have inhibited SRB and MA production. Therefore, the heavily intertwined interactions between sulfide and methane metabolism provided environmental security for SRB and MA, and completely formed the symbiosis between SRB and MA. Based on these findings, an ecological model involving synergistic mechanism between sulfide and methane generation is proposed and this model can also improve understanding on the symbiosis of SRB and MA in the natural environment.},
}
@article {pmid32634643,
year = {2020},
author = {Lin, Z and Huang, W and Zhou, J and He, X and Wang, J and Wang, X and Zhou, J},
title = {The variation on nitrogen removal mechanisms and the succession of ammonia oxidizing archaea and ammonia oxidizing bacteria with temperature in biofilm reactors treating saline wastewater.},
journal = {Bioresource technology},
volume = {314},
number = {},
pages = {123760},
doi = {10.1016/j.biortech.2020.123760},
pmid = {32634643},
issn = {1873-2976},
mesh = {*Ammonia ; *Archaea ; Bacteria ; Biofilms ; Denitrification ; Nitrification ; Nitrogen ; Oxidation-Reduction ; Phylogeny ; Temperature ; Wastewater ; },
abstract = {To reveal nitrogen removal mechanisms under environmental stresses, biofilm reactors were operated at different temperatures (10 °C-35 °C) treating saline wastewater (salinity 3%). The results showed nitrogen removal efficiency was 98.46% at 30 °C and 60.85% at 10 °C, respectively. Both ammonia oxidizing archaea (AOA) and ammonia oxidizing bacteria (AOB) participated in nitrification. 94.9% of the overall ammonia oxidation was attributed to AOA at 10 °C, but only 48.2% of that was undertaken by AOA at 35 °C. AOA had a greater contribution at low temperature, which demonstrated that nitrogen removal pathway varied with temperature. Aerobic denitrification was more stable than anoxic denitrification. High-throughput sequencing showed Crenarchaeota was the dominant AOA (97.02-34.47%), cooperating with various heterotrophic AOB. Real-time PCR indicated that AOA was three orders of magnitude more abundant than AOB. AOA was more resistant to low temperature and high-saline stresses. Ammonia oxidizers had distinct responses to temperature change and showed diverse relationships at different temperatures.},
}
@article {pmid32633872,
year = {2020},
author = {Eichler, J},
title = {N-glycosylation in Archaea-New roles for an ancient posttranslational modification.},
journal = {Molecular microbiology},
volume = {114},
number = {5},
pages = {735-741},
doi = {10.1111/mmi.14569},
pmid = {32633872},
issn = {1365-2958},
mesh = {Archaea/*metabolism ; Archaeal Proteins/metabolism ; Biological Evolution ; Evolution, Molecular ; Genes, Archaeal/genetics ; Glycoproteins/metabolism ; *Glycosylation ; Polysaccharides/genetics/*metabolism ; Protein Processing, Post-Translational/genetics/physiology ; },
abstract = {Genome analysis points to N-glycosylation as being an almost universal posttranslational modification in Archaea. Although such predictions have been confirmed in only a limited number of species, such studies are making it increasingly clear that the N-linked glycans which decorate archaeal glycoproteins present diversity in terms of both glycan composition and architecture far beyond what is seen in the other two domains of life. In addition to continuing to decipher pathways of N-glycosylation, recent efforts have revealed how Archaea exploit this variability in novel roles. As well as encouraging glycoprotein synthesis, folding and assembly into properly functioning higher ordered complexes, N-glycosylation also provides Archaea with a strategy to cope with changing environments. Archaea can, moreover, exploit the apparent species-specific nature of N-glycosylation for selectivity in mating, and hence, to maintain species boundaries, and in other events where cell-selective interactions are required. At the same time, addressing components of N-glycosylation pathways across archaeal phylogeny offers support for the concept of an archaeal origin for eukaryotes. In this MicroReview, these and other recent discoveries related to N-glycosylation in Archaea are considered.},
}
@article {pmid32631866,
year = {2020},
author = {Zou, D and Wan, R and Han, L and Xu, MN and Liu, Y and Liu, H and Kao, SJ and Li, M},
title = {Genomic Characteristics of a Novel Species of Ammonia-Oxidizing Archaea from the Jiulong River Estuary.},
journal = {Applied and environmental microbiology},
volume = {86},
number = {18},
pages = {},
pmid = {32631866},
issn = {1098-5336},
mesh = {Ammonia/*metabolism ; Archaea/classification/*genetics/metabolism ; China ; Estuaries ; *Genome, Archaeal ; Oxidation-Reduction ; Rivers/microbiology ; },
abstract = {Ammonia-oxidizing archaea (AOA) are ubiquitous in diverse ecosystems and play a pivotal role in global nitrogen and carbon cycling. Although AOA diversity and distribution are widely studied, mainly based on the amoA (alpha subunit of ammonia monooxygenase) genotypes, only limited investigations have addressed the relationship between AOA genetic adaptation, metabolic features, and ecological niches, especially in estuaries. Here, we describe the AOA communities along the Jiulong River estuary in southern China. Nine high-quality AOA metagenome-assembled genomes (MAGs) were obtained by metagenomics. Five of the MAGs are proposed to constitute a new species, "Candidatus Nitrosopumilus aestuariumsis" sp. nov., based on the phylogenies of the 16S and 23S rRNA genes and concatenated ribosomal proteins, as well as the average amino acid identity. Comparative genomic analysis revealed unique features of the new species, including a high number of genes related to diverse carbohydrate-active enzymes, phosphatases, heavy-metal transport systems, flagellation, and chemotaxis. These genes may be crucial for AOA adaptation to the eutrophic and heavy-metal-contaminated Jiulong River estuary. The uncovered detailed genomic characteristics of the new estuarine AOA species highlight AOA contributions to ammonia oxidation in the Jiulong River estuary.IMPORTANCE In this study, AOA communities along a river in southern China were characterized, and metagenome-assembled genomes (MAGs) of a novel AOA clade were also obtained. Based on the characterization of AOA genomes, the study suggests adaptation of the novel AOAs to estuarine environments, providing new information on the ecology of estuarine AOA and the nitrogen cycle in contaminated estuarine environments.},
}
@article {pmid32608808,
year = {2020},
author = {Zhang, Y and Zuo, JE and Wang, SK and Alisa, S and Li, AJ and Li, LL},
title = {[Spatial Distribution of Nitrogen Metabolism Functional Genes of Eubacteria and Archaebacteria in Dianchi Lake].},
journal = {Huan jing ke xue= Huanjing kexue},
volume = {41},
number = {6},
pages = {2908-2917},
doi = {10.13227/j.hjkx.201909196},
pmid = {32608808},
issn = {0250-3301},
mesh = {*Archaea ; *Bacteria/genetics ; Biodiversity ; *Genes, Bacterial ; *Lakes ; Nitrogen ; *Nitrogen Cycle ; Phylogeny ; },
abstract = {Nitrogen metabolism plays an important role in the nitrogen cycle and transformation in Dianchi Lake. Not only do eukaryotes participate in nitrogen transformation but prokaryotes, as the main drivers of the nitrogen cycle, also play an extremely important role in the nitrogen cycle. Based on 16S rDNA high-throughput sequencing technology, 13 sites in Caohai and Waihai of Dianchi Lake were monitored, and PICRUSt function analysis method was adopted to analyze the microbial community diversity and key genes of nitrogen metabolism in Dianchi Lake. Bacteria belonging to 35 phyla and 427 genera were found in Dianchi Lake water and mainly included Proteobacteria and Bacteroidetes. Archaea had 14 phyla and 61 genera and mainly belonged to Euryarchaeota. The overall bacterial richness index of Dianchi Lake was higher than that of archaea, and the bacterial diversity index of Caohai was higher than that of Waihai. Functional prediction showed functional richness of bacteria and archaea. There were 35 KO pathways involved in nitrogen metabolism in bacteria, including key genes such as nitrogenous nitrate-reducing gene nirB, nitric oxide reductase gene norB in denitrification, and nitroreductase gene nasK. There were 23 KO pathways involved in nitrogen metabolism in archaea, involving nifH, nifK, and nifD nitrogenase genes in nitrogen fixation. The copy number of nitrogenase genes was significantly higher than that of other nitrogenase genes. The copy number of nitrogen-fixing genes of archaea was higher than that of bacteria, the nitrogen metabolism capacity of archaea in Caohai was higher than that in Waihai, and the potential of nitrogen-fixation of archaea in Dianchi Lake water was higher than that of bacteria. From the perspective of community structure and function prediction of bacteria and archaea, this study discussed the differences of nitrogen cycle in bacteria and archaea in different areas of Dianchi Lake and provided a decision basis for water environment management in Dianchi Lake.},
}
@article {pmid32602260,
year = {2021},
author = {Song, Y and Zhu, Z and Zhou, W and Zhang, YPJ},
title = {High-efficiency transformation of archaea by direct PCR products with its application to directed evolution of a thermostable enzyme.},
journal = {Microbial biotechnology},
volume = {14},
number = {2},
pages = {453-464},
pmid = {32602260},
issn = {1751-7915},
mesh = {Hot Temperature ; Plasmids ; Polymerase Chain Reaction ; *Thermococcus/genetics ; },
abstract = {Hyperthermophilic archaea with unique biochemical and physiological characteristics are important organisms for fundamental research of life science and have great potential for biotechnological applications. However, low transformation efficiency of foreign DNA molecules impedes developments in genetic modification tools and industrial applications. In this study, we applied prolonged overlap extension PCR (POE-PCR) to generate multimeric DNA molecules and then transformed them into two hyperthermophilic archaea, Thermococcus kodakarensis KOD1 and Pyrococcus yayanosii A1. This study was the first example to demonstrate the enhanced transformation efficiencies of POE-PCR products by a factor of approximately 100 for T. kodakarensis KOD1 and 8 for P. yayanosii A1, respectively, relative to circular shuttle plasmids. Furthermore, directed evolution of a modestly thermophilic enzyme, Methanothermococcus okinawensis 3-hydroxy-3-methylglutaryl coenzyme A reductase (HMGR), was conducted to obtain more stable ones due to high transformation efficiency of T. kodakarensis (i.e. ~3 × 10[4] CFU per μg DNA). T. kodakarensis harbouring the most thermostable MoHMGR mutant can grow in the presence of a thermostable antibiotic simvastatin at 85°C and even higher temperatures. This high transformation efficiency technique could not only help develop more hyperthermophilic enzyme mutants via directed evolution but also simplify genetical modification of archaea, which could be novel hosts for industrial biotechnology.},
}
@article {pmid32580393,
year = {2020},
author = {Leoni, C and Volpicella, M and Fosso, B and Manzari, C and Piancone, E and Dileo, MCG and Arcadi, E and Yakimov, M and Pesole, G and Ceci, LR},
title = {A Differential Metabarcoding Approach to Describe Taxonomy Profiles of Bacteria and Archaea in the Saltern of Margherita di Savoia (Italy).},
journal = {Microorganisms},
volume = {8},
number = {6},
pages = {},
pmid = {32580393},
issn = {2076-2607},
support = {634486//Horizon 2020/ ; 97/2018//Banca d'Italia/ ; },
abstract = {Microorganisms inhabiting saline environments are an interesting ecological model for the study of the adaptation of organisms to extreme living conditions and constitute a precious resource of enzymes and bioproducts for biotechnological applications. We analyzed the microbial communities in nine ponds with increasing salt concentrations (salinity range 4.9-36.0%) of the Saltern of Margherita di Savoia (Italy), the largest thalassohaline saltern in Europe. A deep-metabarcoding NGS procedure addressing separately the V5-V6 and V3-V4 hypervariable regions of the 16S rRNA gene of Bacteria and Archaea, respectively, and a CARD-FISH (catalyzed reporter deposition fluorescence in situ hybridization) analysis allowed us to profile the dynamics of microbial populations at the different salt concentrations. Both the domains were detected throughout the saltern, even if the low relative abundance of Archaea in the three ponds with the lowest salinities prevented the construction of the relative amplicon libraries. The highest cell counts were recorded at 14.5% salinity for Bacteria and at 24.1% salinity for Archaea. While Bacteria showed the greatest number of genera in the first ponds (salinity range 4.9-14.5%), archaeal genera were more numerous in the last ponds of the saltern (salinity 24.1-36.0%). Among prokaryotes, Salinibacter was the genus with the maximum abundance (~49% at 34.6% salinity). Other genera detected at high abundance were the archaeal Haloquadratum (~43% at 36.0% salinity) and Natronomonas (~18% at 13.1% salinity) and the bacterial "Candidatus Aquiluna" (~19% at 14.5% salinity). Interestingly, "Candidatus Aquiluna" had not been identified before in thalassohaline waters.},
}
@article {pmid32569776,
year = {2020},
author = {Coker, OO and Wu, WKK and Wong, SH and Sung, JJY and Yu, J},
title = {Altered Gut Archaea Composition and Interaction With Bacteria Are Associated With Colorectal Cancer.},
journal = {Gastroenterology},
volume = {159},
number = {4},
pages = {1459-1470.e5},
doi = {10.1053/j.gastro.2020.06.042},
pmid = {32569776},
issn = {1528-0012},
mesh = {Adenoma/*microbiology/*pathology ; Aged ; Archaea/*isolation &amp; purification ; Case-Control Studies ; Cohort Studies ; Colorectal Neoplasms/*microbiology/*pathology ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Middle Aged ; Sensitivity and Specificity ; },
abstract = {BACKGROUND &amp; AIMS: Changes in the intestinal microbiota have been associated with development and progression of colorectal cancer (CRC). Archaea are stable components of the microbiota, but little is known about their composition or contribution to colorectal carcinogenesis. We analyzed archaea in fecal microbiomes of 2 large cohorts of patients with CRC.<br><br>METHODS: We performed shotgun metagenomic analyses of fecal samples from 585 participants (184 patients with CRC, 197 patients with adenomas, and 204 healthy individuals) from discovery (165 individuals) and validation (420 individuals) cohorts. Assignment of taxonomies was performed by exact k-mer alignment against an integrated microbial reference genome database.<br><br>RESULTS: Principal component analysis of archaeomes showed distinct clusters in fecal samples from patients with CRC, patients with adenomas, and control individuals (P < .001), indicating an alteration in the composition of enteric archaea during tumorigenesis. Fecal samples from patients with CRC had significant enrichment of halophilic and depletion of methanogenic archaea. The halophilic Natrinema sp. J7-2 increased progressively in samples from control individuals, to patients with adenomas, to patients with CRC. Abundances of 9 archaea species that were enriched in fecal samples from patients with CRC distinguished them from control individuals with areas under the receiver operating characteristic curve of 0.82 in the discovery cohort and 0.83 in the validation cohort. An association between archaea and bacteria diversities was observed in fecal samples from control individuals but not from patients with CRC. Archaea that were enriched in fecal samples from patients with CRC had an extensive mutual association with bacteria that were enriched in the same samples and exclusivity with bacteria that were lost from these samples.<br><br>CONCLUSIONS: Archaeomes of fecal samples from patients with CRC are characterized by enrichment of halophiles and depletion of methanogens. Studies are needed to determine whether associations between specific archaea and bacteria species in samples from patients with CRC contribute to or are a response to colorectal tumorigenesis.},
}
@article {pmid32546672,
year = {2020},
author = {Zhao, J and Meng, Y and Drewer, J and Skiba, UM and Prosser, JI and Gubry-Rangin, C},
title = {Differential Ecosystem Function Stability of Ammonia-Oxidizing Archaea and Bacteria following Short-Term Environmental Perturbation.},
journal = {mSystems},
volume = {5},
number = {3},
pages = {},
pmid = {32546672},
issn = {2379-5077},
abstract = {Rapidly expanding conversion of tropical forests to oil palm plantations in Southeast Asia leads to soil acidification following intensive nitrogen fertilization. Changes in soil pH are predicted to have an impact on archaeal ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), and complete (comammox) ammonia oxidizers and, consequently, on nitrification. It is therefore critical to determine whether the predicted effects of pH on ammonia oxidizers and nitrification activity apply in tropical soils subjected to various degrees of anthropogenic activity. This was investigated by experimental manipulation of pH in soil microcosms from a land-use gradient (forest, riparian, and oil palm soils). The nitrification rate was greater in forest soils with native neutral pH than in converted acidic oil palm soils. Ammonia oxidizer activity decreased following acidification of the forest soils but increased after liming of the oil palm soils, leading to a trend of a reversed net nitrification rate after pH modification. AOA and AOB nitrification activity was dependent on pH, but AOB were more sensitive to pH modification than AOA, which demonstrates a greater stability of AOA than AOB under conditions of short-term perturbation. In addition, these results predict AOB to be a good bioindicator of nitrification response following pH perturbation during land-use conversion. AOB and/or comammox species were active in all soils along the land-use gradient, even, unexpectedly, under acidic conditions, suggesting their adaptation to native acidic or acidified soils. The present study therefore provided evidence for limited stability of soil ammonia oxidizer activity following intensive anthropogenic activities, which likely aggravates the vulnerability of nitrogen cycle processes to environmental disturbance.IMPORTANCE Physiological and ecological studies have provided evidence for pH-driven niche specialization of ammonia oxidizers in terrestrial ecosystems. However, the functional stability of ammonia oxidizers following pH change has not been investigated, despite its importance in understanding the maintenance of ecosystem processes following environmental perturbation. This is particularly true after anthropogenic perturbation, such as the conversion of tropical forest to oil palm plantations. This study demonstrated a great impact of land-use conversion on nitrification, which is linked to changes in soil pH due to common agricultural practices (intensive fertilization). In addition, the different communities of ammonia oxidizers were differently affected by short-term pH perturbations, with implications for future land-use conversions but also for increased knowledge of associated global nitrous oxide emissions and current climate change concerns.},
}
@article {pmid32535177,
year = {2020},
author = {Di Giulio, M},
title = {The phylogenetic distribution of the glutaminyl-tRNA synthetase and Glu-tRNA[Gln] amidotransferase in the fundamental lineages would imply that the ancestor of archaea, that of eukaryotes and LUCA were progenotes.},
journal = {Bio Systems},
volume = {196},
number = {},
pages = {104174},
doi = {10.1016/j.biosystems.2020.104174},
pmid = {32535177},
issn = {1872-8324},
mesh = {Amino Acyl-tRNA Synthetases/*genetics/metabolism ; Archaea/enzymology/*genetics ; Eukaryota/enzymology/*genetics ; *Evolution, Molecular ; Nitrogenous Group Transferases/*genetics/metabolism ; *Phylogeny ; },
abstract = {The function of the glutaminyl-tRNA synthetase and Glu-tRNA[Gln] amidotransferase might be related to the origin of the genetic code because, for example, glutaminyl-tRNA synthetase catalyses the fundamental reaction that makes the genetic code. If the evolutionary stage of the origin of these two enzymes could be unambiguously identified, then the genetic code should still have been originating at that particular evolutionary stage because the fundamental reaction that makes the code itself was still evidently evolving. This would result in that particular evolutionary moment being attributed to the evolutionary stage of the progenote because it would have a relationship between the genotype and the phenotype not yet fully realized because the genetic code was precisely still originating. I then analyzed the distribution of the glutaminyl-tRNA synthetase and Glu-tRNA[Gln] aminodotrasferase in the main phyletic lineages. Since in some cases the origin of these two enzymes can be related to the evolutionary stages of ancestors of archaea and eukaryotes, this would indicate these ancestors as progenotes because at that evolutionary moment the genetic code was evidently still evolving, thus realizing the definition of progenote. The conclusion that the ancestor of archaea and that of eukaryotes were progenotes would imply that even the last universal common ancestor (LUCA) was a progenote because it appeared, on the tree of life, temporally before these ancestors.},
}
@article {pmid32534168,
year = {2020},
author = {Pinevich, AV},
title = {The ambiguity of the basic terms related to eukaryotes and the more consistent etymology based on eukaryotic signatures in Asgard archaea.},
journal = {Bio Systems},
volume = {197},
number = {},
pages = {104178},
doi = {10.1016/j.biosystems.2020.104178},
pmid = {32534168},
issn = {1872-8324},
mesh = {Actin Cytoskeleton/genetics ; Archaea/*classification/genetics ; Bacteria/genetics ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; Endosomal Sorting Complexes Required for Transport/genetics ; *Eukaryota ; *Eukaryotic Cells ; Euryarchaeota/*classification/genetics ; GTP Phosphohydrolases/genetics ; Genome, Archaeal/*genetics ; Phylogeny ; Symbiosis/*genetics ; *Terminology as Topic ; },
abstract = {The endosymbiosis theory most widely accepted variant surmises the engulfment of a bacterial cell by an archaeal cell. For decades, this scenario was reputed to be an unconfirmed hypothesis, and only recently it has obtained an indirect proof in Asgard archaea environmental DNA encoding eukaryotic signatures - actin cytoskeleton, small GTPases, and ESCRT complex. In view of growing interest to this aspect of the endosymbiosis theory, it seemed timely to revisit the basic terms eukaryotic cell/eukaryotes/nucleated organisms. The article highlights the ambiguous applications of these terms, and seeks for their consistency with regard to phylogeny and taxonomy. Additionally, new name Caryosignifera is proposed for the phylum represented by: (1) the underexplored Asgard archaea manifested by above-mentioned environmental DNA; (2) cultured species of engulfing Asgard archaea; (3) eukaryotic host cells in nucleated organisms (protists, algae, plants, fungi, and animals).},
}
@article {pmid32527006,
year = {2020},
author = {Gryta, A and Frąc, M},
title = {Methodological Aspects of Multiplex Terminal Restriction Fragment Length Polymorphism-Technique to Describe the Genetic Diversity of Soil Bacteria, Archaea and Fungi.},
journal = {Sensors (Basel, Switzerland)},
volume = {20},
number = {11},
pages = {},
pmid = {32527006},
issn = {1424-8220},
support = {2018/02/X/NZ9/00515//National Science Center/ ; BIOSTRATEG3/347464/5/NCBR/2017//The National Centre for Research and Development/ ; },
mesh = {Archaea/*classification ; Bacteria/*classification ; Fungi/*classification ; Polymerase Chain Reaction ; *Polymorphism, Restriction Fragment Length ; *Soil Microbiology ; },
abstract = {The molecular fingerprinting methods used to evaluate soil microbial diversity could also be used as effective biosensors for the purposes of monitoring ecological soil status. The biodiversity of microorganisms is a relevant index of soil activity and there is a necessity to develop tools to generate reliable results for an emerging approach in the field of environmental control using microbial diversity biosensors. This work reports a method under development for determining soil microbial diversity using high efficiency Multiplex PCR-Terminal Restriction Fragment Length Polymorphism (M-T-RFLP) for the simultaneous detection of bacteria, archaea and fungi. Three different primer sets were used in the reaction and the analytical conditions were optimized. Optimal analytical conditions were achieved using 0.5 µM of primer for bacteria and 1 µM for archaea and fungi, 4 ng of soil DNA template, and HaeIII restriction enzyme. Comparative tests using the proposed analytical approach and a single analysis of each microorganism group were carried out to indicate that both genetic profiles were similar. The Jaccard similarity coefficient between single and multiplexing approach ranged from 0.773 to 0.850 for bacteria and fungi, and 0.208 to 0.905 for archaea. In conclusion, the multiplexing and pooling approaches significantly reduced the costs and time required to perform the analyses, while maintaining a proper effectiveness.},
}
@article {pmid32514073,
year = {2020},
author = {Murray, AE and Freudenstein, J and Gribaldo, S and Hatzenpichler, R and Hugenholtz, P and Kämpfer, P and Konstantinidis, KT and Lane, CE and Papke, RT and Parks, DH and Rossello-Mora, R and Stott, MB and Sutcliffe, IC and Thrash, JC and Venter, SN and Whitman, WB and Acinas, SG and Amann, RI and Anantharaman, K and Armengaud, J and Baker, BJ and Barco, RA and Bode, HB and Boyd, ES and Brady, CL and Carini, P and Chain, PSG and Colman, DR and DeAngelis, KM and de Los Rios, MA and Estrada-de Los Santos, P and Dunlap, CA and Eisen, JA and Emerson, D and Ettema, TJG and Eveillard, D and Girguis, PR and Hentschel, U and Hollibaugh, JT and Hug, LA and Inskeep, WP and Ivanova, EP and Klenk, HP and Li, WJ and Lloyd, KG and Löffler, FE and Makhalanyane, TP and Moser, DP and Nunoura, T and Palmer, M and Parro, V and Pedrós-Alió, C and Probst, AJ and Smits, THM and Steen, AD and Steenkamp, ET and Spang, A and Stewart, FJ and Tiedje, JM and Vandamme, P and Wagner, M and Wang, FP and Yarza, P and Hedlund, BP and Reysenbach, AL},
title = {Roadmap for naming uncultivated Archaea and Bacteria.},
journal = {Nature microbiology},
volume = {5},
number = {8},
pages = {987-994},
pmid = {32514073},
issn = {2058-5276},
mesh = {Archaea/*classification/genetics ; Bacteria/*classification/genetics ; DNA, Bacterial ; Metagenome ; Phylogeny ; Prokaryotic Cells/classification ; Sequence Analysis, DNA ; Terminology as Topic ; },
abstract = {The assembly of single-amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) has led to a surge in genome-based discoveries of members affiliated with Archaea and Bacteria, bringing with it a need to develop guidelines for nomenclature of uncultivated microorganisms. The International Code of Nomenclature of Prokaryotes (ICNP) only recognizes cultures as 'type material', thereby preventing the naming of uncultivated organisms. In this Consensus Statement, we propose two potential paths to solve this nomenclatural conundrum. One option is the adoption of previously proposed modifications to the ICNP to recognize DNA sequences as acceptable type material; the other option creates a nomenclatural code for uncultivated Archaea and Bacteria that could eventually be merged with the ICNP in the future. Regardless of the path taken, we believe that action is needed now within the scientific community to develop consistent rules for nomenclature of uncultivated taxa in order to provide clarity and stability, and to effectively communicate microbial diversity.},
}
@article {pmid32507415,
year = {2020},
author = {Zhou, S and Xiang, H and Liu, JL},
title = {CTP synthase forms cytoophidia in archaea.},
journal = {Journal of genetics and genomics = Yi chuan xue bao},
volume = {47},
number = {4},
pages = {213-223},
doi = {10.1016/j.jgg.2020.03.004},
pmid = {32507415},
issn = {1673-8527},
mesh = {Archaea/enzymology/metabolism ; Carbon-Nitrogen Ligases/*genetics/metabolism ; Cytoskeleton/*enzymology/genetics/metabolism ; Gene Expression Regulation, Archaeal/drug effects ; Glutamine/metabolism/pharmacology ; Haloarcula/*enzymology/genetics ; },
abstract = {CTP synthase (CTPS) is an important metabolic enzyme that catalyzes the rate-limiting reaction of nucleotide CTP de novo synthesis. Since 2010, a series of studies have demonstrated that CTPS can form filamentous structures in bacteria and eukaryotes, which are termed cytoophidia. However, it is unknown whether cytoophidia exist in the third domain of life, archaea. Using Haloarcula hispanica as a model system, here we demonstrate that CTPS forms distinct intracellular compartments in archaea. Under stimulated emission depletion microscopy, we find that the structures of H. hispanica CTPS are elongated, similar to cytoophidia in bacteria and eukaryotes. When Haloarcula cells are cultured in low-salt medium, the occurrence of cytoophidia increases dramatically. In addition, treatment of H. hispanica with a glutamine analog or overexpression of CTPS can promote cytoophidium assembly. Our study reveals that CTPS can form cytoophidia in all three domains of life, suggesting that forming cytoophidia is an ancient property of CTPS.},
}
@article {pmid32503045,
year = {2020},
author = {},
title = {Corrigendum to: D-Galactose catabolism in archaea: Operation of the DeLey-Doudoroff pathway in Haloferax volcanii.},
journal = {FEMS microbiology letters},
volume = {367},
number = {11},
pages = {},
doi = {10.1093/femsle/fnaa069},
pmid = {32503045},
issn = {1574-6968},
}
@article {pmid32499624,
year = {2020},
author = {Tang, L},
title = {Taxonomy of Bacteria and Archaea.},
journal = {Nature methods},
volume = {17},
number = {6},
pages = {562},
doi = {10.1038/s41592-020-0863-3},
pmid = {32499624},
issn = {1548-7105},
mesh = {*Archaea ; *Bacteria ; Phylogeny ; },
}
@article {pmid32499102,
year = {2020},
author = {Peng, X and Mayo-Muñoz, D and Bhoobalan-Chitty, Y and Martínez-Álvarez, L},
title = {Anti-CRISPR Proteins in Archaea.},
journal = {Trends in microbiology},
volume = {28},
number = {11},
pages = {913-921},
doi = {10.1016/j.tim.2020.05.007},
pmid = {32499102},
issn = {1878-4380},
mesh = {Archaea/genetics/*immunology/virology ; Archaeal Proteins/genetics/*immunology ; Archaeal Viruses/genetics/*physiology ; *CRISPR-Cas Systems ; Rudiviridae/genetics/*physiology ; },
abstract = {Anti-CRISPR (Acr) proteins are natural inhibitors of CRISPR-Cas immune systems. To date, Acrs inhibiting types I, II, III, V, and VI CRISPR-Cas systems have been characterized. While most known Acrs are derived from bacterial phages and prophages, very few have been characterized in the domain Archaea, despite the nearly ubiquitous presence of CRISPR-Cas in archaeal cells. Here we summarize the discovery and characterization of the archaeal Acrs with the representatives encoded by a model archaeal virus, Sulfolobus islandicus rod-shaped virus 2 (SIRV2). AcrID1 inhibits subtype I-D CRISPR-Cas immunity through direct interaction with the large subunit Cas10d of the effector complex, and AcrIIIB1 inhibits subtype III-B CRISPR-Cas immunity through a mechanism interfering with middle/late gene targeting. Future development of efficient screening methods will be key to uncovering the diversity of archaeal Acrs.},
}
@article {pmid32449429,
year = {2020},
author = {Qi, L and Li, J and Jia, J and Yue, L and Dong, X},
title = {Comprehensive analysis of the pre-ribosomal RNA maturation pathway in a methanoarchaeon exposes the conserved circularization and linearization mode in archaea.},
journal = {RNA biology},
volume = {17},
number = {10},
pages = {1427-1441},
pmid = {32449429},
issn = {1555-8584},
mesh = {Archaea/*physiology ; Base Sequence ; Conserved Sequence ; Endodeoxyribonucleases/chemistry/metabolism ; *Gene Expression Regulation, Archaeal ; Models, Biological ; Nucleic Acid Conformation ; RNA Cleavage ; RNA Precursors/chemistry/*genetics ; *RNA Processing, Post-Transcriptional ; RNA Splicing ; RNA, Ribosomal/chemistry/*genetics ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 23S/genetics ; RNA, Ribosomal, 5S/genetics ; RNA, Transfer/genetics ; RNA-Binding Motifs ; },
abstract = {The ribosomal RNA (rRNA) genes are generally organized as an operon and cotranscribed into a polycistronic precursor; therefore, processing and maturation of pre-rRNAs are essential for ribosome biogenesis. However, rRNA maturation pathways of archaea, particularly of methanoarchaea, are scarcely known. Here, we thoroughly elucidated the maturation pathway of the rRNA operon (16S-tRNA[Ala]-23S-tRNA[Cys]-5S) in Methanolobus psychrophilus, one representative of methanoarchaea. Enzymatic assay demonstrated that EndA, a tRNA splicing endoribonuclease, cleaved bulge-helix-bulge (BHB) motifs buried in the processing stems of pre-16S and pre-23S rRNAs. Northern blot and quantitative PCR detected splicing-coupled circularization of pre-16S and pre-23S rRNAs, which accounted for 2% and 12% of the corresponding rRNAs, respectively. Importantly, endoribonuclease Nob1 was determined to linearize circular pre-16S rRNA at the mature 3' end so to expose the anti-Shine-Dalgarno sequence, while circular pre-23S rRNA was linearized at the mature 5' end by an unknown endoribonuclease. The resultant 5' and 3' extension in linearized pre-16S and pre-23S rRNAs were finally matured through 5'-3' and 3'-5' exoribonucleolytic trimming, respectively. Additionally, a novel processing pathway of endoribonucleolysis coupled with exoribonucleolysis was identified for the pre-5S rRNA maturation in this methanogen, which could be also conserved in most methanogenic euryarchaea. Based on evaluating the phylogenetic conservation of the key elements that are involved in circularization and linearization of pre-rRNA maturation, we predict that the rRNA maturation mode revealed here could be prevalent among archaea.},
}
@article {pmid32448158,
year = {2020},
author = {Eckert, I and Weinberg, Z},
title = {Discovery of 20 novel ribosomal leader candidates in bacteria and archaea.},
journal = {BMC microbiology},
volume = {20},
number = {1},
pages = {130},
pmid = {32448158},
issn = {1471-2180},
support = {WE6322/1-1//Deutsche Forschungsgemeinschaft/International ; },
mesh = {*5' Untranslated Regions ; Archaea/*genetics/metabolism ; Bacillus subtilis/genetics ; Bacteria/*genetics/metabolism ; Escherichia coli/genetics ; Gene Expression Regulation, Archaeal ; Gene Expression Regulation, Bacterial ; Models, Molecular ; Nucleic Acid Conformation ; Protein Biosynthesis ; RNA, Archaeal/genetics ; RNA, Bacterial/genetics ; RNA, Ribosomal/*chemistry/genetics ; Ribosomal Proteins/metabolism ; },
abstract = {BACKGROUND: RNAs perform many functions in addition to supplying coding templates, such as binding proteins. RNA-protein interactions are important in multiple processes in all domains of life, and the discovery of additional protein-binding RNAs expands the scope for studying such interactions. To find such RNAs, we exploited a form of ribosomal regulation. Ribosome biosynthesis must be tightly regulated to ensure that concentrations of rRNAs and ribosomal proteins (r-proteins) match. One regulatory mechanism is a ribosomal leader (r-leader), which is a domain in the 5' UTR of an mRNA whose genes encode r-proteins. When the concentration of one of these r-proteins is high, the protein binds the r-leader in its own mRNA, reducing gene expression and thus protein concentrations. To date, 35 types of r-leaders have been validated or predicted.<br><br>RESULTS: By analyzing additional conserved RNA structures on a multi-genome scale, we identified 20 novel r-leader structures. Surprisingly, these included new r-leaders in the highly studied organisms Escherichia coli and Bacillus subtilis. Our results reveal several cases where multiple unrelated RNA structures likely bind the same r-protein ligand, and uncover previously unknown r-protein ligands. Each r-leader consistently occurs upstream of r-protein genes, suggesting a regulatory function. That the predicted r-leaders function as RNAs is supported by evolutionary correlations in the nucleotide sequences that are characteristic of a conserved RNA secondary structure. The r-leader predictions are also consistent with the locations of experimentally determined transcription start sites.<br><br>CONCLUSIONS: This work increases the number of known or predicted r-leader structures by more than 50%, providing additional opportunities to study structural and evolutionary aspects of RNA-protein interactions. These results provide a starting point for detailed experimental studies.},
}
@article {pmid32442771,
year = {2020},
author = {Shi, LD and Lv, PL and Wang, M and Lai, CY and Zhao, HP},
title = {A mixed consortium of methanotrophic archaea and bacteria boosts methane-dependent selenate reduction.},
journal = {The Science of the total environment},
volume = {732},
number = {},
pages = {139310},
doi = {10.1016/j.scitotenv.2020.139310},
pmid = {32442771},
issn = {1879-1026},
mesh = {Anaerobiosis ; *Archaea ; Bacteria ; Biofilms ; Bioreactors ; In Situ Hybridization, Fluorescence ; Methane ; Oxidation-Reduction ; RNA, Ribosomal, 16S ; Selenic Acid ; },
abstract = {Though methane-based selenate reduction has been reported, neither the selenate load nor the removal rate could satisfy practical applications, thus limiting this technique to bio-remediate selenate pollution. In the present study, using a membrane biofilm batch reactor (MBBR), we successfully enriched a consortium performing methane-dependent selenate reduction, with enhanced reduction rates from 16.1 to 28.9 μM-day[-1] under a comparable Se concentration to industrial wastewaters (i.e., ~500 μM). During active reduction, 16S rRNA gene copies of Archaea and Bacteria were both increased more than one order of magnitude. Clone library construction and high-throughput sequencing indicated that Methanosarcina and Methylocystis were the only methane-oxidizing microorganisms. The presence of 20 mM bromoethanesulphonate or 0.15 mM acetylene both significantly, but not completely, inhibited methane-dependent selenate reduction, indicating the concurrent contributions of methanotrophic archaea and bacteria. Fluorescence in situ hybridization (FISH) revealed that archaea directly adhered to the surface of the membrane while bacteria were in the outer layer, together forming the mature biofilm. This study highlights the crucial role of both methanotrophic archaea and bacteria in methane-dependent selenate reduction, and lays foundations in applying methane to bio-remediate practical selenate pollution.},
}
@article {pmid32440868,
year = {2020},
author = {Yang, D and Xiao, X and He, N and Zhu, W and Liu, M and Xie, G},
title = {Effects of reducing chemical fertilizer combined with organic amendments on ammonia-oxidizing bacteria and archaea communities in a low-fertility red paddy field.},
journal = {Environmental science and pollution research international},
volume = {27},
number = {23},
pages = {29422-29432},
doi = {10.1007/s11356-020-09120-5},
pmid = {32440868},
issn = {1614-7499},
support = {2016YFD0201200//the National Key Research and Development Program of China/ ; },
mesh = {Ammonia ; Animals ; *Archaea ; Bacteria ; Ecosystem ; Fertility ; *Fertilizers ; Nitrification ; Oxidation-Reduction ; Phylogeny ; Soil ; Soil Microbiology ; Swine ; },
abstract = {Ammonia oxidation process in soil has a great contribution to the emission of nitrous oxide, which is a hot issue in the study of N cycle of rice field ecosystem. Organic amendments which partially substitute chemical nitrogen fertilizer are widely adopted to optimizing N management and reduce the use of chemical nitrogen fertilizers in the paddy ecosystem, but their long-term effects on ammonia-oxidizing archaea (AOA) and bacteria (AOB) were not well understood. Thus, based on a 6-year field trial that comprised four fertilization strategies (CF, chemical fertilizer; PM, pig manure substituting for 20% chemical N; BF, biogas slurry substituting for 20% chemical N; and GM, milk vetch substituting for 20% chemical N) and no N fertilizer application as CK, the abundance and community structure of ammonia oxidizers were examined by using qPCR and Illumina Miseq sequencing approaches based on the functional marker genes (amoA) in a low-fertility paddy field. The results revealed that 6 years of organic-substitute fertilization significantly increased AOA abundance in comparison with NF and CF. However, only CF and PM had a higher AOB abundance than those in NF and no significant difference between CF and organic-substitute treatments was observed. Both AOA and AOB were significantly correlated with soil potential nitrification rate (PNR). Moreover, organic-substitute treatments showed the evident changes in the AOA community, while little were observed in the AOB community. Soil pH was the main predictor for AOA abundance, while NH4[+]-N and NO3[-]-N were the main predictors for AOB abundance. This study suggests that both AOA and AOB were jointly contributed to the variation of soil potential nitrification rate, while the AOA community was shown to be more responsive to organic-substitute fertilization strategies than AOB in the tested soils.},
}
@article {pmid32430468,
year = {2020},
author = {Lu, Z and Fu, T and Li, T and Liu, Y and Zhang, S and Li, J and Dai, J and Koonin, EV and Li, G and Chu, H and Li, M},
title = {Coevolution of Eukaryote-like Vps4 and ESCRT-III Subunits in the Asgard Archaea.},
journal = {mBio},
volume = {11},
number = {3},
pages = {},
pmid = {32430468},
issn = {2150-7511},
mesh = {Adenosine Triphosphatases/genetics ; Archaea/*classification ; Archaeal Proteins/*genetics/metabolism ; Biological Transport ; Endosomal Sorting Complexes Required for Transport/*genetics/metabolism ; *Evolution, Molecular ; Models, Molecular ; Molecular Docking Simulation ; *Phylogeny ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae Proteins/genetics ; },
abstract = {The emergence of the endomembrane system is a key step in the evolution of cellular complexity during eukaryogenesis. The endosomal sorting complex required for transport (ESCRT) machinery is essential and required for the endomembrane system functions in eukaryotic cells. Recently, genes encoding eukaryote-like ESCRT protein components have been identified in the genomes of Asgard archaea, a newly proposed archaeal superphylum that is thought to include the closest extant prokaryotic relatives of eukaryotes. However, structural and functional features of Asgard ESCRT remain uncharacterized. Here, we show that Vps4, Vps2/24/46, and Vps20/32/60, the core functional components of the Asgard ESCRT, coevolved eukaryote-like structural and functional features. Phylogenetic analysis shows that Asgard Vps4, Vps2/24/46, and Vps20/32/60 are closely related to their eukaryotic counterparts. Molecular dynamics simulation and biochemical assays indicate that Asgard Vps4 contains a eukaryote-like microtubule-interacting and transport (MIT) domain that binds the distinct type 1 MIT-interacting motif and type 2 MIT-interacting motif in Vps2/24/46 and Vps20/32/60, respectively. The Asgard Vps4 partly, but much more efficiently than homologs from other archaea, complements the vps4 null mutant of Saccharomyces cerevisiae, further supporting the functional similarity between the membrane remodeling machineries of Asgard archaea and eukaryotes. Thus, this work provides evidence that the ESCRT complexes from Asgard archaea and eukaryotes are evolutionarily related and functionally similar. Thus, despite the apparent absence of endomembranes in Asgard archaea, the eukaryotic ESCRT seems to have been directly inherited from an Asgard ancestor, to become a key component of the emerging endomembrane system.IMPORTANCE The discovery of Asgard archaea has changed the existing ideas on the origins of eukaryotes. Researchers propose that eukaryotic cells evolved from Asgard archaea. This hypothesis partly stems from the presence of multiple eukaryotic signature proteins in Asgard archaea, including homologs of ESCRT proteins that are essential components of the endomembrane system in eukaryotes. However, structural and functional features of Asgard ESCRT remain unknown. Our study provides evidence that Asgard ESCRT is functionally comparable to the eukaryotic counterparts, suggesting that despite the apparent absence of endomembranes in archaea, eukaryotic ESCRT was inherited from an Asgard archaeal ancestor, alongside the emergence of endomembrane system during eukaryogenesis.},
}
@article {pmid32427979,
year = {2020},
author = {Baker, BJ and De Anda, V and Seitz, KW and Dombrowski, N and Santoro, AE and Lloyd, KG},
title = {Author Correction: Diversity, ecology and evolution of Archaea.},
journal = {Nature microbiology},
volume = {5},
number = {7},
pages = {976},
doi = {10.1038/s41564-020-0741-x},
pmid = {32427979},
issn = {2058-5276},
abstract = {An amendment to this paper has been published and can be accessed via a link at the top of the paper.},
}
@article {pmid32426487,
year = {2020},
author = {Meador, TB and Schoffelen, N and Ferdelman, TG and Rebello, O and Khachikyan, A and Könneke, M},
title = {Carbon recycling efficiency and phosphate turnover by marine nitrifying archaea.},
journal = {Science advances},
volume = {6},
number = {19},
pages = {eaba1799},
pmid = {32426487},
issn = {2375-2548},
abstract = {Thaumarchaeotal nitrifiers are among the most abundant organisms in the ocean, but still unknown is the carbon (C) yield from nitrification and the coupling of these fluxes to phosphorus (P) turnover and release of metabolites from the cell. Using a dual radiotracer approach, we found that Nitrosopumilus maritimus fixed roughly 0.3 mol C, assimilated 2 mmol P, and released ca. 10[-2] mol C and 10[-5] mol P as dissolved organics (DOC and DOP) per mole ammonia respired. Phosphate turnover may influence assimilation fluxes by nitrifiers in the euphotic zone, which parallel those of the dark ocean. Collectively, marine nitrifiers assimilate up to 2 Pg C year[-1] and 0.05 Pg P year[-1] and thereby recycle roughly 5% of mineralized C and P into marine biomass. Release of roughly 50 Tg DOC and 0.2 Tg DOP by thaumarchaea each year represents a small but fresh input of reduced substrates throughout the ocean.},
}
@article {pmid32423947,
year = {2020},
author = {Takemata, N and Bell, SD},
title = {Emerging views of genome organization in Archaea.},
journal = {Journal of cell science},
volume = {133},
number = {10},
pages = {},
pmid = {32423947},
issn = {1477-9137},
support = {R01 GM125579/GM/NIGMS NIH HHS/United States ; R01 GM135178/GM/NIGMS NIH HHS/United States ; },
mesh = {*Archaea/genetics ; *Chromatin ; Chromosomes ; Eukaryota ; Genome/genetics ; },
abstract = {Over the past decade, advances in methodologies for the determination of chromosome conformation have provided remarkable insight into the local and higher-order organization of bacterial and eukaryotic chromosomes. Locally folded domains are found in both bacterial and eukaryotic genomes, although they vary in size. Importantly, genomes of metazoans also possess higher-order organization into A- and B-type compartments, regions of transcriptionally active and inactive chromatin, respectively. Until recently, nothing was known about the organization of genomes of organisms in the third domain of life - the archaea. However, despite archaea possessing simple circular genomes that are morphologically reminiscent of those seen in many bacteria, a recent study of archaea of the genus Sulfolobus has revealed that it organizes its genome into large-scale domains. These domains further interact to form defined A- and B-type compartments. The interplay of transcription and localization of a novel structural maintenance of chromosomes (SMC) superfamily protein, termed coalescin, defines compartment identity. In this Review, we discuss the mechanistic and evolutionary implications of these findings.},
}
@article {pmid32422160,
year = {2020},
author = {Lekontseva, N and Mikhailina, A and Fando, M and Kravchenko, O and Balobanov, V and Tishchenko, S and Nikulin, A},
title = {Crystal structures and RNA-binding properties of Lsm proteins from archaea Sulfolobus acidocaldarius and Methanococcus vannielii: Similarity and difference of the U-binding mode.},
journal = {Biochimie},
volume = {175},
number = {},
pages = {1-12},
doi = {10.1016/j.biochi.2020.05.001},
pmid = {32422160},
issn = {1638-6183},
mesh = {Archaeal Proteins/*chemistry ; Binding Sites ; Crystallography, X-Ray ; Methanococcus/*chemistry ; Poly U/*chemistry ; RNA-Binding Proteins/*chemistry ; Sulfolobus acidocaldarius/*chemistry ; },
abstract = {Sm and Sm-like (Lsm) proteins are considered as an evolutionary conserved family involved in RNA metabolism in organisms from bacteria and archaea to human. Currently, the function of Sm-like archaeal proteins (SmAP) is not well understood. Here, we report the crystal structures of SmAP proteins from Sulfolobus acidocaldarius and Methanococcus vannielii and a comparative analysis of their RNA-binding sites. Our data show that these SmAPs have only a uridine-specific RNA-binding site, unlike their bacterial homolog Hfq, which has three different RNA-binding sites. Moreover, variations in the amino acid composition of the U-binding sites of the two SmAPs lead to a difference in protein affinity for oligo(U) RNA. Surface plasmon resonance data and nucleotide-binding analysis confirm the high affinity of SmAPs for uridine nucleotides and oligo(U) RNA and the reduced affinity for adenines, guanines, cytidines and corresponding oligo-RNAs. In addition, we demonstrate that MvaSmAP1 and SacSmAP2 are capable of melting an RNA hairpin and, apparently, promote its interaction with complementary RNA.},
}
@article {pmid32382758,
year = {2020},
author = {Gelsinger, DR and Dallon, E and Reddy, R and Mohammad, F and Buskirk, AR and DiRuggiero, J},
title = {Ribosome profiling in archaea reveals leaderless translation, novel translational initiation sites, and ribosome pausing at single codon resolution.},
journal = {Nucleic acids research},
volume = {48},
number = {10},
pages = {5201-5216},
pmid = {32382758},
issn = {1362-4962},
support = {R01 GM110113/GM/NIGMS NIH HHS/United States ; T32 GM007445/GM/NIGMS NIH HHS/United States ; },
mesh = {5' Untranslated Regions/genetics ; Codon/genetics/*metabolism ; Haloferax volcanii/drug effects/*genetics/*metabolism ; Harringtonines/pharmacology ; Peptide Chain Elongation, Translational/drug effects/genetics ; Peptide Chain Initiation, Translational/drug effects/genetics ; *Protein Biosynthesis/drug effects ; Protein Footprinting ; Reading Frames/genetics ; Ribosomes/drug effects/*metabolism ; Transcriptome/drug effects ; },
abstract = {High-throughput methods, such as ribosome profiling, have revealed the complexity of translation regulation in Bacteria and Eukarya with large-scale effects on cellular functions. In contrast, the translational landscape in Archaea remains mostly unexplored. Here, we developed ribosome profiling in a model archaeon, Haloferax volcanii, elucidating, for the first time, the translational landscape of a representative of the third domain of life. We determined the ribosome footprint of H. volcanii to be comparable in size to that of the Eukarya. We linked footprint lengths to initiating and elongating states of the ribosome on leadered transcripts, operons, and on leaderless transcripts, the latter representing 70% of H. volcanii transcriptome. We manipulated ribosome activity with translation inhibitors to reveal ribosome pausing at specific codons. Lastly, we found that the drug harringtonine arrested ribosomes at initiation sites in this archaeon. This drug treatment allowed us to confirm known translation initiation sites and also reveal putative novel initiation sites in intergenic regions and within genes. Ribosome profiling revealed an uncharacterized complexity of translation in this archaeon with bacteria-like, eukarya-like, and potentially novel translation mechanisms. These mechanisms are likely to be functionally essential and to contribute to an expanded proteome with regulatory roles in gene expression.},
}
@article {pmid32380716,
year = {2020},
author = {Rawat, M and Maupin-Furlow, JA},
title = {Redox and Thiols in Archaea.},
journal = {Antioxidants (Basel, Switzerland)},
volume = {9},
number = {5},
pages = {},
pmid = {32380716},
issn = {2076-3921},
support = {R01 GM057498/GM/NIGMS NIH HHS/United States ; DE-FG02-05ER15650//U.S. Department of Energy/ ; MCB-1642283//National Science Foundation/ ; R01 GM57498/NH/NIH HHS/United States ; SC3GM-100855-03/NH/NIH HHS/United States ; MCB1244611//National Science Foundation/ ; },
abstract = {Low molecular weight (LMW) thiols have many functions in bacteria and eukarya, ranging from redox homeostasis to acting as cofactors in numerous reactions, including detoxification of xenobiotic compounds. The LMW thiol, glutathione (GSH), is found in eukaryotes and many species of bacteria. Analogues of GSH include the structurally different LMW thiols: bacillithiol, mycothiol, ergothioneine, and coenzyme A. Many advances have been made in understanding the diverse and multiple functions of GSH and GSH analogues in bacteria but much less is known about distribution and functions of GSH and its analogues in archaea, which constitute the third domain of life, occupying many niches, including those in extreme environments. Archaea are able to use many energy sources and have many unique metabolic reactions and as a result are major contributors to geochemical cycles. As LMW thiols are major players in cells, this review explores the distribution of thiols and their biochemistry in archaea.},
}
@article {pmid32375092,
year = {2020},
author = {Li, Y and Fan, C and Wang, L and Wang, L and Zhang, W and Zhang, H and Niu, L},
title = {Interaction type of tetrabromobisphenol A and copper manipulates ammonia-oxidizing archaea and bacteria communities in co-contaminated river sediments.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {264},
number = {},
pages = {114671},
doi = {10.1016/j.envpol.2020.114671},
pmid = {32375092},
issn = {1873-6424},
mesh = {*Ammonia ; *Archaea ; Bacteria ; Copper ; Oxidation-Reduction ; Phylogeny ; Polybrominated Biphenyls ; Rivers ; Soil Microbiology ; },
abstract = {The combined contamination of brominated flame retardants (BFRs) and heavy metals in electronic waste (e-waste) recycling and disposal areas has been a serious concern owing to their environmental persistence and chronic toxicities. Ammonia oxidizers, e.g., ammonia-oxidizing archaea (AOA) and bacteria (AOB) play essential roles in nitrogen cycling and can serve as ideal indicators that reflect the changes in sediment health in response to environmental variables. There is currently very little information available on the combined toxic effects of BFRs and heavy metals on AOA and AOB communities. In this study, two typical e-waste pollutants, tetrabromobisphenol A (TBBPA) and copper (Cu), were selected as target contaminants to investigate the individual and combined effects of both pollutants on AOA and AOB communities in river sediments. Respective treatments of TBBPA (1, 10, and 20 mg/kg wet weight), Cu (100 mg/kg wet weight) and their combined treatments (weight ratios of 1:100, 1:10, and 1:5) were performed in laboratory experiments. High-throughput sequencing was applied to explore the response of ammonia oxidizers to TBBPA and Cu. The interaction types of TBBPA and Cu were calculated by the directional classification system to reveal the individual and combined toxicities of both contaminants to the ammonia oxidizers. On days 15 and 30, the dominant interaction type of TBBPA and Cu was synergistic (62.50%), and the combined contamination exacted selective pressure and inhibition on the AOB and AOA communities. On days 45 and 90, the interaction type shifted to be antagonistic (83.33%), with both the AOB and AOA communities gradually reaching stable population equilibria. The alteration of the interaction type is attributed to the elevated TBBPA/Cu tolerance as the incubation time increased. This study disclosed the interaction types of TBBPA and Cu in contaminated river sediments, and revealed that the combined effect could potentially manipulate AOB and AOA communities.},
}
@article {pmid32372550,
year = {2020},
author = {Juottonen, H and Fontaine, L and Wurzbacher, C and Drakare, S and Peura, S and Eiler, A},
title = {Archaea in boreal Swedish lakes are diverse, dominated by Woesearchaeota and follow deterministic community assembly.},
journal = {Environmental microbiology},
volume = {22},
number = {8},
pages = {3158-3171},
doi = {10.1111/1462-2920.15058},
pmid = {32372550},
issn = {1462-2920},
support = {2012-4592//Swedish University of Agricultural Sciences/International ; //Swedish Research Council VR/International ; //University of Oslo/International ; 265902//Academy of Finland/International ; CTS:13-113//Carl Tryggers Foundation/International ; },
mesh = {Archaea/classification/genetics/*isolation &amp; purification ; Biodiversity ; Geologic Sediments/microbiology ; Lakes/*microbiology ; Molecular Typing ; Oxidation-Reduction ; Phylogeny ; RNA, Ribosomal, 16S ; Sequence Analysis, RNA ; Sweden ; *Water Microbiology ; },
abstract = {Despite their key role in biogeochemical processes, particularly the methane cycle, archaea are widely underrepresented in molecular surveys because of their lower abundance compared with bacteria and eukaryotes. Here, we use parallel high-resolution small subunit rRNA gene sequencing to explore archaeal diversity in 109 Swedish lakes and correlate archaeal community assembly mechanisms to large-scale latitudinal, climatic (nemoral to arctic) and nutrient (oligotrophic to eutrophic) gradients. Sequencing with universal primers showed the contribution of archaea was on average 0.8% but increased up to 1.5% of the three domains in forest lakes. Archaea-specific sequencing revealed that freshwater archaeal diversity could be partly explained by lake variables associated with nutrient status. Combined with deterministic co-occurrence patterns this finding suggests that ecological drift is overridden by environmental sorting, as well as other deterministic processes such as biogeographic and evolutionary history, leading to lake-specific archaeal biodiversity. Acetoclastic, hydrogenotrophic and methylotrophic methanogens as well as ammonia-oxidizing archaea were frequently detected across the lakes. Archaea-specific sequencing also revealed representatives of Woesearchaeota and other phyla of the DPANN superphylum. This study adds to our understanding of the ecological range of key archaea in freshwaters and links these taxa to hypotheses about processes governing biogeochemical cycles in lakes.},
}
@article {pmid32371309,
year = {2020},
author = {Xie, F and Ma, A and Zhou, H and Liang, Y and Yin, J and Ma, K and Zhuang, X and Zhuang, G},
title = {Niche differentiation of denitrifying anaerobic methane oxidizing bacteria and archaea leads to effective methane filtration in a Tibetan alpine wetland.},
journal = {Environment international},
volume = {140},
number = {},
pages = {105764},
doi = {10.1016/j.envint.2020.105764},
pmid = {32371309},
issn = {1873-6750},
mesh = {Anaerobiosis ; *Archaea/genetics ; Methane ; *Methylococcaceae ; Oxidation-Reduction ; Tibet ; Wetlands ; },
abstract = {Denitrifying anaerobic methane oxidation (DAMO) is a vital methane sink in wetlands. However, the interactions and niche partitioning of DAMO bacteria and archaea in freshwater wetland soils, in addition to the interactions among microorganisms that couple methane and nitrogen cycling is still unclear, despite that these factors may govern the fate of methane and nitrogen in wetlands. Here, we evaluated the vertical distribution of DAMO bacteria and archaea in soil layers along with the potential interactions among populations in the methane-coupled nitrogen cycling microbial community of Tibetan freshwater wetlands. A combination of molecular biology, stable isotope tracer technology, and microbial bioinformatics was used to evaluate these interrelated dynamics. The abundances and potential methane oxidation rates indicated that DAMO bacteria and archaea differentially occupy surface and subsurface soil layers, respectively. The inferred interactions between DAMO bacteria and nitrogen cycling microorganisms within their communities are complex, DAMO bacteria apparently achieve an advantage in the highly competitive environment of surface soils layers and occupy a specific niche in those environments. Conversely, the apparent relationships between DAMO archaea and nitrogen cycling microorganisms are relatively simple, wherein high levels of cooperation are inferred between DAMO archaea and nitrate-producing organisms in subsurface soils layers. These results suggest that the vertical distribution patterns of DAMO bacteria and archaea enable them to play significant roles in the methane oxidation activity of different soil layers and collectively form an effective methane filtration consortium.},
}
@article {pmid32367670,
year = {2021},
author = {Wang, Y and Wegener, G and Ruff, SE and Wang, F},
title = {Methyl/alkyl-coenzyme M reductase-based anaerobic alkane oxidation in archaea.},
journal = {Environmental microbiology},
volume = {23},
number = {2},
pages = {530-541},
doi = {10.1111/1462-2920.15057},
pmid = {32367670},
issn = {1462-2920},
support = {DY135-B2-12//COMRA Project/ ; 41525011,//National Natural Science Foundation of China/ ; 41902313,//National Natural Science Foundation of China/ ; 91751205//National Natural Science Foundation of China/ ; GKZD010075//State Key Laboratory of Ocean Engineering Foundation/ ; 2016YFA0601102,//State Key R&amp;D Project of China/ ; 2018YFC0310800//State Key R&amp;D Project of China/ ; //DFG Cluster of Excellence 2077/ ; },
mesh = {Alkanes/*metabolism ; Anaerobiosis ; Archaea/chemistry/classification/*enzymology/genetics ; Archaeal Proteins/chemistry/genetics/*metabolism ; Oxidation-Reduction ; Oxidoreductases/chemistry/genetics/*metabolism ; Phylogeny ; },
abstract = {Methyl-coenzyme M reductase (MCR) has been originally identified to catalyse the final step of the methanogenesis pathway. About 20 years ago anaerobic methane-oxidizing archaea (ANME) were discovered that use MCR enzymes to activate methane. ANME thrive at the thermodynamic limit of life, are slow-growing, and in most cases form syntrophic consortia with sulfate-reducing bacteria. Recently, archaea that have the ability to anaerobically oxidize non-methane multi-carbon alkanes such as ethane and n-butane were described in both enrichment cultures and environmental samples. These anaerobic multi-carbon alkane-oxidizing archaea (ANKA) use enzymes homologous to MCR named alkyl-coenzyme M reductase (ACR). Here we review the recent progresses on the diversity, distribution and functioning of both ANME and ANKA by presenting a detailed MCR/ACR-based phylogeny, compare their metabolic pathways and discuss the gaps in our knowledge of physiology of these organisms. To improve our understanding of alkane oxidation in archaea, we identified three directions for future research: (i) expanding cultivation attempts to validate omics-based metabolic models of yet-uncultured organisms, (ii) performing biochemical and structural analyses of key enzymes to understand thermodynamic and steric constraints and (iii) investigating the evolution of anaerobic alkane metabolisms and their impact on biogeochemical cycles.},
}
@article {pmid32367054,
year = {2020},
author = {Baker, BJ and De Anda, V and Seitz, KW and Dombrowski, N and Santoro, AE and Lloyd, KG},
title = {Diversity, ecology and evolution of Archaea.},
journal = {Nature microbiology},
volume = {5},
number = {7},
pages = {887-900},
pmid = {32367054},
issn = {2058-5276},
mesh = {*Archaea/classification/genetics/growth &amp; development/metabolism ; *Biodiversity ; *Biological Evolution ; *Ecology ; Energy Metabolism ; Environmental Microbiology ; Genetic Variation ; Genome, Archaeal ; Phylogeny ; },
abstract = {Compared to bacteria, our knowledge of archaeal biology is limited. Historically, microbiologists have mostly relied on culturing and single-gene diversity surveys to understand Archaea in nature. However, only six of the 27 currently proposed archaeal phyla have cultured representatives. Advances in genomic sequencing and computational approaches are revolutionizing our understanding of Archaea. The recovery of genomes belonging to uncultured groups from the environment has resulted in the description of several new phyla, many of which are globally distributed and are among the predominant organisms on the planet. In this Review, we discuss how these genomes, together with long-term enrichment studies and elegant in situ measurements, are providing insights into the metabolic capabilities of the Archaea. We also debate how such studies reveal how important Archaea are in mediating an array of ecological processes, including global carbon and nutrient cycles, and how this increase in archaeal diversity has expanded our view of the tree of life and early archaeal evolution, and has provided new insights into the origin of eukaryotes.},
}
@article {pmid32345641,
year = {2020},
author = {DeWerff, SJ and Bautista, MA and Pauly, M and Zhang, C and Whitaker, RJ},
title = {Killer Archaea: Virus-Mediated Antagonism to CRISPR-Immune Populations Results in Emergent Virus-Host Mutualism.},
journal = {mBio},
volume = {11},
number = {2},
pages = {},
pmid = {32345641},
issn = {2150-7511},
mesh = {Archaea/*virology ; *Bacteriophages ; Biological Evolution ; CRISPR-Cas Systems/*immunology ; Evolution, Molecular ; Genome, Viral ; *Host Microbial Interactions ; *Sulfolobus/genetics/virology ; Symbiosis ; },
abstract = {Theory, simulation, and experimental evolution demonstrate that diversified CRISPR-Cas immunity to lytic viruses can lead to stochastic virus extinction due to a limited number of susceptible hosts available to each potential new protospacer escape mutation. Under such conditions, theory predicts that to evade extinction, viruses evolve toward decreased virulence and promote vertical transmission and persistence in infected hosts. To better understand the evolution of host-virus interactions in microbial populations with active CRISPR-Cas immunity, we studied the interaction between CRISPR-immune Sulfolobus islandicus cells and immune-deficient strains that are infected by the chronic virus SSV9. We demonstrate that Sulfolobus islandicus cells infected with SSV9, and with other related SSVs, kill uninfected, immune strains through an antagonistic mechanism that is a protein and is independent of infectious virus. Cells that are infected with SSV9 are protected from killing and persist in the population. We hypothesize that this infection acts as a form of mutualism between the host and the virus by removing competitors in the population and ensuring continued vertical transmission of the virus within populations with diversified CRISPR-Cas immunity.IMPORTANCE Multiple studies, especially those focusing on the role of lytic viruses in key model systems, have shown the importance of viruses in shaping microbial populations. However, it has become increasingly clear that viruses with a long host-virus interaction, such as those with a chronic lifestyle, can be important drivers of evolution and have large impacts on host ecology. In this work, we describe one such interaction with the acidic crenarchaeon Sulfolobus islandicus and its chronic virus Sulfolobus spindle-shaped virus 9. Our work expands the view in which this symbiosis between host and virus evolved, describing a killing phenotype which we hypothesize has evolved in part due to the high prevalence and diversity of CRISPR-Cas immunity seen in natural populations. We explore the implications of this phenotype in population dynamics and host ecology, as well as the implications of mutualism between this virus-host pair.},
}
@article {pmid32341564,
year = {2020},
author = {Parks, DH and Chuvochina, M and Chaumeil, PA and Rinke, C and Mussig, AJ and Hugenholtz, P},
title = {A complete domain-to-species taxonomy for Bacteria and Archaea.},
journal = {Nature biotechnology},
volume = {38},
number = {9},
pages = {1079-1086},
pmid = {32341564},
issn = {1546-1696},
mesh = {Archaea/*classification/genetics ; Bacteria/*classification/genetics ; Databases, Genetic ; Genome, Archaeal/genetics ; Genome, Bacterial/genetics ; Nucleic Acid Hybridization ; *Phylogeny ; Reproducibility of Results ; },
abstract = {The Genome Taxonomy Database is a phylogenetically consistent, genome-based taxonomy that provides rank-normalized classifications for ~150,000 bacterial and archaeal genomes from domain to genus. However, almost 40% of the genomes in the Genome Taxonomy Database lack a species name. We address this limitation by using commonly accepted average nucleotide identity criteria to set bounds on species and propose species clusters that encompass all publicly available bacterial and archaeal genomes. Unlike previous average nucleotide identity studies, we chose a single representative genome to serve as the effective nomenclatural 'type' defining each species. Of the 24,706 proposed species clusters, 8,792 are based on published names. We assigned placeholder names to the remaining 15,914 species clusters to provide names to the growing number of genomes from uncultivated species. This resource provides a complete domain-to-species taxonomic framework for bacterial and archaeal genomes, which will facilitate research on uncultivated species and improve communication of scientific results.},
}
@article {pmid32317322,
year = {2020},
author = {Hahn, CJ and Laso-Pérez, R and Vulcano, F and Vaziourakis, KM and Stokke, R and Steen, IH and Teske, A and Boetius, A and Liebeke, M and Amann, R and Knittel, K and Wegener, G},
title = {"Candidatus Ethanoperedens," a Thermophilic Genus of Archaea Mediating the Anaerobic Oxidation of Ethane.},
journal = {mBio},
volume = {11},
number = {2},
pages = {},
pmid = {32317322},
issn = {2150-7511},
mesh = {*Anaerobiosis ; Archaea/classification/genetics/*metabolism ; Bacteria/classification/genetics/metabolism ; Biomarkers ; Energy Metabolism ; Ethane/*metabolism ; Genome, Archaeal ; Genomics/methods ; Geologic Sediments/microbiology ; Hydrothermal Vents/microbiology ; Metabolic Networks and Pathways ; Molecular Typing ; Oxidation-Reduction ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Cold seeps and hydrothermal vents deliver large amounts of methane and other gaseous alkanes into marine surface sediments. Consortia of archaea and partner bacteria thrive on the oxidation of these alkanes and its coupling to sulfate reduction. The inherently slow growth of the involved organisms and the lack of pure cultures have impeded the understanding of the molecular mechanisms of archaeal alkane degradation. Here, using hydrothermal sediments of the Guaymas Basin (Gulf of California) and ethane as the substrate, we cultured microbial consortia of a novel anaerobic ethane oxidizer, "Candidatus Ethanoperedens thermophilum" (GoM-Arc1 clade), and its partner bacterium "Candidatus Desulfofervidus auxilii," previously known from methane-oxidizing consortia. The sulfate reduction activity of the culture doubled within one week, indicating a much faster growth than in any other alkane-oxidizing archaea described before. The dominance of a single archaeal phylotype in this culture allowed retrieval of a closed genome of "Ca. Ethanoperedens," a sister genus of the recently reported ethane oxidizer "Candidatus Argoarchaeum." The metagenome-assembled genome of "Ca. Ethanoperedens" encoded a complete methanogenesis pathway including a methyl-coenzyme M reductase (MCR) that is highly divergent from those of methanogens and methanotrophs. Combined substrate and metabolite analysis showed ethane as the sole growth substrate and production of ethyl-coenzyme M as the activation product. Stable isotope probing demonstrated that the enzymatic mechanism of ethane oxidation in "Ca. Ethanoperedens" is fully reversible; thus, its enzymatic machinery has potential for the biotechnological development of microbial ethane production from carbon dioxide.IMPORTANCE In the seabed, gaseous alkanes are oxidized by syntrophic microbial consortia that thereby reduce fluxes of these compounds into the water column. Because of the immense quantities of seabed alkane fluxes, these consortia are key catalysts of the global carbon cycle. Due to their obligate syntrophic lifestyle, the physiology of alkane-degrading archaea remains poorly understood. We have now cultivated a thermophilic, relatively fast-growing ethane oxidizer in partnership with a sulfate-reducing bacterium known to aid in methane oxidation and have retrieved the first complete genome of a short-chain alkane-degrading archaeon. This will greatly enhance the understanding of nonmethane alkane activation by noncanonical methyl-coenzyme M reductase enzymes and provide insights into additional metabolic steps and the mechanisms underlying syntrophic partnerships. Ultimately, this knowledge could lead to the biotechnological development of alkanogenic microorganisms to support the carbon neutrality of industrial processes.},
}
@article {pmid32316034,
year = {2020},
author = {Berkemer, SJ and McGlynn, SE},
title = {A New Analysis of Archaea-Bacteria Domain Separation: Variable Phylogenetic Distance and the Tempo of Early Evolution.},
journal = {Molecular biology and evolution},
volume = {37},
number = {8},
pages = {2332-2340},
pmid = {32316034},
issn = {1537-1719},
mesh = {Archaea/*genetics ; Archaeal Proteins/genetics ; Bacteria/*genetics ; Bacterial Proteins/genetics ; *Phylogeny ; },
abstract = {Comparative genomics and molecular phylogenetics are foundational for understanding biological evolution. Although many studies have been made with the aim of understanding the genomic contents of early life, uncertainty remains. A study by Weiss et al. (Weiss MC, Sousa FL, Mrnjavac N, Neukirchen S, Roettger M, Nelson-Sathi S, Martin WF. 2016. The physiology and habitat of the last universal common ancestor. Nat Microbiol. 1(9):16116.) identified a number of protein families in the last universal common ancestor of archaea and bacteria (LUCA) which were not found in previous works. Here, we report new research that suggests the clustering approaches used in this previous study undersampled protein families, resulting in incomplete phylogenetic trees which do not reflect protein family evolution. Phylogenetic analysis of protein families which include more sequence homologs rejects a simple LUCA hypothesis based on phylogenetic separation of the bacterial and archaeal domains for a majority of the previously identified LUCA proteins (∼82%). To supplement limitations of phylogenetic inference derived from incompletely populated orthologous groups and to test the hypothesis of a period of rapid evolution preceding the separation of the domains, we compared phylogenetic distances both within and between domains, for thousands of orthologous groups. We find a substantial diversity of interdomain versus intradomain branch lengths, even among protein families which exhibit a single domain separating branch and are thought to be associated with the LUCA. Additionally, phylogenetic trees with long interdomain branches relative to intradomain branches are enriched in information categories of protein families in comparison to those associated with metabolic functions. These results provide a new view of protein family evolution and temper claims about the phenotype and habitat of the LUCA.},
}
@article {pmid32302567,
year = {2020},
author = {López-García, P and Moreira, D},
title = {Cultured Asgard Archaea Shed Light on Eukaryogenesis.},
journal = {Cell},
volume = {181},
number = {2},
pages = {232-235},
doi = {10.1016/j.cell.2020.03.058},
pmid = {32302567},
issn = {1097-4172},
mesh = {*Archaea/genetics ; *Eukaryota/genetics ; Eukaryotic Cells ; Genome, Archaeal ; Phylogeny ; },
abstract = {The first cultured Asgard archaeon lives in metabolic symbiosis with hydrogen-scavenging microbes. Its full-genome analysis authenticates the existence of Asgard archaea, previously only known from metagenome-assembled genomes, confirms their closer phylogenetic relatedness to eukaryotes and reinforces the idea that the eukaryotic cell evolved from an integrated archaeal-bacterial syntrophic consortium.},
}
@article {pmid32302368,
year = {2020},
author = {Molnár, J and Magyar, B and Schneider, G and Laczi, K and Valappil, SK and Kovács, &#xc1;L and Nagy, IK and Rákhely, G and Kovács, T},
title = {Identification of a novel archaea virus, detected in hydrocarbon polluted Hungarian and Canadian samples.},
journal = {PloS one},
volume = {15},
number = {4},
pages = {e0231864},
pmid = {32302368},
issn = {1932-6203},
mesh = {Archaea/isolation &amp; purification/*virology ; Archaeal Viruses/genetics/*isolation &amp; purification ; Canada ; DNA, Viral/chemistry/metabolism ; Environmental Pollution/*analysis ; Genome, Viral ; Hungary ; Hydrocarbons/*analysis ; Soil Microbiology ; Water Microbiology ; },
abstract = {Metagenomics is a helpful tool for the analysis of unculturable organisms and viruses. Viruses that target bacteria and archaea play important roles in the microbial diversity of various ecosystems. Here we show that Methanosarcina virus MV (MetMV), the second Methanosarcina sp. virus with a completely determined genome, is characteristic of hydrocarbon pollution in environmental (soil and water) samples. It was highly abundant in Hungarian hydrocarbon polluted samples and its genome was also present in the NCBI SRA database containing reads from hydrocarbon polluted samples collected in Canada, indicating the stability of its niche and the marker feature of this virus. MetMV, as the only currently identified marker virus for pollution in environmental samples, could contribute to the understanding of the complicated network of prokaryotes and their viruses driving the decomposition of environmental pollutants.},
}
@article {pmid32300653,
year = {2020},
author = {Inoue, K and Tsunoda, SP and Singh, M and Tomida, S and Hososhima, S and Konno, M and Nakamura, R and Watanabe, H and Bulzu, PA and Banciu, HL and Andrei, A&#x15e; and Uchihashi, T and Ghai, R and Béjà, O and Kandori, H},
title = {Schizorhodopsins: A family of rhodopsins from Asgard archaea that function as light-driven inward H[+] pumps.},
journal = {Science advances},
volume = {6},
number = {15},
pages = {eaaz2441},
pmid = {32300653},
issn = {2375-2548},
mesh = {Archaea/genetics/*metabolism ; Cell Membrane/metabolism ; Fluorescent Antibody Technique ; Ion Channel Gating/*radiation effects ; Light ; Models, Molecular ; Multigene Family ; Mutation ; Protein Conformation ; Proton Pumps/chemistry/genetics/*metabolism ; Rhodopsin/chemistry/genetics/*metabolism ; Spectroscopy, Fourier Transform Infrared ; Structure-Activity Relationship ; },
abstract = {Schizorhodopsins (SzRs), a rhodopsin family first identified in Asgard archaea, the archaeal group closest to eukaryotes, are present at a phylogenetically intermediate position between typical microbial rhodopsins and heliorhodopsins. However, the biological function and molecular properties of SzRs have not been reported. Here, SzRs from Asgardarchaeota and from a yet unknown microorganism are expressed in Escherichia coli and mammalian cells, and ion transport assays and patch clamp analyses are used to demonstrate SzR as a novel type of light-driven inward H[+] pump. The mutation of a cytoplasmic glutamate inhibited inward H[+] transport, suggesting that it functions as a cytoplasmic H[+] acceptor. The function, trimeric structure, and H[+] transport mechanism of SzR are similar to that of xenorhodopsin (XeR), a light-driven inward H[+] pumping microbial rhodopsins, implying that they evolved convergently. The inward H[+] pump function of SzR provides new insight into the photobiological life cycle of the Asgardarchaeota.},
}
@article {pmid32296409,
year = {2020},
author = {Tourte, M and Schaeffer, P and Grossi, V and Oger, PM},
title = {Functionalized Membrane Domains: An Ancestral Feature of Archaea?.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {526},
pmid = {32296409},
issn = {1664-302X},
abstract = {Bacteria and Eukarya organize their plasma membrane spatially into domains of distinct functions. Due to the uniqueness of their lipids, membrane functionalization in Archaea remains a debated area. A novel membrane ultrastructure predicts that monolayer and bilayer domains would be laterally segregated in the hyperthermophilic archaeon Thermococcus barophilus. With very different physico-chemical parameters of the mono- and bilayer, each domain type would thus allow the docking of different membrane proteins and express different biological functions in the membrane. To estimate the ubiquity of this putative membrane ultrastructure in and out of the order Thermococcales, we re-analyzed the core lipid composition of all the Thermococcales type species and collected all the literature data available for isolated archaea. We show that all species of Thermococcales synthesize a mixture of diether bilayer forming and tetraether monolayer forming lipids, in various ratio from 10 to 80% diether in Pyrococcus horikoshii and Thermococcus gorgonarius, respectively. Since the domain formation prediction rests only on the coexistence of di- and tetraether lipids, we show that all Thermococcales have the ability for domain formation, i.e., differential functionalization of their membrane. Extrapolating this view to the whole Archaea domain, we show that almost all archaea also have the ability to synthesize di- and tetraether lipids, which supports the view that functionalized membrane domains may be shared between all Archaea. Hence domain formation and membrane compartmentalization may have predated the separation of the three domains of life and be essential for the cell cycle.},
}
@article {pmid32281023,
year = {2020},
author = {Fadhlaoui, K and Arnal, ME and Martineau, M and Camponova, P and Ollivier, B and O'Toole, PW and Brugère, JF},
title = {Archaea, specific genetic traits, and development of improved bacterial live biotherapeutic products: another face of next-generation probiotics.},
journal = {Applied microbiology and biotechnology},
volume = {104},
number = {11},
pages = {4705-4716},
doi = {10.1007/s00253-020-10599-8},
pmid = {32281023},
issn = {1432-0614},
support = {16-IDEX-0001 CAP 20-25//ANR program ''Investissements d'Avenir'' CAP 20-25 "Innovation-Research" grant from Hub Innovergne/ ; },
mesh = {Animals ; Archaea/*genetics/*metabolism ; *Biological Therapy ; Cardiovascular Diseases/prevention &amp; control ; Diet ; Gastrointestinal Microbiome/*physiology ; Humans ; Metabolism, Inborn Errors/prevention &amp; control ; Methylamines/blood/metabolism/urine ; Mice ; Probiotics/*therapeutic use ; },
abstract = {Trimethylamine (TMA) and its oxide TMAO are important biomolecules involved in disease-associated processes in humans (e.g., trimethylaminuria and cardiovascular diseases). TMAO in plasma (pTMAO) stems from intestinal TMA, which is formed from various components of the diet in a complex interplay between diet, gut microbiota, and the human host. Most approaches to prevent the occurrence of such deleterious molecules focus on actions to interfere with gut microbiota metabolism to limit the synthesis of TMA. Some human gut archaea however use TMA as terminal electron acceptor for producing methane, thus indicating that intestinal TMA does not accumulate in some human subjects. Therefore, a rational alternative approach is to eliminate neo-synthesized intestinal TMA. This can be achieved through bioremediation of TMA by these peculiar methanogenic archaea, either by stimulating or providing them, leading to a novel kind of next-generation probiotics referred to as archaebiotics. Finally, specific components which are involved in this archaeal metabolism could also be used as intestinal TMA sequesters, facilitating TMA excretion along with stool. Referring to a standard pharmacological approach, these TMA traps could be synthesized ex vivo and then delivered into the human gut. Another approach is the engineering of known probiotic strain in order to metabolize TMA, i.e., live engineered biotherapeutic products. These alternatives would require, however, to take into account the necessity of synthesizing the 22nd amino acid pyrrolysine, i.e., some specificities of the genetics of TMA-consuming archaea. Here, we present an overview of these different strategies and recent advances in the field that will sustain such biotechnological developments. KEY POINTS: • Some autochthonous human archaea can use TMA for their essential metabolism, a methyl-dependent hydrogenotrophic methanogenesis. • They could therefore be used as next-generation probiotics for preventing some human diseases, especially cardiovascular diseases and trimethylaminuria. • Their genetic capacities can also be used to design live recombinant biotherapeutic products. • Encoding of the 22nd amino acid pyrrolysine is necessary for such alternative developments.},
}
@article {pmid32267873,
year = {2020},
author = {Compte-Port, S and Fillol, M and Gich, F and Borrego, CM},
title = {Metabolic versatility of freshwater sedimentary archaea feeding on different organic carbon sources.},
journal = {PloS one},
volume = {15},
number = {4},
pages = {e0231238},
pmid = {32267873},
issn = {1932-6203},
mesh = {Biodiversity ; Biofilms ; Carbon/metabolism ; Carbon Cycle/*physiology ; Crenarchaeota/*genetics/*metabolism ; DNA, Archaeal/genetics ; Ecosystem ; Euryarchaeota/*genetics/*metabolism ; *Geologic Sediments ; Humic Substances ; *Lakes ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Tryptophan ; },
abstract = {Members of the phylum Bathyarchaeota and the class Thermoplasmata are widespread in marine and freshwater sediments where they have been recognized as key players in the carbon cycle. Here, we tested the responsiveness of archaeal communities on settled plant debris and sediment from a karstic lake to different organic carbon amendments (amino acids, plant-derived carbohydrates, and aromatics) using a lab-scale microcosm. Changes in the composition and abundance of sediment and biofilm archaeal communities in both DNA and RNA fractions were assessed by 16S rRNA gene amplicon sequencing and qPCR, respectively, after 7 and 30 days of incubation. Archaeal communities showed compositional changes in terms of alpha and beta diversity in relation to the type of carbon source (amino acids vs. plant-derived compounds), the nucleic acid fraction (DNA vs. RNA), and the incubation time (7 vs. 30 days). Distinct groups within the Bathyarchaeota (Bathy-15 and Bathy-6) and the Thermoplasmata (MBG-D) differently reacted to carbon supplements as deduced from the analysis of RNA libraries. Whereas Bathyarchaeota in biofilms showed a long-term positive response to humic acids, their counterparts in the sediment were mainly stimulated by the addition of tryptophan, suggesting the presence of different subpopulations in both habitats. Overall, our work presents an in vitro assessment of the versatility of archaea inhabiting freshwater sediments towards organic carbon and introduces settled leaf litter as a new habitat for the Bathyarchaeota and the Thermoplasmata.},
}
@article {pmid32247910,
year = {2020},
author = {Jin, D and Zhang, F and Shi, Y and Kong, X and Xie, Y and Du, X and Li, Y and Zhang, R},
title = {Diversity of bacteria and archaea in the groundwater contaminated by chlorinated solvents undergoing natural attenuation.},
journal = {Environmental research},
volume = {185},
number = {},
pages = {109457},
doi = {10.1016/j.envres.2020.109457},
pmid = {32247910},
issn = {1096-0953},
mesh = {*Archaea/genetics ; Bacteria/genetics ; *Groundwater ; RNA, Ribosomal, 16S/genetics ; Solvents ; },
abstract = {Chlorinated solvents (CS)-contaminated groundwater poses serious risks to the environment and public health. Microorganisms play a vital role in efficient remediation of CS. In this study, the microbial community (bacterial and archaeal) composition of three CS-contaminated groundwater wells located at an abandoned chemical factory which covers three orders of magnitude in concentration (0.02-16.15 mg/L) were investigated via 16S rRNA gene high-throughput sequencing. The results indicated that Proteobacteria and Thaumarchaeota were the most abundant bacterial and archaeal groups at the phylum level in groundwater, respectively. The major bacterial genera (Flavobacterium sp., Mycobacterium sp. and unclassified Parcubacteria taxa, etc.) and archaeal genera (Thaumarchaeota Group C3, Miscellaneous Crenarchaeotic Group and Miscellaneous Euryarchaeotic Group, etc.) might be involved in the dechlorination processes. In addition, Pearson's correlation analyses showed that alpha diversity of the bacterial community was not significantly correlated with CS concentration, while alpha diversity of archaeal community greatly decreased with the increased contamination of CS. Moreover, partial Mantel test indicated that oxidation-reduction potential, dissolved oxygen, temperature and methane concentration were major drivers of bacterial and archaeal community composition, whereas CS concentration had no significant impact, indicating that both indigenous bacterial and archaeal community compositions are capable of withstanding elevated CS contamination. This study improves our understanding of how the natural microbial community responds to high CS-contaminated groundwater.},
}
@article {pmid32232532,
year = {2020},
author = {Abril, AG and Rama, JLR and Sánchez-Pérez, A and Villa, TG},
title = {Prokaryotic sigma factors and their transcriptional counterparts in Archaea and Eukarya.},
journal = {Applied microbiology and biotechnology},
volume = {104},
number = {10},
pages = {4289-4302},
doi = {10.1007/s00253-020-10577-0},
pmid = {32232532},
issn = {1432-0614},
mesh = {Archaea/*genetics ; Bacteria/genetics/metabolism ; DNA, Archaeal/genetics ; DNA-Directed RNA Polymerases/genetics/metabolism ; Eukaryota/*genetics ; Gene Expression Regulation ; Promoter Regions, Genetic ; Sigma Factor/*genetics/metabolism ; Transcription Factors/*genetics ; Transcription Initiation, Genetic ; },
abstract = {RNA polymerases (RNAPs) carry out transcription in the three domains of life, Bacteria, Archaea, and Eukarya. Transcription initiation is highly regulated by a variety of transcription factors, whose number and subunit complexity increase during evolution. This process is regulated in Bacteria by the σ factor, while the three eukaryotic RNAPs require a complex set of transcription factors (TFs) and a TATA-binding protein (TBP). The archaeal transcription system appears to be an ancestral version of the eukaryotic RNAPII, requiring transcription factor B (TFB), TBP, and transcription factor E (TFE). The function of the bacterial sigma (σ) factor has been correlated to the roles played by the eukaryotic RNAP II and the archaeal RNAP. In addition, σ factors, TFB, and TFIIB all contain multiple DNA binding helix-turn-helix (HTH) structural motifs; although TFIIB and TFB display two HTH domains, while the bacterial σ factor spans 4 HTH motifs. The sequence similarities and structure alignments of the bacterial σ factor, eukaryotic TFIIB, and archaeal TFB evidence that these three proteins are homologs.Key Points• Transcription initiation is highly regulated by TFs.• Transcription is finely regulated in all domains of life by different sets of TFs.• Specific TFs in Bacteria, Eukarya and Archaea are homologs.},
}
@article {pmid32201928,
year = {2020},
author = {Cai, M and Liu, Y and Yin, X and Zhou, Z and Friedrich, MW and Richter-Heitmann, T and Nimzyk, R and Kulkarni, A and Wang, X and Li, W and Pan, J and Yang, Y and Gu, JD and Li, M},
title = {Diverse Asgard archaea including the novel phylum Gerdarchaeota participate in organic matter degradation.},
journal = {Science China. Life sciences},
volume = {63},
number = {6},
pages = {886-897},
pmid = {32201928},
issn = {1869-1889},
mesh = {Amino Acids/metabolism ; Archaea/*enzymology ; Carbon Cycle ; Ecosystem ; Fatty Acids/metabolism ; Genomics ; Geologic Sediments/*chemistry ; *Metagenome ; Peptides/metabolism ; *Phylogeny ; },
abstract = {Asgard is an archaeal superphylum that might hold the key to understand the origin of eukaryotes, but its diversity and ecological roles remain poorly understood. Here, we reconstructed 15 metagenomic-assembled genomes from coastal sediments covering most known Asgard archaea and a novel group, which is proposed as a new Asgard phylum named as the "Gerdarchaeota". Genomic analyses predict that Gerdarchaeota are facultative anaerobes in utilizing both organic and inorganic carbon. Unlike their closest relatives Heimdallarchaeota, Gerdarchaeota have genes encoding for cellulase and enzymes involved in the tetrahydromethanopterin-based Wood-Ljungdahl pathway. Transcriptomics showed that most of our identified Asgard archaea are capable of degrading organic matter, including peptides, amino acids and fatty acids, occupying ecological niches in different depths of layers of the sediments. Overall, this study broadens the diversity of the mysterious Asgard archaea and provides evidence for their ecological roles in coastal sediments.},
}
@article {pmid32156797,
year = {2020},
author = {Zhao, R and Dahle, H and Ramírez, GA and Jørgensen, SL},
title = {Indigenous Ammonia-Oxidizing Archaea in Oxic Subseafloor Oceanic Crust.},
journal = {mSystems},
volume = {5},
number = {2},
pages = {},
pmid = {32156797},
issn = {2379-5077},
abstract = {Oceanic ridge flank systems represent one of the largest and least-explored microbial habitats on Earth. Fundamental ecological questions regarding community activity, recruitment, and succession in this environment remain unanswered. Here, we investigated ammonia-oxidizing archaea (AOA) in the sediment-buried basalts on the oxic and young ridge flank at North Pond, a sediment-filled pond on the western flank of the Mid-Atlantic Ridge, and compared them with those in the overlying sediments and bottom seawater. Nitrification in the North Pond basement is thermodynamically favorable and is supported by a reaction-transport model simulating the dynamics of nitrate in the crustal fluids. Nitrification rate is estimated to account for 6% to 7% of oxygen consumption, which is similar to the ratios found in marine oxic sediments, suggesting that aerobic mineralization of organic matter is the major ammonium source for crustal nitrifiers. Using the archaeal 16S rRNA and amoA genes as phylogenetic markers, we show that AOA, composed solely of Nitrosopumilaceae, are the major archaeal dwellers at North Pond. Phylogenetic analysis reveals that the crustal AOA communities are distinct from those in the bottom seawater and the upper oxic sediments but are similar to those in the basal part of the overlying sediment column, suggesting either similar environmental selection or the dispersal of microbes across the sediment-basement interface. Additionally, quantitative abundance data suggest enrichment of the dominant Nitrosopumilaceae clade (Eta clade) in the basement compared to the seawater. This study explored AOA and their activity in the upper oceanic crust, and our results have ecological implications for the biogeochemical cycling of nitrogen in the crustal subsurface.IMPORTANCE Ridge flanks represent the major avenue of chemical and heat exchange between the Earth's oceans and the lithosphere and are thought to harbor an enormous and understudied biosphere. However, little is known about the diversity and functionality of the crustal biosphere. Here, we report an indigenous community of archaea specialized in ammonia oxidation (i.e., AOA) in the oxic oceanic crust at North Pond. These AOA are the dominant archaea and are likely responsible for most of the cycling taking place in the first step of nitrification, a feasible nitrogen cycling step in the oxic basement. The crustal AOA community structure significantly differs from that in deep ocean water but is similar to that of the community in the overlying sediments in close proximity. This report links the occurrence of AOA to their metabolic activity in the oxic subseafloor crust and suggests that ecological selection and in situ proliferation may shape the microbial community structure in the rocky subsurface.},
}
@article {pmid32148848,
year = {2020},
author = {Jeon, JH and Lee, HS and Shin, HC and Kwak, MJ and Kim, YG and Gruber, S and Oh, BH},
title = {Evidence for binary Smc complexes lacking kite subunits in archaea.},
journal = {IUCrJ},
volume = {7},
number = {Pt 2},
pages = {193-206},
pmid = {32148848},
issn = {2052-2525},
abstract = {SMC complexes play a central role in chromosome organization in all domains of life. The bacterial Smc-ScpAB complex is a three-subunit complex composed of Smc, ScpA and ScpB. ScpA bridges the two ATPase domains of the Smc homodimer, while ScpB, which belongs to the kite family of proteins, interacts with ScpA. The three subunits are known to be equally important for the function of Smc-ScpAB in bacteria. From crystallographic and biochemical studies, evidence is provided that six archaeal ScpA proteins are unable to interact with the only putative ScpB found in these species. Structure-based sequence alignment reveals that these archaeal ScpAs lack the ScpB-binding segment that is commonly present in the middle of bacterial ScpA sequences, which is thus responsible for their inability to interact with ScpB. ScpA proteins lacking the ScpB-binding segment are found to prevail in archaea. Moreover, two archaeal ScpA proteins with a longer middle region also failed to bind their putative ScpB partner. Furthermore, all or most species belonging to five out of 14 euryarchaeotal orders contain Smc and ScpA but not a detectable ScpB homologue. These data support the notion that archaeal Smc-based complexes generally function as a two-subunit complex composed of only Smc and ScpA.},
}
@article {pmid32126588,
year = {2020},
author = {Taylor, HB and Kurtz, HD},
title = {Composition, diversity, and activity of aerobic ammonia-oxidizing Bacteria and Archaea in the intertidal sands of a grand strand South Carolina beach.},
journal = {MicrobiologyOpen},
volume = {9},
number = {5},
pages = {e1011},
pmid = {32126588},
issn = {2045-8827},
mesh = {Ammonia/metabolism ; Archaea/*classification/metabolism ; Bacteria/*classification/metabolism ; Betaproteobacteria/classification ; Biodiversity ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; Gammaproteobacteria/classification ; High-Throughput Nucleotide Sequencing ; Oxidation-Reduction ; Oxidoreductases/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sand/*microbiology ; *Soil Microbiology ; South Carolina ; },
abstract = {Aerobic ammonia oxidation to nitrite has been established as an important ecosystem process in regulating the level of nitrogen in marine ecosystems. This process is carried out by ammonia-oxidizing bacteria (AOB) within the classes Betaproteobacteria and Gammaproteobacteria and ammonia-oxidizing Archaea (AOA) from the phylum Thaumarchaeota, and the latter of which has been established as more prevalent in marine systems. This study investigated the presence, abundance, and activity of these groups of microbes at a beach near Springmaid Pier in Myrtle Beach, South Carolina, through the implementation of next generation sequencing, quantitative PCR (qPCR), and microcosm experiments to monitor activity. Sequencing analysis revealed a diverse community of ammonia-oxidizing microbes dominated by AOA classified within the family Nitrosopumilaceae, and qPCR revealed the abundance of AOA amoA genes over AOB by at least an order of magnitude in most samples. Microcosm studies indicate that the rates of potential ammonia oxidation in these communities satisfy Michaelis-Menten substrate kinetics and this process is more active at temperatures corresponding to summer months than winter. Potential rates in AOA medium were higher than that of AOB medium, indicating a potentially greater contribution of AOA to this process in this environment. In conclusion, this study provides further evidence of the dominance of AOA in these environments compared with AOB and highlights the overall efficiency of this process at turning over excess ammonium that may be present in these environments.},
}
@article {pmid32094586,
year = {2020},
author = {Sanders, TJ and Wenck, BR and Selan, JN and Barker, MP and Trimmer, SA and Walker, JE and Santangelo, TJ},
title = {FttA is a CPSF73 homologue that terminates transcription in Archaea.},
journal = {Nature microbiology},
volume = {5},
number = {4},
pages = {545-553},
pmid = {32094586},
issn = {2058-5276},
support = {R01 GM100329/GM/NIGMS NIH HHS/United States ; R35 GM143963/GM/NIGMS NIH HHS/United States ; },
mesh = {Archaeal Proteins/*chemistry/genetics/metabolism ; Bacteria/genetics/metabolism ; Biological Evolution ; Cleavage And Polyadenylation Specificity Factor/*chemistry/genetics/metabolism ; DNA-Directed RNA Polymerases/genetics/metabolism ; *Genome, Archaeal ; Humans ; Models, Molecular ; Protein Biosynthesis ; RNA, Messenger/genetics/metabolism ; Structural Homology, Protein ; Thermococcus/*genetics/metabolism ; Transcription Elongation, Genetic ; Transcription Factors/*chemistry/genetics/metabolism ; Transcription Initiation, Genetic ; *Transcription Termination, Genetic ; },
abstract = {Regulated gene expression is largely achieved by controlling the activities of essential, multisubunit RNA polymerase transcription elongation complexes (TECs). The extreme stability required of TECs to processively transcribe large genomic regions necessitates robust mechanisms to terminate transcription. Efficient transcription termination is particularly critical for gene-dense bacterial and archaeal genomes[1-3] in which continued transcription would necessarily transcribe immediately adjacent genes and result in conflicts between the transcription and replication apparatuses[4-6]; the coupling of transcription and translation[7,8] would permit the loading of ribosomes onto aberrant transcripts. Only select sequences or transcription termination factors can disrupt the otherwise extremely stable TEC and we demonstrate that one of the last universally conserved archaeal proteins with unknown biological function is the Factor that terminates transcription in Archaea (FttA). FttA resolves the dichotomy of a prokaryotic gene structure (operons and polarity) and eukaryotic molecular homology (general transcription apparatus) that is observed in Archaea. This missing link between prokaryotic and eukaryotic transcription regulation provides the most parsimonious link to the evolution of the processing activities involved in RNA 3'-end formation in Eukarya.},
}
@article {pmid32086308,
year = {2020},
author = {Wright, CL and Schatteman, A and Crombie, AT and Murrell, JC and Lehtovirta-Morley, LE},
title = {Inhibition of Ammonia Monooxygenase from Ammonia-Oxidizing Archaea by Linear and Aromatic Alkynes.},
journal = {Applied and environmental microbiology},
volume = {86},
number = {9},
pages = {},
pmid = {32086308},
issn = {1098-5336},
mesh = {Alkynes/*metabolism ; Ammonia/metabolism ; Archaea/*metabolism ; Oxidoreductases/*metabolism ; },
abstract = {Ammonia monooxygenase (AMO) is a key nitrogen-transforming enzyme belonging to the same copper-dependent membrane monooxygenase family (CuMMO) as the particulate methane monooxygenase (pMMO). The AMO from ammonia-oxidizing archaea (AOA) is very divergent from both the AMO of ammonia-oxidizing bacteria (AOB) and the pMMO from methanotrophs, and little is known about the structure or substrate range of the archaeal AMO. This study compares inhibition by C2 to C8 linear 1-alkynes of AMO from two phylogenetically distinct strains of AOA, "Candidatus Nitrosocosmicus franklandus" C13 and "Candidatus Nitrosotalea sinensis" Nd2, with AMO from Nitrosomonas europaea and pMMO from Methylococcus capsulatus (Bath). An increased sensitivity of the archaeal AMO to short-chain-length alkynes (≤C5) appeared to be conserved across AOA lineages. Similarities in C2 to C8 alkyne inhibition profiles between AMO from AOA and pMMO from M. capsulatus suggested that the archaeal AMO has a narrower substrate range than N. europaea AMO. Inhibition of AMO from "Ca Nitrosocosmicus franklandus" and N. europaea by the aromatic alkyne phenylacetylene was also investigated. Kinetic data revealed that the mechanisms by which phenylacetylene inhibits "Ca Nitrosocosmicus franklandus" and N. europaea are different, indicating differences in the AMO active site between AOA and AOB. Phenylacetylene was found to be a specific and irreversible inhibitor of AMO from "Ca Nitrosocosmicus franklandus," and it does not compete with NH3 for binding at the active site.IMPORTANCE Archaeal and bacterial ammonia oxidizers (AOA and AOB, respectively) initiate nitrification by oxidizing ammonia to hydroxylamine, a reaction catalyzed by ammonia monooxygenase (AMO). AMO enzyme is difficult to purify in its active form, and its structure and biochemistry remain largely unexplored. The bacterial AMO and the closely related particulate methane monooxygenase (pMMO) have a broad range of hydrocarbon cooxidation substrates. This study provides insights into the AMO of previously unstudied archaeal genera, by comparing the response of the archaeal AMO, a bacterial AMO, and pMMO to inhibition by linear 1-alkynes and the aromatic alkyne, phenylacetylene. Reduced sensitivity to inhibition by larger alkynes suggests that the archaeal AMO has a narrower hydrocarbon substrate range than the bacterial AMO, as previously reported for other genera of AOA. Phenylacetylene inhibited the archaeal and bacterial AMOs at different thresholds and by different mechanisms of inhibition, highlighting structural differences between the two forms of monooxygenase.},
}
@article {pmid32084690,
year = {2020},
author = {Yang, X and Ni, K and Shi, Y and Yi, X and Ji, L and Ma, L and Ruan, J},
title = {Heavy nitrogen application increases soil nitrification through ammonia-oxidizing bacteria rather than archaea in acidic tea (Camellia sinensis L.) plantation soil.},
journal = {The Science of the total environment},
volume = {717},
number = {},
pages = {137248},
doi = {10.1016/j.scitotenv.2020.137248},
pmid = {32084690},
issn = {1879-1026},
mesh = {Ammonia ; *Archaea ; Bacteria ; *Camellia sinensis ; Ecosystem ; Nitrification ; Nitrogen ; Oxidation-Reduction ; Phylogeny ; Soil ; Soil Microbiology ; Tea ; },
abstract = {Nitrogen (N) fertilizer is widely used in agricultural ecosystems and influences N transformation processes in the soil such as nitrification. However, whether nitrification is primarily dominated by ammonia-oxidizing bacteria (AOB) or archaea (AOA) under heavy N application is still under debate. In the present work, the effect of long-term (12 years) N fertilization on soil nitrification and the key influencing factors were investigated in acidic tea plantation soil that received four different rates of N application (0, 119, 285, and 569 kg N ha[-1] yr[-1]). Nitrification potential was measured and partitioned using chemical inhibitors. The abundance of functional genes involved in ammonia oxidation was quantified using quantitative polymerase chain reaction (qPCR). Ammonia-oxidizing communities were identified by shotgun metagenome sequencing. Potential nitrification rate in tea plantation soil was mainly dominated by autotrophic nitrification (PNRA) (71-79%). PNRA and heterotrophic nitrification (PNRH) were both significantly increased by heavy N (569 kg ha[-1]) application. Moreover, PNRA was mainly due to the contribution of AOB (52-66%) in N-treated soils, and N569 significantly increased the AOB contribution without affecting the AOA contribution. N569 increased the functional gene abundance of AOB and TAO100 (a non-halophilic γ-AOB) but decreased that of AOA. The dominant AOB (Nitrosomonas, Nitrosospira, and Nitrosococcus), AOA (Nitrososphaera and Nitrosopumilus) and commamox (Nitrospira) groups were profoundly altered by long-term N application rates. Partial least squares regression showed that total nitrification (PNRT), PNRA, and PNRAOB were primarily explained by the functional gene abundance of nitrifiers whereas PNRH and PNRAOA were closely associated with soil and pruned litter properties. Moreover, structural equation modeling (SEM) revealed that long-term N application significantly and indirectly affected nitrification potential by directly influencing soil properties, pruned litter properties, and functional gene abundance. Understanding the relative contribution of AOA and AOB to nitrification may help to better regulate N fertilizer use in agricultural ecosystems.},
}
@article {pmid32073658,
year = {2020},
author = {Eckl, DB and Huber, H and Bäumler, W},
title = {First Report on Photodynamic Inactivation of Archaea Including a Novel Method for High-Throughput Reduction Measurement.},
journal = {Photochemistry and photobiology},
volume = {96},
number = {4},
pages = {883-889},
doi = {10.1111/php.13229},
pmid = {32073658},
issn = {1751-1097},
support = {415812443//Deutsche Forschungsgemeinschaft/International ; },
mesh = {Anti-Infective Agents/pharmacology ; Halobacterium salinarum/*drug effects ; Photosensitizing Agents/*pharmacology ; Porphyrins/*pharmacology ; },
abstract = {Archaea are considered third, independent domain of living organisms besides eukaryotic and bacterial cells. To date, no report is available of photodynamic inactivation (PDI) of any archaeal cells. Two commercially available photosensitizers (SAPYR and TMPyP) were used to investigate photodynamic inactivation of Halobacterium salinarum. In addition, a novel high-throughput method was tested to evaluate microbial reduction in vitro. Due to the high salt content of the culture medium, the physical and chemical properties of photosensitizers were analyzed via spectroscopy and fluorescence-based DPBF assays. Attachment or uptake of photosensitizers to or in archaeal cells was investigated. The photodynamic inactivation of Halobacterium salinarum was evaluated via growth curve method allowing a high throughput of samples. The presented results indicate that the photodynamic mechanisms are working even in high salt environments. Either photosensitizer inactivated the archaeal cells with a reduction of 99.9% at least. The growth curves provided a fast and precise measurement of cell viability. The results show for the first time that PDI can kill not only bacterial cells but also robust archaea. The novel method for generating high-throughput growth curves provides benefits for future research regarding antimicrobial substances in general.},
}
@article {pmid32071162,
year = {2020},
author = {Liechty, Z and Santos-Medellín, C and Edwards, J and Nguyen, B and Mikhail, D and Eason, S and Phillips, G and Sundaresan, V},
title = {Comparative Analysis of Root Microbiomes of Rice Cultivars with High and Low Methane Emissions Reveals Differences in Abundance of Methanogenic Archaea and Putative Upstream Fermenters.},
journal = {mSystems},
volume = {5},
number = {1},
pages = {},
pmid = {32071162},
issn = {2379-5077},
abstract = {Rice cultivation worldwide accounts for ∼7 to 17% of global methane emissions. Methane cycling in rice paddies is a microbial process not only involving methane producers (methanogens) and methane metabolizers (methanotrophs) but also other microbial taxa that affect upstream processes related to methane metabolism. Rice cultivars vary in their rates of methane emissions, but the influence of rice genotypes on methane cycling microbiota has been poorly characterized. Here, we profiled the rhizosphere, rhizoplane, and endosphere microbiomes of a high-methane-emitting cultivar (Sabine) and a low-methane-emitting cultivar (CLXL745) throughout the growing season to identify variations in the archaeal and bacterial communities relating to methane emissions. The rhizosphere of the high-emitting cultivar was enriched in methanogens compared to that in the low emitter, whereas the relative abundances of methanotrophs between the cultivars were not significantly different. Further analysis of cultivar-sensitive taxa identified families enriched in the high emitter that are associated with methanogenesis-related processes. The high emitter had greater relative abundances of sulfate-reducing and iron-reducing taxa which peak earlier in the season than methanogens and are necessary to lower soil oxidation reduction potential before methanogenesis can occur. The high emitter also had a greater abundance of fermentative taxa which produce methanogenesis precursors (acetate, CO2, and H2). Furthermore, the high emitter was enriched in taxa related to acetogenesis which compete with methanogens for CO2 and H2 These taxa were enriched in a spatio-specific manner and reveal a complex network of microbial interactions on which plant genotype-dependent factors can act to affect methanogenesis and methane emissions.IMPORTANCE Rice cultivation is a major source of anthropogenic emissions of methane, a greenhouse gas with a potentially severe impact on climate change. Emission variation between rice cultivars suggests the feasibility of breeding low-emission rice, but there is a limited understanding of how genotypes affect the microbiota involved in methane cycling. Here, we show that the root microbiome of the high-emitting cultivar is enriched both in methanogens and in taxa associated with fermentation, iron, and sulfate reduction and acetogenesis, processes that support methanogenesis. Understanding how cultivars affect microbes with methanogenesis-related functions is vital for understanding the genetic basis for methane emission in rice and can aid in the development of breeding programs that reduce the environmental impact of rice cultivation.},
}
@article {pmid32068866,
year = {2020},
author = {Badel, C and Da Cunha, V and Forterre, P and Oberto, J},
title = {Pervasive Suicidal Integrases in Deep-Sea Archaea.},
journal = {Molecular biology and evolution},
volume = {37},
number = {6},
pages = {1727-1743},
pmid = {32068866},
issn = {1537-1719},
mesh = {*Evolution, Molecular ; Hydrothermal Vents ; Integrases/genetics/*metabolism ; Interspersed Repetitive Sequences ; *Pseudogenes ; Thermococcus/*enzymology/genetics/isolation &amp; purification ; },
abstract = {Mobile genetic elements (MGEs) often encode integrases which catalyze the site-specific insertion of their genetic information into the host genome and the reverse reaction of excision. Hyperthermophilic archaea harbor integrases belonging to the SSV-family which carry the MGE recombination site within their open reading frame. Upon integration into the host genome, SSV integrases disrupt their own gene into two inactive pseudogenes and are termed suicidal for this reason. The evolutionary maintenance of suicidal integrases, concurring with the high prevalence and multiples recruitments of these recombinases by archaeal MGEs, is highly paradoxical. To elucidate this phenomenon, we analyzed the wide phylogenomic distribution of a prominent class of suicidal integrases which revealed a highly variable integration site specificity. Our results highlighted the remarkable hybrid nature of these enzymes encoded from the assembly of inactive pseudogenes of different origins. The characterization of the biological properties of one of these integrases, IntpT26-2 showed that this enzyme was active over a wide range of temperatures up to 99 °C and displayed a less-stringent site specificity requirement than comparable integrases. These observations concurred in explaining the pervasiveness of these suicidal integrases in the most hyperthermophilic organisms. The biochemical and phylogenomic data presented here revealed a target site switching system operating on highly thermostable integrases and suggested a new model for split gene reconstitution. By generating fast-evolving pseudogenes at high frequency, suicidal integrases constitute a powerful model to approach the molecular mechanisms involved in the generation of active genes variants by the recombination of proto-genes.},
}
@article {pmid32055827,
year = {2020},
author = {Tästensen, JB and Johnsen, U and Reinhardt, A and Ortjohann, M and Schönheit, P},
title = {D-galactose catabolism in archaea: operation of the DeLey-Doudoroff pathway in Haloferax volcanii.},
journal = {FEMS microbiology letters},
volume = {367},
number = {1},
pages = {},
doi = {10.1093/femsle/fnaa029},
pmid = {32055827},
issn = {1574-6968},
mesh = {Carbohydrate Metabolism/genetics ; Enzymes/genetics/metabolism ; Galactose/*metabolism ; Gene Knockout Techniques ; Genes, Archaeal/*genetics ; *Haloferax volcanii/enzymology/genetics ; Metabolic Networks and Pathways/*genetics ; },
abstract = {The haloarchaeon Haloferax volcanii was found to grow on D-galactose as carbon and energy source. Here we report a comprehensive analysis of D-galactose catabolism in H. volcanii. Genome analyses indicated a cluster of genes encoding putative enzymes of the DeLey-Doudoroff pathway for D-galactose degradation including galactose dehydrogenase, galactonate dehydratase, 2-keto-3-deoxygalactonate kinase and 2-keto-3-deoxy-6-phosphogalactonate (KDPGal) aldolase. The recombinant galactose dehydrogenase and galactonate dehydratase showed high specificity for D-galactose and galactonate, respectively, whereas KDPGal aldolase was promiscuous in utilizing KDPGal and also the C4 epimer 2-keto-3-deoxy-6-phosphogluconate as substrates. Growth studies with knock-out mutants indicated the functional involvement of galactose dehydrogenase, galactonate dehydratase and KDPGal aldolase in D-galactose degradation. Further, the transcriptional regulator GacR was identified, which was characterized as an activator of genes of the DeLey-Doudoroff pathway. Finally, genes were identified encoding components of an ABC transporter and a knock-out mutant of the substrate binding protein indicated the functional involvement of this transporter in D-galactose uptake. This is the first report of D-galactose degradation via the DeLey-Doudoroff pathway in the domain of archaea.},
}
@article {pmid32047285,
year = {2020},
author = {Roux, S and Krupovic, M and Daly, RA and Borges, AL and Nayfach, S and Schulz, F and Sharrar, A and Matheus Carnevali, PB and Cheng, JF and Ivanova, NN and Bondy-Denomy, J and Wrighton, KC and Woyke, T and Visel, A and Kyrpides, NC and Eloe-Fadrosh, EA},
title = {Author Correction: Cryptic inoviruses revealed as pervasive in bacteria and archaea across Earth's biomes.},
journal = {Nature microbiology},
volume = {5},
number = {3},
pages = {527},
doi = {10.1038/s41564-020-0681-5},
pmid = {32047285},
issn = {2058-5276},
abstract = {An amendment to this paper has been published and can be accessed via a link at the top of the paper.},
}
@article {pmid32041059,
year = {2020},
author = {Roy, D and McEvoy, J and Khan, E},
title = {Abundance and activity of ammonia oxidizing archaea and bacteria in bulk water and biofilm in water supply systems practicing chlorination and chloramination: Full and laboratory scale investigations.},
journal = {The Science of the total environment},
volume = {715},
number = {},
pages = {137043},
doi = {10.1016/j.scitotenv.2020.137043},
pmid = {32041059},
issn = {1879-1026},
mesh = {Ammonia ; *Archaea ; Bacteria ; *Biofilms ; Halogenation ; Nitrification ; Oxidation-Reduction ; Phylogeny ; Soil Microbiology ; Water ; Water Supply ; },
abstract = {The abundance and nitrification activity of ammonia oxidizing archaea (AOA) and ammonia oxidizing bacteria (AOB) in bulk water and biofilm in chloraminated and chlorinated water supply systems were investigated. The abundance of AOB varied between cold and warm periods while that was the case for AOA only in biofilm. Lower ammonia concentrations favored the abundance of AOA over AOB. AOA and AOB were found more in distal zones of the distribution system (DS). Higher numbers of AOA and AOB were observed in DS associated with chloramination compared to those associated with chlorination. Significant positive correlations between ammonia-N in bulk water and AOA indicate a possibility of involvement of AOA in nitrification in DS. A separate laboratory-based experiment simulating DS condition was conducted to understand the effects of chlorine and chloramine dosages and temperature on AOA and AOB. AOA were inhibited less than AOB in the presence of lower concentrations of chlorine and chloramine (1.5 and 2.0 mg/L chlorine; 0.05-0.1 and 0.3-0.4 mg/L chloramine) while both of them were not detected at higher dosages (2.5 mg/L chlorine and 1.5-1.6 mg/L chloramine). At a low temperature (10-12 °C), chloramine and chlorine provided similar inhibition trends in which AOB were inhibited more than AOA. At a high temperature (25 °C), chloramine was less inhibitory to AOA and AOB than chlorine.},
}
@article {pmid32030412,
year = {2020},
author = {Phung, DK and Etienne, C and Batista, M and Langendijk-Genevaux, P and Moalic, Y and Laurent, S and Liuu, S and Morales, V and Jebbar, M and Fichant, G and Bouvier, M and Flament, D and Clouet-d'Orval, B},
title = {RNA processing machineries in Archaea: the 5'-3' exoribonuclease aRNase J of the β-CASP family is engaged specifically with the helicase ASH-Ski2 and the 3'-5' exoribonucleolytic RNA exosome machinery.},
journal = {Nucleic acids research},
volume = {48},
number = {7},
pages = {3832-3847},
pmid = {32030412},
issn = {1362-4962},
mesh = {Euryarchaeota/*enzymology ; Exoribonucleases/*metabolism ; Exosome Multienzyme Ribonuclease Complex/*metabolism ; Protein Interaction Mapping ; Pyrococcus abyssi/enzymology ; RNA Helicases/*metabolism ; *RNA Processing, Post-Transcriptional ; RNA, Archaeal/*metabolism ; Thermococcus/enzymology ; },
abstract = {A network of RNA helicases, endoribonucleases and exoribonucleases regulates the quantity and quality of cellular RNAs. To date, mechanistic studies focussed on bacterial and eukaryal systems due to the challenge of identifying the main drivers of RNA decay and processing in Archaea. Here, our data support that aRNase J, a 5'-3' exoribonuclease of the β-CASP family conserved in Euryarchaeota, engages specifically with a Ski2-like helicase and the RNA exosome to potentially exert control over RNA surveillance, at the vicinity of the ribosome. Proteomic landscapes and direct protein-protein interaction analyses, strengthened by comprehensive phylogenomic studies demonstrated that aRNase J interplay with ASH-Ski2 and a cap exosome subunit. Finally, Thermococcus barophilus whole-cell extract fractionation experiments provide evidences that an aRNase J/ASH-Ski2 complex might exist in vivo and hint at an association of aRNase J with the ribosome that is emphasised in absence of ASH-Ski2. Whilst aRNase J homologues are found among bacteria, the RNA exosome and the Ski2-like RNA helicase have eukaryotic homologues, underlining the mosaic aspect of archaeal RNA machines. Altogether, these results suggest a fundamental role of β-CASP RNase/helicase complex in archaeal RNA metabolism.},
}
@article {pmid32025518,
year = {2020},
author = {Lyubetsky, VA and Zverkov, OA and Rubanov, LI and Seliverstov, AV},
title = {Optimal Growth Temperature and Intergenic Distances in Bacteria, Archaea, and Plastids of Rhodophytic Branch.},
journal = {BioMed research international},
volume = {2020},
number = {},
pages = {3465380},
pmid = {32025518},
issn = {2314-6141},
mesh = {Archaea/*genetics/*growth &amp; development/metabolism ; Archaeal Proteins/genetics ; Bacteria/*genetics/*growth &amp; development/metabolism ; Bacterial Proteins/genetics ; Cell Culture Techniques ; Chloroplast Proteins/genetics ; Evolution, Molecular ; Genome, Archaeal ; Genome, Bacterial ; Genome, Plastid ; Linear Models ; Plastids/*genetics/metabolism/*physiology ; *Temperature ; },
abstract = {The lengths of intergenic regions between neighboring genes that are convergent, divergent, or unidirectional were calculated for plastids of the rhodophytic branch and complete archaeal and bacterial genomes. Statistically significant linear relationships between any pair of the medians of these three length types have been revealed in each genomic group. Exponential relationships between the optimal growth temperature and each of the three medians have been revealed as well. The leading coefficients of the regression equations relating all pairs of the medians as well as temperature and any of the medians have the same sign and order of magnitude. The results obtained for plastids, archaea, and bacteria are also similar at the qualitative level. For instance, the medians are always low at high temperatures. At low temperatures, the medians tend to statistically significant greater values and scattering. The original model was used to test our hypothesis that the intergenic distances are optimized in particular to decrease the competition of RNA polymerases within the locus that results in transcribing shortened RNAs. Overall, this points to an effect of temperature for both remote and close genomes.},
}
@article {pmid32014611,
year = {2020},
author = {Fusco, S and Aulitto, M and Iacobucci, I and Crocamo, G and Pucci, P and Bartolucci, S and Monti, M and Contursi, P},
title = {The interaction between the F55 virus-encoded transcription regulator and the RadA host recombinase reveals a common strategy in Archaea and Bacteria to sense the UV-induced damage to the host DNA.},
journal = {Biochimica et biophysica acta. Gene regulatory mechanisms},
volume = {1863},
number = {5},
pages = {194493},
doi = {10.1016/j.bbagrm.2020.194493},
pmid = {32014611},
issn = {1876-4320},
mesh = {Archaeal Proteins/*genetics/metabolism ; *DNA Damage ; DNA-Binding Proteins/*genetics/metabolism ; Escherichia coli/genetics/metabolism/radiation effects ; Escherichia coli Proteins/genetics/metabolism ; Fuselloviridae/genetics/metabolism/pathogenicity ; Promoter Regions, Genetic ; Protein Binding ; Rec A Recombinases/genetics/metabolism ; Sulfolobus/genetics/metabolism/radiation effects/virology ; Transcription Factors/genetics/*metabolism ; Ultraviolet Rays ; Viral Proteins/genetics/*metabolism ; },
abstract = {Sulfolobus spindle-shaped virus 1 is the only UV-inducible member of the virus family Fuselloviridae. Originally isolated from Saccharolobus shibatae B12, it can also infect Saccharolobus solfataricus. Like the CI repressor of the bacteriophage λ, the SSV1-encoded F55 transcription repressor acts as a key regulator for the maintenance of the SSV1 carrier state. In particular, F55 binds to tandem repeat sequences located within the promoters of the early and UV-inducible transcripts. Upon exposure to UV light, a temporally coordinated pattern of gene expression is triggered. In the case of the better characterized bacteriophage λ, the switch from lysogenic to lytic development is regulated by a crosstalk between the virus encoded CI repressor and the host RecA, which regulates also the SOS response. For SSV1, instead, the regulatory mechanisms governing the switch from the carrier to the induced state have not been completely unravelled. In this study we have applied an integrated biochemical approach based on a variant of the EMSA assay coupled to mass spectrometry analyses to identify the proteins associated with F55 when bound to its specific DNA promoter sequences. Among the putative F55 interactors, we identified RadA and showed that the archaeal molecular components F55 and RadA are functional homologs of bacteriophage λ (factor CI) and Escherichia coli (RecA) system.},
}
@article {pmid32013868,
year = {2020},
author = {Zhang, RY and Zou, B and Yan, YW and Jeon, CO and Li, M and Cai, M and Quan, ZX},
title = {Design of targeted primers based on 16S rRNA sequences in meta-transcriptomic datasets and identification of a novel taxonomic group in the Asgard archaea.},
journal = {BMC microbiology},
volume = {20},
number = {1},
pages = {25},
pmid = {32013868},
issn = {1471-2180},
support = {2018YFC0310600//the National Key R&amp;D Program of China/International ; 31870109//National Natural Science Foundation of China/International ; 31170114//National Natural Science Foundation of China/International ; },
mesh = {Archaea/*classification/genetics ; DNA Primers/*genetics ; DNA, Archaeal/genetics ; DNA, Ribosomal/genetics ; Databases, Genetic ; Gene Expression Profiling ; High-Throughput Nucleotide Sequencing ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, RNA/*methods ; },
abstract = {BACKGROUND: Amplification of small subunit (SSU) rRNA genes with universal primers is a common method used to assess microbial populations in various environmental samples. However, owing to limitations in coverage of these universal primers, some microorganisms remain unidentified. The present study aimed to establish a method for amplifying nearly full-length SSU rRNA gene sequences of previously unidentified prokaryotes, using newly designed targeted primers via primer evaluation in meta-transcriptomic datasets.<br><br>METHODS: Primer binding regions of universal primer 8F/Arch21F for bacteria or archaea were used for primer evaluation of SSU rRNA sequences in meta-transcriptomic datasets. Furthermore, targeted forward primers were designed based on SSU rRNA reads from unclassified groups unmatched with the universal primer 8F/Arch21F, and these primers were used to amplify nearly full-length special SSU rRNA gene sequences along with universal reverse primer 1492R. Similarity and phylogenetic analysis were used to confirm their novel status.<br><br>RESULTS: Using this method, we identified unclassified SSU rRNA sequences that were not matched with universal primer 8F and Arch21F. A new group within the Asgard superphylum was amplified by the newly designed specific primer based on these unclassified SSU rRNA sequences by using mudflat samples.<br><br>CONCLUSION: We showed that using specific primers designed based on universal primer evaluation from meta-transcriptomic datasets, identification of novel taxonomic groups from a specific environment is possible.},
}
@article {pmid32006018,
year = {2020},
author = {Menéndez-Serra, M and Ontiveros, VJ and Triadó-Margarit, X and Alonso, D and Casamayor, EO},
title = {Dynamics and ecological distributions of the Archaea microbiome from inland saline lakes (Monegros Desert, Spain).},
journal = {FEMS microbiology ecology},
volume = {96},
number = {3},
pages = {},
doi = {10.1093/femsec/fiaa019},
pmid = {32006018},
issn = {1574-6941},
mesh = {*Archaea/genetics ; Biodiversity ; Lakes ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Spain ; },
abstract = {We characterized the rich Archaea microbiome of shallow inland lakes (Monegros Desert, NE Spain) by 16S rRNA gene tag sequencing covering a wide salinity range (0.1%-40% w/v) along 3 years. Up to 990 operational taxonomic units (OTUs; >97% identity) were detected allocated in 14 major archaeal phyla and heterogeneously distributed along the salt gradient. Dynamics and idiosyncratic ecological distributions were uncovered for the different phyla. A high genetic richness was observed for Woesearchaeota and Pacearchaeota (>370 OTUs each), followed by Halobacteria (105), Nanohaloarchaeota (62) and Thermoplasmata (19). Overall, the distribution of genetic richness was strongly correlated with environmental niche amplitude, but not with occurrence. We unveiled high occurrence for a very rich Woesearchaeota assemblage, and an unexpected positive correlation of Pacearchaeota abundance with salinity at >15% dissolved salt content. The estimated dynamic behaviour (temporal 'turnover' rates of presence/absence data) unveiled Thaumarchaeota and Halobacteria as the most dynamic groups, and Aenigmarchaeota and Thermoplasmata as the most stable. The DPANN Pacearchaeota, Woesearchaeota, and Nanohaloarchaeota showed intermediate rates, suggesting higher resilience to environmental perturbations. A rich and dynamic Archaea microbiome was unveiled, including unseen ecological traits for relevant members of the still largely unknown DPANN group, supporting a strong ecological differentiation between Pacearchaeota and Woesearchaeota.},
}
@article {pmid31999377,
year = {2020},
author = {Roy, C and Kumar, R and Datta, S},
title = {Comparative studies on ion-pair energetic, distribution among three domains of life: Archaea, eubacteria, and eukarya.},
journal = {Proteins},
volume = {88},
number = {7},
pages = {865-873},
doi = {10.1002/prot.25878},
pmid = {31999377},
issn = {1097-0134},
mesh = {Archaea/*chemistry ; Archaeal Proteins/*chemistry ; Bacteria/*chemistry ; Bacterial Proteins/*chemistry ; Crystallography, X-Ray ; Datasets as Topic ; Eukaryota/*chemistry ; Models, Molecular ; Protein Conformation, alpha-Helical ; Protein Conformation, beta-Strand ; Protein Interaction Domains and Motifs ; Protein Stability ; Static Electricity ; Thermodynamics ; },
abstract = {Salt-bridges play a unique role in the structural and functional stability of proteins, especially under harsh environments. How these salt-bridges contribute to the overall thermodynamic stability of protein structure and function across different domains of life is elusive still date. To address the issue, statistical analyses on the energies of salt-bridges, involved in proteins' structure and function, are performed across three domains of life, that is, archaea, eubacteria, and eukarya. Results show that although the majority of salt-bridges are stable and conserved, yet the stability of archaeal proteins (∆∆Gnet = -5.06 ± 3.8) is much more than that of eubacteria (∆∆Gnet = -3.7 ± 2.9) and eukarya (∆∆Gnet = -3.54 ± 3.1). Unlike earlier study with archaea, in eukarya and eubacteria, not all buried salt-bridge in our dataset are stable. Buried salt-bridges play surprising role in protein stability, whose variations are clearly observed among these domains. Greater desolvation penalty of buried salt-bridges is compensated by stable network of salt-bridges apart from equal contribution of bridge and background energy terms. On the basis proteins' secondary structure, topology, and evolution, our observation shows that salt-bridges when present closer to each other in sequence tend to form a greater number. Overall, our comparative study provides insight into the role of specific electrostatic interactions in proteins from different domains of life, which we hope, would be useful for protein engineering and bioinformatics study.},
}
@article {pmid31994760,
year = {2020},
author = {Eichler, J},
title = {Modifying Post-Translational Modifications: A Strategy Used by Archaea for Adapting to Changing Environments?: Manipulating the Extent, Position, or Content of Post-Translational Modifications May Help Archaea Adapt to Environmental Change.},
journal = {BioEssays : news and reviews in molecular, cellular and developmental biology},
volume = {42},
number = {3},
pages = {e1900207},
doi = {10.1002/bies.201900207},
pmid = {31994760},
issn = {1521-1878},
support = {2193/16//ISF-NSFC joint research program/International ; },
mesh = {Adaptation, Physiological/*physiology ; Amino Acid Sequence ; Archaea/*growth &amp; development/*metabolism ; Archaeal Proteins/*metabolism ; *Environment ; Glycosylation ; Methylation ; Phosphorylation/physiology ; Protein Processing, Post-Translational/*physiology ; },
abstract = {In concert with the selective pressures affecting protein folding and function in the extreme environments in which they can exist, proteins in Archaea have evolved to present permanent molecular adaptations at the amino acid sequence level. Such adaptations may not, however, suffice when Archaea encounter transient changes in their surroundings. Post-translational modifications offer a rapid and reversible layer of adaptation for proteins to cope with such situations. Here, it is proposed that Archaea further augment their ability to survive changing growth conditions by modifying the extent, position, and, where relevant, the composition of different post-translational modifications, as a function of the environment. Support for this hypothesis comes from recent reports describing how patterns of protein glycosylation, methylation, and other post-translational modifications of archaeal proteins are altered in response to environmental change. Indeed, adjusting post-translational modifications as a means to cope with environmental variability may also hold true beyond the Archaea.},
}
@article {pmid31949227,
year = {2020},
author = {Guo, H and Ma, L and Liang, Y and Hou, Z and Min, W},
title = {Response of ammonia-oxidizing Bacteria and Archaea to long-term saline water irrigation in alluvial grey desert soils.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {489},
pmid = {31949227},
issn = {2045-2322},
support = {41661055//The National Natural Science Foundation of China/International ; },
mesh = {Agricultural Irrigation/*methods ; Ammonia/*chemistry ; Archaea/*metabolism ; Archaeal Proteins/genetics/metabolism ; Bacteria/*metabolism ; Bacterial Proteins/genetics/metabolism ; DNA Copy Number Variations ; Ecosystem ; *Nitrification ; Saline Waters/*chemistry ; *Soil Microbiology ; },
abstract = {Soil nitrification via ammonia oxidation is a key ecosystem process in terrestrial environments, but little is known of how increasing irrigation of farmland soils with saline waters effects these processes. We investigated the effects of long-term irrigation with saline water on the abundances and community structures of ammonia-oxidizing bacteria (AOB) and archaea (AOA). Irrigation with brackish or saline water increased soil salinity (EC1:5) and NH4-N compared to irrigation with freshwater, while NO3-N, potential nitrification rates (PNR) and amoA gene copy numbers of AOA and AOB decreased markedly under irrigation regimes with saline waters. Moreover, irrigation with brackish water lowered AOA/AOB ratios. PNR was positively correlated with AOA and AOB amoA gene copy numbers across treatments. Saline and brackish water irrigation significantly increased the diversity of AOA, as noted by Shannon index values, while saline water irrigation markedly reduced AOB diversity. In addition, irrigation with brackish or fresh waters resulted in higher proportions of unclassified taxa in the AOB communities. However, irrigation with saline water led to higher proportions of unclassified taxa in the AOA communities along with the Candidatus Nitrosocaldus genus, as compared to soils irrigated with freshwater. AOA community structures were closely associated with soil salinity, NO3[-]N, and pH, while AOB communities were only significantly associated with NO3[-]N and pH. These results suggest that salinity was the dominant factor affecting the growth of ammonia-oxidizing microorganisms and community structure. These results can provide a scientific basis for further exploring the response mechanism of ammonia-oxidizing microorganisms and their roles in nitrogen transformation in alluvial grey desert soils of arid areas.},
}
@article {pmid31942065,
year = {2020},
author = {},
title = {The life of archaea.},
journal = {Nature},
volume = {577},
number = {7790},
pages = {294},
doi = {10.1038/d41586-020-00087-4},
pmid = {31942065},
issn = {1476-4687},
mesh = {*Archaea ; *Eukaryota ; Phylogeny ; Prokaryotic Cells ; },
}
@article {pmid31941956,
year = {2020},
author = {Besseling, MA and Hopmans, EC and Bale, NJ and Schouten, S and Damsté, JSS and Villanueva, L},
title = {The absence of intact polar lipid-derived GDGTs in marine waters dominated by Marine Group II: Implications for lipid biosynthesis in Archaea.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {294},
pmid = {31941956},
issn = {2045-2322},
mesh = {Archaea/classification/genetics/*metabolism ; Atlantic Ocean ; Chromatography, High Pressure Liquid ; Euryarchaeota/classification/genetics/metabolism ; Glyceryl Ethers/analysis/metabolism ; Lipids/analysis/*biosynthesis/isolation &amp; purification ; Mass Spectrometry ; Phylogeny ; RNA, Ribosomal, 16S/chemistry/metabolism ; Solid Phase Extraction ; },
abstract = {The marine pelagic archaeal community is dominated by three major groups, the marine group I (MGI) Thaumarchaeota, and the marine groups II and III (MGII and MGIII) Euryarchaeota. Studies of both MGI cultures and the environment have shown that the MGI core membrane lipids are predominantly composed of glycerol dibiphytanyl glycerol tetraether (GDGT) lipids and the diether lipid archaeol. However, there are no cultured representatives of MGII and III archaea and, therefore, both their membrane lipid composition and potential contribution to the marine archaeal lipid pool remain unknown. Here, we show that GDGTs present in suspended particulate matter of the (sub)surface waters of the North Atlantic Ocean and the coastal North Sea are derived from MGI archaea, and that MGII archaea do not significantly contribute to the pool of GDGTs and archaeol. This implies, in contrast to previous suggestions, that their lipids do not affect the widely used sea surface temperature proxy TEX86. These findings also indicate that MGII archaea are not able to produce any known archaeal lipids, implying that our understanding of the evolution of membrane lipid biosynthesis in Archaea is far from complete.},
}
@article {pmid31937639,
year = {2020},
author = {Barco, RA and Garrity, GM and Scott, JJ and Amend, JP and Nealson, KH and Emerson, D},
title = {A Genus Definition for Bacteria and Archaea Based on a Standard Genome Relatedness Index.},
journal = {mBio},
volume = {11},
number = {1},
pages = {},
pmid = {31937639},
issn = {2150-7511},
mesh = {Archaea/*classification ; Bacteria/*classification ; Classification/*methods ; DNA, Bacterial/genetics ; *Genome, Archaeal ; *Genome, Bacterial ; Genomics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; },
abstract = {Genus assignment is fundamental in the characterization of microbes, yet there is currently no unambiguous way to demarcate genera solely using standard genomic relatedness indices. Here, we propose an approach to demarcate genera that relies on the combined use of the average nucleotide identity, genome alignment fraction, and the distinction between type- and non-type species. More than 3,500 genomes representing type strains of species from >850 genera of either bacterial or archaeal lineages were tested. Over 140 genera were analyzed in detail within the taxonomic context of order/family. Significant genomic differences between members of a genus and type species of other genera in the same order/family were conserved in 94% of the cases. Nearly 90% (92% if polyphyletic genera are excluded) of the type strains were classified in agreement with current taxonomy. The 448 type strains that need reclassification directly impact 33% of the genera analyzed in detail. The results provide a first line of evidence that the combination of genomic indices provides added resolution to effectively demarcate genera within the taxonomic framework that is currently based on the 16S rRNA gene. We also identify the emergence of natural breakpoints at the genome level that can further help in the circumscription of taxa, increasing the proportion of directly impacted genera to at least 43% and pointing at inaccuracies on the use of the 16S rRNA gene as a taxonomic marker, despite its precision. Altogether, these results suggest that genomic coherence is an emergent property of genera in Bacteria and ArchaeaIMPORTANCE In recent decades, the taxonomy of Bacteria and Archaea, and therefore genus designation, has been largely based on the use of a single ribosomal gene, the 16S rRNA gene, as a taxonomic marker. We propose an approach to delineate genera that excludes the direct use of the 16S rRNA gene and focuses on a standard genome relatedness index, the average nucleotide identity. Our findings are of importance to the microbiology community because the emergent properties of Bacteria and Archaea that are identified in this study will help assign genera with higher taxonomic resolution.},
}
@article {pmid31926374,
year = {2020},
author = {Wang, C and Tang, S and He, X and Ji, G},
title = {The abundance and community structure of active ammonia-oxidizing archaea and ammonia-oxidizing bacteria shape their activities and contributions in coastal wetlands.},
journal = {Water research},
volume = {171},
number = {},
pages = {115464},
doi = {10.1016/j.watres.2019.115464},
pmid = {31926374},
issn = {1879-2448},
mesh = {*Ammonia ; *Archaea ; Bacteria ; China ; Nitrification ; Oxidation-Reduction ; Phylogeny ; Soil Microbiology ; Wetlands ; },
abstract = {Aerobic ammonia oxidation, an important part of the global nitrogen cycle, is thought to be jointly driven by ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) in coastal wetlands. However, the activities and contributions of AOA and AOB in coastal wetlands have remained largely unknown. Here, we investigated the oxidation capability of AOA and AOB in four types of typical coastal wetlands (paddy, estuary, shallow and reed wetland) in the Bohai region in China using DNA-based stable-isotope probing (DNA-SIP), quantitative PCR and high-throughput sequencing techniques. We found that the community structure of AOB varied substantially, and the AOA structure was more stable across different coastal wetlands. The rate of AOA was 0.12, 0.84, 0.45 and 0.93 μg N g[-1] soil d[-1] in paddy, estuary, shallow and reed wetlands, and the rate of AOB was 5.61, 10.72, 0.74 and 1.16 μg N g[-1] soil d[-1], respectively. We found that the contribution of AOA gradually increased from paddy to estuary to shallow wetland and finally to reed wetland, with values of 2.03%, 7.25%, 37.53% and 44.51%, respectively. Our results provide new insight into the mechanisms of the differences in activities and the contributions of AOA and AOB in different coastal wetlands, and our findings may contribute to further understanding of the global nitrogen cycle.},
}
@article {pmid31920997,
year = {2019},
author = {Dekas, AE and Parada, AE and Mayali, X and Fuhrman, JA and Wollard, J and Weber, PK and Pett-Ridge, J},
title = {Characterizing Chemoautotrophy and Heterotrophy in Marine Archaea and Bacteria With Single-Cell Multi-isotope NanoSIP.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {2682},
pmid = {31920997},
issn = {1664-302X},
abstract = {Characterizing and quantifying in situ metabolisms remains both a central goal and challenge for environmental microbiology. Here, we used a single-cell, multi-isotope approach to investigate the anabolic activity of marine microorganisms, with an emphasis on natural populations of Thaumarchaeota. After incubating coastal Pacific Ocean water with [13]C-bicarbonate and [15]N-amino acids, we used nanoscale secondary ion mass spectrometry (nanoSIMS) to isotopically screen 1,501 individual cells, and 16S rRNA amplicon sequencing to assess community composition. We established isotopic enrichment thresholds for activity and metabolic classification, and with these determined the percentage of anabolically active cells, the distribution of activity across the whole community, and the metabolic lifestyle-chemoautotrophic or heterotrophic-of each cell. Most cells (>90%) were anabolically active during the incubation, and 4-17% were chemoautotrophic. When we inhibited bacteria with antibiotics, the fraction of chemoautotrophic cells detected via nanoSIMS increased, suggesting archaea dominated chemoautotrophy. With fluorescence in situ hybridization coupled to nanoSIMS (FISH-nanoSIMS), we confirmed that most Thaumarchaeota were living chemoautotrophically, while bacteria were not. FISH-nanoSIMS analysis of cells incubated with dual-labeled ([13]C,[15]N-) amino acids revealed that most Thaumarchaeota cells assimilated amino-acid-derived nitrogen but not carbon, while bacteria assimilated both. This indicates that some Thaumarchaeota do not assimilate intact amino acids, suggesting intra-phylum heterogeneity in organic carbon utilization, and potentially their use of amino acids for nitrification. Together, our results demonstrate the utility of multi-isotope nanoSIMS analysis for high-throughput metabolic screening, and shed light on the activity and metabolism of uncultured marine archaea and bacteria.},
}
@article {pmid31913316,
year = {2020},
author = {Maus, D and Heinz, J and Schirmack, J and Airo, A and Kounaves, SP and Wagner, D and Schulze-Makuch, D},
title = {Methanogenic Archaea Can Produce Methane in Deliquescence-Driven Mars Analog Environments.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {6},
pmid = {31913316},
issn = {2045-2322},
support = {339231//EC | EC Seventh Framework Programm | FP7 Ideas: European Research Council (FP7-IDEAS-ERC - Specific Programme: "Ideas" Implementing the Seventh Framework Programme of the European Community for Research, Technological Development and Demonstration Activities (2007 to 2013))/International ; },
mesh = {Chemoautotrophic Growth ; Exobiology/*methods ; *Extraterrestrial Environment ; *Mars ; Methane/analysis/*metabolism ; Methanosarcina/*physiology ; Salts/*chemistry ; Water/*chemistry ; },
abstract = {The current understanding of the Martian surface indicates that briny environments at the near-surface are temporarily possible, e.g. in the case of the presumably deliquescence-driven Recurring Slope Lineae (RSL). However, whether such dynamic environments are habitable for terrestrial organisms remains poorly understood. This hypothesis was tested by developing a Closed Deliquescence System (CDS) consisting of a mixture of desiccated Martian Regolith Analog (MRA) substrate, salts, and microbial cells, which over the course of days became wetted through deliquescence. The methane produced via metabolic activity for three methanogenic archaea: Methanosarcina mazei, M. barkeri and M. soligelidi, was measured after exposing them to three different MRA substrates using either NaCl or NaClO4 as a hygroscopic salt. Our experiments showed that (1) M. soligelidi rapidly produced methane at 4 °C, (2) M. barkeri produced methane at 28 °C though not at 4 °C, (3) M. mazei was not metabolically reactivated through deliquescence, (4) none of the species produced methane in the presence of perchlorate, and (5) all species were metabolically most active in the phyllosilicate-containing MRA. These results emphasize the importance of the substrate, microbial species, salt, and temperature used in the experiments. Furthermore, we show here for the first time that water provided by deliquescence alone is sufficient to rehydrate methanogenic archaea and to reactivate their metabolism under conditions roughly analogous to the near-subsurface Martian environment.},
}
@article {pmid31900730,
year = {2020},
author = {Cavalier-Smith, T and Chao, EE},
title = {Multidomain ribosomal protein trees and the planctobacterial origin of neomura (eukaryotes, archaebacteria).},
journal = {Protoplasma},
volume = {257},
number = {3},
pages = {621-753},
pmid = {31900730},
issn = {1615-6102},
support = {NE/E004156/1//Natural Environment Research Council/ ; },
mesh = {Archaea/*chemistry ; Biological Evolution ; Eukaryota/*chemistry ; *Phylogeny ; Ribosomes/*chemistry ; },
abstract = {Palaeontologically, eubacteria are > 3× older than neomura (eukaryotes, archaebacteria). Cell biology contrasts ancestral eubacterial murein peptidoglycan walls and derived neomuran N-linked glycoprotein coats/walls. Misinterpreting long stems connecting clade neomura to eubacteria on ribosomal sequence trees (plus misinterpreted protein paralogue trees) obscured this historical pattern. Universal multiprotein ribosomal protein (RP) trees, more accurate than rRNA trees, are taxonomically undersampled. To reduce contradictions with genically richer eukaryote trees and improve eubacterial phylogeny, we constructed site-heterogeneous and maximum-likelihood universal three-domain, two-domain, and single-domain trees for 143 eukaryotes (branching now congruent with 187-protein trees), 60 archaebacteria, and 151 taxonomically representative eubacteria, using 51 and 26 RPs. Site-heterogeneous trees greatly improve eubacterial phylogeny and higher classification, e.g. showing gracilicute monophyly, that many 'rDNA-phyla' belong in Proteobacteria, and reveal robust new phyla Synthermota and Aquithermota. Monoderm Posibacteria and Mollicutes (two separate wall losses) are both polyphyletic: multiple outer membrane losses in Endobacteria occurred separately from Actinobacteria; neither phylum is related to Chloroflexi, the most divergent prokaryotes, which originated photosynthesis (new model proposed). RP trees support an eozoan root for eukaryotes and are consistent with archaebacteria being their sisters and rooted between Filarchaeota (=Proteoarchaeota, including 'Asgardia') and Euryarchaeota sensu-lato (including ultrasimplified 'DPANN' whose long branches often distort trees). Two-domain trees group eukaryotes within Planctobacteria, and archaebacteria with Planctobacteria/Sphingobacteria. Integrated molecular/palaeontological evidence favours negibacterial ancestors for neomura and all life. Unique presence of key pre-neomuran characters favours Planctobacteria only as ancestral to neomura, which apparently arose by coevolutionary repercussions (explained here in detail, including RP replacement) of simultaneous outer membrane and murein loss. Planctobacterial C-1 methanotrophic enzymes are likely ancestral to archaebacterial methanogenesis and β-propeller-α-solenoid proteins to eukaryotic vesicle coats, nuclear-pore-complexes, and intraciliary transport. Planctobacterial chaperone-independent 4/5-protofilament microtubules and MamK actin-ancestors prepared for eukaryote intracellular motility, mitosis, cytokinesis, and phagocytosis. We refute numerous wrong ideas about the universal tree.},
}
@article {pmid31889259,
year = {2020},
author = {Knüppel, R and Fenk, M and Jüttner, M and Ferreira-Cerca, S},
title = {In Vivo RNA Chemical Footprinting Analysis in Archaea.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2106},
number = {},
pages = {193-208},
doi = {10.1007/978-1-0716-0231-7_12},
pmid = {31889259},
issn = {1940-6029},
mesh = {Archaea/chemistry/genetics ; Archaeal Proteins/chemistry/*metabolism ; *Molecular Probe Techniques ; *RNA Folding ; RNA, Archaeal/chemistry/genetics/*metabolism ; RNA-Binding Proteins/chemistry/*metabolism ; },
abstract = {RNA structural conformation and dynamics govern the functional properties of all RNA/RNP. Accordingly, defining changes of RNA structure and dynamics in various conditions may provide detailed insight into how RNA structural properties regulate the function of RNA/RNP. Traditional chemical footprinting analysis using chemical modifiers allows to sample the dynamics and conformation landscape of diverse RNA/RNP. However, many chemical modifiers are limited in their capacity to provide unbiased information reflecting the in vivo RNA/RNP structural landscape. In the recent years, the development of selective-2'-hydroxyl acylation analyzed by primer extension (SHAPE) methodology that uses powerful new chemical modifiers has significantly improved in vitro and in vivo structural probing of secondary and tertiary interactions of diverse RNA species at the single nucleotide level.Although the original discovery of Archaea as an independent domain of life is intimately linked to the technological development of RNA analysis, our understanding of in vivo RNA structural conformation and dynamics in this domain of life remains scarce.This protocol describes the in vivo use of SHAPE chemistry in two evolutionary divergent model Archaea, Sulfolobus acidocaldarius and Haloferax volcanii.},
}
@article {pmid31884971,
year = {2019},
author = {Coutinho, FH and Edwards, RA and Rodríguez-Valera, F},
title = {Charting the diversity of uncultured viruses of Archaea and Bacteria.},
journal = {BMC biology},
volume = {17},
number = {1},
pages = {109},
pmid = {31884971},
issn = {1741-7007},
mesh = {Archaea/*virology ; Bacteria/*virology ; Bacteriophages/*genetics ; *Genome, Viral ; *Microbiota ; Phylogeny ; },
abstract = {BACKGROUND: Viruses of Archaea and Bacteria are among the most abundant and diverse biological entities on Earth. Unraveling their biodiversity has been challenging due to methodological limitations. Recent advances in culture-independent techniques, such as metagenomics, shed light on the unknown viral diversity, revealing thousands of new viral nucleotide sequences at an unprecedented scale. However, these novel sequences have not been properly classified and the evolutionary associations between them were not resolved.<br><br>RESULTS: Here, we performed phylogenomic analysis of nearly 200,000 viral nucleotide sequences to establish GL-UVAB: Genomic Lineages of Uncultured Viruses of Archaea and Bacteria. The pan-genome content of the identified lineages shed light on some of their infection strategies, potential to modulate host physiology, and mechanisms to escape host resistance systems. Furthermore, using GL-UVAB as a reference database for annotating metagenomes revealed elusive habitat distribution patterns of viral lineages and environmental drivers of community composition.<br><br>CONCLUSIONS: These findings provide insights about the genomic diversity and ecology of viruses of prokaryotes. The source code used in these analyses is freely available at https://sourceforge.net/projects/gluvab/.},
}
@article {pmid31869713,
year = {2020},
author = {Li, M and Huang, Y and Yang, Y and Wang, H and Hu, L and Zhong, H and He, Z},
title = {Heavy metal ions removed from imitating acid mine drainages with a thermoacidophilic archaea: Acidianus manzaensis YN25.},
journal = {Ecotoxicology and environmental safety},
volume = {190},
number = {},
pages = {110084},
doi = {10.1016/j.ecoenv.2019.110084},
pmid = {31869713},
issn = {1090-2414},
mesh = {Acidianus/*physiology ; Adsorption ; Archaea/metabolism ; *Biodegradation, Environmental ; Heavy Ions ; Hydrogen-Ion Concentration ; Ions ; Metals, Heavy/analysis/metabolism ; *Mining ; Spectroscopy, Fourier Transform Infrared ; Water Pollutants, Chemical/analysis/*metabolism ; },
abstract = {Metals in acid mine drainages (AMD) have posed a great threat to environment, and in situ economic environment-friendly remediation technologies need to be developed. Moreover, the effects of acidophiles on biosorption and migrating behaviors of metals in AMD have not been previously reported. In this study, the extremely thermoacidophilic Archaea, Acidianus manzaensis YN25 (A. manzaensis YN25) was used as a bio-adsorbent to adsorb metals (Cu[2+], Ni[2+], Cd[2+] and Zn[2+]) from acidic solutions which were taken to imitate AMD. The values of their maximum biosorption capacities at both high (1 mM) and low (0.1 mM) metal concentrations followed the order: Cu[2+] > Ni[2+] > Cd[2+] > Zn[2+]. With the elevations of temperature and pH value, the adsorption amounts of metals increased. The results also indicated that A. manzaensis YN25 had the highest adsorption affinity to Cu[2+] in coexisting system of quaternary metals. Acid-base titration data revealed that carboxyl and phosphoryl groups provided adsorption sites for metals via deprotonation. Fourier transform infrared spectroscopy (FTIR) and X-ray photoelectron spectroscopy (XPS) further corroborated that amino played an important role in the biosorption process. The fitted Langmuir model illustrated monolayer adsorption occurring on cell surface. The possible adsorption mechanism of A. manzaensis YN25 mainly involved in electrostatic attraction and complexes formation. This study gives a profound insight into the biosorption behavior of heavy metals in acidic solution by thermoacidophilic Archaea and provides a probable novel strategy for in situ remediation of heavy metals pollution in AMD.},
}
@article {pmid31856202,
year = {2019},
author = {Hernandez-Guerrero, R and Galán-Vásquez, E and Pérez-Rueda, E},
title = {The protein architecture in Bacteria and Archaea identifies a set of promiscuous and ancient domains.},
journal = {PloS one},
volume = {14},
number = {12},
pages = {e0226604},
pmid = {31856202},
issn = {1932-6203},
mesh = {Archaea/genetics ; Archaeal Proteins/*chemistry/genetics/metabolism ; Bacteria/genetics ; Bacterial Proteins/*chemistry/genetics/metabolism ; Binding Sites ; Conserved Sequence ; *Evolution, Molecular ; Protein Binding ; Proteome ; },
abstract = {In this work, we describe a systematic comparative genomic analysis of promiscuous domains in genomes of Bacteria and Archaea. A quantitative measure of domain promiscuity, the weighted domain architecture score (WDAS), was used and applied to 1317 domains in 1320 genomes of Bacteria and Archaea. A functional analysis associated with the WDAS per genome showed that 18 of 50 functional categories were identified as significantly enriched in the promiscuous domains; in particular, small-molecule binding domains, transferases domains, DNA binding domains (transcription factors), and signal transduction domains were identified as promiscuous. In contrast, non-promiscuous domains were identified as associated with 6 of 50 functional categories, and the category Function unknown was enriched. In addition, the WDASs of 52 domains correlated with genome size, i.e., WDAS values decreased as the genome size increased, suggesting that the number of combinations at larger domains increases, including domains in the superfamilies Winged helix-turn-helix and P-loop-containing nucleoside triphosphate hydrolases. Finally, based on classification of the domains according to their ancestry, we determined that the set of 52 promiscuous domains are also ancient and abundant among all the genomes, in contrast to the non-promiscuous domains. In summary, we consider that the association between these two classes of protein domains (promiscuous and non-promiscuous) provides bacterial and archaeal cells with the ability to respond to diverse environmental challenges.},
}
@article {pmid31854886,
year = {2019},
author = {Bao, QL and Wang, FH and Bao, WK and Huang, YZ},
title = {[Effects of Rice Straw Addition on Methanogenic Archaea and Bacteria in Two Paddy Soils].},
journal = {Huan jing ke xue= Huanjing kexue},
volume = {40},
number = {9},
pages = {4202-4212},
doi = {10.13227/j.hjkx.201901195},
pmid = {31854886},
issn = {0250-3301},
mesh = {*Archaea ; Bacteria ; Methane ; *Oryza ; RNA, Ribosomal, 16S ; Soil ; *Soil Microbiology ; },
abstract = {Rice straw (RS) returning has an important effect on CH4 emission in rice paddy soil. In the present study, two paddy soil types from Jiangxi (JX) and Guangdong (GD), respectively, with different amounts of added RS were incubated through microcosmic anaerobic incubation experiments to investigate the responses of methanogenic archaea and bacteria communities after relatively long-term incubation. The different amounts of added RS affected methanogenic archaea community structures in the JX soil to some extent but did not affect the GD soil. The mcrA gene copy number increased with an increase in RS amount in both soils. Under the same amount of RS, the copy number of this gene in the JX soil was greater than that in the GD soil. In addition, significant positive correlations were shown between the RS amount and the copy number of the mcrA gene, and the response of the copy number was more sensitive to the RS amount in the JX soil. Obvious differences in methanogenic archaea community structures were shown between two soils. Methanosarcinaceae, Methanocellaceae, Methanomicrobiaceae, Methanobacteriaceae, and unknown microorganism (494 bp) were detected in the JX soil, and Methanobacteriaceae, Methanosarcinaceae, and Methanocellaceae were observed in the GD soil. The bacterial communities exhibited obvious differences between the two soil types after 180 days of incubation. The bacterial diversity in the GD soil was higher than that in the JX soil, although the amounts of dominant bacteria in the JX soil, including Bacillus, Desulfovirgula, Thermosporothrix, Acidobacteria/Gp1, Acidobacteria/Gp3, and Ktedonobacter, were higher than those of the GD soil, including Longilinea, Acidobacteria/Gp6, Bellilinea, and Thermosporothrix. RS application promoted the growth of methanogenic archaea as important substrates. Moreover, different structures of methanogens and bacteria were shown between the two soil types after relatively long-term incubation.},
}
@article {pmid31854584,
year = {2019},
author = {Guo, JL and Liu, Y and Wei, WX and Ge, TD and Wang, GJ},
title = {[Impact of Dicyandiamide (DCD) and 3,4-Dimethylpyrazole Phosphate (DMPP) on Ammonia-oxidizing Bacteria and Archaea in a Vegetable Planting Soil].},
journal = {Huan jing ke xue= Huanjing kexue},
volume = {40},
number = {11},
pages = {5142-5150},
doi = {10.13227/j.hjkx.201902031},
pmid = {31854584},
issn = {0250-3301},
mesh = {Ammonia ; *Archaea ; Bacteria ; Guanidines ; Nitrification ; Oxidation-Reduction ; Phosphates ; Phylogeny ; *Pyrazoles ; *Soil ; *Soil Microbiology ; *Vegetables ; },
abstract = {Nitrification inhibitors (NIs) dicyandiamide (DCD) and 3,4-dimethylpyrazole phosphate (DMPP) showed significant effects in the inhibition of nitrification and the improvement of the utilization efficiency of nitrogen fertilizer in agricultural soils. However, the effects of different NIs on ammonia-oxidizing bacteria (AOB) and archaea (AOA) is still unclear. To verify the inhibitory effect of DCD and DMPP on AOB and AOA, a pot experiment was performed, including Urea, Urea+DCD, and Urea+DMPP treatments. The dynamics of NH4[+]-N and NO3[-]-N and nitrification potential among different treatments were measured. In addition, real-time PCR and high-throughput sequencing approaches were applied to investigate the changes in the AOB and AOA population abundance and composition. The results revealed that the concentrations of NH4[+]-N in Urea+DCD and Urea+DMPP treatments were 213% and 675% higher than that in the CK treatment, respectively. However, the concentrations of NO3[-]-N and the nitrification potentials were 13.3% and 37.2%, and 20.4% and 82.4% lower than that in CK treatment, respectively; Furthermore, the copy numbers of the bacterial and archaeal amoA gene were 51.2% and 56.5%, and 6.0% and 27.0% lower than that in the CK treatment, respectively. However, the diversity indexes of AOB and AOA communities, including evenness and richness, exhibited no significant differences after addition of DCD and DMPP. The nork-environmental-samples, unclassified-Nitrosomonadaceae, unclassified-Bacteria, and Nitrosospira, were the predominant genera of the AOB community. The no rank-Crenarchaeota, no rank-environmental-samples and Nitrososphaera were the predominant groups in the AOA community. Summarily, application of DCD and DMPP significantly delayed the transformation of NH4[+]-N, decreased the formation of NO3[-]-N, inhibited the abundance and changed the composition of AOB and AOA communities. DMPP had a stronger inhibitory effect on nitrification, and on AOB and AOA than DCD. Therefore, compared with DCD, DMPP had a better application prospect regarding the improvement of the nitrogen utilization efficiency in vegetable soil.},
}
@article {pmid31836857,
year = {2020},
author = {Gribaldo, S and Brochier-Armanet, C},
title = {Evolutionary relationships between archaea and eukaryotes.},
journal = {Nature ecology &amp; evolution},
volume = {4},
number = {1},
pages = {20-21},
pmid = {31836857},
issn = {2397-334X},
mesh = {*Archaea ; Biological Evolution ; *Eukaryota ; Evolution, Molecular ; Phylogeny ; },
}
@article {pmid31828323,
year = {2020},
author = {Jüttner, M and Weiß, M and Ostheimer, N and Reglin, C and Kern, M and Knüppel, R and Ferreira-Cerca, S},
title = {A versatile cis-acting element reporter system to study the function, maturation and stability of ribosomal RNA mutants in archaea.},
journal = {Nucleic acids research},
volume = {48},
number = {4},
pages = {2073-2090},
pmid = {31828323},
issn = {1362-4962},
mesh = {Gene Regulatory Networks/*genetics ; Haloferax volcanii/genetics ; Mutation/genetics ; Phylogeny ; RNA Precursors/genetics ; RNA Processing, Post-Transcriptional/*genetics ; RNA Stability/genetics ; RNA, Archaeal/genetics ; RNA, Ribosomal/*genetics ; Ribosomes/*genetics ; },
abstract = {General molecular principles of ribosome biogenesis have been well explored in bacteria and eukaryotes. Collectively, these studies have revealed important functional differences and few similarities between these processes. Phylogenetic studies suggest that the information processing machineries from archaea and eukaryotes are evolutionary more closely related than their bacterial counterparts. These observations raise the question of how ribosome synthesis in archaea may proceed in vivo. In this study, we describe a versatile plasmid-based cis-acting reporter system allowing to analyze in vivo the consequences of ribosomal RNA mutations in the model archaeon Haloferax volcanii. Applying this system, we provide evidence that the bulge-helix-bulge motif enclosed within the ribosomal RNA processing stems is required for the formation of archaeal-specific circular-pre-rRNA intermediates and mature rRNAs. In addition, we have collected evidences suggesting functional coordination of the early steps of ribosome synthesis in H. volcanii. Together our investigation describes a versatile platform allowing to generate and functionally analyze the fate of diverse rRNA variants, thereby paving the way to better understand the cis-acting molecular determinants necessary for archaeal ribosome synthesis, maturation, stability and function.},
}
@article {pmid31827386,
year = {2019},
author = {Zheng, P and Wang, C and Zhang, X and Gong, J},
title = {Community Structure and Abundance of Archaea in a Zostera marina Meadow: A Comparison between Seagrass-Colonized and Bare Sediment Sites.},
journal = {Archaea (Vancouver, B.C.)},
volume = {2019},
number = {},
pages = {5108012},
pmid = {31827386},
issn = {1472-3654},
mesh = {Archaea/classification/genetics/*growth &amp; development/*isolation &amp; purification ; Biodiversity ; Genes, Archaeal ; Genes, rRNA ; Geologic Sediments/*microbiology ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Zosteraceae/*growth &amp; development ; },
abstract = {Seagrass colonization alters sediment physicochemical properties by depositing seagrass fibers and releasing organic carbon and oxygen from the roots. How this seagrass colonization-induced spatial heterogeneity affects archaeal community structure and abundance remains unclear. In this study, we investigated archaeal abundance, diversity, and composition in both vegetated and adjacent bare surface sediments of a Zostera marina meadow. High-throughput sequencing of 16S rDNA showed that Woesearchaeota, Bathyarchaeota, and Thaumarchaeota were the most abundant phyla across all samples, accounting for approximately 42%, 21%, and 17% of the total archaeal communities, respectively. In terms of relative abundance, Woesearchaeota and Bathyarchaeota were not significantly different between these two niches; however, specific subclades (Woese-3, Woese-21, Bathy-6, Bathy-18) were significantly enriched in vegetated sediments (P < 0.05), while Thaumarchaeota was favored in unvegetated sites (P = 0.02). The quantification of archaeal 16S rRNA genes showed that the absolute abundance of the whole archaeal community, Bathyarchaeota, and Woese-3, Woese-10, Woese-13, and Woese-21 was significantly more abundant in vegetated sediments than in bare sediments (P < 0.05). Our study expands the available knowledge of the distribution patterns and niche preferences of archaea in seagrass systems, especially for the different subclades of Woesearchaeota and Bathyarchaeota, in terms of both relative proportions and absolute quantities.},
}
@article {pmid31819085,
year = {2019},
author = {Togo, AH and Grine, G and Khelaifia, S and des Robert, C and Brevaut, V and Caputo, A and Baptiste, E and Bonnet, M and Levasseur, A and Drancourt, M and Million, M and Raoult, D},
title = {Culture of Methanogenic Archaea from Human Colostrum and Milk.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {18653},
pmid = {31819085},
issn = {2045-2322},
mesh = {Animals ; Body Mass Index ; Breast Feeding/*adverse effects ; Chemoautotrophic Growth/genetics ; Colostrum/*microbiology ; DNA, Archaeal/genetics/isolation &amp; purification ; Euryarchaeota/genetics/pathogenicity ; Feces/microbiology ; Female ; Humans ; Infant ; Methanobrevibacter/genetics/*isolation &amp; purification/pathogenicity ; Microbiota/genetics ; Milk, Human/*microbiology ; Mothers ; Pregnancy ; },
abstract = {Archaeal sequences have been detected in human colostrum and milk, but no studies have determined whether living archaea are present in either of these fluids. Methanogenic archaea are neglected since they are not detected by usual molecular and culture methods. By using improved DNA detection protocols and microbial culture techniques associated with antioxidants previously developed in our center, we investigated the presence of methanogenic archaea using culture and specific Methanobrevibacter smithii and Methanobrevibacter oralis real-time PCR in human colostrum and milk. M. smithii was isolated from 3 colostrum and 5 milk (day 10) samples. M. oralis was isolated from 1 milk sample. For 2 strains, the genome was sequenced, and the rhizome was similar to that of strains previously isolated from the human mouth and gut. M. smithii was detected in the colostrum or milk of 5/13 (38%) and 37/127 (29%) mothers by culture and qPCR, respectively. The different distribution of maternal body mass index according to the detection of M. smithii suggested an association with maternal metabolic phenotype. M. oralis was not detected by molecular methods. Our results suggest that breastfeeding may contribute to the vertical transmission of these microorganisms and may be essential to seed the infant's microbiota with these neglected critical commensals from the first hour of life.},
}
@article {pmid31801875,
year = {2019},
author = {Prakash, D and Iyer, PR and Suharti, S and Walters, KA and Santiago-Martinez, MG and Golbeck, JH and Murakami, KS and Ferry, JG},
title = {Structure and function of an unusual flavodoxin from the domain Archaea.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {116},
number = {51},
pages = {25917-25922},
pmid = {31801875},
issn = {1091-6490},
support = {P41 GM103485/GM/NIGMS NIH HHS/United States ; R01 GM087350/GM/NIGMS NIH HHS/United States ; },
mesh = {Acetates/metabolism ; Bacterial Proteins/chemistry ; Binding Sites ; Cloning, Molecular ; Crystallography, X-Ray ; Ferredoxins/chemistry/metabolism ; Flavin Mononucleotide/chemistry ; Flavodoxin/*chemistry/genetics/isolation &amp; purification/*metabolism ; Flavoproteins/chemistry ; Global Warming ; Hydroquinones ; Methane/metabolism ; Methanosarcina/*metabolism ; Models, Molecular ; Oxidation-Reduction ; Protein Conformation ; },
abstract = {Flavodoxins, electron transfer proteins essential for diverse metabolisms in microbes from the domain Bacteria, are extensively characterized. Remarkably, although genomic annotations of flavodoxins are widespread in microbes from the domain Archaea, none have been isolated and characterized. Herein is described the structural, biochemical, and physiological characterization of an unusual flavodoxin (FldA) from Methanosarcina acetivorans, an acetate-utilizing methane-producing microbe of the domain Archaea In contrast to all flavodoxins, FldA is homodimeric, markedly less acidic, and stabilizes an anionic semiquinone. The crystal structure reveals an flavin mononucleotide (FMN) binding site unique from all other flavodoxins that provides a rationale for stabilization of the anionic semiquinone and a remarkably low reduction potentials for both the oxidized/semiquinone (-301 mV) and semiquinone/hydroquinone couples (-464 mV). FldA is up-regulated in acetate-grown versus methanol-grown cells and shown here to substitute for ferredoxin in mediating the transfer of low potential electrons from the carbonyl of acetate to the membrane-bound electron transport chain that generates ion gradients driving ATP synthesis. FldA offers potential advantages over ferredoxin by (i) sparing iron for abundant iron-sulfur proteins essential for acetotrophic growth and (ii) resilience to oxidative damage.},
}
@article {pmid31792218,
year = {2019},
author = {Zhu, Q and Mai, U and Pfeiffer, W and Janssen, S and Asnicar, F and Sanders, JG and Belda-Ferre, P and Al-Ghalith, GA and Kopylova, E and McDonald, D and Kosciolek, T and Yin, JB and Huang, S and Salam, N and Jiao, JY and Wu, Z and Xu, ZZ and Cantrell, K and Yang, Y and Sayyari, E and Rabiee, M and Morton, JT and Podell, S and Knights, D and Li, WJ and Huttenhower, C and Segata, N and Smarr, L and Mirarab, S and Knight, R},
title = {Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea.},
journal = {Nature communications},
volume = {10},
number = {1},
pages = {5477},
pmid = {31792218},
issn = {2041-1723},
support = {P30 MH062512/MH/NIMH NIH HHS/United States ; },
mesh = {Archaea/*classification/genetics ; Bacteria/*classification/genetics ; *Evolution, Molecular ; *Genome, Archaeal ; *Genome, Bacterial ; *Phylogeny ; },
abstract = {Rapid growth of genome data provides opportunities for updating microbial evolutionary relationships, but this is challenged by the discordant evolution of individual genes. Here we build a reference phylogeny of 10,575 evenly-sampled bacterial and archaeal genomes, based on a comprehensive set of 381 markers, using multiple strategies. Our trees indicate remarkably closer evolutionary proximity between Archaea and Bacteria than previous estimates that were limited to fewer "core" genes, such as the ribosomal proteins. The robustness of the results was tested with respect to several variables, including taxon and site sampling, amino acid substitution heterogeneity and saturation, non-vertical evolution, and the impact of exclusion of candidate phyla radiation (CPR) taxa. Our results provide an updated view of domain-level relationships.},
}
@article {pmid31787176,
year = {2019},
author = {Islam, GM and Vi, P and Gilbride, KA},
title = {Functional relationship between ammonia-oxidizing bacteria and ammonia-oxidizing archaea populations in the secondary treatment system of a full-scale municipal wastewater treatment plant.},
journal = {Journal of environmental sciences (China)},
volume = {86},
number = {},
pages = {120-130},
doi = {10.1016/j.jes.2019.04.031},
pmid = {31787176},
issn = {1001-0742},
mesh = {Ammonia/*metabolism ; Archaea/*genetics ; Bacteria/genetics ; Denaturing Gradient Gel Electrophoresis ; Sewage/*microbiology ; Waste Disposal, Fluid/*methods ; Wastewater/*microbiology ; Water Pollutants, Chemical/*metabolism ; },
abstract = {The abundance of ammonia-oxidizing bacteria and archaea and their amoA genes from the aerobic activated sludge tanks, recycled sludge and anaerobic digesters of a full-scale wastewater treatment plant (WWTP) was determined. Polymerase chain reaction and denaturing gradient gel electrophoresis were used to generate diversity profiles, which showed that each population had a consistent profile although the abundance of individual members varied. In the aerobic tanks, the ammonia-oxidizing bacterial (AOB) population was more than 350 times more abundant than the ammonia-oxidizing archaeal (AOA) population, however in the digesters, the AOA population was more than 10 times more abundant. Measuring the activity of the amoA gene expression of the two populations using RT-PCR also showed that the AOA amoA gene was more active in the digesters than in the activated sludge tanks. Using batch reactors and ddPCR, amoA activity could be measured and it was found that when the AOB amoA activity was inhibited in the anoxic reactors, the expression of the AOA amoA gene increased fourfold. This suggests that these two populations may have a cooperative relationship for the oxidation of ammonia.},
}
@article {pmid31754204,
year = {2020},
author = {Rinke, C and Rubino, F and Messer, LF and Youssef, N and Parks, DH and Chuvochina, M and Brown, M and Jeffries, T and Tyson, GW and Seymour, JR and Hugenholtz, P},
title = {Correction: A phylogenomic and ecological analysis of the globally abundant Marine Group II archaea (Ca. Poseidoniales ord. nov.).},
journal = {The ISME journal},
volume = {14},
number = {3},
pages = {878},
doi = {10.1038/s41396-019-0556-z},
pmid = {31754204},
issn = {1751-7370},
abstract = {An amendment to this paper has been published and can be accessed via a link at the top of the paper.},
}
@article {pmid31745137,
year = {2019},
author = {Paula, FS and Chin, JP and Schnürer, A and Müller, B and Manesiotis, P and Waters, N and Macintosh, KA and Quinn, JP and Connolly, J and Abram, F and McGrath, JW and O'Flaherty, V},
title = {The potential for polyphosphate metabolism in Archaea and anaerobic polyphosphate formation in Methanosarcina mazei.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {17101},
pmid = {31745137},
issn = {2045-2322},
mesh = {Anaerobiosis ; Archaeal Proteins/genetics/*metabolism ; Methanosarcina/*growth &amp; development/*metabolism ; Phosphotransferases (Phosphate Group Acceptor)/*metabolism ; Polyphosphates/*metabolism ; },
abstract = {Inorganic polyphosphate (polyP) is ubiquitous across all forms of life, but the study of its metabolism has been mainly confined to bacteria and yeasts. Few reports detail the presence and accumulation of polyP in Archaea, and little information is available on its functions and regulation. Here, we report that homologs of bacterial polyP metabolism proteins are present across the major taxa in the Archaea, suggesting that archaeal populations may have a greater contribution to global phosphorus cycling than has previously been recognised. We also demonstrate that polyP accumulation can be induced under strictly anaerobic conditions, in response to changes in phosphate (Pi) availability, i.e. Pi starvation, followed by incubation in Pi replete media (overplus), in cells of the methanogenic archaeon Methanosarcina mazei. Pi-starved M. mazei cells increased transcript abundance of the alkaline phosphatase (phoA) gene and of the high-affinity phosphate transport (pstSCAB-phoU) operon: no increase in polyphosphate kinase 1 (ppk1) transcript abundance was observed. Subsequent incubation of Pi-starved M. mazei cells under Pi replete conditions, led to a 237% increase in intracellular polyphosphate content and a > 5.7-fold increase in ppk1 gene transcripts. Ppk1 expression in M. mazei thus appears not to be under classical phosphate starvation control.},
}
@article {pmid31739075,
year = {2020},
author = {Dame-Teixeira, N and de Cena, JA and Côrtes, DA and Belmok, A and Dos Anjos Borges, LG and Marconatto, L and Giongo, A and Kyaw, CM},
title = {Presence of Archaea in dental caries biofilms.},
journal = {Archives of oral biology},
volume = {110},
number = {},
pages = {104606},
doi = {10.1016/j.archoralbio.2019.104606},
pmid = {31739075},
issn = {1879-1506},
mesh = {*Archaea/genetics/isolation &amp; purification ; Bacteria ; *Biofilms ; *DNA, Bacterial/analysis ; *Dental Caries/microbiology ; Humans ; Phylogeny ; RNA, Ribosomal, 16S ; Sequence Analysis, DNA ; },
abstract = {OBJECTIVE: Although the prevalence and functions associated with members of Bacteria are well known in dental caries, the role of Archaea in cariogenic biofilms has not been studied yet.<br><br>DESIGN: To detect the presence of Archaea in dental caries, a triplicate of carious dentine samples and duplicate of supragingival biofilms were collected, total microbial DNA was extracted and the composition of the microbiota was investigated. Total DNA was submitted to 16S rRNA gene amplification using universal prokaryotic primers; amplicons were sequenced by high-throughput DNA sequencing. As a second strategy to detect Archaea, a representative sample of caries was chosen and other PCR reactions were performed using specific primers targeting the archaeal 16S rRNA gene; amplicons were cloned and sequenced. Annotation of sequences was performed using SILVA database and the relative abundance of genus level OTUs was calculated.<br><br>RESULTS: The high-throughput sequencing method detected archaeal sequences in all samples (identified as group I.1c of the phylum Thaumarchaeota), although in a very low abundance (&#x2264;0.03 % of the total sequences). For the second strategy, 14 archaeal clones were detected, with an OTU affiliated to Methanocella clade, and another one affiliated to group I.1b of the phylum Thaumarchaeota.<br><br>CONCLUSIONS: Archaeal sequences were detected in dental caries and biofilms from surfaces without caries lesions. DNA sequences of Thaumarchaeota were also identified, showing that overall archaeal diversity in the human oral cavity could be currently underestimated and not restricted to methanogens.},
}
@article {pmid31712737,
year = {2020},
author = {Brewer, TE and Albertsen, M and Edwards, A and Kirkegaard, RH and Rocha, EPC and Fierer, N},
title = {Unlinked rRNA genes are widespread among bacteria and archaea.},
journal = {The ISME journal},
volume = {14},
number = {2},
pages = {597-608},
pmid = {31712737},
issn = {1751-7370},
mesh = {Archaea/*genetics ; Bacteria/*genetics ; Environmental Microbiology ; Gastrointestinal Microbiome ; Genes, rRNA ; Humans ; Metagenomics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 23S ; rRNA Operon/*genetics ; },
abstract = {Ribosomes are essential to cellular life and the genes for their RNA components are the most conserved and transcribed genes in bacteria and archaea. Ribosomal RNA genes are typically organized into a single operon, an arrangement thought to facilitate gene regulation. In reality, some bacteria and archaea do not share this canonical rRNA arrangement-their 16S and 23S rRNA genes are separated across the genome and referred to as "unlinked". This rearrangement has previously been treated as an anomaly or a byproduct of genome degradation in intracellular bacteria. Here, we leverage complete genome and long-read metagenomic data to show that unlinked 16S and 23S rRNA genes are more common than previously thought. Unlinked rRNA genes occur in many phyla, most significantly within Deinococcus-Thermus, Chloroflexi, and Planctomycetes, and occur in differential frequencies across natural environments. We found that up to 41% of rRNA genes in soil were unlinked, in contrast to the human gut, where all sequenced rRNA genes were linked. The frequency of unlinked rRNA genes may reflect meaningful life history traits, as they tend to be associated with a mix of slow-growing free-living species and intracellular species. We speculate that unlinked rRNA genes may confer selective advantages in some environments, though the specific nature of these advantages remains undetermined and worthy of further investigation. More generally, the prevalence of unlinked rRNA genes in poorly-studied taxa serves as a reminder that paradigms derived from model organisms do not necessarily extend to the broader diversity of bacteria and archaea.},
}
@article {pmid31712277,
year = {2020},
author = {Johnsen, U and Sutter, JM and Reinhardt, A and Pickl, A and Wang, R and Xiang, H and Schönheit, P},
title = {d-Ribose Catabolism in Archaea: Discovery of a Novel Oxidative Pathway in Haloarcula Species.},
journal = {Journal of bacteriology},
volume = {202},
number = {3},
pages = {},
pmid = {31712277},
issn = {1098-5530},
mesh = {Arabinose/metabolism ; Archaea/*metabolism ; Haloarcula/*metabolism ; Oxidation-Reduction ; Ribose/*metabolism ; Xylose/metabolism ; },
abstract = {The Haloarcula species H. marismortui and H. hispanica were found to grow on d-ribose, d-xylose, and l-arabinose. Here, we report the discovery of a novel promiscuous oxidative pathway of pentose degradation based on genome analysis, identification and characterization of enzymes, transcriptional analysis, and growth experiments with knockout mutants. Together, the data indicate that in Haloarcula spp., d-ribose, d-xylose, and l-arabinose were degraded to α-ketoglutarate involving the following enzymes: (i) a promiscuous pentose dehydrogenase that catalyzed the oxidation of d-ribose, d-xylose, and l-arabinose; (ii) a promiscuous pentonolactonase that was involved in the hydrolysis of ribonolactone, xylonolactone, and arabinolactone; (iii) a highly specific dehydratase, ribonate dehydratase, which catalyzed the dehydration of ribonate, and a second enzyme, a promiscuous xylonate/gluconate dehydratase, which was involved in the conversion of xylonate, arabinonate, and gluconate. Phylogenetic analysis indicated that the highly specific ribonate dehydratase constitutes a novel sugar acid dehydratase family within the enolase superfamily; and (iv) finally, 2-keto-3-deoxypentanonate dehydratase and α-ketoglutarate semialdehyde dehydrogenase catalyzed the conversion of 2-keto-3-deoxypentanonate to α-ketoglutarate via α-ketoglutarate semialdehyde. We conclude that the expanded substrate specificities of the pentose dehydrogenase and pentonolactonase toward d-ribose and ribonolactone, respectively, and the presence of a highly specific ribonate dehydratase are prerequisites of the oxidative degradation of d-ribose in Haloarcula spp. This is the first characterization of an oxidative degradation pathway of d-ribose to α-ketoglutarate in archaea.IMPORTANCE The utilization and degradation of d-ribose in archaea, the third domain of life, have not been analyzed so far. We show that Haloarcula species utilize d-ribose, which is degraded to α-ketoglutarate via a novel oxidative pathway. Evidence is presented that the oxidative degradation of d-ribose involves novel promiscuous enzymes, pentose dehydrogenase and pentonolactonase, and a novel sugar acid dehydratase highly specific for ribonate. This is the first report of an oxidative degradation pathway of d-ribose in archaea, which differs from the canonical nonoxidative pathway of d-ribose degradation reported for most bacteria. The data contribute to our understanding of the unusual sugar degradation pathways and enzymes in archaea.},
}
@article {pmid31709520,
year = {2020},
author = {Zhao, C and Lyu, Z and Long, F and Akinyemi, T and Manakongtreecheep, K and Söll, D and Whitman, WB and Vinyard, DJ and Liu, Y},
title = {The Nbp35/ApbC homolog acts as a nonessential [4Fe-4S] transfer protein in methanogenic archaea.},
journal = {FEBS letters},
volume = {594},
number = {5},
pages = {924-932},
doi = {10.1002/1873-3468.13673},
pmid = {31709520},
issn = {1873-3468},
mesh = {Archaeal Proteins/genetics/metabolism ; Cell Nucleus/metabolism ; Cytosol/metabolism ; Gene Deletion ; Iron-Sulfur Proteins/genetics/*metabolism ; Methanococcus/genetics/*growth &amp; development/metabolism ; Phylogeny ; },
abstract = {The nucleotide binding protein 35 (Nbp35)/cytosolic Fe-S cluster deficient 1 (Cfd1)/alternative pyrimidine biosynthetic protein C (ApbC) protein homologs have been identified in all three domains of life. In eukaryotes, the Nbp35/Cfd1 heterocomplex is an essential Fe-S cluster assembly scaffold required for the maturation of Fe-S proteins in the cytosol and nucleus, whereas the bacterial ApbC is an Fe-S cluster transfer protein only involved in the maturation of a specific target protein. Here, we show that the Nbp35/ApbC homolog MMP0704 purified from its native archaeal host Methanococcus maripaludis contains a [4Fe-4S] cluster that can be transferred to a [4Fe-4S] apoprotein. Deletion of mmp0704 from M. maripaludis does not cause growth deficiency under our tested conditions. Our data indicate that Nbp35/ApbC is a nonessential [4Fe-4S] cluster transfer protein in methanogenic archaea.},
}
@article {pmid31705614,
year = {2020},
author = {Kubatova, N and Pyper, DJ and Jonker, HRA and Saxena, K and Remmel, L and Richter, C and Brantl, S and Evguenieva-Hackenberg, E and Hess, WR and Klug, G and Marchfelder, A and Soppa, J and Streit, W and Mayzel, M and Orekhov, VY and Fuxreiter, M and Schmitz, RA and Schwalbe, H},
title = {Rapid Biophysical Characterization and NMR Spectroscopy Structural Analysis of Small Proteins from Bacteria and Archaea.},
journal = {Chembiochem : a European journal of chemical biology},
volume = {21},
number = {8},
pages = {1178-1187},
pmid = {31705614},
issn = {1439-7633},
mesh = {Archaea/*metabolism ; Archaeal Proteins/*chemistry ; Bacteria/*metabolism ; Bacterial Proteins/*chemistry ; Computational Biology/*methods ; Nuclear Magnetic Resonance, Biomolecular/*methods ; Open Reading Frames ; Protein Conformation ; *Protein Folding ; },
abstract = {Proteins encoded by small open reading frames (sORFs) have a widespread occurrence in diverse microorganisms and can be of high functional importance. However, due to annotation biases and their technically challenging direct detection, these small proteins have been overlooked for a long time and were only recently rediscovered. The currently rapidly growing number of such proteins requires efficient methods to investigate their structure-function relationship. Herein, a method is presented for fast determination of the conformational properties of small proteins. Their small size makes them perfectly amenable for solution-state NMR spectroscopy. NMR spectroscopy can provide detailed information about their conformational states (folded, partially folded, and unstructured). In the context of the priority program on small proteins funded by the German research foundation (SPP2002), 27 small proteins from 9 different bacterial and archaeal organisms have been investigated. It is found that most of these small proteins are unstructured or partially folded. Bioinformatics tools predict that some of these unstructured proteins can potentially fold upon complex formation. A protocol for fast NMR spectroscopy structure elucidation is described for the small proteins that adopt a persistently folded structure by implementation of new NMR technologies, including automated resonance assignment and nonuniform sampling in combination with targeted acquisition.},
}
@article {pmid31704973,
year = {2019},
author = {Chénard, C and Wijaya, W and Vaulot, D and Lopes Dos Santos, A and Martin, P and Kaur, A and Lauro, FM},
title = {Temporal and spatial dynamics of Bacteria, Archaea and protists in equatorial coastal waters.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {16390},
pmid = {31704973},
issn = {2045-2322},
mesh = {Archaea/genetics/isolation &amp; purification ; Bacteria/classification/genetics/isolation &amp; purification ; Biodiversity ; Eukaryota/genetics/isolation &amp; purification ; *Microbiota/genetics ; Seasons ; Seawater/*microbiology ; Singapore ; Spatio-Temporal Analysis ; Wind ; },
abstract = {Singapore, an equatorial island in South East Asia, is influenced by a bi-annual reversal of wind directions which defines two monsoon seasons. We characterized the dynamics of the microbial communities of Singapore coastal waters by collecting monthly samples between February 2017 and July 2018 at four sites located across two straits with different trophic status, and sequencing the V6-V8 region of the small sub-unit ribosomal RNA gene (rRNA gene) of Bacteria, Archaea, and Eukaryota. Johor Strait, which is subjected to wider environmental fluctuations from anthropogenic activities, presented a higher abundance of copiotrophic microbes, including Cellvibrionales and Rhodobacterales. The mesotrophic Singapore Strait, where the seasonal variability is caused by changes in the oceanographic conditions, harboured a higher proportion of typically marine microbe groups such as Synechococcales, Nitrosupumilales, SAR11, SAR86, Marine Group II Archaea and Radiolaria. In addition, we observed seasonal variability of the microbial communities in the Singapore Strait, which was possibly influenced by the alternating monsoon regime, while no seasonal pattern was detected in the Johor Strait.},
}
@article {pmid31690001,
year = {2019},
author = {Mukhtar, H and Lin, YP and Lin, CM and Lin, YR},
title = {Relative Abundance of Ammonia Oxidizing Archaea and Bacteria Influences Soil Nitrification Responses to Temperature.},
journal = {Microorganisms},
volume = {7},
number = {11},
pages = {},
pmid = {31690001},
issn = {2076-2607},
abstract = {Ammonia oxidizing archaea (AOA) and bacteria (AOB) are thought to contribute differently to soil nitrification, yet the extent to which their relative abundances influence the temperature response of nitrification is poorly understood. Here, we investigated the impact of different AOA to AOB ratios on soil nitrification potential (NP) across a temperature gradient from 4 °C to 40 °C in twenty different organic and inorganic fertilized soils. The temperature responses of different relative abundance of ammonia oxidizers for nitrification were modeled using square rate theory (SQRT) and macromolecular rate theory (MMRT) models. We found that the proportional nitrification rates at different temperatures varied among AOA to AOB ratios. Predicted by both models, an optimum temperature (Topt) for nitrification in AOA dominated soils was significantly higher than for soils where AOA and AOB abundances are within the same order of magnitude. Moreover, the change in heat capacity (Δ C P ‡) associated with the temperature dependence of nitrification was positively correlated with Topt and significantly varied among the AOA to AOB ratios. The temperature ranges for NP decreased with increasing AOA abundance for both organic and inorganic fertilized soils. These results challenge the widely accepted approach of comparing NP rates in different soils at a fixed temperature. We conclude that a shift in AOA to AOB ratio in soils exhibits distinguished temperature-dependent characteristics that have an important impact on nitrification responses across the temperature gradient. The proposed approach benefits the accurate discernment of the true contribution of fertilized soils to nitrification for improvement of nitrogen management.},
}
@article {pmid31683078,
year = {2020},
author = {Magdalena, JA and González-Fernández, C},
title = {Archaea inhibition: Strategies for the enhancement of volatile fatty acids production from microalgae.},
journal = {Waste management (New York, N.Y.)},
volume = {102},
number = {},
pages = {222-230},
doi = {10.1016/j.wasman.2019.10.044},
pmid = {31683078},
issn = {1879-2456},
mesh = {Anaerobiosis ; Archaea ; Fatty Acids, Volatile ; Fermentation ; *Microalgae ; Sewage ; },
abstract = {In the present study, anaerobic sludge was subjected to thermal and chemical pretreatments to favour VFAs production from a protein-rich waste (i.e. microalgae biomass). Sludge pretreatments have been previously used in hydrogen production; however, information about how they can affect VFAs production from microalgae is still lacking. Thermal pretreatment was studied at: (i) 80 °C for 10 and 30 min; (ii) 120 °C for 10 and 30 min; and (iii) 100 °C for 20 min. 2-bromoethanesulfonate (BES) at 10 mM and 30 mM was used as chemical pretreatment. Besides, a combination of both pretreatment methods (80 °C and 120 °C at 10 mM and 30 mM BES) was also tested. Thermal pretreatment increased organic matter conversions into VFAs (up to 71% COD-VFAs/CODin) when compared to control values (40% in the untreated anaerobic sludge). Acetic acid was the most abundant VFAs at high temperatures (120 °C) and when BES was employed (up to 60% and 40%, respectively, in terms of COD). On the other hand, propionic acid was the most abundant product at low temperatures and in the untreated anaerobic sludge (up to 60% in terms of COD). This research work might set guidelines in order to choose a suitable sludge pretreatment for VFAs production from microalgae.},
}
@article {pmid31681249,
year = {2019},
author = {He, H and Fu, L and Liu, Q and Fu, L and Bi, N and Yang, Z and Zhen, Y},
title = {Community Structure, Abundance and Potential Functions of Bacteria and Archaea in the Sansha Yongle Blue Hole, Xisha, South China Sea.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {2404},
pmid = {31681249},
issn = {1664-302X},
abstract = {The Sansha Yongle Blue Hole is the deepest blue hole in the world and exhibits unique environmental characteristics. In this paper, Illumina sequencing and qPCR analysis were conducted to obtain the microbial information in this special ecosystem. The results showed that the richness and diversity of bacterial communities in the hole was greater than those of archaeal communities, and bacterial and archaeal communities were dominated by Proteobacteria and Euryarchaeota, respectively. Temperature and nitrate concentration significantly contributed to the heterogeneous distribution of major bacterial clades; salinity explained most variations of the archaeal communities, but not significant. A sudden increase of bacterial 16S rRNA, archaeal 16S rRNA, ANAMMOX 16S rRNA, nirS and dsrB gene was noticed from 90 to 100 m in the hole probably due to more phytoplankton at this depth. Sulfur oxidation and nitrate reduction were the most abundant predicted ecological functions in the hole, while lots of archaea were predicted to be involved in aerobic ammonia oxidation and methanogenesis. The co-occurrence network analysis illustrated that a synergistic effect between sulfate reduction and sulfur oxidation, and between nitrogen fixation and denitrification, a certain degree of coupling between sulfur and nitrogen cycle was also observed in the hole. The comparisons of bacterial and archaeal communities between the hole and other caves in the world (or other areas of the South China Sea) suggest that similar conditions are hypothesized to give rise to similar microbial communities, and environmental conditions may contribute significantly to the bacterial and archaeal communities.},
}
@article {pmid31669955,
year = {2019},
author = {Tu, R and Jin, W and Han, SF and Zhou, X and Wang, T and Gao, SH and Wang, Q and Chen, C and Xie, GJ and Wang, Q},
title = {Rapid enrichment and ammonia oxidation performance of ammonia-oxidizing archaea from an urban polluted river of China.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {255},
number = {Pt 2},
pages = {113258},
doi = {10.1016/j.envpol.2019.113258},
pmid = {31669955},
issn = {1873-6424},
mesh = {Ammonia/*metabolism ; Archaea/*metabolism ; Bacteria/genetics ; Betaproteobacteria ; *Biodegradation, Environmental ; China ; Nitrification ; Oxidation-Reduction ; Phylogeny ; Rivers/microbiology ; Soil Microbiology ; Water Pollutants, Chemical/*metabolism ; },
abstract = {Ammonia oxidation is the rate-limiting step in nitrification process and dominated by ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA). In the present study, a highly enriched culture of AOA was obtained from urban polluted water in Shahe River, Shenzhen, China. The optimum growth conditions were identified by orthogonal analysis as 37 °C, with pH 7.0 and initial ammonia concentration of 1.0 mM. Under these conditions, the highest abundance of AOA was obtained as 4.6 × 10[7] copies/ng DNA. Growth of AOA in polluted river water showed significant reduction in ammonia concentration in AOA-enriched cultures without antibiotics after 10 days of incubation, while synchronous increase in nitrate concentration was up to 12.7 mg/L. However, AOA-enriched by antibiotic showed insignificant changes in ammonia or nitrite concentration. This study showed that AOB play an important role in ammonia oxidation of polluted river water, and AOA alone showed insignificant changes in ammonia or nitrite concentrations. Therefore, the ammonia oxidation performance of natural water could not be improved by adding high concentration AOA bacterial liquid.},
}
@article {pmid31666740,
year = {2019},
author = {Belilla, J and Moreira, D and Jardillier, L and Reboul, G and Benzerara, K and López-García, JM and Bertolino, P and López-Archilla, AI and López-García, P},
title = {Hyperdiverse archaea near life limits at the polyextreme geothermal Dallol area.},
journal = {Nature ecology &amp; evolution},
volume = {3},
number = {11},
pages = {1552-1561},
pmid = {31666740},
issn = {2397-334X},
support = {322669/ERC_/European Research Council/International ; },
mesh = {*Archaea ; *Bacteria ; Phylogeny ; RNA, Ribosomal, 16S ; },
abstract = {Microbial life has adapted to various individual extreme conditions; yet, organisms simultaneously adapted to very low pH, high salt and high temperature are unknown. We combined environmental 16S/18S ribosomal RNA gene metabarcoding, cultural approaches, fluorescence-activated cell sorting, scanning electron microscopy and chemical analyses to study samples along such unique polyextreme gradients in the Dallol-Danakil area in Ethiopia. We identified two physicochemical barriers to life in the presence of surface liquid water defined by (1) high chaotropicity-low water activity in Mg[2+]/Ca[2+]-dominated brines and (2) hyperacidity-salt combinations (pH ~0/NaCl-dominated salt saturation). When detected, life was dominated by highly diverse ultrasmall archaea that were widely distributed across phyla with and without previously known halophilic members. We hypothesize that a high cytoplasmic K[+]-level was an original archaeal adaptation to hyperthermophily, subsequently exapted during several transitions to extreme halophily. We detect active silica encrustment/fossilization of cells but also abiotic biomorphs of varied chemistry. Our work helps circumscribing habitability and calls for cautionary interpretations of morphological biosignatures on Earth and beyond.},
}
@article {pmid31654454,
year = {2020},
author = {Xu, S and Lu, W and Mustafa, MF and Liu, Y and Wang, H},
title = {Presence of diverse nitrate-dependent anaerobic methane oxidizing archaea in sewage sludge.},
journal = {Journal of applied microbiology},
volume = {128},
number = {3},
pages = {775-783},
doi = {10.1111/jam.14502},
pmid = {31654454},
issn = {1365-2672},
support = {BK20190481//Natural Science Foundation of Jiangsu Province/ ; 30919011212//Fundamental Research Funds for the Central Universities/ ; },
mesh = {Anaerobiosis ; Archaea/classification/genetics/*isolation &amp; purification/*metabolism ; China ; Methane/*metabolism ; Methanosarcinales/classification/genetics/isolation &amp; purification/metabolism ; Microbiota ; Nitrates/*metabolism ; Oxidation-Reduction ; Phylogeny ; Seasons ; Sewage/chemistry/*microbiology ; },
abstract = {AIM: The aim of this study was to explore the community diversity and abundance of nitrate-dependent anaerobic methane oxidizing archaea, Candidatus Methanoperedens nitroreducens, in sewage sludge from wastewater treatment plants.<br><br>METHODS AND RESULTS: Seasonal sampling of the sewage sludge was carried out from two wastewater treatment plants (WWTPs) located in the northern and southern parts of China. Through amplicon sequencing using our newly designed primers, a large number of Candidatus Methanoperedens nitroreducens-like (M. nitroreducens) archaeal sequences (638&#xa0;743) were generated. These sequences were assigned into 742 operational protein units (OPUs) at 90% cut-off level and classified as Group B member of M. nitroreducens archaea in the phylogenetic tree. More than 80% of the OPUs were not shared between these two WWTPs, showing the M. nitroreducens-like archaeal community in each WWTP was unique. Quantitative PCR assays also confirmed the presence of M. nitroreducens-like archaea and revealed a higher abundance in autumn and winter than other seasons, indicating that the environmental attributes in these seasons might favour the growth of this archaea. Further redundancy analysis revealed that volatile solid and pH were the significant environmental attributes (P&#xa0;<&#xa0;0&#xb7;05) in shaping the M. nitroreducens-like archaeal community based on variance inflation factor selection and Monte Carlo permutation test.<br><br>CONCLUSIONS: The results confirmed the presence of diverse M. nitroreducens-like archaea in sewage sludge using Illumina-based mcrA gene sequencing and quantitative PCR assays.<br><br>The results of this study revealed the ecological characteristics of M. nitroreducens-like archaea in sewage sludge that improved our understanding of nitrate-dependent anaerobic methane oxidation process and may be the basis for future application of M. nitroreducens-like archaea for new nitrogen removal in WWTPs.},
}
@article {pmid31637140,
year = {2019},
author = {Yuan, M and Liu, S and Wang, Z and Wang, L and Xue, B and Zou, H and Tian, G and Cai, J and Peng, Q},
title = {Effects of particle size of ground alfalfa hay on caecal bacteria and archaea populations of rabbits.},
journal = {PeerJ},
volume = {7},
number = {},
pages = {e7910},
pmid = {31637140},
issn = {2167-8359},
abstract = {This work was aimed to investigate the effects of the different particle size of ground alfalfa hay on caecal microbial and archeal communities of rabbits. One hundred-twenty New Zealand rabbits (950.3 ± 8.82 g) were allocated into four treatments, with five replicates in each treatment and six rabbits in each replicate. The particle sizes of the alfalfa meal in the four treatment diets were 2,500, 1,000, 100 and 10 µm respectively, while the other ingredients were ground through a 2.5 mm sieve. High-throughput sequencing technology was applied to examine the differences in bacteria and methanogenic archaea diversity in the caecum of the four treatment groups of rabbits. A total of 745,946 bacterial sequences (a mean of 31,081 ± 13,901 sequences per sample) and 539,227 archaeal sequences (a mean of 22,468 ± 2,443 sequences per sample) were recovered from twenty-four caecal samples, and were clustered into 9,953 and 2,246 OTUs respectively. A total of 26 bacterial phyla with 465 genera and three archaeal phyla with 10 genera were identified after taxonomic summarization. Bioinformatic analyses illustrated that Firmicutes (58.69% ∼ 68.50%) and Bacteroidetes (23.96% ∼ 36.05%) were the two most predominant bacterial phyla and Euryarchaeota (over 99.9%) was the most predominant archaeal phyla in the caecum of all rabbits. At genus level, as the particle size of alfalfa decreased from 2,500 to 10 µm, the relative abundances of Ruminococcaceae UCG-014 (P < 0.001) and Lactobacillus (P = 0.043) were increased and Ruminococcaceae UCG-005 (P = 0.012) was increased first and then decreased when the alfalfa particle size decreased, while Lachnospiraceae NK4A136 group (P = 0.016), Ruminococcaceae NK4A214 (P = 0.044), Christensenellaceae R-7 group (P = 0.019), Lachnospiraceae other (Family) (P = 0.011) and Ruminococcaceae UCG-013 (P = 0.021) were decreased. The relative abundance of Methanobrevibacter was increased from 62.48% to 90.40% (P < 0.001), whereas the relative abundance of Methanosphaera was reduced from 35.47% to 8.62% (P < 0.001). In conclusion, as the particle size of alfalfa meal decreased, both the bacterial and archaeal population in the caecum of rabbit experienced alterations, however archaea response earlier than bacteria to the decrease of alfalfa meal particle size.},
}
@article {pmid31618850,
year = {2019},
author = {Lu, Y and Xia, X and Cheung, S and Jing, H and Liu, H},
title = {Differential Distribution and Determinants of Ammonia Oxidizing Archaea Sublineages in the Oxygen Minimum Zone off Costa Rica.},
journal = {Microorganisms},
volume = {7},
number = {10},
pages = {},
pmid = {31618850},
issn = {2076-2607},
support = {2015CB954003//Ministry of Science and Technology of the People's Republic of China/ ; N-HKUST609/15//Research Grants Council, University Grants Committee/ ; 16128416//Research Grants Council, University Grants Committee/ ; 16101318//Research Grants Council, University Grants Committee/ ; Y8SL031001//CAS Pioneer Hundred Talents Program, the South China Sea Institute of Oceanography/ ; Y9YB021001//CAS Pioneer Hundred Talents Program, the South China Sea Institute of Oceanography/ ; 31971501//National Natural Science Foundation of China/ ; },
abstract = {Ammonia oxidizing archaea (AOA) are microbes that are widely distributed in the ocean that convert ammonia to nitrite for energy acquisition in the presence of oxygen. Recent study has unraveled highly diverse sublineages within the previously defined AOA ecotypes (i.e., water column A (WCA) and water column B (WCB)), although the eco-physiology and environmental determinants of WCB subclades remain largely unclear. In this study, we examined the AOA communities along the water columns (40-3000 m depth) in the Costa Rica Dome (CRD) upwelling region in the eastern tropical North Pacific Ocean. Highly diverse AOA communities that were significantly different from those in oxygenated water layers were observed in the core layer of the oxygen minimum zone (OMZ), where the dissolved oxygen (DO) concentration was < 2μM. Moreover, a number of AOA phylotypes were found to be enriched in the OMZ core. Most of them were negatively correlated with DO and were also detected in other OMZs in the Arabian Sea and Gulf of California, which suggests low oxygen adaptation. This study provided the first insight into the differential niche partitioning and environmental determinants of various subclades within the ecotype WCB. Our results indicated that the ecotype WCB did indeed consist of various sublineages with different eco-physiologies, which should be further explored.},
}
@article {pmid31614851,
year = {2019},
author = {Odelade, KA and Babalola, OO},
title = {Bacteria, Fungi and Archaea Domains in Rhizospheric Soil and Their Effects in Enhancing Agricultural Productivity.},
journal = {International journal of environmental research and public health},
volume = {16},
number = {20},
pages = {},
pmid = {31614851},
issn = {1660-4601},
mesh = {Agriculture/*statistics &amp; numerical data ; Archaea/*metabolism ; Bacteria/*metabolism ; Fungi/*metabolism ; *Microbiota ; Plant Roots/*metabolism ; *Rhizosphere ; Soil Microbiology ; },
abstract = {The persistent and undiscriminating application of chemicals as means to improve crop growth, development and yields for several years has become problematic to agricultural sustainability because of the adverse effects these chemicals have on the produce, consumers and beneficial microbes in the ecosystem. Therefore, for agricultural productivity to be sustained there are needs for better and suitable preferences which would be friendly to the ecosystem. The use of microbial metabolites has become an attractive and more feasible preference because they are versatile, degradable and ecofriendly, unlike chemicals. In order to achieve this aim, it is then imperative to explore microbes that are very close to the root of a plant, especially where they are more concentrated and have efficient activities called the rhizosphere. Extensive varieties of bacteria, archaea, fungi and other microbes are found inhabiting the rhizosphere with various interactions with the plant host. Therefore, this review explores various beneficial microbes such as bacteria, fungi and archaea and their roles in the environment in terms of acquisition of nutrients for plants for the purposes of plant growth and health. It also discusses the effect of root exudate on the rhizosphere microbiome and compares the three domains at molecular levels.},
}
@article {pmid31605529,
year = {2019},
author = {Farley, KR and Metcalf, WW},
title = {The streptothricin acetyltransferase (sat) gene as a positive selectable marker for methanogenic archaea.},
journal = {FEMS microbiology letters},
volume = {366},
number = {17},
pages = {},
pmid = {31605529},
issn = {1574-6968},
support = {R21 AI122019/AI/NIAID NIH HHS/United States ; },
mesh = {Acetyltransferases/*genetics ; Anti-Infective Agents/pharmacology ; Archaea/drug effects/*genetics ; Drug Resistance, Microbial ; *Evolution, Molecular ; Genes, Archaeal ; Humans ; Microbial Sensitivity Tests ; Mutation ; *Selection, Genetic ; Sequence Deletion ; },
abstract = {A repertoire of sophisticated genetic tools has significantly enhanced studies of Methanosarcina genera, yet the lack of multiple positive selectable markers has limited the types of genetic experiments that can be performed. In this study, we report the development of an additional positive selection system for Methanosarcina that utilizes the antibiotic nourseothricin and the Streptomyces rochei streptothricin acetyltransferase (sat) gene, which may be broadly applicable to other groups of methanogenic archaea. Nourseothricin was found to inhibit growth of four different methanogen species at concentrations ≤300 μg/ml in liquid or on solid media. Selection of nourseothricin resistant transformants was possible in two genetically tractable Methanosarcina species, M. acetivorans and M. barkeri, using the sat gene as a positive selectable marker. Additionally, the sat marker was useful for constructing a gene deletion mutant strain of M. acetivorans, emphasizing its utility as a second positive selectable marker for genetic analyses of Methanosarcina genera. Interestingly, two human gut-associated methanogens Methanobrevibacter smithii and Methanomassillicoccus luminyensis were more sensitive to nourseothricin than either Methanosarcina species, suggesting the nourseothricin-sat gene pair may provide a robust positive selection system for development of genetic tools in these and other methanogens.},
}
@article {pmid31594929,
year = {2019},
author = {Hua, ZS and Wang, YL and Evans, PN and Qu, YN and Goh, KM and Rao, YZ and Qi, YL and Li, YX and Huang, MJ and Jiao, JY and Chen, YT and Mao, YP and Shu, WS and Hozzein, W and Hedlund, BP and Tyson, GW and Zhang, T and Li, WJ},
title = {Insights into the ecological roles and evolution of methyl-coenzyme M reductase-containing hot spring Archaea.},
journal = {Nature communications},
volume = {10},
number = {1},
pages = {4574},
pmid = {31594929},
issn = {2041-1723},
mesh = {Alkanes/metabolism ; Archaea/enzymology/*genetics/isolation &amp; purification ; *Biological Evolution ; China ; Computational Biology ; Genome, Archaeal ; Hot Springs/*microbiology ; Hot Temperature ; Metabolic Networks and Pathways/genetics ; *Metagenome ; Methane/metabolism ; Multigene Family/genetics ; Oxidoreductases/*genetics/metabolism ; Phylogeny ; },
abstract = {Several recent studies have shown the presence of genes for the key enzyme associated with archaeal methane/alkane metabolism, methyl-coenzyme M reductase (Mcr), in metagenome-assembled genomes (MAGs) divergent to existing archaeal lineages. Here, we study the mcr-containing archaeal MAGs from several hot springs, which reveal further expansion in the diversity of archaeal organisms performing methane/alkane metabolism. Significantly, an MAG basal to organisms from the phylum Thaumarchaeota that contains mcr genes, but not those for ammonia oxidation or aerobic metabolism, is identified. Together, our phylogenetic analyses and ancestral state reconstructions suggest a mostly vertical evolution of mcrABG genes among methanogens and methanotrophs, along with frequent horizontal gene transfer of mcr genes between alkanotrophs. Analysis of all mcr-containing archaeal MAGs/genomes suggests a hydrothermal origin for these microorganisms based on optimal growth temperature predictions. These results also suggest methane/alkane oxidation or methanogenesis at high temperature likely existed in a common archaeal ancestor.},
}
@article {pmid31587640,
year = {2019},
author = {Santoro, AE and Kellom, M and Laperriere, SM},
title = {Contributions of single-cell genomics to our understanding of planktonic marine archaea.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {374},
number = {1786},
pages = {20190096},
pmid = {31587640},
issn = {1471-2970},
mesh = {Archaea/*genetics ; *Genome, Archaeal ; *Genomics ; Plankton/*genetics ; *Single-Cell Analysis ; },
abstract = {Single-cell genomics has transformed many fields of biology, marine microbiology included. Here, we consider the impact of single-cell genomics on a specific group of marine microbes-the planktonic marine archaea. Despite single-cell enabled discoveries of novel metabolic function in the marine thaumarchaea, population-level investigations are hindered by an overall lower than expected recovery of thaumarchaea in single-cell studies. Metagenome-assembled genomes have so far been a more useful method for accessing genome-resolved insights into the Marine Group II euryarchaea. Future progress in the application of single-cell genomics to archaeal biology in the ocean would benefit from more targeted sorting approaches, and a more systematic investigation of potential biases against archaea in single-cell workflows including cell lysis, genome amplification and genome screening. This article is part of a discussion meeting issue 'Single cell ecology'.},
}
@article {pmid31582767,
year = {2019},
author = {Loth, K and Largillière, J and Coste, F and Culard, F and Landon, C and Castaing, B and Delmas, AF and Paquet, F},
title = {New protein-DNA complexes in archaea: a small monomeric protein induces a sharp V-turn DNA structure.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {14253},
pmid = {31582767},
issn = {2045-2322},
mesh = {Archaeal Proteins/chemistry/*metabolism ; DNA, Archaeal/chemistry/*metabolism ; DNA-Binding Proteins/chemistry/*metabolism ; Methanosarcina/chemistry/*metabolism ; Models, Molecular ; Nuclear Magnetic Resonance, Biomolecular ; Nucleic Acid Conformation ; Protein Binding ; Protein Conformation ; Ribonucleoproteins/chemistry/*metabolism ; },
abstract = {MC1, a monomeric nucleoid-associated protein (NAP), is structurally unrelated to other DNA-binding proteins. The protein participates in the genome organization of several Euryarchaea species through an atypical compaction mechanism. It is also involved in DNA transcription and cellular division through unknown mechanisms. We determined the 3D solution structure of a new DNA-protein complex formed by MC1 and a strongly distorted 15 base pairs DNA. While the protein just needs to adapt its conformation slightly, the DNA undergoes a dramatic curvature (the first two bend angles of 55° and 70°, respectively) and an impressive torsional stress (dihedral angle of 106°) due to several kinks upon binding of MC1 to its concave side. Thus, it adopts a V-turn structure. For longer DNAs, MC1 stabilizes multiple V-turn conformations in a flexible and dynamic manner. The existence of such V-turn conformations of the MC1-DNA complexes leads us to propose two binding modes of the protein, as a bender (primary binding mode) and as a wrapper (secondary binding mode). Moreover, it opens up new opportunities for studying and understanding the repair, replication and transcription molecular machineries of Archaea.},
}
@article {pmid31568679,
year = {2020},
author = {Ding, J and Ma, M and Jiang, X and Liu, Y and Zhang, J and Suo, L and Wang, L and Wei, D and Li, J},
title = {Effects of applying inorganic fertilizer and organic manure for 35 years on the structure and diversity of ammonia-oxidizing archaea communities in a Chinese Mollisols field.},
journal = {MicrobiologyOpen},
volume = {9},
number = {1},
pages = {e00942},
pmid = {31568679},
issn = {2045-8827},
mesh = {Ammonia/*metabolism ; Archaea/*classification/growth &amp; development/*metabolism ; China ; Fertilizers/*analysis ; Nitrogen Compounds/analysis ; Oxidation-Reduction ; Phosphorus/analysis ; Potassium/analysis ; Soil/*chemistry ; Soil Microbiology ; Glycine max/growth &amp; development ; },
abstract = {In this study, we investigated the physicochemical properties of soil, and the diversity and structure of the soil ammonia-oxidizing archaea (AOA) community, when subjected to fertilizer treatments for over 35 years. We collected soil samples from a black soil fertilization trial in northeast China. Four treatments were tested: no fertilization (CK); manure (M); nitrogen (N), phosphorus (P), and potassium (K) chemical fertilizer (NPK); and N, P, and K plus M (MNPK). We employed 454 high-throughput pyrosequencing to measure the response of the soil AOA community to the long-term fertilization. The fertilization treatments had different impacts on the shifts in the soil properties and AOA community. The utilization of manure alleviated soil acidification and enhanced the soybean yield. The soil AOA abundance was increased greatly by inorganic and organic fertilizers. In addition, the community Chao1 and ACE were highest in the MNPK treatment. In terms of the AOA community composition, Thaumarchaeota and Crenarchaeota were the main AOA phyla in all samples. Compared with CK and M, the abundances of Thaumarchaeota were remarkably lower in the MNPK and NPK treatments. There were distinct shifts in the compositions of the AOA operational taxonomic units (OTUs) under different fertilization management practices. OTU51 was the dominant OTU in all treatments, except for NPK. OTU79 and OTU11 were relatively abundant OTUs in NPK. Only Nitrososphaera AOA were tracked from the black soil. Redundancy analysis indicated that the soil pH and soil available P were the two main factors that affected the AOA community structure. The abundances of AOA were positively correlated with the total N and available P concentrations, and negatively correlated with the soil pH.},
}
@article {pmid31552452,
year = {2019},
author = {He, S and Tan, J and Hu, W and Mo, C},
title = {Diversity of Archaea and Its Correlation with Environmental Factors in the Ebinur Lake Wetland.},
journal = {Current microbiology},
volume = {76},
number = {12},
pages = {1417-1424},
pmid = {31552452},
issn = {1432-0991},
support = {31160026//National Natural Science Foundation of China/ ; },
mesh = {Archaea/*classification/genetics/isolation &amp; purification ; *Biodiversity ; China ; DNA, Archaeal/genetics ; Lakes ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Soil/chemistry ; *Soil Microbiology ; *Wetlands ; },
abstract = {The diversity and community composition of archaea in soil samples from three wetlands (SP1, SP2, and SP3) of Ebinur Lake were studied by constructing 16S rDNA cloning library. The correlation between the diversity of archaea and soil environmental factors was analyzed by CANOCO software. The aim of this study was to reveal the differences of community structures of archaea in different sample sites, to provide a theoretical basis for further study on degradation and restoration of Ebinur Lake wetland. The results showed that Euryarchaeota accounted for 57.1% was the most dominant phylum observed, followed by Thaumarchaeota and Crenarchaeota for the three wetland soil analyzed. Compared with SP3 site, the proportions of Euryarchaeota were decreased by 16.70% and 31.78%, while Thaumarchaeota increased by 7.26% and 17.64% in the SP1 and SP2, respectively. Crenarchaeota was found only in SP3. Shannon-wiener diversity indices in SP1, SP2, and SP3 sites were 3.44, 3.87, and 3.94, respectively, indicating that the diversity of archaea in three plots was: SP3 > SP2 > SP1. Redundancy analysis (RDA) showed that electrical conductivity (EC), soil moisture (SM), hydrogen potential (pH), and soil organic matter content (SOM) may affect archaeal communities. Compared to EC and pH, SM and SOM may have a greater impact on the community composition of archaea.},
}
@article {pmid31533962,
year = {2019},
author = {Mand, TD and Metcalf, WW},
title = {Energy Conservation and Hydrogenase Function in Methanogenic Archaea, in Particular the Genus Methanosarcina.},
journal = {Microbiology and molecular biology reviews : MMBR},
volume = {83},
number = {4},
pages = {},
pmid = {31533962},
issn = {1098-5557},
mesh = {Cytochromes/metabolism ; *Energy Metabolism ; Hydrogen/metabolism ; Hydrogenase/*metabolism ; Methane/metabolism ; Methanosarcina/*enzymology ; Phylogeny ; },
abstract = {The biological production of methane is vital to the global carbon cycle and accounts for ca. 74% of total methane emissions. The organisms that facilitate this process, methanogenic archaea, belong to a large and phylogenetically diverse group that thrives in a wide range of anaerobic environments. Two main subgroups exist within methanogenic archaea: those with and those without cytochromes. Although a variety of metabolisms exist within this group, the reduction of growth substrates to methane using electrons from molecular hydrogen is, in a phylogenetic sense, the most widespread methanogenic pathway. Methanogens without cytochromes typically generate methane by the reduction of CO2 with electrons derived from H2, formate, or secondary alcohols, generating a transmembrane ion gradient for ATP production via an Na[+]-translocating methyltransferase (Mtr). These organisms also conserve energy with a novel flavin-based electron bifurcation mechanism, wherein the endergonic reduction of ferredoxin is facilitated by the exergonic reduction of a disulfide terminal electron acceptor coupled to either H2 or formate oxidation. Methanogens that utilize cytochromes have a broader substrate range, and can convert acetate and methylated compounds to methane, in addition to the ability to reduce CO2 Cytochrome-containing methanogens are able to supplement the ion motive force generated by Mtr with an H[+]-translocating electron transport system. In both groups, enzymes known as hydrogenases, which reversibly interconvert protons and electrons to molecular hydrogen, play a central role in the methanogenic process. This review discusses recent insight into methanogen metabolism and energy conservation mechanisms with a particular focus on the genus Methanosarcina.},
}
@article {pmid31522353,
year = {2019},
author = {Sereme, Y and Mezouar, S and Grine, G and Mege, JL and Drancourt, M and Corbeau, P and Vitte, J},
title = {Methanogenic Archaea: Emerging Partners in the Field of Allergic Diseases.},
journal = {Clinical reviews in allergy &amp; immunology},
volume = {57},
number = {3},
pages = {456-466},
pmid = {31522353},
issn = {1559-0267},
support = {10-IAHU-03//Agence Nationale de la Recherche/ ; PhD//Fondation M&#xe9;diterran&#xe9;e Infection/ ; post-doctoral//Fondation M&#xe9;diterran&#xe9;e Infection/ ; PhD//Fondation M&#xe9;diterran&#xe9;e Infection/ ; },
mesh = {Allergens/*immunology ; Animals ; Archaea/*immunology ; Disease Susceptibility ; Host-Pathogen Interactions/immunology ; Humans ; Hypersensitivity/diagnosis/*etiology ; Microbiota/immunology ; },
abstract = {Archaea, which form one of four domains of life alongside Eukarya, Bacteria, and giant viruses, have long been neglected as components of the human microbiota and potential opportunistic infectious pathogens. In this review, we focus on methanogenic Archaea, which rely on hydrogen for their metabolism and growth. On one hand, methanogenic Archaea in the gut are functional associates of the fermentative digestion of dietary fibers, favoring the production of beneficial short-chain fatty acids and likely contributing to the weaning reaction during the neonatal window of opportunity. On the other hand, methanogenic Archaea trigger the activation of innate and adaptive responses and the generation of specific T and B cells in animals and humans. In mouse models, lung hypersensitivity reactions can be induced by inhaled methanogenic Archaea mimicking human professional exposure to organic dust. Changes in methanogenic Archaea of the microbiota are detected in an array of dysimmune conditions comprising inflammatory bowel disease, obesity, malnutrition, anorexia, colorectal cancer, and diverticulosis. At the subcellular level, methanogenic Archaea are activators of the TLR8-dependent NLRP3 inflammasome, modulate the release of antimicrobial peptides and drive the production of proinflammatory, Th-1, Th-2, and Th-17 cytokines. Our objective was to introduce the most recent and major pieces of evidence supporting the involvement of Archaea in the balance between health and dysimmune diseases, with a particular focus on atopic and allergic conditions.},
}
@article {pmid31520950,
year = {2019},
author = {Pal, S and Sar, A and Dam, B},
title = {Moderate halophilic bacteria, but not extreme halophilic archaea can alleviate the toxicity of short-alkyl side chain imidazolium-based ionic liquids.},
journal = {Ecotoxicology and environmental safety},
volume = {184},
number = {},
pages = {109634},
doi = {10.1016/j.ecoenv.2019.109634},
pmid = {31520950},
issn = {1090-2414},
mesh = {Geologic Sediments/chemistry/microbiology ; Halobacteriaceae/*drug effects ; Halomonas/*drug effects ; Imidazoles/*toxicity ; India ; Ionic Liquids/*toxicity ; Lakes/chemistry/microbiology ; Salinity ; Salt Tolerance ; },
abstract = {Imidazolium-based ionic liquids (IL) with short-alkyl side chain such as 1-ethyl-3-methyl-imidazolium chloride ([Emim]Cl) and 1-butyl-3-methyl-imidazolium chloride ([Bmim]Cl) has immense application potential including in lignocellulosic bioenergy production. But they are toxic to most microorganisms, and those isolated from different environments as IL-tolerant have salt tolerance capabilities. This study evaluates the relationship between salt and [Emim]Cl tolerance of microorganisms using different salinity sediments (2-19%) and brines (35%) of India's largest inland hypersaline lake, Sambhar in Rajasthan as the model system. While samples with 2% and 35% salinities do not yield any [Emim]Cl (100 mM) tolerant colonies, others have 6-50% colonies tolerant to the IL. Similar trend was observed with 50 mM [Bmim]Cl. Moderate halophilic isolates of genera Halomonas and Bacillus (growth in 0.7-3.0 M NaCl) isolated from the sediments could grow in as high as 375 mM [Emim]Cl, or 125 mM [Bmim]Cl facilitated by higher synthesis, and uptake of organic osmolytes; and up to 1.7-fold increased activity of active efflux pumps. [Bmim]Cl was more toxic than [Emim]Cl in all performed experiments. [Emim]Cl-adapted cells could trounce IL-induced stress. Interestingly, enrichment with 100 mM [Emim]Cl resulted in increase of IL-tolerant colonies in all sediments including the one with 2% salinity. However, the salt saturated brines (35%) do not yield any such colony even after repeated incubations. Extreme halophilic archaea, Natronomonas (growth in 3.0-4.0 M NaCl) isolated from such brines, were exceedingly sensitive to even 5 mM [Emim]Cl, or 1 mM [Bmim]Cl. Two additional extremophilic archaea, namely Haloferax and Haladaptatus were also sensitive to the tested ILs. Archaeal sensitivity is possibly due to the competitive interaction of [Emim][+] with their acidic proteome (15.4-17.5% aspartic and glutamic acids, against 10.7-12.9% in bacteria) that they maintain to stabilize the high amount of K[+] ion accumulated by salt-in strategy. Thus, general salt adaptation strategies of moderate halophilic bacteria help them to restrain toxicity of these ILs, but extremophilic archaea are highly sensitive and demands meticulous use of these solvents to prevent environmental contamination.},
}
@article {pmid31505830,
year = {2019},
author = {Salvador-Castell, M and Tourte, M and Oger, PM},
title = {In Search for the Membrane Regulators of Archaea.},
journal = {International journal of molecular sciences},
volume = {20},
number = {18},
pages = {},
pmid = {31505830},
issn = {1422-0067},
support = {ANR 17-CE11-0012-01//Agence Nationale de la Recherche/ ; Origines "ReseArch"//Centre National de la Recherche Scientifique/ ; },
mesh = {*Adaptation, Physiological ; Archaea/*physiology ; Cell Membrane/*metabolism ; Membrane Lipids/*metabolism ; },
abstract = {Membrane regulators such as sterols and hopanoids play a major role in the physiological and physicochemical adaptation of the different plasmic membranes in Eukarya and Bacteria. They are key to the functionalization and the spatialization of the membrane, and therefore indispensable for the cell cycle. No archaeon has been found to be able to synthesize sterols or hopanoids to date. They also lack homologs of the genes responsible for the synthesis of these membrane regulators. Due to their divergent membrane lipid composition, the question whether archaea require membrane regulators, and if so, what is their nature, remains open. In this review, we review evidence for the existence of membrane regulators in Archaea, and propose tentative location and biological functions. It is likely that no membrane regulator is shared by all archaea, but that they may use different polyterpenes, such as carotenoids, polyprenols, quinones and apolar polyisoprenoids, in response to specific stressors or physiological needs.},
}
@article {pmid31504156,
year = {2019},
author = {Bønløkke, JH and Duchaine, C and Schlünssen, V and Sigsgaard, T and Veillette, M and Basinas, I},
title = {Archaea and Bacteria Exposure in Danish Livestock Farmers.},
journal = {Annals of work exposures and health},
volume = {63},
number = {9},
pages = {965-974},
pmid = {31504156},
issn = {2398-7316},
mesh = {*Agriculture ; Air Pollutants, Occupational/*analysis ; Animal Husbandry/*statistics &amp; numerical data ; Animals ; Archaea/*isolation &amp; purification ; Bacteria/*isolation &amp; purification ; Denmark ; Dust/analysis ; Endotoxins/analysis ; Environmental Monitoring/methods ; Humans ; Inhalation Exposure/*analysis ; Livestock ; Occupational Exposure/*analysis ; RNA, Ribosomal, 16S/analysis ; Ventilation ; },
abstract = {OBJECTIVES: Methanogenic archaea have been found to make up part of the bioaerosols in pig, cattle, and poultry farms. So far no attempts have been made to determine how season, farm type, and farm characteristics may affect workers' exposure to archaea.<br><br>METHODS: Personal filter samples from 327 farmers working on 89 Danish farms were analysed for the number of 16S rRNA gene copies from archaea and bacteria and for their dust and endotoxin content. The farms were visited during summer and winter. Information on farm type and stable characteristics were collected using self-reported activity diaries and walk-through surveys. Differences in archaea and bacteria levels with farm type and stable characteristics and correlations with dust and endotoxin levels were examined.<br><br>RESULTS: Personal archaea exposure was documented in all farm types including, for the first time, during mink farming. At 7.3*104 gene copies m-3 the archaea levels were around two orders of magnitude lower than bacteria levels at 5.7*106 gene copies m-3. At 1.7*105 gene copies m-3 among pig farmers and 1.9*104 gene copies m-3 among cattle farmers the archaea levels differed with farm type (P < 0.0005). The archaea and bacteria levels correlated weakly with a Pearson correlation coefficient of 0.17. Neither archaea nor bacteria levels differed by season. In pig farms the archaea levels differed by type of ventilation and by wetness of the floor.<br><br>CONCLUSIONS: Archaea levels were not neglible and appeared to vary greatly between farm types. In pig farms they varied with some farm characteristics. Archaea levels appeared to depend on factors that differed from those of bacteria.},
}
@article {pmid31488843,
year = {2019},
author = {Huber, M and Faure, G and Laass, S and Kolbe, E and Seitz, K and Wehrheim, C and Wolf, YI and Koonin, EV and Soppa, J},
title = {Translational coupling via termination-reinitiation in archaea and bacteria.},
journal = {Nature communications},
volume = {10},
number = {1},
pages = {4006},
pmid = {31488843},
issn = {2041-1723},
mesh = {Archaea/*genetics/metabolism ; Bacteria/*genetics/metabolism ; Base Sequence ; Codon, Initiator ; Escherichia coli/genetics ; Genes, Archaeal/*genetics ; Genes, Bacterial/*genetics ; Genes, Overlapping ; Genes, Reporter ; Open Reading Frames/genetics ; Peptide Chain Initiation, Translational/*physiology ; Peptide Chain Termination, Translational/*physiology ; Protein Biosynthesis/*physiology ; RNA, Messenger ; Terminator Regions, Genetic ; },
abstract = {The genomes of many prokaryotes contain substantial fractions of gene pairs with overlapping stop and start codons (ATGA or TGATG). A potential benefit of overlapping gene pairs is translational coupling. In 720 genomes of archaea and bacteria representing all major phyla, we identify substantial, albeit highly variable, fractions of co-directed overlapping gene pairs. Various patterns are observed for the utilization of the SD motif for de novo initiation at upstream genes versus reinitiation at overlapping gene pairs. We experimentally test the predicted coupling in 9 gene pairs from the archaeon Haloferax volcanii and 5 gene pairs from the bacterium Escherichia coli. In 13 of 14 cases, translation of both genes is strictly coupled. Mutational analysis of SD motifs located upstream of the downstream genes indicate that the contribution of the SD to translational coupling widely varies from gene to gene. The nearly universal, abundant occurrence of overlapping gene pairs suggests that tight translational coupling is widespread in archaea and bacteria.},
}
@article {pmid31437442,
year = {2019},
author = {Hackley, RK and Schmid, AK},
title = {Global Transcriptional Programs in Archaea Share Features with the Eukaryotic Environmental Stress Response.},
journal = {Journal of molecular biology},
volume = {431},
number = {20},
pages = {4147-4166},
pmid = {31437442},
issn = {1089-8638},
support = {T32 GM007754/GM/NIGMS NIH HHS/United States ; },
mesh = {*Adaptation, Physiological ; Fungi/genetics ; Gene Expression Profiling ; *Gene Expression Regulation, Archaeal ; Halobacterium salinarum/*genetics ; *Stress, Physiological ; *Transcription, Genetic ; },
abstract = {The environmental stress response (ESR), a global transcriptional program originally identified in yeast, is characterized by a rapid and transient transcriptional response composed of large, oppositely regulated gene clusters. Genes induced during the ESR encode core components of stress tolerance, macromolecular repair, and maintenance of homeostasis. In this review, we investigate the possibility for conservation of the ESR across the eukaryotic and archaeal domains of life. We first re-analyze existing transcriptomics data sets to illustrate that a similar transcriptional response is identifiable in Halobacterium salinarum, an archaeal model organism. To substantiate the archaeal ESR, we calculated gene-by-gene correlations, gene function enrichment, and comparison of temporal dynamics. We note reported examples of variation in the ESR across fungi, then synthesize high-level trends present in expression data of other archaeal species. In particular, we emphasize the need for additional high-throughput time series expression data to further characterize stress-responsive transcriptional programs in the Archaea. Together, this review explores an open question regarding features of global transcriptional stress response programs shared across domains of life.},
}
@article {pmid31435153,
year = {2019},
author = {Bandyopadhyay, AK and Islam, RNU and Mitra, D and Banerjee, S and Goswami, A},
title = {Structural insights from water-ferredoxin interaction in mesophilic algae and halophilic archaea.},
journal = {Bioinformation},
volume = {15},
number = {2},
pages = {79-89},
pmid = {31435153},
issn = {0973-2063},
abstract = {We analyzed the water-ferredoxin interaction in mesophilic (moderate temperature) algae (PDB ID: 1AWD) and halophilic (salt-tolerant) archaea (PDB ID: 1DOI) using POWAIND version 2.0 (a protein-water interactions calculation program). It is found that the shell water (SW) is 2.5 fold greater in halophilic ferredoxin than mesophilic ferredoxin. Water-ferredoxin interactions in the core and cavity are the signature of stability. The normalized frequency of such interactions is less in halophilic relative to mesophilic ferredoxin and the halophilic signature for stability by such interactions is negligible. However, the surface dominated with such interactions seems to be important for ferredoxin and oxido-reductase recognition.},
}
@article {pmid31432245,
year = {2020},
author = {Sun, Y and Liu, Y and Pan, J and Wang, F and Li, M},
title = {Perspectives on Cultivation Strategies of Archaea.},
journal = {Microbial ecology},
volume = {79},
number = {3},
pages = {770-784},
pmid = {31432245},
issn = {1432-184X},
support = {31622002//NSFC/ ; 91851105//NSFC/ ; },
mesh = {Archaea/*growth &amp; development ; Bacteriological Techniques/instrumentation/*methods ; },
abstract = {Archaea have been recognized as a major domain of life since the 1970s and occupy a key position in the tree of life. Recent advances in culture-independent approaches have greatly accelerated the research son Archaea. However, many hypotheses concerning the diversity, physiology, and evolution of archaea are waiting to be confirmed by culture-base experiments. Consequently, archaeal isolates are in great demand. On the other hand, traditional approaches of archaeal cultivation are rarely successful and require urgent improvement. Here, we review the current practices and applicable microbial cultivation techniques, to inform on potential strategies that could improve archaeal cultivation in the future. We first summarize the current knowledge on archaeal diversity, with an emphasis on cultivated and uncultivated lineages pertinent to future research. Possible causes for the low success rate of the current cultivation practices are then discussed to propose future improvements. Finally, innovative insights for archaeal cultivation are described, including (1) medium refinement for selective cultivation based on the genetic and transcriptional information; (2) consideration of the up-to-date archaeal culturing skills; and (3) application of multiple cultivation techniques, such as co-culture, direct interspecies electron transfer (DIET), single-cell isolation, high-throughput culturing (HTC), and simulation of the natural habitat. Improved cultivation efforts should allow successful isolation of as yet uncultured archaea, contributing to the much-needed physiological investigation of archaea.},
}
@article {pmid31416876,
year = {2019},
author = {DasSarma, P and Anton, BP and DasSarma, SL and Martinez, FL and Guzman, D and Roberts, RJ and DasSarma, S},
title = {Genome Sequences and Methylation Patterns of Natrinema versiforme BOL5-4 and Natrinema pallidum BOL6-1, Two Extremely Halophilic Archaea from a Bolivian Salt Mine.},
journal = {Microbiology resource announcements},
volume = {8},
number = {33},
pages = {},
pmid = {31416876},
issn = {2576-098X},
abstract = {Two extremely halophilic archaea, namely, Natrinema versiforme BOL5-4 and Natrinema pallidum BOL6-1, were isolated from a Bolivian salt mine and their genomes sequenced using single-molecule real-time sequencing. The GC-rich genomes of BOL5-4 and BOL6-1 were 4.6 and 3.8 Mbp, respectively, with large chromosomes and multiple megaplasmids. Genome annotation was incorporated into HaloWeb and methylation patterns incorporated into REBASE.},
}
@article {pmid31411686,
year = {2019},
author = {Tang, Z and Chen, S and Chen, A and He, B and Zhou, Y and Chai, G and Guo, F and Huang, J},
title = {CasPDB: an integrated and annotated database for Cas proteins from bacteria and archaea.},
journal = {Database : the journal of biological databases and curation},
volume = {2019},
number = {},
pages = {},
pmid = {31411686},
issn = {1758-0463},
mesh = {Archaea/*genetics ; Archaeal Proteins/*genetics ; Bacteria/*genetics ; Bacterial Proteins/*genetics ; CRISPR-Associated Proteins/*genetics ; *CRISPR-Cas Systems ; *Databases, Protein ; },
abstract = {Clustered regularly interspaced short palindromic repeats (CRISPR) and associated proteins (Cas) constitute CRISPR-Cas systems, which are antiphage immune systems present in numerous bacterial and most archaeal species. In recent years, CRISPR-Cas systems have been developed into reliable and powerful genome editing tools. Nevertheless, finding similar or better tools from bacteria or archaea remains crucial. This requires the exploration of different CRISPR systems, identification and characterization new Cas proteins. Archives tailored for Cas proteins are urgently needed and necessitate the prediction and grouping of Cas proteins into an information center with all available experimental evidence. Here, we constructed Cas Protein Data Bank (CasPDB), an integrated and annotated online database for Cas proteins from bacteria and archaea. The CasPDB database contains 287 reviewed Cas proteins, 257 745 putative Cas proteins and 3593 Cas operons from 32 023 bacteria species and 1802 archaea species. The database can be freely browsed and searched. The CasPDB web interface also represents all the 3593 putative Cas operons and its components. Among these operons, 328 are members of the type II CRISPR-Cas system.},
}
@article {pmid31407306,
year = {2019},
author = {Yin, X and Kulkarni, AC and Friedrich, MW},
title = {DNA and RNA Stable Isotope Probing of Methylotrophic Methanogenic Archaea.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2046},
number = {},
pages = {189-206},
doi = {10.1007/978-1-4939-9721-3_15},
pmid = {31407306},
issn = {1940-6029},
mesh = {Archaea/*genetics ; Carbon/metabolism ; Carbon Isotopes/*analysis/chemistry ; Centrifugation, Density Gradient ; DNA Probes ; DNA, Archaeal/analysis/isolation &amp; purification/*metabolism ; Geologic Sediments/analysis/chemistry/microbiology ; Isotope Labeling/*methods ; Methane/metabolism ; Methanol ; Phylogeny ; RNA Probes ; RNA, Archaeal/analysis/isolation &amp; purification/*metabolism ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Methylotrophic methanogenic archaea are an integral part of the carbon cycle in various anaerobic environments. Different from methylotrophic bacteria, methylotrophic methanogens assimilate both, the methyl compound and dissolved inorganic carbon. Here, we present DNA- and RNA-stable isotope probing (SIP) methods involving an effective labeling strategy using [13]C-labeled dissolved inorganic carbon (DIC) as carbon source along with methanol as dissimilatory substrate.},
}
@article {pmid31397430,
year = {2019},
author = {Khlebodarova, TM and Likhoshvai, VA},
title = {[Molecular Mechanisms of Non-Inherited Antibiotic Tolerance in Bacteria and Archaea].},
journal = {Molekuliarnaia biologiia},
volume = {53},
number = {4},
pages = {531-540},
doi = {10.1134/S0026898419040050},
pmid = {31397430},
issn = {0026-8984},
mesh = {Anti-Bacterial Agents/*pharmacology ; Archaea/cytology/*drug effects ; Bacteria/cytology/*drug effects ; *Drug Tolerance ; Toxin-Antitoxin Systems ; },
abstract = {The phenomenon of bacterial persistence, also known as non-inherited antibiotic tolerance in a part of bacterial populations, was described more than 70 years ago. This type of tolerance contributes to the chronization of infectious diseases, including tuberculosis. Currently, the emergence of persistent cells in bacterial populations is associated with the functioning of some stress-induced molecular triggers, including toxin-antitoxin systems. In the presented review, genetic and metabolic peculiarities of persistent cells are considered and the mechanisms of their occurrence are discussed. The hypothesis of the origin of persister cells based on bistability, arising due to the non-linear properties of a coupled transcription-translation system, was proposed. Within this hypothesis, the phenomenon of the bacterial persistence of modern cells is considered as a result of the genetic fixation of the phenotypic multiplicity that emerged in primitive cells in the process of neutrally coupled co-evolution (genetic drift of multiple neutrally coupled mutations). Our hypothesis explains the properties of persister cells, as well as their origin and "ineradicable" nature.},
}
@article {pmid31388130,
year = {2019},
author = {Steen, AD and Crits-Christoph, A and Carini, P and DeAngelis, KM and Fierer, N and Lloyd, KG and Cameron Thrash, J},
title = {High proportions of bacteria and archaea across most biomes remain uncultured.},
journal = {The ISME journal},
volume = {13},
number = {12},
pages = {3126-3130},
pmid = {31388130},
issn = {1751-7370},
mesh = {Archaea/*genetics ; Bacteria/*genetics ; Ecosystem ; Phylogeny ; RNA, Ribosomal, 16S ; },
abstract = {A recent paper by Martiny argues that "high proportions" of bacteria in diverse Earth environments have been cultured. Here we reanalyze a portion of the data in that paper, and argue that the conclusion is based on several technical errors, most notably a calculation of sequence similarity that does not account for sequence gaps, and the reliance on 16S rRNA gene amplicons that are known to be biased towards cultured organisms. We further argue that the paper is also based on a conceptual error: namely, that sequence similarity cannot be used to infer "culturability" because one cannot infer physiology from 16S rRNA gene sequences. Combined with other recent, more reliable studies, the evidence supports the conclusion that most bacterial and archaeal taxa remain uncultured.},
}
@article {pmid31384725,
year = {2019},
author = {Blum, P and Payne, S},
title = {Evidence of an Epigenetics System in Archaea.},
journal = {Epigenetics insights},
volume = {12},
number = {},
pages = {2516865719865280},
pmid = {31384725},
issn = {2516-8657},
abstract = {Changes in the phenotype of a cell or organism that are heritable but do not involve changes in DNA sequence are referred to as epigenetic. They occur primarily through the gain or loss of chemical modification of chromatin protein or DNA. Epigenetics is therefore a non-Mendelian process. The study of epigenetics in eukaryotes is expanding with advances in knowledge about the relationship between mechanism and phenotype and as a requirement for multicellularity and cancer. However, life also includes other groups or domains, notably the bacteria and archaea. The occurrence of epigenetics in these deep lineages is an emerging topic accompanied by controversy. In these non-eukaryotic organisms, epigenetics is critically important because it stimulates new evolutionary theory and refines perspective about biological action.},
}
@article {pmid31384702,
year = {2019},
author = {MacLeod, F and Kindler, GS and Wong, HL and Chen, R and Burns, BP},
title = {Asgard archaea: Diversity, function, and evolutionary implications in a range of microbiomes.},
journal = {AIMS microbiology},
volume = {5},
number = {1},
pages = {48-61},
pmid = {31384702},
issn = {2471-1888},
abstract = {Elucidating the diversity of the Archaea has many important ecological and evolutionary implications. The Asgard superphylum of the archaea, described recently from metagenomic data, has reignited the decades-old debate surrounding the topology of the tree of life. This review synthesizes recent findings through publicly available genomes and literature to describe the current ecological and evolutionary significance of the Asgard superphylum. Asgard archaea have been found in a diverse range of microbiomes across the globe, primarily from sedimentary environments. Within these environments, positive correlations between specific members of the Asgard archaea and Candidate Division TA06 bacteria have been observed, opening up the possibility of symbiotic interactions between the groupings. Asgard archaeal genomes encode functionally diverse metabolic pathways, including the Wood-Ljungdahl pathway as a carbon-fixation strategy, putative nucleotide salvaging pathways, and novel mechanisms of phototrophy including new rhodopsins. Asgard archaea also appear to be active in nitrogen cycling. Asgard archaea encode genes involved in both dissimilatory nitrate reduction and denitrification, and for the potential to use atmospheric nitrogen or nitrite as nitrogen sources. Asgard archaea also may be involved in the transformation of sulfur compounds, indicating a putative role in sulfur cycling. To date, all Asgard archaeal genomes identified were described as obligately anaerobic. The Asgard archaea also appear to have important evolutionary implications. The presence of eukaryotic signature proteins and the affiliation of Asgard archaea in phylogenetic analyses appears to support two-domain topologies of the tree of life with eukaryotes emerging from within the domain of archaea, as opposed to the eukaryotes being a separate domain of life. Thus far, Heimdallarchaeota appears as the closest archaeal relative of eukaryotes.},
}
@article {pmid31377507,
year = {2019},
author = {Pan, KL and Gao, JF and Li, DC and Fan, XY},
title = {The dominance of non-halophilic archaea in autotrophic ammonia oxidation of activated sludge under salt stress: A DNA-based stable isotope probing study.},
journal = {Bioresource technology},
volume = {291},
number = {},
pages = {121914},
doi = {10.1016/j.biortech.2019.121914},
pmid = {31377507},
issn = {1873-2976},
mesh = {*Ammonia ; Archaea ; DNA ; Isotopes ; Nitrification ; Oxidation-Reduction ; Phylogeny ; Salt Stress ; *Sewage ; Soil Microbiology ; },
abstract = {Dynamics of nitrification activity, ammonia-oxidizing archaea (AOA) and bacteria (AOB) abundance and active ammonia oxidizers of activated sludge were explored under different salinities. Results showed that specific ammonium oxidation rates were significantly negative with increasing salinity. The responses of AOA and AOB populations to salt stress were distinct. AOA abundance decreased at moderate salinities (2.5, 5 and 7 g L[-1]) and increased at high salinities (10, 15, 20 and 30 g L[-1]), while AOB abundance showed opposite tendency. DNA-based stable isotope probing assays indicated AOA exclusively dominated active ammonia oxidation of test samples under different salinities. The active AOA communities retrieved were all non-halophilic and regulated by salinities. Candidatus Nitrosocosmicus exaquare and Ca. Nitrosocosmicus franklandus were the predominantly active AOA in both salt-free and salt-containing microcosms, while [13]C-labeled Nitrososphaera viennensis and Ca. Nitrososphaera gargensis were only retrieved from the microcosms amended with 0 and 30 g L[-1] salinity, respectively.},
}
@article {pmid31364272,
year = {2019},
author = {Bird, LR and Dawson, KS and Chadwick, GL and Fulton, JM and Orphan, VJ and Freeman, KH},
title = {Carbon isotopic heterogeneity of coenzyme F430 and membrane lipids in methane-oxidizing archaea.},
journal = {Geobiology},
volume = {17},
number = {6},
pages = {611-627},
doi = {10.1111/gbi.12354},
pmid = {31364272},
issn = {1472-4669},
mesh = {Archaea/*chemistry ; California ; Carbon Isotopes/*analysis ; Geologic Sediments/microbiology ; Membrane Lipids/*chemistry ; Metalloporphyrins/*chemistry ; Methane/metabolism ; Oregon ; Oxidation-Reduction ; Pacific Ocean ; },
abstract = {Archaeal ANaerobic MEthanotrophs (ANME) facilitate the anaerobic oxidation of methane (AOM), a process that is believed to proceed via the reversal of the methanogenesis pathway. Carbon isotopic composition studies indicate that ANME are metabolically diverse and able to assimilate metabolites including methane, methanol, acetate, and dissolved inorganic carbon (DIC). Our data support the interpretation that ANME in marine sediments at methane seeps assimilate both methane and DIC, and the carbon isotopic compositions of the tetrapyrrole coenzyme F430 and the membrane lipids archaeol and hydroxy-archaeol reflect their relative proportions of carbon from these substrates. Methane is assimilated via the methyl group of CH3 -tetrahydromethanopterin (H4 MPT) and DIC from carboxylation reactions that incorporate free intracellular DIC. F430 was enriched in [13] C (mean δ[13] C = -27‰ for Hydrate Ridge and -80‰ for the Santa Monica Basin) compared to the archaeal lipids (mean δ[13] C = -97‰ for Hydrate Ridge and -122‰ for the Santa Monica Basin). We propose that depending on the side of the tricarboxylic acid (TCA) cycle used to synthesize F430, its carbon was derived from 76% DIC and 24% methane via the reductive side or 57% DIC and 43% methane via the oxidative side. ANME lipids are predicted to contain 42% DIC and 58% methane, reflecting the amount of each assimilated into acetyl-CoA. With isotope models that include variable fractionation during biosynthesis for different carbon substrates, we show the estimated amounts of DIC and methane can result in carbon isotopic compositions of - 73‰ to - 77‰ for F430 and - 105‰ for archaeal lipids, values close to those for Santa Monica Basin. The F430 δ[13] C value for Hydrate Ridge was [13] C-enriched compared with the modeled value, suggesting there is divergence from the predicted two carbon source models.},
}
@article {pmid31363851,
year = {2019},
author = {Beyer, HM and Mikula, KM and Kudling, TV and Iwaï, H},
title = {Crystal structures of CDC21-1 inteins from hyperthermophilic archaea reveal the selection mechanism for the highly conserved homing endonuclease insertion site.},
journal = {Extremophiles : life under extreme conditions},
volume = {23},
number = {6},
pages = {669-679},
pmid = {31363851},
issn = {1433-4909},
support = {131413//Biotieteiden ja Ymp&#xe4;rist&#xf6;n Tutkimuksen Toimikunta/ ; 137995//Biotieteiden ja Ymp&#xe4;rist&#xf6;n Tutkimuksen Toimikunta/ ; 277335//Biotieteiden ja Ymp&#xe4;rist&#xf6;n Tutkimuksen Toimikunta/ ; NNF17OC0025402//Novo Nordisk Foundation/ ; NNF17OC0027550//Novo Nordisk Foundation/ ; },
mesh = {Archaeal Proteins/*chemistry/genetics ; Endonucleases/*chemistry/genetics ; Enzyme Stability ; Hot Temperature ; *Inteins ; Protein Domains ; Pyrococcus abyssi/*enzymology/genetics ; Pyrococcus horikoshii/*enzymology/genetics ; },
abstract = {Self-splicing inteins are mobile genetic elements invading host genes via nested homing endonuclease (HEN) domains. All HEN domains residing within inteins are inserted at a highly conserved insertion site. A purifying selection mechanism directing the location of the HEN insertion site has not yet been identified. In this work, we solved the three-dimensional crystal structures of two inteins inserted in the cell division control protein 21 of the hyperthermophilic archaea Pyrococcus abyssi and Pyrococcus horikoshii. A comparison between the structures provides the structural basis for the thermo-stabilization mechanism of inteins that have lost the HEN domain during evolution. The presence of an entire extein domain in the intein structure from Pyrococcus horikoshii suggests the selection mechanism for the highly conserved HEN insertion point.},
}
@article {pmid31341668,
year = {2019},
author = {Taffner, J and Cernava, T and Erlacher, A and Berg, G},
title = {Novel insights into plant-associated archaea and their functioning in arugula (Eruca sativa Mill.).},
journal = {Journal of advanced research},
volume = {19},
number = {},
pages = {39-48},
pmid = {31341668},
issn = {2090-1232},
abstract = {A plant's microbiota has various implications for the plant's health and performance; however, the roles of many microbial lineages, particularly Archaea, have not been explored in detail. In the present study, analysis of archaea-specific 16S rRNA gene fragments and shotgun-sequenced metagenomes was combined with visualization techniques to obtain the first insights into the archaeome of a common salad plant, arugula (Eruca sativa Mill.). The archaeal communities associated with the soil, rhizosphere and phyllosphere were distinct, but a high proportion of community members were shared among all analysed habitats. Soil habitats exhibited the highest diversity of Archaea, followed by the rhizosphere and the phyllosphere. The archaeal community was dominated by Thaumarchaeota and Euryarchaeota, with the most abundant taxa assigned to Candidatus Nitrosocosmicus, species of the 'Soil Crenarchaeotic Group' and, interestingly, Methanosarcina. Moreover, a large number of archaea-assigned sequences remained unassigned at lower taxonomic levels. Overall, analysis of shotgun-sequenced total-community DNA revealed a more diverse archaeome. Differences were evident at the class level and at higher taxonomic resolutions when compared to results from the 16S rRNA gene fragment amplicon library. Functional assessments primarily revealed archaeal genes related to response to stress (especially oxidative stress), CO2 fixation, and glycogen degradation. Microscopic visualizations of fluorescently labelled archaea in the phyllosphere revealed small scattered colonies, while archaea in the rhizosphere were found to be embedded within large bacterial biofilms. Altogether, Archaea were identified as a rather small but niche-specific component of the microbiomes of the widespread leafy green plant arugula.},
}
@article {pmid31337720,
year = {2019},
author = {Shimosaka, T and Makarova, KS and Koonin, EV and Atomi, H},
title = {Identification of Dephospho-Coenzyme A (Dephospho-CoA) Kinase in Thermococcus kodakarensis and Elucidation of the Entire CoA Biosynthesis Pathway in Archaea.},
journal = {mBio},
volume = {10},
number = {4},
pages = {},
pmid = {31337720},
issn = {2150-7511},
mesh = {Biosynthetic Pathways ; Coenzyme A/*biosynthesis/metabolism ; Computational Biology ; Peptide Synthases/metabolism ; Phosphorylation ; Phosphotransferases (Alcohol Group Acceptor)/*genetics/*metabolism ; Thermococcus/*enzymology/*genetics ; },
abstract = {Dephospho-coenzyme A (dephospho-CoA) kinase (DPCK) catalyzes the ATP-dependent phosphorylation of dephospho-CoA, the final step in coenzyme A (CoA) biosynthesis. DPCK has been identified and characterized in bacteria and eukaryotes but not in archaea. The hyperthermophilic archaeon Thermococcus kodakarensis encodes two homologs of bacterial DPCK and the DPCK domain of eukaryotic CoA synthase, TK1334 and TK2192. We purified the recombinant TK1334 and TK2192 proteins and found that they lacked DPCK activity. Bioinformatic analyses showed that, in several archaea, the uncharacterized gene from arCOG04076 protein is fused with the gene for phosphopantetheine adenylyltransferase (PPAT), which catalyzes the reaction upstream of the DPCK reaction in CoA biosynthesis. This observation suggested that members of arCOG04076, both fused to PPAT and standalone, could be the missing archaeal DPCKs. We purified the recombinant TK1697 protein, a standalone member of arCOG04076 from T. kodakarensis, and demonstrated its GTP-dependent DPCK activity. Disruption of the TK1697 resulted in CoA auxotrophy, indicating that TK1697 encodes a DPCK that contributes to CoA biosynthesis in T. kodakarensis TK1697 homologs are widely distributed in archaea, suggesting that the arCOG04076 protein represents a novel family of DPCK that is not homologous to bacterial and eukaryotic DPCKs but is distantly related to bacterial and eukaryotic thiamine pyrophosphokinases. We also constructed and characterized gene disruption strains of TK0517 and TK2128, homologs of bifunctional phosphopantothenoylcysteine synthetase-phosphopantothenoylcysteine decarboxylase and PPAT, respectively. Both strains displayed CoA auxotrophy, indicating their contribution to CoA biosynthesis. Taken together with previous studies, the results experimentally validate the entire CoA biosynthesis pathway in T. kodakarensisIMPORTANCE CoA is utilized in a wide range of metabolic pathways, and its biosynthesis is essential for all life. Pathways for CoA biosynthesis in bacteria and eukaryotes have been established. In archaea, however, the enzyme that catalyzes the final step in CoA biosynthesis, dephospho-CoA kinase (DPCK), had not been identified. In the present study, bioinformatic analyses identified a candidate for the DPCK in archaea, which was biochemically and genetically confirmed in the hyperthermophilic archaeon Thermococcus kodakarensis Genetic analyses on genes presumed to encode bifunctional phosphopantothenoylcysteine synthetase-phosphopantothenoylcysteine decarboxylase and phosphopantetheine adenylyltransferase confirmed their involvement in CoA biosynthesis. Taken together with previous studies, the results reveal the entire pathway for CoA biosynthesis in a single archaeon and provide insight into the different mechanisms of CoA biosynthesis and their distribution in nature.},
}
@article {pmid31336026,
year = {2019},
author = {Bayer, B and Hansman, RL and Bittner, MJ and Noriega-Ortega, BE and Niggemann, J and Dittmar, T and Herndl, GJ},
title = {Ammonia-oxidizing archaea release a suite of organic compounds potentially fueling prokaryotic heterotrophy in the ocean.},
journal = {Environmental microbiology},
volume = {21},
number = {11},
pages = {4062-4075},
pmid = {31336026},
issn = {1462-2920},
support = {P28781-B21//Austrian Science Fund/International ; W1257-B20//Austrian Science Fund/International ; },
mesh = {Ammonia/*metabolism ; Archaea/*metabolism ; Carbon/metabolism ; Chemoautotrophic Growth/physiology ; Heterotrophic Processes/*physiology ; Oceans and Seas ; Organic Chemicals/*metabolism ; Oxidation-Reduction ; Phylogeny ; },
abstract = {Ammonia-oxidizing archaea (AOA) constitute a considerable fraction of microbial biomass in the global ocean, comprising 20%-40% of the ocean's prokaryotic plankton. However, it remains enigmatic to what extent these chemolithoautotrophic archaea release dissolved organic carbon (DOC). A combination of targeted and untargeted metabolomics was used to characterize the exometabolomes of three model AOA strains of the Nitrosopumilus genus. Our results indicate that marine AOA exude a suite of organic compounds with potentially varying reactivities, dominated by nitrogen-containing compounds. A significant fraction of the released dissolved organic matter (DOM) consists of labile compounds, which typically limit prokaryotic heterotrophic activity in open ocean waters, including amino acids, thymidine and B vitamins. Amino acid release rates corresponded with ammonia oxidation activity and the three Nitrosopumilus strains predominantly released hydrophobic amino acids, potentially as a result of passive diffusion. Despite the low contribution of DOC released by AOA (~0.08%-1.05%) to the heterotrophic prokaryotic carbon demand, the release of physiologically relevant metabolites could be crucial for microbes that are auxotrophic for some of these compounds, including members of the globally abundant and ubiquitous SAR11 clade.},
}
@article {pmid31332386,
year = {2019},
author = {Roux, S and Krupovic, M and Daly, RA and Borges, AL and Nayfach, S and Schulz, F and Sharrar, A and Matheus Carnevali, PB and Cheng, JF and Ivanova, NN and Bondy-Denomy, J and Wrighton, KC and Woyke, T and Visel, A and Kyrpides, NC and Eloe-Fadrosh, EA},
title = {Cryptic inoviruses revealed as pervasive in bacteria and archaea across Earth's biomes.},
journal = {Nature microbiology},
volume = {4},
number = {11},
pages = {1895-1906},
pmid = {31332386},
issn = {2058-5276},
support = {DP5 OD021344/OD/NIH HHS/United States ; R01 GM127489/GM/NIGMS NIH HHS/United States ; T32 AI060537/AI/NIAID NIH HHS/United States ; },
mesh = {Archaea/*virology ; Archaeal Viruses/classification/genetics ; Bacteria/*virology ; Bacteriophages/classification/genetics ; Computational Biology/*methods ; Genome, Viral ; Inoviridae/*classification/genetics ; Machine Learning ; Phylogeny ; },
abstract = {Bacteriophages from the Inoviridae family (inoviruses) are characterized by their unique morphology, genome content and infection cycle. One of the most striking features of inoviruses is their ability to establish a chronic infection whereby the viral genome resides within the cell in either an exclusively episomal state or integrated into the host chromosome and virions are continuously released without killing the host. To date, a relatively small number of inovirus isolates have been extensively studied, either for biotechnological applications, such as phage display, or because of their effect on the toxicity of known bacterial pathogens including Vibrio cholerae and Neisseria meningitidis. Here, we show that the current 56 members of the Inoviridae family represent a minute fraction of a highly diverse group of inoviruses. Using a machine learning approach leveraging a combination of marker gene and genome features, we identified 10,295 inovirus-like sequences from microbial genomes and metagenomes. Collectively, our results call for reclassification of the current Inoviridae family into a viral order including six distinct proposed families associated with nearly all bacterial phyla across virtually every ecosystem. Putative inoviruses were also detected in several archaeal genomes, suggesting that, collectively, members of this supergroup infect hosts across the domains Bacteria and Archaea. Finally, we identified an expansive diversity of inovirus-encoded toxin-antitoxin and gene expression modulation systems, alongside evidence of both synergistic (CRISPR evasion) and antagonistic (superinfection exclusion) interactions with co-infecting viruses, which we experimentally validated in a Pseudomonas model. Capturing this previously obscured component of the global virosphere may spark new avenues for microbial manipulation approaches and innovative biotechnological applications.},
}
@article {pmid31320751,
year = {2019},
author = {Eloe-Fadrosh, EA},
title = {Genome gazing in ammonia-oxidizing archaea.},
journal = {Nature reviews. Microbiology},
volume = {17},
number = {9},
pages = {531},
doi = {10.1038/s41579-019-0248-8},
pmid = {31320751},
issn = {1740-1534},
mesh = {Ammonia/metabolism ; Archaea/*genetics/metabolism/virology ; *Genome, Archaeal ; *Interspersed Repetitive Sequences ; Metabolic Networks and Pathways/*genetics ; Oxidation-Reduction ; Viruses/genetics ; },
}
@article {pmid31314099,
year = {2019},
author = {Liu, TT and Yang, H},
title = {An RNA-based quantitative and compositional study of ammonium-oxidizing bacteria and archaea in Lake Taihu, a eutrophic freshwater lake.},
journal = {FEMS microbiology ecology},
volume = {95},
number = {9},
pages = {},
doi = {10.1093/femsec/fiz117},
pmid = {31314099},
issn = {1574-6941},
mesh = {Ammonium Compounds/*metabolism ; Archaea/classification/genetics/growth &amp; development/*metabolism ; Bacteria/classification/genetics/growth &amp; development/*metabolism ; Biodiversity ; Geologic Sediments/microbiology ; Lakes/chemistry/*microbiology ; Microbiota ; Nitrification ; Oxidation-Reduction ; Phylogeny ; RNA, Bacterial/genetics ; },
abstract = {Ammonium-oxidizing archaea (AOA) and bacteria (AOB) play crucial roles in ammonium oxidation in freshwater lake sediment. However, previous reports on the predominance of AOA and AOB in the surface sediment of Lake Taihu have been based on DNA levels, detecting the total abundance of microbiota (including inactive cells), and have resulted in numerous contradictory conclusions. Existing RNA-level studies detecting active transcription are very limited. The current study, using RNA-based real-time quantification and clone library analysis, demonstrated that the amoA gene abundance of active AOB was higher than that of active AOA, despite conflicting results at the DNA level. Further exploration revealed a significant positive correlation between the potential nitrification rate (PNR) and the abundance of AOA and AOB at the RNA level, with irregular or contradictory correlation found at the DNA level. Ultimately, using quantitative analysis of RNA levels, we show AOB to be the active dominant contributor to ammonium oxidation. Our investigations also indicated that AOB were more diverse in high-ammonium lake regions, with Nitrosomonas being the active and dominating cluster, but that AOA had an advantage in the low-ammonium lake regions.},
}
@article {pmid31312729,
year = {2019},
author = {DeMott, MS and Dedon, PC},
title = {The road less traveled: A new phosphorothioate antiviral defense mechanism discovered in Archaea.},
journal = {Synthetic and systems biotechnology},
volume = {4},
number = {3},
pages = {132-133},
pmid = {31312729},
issn = {2405-805X},
}
@article {pmid31283101,
year = {2019},
author = {Schwarz, TS and Wäber, NB and Feyh, R and Weidenbach, K and Schmitz, RA and Marchfelder, A and Hartmann, RK},
title = {Homologs of aquifex aeolicus protein-only RNase P are not the major RNase P activities in the archaea haloferax volcanii and methanosarcina mazei.},
journal = {IUBMB life},
volume = {71},
number = {8},
pages = {1109-1116},
doi = {10.1002/iub.2122},
pmid = {31283101},
issn = {1521-6551},
mesh = {Aquifex ; Bacteria/*enzymology ; Catalysis ; Circular Dichroism ; Escherichia coli/metabolism ; Gene Deletion ; Genetic Complementation Test ; Haloferax volcanii/*enzymology ; Methanosarcina/*enzymology ; Nucleic Acid Conformation ; Phenotype ; Plasmids/genetics ; RNA, Transfer/genetics ; Recombinant Proteins/metabolism ; Ribonuclease P/*metabolism ; Species Specificity ; Temperature ; Thermus thermophilus/enzymology ; },
abstract = {The mature 5'-ends of tRNAs are generated by RNase P in all domains of life. The ancient form of the enzyme is a ribonucleoprotein consisting of a catalytic RNA and one or more protein subunits. However, in the hyperthermophilic bacterium Aquifex aeolicus and close relatives, RNase P is a protein-only enzyme consisting of a single type of polypeptide (Aq_880, ~23 kDa). In many archaea, homologs of Aq_880 were identified (termed HARPs for Homologs of Aquifex RNase P) in addition to the RNA-based RNase P, raising the question about the functions of HARP and the classical RNase P in these archaea. Here we investigated HARPs from two euryarchaeotes, Haloferax volcanii and Methanosarcina mazei. Archaeal strains with HARP gene knockouts showed no growth phenotypes under standard conditions, temperature and salt stress (H. volcanii) or nitrogen deficiency (M. mazei). Recombinant H. volcanii and M. mazei HARPs were basically able to catalyse specific tRNA 5'-end maturation in vitro. Furthermore, M. mazei HARP was able to rescue growth of an Escherichia coli RNase P depletion strain with comparable efficiency as Aq_880, while H. volcanii HARP was unable to do so. In conclusion, both archaeal HARPs showed the capacity (in at least one functional assay) to act as RNases P. However, the ease to obtain knockouts of the singular HARP genes and the lack of growth phenotypes upon HARP gene deletion contrasts with the findings that the canonical RNase P RNA gene cannot be deleted in H. volcanii, and a knockdown of RNase P RNA in H. volcanii results in severe tRNA processing defects. We conclude that archaeal HARPs do not make a major contribution to global tRNA 5'-end maturation in archaea, but may well exert a specialised, yet unknown function in (t)RNA metabolism. © 2019 IUBMB Life, 2019 © 2019 IUBMB Life, 71(8):1109-1116, 2019.},
}
@article {pmid31270201,
year = {2019},
author = {DasSarma, S and Fomenkov, A and DasSarma, SL and Vincze, T and DasSarma, P and Roberts, RJ},
title = {Methylomes of Two Extremely Halophilic Archaea Species, Haloarcula marismortui and Haloferax mediterranei.},
journal = {Microbiology resource announcements},
volume = {8},
number = {27},
pages = {},
pmid = {31270201},
issn = {2576-098X},
abstract = {The genomes of two extremely halophilic Archaea species, Haloarcula marismortui and Haloferax mediterranei, were sequenced using single-molecule real-time sequencing. The ∼4-Mbp genomes are GC rich with multiple large plasmids and two 4-methyl-cytosine patterns. Methyl transferases were incorporated into the Restriction Enzymes Database (REBASE), and gene annotation was incorporated into the Haloarchaeal Genomes Database (HaloWeb).},
}
@article {pmid31264806,
year = {2019},
author = {Pereira, O and Hochart, C and Auguet, JC and Debroas, D and Galand, PE},
title = {Genomic ecology of Marine Group II, the most common marine planktonic Archaea across the surface ocean.},
journal = {MicrobiologyOpen},
volume = {8},
number = {9},
pages = {e00852},
pmid = {31264806},
issn = {2045-8827},
mesh = {Aquatic Organisms/*classification/*genetics ; Euryarchaeota/*classification/*genetics ; Metabolic Networks and Pathways/genetics ; Metagenomics ; *Microbiota ; *Oceans and Seas ; Phylogeny ; Rhodopsins, Microbial/genetics ; Seawater/*microbiology ; },
abstract = {Planktonic Archaea have been detected in all the world's oceans and are found from surface waters to the deep sea. The two most common Archaea phyla are Thaumarchaeota and Euryarchaeota. Euryarchaeota are generally more common in surface waters, but very little is known about their ecology and their potential metabolisms. In this study, we explore the genomic ecology of the Marine Group II (MGII), the main marine planktonic Euryarchaeota, and test if it is composed of different ecologically relevant units. We re-analyzed Tara Oceans metagenomes from the photic layer and the deep ocean by annotating sequences against a custom MGII database and by mapping gene co-occurrences. Our data provide a global view of the distribution of Euryarchaeota, and more specifically of MGII subgroups, and reveal their association to a number of gene-coding sequences. In particular, we show that MGII proteorhodopsins were detected in both the surface and the deep chlorophyll maximum layer and that different clusters of these light harvesting proteins were present. Our approach helped describing the set of genes found together with specific MGII subgroups. We could thus define genomic environments that could theoretically describe ecologically meaningful units and the ecological niche that they occupy.},
}
@article {pmid31249623,
year = {2019},
author = {Zhao, X and Li, X and Li, Y and Sun, Y and Zhang, X and Weng, L and Ren, T and Li, Y},
title = {Shifting interactions among bacteria, fungi and archaea enhance removal of antibiotics and antibiotic resistance genes in the soil bioelectrochemical remediation.},
journal = {Biotechnology for biofuels},
volume = {12},
number = {},
pages = {160},
pmid = {31249623},
issn = {1754-6834},
abstract = {BACKGROUND: Antibiotics and antibiotic resistance genes (ARGs) are two pollutants in soil, especially ARGs as one of the top three threats to human health. The performance of soil microbial fuel cells (MFCs) fuelled with antibiotics was investigated.<br><br>RESULTS: In this study, soil MFCs spiked with tetracycline exhibited optimal bioelectricity generation, which was 25% and 733% higher than those of MFCs spiked with sulfadiazine and control, respectively. Compared with the non-electrode treatment, not only did functional micro-organisms change in open- and closed-circuit treatments, but also the microbial affinities, respectively, increased by 50% and 340% to adapt to higher removal of antibiotics. For the open-circuit treatment, the ineffective interspecific relation of micro-organisms was reduced to assist the removal efficiency of antibiotics by 7-27%. For the closed-circuit treatment, an intensive metabolic network capable of bioelectricity generation, degradation and nitrogen transformation was established, which led to 10-35% higher removal of antibiotics. Importantly, the abundances of ARGs and mobile genetic element (MGE) genes decreased after the introduction of electrodes; especially in the closed-circuit treatment, the highest reduction of 47% and 53% was observed, respectively.<br><br>CONCLUSIONS: Soil MFCs possess advantages for the elimination of antibiotics and ARGs with sevenfold to eightfold higher electricity generation than that of the control treatment. Compared with sulphonamides, the enhancement removal of tetracycline is higher, while both potential ARG propagation risk is reduced in soil MFCs. This study firstly synchronously reveals the relationships among bacteria, fungi and archaea and with ARGs and MGE genes in soil bioelectrochemical systems.},
}
@article {pmid31249390,
year = {2019},
author = {Trivedi, C and Reich, PB and Maestre, FT and Hu, HW and Singh, BK and Delgado-Baquerizo, M},
title = {Plant-driven niche differentiation of ammonia-oxidizing bacteria and archaea in global drylands.},
journal = {The ISME journal},
volume = {13},
number = {11},
pages = {2727-2736},
pmid = {31249390},
issn = {1751-7370},
mesh = {Ammonia/*metabolism ; Archaea/genetics/*metabolism ; Bacteria/classification/genetics/*metabolism ; Betaproteobacteria/metabolism ; Climate ; Ecosystem ; Environment ; Nitrification ; Oxidation-Reduction ; Phylogeny ; *Soil Microbiology ; },
abstract = {Under controlled laboratory conditions, high and low ammonium availability are known to favor soil ammonia-oxidizing bacteria (AOB) and archaea (AOA) communities, respectively. However, whether this niche segregation is maintained under field conditions in terrestrial ecosystems remains unresolved, particularly at the global scale. We hypothesized that perennial vegetation might favor AOB vs. AOA communities compared with adjacent open areas devoid of perennial vegetation (i.e., bare soil) via several mechanisms, including increasing the amount of ammonium in soil. To test this niche-differentiation hypothesis, we conducted a global field survey including 80 drylands from 6 continents. Data supported our hypothesis, as soils collected under plant canopies had higher levels of ammonium, as well as higher richness (number of terminal restriction fragments; T-RFs) and abundance (qPCR amoA genes) of AOB, and lower richness and abundance of AOA, than those collected in open areas located between plant canopies. Some of the reported associations between plant canopies and AOA and AOB communities can be a consequence of the higher organic matter and available N contents found under plant canopies. Other aspects of soils associated with vegetation including shading and microclimatic conditions might also help explain our results. Our findings provide strong evidence for niche differentiation between AOA and AOB communities in drylands worldwide, advancing our understanding of their ecology and biogeography at the global scale.},
}
@article {pmid31249385,
year = {2019},
author = {Zhang, H and Sun, H and Zhou, S and Bai, N and Zheng, X and Li, S and Zhang, J and Lv, W},
title = {Effect of Straw and Straw Biochar on the Community Structure and Diversity of Ammonia-oxidizing Bacteria and Archaea in Rice-wheat Rotation Ecosystems.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {9367},
pmid = {31249385},
issn = {2045-2322},
mesh = {Agriculture/methods ; *Ammonia/metabolism ; *Archaea/classification/genetics/metabolism ; *Bacteria/classification/genetics/metabolism ; Crops, Agricultural ; *Ecosystem ; Fertilizers ; Nitrification ; *Oryza/growth &amp; development ; *Oxidation-Reduction ; Soil/chemistry ; *Soil Microbiology ; *Triticum/growth &amp; development ; },
abstract = {Ammonia oxidation is the first and rate-limiting step of nitrification, driven by ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA). Straw and straw biochar retention are the popular ways to utilize the agricultural by-products in China, but their long-term effects on AOB and AOA still remain poorly understood. Based on a 7-year plot experiment, which had 4 fertilization regimes: no fertilizer (CK), regular fertilization (RT), straw retention (SR) and straw biochar retention (SB), the abundance and the composition of AOB and AOA was investigated before both the harvest of rice and wheat season by quantitative PCR and 454 high-throughput pyrosequencing, respectively. (1) Compared to RT, straw and straw biochar increased AOB abundance and diversity significantly only in wheat season (P < 0.05), and they both ranked as SB > SR > RT. Among fertilized treatments, a significant difference between SR and RT was found in AOB community composition of the winter season (R value = 0.58, P value = 0.02); (2) In contrast, AOA was almost not responsive to organic addition, except the significant enhancement of abundance by biochar in wheat season; (3) After straw and straw biochar addition, soil potential nitrification rates (PNR) was positive correlated to AOB abundance in both rice and wheat season (P < 0.01), not to AOA abundance (P = 0.211 and 0.068, respectively). This study provides scientific support for the potential of straw utilization to improve nitrification in rice-wheat rotation system with respect to soil ammonia oxidation microorganism.},
}
@article {pmid31239395,
year = {2019},
author = {Bayer, B and Pelikan, C and Bittner, MJ and Reinthaler, T and Könneke, M and Herndl, GJ and Offre, P},
title = {Proteomic Response of Three Marine Ammonia-Oxidizing Archaea to Hydrogen Peroxide and Their Metabolic Interactions with a Heterotrophic Alphaproteobacterium.},
journal = {mSystems},
volume = {4},
number = {4},
pages = {},
pmid = {31239395},
issn = {2379-5077},
abstract = {Ammonia-oxidizing archaea (AOA) play an important role in the nitrogen cycle and account for a considerable fraction of the prokaryotic plankton in the ocean. Most AOA lack the hydrogen peroxide (H2O2)-detoxifying enzyme catalase, and some AOA have been shown to grow poorly under conditions of exposure to H2O2 However, differences in the degrees of H2O2 sensitivity of different AOA strains, the physiological status of AOA cells exposed to H2O2, and their molecular response to H2O2 remain poorly characterized. Further, AOA might rely on heterotrophic bacteria to detoxify H2O2, and yet the extent and variety of costs and benefits involved in these interactions remain unclear. Here, we used a proteomics approach to compare the protein profiles of three Nitrosopumilus strains grown in the presence and absence of catalase and in coculture with the heterotrophic alphaproteobacterium Oceanicaulis alexandrii We observed that most proteins detected at a higher relative abundance in H2O2-exposed Nitrosopumilus cells had no known function in oxidative stress defense. Instead, these proteins were putatively involved in the remodeling of the extracellular matrix, which we hypothesize to be a strategy limiting the influx of H2O2 into the cells. Using RNA-stable isotope probing, we confirmed that O. alexandrii cells growing in coculture with the Nitrosopumilus strains assimilated Nitrosopumilus-derived organic carbon, suggesting that AOA could recruit H2O2-detoxifying bacteria through the release of labile organic matter. Our results contribute new insights into the response of AOA to H2O2 and highlight the potential ecological importance of their interactions with heterotrophic free-living bacteria in marine environments.IMPORTANCE Ammonia-oxidizing archaea (AOA) are the most abundant chemolithoautotrophic microorganisms in the oxygenated water column of the global ocean. Although H2O2 appears to be a universal by-product of aerobic metabolism, genes encoding the hydrogen peroxide (H2O2)-detoxifying enzyme catalase are largely absent in genomes of marine AOA. Here, we provide evidence that closely related marine AOA have different degrees of sensitivity to H2O2, which may contribute to niche differentiation between these organisms. Furthermore, our results suggest that marine AOA rely on H2O2 detoxification during periods of high metabolic activity and release organic compounds, thereby potentially attracting heterotrophic prokaryotes that provide this missing function. In summary, this report provides insights into the metabolic interactions between AOA and heterotrophic bacteria in marine environments and suggests that AOA play an important role in the biogeochemical carbon cycle by making organic carbon available for heterotrophic microorganisms.},
}
@article {pmid31237975,
year = {2019},
author = {Horai, S and Yamauchi, N and Naraoka, H},
title = {Simultaneous total analysis of core and polar membrane lipids in archaea by high-performance liquid chromatography/high-resolution mass spectrometry coupled with heated electrospray ionization.},
journal = {Rapid communications in mass spectrometry : RCM},
volume = {33},
number = {20},
pages = {1571-1577},
doi = {10.1002/rcm.8506},
pmid = {31237975},
issn = {1097-0231},
support = {KAKENHI Grant JP15H05749//Japan Society for the Promotion of Science/ ; },
abstract = {RATIONALE: Archaea have characteristic membrane lipids including diether and/or tetraether isoprenoidal core lipids with various polar head groups. Since the polar group is removed soon after the end of archaeal activity, the occurrences of core and polar lipids are regarded as dead and active signals, respectively. The core and polar lipids have generally been analyzed separately using atmospheric pressure chemical ionization (APCI) and electrospray ionization (ESI), respectively, coupled with mass spectrometry.<br><br>METHODS: In this study, simultaneous analyses of core and polar archaeal lipids have been examined using heated electrospray ionization (HESI) by high-performance liquid chromatography/high-resolution mass spectrometry (HPLC/HRMS).<br><br>RESULTS: Both core and intact polar lipids can be analyzed simultaneously by HESI with good sensitivity (sub ng to 100&#x2009;ng) and separation using a semi-bore diol column by normal-phase chromatography. The core lipids eluted firstly to separate archeaol, then glycerol dibiphytanyl glycerol tetraethers (GDGTs), followed by the polar lipids with glycosides and glycophosphates. The relative GDGT composition is identical between HESI and APCI methods.<br><br>CONCLUSIONS: The simultaneous analysis has the benefit of minimizing sample amount and elution solvent as well as preparation work. The method can also be applied to a compound class fractionation for compound-specific carbon and hydrogen isotope analysis.},
}
@article {pmid31223656,
year = {2019},
author = {Vuillemin, A and Wankel, SD and Coskun, &#xd6;K and Magritsch, T and Vargas, S and Estes, ER and Spivack, AJ and Smith, DC and Pockalny, R and Murray, RW and D'Hondt, S and Orsi, WD},
title = {Archaea dominate oxic subseafloor communities over multimillion-year time scales.},
journal = {Science advances},
volume = {5},
number = {6},
pages = {eaaw4108},
pmid = {31223656},
issn = {2375-2548},
mesh = {Ammonia/metabolism ; Archaea/*metabolism/*physiology ; Carbon Cycle/physiology ; Geologic Sediments/microbiology ; Microbiota/physiology ; Nitrogen/metabolism ; Nitrogen Cycle/physiology ; Oxidation-Reduction ; Water Microbiology ; },
abstract = {Ammonia-oxidizing archaea (AOA) dominate microbial communities throughout oxic subseafloor sediment deposited over millions of years in the North Atlantic Ocean. Rates of nitrification correlated with the abundance of these dominant AOA populations, whose metabolism is characterized by ammonia oxidation, mixotrophic utilization of organic nitrogen, deamination, and the energetically efficient chemolithoautotrophic hydroxypropionate/hydroxybutyrate carbon fixation cycle. These AOA thus have the potential to couple mixotrophic and chemolithoautotrophic metabolism via mixotrophic deamination of organic nitrogen, followed by oxidation of the regenerated ammonia for additional energy to fuel carbon fixation. This metabolic feature likely reduces energy loss and improves AOA fitness under energy-starved, oxic conditions, thereby allowing them to outcompete other taxa for millions of years.},
}
@article {pmid31212151,
year = {2019},
author = {Zhang, X and Duan, P and Wu, Z and Xiong, Z},
title = {Aged biochar stimulated ammonia-oxidizing archaea and bacteria-derived N2O and NO production in an acidic vegetable soil.},
journal = {The Science of the total environment},
volume = {687},
number = {},
pages = {433-440},
doi = {10.1016/j.scitotenv.2019.06.128},
pmid = {31212151},
issn = {1879-1026},
mesh = {Agriculture ; Ammonia/*metabolism ; Archaea ; Bacteria ; Charcoal/*chemistry ; Nitrogen Oxides/analysis/*metabolism ; Soil/chemistry ; *Soil Microbiology ; },
abstract = {Both nitrous oxide (N2O) and nitric oxide (NO) emissions are typically high in greenhouse-based high N input vegetable soils. Biochar amendment has been widely recommended for mitigating soil N2O emissions in agriculture. However, knowledge of the regulatory mechanisms of fresh and aged biochar for both N2O and NO production during ammonia oxidation is lacking. Two vegetable soils with different pH values were used in aerobic incubation experiments with 2-phenyl-4,4,5,5-tetramethylimidazoline-1-oxyl 3-oxide (PTIO), 1-octyne and acetylene. The relative importance of ammonia-oxidizing archaea (AOA) and bacteria (AOB) to N2O and NO production was investigated as influenced by fresh and aged biochar amendments. The results showed that AOA dominated N2O production in acidic soil, while AOB dominated N2O production in alkaline soil. Aged biochar stimulated both AOA- and AOB-derived N2O and NO production by 84.8 and 340%, respectively, in acidic soil but only increased AOA-derived N2O and NO production in alkaline soil. Fresh biochar amendment increased AOA- and AOB-derived NO in acidic soil and AOA-derived NO in alkaline soil but had negligible effects on AOA- and AOB-derived N2O in both soils. Fresh biochar decreased AOA-amoA but increased AOB-amoA gene abundances in acidic soil, whereas aged biochar increased AOA- and AOB-amoA gene abundances in both soils. These findings improved our understanding of N2O and NO production mechanisms under different biochar amendments in alkaline and acidic vegetable soils.},
}
@article {pmid31196534,
year = {2019},
author = {Kırtel, O and Lescrinier, E and Van den Ende, W and Toksoy Öner, E},
title = {Discovery of fructans in Archaea.},
journal = {Carbohydrate polymers},
volume = {220},
number = {},
pages = {149-156},
doi = {10.1016/j.carbpol.2019.05.064},
pmid = {31196534},
issn = {1879-1344},
mesh = {Evolution, Molecular ; *Fructans/chemistry/metabolism ; *Halobacteriaceae/classification/metabolism ; *Inulin/chemistry/metabolism ; Lakes/*microbiology ; Salinity ; Turkey ; Water Microbiology ; },
abstract = {Fructans are fructose-based oligo- and polysaccharides derived from sucrose that occur in a plethora of Eubacteria and plants. While fructan-producing (fructanogenic) Eubacteria are abundant in hypersaline environments, fructan production by Archaea has never been reported before. Exopolysaccharides accumulated by various Archaea from the Halobacteria class (belonging to the genera of Halomicrobium, Haloferax and Natronococcus) originating from different locations on Earth were structurally characterized as either levans or inulins with varying branching degrees (10%-16%). Thus, we show for the first time in the literature that fructans are produced in all three domains of life, including Archaea. This proof of concept will not only provide insight into Archaeal glycans and evolution but it may also open new frontiers for innovative strategies to overcome the ever-increasing threat of excessive salinization.},
}
@article {pmid31195017,
year = {2019},
author = {Lemmens, L and Maklad, HR and Bervoets, I and Peeters, E},
title = {Transcription Regulators in Archaea: Homologies and Differences with Bacterial Regulators.},
journal = {Journal of molecular biology},
volume = {431},
number = {20},
pages = {4132-4146},
doi = {10.1016/j.jmb.2019.05.045},
pmid = {31195017},
issn = {1089-8638},
mesh = {Archaea/*genetics/metabolism ; Evolution, Molecular ; Gene Expression Regulation, Archaeal ; Transcription Factors/genetics/*metabolism ; *Transcription, Genetic ; },
abstract = {The fitness and survival of prokaryotic microorganisms depends on their ability to adequately respond to environmental changes, sudden stress conditions and metabolic shifts. An important mechanism underlying this response is the regulation of gene expression mediated by transcription factors that are responsive to small-molecule ligands or other intracellular signals. Despite constituting a distinct domain of life from bacteria and harboring a eukaryotic-like basal transcription apparatus, it is well established that archaea have similar transcription factors pointing to the existence of shared ancestral proteins and to the occurrence of inter-domain horizontal gene transfer events. However, while global structural features of bacterial and archaeal transcription factors are indeed similar, other characteristics imply that archaeal regulators have undergone independent evolution. Here, we discuss the characteristics of Lrp/AsnC, MarR, ArsR/SmtB and TrmB families of transcription factors, which are the dominant families that constitute the transcription factor repertoire in archaea. We exemplify the evolutionary expansion of these families in archaeal lineages by emphasizing homologies and differences with bacterial counterparts in terms of ligand or signal response, physiological functions and mechanistic principles of regulation. As such, we aim to define future research approaches that enable further characterization of the functions and mechanisms of archaeal transcription factors.},
}
@article {pmid31189733,
year = {2019},
author = {Ludt, K and Soppa, J},
title = {Polyploidy in halophilic archaea: regulation, evolutionary advantages, and gene conversion.},
journal = {Biochemical Society transactions},
volume = {47},
number = {3},
pages = {933-944},
doi = {10.1042/BST20190256},
pmid = {31189733},
issn = {1470-8752},
mesh = {Archaea/*genetics ; Chromosomes, Archaeal ; *Evolution, Molecular ; *Gene Conversion ; *Genes, Archaeal ; *Polyploidy ; Replication Origin ; },
abstract = {All analyzed haloarachea are polyploid. In addition, haloarchaea contain more than one type of chromosome, and thus the gene dosage can be regulated independently on different replicons. Haloarchaea and several additional archaea have more than one replication origin on their major chromosome, in stark contrast with bacteria, which have a single replication origin. Two of these replication origins of Haloferax volcanii have been studied in detail and turned out to have very different properties. The chromosome copy number appears to be regulated in response to growth phases and environmental factors. Archaea typically contain about two Origin Recognition Complex (ORC) proteins, which are homologous to eukaryotic ORC proteins. However, haloarchaea are the only archaeal group that contains a multitude of ORC proteins. All 16 ORC protein paralogs from H. volcanii are involved in chromosome copy number regulation. Polyploidy has many evolutionary advantages for haloarchaea, e.g. a high resistance to desiccation, survival over geological times, and the relaxation of cell cycle-specific replication control. A further advantage is the ability to grow in the absence of external phosphate while using the many genome copies as internal phosphate storage polymers. Very efficient gene conversion operates in haloarchaea and results in the unification of genome copies. Taken together, haloarchaea are excellent models to study many aspects of genome biology in prokaryotes, exhibiting properties that have not been found in bacteria.},
}
@article {pmid31184586,
year = {2019},
author = {Killelea, T and Palud, A and Akcha, F and Lemor, M and L'haridon, S and Godfroy, A and Henneke, G},
title = {The interplay at the replisome mitigates the impact of oxidative damage on the genetic integrity of hyperthermophilic Archaea.},
journal = {eLife},
volume = {8},
number = {},
pages = {},
pmid = {31184586},
issn = {2050-084X},
support = {ANR-10-JCJC-1501-01//Agence Nationale de la Recherche/International ; },
mesh = {8-Hydroxy-2'-Deoxyguanosine/*metabolism ; Archaea/*genetics/metabolism ; *DNA Damage ; DNA Repair ; DNA Replication/*genetics ; DNA, Archaeal/*genetics/metabolism ; DNA-Directed DNA Polymerase/genetics/metabolism ; Genome, Archaeal/*genetics ; Models, Genetic ; Mutation ; Oxidative Stress ; Protein Biosynthesis/genetics ; },
abstract = {8-oxodeoxyguanosine (8-oxodG), a major oxidised base modification, has been investigated to study its impact on DNA replication in hyperthermophilic Archaea. Here we show that 8-oxodG is formed in the genome of growing cells, with elevated levels following exposure to oxidative stress. Functional characterisation of cell-free extracts and the DNA polymerisation enzymes, PolB, PolD, and the p41/p46 complex, alone or in the presence of accessory factors (PCNA and RPA) indicates that translesion synthesis occurs under replicative conditions. One of the major polymerisation effects was stalling, but each of the individual proteins could insert and extend past 8-oxodG with differing efficiencies. The introduction of RPA and PCNA influenced PolB and PolD in similar ways, yet provided a cumulative enhancement to the polymerisation performance of p41/p46. Overall, 8-oxodG translesion synthesis was seen to be potentially mutagenic leading to errors that are reminiscent of dA:8-oxodG base pairing.},
}
@article {pmid31170597,
year = {2019},
author = {Wang, W and Su, Y and Wang, B and Wang, Y and Zhuang, L and Zhu, G},
title = {Spatiotemporal shifts of ammonia-oxidizing archaea abundance and structure during the restoration of a multiple pond and plant-bed/ditch wetland.},
journal = {The Science of the total environment},
volume = {684},
number = {},
pages = {629-640},
doi = {10.1016/j.scitotenv.2019.04.415},
pmid = {31170597},
issn = {1879-1026},
mesh = {Ammonia/metabolism ; Archaea/classification/*physiology ; *Conservation of Natural Resources ; *Microbiota ; Oxidation-Reduction ; Population Dynamics ; Spatio-Temporal Analysis ; *Wetlands ; },
abstract = {Ammonia-oxidizing archaea (AOA) microorganisms have been increasingly found in aquatic and terrestrial environments. These microorganisms make vital contributions to ammonia oxidation in such systems. However, their community succession characteristics in man-made wetland ecosystems have scarcely been reported. We assessed the AOA's spatiotemporal shifts in the sediments of a constructed wetland (CW) - the Shijiuyang constructed wetland (SJY-CW) - in China from the third year (2011) to the fifth year (2013) of the CW operation. The SJY-CW is composed of a pretreatment pond, a multiple plant-bed/ditch system, and a post-treatment pond. Results showed that AOA abundance in the pre- and post-treatment ponds remained invariant through 2011-2012 and decreased in 2013, while the abundance in the plant-bed/ditch system decreased gradually with wetland operation. The AOA abundance in 2013 was one order of magnitude lower than that through 2011-2012, and the AOA abundance in the plant-bed/ditch system was generally higher than that in the pre- and post-treatment ponds from 2011 to 2013. AOA diversity showed little temporal differentiation with a slightly decreasing trend for community richness index Chao1 and diversity index Shannon H' from 2011 to 2013. The AOA community was dominated by the Nitrososphaera cluster accompanied by an increasing Nitrosopumilus cluster and Nitrososphaera sister cluster within the wetland operation. Hierarchical clustering and redundancy analysis verified the horizontal shifts of AOA communities. The shifts occurred preferentially in the central plant-bed/ditch system. The operational duration of the wetland became a key factor influencing AOA abundance and community shift in SJY-CW sediments.},
}
@article {pmid31150759,
year = {2020},
author = {Stachler, AE and Schwarz, TS and Schreiber, S and Marchfelder, A},
title = {CRISPRi as an efficient tool for gene repression in archaea.},
journal = {Methods (San Diego, Calif.)},
volume = {172},
number = {},
pages = {76-85},
doi = {10.1016/j.ymeth.2019.05.023},
pmid = {31150759},
issn = {1095-9130},
mesh = {CRISPR-Cas Systems/*genetics ; Chromosomes, Archaeal/genetics ; Gene Editing/*methods ; *Gene Expression Regulation, Archaeal ; Gene Knockdown Techniques/methods ; Genes, Archaeal/genetics ; Genes, Essential/genetics ; Haloferax volcanii/*genetics ; Plasmids/genetics ; },
abstract = {In the years following its discovery and characterization, the CRISPR-Cas system has been modified and converted into a multitude of applications for eukaryotes and bacteria, such as genome editing and gene regulation. Since no such method has been available for archaea, we developed a tool for gene repression in the haloarchaeon Haloferax volcanii by repurposing its endogenous type I-B CRISPR-Cas system. Here, we present the two possible approaches for gene repression as well as our workflow to achieve and assess gene knockdown, offer recommendations on protospacer selection and give some examples of genes we have successfully silenced.},
}
@article {pmid31150548,
year = {2019},
author = {Kurth, JM and Smit, NT and Berger, S and Schouten, S and Jetten, MSM and Welte, CU},
title = {Anaerobic methanotrophic archaea of the ANME-2d clade feature lipid composition that differs from other ANME archaea.},
journal = {FEMS microbiology ecology},
volume = {95},
number = {7},
pages = {},
pmid = {31150548},
issn = {1574-6941},
support = {339880/ERC_/European Research Council/International ; },
mesh = {Anaerobiosis ; Archaea/*chemistry/classification/*metabolism ; Carbon/metabolism ; Lipids/biosynthesis/*chemistry ; Methane/*metabolism ; Nitrates/metabolism ; Oxidation-Reduction ; Seawater/chemistry/*microbiology ; },
abstract = {The anaerobic oxidation of methane (AOM) is a microbial process present in marine and freshwater environments. AOM is important for reducing the emission of the second most important greenhouse gas methane. In marine environments anaerobic methanotrophic archaea (ANME) are involved in sulfate-reducing AOM. In contrast, Ca. Methanoperedens of the ANME-2d cluster carries out nitrate AOM in freshwater ecosystems. Despite the importance of those organisms for AOM in non-marine environments little is known about their lipid composition or carbon sources. To close this gap, we analysed the lipid composition of ANME-2d archaea and found that they mainly synthesise archaeol and hydroxyarchaeol as well as different (hydroxy-) glycerol dialkyl glycerol tetraethers, albeit in much lower amounts. Abundant lipid headgroups were dihexose, monomethyl-phosphatidyl ethanolamine and phosphatidyl hexose. Moreover, a monopentose was detected as a lipid headgroup that is rare among microorganisms. Batch incubations with 13C labelled bicarbonate and methane showed that methane is the main carbon source of ANME-2d archaea varying from ANME-1 archaea that primarily assimilate dissolved inorganic carbon (DIC). ANME-2d archaea also assimilate DIC, but to a lower extent than methane. The lipid characterisation and analysis of the carbon source of Ca. Methanoperedens facilitates distinction between ANME-2d and other ANMEs.},
}
@article {pmid32625030,
year = {2019},
author = {Pappenreiter, PA and Zwirtmayr, S and Mauerhofer, LM and Rittmann, SKR and Paulik, C},
title = {Development of a simultaneous bioreactor system for characterization of gas production kinetics of methanogenic archaea at high pressure.},
journal = {Engineering in life sciences},
volume = {19},
number = {7},
pages = {537-544},
pmid = {32625030},
issn = {1618-0240},
abstract = {Cultivation of methanogens under high pressure offers a great opportunity in biotechnological processes, one of which is the improvement of the gas-liquid transfer of substrate gases into the medium broth. This article describes a newly developed simultaneous bioreactor system consisting of four identical cultivation vessels suitable for investigation of microbial activity at pressures up to 50 bar and temperatures up to 145°C. Initial pressure studies at 10 and 50 bar of the autotrophic and hydrogenotrophic methanogens Methanothermobacter marburgensis, Methanobacterium palustre, and Methanobacterium thermaggregans were performed to evaluate the reproducibility of the system as well as to test the productivity of these strains. The strains were compared with respect to gas conversion (%), methane evolution rate (MER) (mmol L[-1 ]h[-1]), turnover rate (h[-1]), and maximum conversion rate (k min) (bar h[-1]). A pressure drop that can be explained by the reaction stoichiometry showed that all tested strains were active under pressurized conditions. Our study sheds light on the production kinetics of methanogenic strains under high-pressure conditions. In addition, the simultaneous bioreactor system is a suitable first step screening system for analyzing the substrate uptake and/or production kinetics of gas conversion and/or gas production processes for barophilic or barotolerant microbes.},
}
@article {pmid31147749,
year = {2019},
author = {Ijichi, M and Itoh, H and Hamasaki, K},
title = {Vertical distribution of particle-associated and free-living ammonia-oxidizing archaea in Suruga Bay, a deep coastal embayment of Japan.},
journal = {Archives of microbiology},
volume = {201},
number = {8},
pages = {1141-1146},
doi = {10.1007/s00203-019-01680-6},
pmid = {31147749},
issn = {1432-072X},
support = {JP24121004//Japan Society for the Promotion of Science/ ; },
mesh = {Ammonia/*metabolism ; Archaea/*genetics/*metabolism ; Bays/*microbiology ; Japan ; Oxidation-Reduction ; Oxidoreductases/*genetics ; Phylogeny ; Seawater/microbiology ; },
abstract = {We analyzed the vertical distributions of ammonia-oxidizing archaea (AOA) in terms of abundance in Suruga Bay, Japan. We distinguished particle-associated (PA) from free-living (FL) assemblages. According to quantitative PCR measurements of the ammonia monooxygenase subunit A gene (amoA), most marine AOA were in an FL state. The vertical distributions of PA AOA ecotypes differed from the general trend; the Shallow Marine clade was dominant in both the surface and deep layers. Thus, although PA AOA account for a small percentage of AOA abundance, they have a community structure distinct from that of FL AOA in planktonic environments. Marine particles should be investigated further as an unexplored niche of AOA in the ocean.},
}
@article {pmid31136034,
year = {2019},
author = {Walsh, JC and Angstmann, CN and Bisson-Filho, AW and Garner, EC and Duggin, IG and Curmi, PMG},
title = {Division plane placement in pleomorphic archaea is dynamically coupled to cell shape.},
journal = {Molecular microbiology},
volume = {112},
number = {3},
pages = {785-799},
pmid = {31136034},
issn = {1365-2958},
support = {DP2 AI117923/AI/NIAID NIH HHS/United States ; 203276/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Archaeal Proteins/genetics/metabolism ; *Cell Division ; Cell Shape ; Haloferax/cytology/genetics/metabolism ; Haloferax volcanii/*cytology/genetics/*metabolism ; },
abstract = {One mechanism for achieving accurate placement of the cell division machinery is via Turing patterns, where nonlinear molecular interactions spontaneously produce spatiotemporal concentration gradients. The resulting patterns are dictated by cell shape. For example, the Min system of Escherichia coli shows spatiotemporal oscillation between cell poles, leaving a mid-cell zone for division. The universality of pattern-forming mechanisms in divisome placement is currently unclear. We examined the location of the division plane in two pleomorphic archaea, Haloferax volcanii and Haloarcula japonica, and showed that it correlates with the predictions of Turing patterning. Time-lapse analysis of H. volcanii shows that divisome locations after successive rounds of division are dynamically determined by daughter cell shape. For H. volcanii, we show that the location of DNA does not influence division plane location, ruling out nucleoid occlusion. Triangular cells provide a stringent test for Turing patterning, where there is a bifurcation in division plane orientation. For the two archaea examined, most triangular cells divide as predicted by a Turing mechanism; however, in some cases multiple division planes are observed resulting in cells dividing into three viable progeny. Our results suggest that the division site placement is consistent with a Turing patterning system in these archaea.},
}
@article {pmid31133998,
year = {2019},
author = {Zhang, R and Neu, TR and Li, Q and Blanchard, V and Zhang, Y and Schippers, A and Sand, W},
title = {Insight Into Interactions of Thermoacidophilic Archaea With Elemental Sulfur: Biofilm Dynamics and EPS Analysis.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {896},
pmid = {31133998},
issn = {1664-302X},
abstract = {Biooxidation of reduced inorganic sulfur compounds (RISCs) by thermoacidophiles is of particular interest for the biomining industry and for environmental issues, e.g., formation of acid mine drainage (AMD). Up to now, interfacial interactions of acidophiles with elemental sulfur as well as the mechanisms of sulfur oxidation by acidophiles, especially thermoacidophiles, are not yet fully clear. This work focused on how a crenarchaeal isolate Acidianus sp. DSM 29099 interacts with elemental sulfur. Analysis by Confocal laser scanning microscopy (CLSM) and Atomic force microscopy (AFM) in combination with Epifluorescence microscopy (EFM) shows that biofilms on elemental sulfur are characterized by single colonies and a monolayer in first stage and later on 3-D structures with a diameter of up to 100 μm. The analysis of extracellular polymeric substances (EPS) by a non-destructive lectin approach (fluorescence lectin-barcoding analysis) using several fluorochromes shows that intial attachment was featured by footprints rich in biofilm cells that were embedded in an EPS matrix consisting of various glycoconjugates. Wet chemistry data indicate that carbohydrates, proteins, lipids and uronic acids are the main components. Attenuated reflectance (ATR)-Fourier transformation infrared spectroscopy (FTIR) and high-performance anion exchange chromatography with pulsed amperometric detection (HPAE-PAD) indicate glucose and mannose as the main monosaccharides in EPS polysaccharides. EPS composition as well as sugar types in EPS vary according to substrate (sulfur or tetrathionate) and lifestyle (biofilms and planktonic cells). This study provides information on the building blocks/make up as well as dynamics of biofilms of thermoacidophilic archaea in extremely acidic environments.},
}
@article {pmid31121445,
year = {2019},
author = {Zhang, L and Dong, H and Zhang, J and Chen, Y and Zeng, G and Yuan, Y and Cao, W and Fang, W and Hou, K and Wang, B and Li, L},
title = {Influence of FeONPs amendment on nitrogen conservation and microbial community succession during composting of agricultural waste: Relative contributions of ammonia-oxidizing bacteria and archaea to nitrogen conservation.},
journal = {Bioresource technology},
volume = {287},
number = {},
pages = {121463},
doi = {10.1016/j.biortech.2019.121463},
pmid = {31121445},
issn = {1873-2976},
mesh = {Ammonia ; Archaea ; Bacteria ; *Composting ; *Microbiota ; Nitrogen ; Oxidation-Reduction ; Soil ; Soil Microbiology ; },
abstract = {Composting amended with iron oxide nanoparticles (FeONPs, α-Fe2O3 and Fe3O4 NPs) were conducted to study the impacts of FeONPs on nitrogen conservation and microbial community. It was found that amendment of FeONPs, especially α-Fe2O3 NPs, reduced total nitrogen (TN) loss, and reserved more NH4[+]-N and mineral N. Pearson correlation analysis revealed that decrease of ammonia-oxidizing bacteria (AOB) in FeONPs treatments played more important role than ammonia-oxidizing archaea (AOA) in reserving more NH4[+]-N and mineral N, and reducing TN loss. Bacterial community composition at phylum level did not shift with addition of FeONPs. Firmicutes, Actinobacteria, and Proteobacteria were the three most dominant phyla in all treatments. Overall, this study provides a method to reduce TN loss and improve mineral N reservation during composting, and gives a deep insight into the role of AOB and AOA in nitrogen transformation.},
}
@article {pmid31089359,
year = {2019},
author = {Safarpour, A and Ebrahimi, M and Shahzadeh Fazeli, SA and Amoozegar, MA},
title = {Supernatant Metabolites from Halophilic Archaea to Reduce Tumorigenesis in Prostate Cancer In-vitro and In-vivo.},
journal = {Iranian journal of pharmaceutical research : IJPR},
volume = {18},
number = {1},
pages = {241-253},
pmid = {31089359},
issn = {1735-0328},
abstract = {Halophilic archaea are known as the novel producers of natural products and their supernatant metabolites could have cytotoxic effects on cancer cells. In the present study, we screened the anticancer potential of supernatant metabolites from eight native haloarchaeal strains obtained from a culture collection in Iran. Five human cancer cell lines including breast, lung, prostate and also human fibroblast cells as the normal control were used in the present study. Moreover, to evaluate the anti-tumor effect of the selected supernatant, inhibition of sphere formation and tumor development was assessed in-vitro and in-vivo, respectively. Among all strains, supernatant metabolites from Halobacterium salinarum IBRC M10715 had the most potent cytotoxic effect on prostate cancer cell lines (IC50 = 0.5 mg/mL) without any effects on normal cells. It significantly increased both early and late apoptosis (about 11% and 9%, respectively) in the androgen-dependent PC3 cell line, reduced sphere formation ability of DU145 and PC3 cells with down-regulation of SOX2 gene expression. Furthermore, our results revealed that tumors developed in nude mice significantly shrank post intratumor injection of metabolites of the haloarchaeal strain. In conclusion, we suggested here for the first time that supernatant metabolites from Halobacterium salinarum IBRC M10715 could be a novel component against prostate cancer in-vitro and in-vivo with remarkable reduction in stem-like properties of tumor.},
}
@article {pmid31085691,
year = {2019},
author = {Hepowit, NL and Maupin-Furlow, JA},
title = {Rhodanese-Like Domain Protein UbaC and Its Role in Ubiquitin-Like Protein Modification and Sulfur Mobilization in Archaea.},
journal = {Journal of bacteriology},
volume = {201},
number = {15},
pages = {},
pmid = {31085691},
issn = {1098-5530},
support = {R01 GM057498/GM/NIGMS NIH HHS/United States ; },
mesh = {Archaeal Proteins/chemistry/genetics/*metabolism ; Haloferax volcanii/chemistry/*enzymology/genetics/metabolism ; Protein Domains ; Sulfur/*metabolism ; Sulfurtransferases/genetics/metabolism ; Thiosulfate Sulfurtransferase ; Ubiquitin/metabolism ; Ubiquitins/metabolism ; },
abstract = {Ubiquitin-like protein (Ubl) modification targets proteins for transient inactivation and/or proteasome-mediated degradation in archaea. Here the rhodanese-like domain (RHD) protein UbaC (HVO_1947) was found to copurify with the E1-like enzyme (UbaA) of the Ubl modification machinery in the archaeon Haloferax volcanii UbaC was shown to be important for Ubl ligation, particularly for the attachment of the Ubl SAMP2/3s to protein targets after exposure to oxidants (NaOCl, dimethyl sulfoxide [DMSO], and methionine sulfoxide [MetO]) and the proteasome inhibitor bortezomib. While UbaC was needed for ligation of the Ubl SAMP1 to MoaE (the large subunit of molybdopterin synthase), it was not important in the formation of oxidant-induced SAMP1 protein conjugates. Indicative of defects in sulfur relay, mutation of ubaC impaired molybdenum cofactor (Moco)-dependent DMSO reductase activity and cell survival at elevated temperature, suggesting a correlation with defects in the 2-thiolated state of wobble uridine tRNA. Overall, the archaeal stand-alone RHD UbaC has an important function in Ubl ligation and is associated with sulfur relay processes.IMPORTANCE Canonical E2 Ub/Ubl-conjugating enzymes are not conserved in the dual-function Ubl systems associated with protein modification and sulfur relay. Instead, the C-terminal RHDs of E1-RHD fusion proteins are the apparent E2 modules of these systems in eukaryotes. E1s that lack an RHD are common in archaea. Here we identified an RHD (UbaC) that serves as an apparent E2 analog with the E1-like UbaA in the dual-function Ubl sampylation system of archaea. Unlike the eukaryotic E1-RHD fusion, the archaeal RHD is a stand-alone protein. This new insight suggests that E1 function in Ubl pathways could be influenced by shifts in RHD abundance and/or competition with other protein partners in the cell.},
}
@article {pmid31069963,
year = {2019},
author = {Lu, S and Zhang, X and Chen, K and Chen, Z and Li, Y and Qi, Z and Shen, Y and Li, Z},
title = {The small subunit of DNA polymerase D (DP1) associates with GINS-GAN complex of the thermophilic archaea in Thermococcus sp. 4557.},
journal = {MicrobiologyOpen},
volume = {8},
number = {9},
pages = {e00848},
pmid = {31069963},
issn = {2045-8827},
mesh = {Archaeal Proteins/*metabolism ; DNA Replication ; *Protein Interaction Maps ; *Protein Multimerization ; Thermococcus/*enzymology ; Transcription Factor DP1/*metabolism ; },
abstract = {The eukaryotic GINS, Cdc45, and minichromosome maintenance proteins form an essential complex that moves with the DNA replication fork. The GINS protein complex has also been reported to associate with DNA polymerase. In archaea, the third domain of life, DNA polymerase D (PolD) is essential for DNA replication, and the genes encoding PolDs exist only in the genomes of archaea. The archaeal GAN (GINS-associated nuclease) is believed to be a homolog of the eukaryotic Cdc45. In this study, we found that the Thermococcus sp. 4557 DP1 (small subunit of PolD) interacted with GINS15 in vitro, and the 3'-5' exonuclease activity of DP1 was inhibited by GINS15. We also demonstrated that the GAN, GINS15, and DP1 proteins interact to form a complex adapting a GAN-GINS15-DP1 order. The results of this study imply that the complex constitutes a core of the DNA replisome in archaea.},
}
@article {pmid31064832,
year = {2019},
author = {Makarova, KS and Wolf, YI and Karamycheva, S and Zhang, D and Aravind, L and Koonin, EV},
title = {Antimicrobial Peptides, Polymorphic Toxins, and Self-Nonself Recognition Systems in Archaea: an Untapped Armory for Intermicrobial Conflicts.},
journal = {mBio},
volume = {10},
number = {3},
pages = {},
pmid = {31064832},
issn = {2150-7511},
mesh = {Amino Acid Sequence ; Antimicrobial Cationic Peptides/*genetics ; Archaea/*genetics ; Archaeal Proteins/*genetics ; Bacterial Proteins/genetics ; Evolution, Molecular ; *Genome, Archaeal ; Genome, Bacterial ; Genomics ; Microbial Interactions ; Toxins, Biological/*genetics ; },
abstract = {Numerous, diverse, highly variable defense and offense genetic systems are encoded in most bacterial genomes and are involved in various forms of conflict among competing microbes or their eukaryotic hosts. Here we focus on the offense and self-versus-nonself discrimination systems encoded by archaeal genomes that so far have remained largely uncharacterized and unannotated. Specifically, we analyze archaeal genomic loci encoding polymorphic and related toxin systems and ribosomally synthesized antimicrobial peptides. Using sensitive methods for sequence comparison and the "guilt by association" approach, we identified such systems in 141 archaeal genomes. These toxins can be classified into four major groups based on the structure of the components involved in the toxin delivery. The toxin domains are often shared between and within each system. We revisit halocin families and substantially expand the halocin C8 family, which was identified in diverse archaeal genomes and also certain bacteria. Finally, we employ features of protein sequences and genomic locus organization characteristic of archaeocins and polymorphic toxins to identify candidates for analogous but not necessarily homologous systems among uncharacterized protein families. This work confidently predicts that more than 1,600 archaeal proteins, currently annotated as "hypothetical" in public databases, are components of conflict and self-versus-nonself discrimination systems.IMPORTANCE Diverse and highly variable systems involved in biological conflicts and self-versus-nonself discrimination are ubiquitous in bacteria but much less studied in archaea. We performed comprehensive comparative genomic analyses of the archaeal systems that share components with analogous bacterial systems and propose an approach to identify new systems that could be involved in these functions. We predict polymorphic toxin systems in 141 archaeal genomes and identify new, archaea-specific toxin and immunity protein families. These systems are widely represented in archaea and are predicted to play major roles in interactions between species and in intermicrobial conflicts. This work is expected to stimulate experimental research to advance the understanding of poorly characterized major aspects of archaeal biology.},
}
@article {pmid31064826,
year = {2019},
author = {Li, Z and Kinosita, Y and Rodriguez-Franco, M and Nußbaum, P and Braun, F and Delpech, F and Quax, TEF and Albers, SV},
title = {Positioning of the Motility Machinery in Halophilic Archaea.},
journal = {mBio},
volume = {10},
number = {3},
pages = {},
pmid = {31064826},
issn = {2150-7511},
mesh = {Archaeal Proteins/*chemistry ; *Cell Polarity ; *Chemotaxis ; Cytoplasm/chemistry ; Flagella/physiology ; Haloferax volcanii/*physiology/ultrastructure ; Microscopy, Electron ; Time-Lapse Imaging ; },
abstract = {Bacteria and archaea exhibit tactical behavior and can move up and down chemical gradients. This tactical behavior relies on a motility structure, which is guided by a chemosensory system. Environmental signals are sensed by membrane-inserted chemosensory receptors that are organized in large ordered arrays. While the cellular positioning of the chemotaxis machinery and that of the flagellum have been studied in detail in bacteria, we have little knowledge about the localization of such macromolecular assemblies in archaea. Although the archaeal motility structure, the archaellum, is fundamentally different from the flagellum, archaea have received the chemosensory machinery from bacteria and have connected this system with the archaellum. Here, we applied a combination of time-lapse imaging and fluorescence and electron microscopy using the model euryarchaeon Haloferax volcanii and found that archaella were specifically present at the cell poles of actively dividing rod-shaped cells. The chemosensory arrays also had a polar preference, but in addition, several smaller arrays moved freely in the lateral membranes. In the stationary phase, rod-shaped cells became round and chemosensory arrays were disassembled. The positioning of archaella and that of chemosensory arrays are not interdependent and likely require an independent form of positioning machinery. This work showed that, in the rod-shaped haloarchaeal cells, the positioning of the archaellum and of the chemosensory arrays is regulated in time and in space. These insights into the cellular organization of H. volcanii suggest the presence of an active mechanism responsible for the positioning of macromolecular protein complexes in archaea.IMPORTANCE Archaea are ubiquitous single cellular microorganisms that play important ecological roles in nature. The intracellular organization of archaeal cells is among the unresolved mysteries of archaeal biology. With this work, we show that cells of haloarchaea are polarized. The cellular positioning of proteins involved in chemotaxis and motility is spatially and temporally organized in these cells. This suggests the presence of a specific mechanism responsible for the positioning of macromolecular protein complexes in archaea.},
}
@article {pmid31058146,
year = {2019},
author = {Isupov, MN and Boyko, KM and Sutter, JM and James, P and Sayer, C and Schmidt, M and Schönheit, P and Nikolaeva, AY and Stekhanova, TN and Mardanov, AV and Ravin, NV and Bezsudnova, EY and Popov, VO and Littlechild, JA},
title = {Corrigendum: Thermostable Branched-Chain Amino Acid Transaminases From the Archaea Geoglobus acetivorans and Archaeoglobus fulgidus: Biochemical and Structural Characterization.},
journal = {Frontiers in bioengineering and biotechnology},
volume = {7},
number = {},
pages = {79},
doi = {10.3389/fbioe.2019.00079},
pmid = {31058146},
issn = {2296-4185},
abstract = {[This corrects the article DOI: 10.3389/fbioe.2019.00007.].},
}
@article {pmid31048384,
year = {2019},
author = {Webster, G and Mullins, AJ and Watkins, AJ and Cunningham-Oakes, E and Weightman, AJ and Mahenthiralingam, E and Sass, H},
title = {Genome Sequences of Two Choline-Utilizing Methanogenic Archaea, Methanococcoides spp., Isolated from Marine Sediments.},
journal = {Microbiology resource announcements},
volume = {8},
number = {18},
pages = {},
pmid = {31048384},
issn = {2576-098X},
support = {//Wellcome Trust/United Kingdom ; MR/L015080/1/MRC_/Medical Research Council/United Kingdom ; },
abstract = {The genomes of two Methanococcoides spp. that were isolated from marine sediments and are capable of carrying out methanogenesis from choline and other methylotrophic substrates were sequenced. The average nucleotide identity and in silico DNA-DNA hybridization analyses demonstrate that they represent species different from those previously described.},
}
@article {pmid31020937,
year = {2019},
author = {Gupta, A and Swati, D},
title = {Riboswitches in Archaea.},
journal = {Combinatorial chemistry &amp; high throughput screening},
volume = {22},
number = {2},
pages = {135-149},
doi = {10.2174/1386207322666190425143301},
pmid = {31020937},
issn = {1875-5402},
mesh = {5' Untranslated Regions ; Archaea/genetics/*metabolism ; Databases, Genetic ; Genes, Archaeal ; *Riboswitch ; },
abstract = {BACKGROUND: Riboswitches are cis-acting, non-coding RNA elements found in the 5'UTR of bacterial mRNA and 3' UTR of eukaryotic mRNA, that fold in a complex manner to act as receptors for specific metabolites hence altering their conformation in response to the change in concentrations of a ligand or metabolite. Riboswitches function as gene regulators in numerous bacteria, archaea, fungi, algae and plants.<br><br>AIM AND OBJECTIVE: This study identifies different classes of riboswitches in the Archaeal domain of life. Previous studies have suggested that riboswitches carry a conserved aptameric domain in different domains of life. Since Archaea are considered to be the most idiosyncratic organisms it was interesting to look for the conservation pattern of riboswitches in these obviously strange microorganisms.<br><br>MATERIALS AND METHODS: Completely sequenced Archaeal Genomes present in the NCBI repository were used for studying riboswitches and other ncRNAs. The sequence files in FASTA format were downloaded from NCBI Genome database and information related to these genomes was retrieved from GenBank. Three bioinformatics approaches were used namely, ab initio, consensus structure prediction and statistical model-based prediction for identifying riboswitches.<br><br>RESULTS: Archaeal genomes have a sporadic distribution of putative riboswitches like the TPP, FMN, Guanidine, Lysine and c-di-AMP riboswitches, which are known to occur in bacteria. Also, a class of riboswitch sensing c-di-GMP, a second messenger, has been identified in a few Archaeal organisms.<br><br>CONCLUSION: This study clearly reveals that bioinformatics methods are likely to play a major role in identifying conserved riboswitches and in establishing how widespread these classes are in all domains of life, even though the final confirmation may come from wet lab methods.},
}
@article {pmid31016969,
year = {2019},
author = {Cândido, ES and Cardoso, MH and Chan, LY and Torres, MDT and Oshiro, KGN and Porto, WF and Ribeiro, SM and Haney, EF and Hancock, REW and Lu, TK and de la Fuente-Nunez, C and Craik, DJ and Franco, OL},
title = {Short Cationic Peptide Derived from Archaea with Dual Antibacterial Properties and Anti-Infective Potential.},
journal = {ACS infectious diseases},
volume = {5},
number = {7},
pages = {1081-1086},
doi = {10.1021/acsinfecdis.9b00073},
pmid = {31016969},
issn = {2373-8227},
mesh = {Amino Acid Sequence ; Animals ; Antimicrobial Cationic Peptides/chemistry/*pharmacology ; Archaeal Proteins/chemistry ; Biofilms/drug effects/growth &amp; development ; Disease Models, Animal ; Humans ; Mice ; Microbial Sensitivity Tests ; Protein Structure, Secondary ; Pseudomonas Infections/*drug therapy ; Pseudomonas aeruginosa/*drug effects/physiology ; Pyrobaculum/*metabolism ; Ribosomal Proteins/*chemistry ; },
abstract = {Bacterial biofilms and associated infections represent one of the biggest challenges in the clinic, and as an alternative to counter bacterial infections, antimicrobial peptides have attracted great attention in the past decade. Here, ten short cationic antimicrobial peptides were generated through a sliding-window strategy on the basis of the 19-amino acid residue peptide, derived from a Pyrobaculum aerophilum ribosomal protein. PaDBS1R6F10 exhibited anti-infective potential as it decreased the bacterial burden in murine Pseudomonas aeruginosa cutaneous infections by more than 1000-fold. Adverse cytotoxic and hemolytic effects were not detected against mammalian cells. The peptide demonstrated structural plasticity in terms of its secondary structure in the different environments tested. PaDBS1R6F10 represents a promising antimicrobial agent against bacteria infections, without harming human cells.},
}
@article {pmid31015799,
year = {2019},
author = {Wemheuer, F and von Hoyningen-Huene, AJE and Pohlner, M and Degenhardt, J and Engelen, B and Daniel, R and Wemheuer, B},
title = {Primary Production in the Water Column as Major Structuring Element of the Biogeographical Distribution and Function of Archaea in Deep-Sea Sediments of the Central Pacific Ocean.},
journal = {Archaea (Vancouver, B.C.)},
volume = {2019},
number = {},
pages = {3717239},
pmid = {31015799},
issn = {1472-3654},
mesh = {Archaea/classification/genetics/*physiology ; Chlorophyll/analysis ; Ferric Compounds/analysis ; Geography ; Geologic Sediments/chemistry/*microbiology ; *Microbiota ; Pacific Ocean ; RNA, Archaeal/genetics ; RNA, Ribosomal, 16S/genetics ; Seawater/chemistry/*microbiology ; },
abstract = {Information on environmental conditions shaping archaeal communities thriving at the seafloor of the central Pacific Ocean is limited. The present study was conducted to investigate the diversity, composition, and function of both entire and potentially active archaeal communities within Pacific deep-sea sediments. For this purpose, sediment samples were taken along the 180° meridian of the central Pacific Ocean. Community composition and diversity were assessed by Illumina tag sequencing targeting archaeal 16S rRNA genes and transcripts. Archaeal communities were dominated by Candidatus Nitrosopumilus (Thaumarchaeota) and other members of the Nitrosopumilaceae (Thaumarchaeota), but higher relative abundances of the Marine Group II (Euryarchaeota) were observed in the active compared to the entire archaeal community. The composition of the entire and the active archaeal communities was strongly linked to primary production (chlorophyll content), explaining more than 40% of the variance. Furthermore, we found a strong correlation of the entire archaeal community composition to latitude and silicic acid content, while the active community was significantly correlated with primary production and ferric oxide content. We predicted functional profiles from 16S rRNA data to assess archaeal community functions. Latitude was significantly correlated with functional profiles of the entire community, whereas those of the active community were significantly correlated with nitrate and chlorophyll content. The results of the present study provide first insights into benthic archaeal communities in the Pacific Ocean and environmental conditions shaping their diversity, distribution, and function. Additionally, they might serve as a template for further studies investigating archaea colonizing deep-sea sediments.},
}
@article {pmid31015394,
year = {2019},
author = {Seitz, KW and Dombrowski, N and Eme, L and Spang, A and Lombard, J and Sieber, JR and Teske, AP and Ettema, TJG and Baker, BJ},
title = {Asgard archaea capable of anaerobic hydrocarbon cycling.},
journal = {Nature communications},
volume = {10},
number = {1},
pages = {1822},
pmid = {31015394},
issn = {2041-1723},
support = {OCE-0647633//National Science Foundation/International ; OCE-1357238//National Science Foundation/International ; DE-AC02-05CH11231//US Department of Energy/International ; },
mesh = {Anaerobiosis ; Archaea/genetics/*metabolism ; Archaeal Proteins/genetics/*metabolism ; Genome, Archaeal/*genetics ; Geologic Sediments/microbiology ; Hydrocarbons/*metabolism ; Hydrothermal Vents/microbiology ; Metabolic Networks and Pathways/genetics ; Metagenomics ; Oceans and Seas ; Oxidoreductases/genetics/*metabolism ; Phylogeny ; },
abstract = {Large reservoirs of natural gas in the oceanic subsurface sustain complex communities of anaerobic microbes, including archaeal lineages with potential to mediate oxidation of hydrocarbons such as methane and butane. Here we describe a previously unknown archaeal phylum, Helarchaeota, belonging to the Asgard superphylum and with the potential for hydrocarbon oxidation. We reconstruct Helarchaeota genomes from metagenomic data derived from hydrothermal deep-sea sediments in the hydrocarbon-rich Guaymas Basin. The genomes encode methyl-CoM reductase-like enzymes that are similar to those found in butane-oxidizing archaea, as well as several enzymes potentially involved in alkyl-CoA oxidation and the Wood-Ljungdahl pathway. We suggest that members of the Helarchaeota have the potential to activate and subsequently anaerobically oxidize hydrothermally generated short-chain hydrocarbons.},
}
@article {pmid31000700,
year = {2019},
author = {Dong, X and Greening, C and Rattray, JE and Chakraborty, A and Chuvochina, M and Mayumi, D and Dolfing, J and Li, C and Brooks, JM and Bernard, BB and Groves, RA and Lewis, IA and Hubert, CRJ},
title = {Metabolic potential of uncultured bacteria and archaea associated with petroleum seepage in deep-sea sediments.},
journal = {Nature communications},
volume = {10},
number = {1},
pages = {1816},
pmid = {31000700},
issn = {2041-1723},
mesh = {Acetates/metabolism ; Archaea/genetics/isolation &amp; purification/*metabolism ; Bacteria/genetics/isolation &amp; purification/*metabolism ; Geologic Sediments/chemistry/*microbiology ; Hydrocarbons/metabolism ; Hydrogen/metabolism ; Metagenome ; Metagenomics/methods ; Mexico ; Microbial Interactions/physiology ; Microbiota/*physiology ; Petroleum/*metabolism ; },
abstract = {The lack of microbial genomes and isolates from the deep seabed means that very little is known about the ecology of this vast habitat. Here, we investigate energy and carbon acquisition strategies of microbial communities from three deep seabed petroleum seeps (3 km water depth) in the Eastern Gulf of Mexico. Shotgun metagenomic analysis reveals that each sediment harbors diverse communities of chemoheterotrophs and chemolithotrophs. We recovered 82 metagenome-assembled genomes affiliated with 21 different archaeal and bacterial phyla. Multiple genomes encode enzymes for anaerobic oxidation of aliphatic and aromatic compounds, including those of candidate phyla Aerophobetes, Aminicenantes, TA06 and Bathyarchaeota. Microbial interactions are predicted to be driven by acetate and molecular hydrogen. These findings are supported by sediment geochemistry, metabolomics, and thermodynamic modelling. Overall, we infer that deep-sea sediments experiencing thermogenic hydrocarbon inputs harbor phylogenetically and functionally diverse communities potentially sustained through anaerobic hydrocarbon, acetate and hydrogen metabolism.},
}
@article {pmid30997302,
year = {2019},
author = {Verma, S and Kumar, R and Meghwanshi, GK},
title = {Identification of new members of alkaliphilic lipases in archaea and metagenome database using reconstruction of ancestral sequences.},
journal = {3 Biotech},
volume = {9},
number = {5},
pages = {165},
pmid = {30997302},
issn = {2190-572X},
abstract = {The application of bioinformatics in lipase research has the potential to discover robust members from different genomic/metagenomic databses. In this study, we explored the diversity and distribution of alkaliphilic lipases in archaea domain and metagenome data sets through phylogenetic survey. Reconstructed ancestral sequence of alkaphilic lipase was used to search the homologous alkaliphilic lipases among the archaea and metagenome public databases. Our investigation revealed a total 21 unique sequences of new alkaliphilic lipases in the archaeal and environmental metagenomic protein databases that shared significant sequence similarity to the bacterial alkaliphilic lipases. Most of the identified new members of alkaliphilic lipases belong to class Haloarchaea. The searched list of homologs also comprised of one characterized lipase from alkalohyperthermophilic Archaeoglobus fulgidus. All the newly identified alkaliphilic lipase members showed conserved pentapeptide [X-His-Ser-X-Gly] motif, a key feature of lipase family. Furthermore, detailed analysis of all these new sequences showed homology either with thermostable or alkalophilic lipases. The reconstructed ancestral sequence-based searches increased the sensitivity and efficacies to detect remotely homologous sequences. We hypothesize that this study can enrich our current knowledge on lipases in designing more potential thermo-alkaliphilic lipases for industrial applications.},
}
@article {pmid30995692,
year = {2019},
author = {Langer, SG and Gabris, C and Einfalt, D and Wemheuer, B and Kazda, M and Bengelsdorf, FR},
title = {Different response of bacteria, archaea and fungi to process parameters in nine full-scale anaerobic digesters.},
journal = {Microbial biotechnology},
volume = {12},
number = {6},
pages = {1210-1225},
pmid = {30995692},
issn = {1751-7915},
mesh = {Anaerobiosis ; Archaea/classification/genetics/*growth &amp; development ; Bacteria, Anaerobic/classification/genetics/*growth &amp; development ; Biofuels ; Bioreactors/*microbiology ; Cluster Analysis ; DNA, Archaeal/chemistry/genetics ; DNA, Bacterial/chemistry/genetics ; DNA, Fungal/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Fungi/classification/genetics/*growth &amp; development ; Manure/*microbiology ; Metagenomics ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 28S/genetics ; Sequence Analysis, DNA ; },
abstract = {Biogas production is a biotechnological process realized by complex bacterial, archaeal and likely fungal communities. Their composition was assessed in nine full-scale biogas plants with distinctly differing feedstock input and process parameters. This study investigated the actually active microbial community members by using a comprehensive sequencing approach based on ribosomal 16S and 28S rRNA fragments. The prevailing taxonomical units of each respective community were subsequently linked to process parameters. Ribosomal rRNA of bacteria, archaea and fungi, respectively, showed different compositions with respect to process parameters and supplied feedstocks: (i) bacterial communities were affected by the key factors temperature and ammonium concentration; (ii) composition of archaea was mainly related to process temperature; and (iii) relative abundance of fungi was linked to feedstocks supplied to the digesters. Anaerobic digesters with a high methane yield showed remarkably similar bacterial communities regarding identified taxonomic families. Although archaeal communities differed strongly on genus level from each other, the respective digesters still showed high methane yields. Functional redundancy of the archaeal communities may explain this effect. 28S rRNA sequences of fungi in all nine full-scale anaerobic digesters were primarily classified as facultative anaerobic Ascomycota and Basidiomycota. Since the presence of ribosomal 28S rRNA indicates that fungi may be active in the biogas digesters, further research should be carried out to examine to which extent they are important players in anaerobic digestion processes.},
}
@article {pmid30994930,
year = {2019},
author = {Gomes-Filho, JV and Randau, L},
title = {RNA stabilization in hyperthermophilic archaea.},
journal = {Annals of the New York Academy of Sciences},
volume = {1447},
number = {1},
pages = {88-96},
doi = {10.1111/nyas.14060},
pmid = {30994930},
issn = {1749-6632},
support = {RA 2169/3-1//Deutsche Forschungsgemeinschaft/International ; },
mesh = {Animals ; Archaea/*chemistry/*genetics ; Humans ; Proteolysis ; RNA Stability/*genetics ; RNA, Archaeal/*chemistry/*genetics ; },
abstract = {Analyses of the RNA metabolism of hyperthermophilic archaea highlight the efficiency of regulatory RNAs and RNA-guided processes at extreme temperatures. These organisms must overcome the intrinsic thermolability of RNAs. Elevated levels of RNA modifications and structured GC-rich regions are observed for many universal noncoding RNA families. Guide RNAs are often protected from degradation by their presence within ribonucleoprotein complexes. Modification and ligation of RNA termini can be employed to impair exonucleolytic degradation. Finally, antisense strand transcription promotes the formation of RNA duplexes and can be used to stabilize RNA regions. In our review, we provide examples of these RNA stabilization mechanisms that have been observed in hyperthermophilic archaeal model organisms.},
}
@article {pmid30991941,
year = {2019},
author = {Santos-Zavaleta, A and Pérez-Rueda, E and Sánchez-Pérez, M and Velázquez-Ramírez, DA and Collado-Vides, J},
title = {Tracing the phylogenetic history of the Crl regulon through the Bacteria and Archaea genomes.},
journal = {BMC genomics},
volume = {20},
number = {1},
pages = {299},
pmid = {30991941},
issn = {1471-2164},
support = {R01GM110597//Foundation for the National Institutes of Health/ ; PAPIIT IN-201117//Direcci&#xf3;n General de Asuntos del Personal Acad&#xe9;mico, Universidad Nacional Aut&#xf3;noma de M&#xe9;xico (MX)/ ; R01 GM110597/GM/NIGMS NIH HHS/United States ; U24GM077678//Foundation for the National Institutes of Health/ ; U24 GM077678/GM/NIGMS NIH HHS/United States ; },
mesh = {Evolution, Molecular ; Genome, Archaeal/*genetics ; Genome, Bacterial/*genetics ; *Phylogeny ; Regulon/*genetics ; },
abstract = {BACKGROUND: Crl, identified for curli production, is a small transcription factor that stimulates the association of the σ[S] factor (RpoS) with the RNA polymerase core through direct and specific interactions, increasing the transcription rate of genes during the transition from exponential to stationary phase at low temperatures, using indole as an effector molecule. The lack of a comprehensive collection of information on the Crl regulon makes it difficult to identify a dominant function of Crl and to generate any hypotheses concerning its taxonomical distribution in archaeal and bacterial organisms.<br><br>RESULTS: In this work, based on a systematic literature review, we identified the first comprehensive dataset of 86 genes under the control of Crl in the bacterium Escherichia coli K-12; those genes correspond to 40% of the &#x3c3;[S] regulon in this bacterium. Based on an analysis of orthologs in 18 archaeal and 69 bacterial taxonomical divisions and using E. coli K-12 as a framework, we suggest three main events that resulted in this regulon's actual form: (i) in a first step, rpoS, a gene widely distributed in bacteria and archaea cellular domains, was recruited to regulate genes involved in ancient metabolic processes, such as those associated with glycolysis and the tricarboxylic acid cycle; (ii) in a second step, the regulon recruited those genes involved in metabolic processes, which are mainly taxonomically constrained to Proteobacteria, with some secondary losses, such as those genes involved in responses to stress or starvation and cell adhesion, among others; and (iii) in a posterior step, Crl might have been recruited in Enterobacteriaceae; because its taxonomical pattern constrained to this bacterial order, however further analysis are necessary.<br><br>CONCLUSIONS: Therefore, we suggest that the regulon Crl is highly flexible for phenotypic adaptation, probably as consequence of the diverse growth environments associated with all organisms in which members of this regulatory network are present.},
}
@article {pmid30991368,
year = {2019},
author = {Eggenberger, OM and Leriche, G and Koyanagi, T and Ying, C and Houghtaling, J and Schroeder, TBH and Yang, J and Li, J and Hall, A and Mayer, M},
title = {Fluid surface coatings for solid-state nanopores: comparison of phospholipid bilayers and archaea-inspired lipid monolayers.},
journal = {Nanotechnology},
volume = {30},
number = {32},
pages = {325504},
doi = {10.1088/1361-6528/ab19e6},
pmid = {30991368},
issn = {1361-6528},
mesh = {Archaea/*metabolism ; Diffusion ; Lipid Bilayers/*chemistry ; *Nanopores ; Phosphatidylcholines/chemistry ; Phospholipids/chemistry ; Surface Properties ; Unilamellar Liposomes/*chemistry ; },
abstract = {In the context of sensing and characterizing single proteins with synthetic nanopores, lipid bilayer coatings provide at least four benefits: first, they minimize unwanted protein adhesion to the pore walls by exposing a zwitterionic, fluid surface. Second, they can slow down protein translocation and rotation by the opportunity to tether proteins with a lipid anchor to the fluid bilayer coating. Third, they provide the possibility to impart analyte specificity by including lipid anchors with a specific receptor or ligand in the coating. Fourth, they offer a method for tuning nanopore diameters by choice of the length of the lipid's acyl chains. The work presented here compares four properties of various lipid compositions with regard to their suitability as nanopore coatings for protein sensing experiments: (1) electrical noise during current recordings through solid-state nanopores before and after lipid coating, (2) long-term stability of the recorded current baseline and, by inference, of the coating, (3) viscosity of the coating as quantified by the lateral diffusion coefficient of lipids in the coating, and (4) the success rate of generating a suitable coating for quantitative nanopore-based resistive pulse recordings. We surveyed lipid coatings prepared from bolaamphiphilic, monolayer-forming lipids inspired by extremophile archaea and compared them to typical bilayer-forming phosphatidylcholine lipids containing various fractions of curvature-inducing lipids or cholesterol. We found that coatings from archaea-inspired lipids provide several advantages compared to conventional phospholipids; the stable, low noise baseline qualities and high viscosity make these membranes especially suitable for analysis that estimates physical protein parameters such as the net charge of proteins as they enable translocation events with sufficiently long duration to time-resolve dwell time distributions completely. The work presented here reveals that the ease or difficulty of coating a nanopore with lipid membranes did not depend significantly on the composition of the lipid mixture, but rather on the geometry and surface chemistry of the nanopore in the solid state substrate. In particular, annealing substrates containing the nanopore increased the success rate of generating stable lipid coatings.},
}
@article {pmid30975999,
year = {2019},
author = {Xiong, L and Liu, S and Chen, S and Xiao, Y and Zhu, B and Gao, Y and Zhang, Y and Chen, B and Luo, J and Deng, Z and Chen, X and Wang, L and Chen, S},
title = {A new type of DNA phosphorothioation-based antiviral system in archaea.},
journal = {Nature communications},
volume = {10},
number = {1},
pages = {1688},
pmid = {30975999},
issn = {2041-1723},
mesh = {Archaea/*physiology/virology ; Archaeal Proteins/genetics/immunology/*metabolism ; Archaeal Viruses/*genetics/pathogenicity ; DNA Replication/immunology ; DNA, Viral/*metabolism ; Gene Transfer, Horizontal/immunology ; Host Microbial Interactions/*genetics ; Immunity, Innate/genetics/immunology ; Phosphorothioate Oligonucleotides/metabolism ; RNA, Archaeal/genetics/isolation &amp; purification ; Sequence Analysis, DNA ; },
abstract = {Archaea and Bacteria have evolved different defence strategies that target virtually all steps of the viral life cycle. The diversified virion morphotypes and genome contents of archaeal viruses result in a highly complex array of archaea-virus interactions. However, our understanding of archaeal antiviral activities lags far behind our knowledges of those in bacteria. Here we report a new archaeal defence system that involves DndCDEA-specific DNA phosphorothioate (PT) modification and the PbeABCD-mediated halt of virus propagation via inhibition of DNA replication. In contrast to the breakage of invasive DNA by DndFGH in bacteria, DndCDEA-PbeABCD does not degrade or cleave viral DNA. The PbeABCD-mediated PT defence system is widespread and exhibits extensive interdomain and intradomain gene transfer events. Our results suggest that DndCDEA-PbeABCD is a new type of PT-based virus resistance system, expanding the known arsenal of defence systems as well as our understanding of host-virus interactions.},
}
@article {pmid30938665,
year = {2019},
author = {Bayer, B and Vojvoda, J and Reinthaler, T and Reyes, C and Pinto, M and Herndl, GJ},
title = {Nitrosopumilus adriaticus sp. nov. and Nitrosopumilus piranensis sp. nov., two ammonia-oxidizing archaea from the Adriatic Sea and members of the class Nitrososphaeria.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {69},
number = {7},
pages = {1892-1902},
doi = {10.1099/ijsem.0.003360},
pmid = {30938665},
issn = {1466-5034},
mesh = {Ammonia/*metabolism ; Archaea/*classification/isolation &amp; purification ; Base Composition ; DNA, Archaeal/genetics ; Glyceryl Ethers/chemistry ; Hydrogen Peroxide ; Oceans and Seas ; Oxidation-Reduction ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; Sequence Analysis, DNA ; Vitamin K 2/analogs &amp; derivatives/chemistry ; },
abstract = {Two mesophilic, neutrophilic and aerobic marine ammonia-oxidizing archaea, designated strains NF5[T] and D3C[T], were isolated from coastal surface water of the Northern Adriatic Sea. Cells were straight small rods 0.20-0.25 µm wide and 0.49-2.00 µm long. Strain NF5[T] possessed archaella as cell appendages. Glycerol dibiphytanyl glycerol tetraethers with zero to four cyclopentane moieties (GDGT-0 to GDGT-4) and crenarchaeol were the major core lipids. Menaquinone MK6 : 0 was the major respiratory quinone. Both isolates gained energy by oxidizing ammonia (NH3) to nitrite (NO2[-]) and used bicarbonate as a carbon source. Strain D3C[T] was able use urea as a source of ammonia for energy production and growth. Addition of hydrogen peroxide (H2O2) scavengers (catalase or α-keto acids) was required to sustain growth. Optimal growth occurred between 30 and 32 °C, pH 7.1 and 7.3 and between 34 and 37‰ salinity. The cellular metal abundance ranking of both strains was Fe>Zn>Cu>Mn>Co. The genomes of strains NF5[T] and D3C[T] have a DNA G+C content of 33.4 and 33.8 mol%, respectively. Phylogenetic analyses of 16S rRNA gene sequences revealed that both strains are affiliated with the class Nitrososphaeria, sharing ~85 % 16S rRNA gene sequence identity with Nitrososphaera viennensis EN76[T]. The two isolates are separated by phenotypic and genotypic characteristics and are assigned to distinct species within the genus Nitrosopumilus gen. nov. according to average nucleotide identity thresholds of their closed genomes. Isolates NF5[T] (=JCM 32270[T] =NCIMB 15114[T]) and D3C[T] (=JCM 32271[T] =DSM 106147[T] =NCIMB 15115[T]) are type strains of the species Nitrosopumilusadriaticus sp. nov. and Nitrosopumiluspiranensis sp. nov., respectively.},
}
@article {pmid30936420,
year = {2019},
author = {Straka, LL and Meinhardt, KA and Bollmann, A and Stahl, DA and Winkler, MH},
title = {Affinity informs environmental cooperation between ammonia-oxidizing archaea (AOA) and anaerobic ammonia-oxidizing (Anammox) bacteria.},
journal = {The ISME journal},
volume = {13},
number = {8},
pages = {1997-2004},
pmid = {30936420},
issn = {1751-7370},
mesh = {Ammonia/chemistry/metabolism ; Anaerobiosis ; Archaea/chemistry/classification/isolation &amp; purification/*metabolism ; Bacteria/chemistry/classification/isolation &amp; purification/*metabolism ; Kinetics ; Lakes/microbiology ; Oxidation-Reduction ; Oxygen/metabolism ; Phylogeny ; Soil/chemistry ; Soil Microbiology ; },
abstract = {Anaerobic ammonia-oxidizing (Anammox) bacteria (AnAOB) rely on nitrite supplied by ammonia-oxidizing bacteria (AOB) and archaea (AOA). Affinities for ammonia and oxygen play a crucial role in AOA/AOB competition and their association with AnAOB. In this work we measured the affinity constants for ammonia and oxygen (half-saturation; km) of two freshwater AOA enrichments, an AOA soil isolate (N. viennensis), and a freshwater AnAOB enrichment. The AOA enrichments had similar kinetics (μmax ≈ 0.36 d[-1], km,NH4 ≈ 0.78 µM, and km,O2 ≈ 2.9 µM), whereas N. viennensis had similar km values but lower μmax (0.23 d[-1]). In agreement with the current paradigm, these AOA strains showed a higher affinity for ammonia (lower km,NH4; 0.34-1.27 µM) than published AOB measurements (>20 µM). The slower growing AnAOB (μmax ≈ 0.16 d[-1]) had much higher km values (km,NH4 ≈ 132 µM, km,NO2 ≈ 48 µM) and were inhibited by oxygen at low levels (half-oxygen inhibition; ki,O2 ≈ 0.092 µM). The higher affinity of AOA for ammonia relative to AnAOB, suggests AOA/AnAOB cooperation is only possible where AOA do not outcompete AnAOB for ammonia. Using a biofilm model, we show that environments of ammonia/oxygen counter diffusion, such as stratified lakes, favors this cooperation.},
}
@article {pmid30924222,
year = {2019},
author = {Zou, D and Li, Y and Kao, SJ and Liu, H and Li, M},
title = {Genomic adaptation to eutrophication of ammonia-oxidizing archaea in the Pearl River estuary.},
journal = {Environmental microbiology},
volume = {21},
number = {7},
pages = {2320-2332},
doi = {10.1111/1462-2920.14613},
pmid = {30924222},
issn = {1462-2920},
support = {JCYJ20170818091727570//Science and Technology Innovation Committee of Shenzhen/International ; 91851105&#xff0c;31622002//National Natural Science Foundation of China/International ; //State Key Laboratory of Marine Pollution/International ; //Research Grants Council of the Hong Kong Special Administrative Region/International ; },
mesh = {Ammonia/*metabolism ; Archaea/*genetics/*physiology ; California ; China ; Ecosystem ; Estuaries ; Eutrophication/*physiology ; Genome, Archaeal/genetics ; Genomics ; Geologic Sediments/microbiology ; Metals, Heavy/metabolism ; Nitrification ; Oxidation-Reduction ; Oxidoreductases/*genetics ; Phosphate Transport Proteins/genetics ; Phylogeny ; Rivers/microbiology ; },
abstract = {Ammonia-oxidizing archaea (AOA) are ubiquitous in natural ecosystems, and they are responsible for a significant fraction of ammonia oxidation globally. Since the first AOA isolate was established a decade ago, molecular surveys of their environmental distribution [based primarily on amplicon sequencing of the amoA, which codes for the alpha subunit of ammonia monooxygenase (AMO)], show that their habitats are believed to range from marine to terrestrial environments. However, the mechanisms of adaptation underpinning to their habitat expansion remain poorly understood. Here, we report that AOA accounts for almost all of the ammonia oxidizers in the shelf water adjacent to the Pearl River estuary (PRE), with the Nitrosopumilus maritimus SCM1-like (SCM1-like) being the main amoA genotype. Using a metagenomic approach, seven high-quality AOA genomes were reconstructed from the PRE. Phylogenetic analysis indicated that four of these genomes with high completeness were closely affiliated with the Nitrosomatrinus catalina strain SPOT01, which was originally isolated off the coast of California. Genomic comparison revealed that the PRE AOA genomes encoded genes functioning in amino acid synthesis, xenobiotic biodegradation metabolism and transportation of inorganic phosphate and heavy metals. This illustrates the different adaptations of AOA in one of the largest estuaries in China, which is strongly influenced by anthropogenic input. Overall, this study provides additional genomic information about estuarine AOA and highlights the importance of their contribution to nitrification in eutrophic coastal environments.},
}
@article {pmid30923872,
year = {2019},
author = {Wu, RN and Meng, H and Wang, YF and Gu, JD},
title = {Functional dominance and community compositions of ammonia-oxidizing archaea in extremely acidic soils of natural forests.},
journal = {Applied microbiology and biotechnology},
volume = {103},
number = {10},
pages = {4229-4240},
doi = {10.1007/s00253-019-09721-2},
pmid = {30923872},
issn = {1432-0614},
support = {31470562//National Natural Science Foundation of China/ ; },
mesh = {Ammonia/*metabolism ; Archaea/*classification/enzymology/genetics/*metabolism ; *Forests ; Hydrogen-Ion Concentration ; *Microbiota ; Oxidation-Reduction ; Oxidoreductases/analysis/genetics ; RNA, Messenger/analysis/genetics ; Soil/chemistry ; *Soil Microbiology ; },
abstract = {Extremely acidic soils of natural forests in Nanling National Nature Reserve have been previously investigated and revisited in two successive years to reveal the active ammonia oxidizers. Ammonia-oxidizing archaea (AOA) rather than ammonia-oxidizing bacteria (AOB) were found more functionally important in the extremely acidic soils of the natural forests in Nanling National Nature Reserve. The relative abundances of Nitrosotalea, Nitrososphaera sister group, and Nitrososphaera lineages recovered by ammonia monooxygenase subunit A (amoA) transcripts were reassessed and compared to AOA communities formerly detected by genomic DNA. Nitrosotalea, previously found the most abundant AOA, were the second-most-active lineage after Nitrososphaera sister group. Our field study results, therefore, propose the acidophilic AOA, Nitrosotalea, can better reside in extremely acidic soils while they may not contribute to nitrification proportionately according to their abundances or they are less functionally active. In contrast, the functional importance of Nitrososphaera sister group may be previously underestimated and the functional dominance further extends their ecological distribution as little has been reported. Nitrososphaera gargensis-like AOA, the third abundant lineage, were more active in summer. The analyses of AOA community composition and its correlation with environmental parameters support the previous observations of the potential impact of organic matter on AOA composition. Al[3+], however, did not show a strong adverse correlation with the abundances of functional AOA unlike in the DNA-based study. The new data further emphasize the functional dominance of AOA in extremely acidic soils, and unveil the relative contributions of AOA lineages to nitrification and their community transitions under the environmental influences.},
}
@article {pmid30918404,
year = {2019},
author = {Chen, SC and Musat, N and Lechtenfeld, OJ and Paschke, H and Schmidt, M and Said, N and Popp, D and Calabrese, F and Stryhanyuk, H and Jaekel, U and Zhu, YG and Joye, SB and Richnow, HH and Widdel, F and Musat, F},
title = {Anaerobic oxidation of ethane by archaea from a marine hydrocarbon seep.},
journal = {Nature},
volume = {568},
number = {7750},
pages = {108-111},
pmid = {30918404},
issn = {1476-4687},
mesh = {Anaerobiosis ; Aquatic Organisms/*metabolism ; Archaea/classification/enzymology/genetics/*metabolism ; Deltaproteobacteria/metabolism ; Ethane/chemistry/*metabolism ; Gases/chemistry/metabolism ; Gulf of Mexico ; Methane/biosynthesis ; Oxidation-Reduction ; Oxidoreductases/genetics/isolation &amp; purification/metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sulfates/metabolism ; Sulfides/metabolism ; },
abstract = {Ethane is the second most abundant component of natural gas in addition to methane, and-similar to methane-is chemically unreactive. The biological consumption of ethane under anoxic conditions was suggested by geochemical profiles at marine hydrocarbon seeps[1-3], and through ethane-dependent sulfate reduction in slurries[4-7]. Nevertheless, the microorganisms and reactions that catalyse this process have to date remained unknown[8]. Here we describe ethane-oxidizing archaea that were obtained by specific enrichment over ten years, and analyse these archaea using phylogeny-based fluorescence analyses, proteogenomics and metabolite studies. The co-culture, which oxidized ethane completely while reducing sulfate to sulfide, was dominated by an archaeon that we name 'Candidatus Argoarchaeum ethanivorans'; other members were sulfate-reducing Deltaproteobacteria. The genome of Ca. Argoarchaeum contains all of the genes that are necessary for a functional methyl-coenzyme M reductase, and all subunits were detected in protein extracts. Accordingly, ethyl-coenzyme M (ethyl-CoM) was identified as an intermediate by liquid chromatography-tandem mass spectrometry. This indicated that Ca. Argoarchaeum initiates ethane oxidation by ethyl-CoM formation, analogous to the recently described butane activation by 'Candidatus Syntrophoarchaeum'[9]. Proteogenomics further suggests that oxidation of intermediary acetyl-CoA to CO2 occurs through the oxidative Wood-Ljungdahl pathway. The identification of an archaeon that uses ethane (C2H6) fills a gap in our knowledge of microorganisms that specifically oxidize members of the homologous alkane series (CnH2n+2) without oxygen. Detection of phylogenetic and functional gene markers related to those of Ca. Argoarchaeum at deep-sea gas seeps[10-12] suggests that archaea that are able to oxidize ethane through ethyl-CoM are widespread members of the local communities fostered by venting gaseous alkanes around these seeps.},
}
@article {pmid30915060,
year = {2019},
author = {Qiu, X and Yao, Y and Wang, H and Shen, A and Zhang, J},
title = {Halophilic Archaea Mediate the Formation of Proto-Dolomite in Solutions With Various Sulfate Concentrations and Salinities.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {480},
pmid = {30915060},
issn = {1664-302X},
abstract = {In the past several decades, sulfate concentration and salinity have been considered to be the two essential hydrochemical factors in the formation of dolomite, yet arguments against this hypothesis have existed simultaneously. To clarify the effects of sulfate concentration and salinity in the mineralization of dolomite, we conducted experiments on dolomite precipitation mediated by a halophilic archaeon, Natrinema sp. J7-1 with various sulfate concentrations and salinities. This strain was cultured in a series of modified growth media (MGM) with salinities of 140, 200, and 280‰. Cells in the post-log phase were harvested and used to mediate the formation of dolomite in solutions with various sulfate concentrations of 0, 3, 29.8, and 100 mM and salinities of 140, 200, and 280‰. X-ray diffraction (XRD) spectra showed that proto-dolomite, monohydrocalcite, and aragonite formed in samples with cells, yet only aragonite was detected in samples without cells. Proto-dolomite was found in all biotic samples, regardless of the variation in salinity and sulfate concentration. Moreover, the relative abundances of proto-dolomite in the precipitates were positively correlated with the salinities of the media but were uncorrelated with the sulfate concentrations of the solutions. Scanning electronic microscopy (SEM) and energy dispersive spectroscopy (EDS) results showed that all the proto-dolomites were sphere or sphere aggregates with a mole ratio of Mg/Ca close to 1.0. No obvious variations in morphology and Mg/Ca were found among samples with various sulfate concentrations or salinities. This work reveals that a variation of sulfate concentration in solution (from 0 to 100 mM) does not affect the formation of dolomite mediated by halophilic archaea, but an increase of salinity (from 140 to 280‰) enhances this process. Our results indicate that under natural conditions, an increase in salinity may be more significant than the decrease of sulfates in microbe-mediated dolomite formation.},
}
@article {pmid30910020,
year = {2019},
author = {Fu, X and Adams, Z and Maupin-Furlow, J},
title = {Assays for ubiquitin-like protein ligation and proteasome function in archaea.},
journal = {Methods in enzymology},
volume = {619},
number = {},
pages = {161-178},
pmid = {30910020},
issn = {1557-7988},
support = {R01 GM057498/GM/NIGMS NIH HHS/United States ; },
mesh = {Archaeal Proteins/*metabolism ; Enzyme Assays/methods ; Haloferax volcanii/*metabolism ; Immunoblotting/methods ; Proteasome Endopeptidase Complex/*metabolism ; Ubiquitins/*metabolism ; },
abstract = {Ubiquitin-like protein (Ubl) ligation is common to diverse archaea and targets many cellular pathways, including those associated with sulfur mobilization, and also tags proteins as substrates for degradation by the proteasome. Here we highlight protocols to assay proteasome function and Ubl ligation in archaea. A chase assay is described to monitor the impact of proteasome function on the stability of Ubl-modified proteins in the cell. A method to reconstitute Ubl ligation using a purified E1-like enzyme (UbaA), Ubl (SAMP2), methionine sulfoxide reductase A (MsrA), and cell lysate of an ΔmsrA ΔubaA Δsamp1-3 mutant is also described. MsrA is found to have the surprising ability to stimulate the formation of Ubl bonds. Haloferax volcanii, a halophilic archaeon originally isolated from the Dead Sea, serves as the model organism for these protocols.},
}
@article {pmid30886840,
year = {2019},
author = {Sogodogo, E and Fellag, M and Loukil, A and Nkamga, VD and Michel, J and Dessi, P and Fournier, PE and Drancourt, M},
title = {Nine Cases of Methanogenic Archaea in Refractory Sinusitis, an Emerging Clinical Entity.},
journal = {Frontiers in public health},
volume = {7},
number = {},
pages = {38},
pmid = {30886840},
issn = {2296-2565},
abstract = {The authors report the cases of 9 patients eventually diagnosed with methanogenic archaea refractory or recalcitrant chronic rhinosinusitis, a condition known to involve various anaerobic bacteria but in which the role of methanogenic archaea is unknown. The authors retrospectively searched these microorganisms by PCR in surgically-collected sinusal pus specimens from patients diagnosed with refractory sinusitis, defined by the persistance of sinus inflammation and related-symptoms for more than 12 weeks despite appropriate treatment. Of the 116 tested sinus surgical specimens, 12 (10.3%) from 9 patients (six females, three males; aged 20-71 years) were PCR-positive. These specimens were further investigated by fluorescence in-situ hybridization, PCR amplicon-sequencing and culture. Methanobrevibacter smithii was documented in four patients and Methanobrevibacter oralis in another four, one of whom was also culture-positive. They were associated with a mixed flora including Gram-positive and Gram-negative bacteria. In the latter patient, "Methanobrevibacter massiliense" was the sole microorganism detected. These results highlight methanogenic archaea as being part of a mixed anaerobic flora involved in refractory sinusitis, and suggest that the treatment of this condition should include an antibiotic active against methanogens, notably a nitroimidazole derivative.},
}
@article {pmid30884174,
year = {2019},
author = {Braun, F and Thomalla, L and van der Does, C and Quax, TEF and Allers, T and Kaever, V and Albers, SV},
title = {Cyclic nucleotides in archaea: Cyclic di-AMP in the archaeon Haloferax volcanii and its putative role.},
journal = {MicrobiologyOpen},
volume = {8},
number = {9},
pages = {e00829},
pmid = {30884174},
issn = {2045-8827},
mesh = {Adenylyl Cyclases/genetics ; Dinucleoside Phosphates/*metabolism ; Gene Expression Regulation, Archaeal ; Genes, Essential ; Genome, Bacterial ; Haloferax volcanii/enzymology/genetics/*metabolism ; Osmoregulation ; Signal Transduction ; },
abstract = {The role of cyclic nucleotides as second messengers for intracellular signal transduction has been well described in bacteria. One recently discovered bacterial second messenger is cyclic di-adenylate monophosphate (c-di-AMP), which has been demonstrated to be essential in bacteria. Compared to bacteria, significantly less is known about second messengers in archaea. This study presents the first evidence of in vivo presence of c-di-AMP in an archaeon. The model organism Haloferax volcanii was demonstrated to produce c-di-AMP. Its genome encodes one diadenylate cyclase (DacZ) which was shown to produce c-di-AMP in vitro. Similar to bacteria, the dacZ gene is essential and homologous overexpression of DacZ leads to cell death, suggesting the need for tight regulation of c-di-AMP levels. Such tight regulation often indicates the control of important regulatory processes. A central target of c-di-AMP signaling in bacteria is cellular osmohomeostasis. The results presented here suggest a comparable function in H. volcanii. A strain with decreased c-di-AMP levels exhibited an increased cell area in hypo-salt medium, implying impaired osmoregulation. In summary, this study expands the field of research on c-di-AMP and its physiological function to archaea and indicates that osmoregulation is likely to be a common function of c-di-AMP in bacteria and archaea.},
}
@article {pmid30859290,
year = {2019},
author = {Du, Y and Shu, K and Guo, X and Pengjin, Z},
title = {Moderate Grazing Promotes Grassland Nitrous Oxide Emission by Increasing Ammonia-Oxidizing Archaea Abundance on the Tibetan Plateau.},
journal = {Current microbiology},
volume = {76},
number = {5},
pages = {620-625},
pmid = {30859290},
issn = {1432-0991},
support = {31770532//National Natural Science Foundation of China/ ; },
mesh = {Ammonia/*metabolism ; Animals ; Archaea/*metabolism ; Fertilizers/analysis ; *Grassland ; *Herbivory ; Nitrous Oxide/*analysis ; Oxidation-Reduction ; Sheep ; Soil ; Tibet ; },
abstract = {Grasslands are suffering from long-term overgrazing because of the population inflation. Furthermore, nitrous oxide (N2O) is a major greenhouse gas that also depletes stratospheric ozone. However, the emission rate of grassland N2O and underlying mechanisms remained unclear under different grazing intensities. We conducted a field manipulation under four grazing intensities to compare its N2O fluxes and main affected factors. It was indicated that alpine meadow N2O emission rates increased from 39.7 ± 3.1 to 47.8 ± 2.3 μg m[-2] h[-1] (p < 0.05), then decreased to 43.4 ± 4.1 and 32.9 ± 1.4 μg m[-2] h[-1] with grazing intensity increasing from 4 to 8, 12 and 16 sheep ha-1, respectively. Multiple-stepwise regression analysis indicated that the predominant affected soil factors were separately TN and BD, pH and BD, also pH and BD, SOC and BD. Simple linear regression models revealed that ammonia-oxidizing archaea (AOA) contributed much to N2O emission (R[2] = 0.77). Additionally, the R[2] coefficient of linear regression was 0.87 between nosZ genes and N2O emission rates in alpine meadow. Much attention should be paid to protecting alpine meadow from degradation to mitigate N2O emission source on the Tibetan Plateau.},
}
@article {pmid30837306,
year = {2019},
author = {He, D and Piergentili, C and Ross, J and Tarrant, E and Tuck, LR and Mackay, CL and McIver, Z and Waldron, KJ and Clarke, DJ and Marles-Wright, J},
title = {Conservation of the structural and functional architecture of encapsulated ferritins in bacteria and archaea.},
journal = {The Biochemical journal},
volume = {476},
number = {6},
pages = {975-989},
doi = {10.1042/BCJ20180922},
pmid = {30837306},
issn = {1470-8728},
support = {BB/N005570/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/M010996/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 098375/Z/12/Z/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Archaeal Proteins/*chemistry ; Bacterial Proteins/*chemistry ; Ferritins/*chemistry ; Myxococcales/*chemistry ; Protein Domains ; Pyrococcus furiosus/*chemistry ; Rhodospirillum rubrum/*chemistry ; Structural Homology, Protein ; Structure-Activity Relationship ; },
abstract = {Ferritins are a large family of intracellular proteins that protect the cell from oxidative stress by catalytically converting Fe(II) into less toxic Fe(III) and storing iron minerals within their core. Encapsulated ferritins (EncFtn) are a sub-family of ferritin-like proteins, which are widely distributed in all bacterial and archaeal phyla. The recently characterized Rhodospirillum rubrum EncFtn displays an unusual structure when compared with classical ferritins, with an open decameric structure that is enzymatically active, but unable to store iron. This EncFtn must be associated with an encapsulin nanocage in order to act as an iron store. Given the wide distribution of the EncFtn family in organisms with diverse environmental niches, a question arises as to whether this unusual structure is conserved across the family. Here, we characterize EncFtn proteins from the halophile Haliangium ochraceum and the thermophile Pyrococcus furiosus, which show the conserved annular pentamer of dimers topology. Key structural differences are apparent between the homologues, particularly in the centre of the ring and the secondary metal-binding site, which is not conserved across the homologues. Solution and native mass spectrometry analyses highlight that the stability of the protein quaternary structure differs between EncFtn proteins from different species. The ferroxidase activity of EncFtn proteins was confirmed, and we show that while the quaternary structure around the ferroxidase centre is distinct from classical ferritins, the ferroxidase activity is still inhibited by Zn(II). Our results highlight the common structural organization and activity of EncFtn proteins, despite diverse host environments and contexts within encapsulins.},
}
@article {pmid30833729,
year = {2019},
author = {Borrel, G and Adam, PS and McKay, LJ and Chen, LX and Sierra-García, IN and Sieber, CMK and Letourneur, Q and Ghozlane, A and Andersen, GL and Li, WJ and Hallam, SJ and Muyzer, G and de Oliveira, VM and Inskeep, WP and Banfield, JF and Gribaldo, S},
title = {Wide diversity of methane and short-chain alkane metabolisms in uncultured archaea.},
journal = {Nature microbiology},
volume = {4},
number = {4},
pages = {603-613},
pmid = {30833729},
issn = {2058-5276},
mesh = {Alkanes/*chemistry/metabolism ; Archaea/classification/genetics/growth &amp; development/*metabolism ; *Biodiversity ; DNA, Archaeal ; Metagenome ; Methane/chemistry/*metabolism ; Oxidation-Reduction ; Phylogeny ; },
abstract = {Methanogenesis is an ancient metabolism of key ecological relevance, with direct impact on the evolution of Earth's climate. Recent results suggest that the diversity of methane metabolisms and their derivations have probably been vastly underestimated. Here, by probing thousands of publicly available metagenomes for homologues of methyl-coenzyme M reductase complex (MCR), we have obtained ten metagenome-assembled genomes (MAGs) belonging to potential methanogenic, anaerobic methanotrophic and short-chain alkane-oxidizing archaea. Five of these MAGs represent under-sampled (Verstraetearchaeota, Methanonatronarchaeia, ANME-1 and GoM-Arc1) or previously genomically undescribed (ANME-2c) archaeal lineages. The remaining five MAGs correspond to lineages that are only distantly related to previously known methanogens and span the entire archaeal phylogeny. Comprehensive comparative annotation substantially expands the metabolic diversity and energy conservation systems of MCR-bearing archaea. It also suggests the potential existence of a yet uncharacterized type of methanogenesis linked to short-chain alkane/fatty acid oxidation in a previously undescribed class of archaea ('Candidatus Methanoliparia'). We redefine a common core of marker genes specific to methanogenic, anaerobic methanotrophic and short-chain alkane-oxidizing archaea, and propose a possible scenario for the evolutionary and functional transitions that led to the emergence of such metabolic diversity.},
}
@article {pmid30833728,
year = {2019},
author = {Wang, Y and Wegener, G and Hou, J and Wang, F and Xiao, X},
title = {Expanding anaerobic alkane metabolism in the domain of Archaea.},
journal = {Nature microbiology},
volume = {4},
number = {4},
pages = {595-602},
pmid = {30833728},
issn = {2058-5276},
mesh = {Alkanes/chemistry/*metabolism ; Archaea/chemistry/*classification/genetics/*metabolism ; Archaeal Proteins/genetics/metabolism ; Methane/metabolism ; Phylogeny ; },
abstract = {Methanogenesis and anaerobic methane oxidation through methyl-coenzyme M reductase (MCR) as a key enzyme have been suggested to be basal pathways of archaea[1]. How widespread MCR-based alkane metabolism is among archaea, where it occurs and how it evolved remain elusive. Here, we performed a global survey of MCR-encoding genomes based on metagenomic data from various environments. Eleven high-quality mcr-containing metagenomic-assembled genomes were obtained belonging to the Archaeoglobi in the Euryarchaeota, Hadesarchaeota and different TACK superphylum archaea, including the Nezhaarchaeota, Korarchaeota and Verstraetearchaeota. Archaeoglobi WYZ-LMO1 and WYZ-LMO3 and Korarchaeota WYZ-LMO9 encode both the (reverse) methanogenesis and the dissimilatory sulfate reduction pathway, suggesting that they have the genomic potential to couple both pathways in individual organisms. The Hadesarchaeota WYZ-LMO4-6 and Archaeoglobi JdFR-42 encode highly divergent MCRs, enzymes that may enable them to thrive on non-methane alkanes. The occurrence of mcr genes in different archaeal phyla indicates that MCR-based alkane metabolism is common in the domain of Archaea.},
}
@article {pmid30810807,
year = {2019},
author = {Lopes-Dos-Santos, RMA and De Troch, M and Bossier, P and Van Stappen, G},
title = {Labelling halophilic Archaea using [13]C and [15]N stable isotopes: a potential tool to investigate haloarchaea consumption by metazoans.},
journal = {Extremophiles : life under extreme conditions},
volume = {23},
number = {3},
pages = {359-365},
pmid = {30810807},
issn = {1433-4909},
support = {BOF/01N01615//Universiteit Gent, Special Research Fund (BOF)/ ; },
mesh = {Animals ; *Biomass ; Carbon Isotopes/*chemistry ; *Food Chain ; Halobacteriales/*growth &amp; development ; Isotope Labeling/*methods ; Nitrogen Isotopes/*chemistry ; },
abstract = {The use of stable isotope (SI) labelling and tracing of live diets is currently considered one of the most comprehensive tools to detect their uptake and assimilation by aquatic organisms. These techniques are indeed widely used in nutritional studies to follow the fate of specific microbial dietary components, unraveling trophic interactions. Nevertheless, to the current date our understanding of aquatic trophic relationships has yet to include a whole domain of life, the Archaea. The aim of the present research was, therefore, to describe a halophilic Archaea (haloarchaea) labelling procedure, using the SI [13]C and [15]N, to enable the application of SI tracing in future studies of haloarchaea consumption by aquatic metazoans. To this end, three [13]C enriched carbon sources and two [15]N enriched nitrogen sources were tested as potential labels to enrich cells of three haloarchaea strains when supplemented to the culture medium. Our overall results indicate [13]C-glycerol as the most effective carbon source to achieve an efficient [13]C enrichment in haloarchaea cells, with Δδ[13]C values above 5000‰ in all tested haloarchaea strains. As for [15]N enriched nitrogen sources, both ([15]NH4)2SO4 and [15]NH4Cl seem to be readily assimilated, also resulting in efficient [15]N enrichment in haloarchaea cells, with Δδ[15]N values higher than 20,000‰. We believe that the proposed methodology will allow for the use of SI labelled haloarchaea biomass in feeding tests, potentially providing unambiguous confirmation of the assimilation of haloarchaea biomass by aquatic metazoans.},
}
@article {pmid30808005,
year = {2019},
author = {Díaz-Perales, A and Quesada, V and Peinado, JR and Ugalde, AP and Álvarez, J and Suárez, MF and Gomis-Rüth, FX and López-Otín, C},
title = {Withdrawal: Identification and characterization of human archaemetzincin-1 and -2, two novel members of a family of metalloproteases widely distributed in Archaea.},
journal = {The Journal of biological chemistry},
volume = {294},
number = {4},
pages = {1434},
doi = {10.1074/jbc.W118.007328},
pmid = {30808005},
issn = {1083-351X},
}
@article {pmid30806656,
year = {2019},
author = {Rissanen, AJ and Peura, S and Mpamah, PA and Taipale, S and Tiirola, M and Biasi, C and Mäki, A and Nykänen, H},
title = {Vertical stratification of bacteria and archaea in sediments of a small boreal humic lake.},
journal = {FEMS microbiology letters},
volume = {366},
number = {5},
pages = {},
pmid = {30806656},
issn = {1574-6968},
mesh = {Archaea/*classification/genetics/isolation &amp; purification ; Bacteria/*classification/genetics/isolation &amp; purification ; Biodiversity ; Biomass ; DNA Restriction Enzymes/genetics ; Geologic Sediments/chemistry/*microbiology ; Humic Substances/analysis ; Lakes/chemistry/*microbiology ; Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; Water Microbiology ; },
abstract = {Although sediments of small boreal humic lakes are important carbon stores and greenhouse gas sources, the composition and structuring mechanisms of their microbial communities have remained understudied. We analyzed the vertical profiles of microbial biomass indicators (PLFAs, DNA and RNA) and the bacterial and archaeal community composition (sequencing of 16S rRNA gene amplicons and qPCR of mcrA) in sediment cores collected from a typical small boreal lake. While microbial biomass decreased with sediment depth, viable microbes (RNA and PLFA) were present all through the profiles. The vertical stratification patterns of the bacterial and archaeal communities resembled those in marine sediments with well-characterized groups (e.g. Methanomicrobia, Proteobacteria, Cyanobacteria, Bacteroidetes) dominating in the surface sediment and being replaced by poorly-known groups (e.g. Bathyarchaeota, Aminicenantes and Caldiserica) in the deeper layers. The results also suggested that, similar to marine systems, the deep bacterial and archaeal communities were predominantly assembled by selective survival of taxa able to persist in the low energy conditions. Methanotrophs were rare, further corroborating the role of these methanogen-rich sediments as important methane emitters. Based on their taxonomy, the deep-dwelling groups were putatively organo-heterotrophic, organo-autotrophic and/or acetogenic and thus may contribute to changes in the lake sediment carbon storage.},
}
@article {pmid30796982,
year = {2019},
author = {Barnett, DJM and Mommers, M and Penders, J and Arts, ICW and Thijs, C},
title = {Intestinal archaea inversely associated with childhood asthma.},
journal = {The Journal of allergy and clinical immunology},
volume = {143},
number = {6},
pages = {2305-2307},
doi = {10.1016/j.jaci.2019.02.009},
pmid = {30796982},
issn = {1097-6825},
mesh = {Allergens/immunology ; *Archaea ; Asthma/immunology/*microbiology ; Child ; Eczema/immunology/microbiology ; Feces/microbiology ; Female ; Food Hypersensitivity/immunology/microbiology ; Humans ; Immunoglobulin E/blood ; Intestines/*microbiology ; Male ; },
}
@article {pmid30796347,
year = {2019},
author = {Wang, L and Li, K and Sheng, R and Li, Z and Wei, W},
title = {Remarkable N2O emissions by draining fallow paddy soil and close link to the ammonium-oxidizing archaea communities.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {2550},
pmid = {30796347},
issn = {2045-2322},
mesh = {Ammonium Compounds/*metabolism ; Archaea/genetics/*metabolism ; Floods ; Nitrification ; Nitrous Oxide/*analysis ; Soil/*chemistry ; Soil Microbiology ; },
abstract = {Fallow paddies experience natural flooding and draining water status due to rainfall and evaporation, which could induce considerable nitrous oxide (N2O) emissions and need to be studied specially. In this study, intact soil columns were collected from a fallow paddy field and the flooding-draining process was simulated in a microcosm experiment. The results showed that both N2O concentrations in the soil and N2O emission rates were negligible during flooding period, which were greatly elevated by draining the fallow paddy soil. The remarkable N2O concentrations in the soil and N2O emission/h during draining both had significant relationships with the Arch-amoA gene (P < 0.01) but not the Bac-amoA, narG, nirK, nirS, and nosZ genes, indicating that the ammonium-oxidizing archaea (AOA) might be the important players in soil N2O net production and emissions after draining. Moreover, we observed that N2O concentrations in the upper soil layers (0-10 cm) were not significantly different from that in the 10-20 cm layer under draining condition (P > 0.05). However, the number of AOA and the nitrification substrate (NH4[+]-N) in the 0-10 cm layer were significantly higher than in the 10-20 cm layer (P < 0.01), indicating N2O production in the 0-10 cm layer might be higher than the measured concentration and would contribute considerably to N2O emissions as shorter distance of gas diffusion to the soil surface.},
}
@article {pmid30790413,
year = {2019},
author = {Wang, Y and Feng, X and Natarajan, VP and Xiao, X and Wang, F},
title = {Diverse anaerobic methane- and multi-carbon alkane-metabolizing archaea coexist and show activity in Guaymas Basin hydrothermal sediment.},
journal = {Environmental microbiology},
volume = {21},
number = {4},
pages = {1344-1355},
doi = {10.1111/1462-2920.14568},
pmid = {30790413},
issn = {1462-2920},
support = {2018T110390//China Postdoctoral Science Foundation Grant/International ; 41525011//National Natural Science Foundation of China/International ; 91428308//National Natural Science Foundation of China/International ; 91751205//National Natural Science Foundation of China/International ; 2018YFC0310800//State Key R&amp;D Project of China/International ; 2016YFA0601102//State Key R&amp;D Project of China/International ; 2018T110390//China Postdoctoral Science Foundation/International ; 91428308//Natural Science Foundation of China/International ; 91751205//Natural Science Foundation of China/International ; 41525011//Natural Science Foundation of China/International ; },
mesh = {Alkanes/*metabolism ; Anaerobiosis/genetics ; Archaea/*classification/*genetics ; Carbon/metabolism ; Ecosystem ; Genes, Archaeal/genetics ; Geologic Sediments/*microbiology ; Hydrothermal Vents ; Metagenome ; Methane/*metabolism ; Oxidation-Reduction ; Phylogeny ; },
abstract = {Anaerobic oxidation of methane greatly contributes to global carbon cycling, yet the anaerobic oxidation of non-methane alkanes by archaea was only recently detected in lab enrichments. The distribution and activity of these archaea in natural environments are not yet reported and understood. Here, a combination of metagenomic and metatranscriptomic approaches was utilized to understand the ecological roles and metabolic potentials of methyl-coenzyme M reductase (MCR)-based alkane oxidizing (MAO) archaea in Guaymas Basin sediments. Diverse MAO archaea, including multi-carbon alkane oxidizer Ca. Syntrophoarchaeum spp., anaerobic methane oxidizing archaea ANME-1 and ANME-2c as well as sulfate-reducing bacteria HotSeep-1 and Seep-SRB2 that potentially involved in MAO processes, coexisted and showed activity in Guaymas Basin sediments. High-quality genomic bins of Ca. Syntrophoarchaeum spp., ANME-1 and ANME-2c were retrieved. They all contain and expressed mcr genes and genes in Wood-Ljungdahl pathway for the complete oxidation from alkane to CO2 in local environment, while Ca. Syntrophoarchaeum spp. also possess beta-oxidation genes for multi-carbon alkane degradation. A global survey of potential multi-carbon alkane metabolism archaea shows that they are usually present in organic rich environments but are not limit to hydrothermal or marine ecosystems. Our study provided new insights into ecological and metabolic potentials of MAO archaea in natural environments.},
}
@article {pmid30783016,
year = {2019},
author = {Maier, LK and Marchfelder, A},
title = {It's all about the T: transcription termination in archaea.},
journal = {Biochemical Society transactions},
volume = {47},
number = {1},
pages = {461-468},
doi = {10.1042/BST20180557},
pmid = {30783016},
issn = {1470-8752},
mesh = {Archaea/*genetics ; Genome, Archaeal ; High-Throughput Nucleotide Sequencing ; Terminator Regions, Genetic ; *Transcription Termination, Genetic ; },
abstract = {One of the most fundamental biological processes driving all life on earth is transcription. The, at first glance, relatively simple cycle is divided into three stages: initiation at the promoter site, elongation throughout the open reading frame, and finally termination and product release at the terminator. In all three processes, motifs of the template DNA and protein factors of the transcription machinery including the multisubunit polymerase itself as well as a broad range of associated transcription factors work together and mutually influence each other. Despite several decades of research, this interplay holds delicate mechanistic and structural details as well as interconnections yet to be explored. One of the surprising characteristics of archaeal biology is the use of eukaryotic-like information processing systems against a backdrop of a bacterial-like genome. Archaeal genomes usually comprise main chromosomes alongside chromosomal plasmids, and the genetic information is encoded in single transcriptional units as well as in multicistronic operons alike their bacterial counterparts. Moreover, archaeal genomes are densely packed and this necessitates a tight regulation of transcription and especially assured termination events in order to prevent read-through into downstream coding regions and the accumulation of antisense transcripts.},
}
@article {pmid30763377,
year = {2019},
author = {Ul-Hasan, S and Bowers, RM and Figueroa-Montiel, A and Licea-Navarro, AF and Beman, JM and Woyke, T and Nobile, CJ},
title = {Community ecology across bacteria, archaea and microbial eukaryotes in the sediment and seawater of coastal Puerto Nuevo, Baja California.},
journal = {PloS one},
volume = {14},
number = {2},
pages = {e0212355},
pmid = {30763377},
issn = {1932-6203},
support = {R35 GM124594/GM/NIGMS NIH HHS/United States ; },
mesh = {Archaea/genetics/*isolation &amp; purification ; Bacteria/genetics/*isolation &amp; purification ; Eukaryota/genetics/*isolation &amp; purification ; Geologic Sediments/*microbiology ; Mexico ; Microbiota ; RNA, Ribosomal, 16S/chemistry/metabolism ; RNA, Ribosomal, 18S/chemistry/metabolism ; Seawater/*microbiology ; Sequence Analysis, DNA ; },
abstract = {Microbial communities control numerous biogeochemical processes critical for ecosystem function and health. Most analyses of coastal microbial communities focus on the characterization of bacteria present in either sediment or seawater, with fewer studies characterizing both sediment and seawater together at a given site, and even fewer studies including information about non-bacterial microbial communities. As a result, knowledge about the ecological patterns of microbial biodiversity across domains and habitats in coastal communities is limited-despite the fact that archaea, bacteria, and microbial eukaryotes are present and known to interact in coastal habitats. To better understand microbial biodiversity patterns in coastal ecosystems, we characterized sediment and seawater microbial communities for three sites along the coastline of Puerto Nuevo, Baja California, Mexico using both 16S and 18S rRNA gene amplicon sequencing. We found that sediment hosted approximately 500-fold more operational taxonomic units (OTUs) for bacteria, archaea, and microbial eukaryotes than seawater (p < 0.001). Distinct phyla were found in sediment versus seawater samples. Of the top ten most abundant classes, Cytophagia (bacterial) and Chromadorea (eukaryal) were specific to the sediment environment, whereas Cyanobacteria and Bacteroidia (bacterial) and Chlorophyceae (eukaryal) were specific to the seawater environment. A total of 47 unique genera were observed to comprise the core taxa community across environment types and sites. No archaeal taxa were observed as part of either the abundant or core taxa. No significant differences were observed for sediment community composition across domains or between sites. For seawater, the bacterial and archaeal community composition was statistically different for the Major Outlet site (p < 0.05), the site closest to a residential area, and the eukaryal community composition was statistically different between all sites (p < 0.05). Our findings highlight the distinct patterns and spatial heterogeneity in microbial communities of a coastal region in Baja California, Mexico.},
}
@article {pmid30760902,
year = {2019},
author = {Flemming, HC and Wuertz, S},
title = {Bacteria and archaea on Earth and their abundance in biofilms.},
journal = {Nature reviews. Microbiology},
volume = {17},
number = {4},
pages = {247-260},
doi = {10.1038/s41579-019-0158-9},
pmid = {30760902},
issn = {1740-1534},
mesh = {Archaea/*physiology ; *Bacteria ; *Biofilms ; *Earth, Planet ; Ecosystem ; Geologic Sediments/microbiology ; Phylogeny ; },
abstract = {Biofilms are a form of collective life with emergent properties that confer many advantages on their inhabitants, and they represent a much higher level of organization than single cells do. However, to date, no global analysis on biofilm abundance exists. We offer a critical discussion of the definition of biofilms and compile current estimates of global cell numbers in major microbial habitats, mindful of the associated uncertainty. Most bacteria and archaea on Earth (1.2 × 10[30] cells) exist in the 'big five' habitats: deep oceanic subsurface (4 × 10[29]), upper oceanic sediment (5 × 10[28]), deep continental subsurface (3 × 10[29]), soil (3 × 10[29]) and oceans (1 × 10[29]). The remaining habitats, including groundwater, the atmosphere, the ocean surface microlayer, humans, animals and the phyllosphere, account for fewer cells by orders of magnitude. Biofilms dominate in all habitats on the surface of the Earth, except in the oceans, accounting for ~80% of bacterial and archaeal cells. In the deep subsurface, however, they cannot always be distinguished from single sessile cells; we estimate that 20-80% of cells in the subsurface exist as biofilms. Hence, overall, 40-80% of cells on Earth reside in biofilms. We conclude that biofilms drive all biogeochemical processes and represent the main way of active bacterial and archaeal life.},
}
@article {pmid30742498,
year = {2019},
author = {Serrano, P and Alawi, M and de Vera, JP and Wagner, D},
title = {Response of Methanogenic Archaea from Siberian Permafrost and Non-permafrost Environments to Simulated Mars-like Desiccation and the Presence of Perchlorate.},
journal = {Astrobiology},
volume = {19},
number = {2},
pages = {197-208},
doi = {10.1089/ast.2018.1877},
pmid = {30742498},
issn = {1557-8070},
mesh = {Desiccation ; *Exobiology ; *Extraterrestrial Environment ; Freezing ; Magnesium Compounds ; *Mars ; Methanosarcina/cytology/*metabolism ; Perchlorates ; },
abstract = {Numerous preflight investigations were necessary prior to the exposure experiment BIOMEX on the International Space Station to test the basic potential of selected microorganisms to resist or even to be active under Mars-like conditions. In this study, methanogenic archaea, which are anaerobic chemolithotrophic microorganisms whose lifestyle would allow metabolism under the conditions on early and recent Mars, were analyzed. Some strains from Siberian permafrost environments have shown a particular resistance. In this investigation, we analyzed the response of three permafrost strains (Methanosarcina soligelidi SMA-21, Candidatus Methanosarcina SMA-17, Candidatus Methanobacterium SMA-27) and two related strains from non-permafrost environments (Methanosarcina mazei, Methanosarcina barkeri) to desiccation conditions (-80°C for 315 days, martian regolith analog simulants S-MRS and P-MRS, a 128-day period of simulated Mars-like atmosphere). Exposure of the different methanogenic strains to increasing concentrations of magnesium perchlorate allowed for the study of their metabolic shutdown in a Mars-relevant perchlorate environment. Survival and metabolic recovery were analyzed by quantitative PCR, gas chromatography, and a new DNA-extraction method from viable cells embedded in S-MRS and P-MRS. All strains survived the two Mars-like desiccating scenarios and recovered to different extents. The permafrost strain SMA-27 showed an increased methanogenic activity by at least 10-fold after deep-freezing conditions. The methanogenic rates of all strains did not decrease significantly after 128 days S-MRS exposure, except for SMA-27, which decreased 10-fold. The activity of strains SMA-17 and SMA-27 decreased after 16 and 60 days P-MRS exposure. Non-permafrost strains showed constant survival and methane production when exposed to both desiccating scenarios. All strains showed unaltered methane production when exposed to the perchlorate concentration reported at the Phoenix landing site (2.4 mM) or even higher concentrations. We conclude that methanogens from (non-)permafrost environments are suitable candidates for potential life in the martian subsurface and therefore are worthy of study after space exposure experiments that approach Mars-like surface conditions.},
}
@article {pmid30733943,
year = {2019},
author = {Isupov, MN and Boyko, KM and Sutter, JM and James, P and Sayer, C and Schmidt, M and Schönheit, P and Nikolaeva, AY and Stekhanova, TN and Mardanov, AV and Ravin, NV and Bezsudnova, EY and Popov, VO and Littlechild, JA},
title = {Thermostable Branched-Chain Amino Acid Transaminases From the Archaea Geoglobus acetivorans and Archaeoglobus fulgidus: Biochemical and Structural Characterization.},
journal = {Frontiers in bioengineering and biotechnology},
volume = {7},
number = {},
pages = {7},
pmid = {30733943},
issn = {2296-4185},
abstract = {Two new thermophilic branched chain amino acid transaminases have been identified within the genomes of different hyper-thermophilic archaea, Geoglobus acetivorans, and Archaeoglobus fulgidus. These enzymes belong to the class IV of transaminases as defined by their structural fold. The enzymes have been cloned and over-expressed in Escherichia coli and the recombinant enzymes have been characterized both biochemically and structurally. Both enzymes showed high thermostability with optimal temperature for activity at 80 and 85°C, respectively. They retain good activity after exposure to 50% of the organic solvents, ethanol, methanol, DMSO and acetonitrile. The enzymes show a low activity to (R)-methylbenzylamine but no activity to (S)-methylbenzylamine. Both enzymes have been crystallized and their structures solved in the internal aldimine form, to 1.9 Å resolution for the Geoglobus enzyme and 2.0 Å for the Archaeoglobus enzyme. Also the Geoglobus enzyme structure has been determined in complex with the amino acceptor α-ketoglutarate and the Archaeoglobus enzyme in complex with the inhibitor gabaculine. These two complexes have helped to determine the conformation of the enzymes during enzymatic turnover and have increased understanding of their substrate specificity. A comparison has been made with another (R) selective class IV transaminase from the fungus Nectria haematococca which was previously studied in complex with gabaculine. The subtle structural differences between these enzymes has provided insight regarding their different substrate specificities.},
}
@article {pmid30714894,
year = {2019},
author = {Portugal, R and Shao, N and Whitman, WB and Allen, KD and White, RH},
title = {Identification and biosynthesis of 2-(1H-imidazol-5-yl) ethan-1-ol (histaminol) in methanogenic archaea.},
journal = {Microbiology (Reading, England)},
volume = {165},
number = {4},
pages = {455-462},
doi = {10.1099/mic.0.000779},
pmid = {30714894},
issn = {1465-2080},
mesh = {Archaea/*chemistry/*metabolism ; Biosynthetic Pathways ; Culture Media, Conditioned/chemistry ; Histamine/*analogs &amp; derivatives/analysis/biosynthesis/chemistry ; Histidine/metabolism ; Methanococcus/metabolism ; Molecular Structure ; },
abstract = {Histaminol is a relatively rare metabolite most commonly resulting from histidine metabolism. Here we describe histaminol production and secretion into the culture broth by the methanogen Methanococcus maripaludis S2 as well as a number of other methanogens. This work is the first identification of this compound as a natural product in methanogens. Its biosynthesis from histidine was confirmed by the incorporation of [2]H3-histidine into histaminol by growing cells of M. maripaludis S2. Possible functions of this molecule could be cell signaling as observed with histamine in eukaryotes or uptake of metal ions.},
}
@article {pmid30709414,
year = {2019},
author = {Jiao, S and Xu, Y and Zhang, J and Lu, Y},
title = {Environmental filtering drives distinct continental atlases of soil archaea between dryland and wetland agricultural ecosystems.},
journal = {Microbiome},
volume = {7},
number = {1},
pages = {15},
pmid = {30709414},
issn = {2049-2618},
mesh = {Agriculture ; Archaea/*classification/genetics ; Crops, Agricultural/*microbiology ; Environment ; Oryza/*microbiology ; RNA, Ribosomal, 16S/genetics ; Soil/chemistry ; *Soil Microbiology ; Wetlands ; Zea mays/*microbiology ; },
abstract = {BACKGROUND: Understanding the spatial distributions and ecological diversity of soil archaeal communities in agricultural ecosystems is crucial for improvements in crop productivity. Here, we conducted a comprehensive, continental-scale survey of soil archaeal communities in adjacent pairs of maize (dryland) and rice (wetland) fields in eastern China.<br><br>RESULTS: We revealed the consequential roles of environmental filtering in driving archaeal community assembly for both maize and rice fields. Rice fields, abundant with Euryarchaeota, had higher archaeal diversity and steeper distance-decay slopes than maize fields dominated by Thaumarchaeota. Dominant soil archaea showed distinct continental atlases and niche differentiation between dryland and wetland habitats, where they were associated with soil pH and mean annual temperature, respectively. After identifying their environmental preferences, we grouped the dominant archaeal taxa into different ecological clusters and determined the unique co-occurrence patterns within each cluster. Using this empirical dataset, we built a continental atlas of soil archaeal communities to provide reliable estimates of their spatial distributions in agricultural ecosystems.<br><br>CONCLUSIONS: Environmental filtering plays a crucial role in driving the distinct continental atlases of dominant soil archaeal communities between dryland and wetland, with contrasting strategies of archaeal-driven nutrient cycling within these two agricultural ecosystems. These findings improve our ability to predict how soil archaeal communities respond to environmental changes and to manage soil archaeal communities for provisioning of agricultural ecosystem services.},
}
@article {pmid30707467,
year = {2019},
author = {Reinhardt, A and Johnsen, U and Schönheit, P},
title = {l-Rhamnose catabolism in archaea.},
journal = {Molecular microbiology},
volume = {111},
number = {4},
pages = {1093-1108},
doi = {10.1111/mmi.14213},
pmid = {30707467},
issn = {1365-2958},
mesh = {ATP-Binding Cassette Transporters/metabolism ; Carbohydrate Dehydrogenases/metabolism ; Carbohydrate Metabolism ; *Genes, Archaeal ; Haloferax volcanii/*enzymology/*genetics ; Multigene Family ; Oxidoreductases/metabolism ; Rhamnose/*metabolism ; Sulfolobus solfataricus/genetics/metabolism ; },
abstract = {The halophilic archaeon Haloferax volcanii utilizes l-rhamnose as a sole carbon and energy source. It is shown that l-rhamnose is taken up by an ABC transporter and is oxidatively degraded to pyruvate and l-lactate via the diketo-hydrolase pathway. The genes involved in l-rhamnose uptake and degradation form a l-rhamnose catabolism (rhc) gene cluster. The rhc cluster also contains a gene, rhcR, that encodes the transcriptional regulator RhcR which was characterized as an activator of all rhc genes. 2-keto-3-deoxy-l-rhamnonate, a metabolic intermediate of l-rhamnose degradation, was identified as inducer molecule of RhcR. The essential function of rhc genes for uptake and degradation of l-rhamnose was proven by the respective knockout mutants. Enzymes of the diketo-hydrolase pathway, including l-rhamnose dehydrogenase, l-rhamnonolactonase, l-rhamnonate dehydratase, 2-keto-3-deoxy-l-rhamnonate dehydrogenase and 2,4-diketo-3-deoxy-l-rhamnonate hydrolase, were characterized. Further, genes of the diketo-hydrolase pathway were also identified in the hyperthermophilic crenarchaeota Vulcanisaeta distributa and Sulfolobus solfataricus and selected enzymes were characterized, indicating the presence of the diketo-hydrolase pathway in these archaea. Together, this is the first comprehensive description of l-rhamnose catabolism in the domain of archaea.},
}
@article {pmid30691532,
year = {2019},
author = {Korzhenkov, AA and Toshchakov, SV and Bargiela, R and Gibbard, H and Ferrer, M and Teplyuk, AV and Jones, DL and Kublanov, IV and Golyshin, PN and Golyshina, OV},
title = {Archaea dominate the microbial community in an ecosystem with low-to-moderate temperature and extreme acidity.},
journal = {Microbiome},
volume = {7},
number = {1},
pages = {11},
pmid = {30691532},
issn = {2049-2618},
support = {BB/M029085/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Acids/metabolism ; Archaea/*classification/genetics/*isolation &amp; purification ; Bacteria/classification/genetics/*isolation &amp; purification ; Cold Temperature ; Ecosystem ; Geologic Sediments/*microbiology ; Metagenome/genetics ; Microbiota/physiology ; RNA, Ribosomal, 16S/genetics ; Wales ; },
abstract = {BACKGROUND: The current view suggests that in low-temperature acidic environments, archaea are significantly less abundant than bacteria. Thus, this study of the microbiome of Parys Mountain (Anglesey, UK) sheds light on the generality of this current assumption. Parys Mountain is a historically important copper mine and its acid mine drainage (AMD) water streams are characterised by constant moderate temperatures (8-18 °C), extremely low pH (1.7) and high concentrations of soluble iron and other metal cations.<br><br>RESULTS: Metagenomic and SSU rRNA amplicon sequencing of DNA from Parys Mountain revealed a significant proportion of archaea affiliated with Euryarchaeota, which accounted for ca. 67% of the community. Within this phylum, potentially new clades of Thermoplasmata were overrepresented (58%), with the most predominant group being "E-plasma", alongside low-abundant Cuniculiplasmataceae, 'Ca. Micrarchaeota' and 'Terrestrial Miscellaneous Euryarchaeal Group' (TMEG) archaea, which were phylogenetically close to Methanomassilicoccales and clustered with counterparts from acidic/moderately acidic settings. In the sediment, archaea and Thermoplasmata contributed the highest numbers in V3-V4 amplicon reads, in contrast with the water body community, where Proteobacteria, Nitrospirae, Acidobacteria and Actinobacteria outnumbered archaea. Cultivation efforts revealed the abundance of archaeal sequences closely related to Cuniculiplasma divulgatum in an enrichment culture established from the filterable fraction of the water sample. Enrichment cultures with unfiltered samples showed the presence of Ferrimicrobium acidiphilum, C. divulgatum, 'Ca. Mancarchaeum acidiphilum Mia14', 'Ca. Micrarchaeota'-related and diverse minor (<&#x2009;2%) bacterial metagenomic reads.<br><br>CONCLUSION: Contrary to expectation, our study showed a high abundance of archaea in this extremely acidic mine-impacted environment. Further, archaeal populations were dominated by one particular group, suggesting that they are functionally important. The prevalence of archaea over bacteria in these microbiomes and their spatial distribution patterns represents a novel and important advance in our understanding of acidophile ecology. We also demonstrated a procedure for the specific enrichment of cell wall-deficient members of the archaeal component of this community, although the large fraction of archaeal taxa remained unculturable. Lastly, we identified a separate clustering of globally occurring acidophilic members of TMEG that collectively belong to a distinct order within Thermoplasmata with yet unclear functional roles in the ecosystem.},
}
@article {pmid30664670,
year = {2019},
author = {Evans, PN and Boyd, JA and Leu, AO and Woodcroft, BJ and Parks, DH and Hugenholtz, P and Tyson, GW},
title = {An evolving view of methane metabolism in the Archaea.},
journal = {Nature reviews. Microbiology},
volume = {17},
number = {4},
pages = {219-232},
doi = {10.1038/s41579-018-0136-7},
pmid = {30664670},
issn = {1740-1534},
mesh = {Archaea/*enzymology/*genetics ; Bacterial Proteins/*genetics ; Carbon Cycle ; *Evolution, Molecular ; Methane/*metabolism ; Oxidation-Reduction ; Oxidoreductases/*genetics ; Phylogeny ; },
abstract = {Methane is a key compound in the global carbon cycle that influences both nutrient cycling and the Earth's climate. A limited number of microorganisms control the flux of biologically generated methane, including methane-metabolizing archaea that either produce or consume methane. Methanogenic and methanotrophic archaea belonging to the phylum Euryarchaeota share a genetically similar, interrelated pathway for methane metabolism. The key enzyme in this pathway, the methyl-coenzyme M reductase (Mcr) complex, catalyses the last step in methanogenesis and the first step in methanotrophy. The discovery of mcr and divergent mcr-like genes in new euryarchaeotal lineages and novel archaeal phyla challenges long-held views of the evolutionary origin of this metabolism within the Euryarchaeota. Divergent mcr-like genes have recently been shown to oxidize short-chain alkanes, indicating that these complexes have evolved to metabolize substrates other than methane. In this Review, we examine the diversity, metabolism and evolutionary history of mcr-containing archaea in light of these recent discoveries.},
}
@article {pmid30655519,
year = {2019},
author = {Díez-Villaseñor, C and Rodriguez-Valera, F},
title = {CRISPR analysis suggests that small circular single-stranded DNA smacoviruses infect Archaea instead of humans.},
journal = {Nature communications},
volume = {10},
number = {1},
pages = {294},
pmid = {30655519},
issn = {2041-1723},
mesh = {Archaea/*genetics/virology ; CRISPR-Cas Systems/genetics ; Clustered Regularly Interspaced Short Palindromic Repeats/genetics ; DNA Viruses/genetics/isolation &amp; purification/*pathogenicity ; DNA, Single-Stranded/*genetics ; Feces/microbiology ; Gastrointestinal Microbiome/*genetics ; Host-Pathogen Interactions/*genetics ; Humans ; Phylogeny ; },
abstract = {Smacoviridae is a family of small (~2.5 Kb) CRESS-DNA (Circular Rep Encoding Single-Stranded (ss) DNA) viruses. These viruses have been found in faeces, were thought to infect eukaryotes and are suspected to cause gastrointestinal disease in humans. CRISPR-Cas systems are adaptive immune systems in prokaryotes, wherein snippets of genomes from invaders are stored as spacers that are interspersed between a repeated CRISPR sequence. Here we report several spacer sequences in the faecal archaeon Candidatus Methanomassiliicoccus intestinalis matching smacoviruses, implicating the archaeon as a firm candidate for a host. This finding may be relevant to understanding the potential origin of smacovirus-associated human diseases. Our results support that CRESS-DNA viruses can infect non-eukaryotes, which would mean that smacoviruses are the viruses with the smallest genomes to infect prokaryotes known to date. A probable target strand bias suggests that, in addition to double-stranded DNA, the CRISPR-Cas system can target ssDNA.},
}
@article {pmid30640434,
year = {2019},
author = {Jeter, VL and Mattes, TA and Beattie, NR and Escalante-Semerena, JC},
title = {A New Class of Phosphoribosyltransferases Involved in Cobamide Biosynthesis Is Found in Methanogenic Archaea and Cyanobacteria.},
journal = {Biochemistry},
volume = {58},
number = {7},
pages = {951-964},
pmid = {30640434},
issn = {1520-4995},
support = {R37 GM040313/GM/NIGMS NIH HHS/United States ; },
mesh = {Archaea/metabolism ; Archaeal Proteins/chemistry/genetics/*metabolism ; Bacterial Proteins/chemistry/genetics/*metabolism ; Cobamides/*biosynthesis ; Cyanobacteria/metabolism ; Hydrogen-Ion Concentration ; Methanococcus/enzymology/genetics ; Multienzyme Complexes/chemistry/genetics/metabolism ; Nucleotidyltransferases/chemistry/genetics/metabolism ; Osmolar Concentration ; Pentosyltransferases/chemistry/genetics/metabolism ; Phosphates/chemistry/metabolism ; Phylogeny ; Potassium Compounds/chemistry/metabolism ; Salmonella enterica/genetics/metabolism ; Substrate Specificity ; },
abstract = {Cobamides are coenzymes used by cells from all domains of life but made de novo by only some bacteria and archaea. The last steps of the cobamide biosynthetic pathway activate the corrin ring and the lower ligand base, condense the activated intermediates, and dephosphorylate the product prior to the release of the biologically active coenzyme. In bacteria, a phosphoribosyltransferase (PRTase) enyzme activates the base into its α-mononucleotide. The enzyme from Salmonella enterica (SeCobT) has been extensively biochemically and structurally characterized. The crystal structure of the putative PRTase from the archaeum Methanocaldococcus jannaschii (MjCobT) is known, but its function has not been validated. Here we report the in vivo and in vitro characterization of MjCobT. In vivo, in vitro, and phylogenetic data reported here show that MjCobT belongs to a new class of NaMN-dependent PRTases. We also show that the Synechococcus sp. WH7803 CobT protein has PRTase activity in vivo. Lastly, results of isothermal titration calorimetry and analytical ultracentrifugation analysis show that the biologically active form of MjCobT is a dimer, not a trimer, as suggested by its crystal structure.},
}
@article {pmid30629179,
year = {2019},
author = {Dombrowski, N and Lee, JH and Williams, TA and Offre, P and Spang, A},
title = {Genomic diversity, lifestyles and evolutionary origins of DPANN archaea.},
journal = {FEMS microbiology letters},
volume = {366},
number = {2},
pages = {},
pmid = {30629179},
issn = {1574-6968},
mesh = {Archaea/classification/*genetics/isolation &amp; purification/metabolism ; *Evolution, Molecular ; *Genetic Variation ; Genome, Archaeal ; Phylogeny ; },
abstract = {Archaea-a primary domain of life besides Bacteria-have for a long time been regarded as peculiar organisms that play marginal roles in biogeochemical cycles. However, this picture changed with the discovery of a large diversity of archaea in non-extreme environments enabled by the use of cultivation-independent methods. These approaches have allowed the reconstruction of genomes of uncultivated microorganisms and revealed that archaea are diverse and broadly distributed in the biosphere and seemingly include a large diversity of putative symbiotic organisms, most of which belong to the tentative archaeal superphylum referred to as DPANN. This archaeal group encompasses at least 10 different lineages and includes organisms with extremely small cell and genome sizes and limited metabolic capabilities. Therefore, many members of DPANN may be obligately dependent on symbiotic interactions with other organisms and may even include novel parasites. In this contribution, we review the current knowledge of the gene repertoires and lifestyles of members of this group and discuss their placement in the tree of life, which is the basis for our understanding of the deep microbial roots and the role of symbiosis in the evolution of life on Earth.},
}
@article {pmid30624459,
year = {2019},
author = {Morgado, SM and Vicente, ACP},
title = {Exploring tRNA gene cluster in archaea.},
journal = {Memorias do Instituto Oswaldo Cruz},
volume = {114},
number = {},
pages = {e180348},
pmid = {30624459},
issn = {1678-8060},
mesh = {Archaea/*genetics ; Evolution, Molecular ; Genome, Archaeal/*genetics ; Multigene Family/*genetics ; Phylogeny ; RNA, Archaeal/*genetics ; RNA, Transfer/*genetics ; Sequence Alignment ; },
abstract = {BACKGROUND: Shared traits between prokaryotes and eukaryotes are helpful in the understanding of the tree of life evolution. In bacteria and eukaryotes, it has been shown a particular organisation of tRNA genes as clusters, but this trait has not been explored in the archaea domain.<br><br>OBJECTIVE: Explore the occurrence of tRNA gene clusters in archaea.<br><br>METHODS: In-silico analyses of complete and draft archaeal genomes based on tRNA gene isotype and synteny, tRNA gene cluster content and mobilome elements.<br><br>FINDINGS: We demonstrated the prevalence of tRNA gene clusters in archaea. tRNA gene clusters, composed of archaeal-type tRNAs, were identified in two Archaea class, Halobacteria and Methanobacteria from Euryarchaeota supergroup. Genomic analyses also revealed evidence of the association between tRNA gene clusters to mobile genetic elements and intra-domain horizontal gene transfer.<br><br>MAIN CONCLUSIONS: tRNA gene cluster occurs in the three domains of life, suggesting a role of this type of tRNA gene organisation in the biology of the living organisms.},
}
@article {pmid30606162,
year = {2019},
author = {Xue, F and Nan, X and Li, Y and Pan, X and Guo, Y and Jiang, L and Xiong, B},
title = {Metagenomic insights into effects of thiamine supplementation on ruminal non-methanogen archaea in high-concentrate diets feeding dairy cows.},
journal = {BMC veterinary research},
volume = {15},
number = {1},
pages = {7},
pmid = {30606162},
issn = {1746-6148},
support = {Grant No. 31572435//Project of National Nature Science Foundation of China/ ; 2016YFD0700205//National Key Research and Development Plan/ ; },
mesh = {Animal Feed ; Animals ; Archaea/*drug effects/genetics ; Cattle ; Diet/*veterinary ; *Dietary Supplements ; Eating/drug effects ; Female ; Gastrointestinal Microbiome/drug effects ; Hydrogen-Ion Concentration ; Lactation/drug effects ; Metagenomics ; Rumen/chemistry/*microbiology ; Thiamine/analysis/*pharmacology ; },
abstract = {BACKGROUND: Overfeeding of high-concentrate diet (HC) frequently leads to subacute ruminal acidosis (SARA) in modern dairy cows' production. Thiamine supplementation has been confirmed to attenuate HC induced SARA by increasing ruminal pH and ratio of acetate to propionate, and decreasing rumen lactate, biogenic amines and lipopolysaccharide (LPS). The effects of thiamine supplementation in HC on rumen bacteria and fungi profile had been detected in our previous studies, however, effects of thiamine supplementation in HC on rumen non-methanogen archaea is still unclear. The objective of the present study was therefore to investigate the effects of thiamine supplementation on ruminal archaea, especially non-methanogens in HC induced SARA cows.<br><br>RESULTS: HC feeding significantly decreased dry matter intake, milk production, milk fat content, ruminal pH and the concentrations of thiamine and acetate in rumen fluid compared with control diet (CON) (P&#x2009;<&#x2009;0.05), while the concentrations of propionate and ammonia-nitrogen (NH3-N) were significantly increased compared with CON (P&#x2009;<&#x2009;0.05). These changes caused by HC were inversed by thiamine supplementation (P&#x2009;<&#x2009;0.05). The taxonomy results showed that ruminal archaea ranged from 0.37 to 0.47% of the whole microbiota. Four characterized phyla, a number of Candidatus archaea and almost 660 species were identified in the present study. In which Euryarchaeota occupied the largest proportion of the whole archaea. Furthermore, thiamine supplementation treatment significantly increased the relative abundance of non-methanogens compared with CON and HC treatments. Thaumarchaeota was increased in HC compared with CON. Thiamine supplementation significantly increased Crenarchaeota, Nanoarchaeota and the Candidatus phyla, however decreased Thaumarchaeota compared with HC treatment.<br><br>CONCLUSIONS: HC feeding significantly decreased ruminal pH and increased the content of NH3-N which led to N loss and the increase of the relative abundance of Thaumarchaeota. Thiamine supplementation increased ruminal pH, improved the activity of ammonia utilizing bacteria, and decreased Thaumarchaeota abundance to reduce the ruminal NH3 content and finally reduced N loss. Overall, these findings contributed to the understanding of thiamine's function in dairy cows and provided new strategies to improve dairy cows' health under high-concentrate feeding regime.},
}
@article {pmid30592124,
year = {2019},
author = {Wang, Y and Huang, JM and Cui, GJ and Nunoura, T and Takaki, Y and Li, WL and Li, J and Gao, ZM and Takai, K and Zhang, AQ and Stepanauskas, R},
title = {Genomics insights into ecotype formation of ammonia-oxidizing archaea in the deep ocean.},
journal = {Environmental microbiology},
volume = {21},
number = {2},
pages = {716-729},
doi = {10.1111/1462-2920.14518},
pmid = {30592124},
issn = {1462-2920},
support = {EF-0826924//NSF/International ; OCE-1335810//NSF/International ; OCE-1232982//NSF/International ; 30070015//Japan Society for the Promotion of Science/International ; 2016YFC0302500//Research and Development/International ; XDB06040101//Chinese Academy of Sciences/International ; XDB06010201//Chinese Academy of Sciences/International ; 31460001//National Science Foundation of China/International ; 41476104//National Science Foundation of China/International ; },
mesh = {Ammonia/*metabolism ; Archaea/classification/*genetics/isolation &amp; purification/*metabolism ; Carbon Cycle ; Ecotype ; Genomics ; Nitrogen/metabolism ; Oceans and Seas ; Oxidation-Reduction ; Phylogeny ; Seawater/*microbiology ; },
abstract = {Various lineages of ammonia-oxidizing archaea (AOA) are present in deep waters, but the mechanisms that determine ecotype formation are obscure. We studied 18 high-quality genomes of the marine group I AOA lineages (alpha, gamma and delta) from the Mariana and Ogasawara trenches. The genomes of alpha AOA resembled each other, while those of gamma and delta lineages were more divergent and had even undergone insertion of some phage genes. The instability of the gamma and delta AOA genomes could be partially due to the loss of DNA polymerase B (polB) and methyladenine DNA glycosylase (tag) genes responsible for the repair of point mutations. The alpha AOA genomes harbour genes encoding a thrombospondin-like outer membrane structure that probably serves as a barrier to gene flow. Moreover, the gamma and alpha AOA lineages rely on vitamin B12 -independent MetE and B12 -dependent MetH, respectively, for methionine synthesis. The delta AOA genome contains genes involved in uptake of sugar and peptide perhaps for heterotrophic lifestyle. Our study provides insights into co-occurrence of cladogenesis and anagenesis in the formation of AOA ecotypes that perform differently in nitrogen and carbon cycling in dark oceans.},
}
@article {pmid30581371,
year = {2018},
author = {Li, J and Liu, R and Tao, Y and Li, G},
title = {Archaea in Wastewater Treatment: Current Research and Emerging Technology.},
journal = {Archaea (Vancouver, B.C.)},
volume = {2018},
number = {},
pages = {6973294},
doi = {10.1155/2018/6973294},
pmid = {30581371},
issn = {1472-3654},
mesh = {Archaea/*growth &amp; development/*metabolism ; Biotechnology/*methods/trends ; Wastewater/*microbiology ; Water Purification/*methods ; },
}
@article {pmid30573104,
year = {2019},
author = {Li, N and Chen, Y and Zhang, Z and Chang, S and Huang, D and Chen, S and Guo, Q and Xie, S and Bing, Y},
title = {Response of ammonia-oxidizing archaea to heavy metal contamination in freshwater sediment.},
journal = {Journal of environmental sciences (China)},
volume = {77},
number = {},
pages = {392-399},
doi = {10.1016/j.jes.2018.09.020},
pmid = {30573104},
issn = {1001-0742},
mesh = {Ammonia/*metabolism ; Archaea/classification/*drug effects/*metabolism ; Biodiversity ; Cluster Analysis ; Fresh Water/*microbiology ; Geologic Sediments/*chemistry ; Metals, Heavy/analysis/*pharmacology ; Oxidation-Reduction ; Phylogeny ; Water Pollutants, Chemical/analysis/*pharmacology ; },
abstract = {It has been well-documented that the distribution of ammonia-oxidizing bacteria (AOB) and archaea (AOA) in soils can be affected by heavy metal contamination, whereas information about the impact of heavy metal on these ammonia-oxidizing microorganisms in freshwater sediment is still lacking. The present study explored the change of sediment ammonia-oxidizing microorganisms in a freshwater reservoir after being accidentally contaminated by industrial discharge containing high levels of metals. Bacterial amoA gene was found to be below the quantitative PCR detection and was not successfully amplified by conventional PCR. The number of archaeal amoA gene in reservoir sediments were 9.62 × 10[2]-1.35 × 10[7] copies per gram dry sediment. AOA abundance continuously decreased, and AOA richness, diversity and community structure also considerably varied with time. Therefore, heavy metal pollution could have a profound impact on freshwater sediment AOA community. This work could expand our knowledge of the effect of heavy metal contamination on nitrification in natural ecosystems.},
}
@article {pmid30559729,
year = {2018},
author = {Yu, H and Susanti, D and McGlynn, SE and Skennerton, CT and Chourey, K and Iyer, R and Scheller, S and Tavormina, PL and Hettich, RL and Mukhopadhyay, B and Orphan, VJ},
title = {Comparative Genomics and Proteomic Analysis of Assimilatory Sulfate Reduction Pathways in Anaerobic Methanotrophic Archaea.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2917},
pmid = {30559729},
issn = {1664-302X},
abstract = {Sulfate is the predominant electron acceptor for anaerobic oxidation of methane (AOM) in marine sediments. This process is carried out by a syntrophic consortium of anaerobic methanotrophic archaea (ANME) and sulfate reducing bacteria (SRB) through an energy conservation mechanism that is still poorly understood. It was previously hypothesized that ANME alone could couple methane oxidation to dissimilatory sulfate reduction, but a genetic and biochemical basis for this proposal has not been identified. Using comparative genomic and phylogenetic analyses, we found the genetic capacity in ANME and related methanogenic archaea for sulfate reduction, including sulfate adenylyltransferase, APS kinase, APS/PAPS reductase and two different sulfite reductases. Based on characterized homologs and the lack of associated energy conserving complexes, the sulfate reduction pathways in ANME are likely used for assimilation but not dissimilation of sulfate. Environmental metaproteomic analysis confirmed the expression of 6 proteins in the sulfate assimilation pathway of ANME. The highest expressed proteins related to sulfate assimilation were two sulfite reductases, namely assimilatory-type low-molecular-weight sulfite reductase (alSir) and a divergent group of coenzyme F420-dependent sulfite reductase (Group II Fsr). In methane seep sediment microcosm experiments, however, sulfite and zero-valent sulfur amendments were inhibitory to ANME-2a/2c while growth in their syntrophic SRB partner was not observed. Combined with our genomic and metaproteomic results, the passage of sulfur species by ANME as metabolic intermediates for their SRB partners is unlikely. Instead, our findings point to a possible niche for ANME to assimilate inorganic sulfur compounds more oxidized than sulfide in anoxic marine environments.},
}
@article {pmid30550095,
year = {2018},
author = {Lvov, DK and Sizikova, TE and Lebedev, VN and Borisevich, SV},
title = {[Plasmids of archaea as possible ancestors of DNA-containing viruses].},
journal = {Voprosy virusologii},
volume = {63},
number = {5},
pages = {197-201},
doi = {10.18821/0507-4088-2018-63-5-197-201},
pmid = {30550095},
issn = {2411-2097},
mesh = {Antarctic Regions ; Archaea/genetics/virology ; DNA, Viral/*genetics ; Halobacteriales/*genetics ; Halorubrum/*genetics/virology ; Lakes/microbiology ; Plasmids/genetics ; Salt Tolerance/genetics ; Viruses/*genetics ; },
abstract = {Тhе kingdom Archaea, as well as Bacteria, belongs to the overkingdom Prokaryota. Halophilic archaea (Halorubrum lacusprofundi) isolated from Antarctic saline lakes contain plasmids (pR1SE) that code proteins taking part in the formation of membranes of archaea vesicles. The molecular and biological properties of pR1SE and the peculiarity of its interaction with sensitive cells are considered in this article. The role of structural proteins coded by pR1S in the process of formation of vesicle membrane complex is paid special attention. Plasmid-containing archaea vesicles model some properties of viruses. Archaea plasmids can be viewed as possible ancestors of DNA-containing viruses.},
}
@article {pmid33525836,
year = {2018},
author = {Brugère, JF and Atkins, JF and O'Toole, PW and Borrel, G},
title = {Pyrrolysine in archaea: a 22nd amino acid encoded through a genetic code expansion.},
journal = {Emerging topics in life sciences},
volume = {2},
number = {4},
pages = {607-618},
doi = {10.1042/ETLS20180094},
pmid = {33525836},
issn = {2397-8554},
abstract = {The 22nd amino acid discovered to be directly encoded, pyrrolysine, is specified by UAG. Until recently, pyrrolysine was only known to be present in archaea from a methanogenic lineage (Methanosarcinales), where it is important in enzymes catalysing anoxic methylamines metabolism, and a few anaerobic bacteria. Relatively new discoveries have revealed wider presence in archaea, deepened functional understanding, shown remarkable carbon source-dependent expression of expanded decoding and extended exploitation of the pyrrolysine machinery for synthetic code expansion. At the same time, other studies have shown the presence of pyrrolysine-containing archaea in the human gut and this has prompted health considerations. The article reviews our knowledge of this fascinating exception to the 'standard' genetic code.},
}
@article {pmid33525832,
year = {2018},
author = {Schmid, AK},
title = {Conserved principles of transcriptional networks controlling metabolic flexibility in archaea.},
journal = {Emerging topics in life sciences},
volume = {2},
number = {4},
pages = {659-669},
pmid = {33525832},
issn = {2397-8554},
abstract = {Gene regulation is intimately connected with metabolism, enabling the appropriate timing and tuning of biochemical pathways to substrate availability. In microorganisms, such as archaea and bacteria, transcription factors (TFs) often directly sense external cues such as nutrient substrates, metabolic intermediates, or redox status to regulate gene expression. Intense recent interest has characterized the functions of a large number of such regulatory TFs in archaea, which regulate a diverse array of unique archaeal metabolic capabilities. However, it remains unclear how the co-ordinated activity of the interconnected metabolic and transcription networks produces the dynamic flexibility so frequently observed in archaeal cells as they respond to energy limitation and intermittent substrate availability. In this review, we communicate the current state of the art regarding these archaeal networks and their dynamic properties. We compare the topology of these archaeal networks to those known for bacteria to highlight conserved and unique aspects. We present a new computational model for an exemplar archaeal network, aiming to lay the groundwork toward understanding general principles that unify the dynamic function of integrated metabolic-transcription networks across archaea and bacteria.},
}
@article {pmid33525831,
year = {2018},
author = {Quax, TEF and Albers, SV and Pfeiffer, F},
title = {Taxis in archaea.},
journal = {Emerging topics in life sciences},
volume = {2},
number = {4},
pages = {535-546},
pmid = {33525831},
issn = {2397-8554},
abstract = {Microorganisms can move towards favorable growth conditions as a response to environmental stimuli. This process requires a motility structure and a system to direct the movement. For swimming motility, archaea employ a rotating filament, the archaellum. This archaea-specific structure is functionally equivalent, but structurally different, from the bacterial flagellum. To control the directionality of movement, some archaea make use of the chemotaxis system, which is used for the same purpose by bacteria. Over the past decades, chemotaxis has been studied in detail in several model bacteria. In contrast, archaeal chemotaxis is much less explored and largely restricted to analyses in halophilic archaea. In this review, we summarize the available information on archaeal taxis. We conclude that archaeal chemotaxis proteins function similarly as their bacterial counterparts. However, because the motility structures are fundamentally different, an archaea-specific docking mechanism is required, for which initial experimental data have only recently been obtained.},
}
@article {pmid33525830,
year = {2018},
author = {Bang, C and Schmitz, RA},
title = {Archaea: forgotten players in the microbiome.},
journal = {Emerging topics in life sciences},
volume = {2},
number = {4},
pages = {459-468},
doi = {10.1042/ETLS20180035},
pmid = {33525830},
issn = {2397-8554},
abstract = {Archaea, the third domain of life containing unique membrane composition and highly diverse cell wall structures, were only recognized 40 years ago. Initially identified in extreme environments, they are currently recognized as organisms ubiquitously present in most, if not all, microbiomes associated with eukaryotic hosts. However, they have been mostly overseen in microbiome studies due to the lack of standardized detection protocols and to the fact that no archaeal pathogen is currently known. Recent years clearly showed that (i) archaea are part of the microbiomes associated with plants, animals and humans, (ii) form biofilms and (iii) interact and activate the human immune system. Future studies will not only define the host-associated diversity of archaea (referred to as 'archaeome') but also contribute to our understanding of the comprehensive metabolic interplay between archaea and bacteria and the long-term gain insights into their role in human health and their potential role(s) during disease development.},
}
@article {pmid33525827,
year = {2018},
author = {Lemmens, L and Baes, R and Peeters, E},
title = {Heat shock response in archaea.},
journal = {Emerging topics in life sciences},
volume = {2},
number = {4},
pages = {581-593},
doi = {10.1042/ETLS20180024},
pmid = {33525827},
issn = {2397-8554},
abstract = {An adequate response to a sudden temperature rise is crucial for cellular fitness and survival. While heat shock response (HSR) is well described in bacteria and eukaryotes, much less information is available for archaea, of which many characterized species are extremophiles thriving in habitats typified by large temperature gradients. Here, we describe known molecular aspects of archaeal heat shock proteins (HSPs) as key components of the protein homeostasis machinery and place this in a phylogenetic perspective with respect to bacterial and eukaryotic HSPs. Particular emphasis is placed on structure-function details of the archaeal thermosome, which is a major element of the HSR and of which subunit composition is altered in response to temperature changes. In contrast with the structural response, it is largely unclear how archaeal cells sense temperature fluctuations and which molecular mechanisms underlie the corresponding regulation. We frame this gap in knowledge by discussing emerging questions related to archaeal HSR and by proposing methodologies to address them. Additionally, as has been shown in bacteria and eukaryotes, HSR is expected to be relevant for the control of physiology and growth in various stress conditions beyond temperature stress. A better understanding of this essential cellular process in archaea will not only provide insights into the evolution of HSR and of its sensing and regulation, but also inspire the development of biotechnological applications, by enabling transfer of archaeal heat shock components to other biological systems and for the engineering of archaea as robust cell factories.},
}
@article {pmid33525826,
year = {2018},
author = {Kellner, S and Spang, A and Offre, P and Szöllősi, GJ and Petitjean, C and Williams, TA},
title = {Genome size evolution in the Archaea.},
journal = {Emerging topics in life sciences},
volume = {2},
number = {4},
pages = {595-605},
pmid = {33525826},
issn = {2397-8554},
abstract = {What determines variation in genome size, gene content and genetic diversity at the broadest scales across the tree of life? Much of the existing work contrasts eukaryotes with prokaryotes, the latter represented mainly by Bacteria. But any general theory of genome evolution must also account for the Archaea, a diverse and ecologically important group of prokaryotes that represent one of the primary domains of cellular life. Here, we survey the extant diversity of Bacteria and Archaea, and ask whether the general principles of genome evolution deduced from the study of Bacteria and eukaryotes also apply to the archaeal domain. Although Bacteria and Archaea share a common prokaryotic genome architecture, the extant diversity of Bacteria appears to be much higher than that of Archaea. Compared with Archaea, Bacteria also show much greater genome-level specialisation to specific ecological niches, including parasitism and endosymbiosis. The reasons for these differences in long-term diversification rates are unclear, but might be related to fundamental differences in informational processing machineries and cell biological features that may favour archaeal diversification in harsher or more energy-limited environments. Finally, phylogenomic analyses suggest that the first Archaea were anaerobic autotrophs that evolved on the early Earth.},
}
@article {pmid33525825,
year = {2018},
author = {Zhang, Y and Lin, J and Feng, M and She, Q},
title = {Molecular mechanisms of III-B CRISPR-Cas systems in archaea.},
journal = {Emerging topics in life sciences},
volume = {2},
number = {4},
pages = {483-491},
doi = {10.1042/ETLS20180023},
pmid = {33525825},
issn = {2397-8554},
abstract = {Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) systems provide the adaptive antiviral immunity against invasive genetic elements in archaea and bacteria. These immune systems are divided into at least six different types, among which Type III CRISPR-Cas systems show several distinct antiviral activities as demonstrated from the investigation of bacterial III-A and archaeal III-B systems in the past decade. First, although initial experiments suggested that III-A systems provided DNA interference activity, whereas III-B system was active only in RNA interference, these immune systems were subsequently found to mediate the transcription-dependent DNA interference and the dual DNA/RNA interference. Second, their ribonucleoprotein (RNP) complexes show target RNA (tgRNA) cleavage by a ruler mechanism and RNA-activated indiscriminate single-stranded DNA cleavage, the latter of which is subjected to spatiotemporal regulation such that the DNase activity occurs only at the right place in the right time. Third, RNPs of Type III systems catalyse the synthesis of cyclic oligoadenylates (cOAs) that function as second messengers to activate Csm6 and Csx1, both of which are potent Cas accessory RNases after activation. To date, Type III CRISPR systems are the only known antiviral immunity that utilizes multiple interference mechanisms for antiviral defence.},
}
@article {pmid33525822,
year = {2018},
author = {Robinson, NP},
title = {Archaea, from obscurity to superhero microbes: 40 years of surprises and critical biological insights.},
journal = {Emerging topics in life sciences},
volume = {2},
number = {4},
pages = {453-458},
pmid = {33525822},
issn = {2397-8554},
abstract = {This issue of Emerging Topics in the Life Sciences highlights current areas of research in the field of archaeal biology and the following introductory editorial sets the stage by considering some of the key developments over the last four decades since the initial identification of the archaea as a unique form of life. Emerging topics from this vibrant and rapidly expanding field of research are considered and detailed further in the articles within this issue.},
}
@article {pmid33525820,
year = {2018},
author = {Lemmens, L and Baes, R and Peeters, E},
title = {Correction: Heat shock response in archaea.},
journal = {Emerging topics in life sciences},
volume = {2},
number = {4},
pages = {671-672},
doi = {10.1042/ETLS-2018-0024C_COR},
pmid = {33525820},
issn = {2397-8554},
}
@article {pmid30544151,
year = {2019},
author = {Jaffe, AL and Castelle, CJ and Dupont, CL and Banfield, JF},
title = {Lateral Gene Transfer Shapes the Distribution of RuBisCO among Candidate Phyla Radiation Bacteria and DPANN Archaea.},
journal = {Molecular biology and evolution},
volume = {36},
number = {3},
pages = {435-446},
pmid = {30544151},
issn = {1537-1719},
mesh = {Archaea/*genetics ; Bacteria/*genetics ; Bacteriophages/*genetics ; *Gene Transfer, Horizontal ; Metagenomics ; Phosphotransferases (Alcohol Group Acceptor)/genetics ; Phylogeny ; Ribulose-Bisphosphate Carboxylase/*genetics ; },
abstract = {Ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) is considered to be the most abundant enzyme on Earth. Despite this, its full diversity and distribution across the domains of life remain to be determined. Here, we leverage a large set of bacterial, archaeal, and viral genomes recovered from the environment to expand our understanding of existing RuBisCO diversity and the evolutionary processes responsible for its distribution. Specifically, we report a new type of RuBisCO present in Candidate Phyla Radiation (CPR) bacteria that is related to the archaeal Form III enzyme and contains the amino acid residues necessary for carboxylase activity. Genome-level metabolic analyses supported the inference that these RuBisCO function in a CO2-incorporating pathway that consumes nucleotides. Importantly, some Gottesmanbacteria (CPR) also encode a phosphoribulokinase that may augment carbon metabolism through a partial Calvin-Benson-Bassham cycle. Based on the scattered distribution of RuBisCO and its discordant evolutionary history, we conclude that this enzyme has been extensively laterally transferred across the CPR bacteria and DPANN archaea. We also report RuBisCO-like proteins in phage genomes from diverse environments. These sequences cluster with proteins in the Beckwithbacteria (CPR), implicating phage as a possible mechanism of RuBisCO transfer. Finally, we synthesize our metabolic and evolutionary analyses to suggest that lateral gene transfer of RuBisCO may have facilitated major shifts in carbon metabolism in several important bacterial and archaeal lineages.},
}
@article {pmid30530297,
year = {2019},
author = {Wang, S and Zheng, Z and Zou, H and Li, N and Wu, M},
title = {Characterization of the secondary metabolite biosynthetic gene clusters in archaea.},
journal = {Computational biology and chemistry},
volume = {78},
number = {},
pages = {165-169},
doi = {10.1016/j.compbiolchem.2018.11.019},
pmid = {30530297},
issn = {1476-928X},
mesh = {Archaea/*genetics/metabolism ; Bacteriocins/*biosynthesis/chemistry/genetics ; *Multigene Family ; },
abstract = {Secondary metabolites are a range of bioactive compounds yielded by bacteria, fungi and plants, etc. The published archaea genomic data provide the opportunity for efficient identification of secondary metabolite biosynthetic gene clusters (BGCs) by genome mining. However, the study of secondary metabolites in archaea is still rare. By using the antiSMASH, we found two main putative secondary metabolite BGCs, bacteriocin and terpene in 203 Archaea genomes. Compared with the genomes of Euryarchaeota that usually lives in less complexity of environment, the genomes of Crenarchaeota usually contained more abundant bacteriocin. In these archaea genomes, we also found the positive correlation between the abundance of bacteriocin and the abundance of CRISPR spacer, suggesting the bacteriocin might be a crucial component of the innate immune system that defense the microbe living in the common environment. The structure analysis of the bacteriocin gene clusters gave a clue that the assisted genes located at the edge of clusters evolved faster than the core biosynthetic genes. To the best of our knowledge, we are the first to systematically explore the distribution of secondary metabolites in archaea, and the investigation of the relationship between BGC and CRISPR spacer expands our understanding of the evolutionary dynamic of these functional molecules.},
}
@article {pmid30520969,
year = {2019},
author = {Alva, V and Lupas, AN},
title = {Histones predate the split between bacteria and archaea.},
journal = {Bioinformatics (Oxford, England)},
volume = {35},
number = {14},
pages = {2349-2353},
doi = {10.1093/bioinformatics/bty1000},
pmid = {30520969},
issn = {1367-4811},
mesh = {*Archaea ; *Bacteria ; Histones ; Nucleosomes ; },
abstract = {MOTIVATION: Histones form octameric complexes called nucleosomes, which organize the genomic DNA of eukaryotes into chromatin. Each nucleosome comprises two copies each of the histones H2A, H2B, H3 and H4, which share a common ancestry. Although histones were initially thought to be a eukaryotic innovation, the subsequent identification of archaeal homologs led to the notion that histones emerged before the divergence of archaea and eukaryotes.<br><br>RESULTS: Here, we report the detection and classification of two new groups of histone homologs, which are present in both archaea and bacteria. Proteins in one group consist of two histone subunits welded into single-chain pseudodimers, whereas in the other they resemble eukaryotic core histone subunits and show sequence patterns characteristic of DNA binding. The sequences come from a broad spectrum of deeply-branching lineages, excluding their genesis by horizontal gene transfer. Our results extend the origin of histones to the last universal common ancestor.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
}
@article {pmid30519544,
year = {2018},
author = {Higuchi, ML and Kawakami, JT and Ikegami, RN and Reis, MM and Pereira, JJ and Ianni, BM and Buck, P and Oliveira, LMDS and Santos, MHH and Hajjar, LA and Bocchi, EA},
title = {Archaea Symbiont of T. cruzi Infection May Explain Heart Failure in Chagas Disease.},
journal = {Frontiers in cellular and infection microbiology},
volume = {8},
number = {},
pages = {412},
pmid = {30519544},
issn = {2235-2988},
mesh = {Adult ; Aged ; Aged, 80 and over ; Antigens, Bacterial/blood ; Archaea/*physiology ; Biomarkers ; Chagas Disease/blood/*immunology ; Collagenases ; Exosomes ; Female ; Flow Cytometry ; Heart Failure/blood/*immunology ; Humans ; Male ; Metalloproteases ; Microscopy, Electron, Transmission ; Middle Aged ; Trypanosoma cruzi/*immunology/*microbiology ; },
abstract = {Background: Archaeal genes present in Trypanosoma cruzi may represent symbionts that would explain development of heart failure in 30% of Chagas disease patients. Extracellular vesicles in peripheral blood, called exosomes (< 0.1 μm) or microvesicles (>0.1 μm), present in larger numbers in heart failure, were analyzed to determine whether they are derived from archaea in heart failure Chagas disease. Methods: Exosomes and microvesicles in serum supernatant from 3 groups were analyzed: heart failure Chagas disease (N = 26), asymptomatic indeterminate form (N = 21) and healthy non-chagasic control (N = 16). Samples were quantified with transmission electron microscopy, flow cytometer immunolabeled with anti-archaemetzincin-1 antibody (AMZ 1, archaea collagenase) and probe anti-archaeal DNA and zymography to determine AMZ1 (Archaeal metalloproteinase) activity. Results: Indeterminate form patients had higher median numbers of exosomes/case vs. heart failure patients (58.5 vs. 25.5, P < 0.001), higher exosome content of AMZ1 antigens (2.0 vs. 0.0; P < 0.001), and lower archaeal DNA content (0.2 vs. 1.5, P = 0.02). A positive correlation between exosomes and AMZ1 content was seen in indeterminate form (r = 0.5, P < 0.001), but not in heart failure patients (r = 0.002, P = 0.98). Higher free archaeal DNA (63.0 vs. 11.1, P < 0.001) in correlation with exosome numbers (r = 0.66, P = 0.01) was seen in heart failure but not in indeterminate form (r = 0.29, P = 0.10). Flow cytometer showed higher numbers of AMZ1 microvesicles in indeterminate form (64 vs. 36, P = 0.02) and higher archaeal DNA microvesicles in heart failure (8.1 vs. 0.9, P < 0.001). Zymography showed strong% collagenase activity in HF group, mild activity in IF compared to non-chagasic healthy group (121 ± 14, 106 ± 13 and 100; P < 0.001). Conclusions: Numerous exosomes, possibly removing and degrading abnormal AMZ1 collagenase, are associated with indeterminate form. Archaeal microvesicles and their exosomes, possibly associated with release of archaeal AMZ1 in heart failure, are future candidates of heart failure biomarkers if confirmed in larger series, and the therapeutic focus in the treatment of Chagas disease.},
}
@article {pmid30502951,
year = {2018},
author = {Buddeweg, A and Daume, M and Randau, L and Schmitz, RA},
title = {Noncoding RNAs in Archaea: Genome-Wide Identification and Functional Classification.},
journal = {Methods in enzymology},
volume = {612},
number = {},
pages = {413-442},
doi = {10.1016/bs.mie.2018.08.003},
pmid = {30502951},
issn = {1557-7988},
mesh = {Archaea/*genetics ; RNA, Untranslated/*genetics ; Sequence Analysis, RNA ; },
abstract = {Noncoding RNAs (ncRNAs) fulfill essential functions in eukaryotes and bacteria, but also in the third domain of life, the Archaea. Many archaeal organisms live in hostile environments that provide unique challenges for their transcriptional and translational regulatory pathways. Computational analyses and RNA-sequencing methodologies allowed for the genome-wide detection of ncRNA molecules in archaea. Several new classes of ncRNAs have been discovered and are expected to enable life in these extreme habitats. Here, we provide an overview of the current knowledge on archaeal ncRNAs and their deduced or biochemically verified functions. In addition, details of applying RNA-seq methodology for the detection of ncRNAs in Sulfolobus acidocaldarius are provided. Identified ncRNAs include small RNAs (sRNAs) that regulate gene expression and C/D box sRNAs that guide 2'-O methylation of target RNAs.},
}
@article {pmid30514872,
year = {2019},
author = {Zhou, Z and Liu, Y and Lloyd, KG and Pan, J and Yang, Y and Gu, JD and Li, M},
title = {Genomic and transcriptomic insights into the ecology and metabolism of benthic archaeal cosmopolitan, Thermoprofundales (MBG-D archaea).},
journal = {The ISME journal},
volume = {13},
number = {4},
pages = {885-901},
pmid = {30514872},
issn = {1751-7370},
mesh = {Archaea/*classification/genetics/*physiology ; Carbon Cycle ; Ecology ; Genomics ; Geologic Sediments/chemistry/*microbiology ; Metagenome ; Methane/metabolism ; Phylogeny ; RNA, Archaeal/genetics ; RNA, Ribosomal, 16S/genetics ; Transcriptome ; *Water Microbiology ; },
abstract = {Marine Benthic Group D (MBG-D) archaea, discovered by 16S rRNA gene survey decades ago, are ecologically important, yet understudied and uncultured sedimentary archaea. In this study, a comprehensive meta-analysis based on the 16S rRNA genes of MBG-D archaea showed that MBG-D archaea are one of the most frequently found archaeal lineages in global sediment with widespread distribution and high abundance, including 16 subgroups in total. Interestingly, some subgroups show significant segregations toward salinity and methane seeps. Co-occurrence analyses indicate significant non-random association of MBG-D archaea with Lokiarchaeota (in both saline and freshwater sediments) and Hadesarchaea, suggesting potential interactions among these archaeal groups. Meanwhile, based on four nearly complete metagenome-assembled genomes (MAGs) and corresponding metatranscriptomes reconstructed from mangrove and intertidal mudflat sediments, we provide insights on metabolic potentials and ecological functions of MBG-D archaea. MBG-D archaea appear to be capable of transporting and assimilating peptides and generating acetate and ethanol through fermentation. Metatranscriptomic analysis suggests high expression of genes for acetate and amino acid utilization and for peptidases, especially the M09B-type extracellular peptidase (collagenase) showing high expression levels in all four mangrove MAGs. Beyond heterotrophic central carbon metabolism, the MBG-D genomes include genes that might encode two autotrophic pathways: Wood-Ljundahl (WL) pathways using both H4MPT and H4folate as C1 carriers, and an incomplete dicarboxylate/4-hydroxybutyrate cycle with alternative bypasses from pyruvate to malate/oxaloacetate during dicarboxylation. These findings reveal MBG-D archaea as an important ubiquitous benthic sedimentary archaeal group with specific mixotrophic metabolisms, so we proposed the name Thermoprofundales as a new Order within the Class Thermoplasmata. Globally, Thermoprofundales and other benthic archaea might synergistically transform benthic organic matter, possibly playing a vital role in sedimentary carbon cycle.},
}
@article {pmid30511184,
year = {2018},
author = {Vipindas, PV and Jabir, T and Jasmin, C and Balu, T and Rehitha, TV and Adarsh, BM and Nair, S and Abdulla, MH and Abdulaziz, A},
title = {Diversity and seasonal distribution of ammonia-oxidizing archaea in the water column of a tropical estuary along the southeast Arabian Sea.},
journal = {World journal of microbiology &amp; biotechnology},
volume = {34},
number = {12},
pages = {188},
pmid = {30511184},
issn = {1573-0972},
mesh = {Ammonia/*metabolism ; Archaea/*classification/genetics/*metabolism ; Bacteria/classification/genetics/metabolism ; *Biodiversity ; DNA, Archaeal ; DNA, Bacterial/genetics ; Environment ; *Estuaries ; Genes, Archaeal/genetics ; Geologic Sediments/microbiology ; India ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Seasons ; Seawater/*microbiology ; Sequence Analysis, DNA ; Tropical Climate ; },
abstract = {Diversity and distribution pattern of ammonia-oxidizing archaea (AOA) were studied across a salinity gradient in the water column of Cochin Estuary (CE), a tropical monsoonal estuary along the southeast Arabian Sea. The water column of CE was found to be nutrient rich with high bacterial (3.7-6.7 × 10[8] cells L[-1]) and archaeal abundance (1.9-4.5 × 10[8] cells L[-1]). Diversity and seasonal variation in the distribution pattern of AOA were studied using clone library analysis and Denaturing gradient gel electrophoresis (DGGE). Clone library analysis of both the amoA and 16S rRNA gene sequences showed similar diversity pattern, however the diversity was more clear when the 16S rRNA gene sequences were analyzed. More than 70% of the sequences retrieved were clustered under uncultured Thaumarchaeota group 1 lineage and the major fractions of the remaining sequences were grouped into the Nitrosopumilus lineage and Nitrosopelagicus lineage. The AOA community in the CE was less adaptable to changing environmental conditions and its distribution showed seasonal variations within the DGGE banding pattern with higher diversity during the pre-monsoon period. The distribution of AOA also showed its preference to intermediate salinity for their higher diversity. Summer monsoon associated runoff and flushing played a critical role in regulating the seasonality of AOA distribution.},
}
@article {pmid32953999,
year = {2018},
author = {Maupin-Furlow, JA},
title = {Proteolytic systems of archaea: slicing, dicing, and mincing in the extreme.},
journal = {Emerging topics in life sciences},
volume = {2},
number = {4},
pages = {561-580},
pmid = {32953999},
issn = {2397-8554},
support = {R01 GM057498/GM/NIGMS NIH HHS/United States ; },
abstract = {Archaea are phylogenetically distinct from bacteria, and some of their proteolytic systems reflect this distinction. Here, the current knowledge of archaeal proteolysis is reviewed as it relates to protein metabolism, protein homeostasis, and cellular regulation including targeted proteolysis by proteasomes associated with AAA-ATPase networks and ubiquitin-like modification. Proteases and peptidases that facilitate the recycling of peptides to amino acids as well as membrane-associated and integral membrane proteases are also reviewed.},
}
@article {pmid30485275,
year = {2018},
author = {Woodall, LC and Jungblut, AD and Hopkins, K and Hall, A and Robinson, LF and Gwinnett, C and Paterson, GLJ},
title = {Deep-sea anthropogenic macrodebris harbours rich and diverse communities of bacteria and archaea.},
journal = {PloS one},
volume = {13},
number = {11},
pages = {e0206220},
pmid = {30485275},
issn = {1932-6203},
mesh = {Archaea/*metabolism ; Atlantic Ocean ; Bacteria/*metabolism ; *Biodiversity ; Biofilms ; Geography ; Geologic Sediments/microbiology ; *Human Activities ; Humans ; Phylogeny ; Seawater ; *Waste Products ; },
abstract = {The deep sea is the largest biome on earth, and microbes dominate in biomass and abundance. Anthropogenic litter is now almost ubiquitous in this biome, and its deposition creates new habitats and environments, including for microbial assemblages. With the ever increasing accumulation of this debris, it is timely to identify and describe the bacterial and archaeal communities that are able to form biofilms on macrodebris in the deep sea. Using 16S rRNA gene high throughput sequencing, we show for the first time the composition of bacteria and archaea on macrodebris collected from the deep sea. Our data suggest differences in the microbial assemblage composition across litter of different materials including metal, rubber, glass, fabric and plastic. These results imply that anthropogenic macrodebris provide diverse habitats for bacterial and archaeal biofilms and each may harbour distinct microbial communities.},
}
@article {pmid30484150,
year = {2018},
author = {Lim, S and Glover, DJ and Clark, DS},
title = {Prefoldins in Archaea.},
journal = {Advances in experimental medicine and biology},
volume = {1106},
number = {},
pages = {11-23},
doi = {10.1007/978-3-030-00737-9_2},
pmid = {30484150},
issn = {0065-2598},
mesh = {*Archaea ; Archaeal Proteins/*physiology ; Molecular Chaperones/*physiology ; *Protein Folding ; },
abstract = {Molecular chaperones promote the correct folding of proteins in aggregation-prone cellular environments by stabilizing nascent polypeptide chains and providing appropriate folding conditions. Prefoldins (PFDs) are molecular chaperones found in archaea and eukaryotes, generally characterized by a unique jellyfish-like hexameric structure consisting of a rigid beta-barrel backbone with protruding flexible coiled-coils. Unlike eukaryotic PFDs that mainly interact with cytoskeletal components, archaeal PFDs can stabilize a wide range of substrates; such versatility reflects PFD's role as a key element in archaeal chaperone systems, which often lack general nascent-chain binding chaperone components such as Hsp70. While archaeal PFDs mainly exist as hexameric complexes, their structural diversity ranges from tetramers to filamentous oligomers. PFDs bind and stabilize nonnative proteins using varying numbers of coiled-coils, and subsequently transfer the substrate to a group II chaperonin (CPN) for refolding. The distinct structure and specific function of archaeal PFDs have been exploited for a broad range of applications in biotechnology; furthermore, a filament-forming variant of PFD has been used to fabricate nanoscale architectures of defined shapes, demonstrating archaeal PFDs' potential applicability in nanotechnology.},
}
@article {pmid30478289,
year = {2019},
author = {Turgeman-Grott, I and Joseph, S and Marton, S and Eizenshtein, K and Naor, A and Soucy, SM and Stachler, AE and Shalev, Y and Zarkor, M and Reshef, L and Altman-Price, N and Marchfelder, A and Gophna, U},
title = {Pervasive acquisition of CRISPR memory driven by inter-species mating of archaea can limit gene transfer and influence speciation.},
journal = {Nature microbiology},
volume = {4},
number = {1},
pages = {177-186},
pmid = {30478289},
issn = {2058-5276},
mesh = {CRISPR-Cas Systems/*genetics ; Clustered Regularly Interspaced Short Palindromic Repeats/*genetics ; DNA, Intergenic/*genetics ; Gene Transfer, Horizontal/*genetics ; Genetic Speciation ; Haloferax mediterranei/*genetics/growth &amp; development ; Haloferax volcanii/*genetics/growth &amp; development ; },
abstract = {CRISPR-Cas systems provide prokaryotes with sequence-specific immunity against viruses and plasmids based on DNA acquired from these invaders, known as spacers. Surprisingly, many archaea possess spacers that match chromosomal genes of related species, including those encoding core housekeeping genes. By sequencing genomes of environmental archaea isolated from a single site, we demonstrate that inter-species spacers are common. We show experimentally, by mating Haloferax volcanii and Haloferax mediterranei, that spacers are indeed acquired chromosome-wide, although a preference for integrated mobile elements and nearby regions of the chromosome exists. Inter-species mating induces increased spacer acquisition and may result in interactions between the acquisition machinery of the two species. Surprisingly, many of the spacers acquired following inter-species mating target self-replicons along with those originating from the mating partner, indicating that the acquisition machinery cannot distinguish self from non-self under these conditions. Engineering the chromosome of one species to be targeted by the other's CRISPR-Cas reduces gene exchange between them substantially. Thus, spacers acquired during inter-species mating could limit future gene transfer, resulting in a role for CRISPR-Cas systems in microbial speciation.},
}
@article {pmid30461142,
year = {2019},
author = {Song, GC and Im, H and Jung, J and Lee, S and Jung, MY and Rhee, SK and Ryu, CM},
title = {Plant growth-promoting archaea trigger induced systemic resistance in Arabidopsis thaliana against Pectobacterium carotovorum and Pseudomonas syringae.},
journal = {Environmental microbiology},
volume = {21},
number = {3},
pages = {940-948},
doi = {10.1111/1462-2920.14486},
pmid = {30461142},
issn = {1462-2920},
support = {KGM2111844//Korea Research Institute of Bioscience and Biotechnology/International ; 918017-4//Ministry of Agriculture, Food and Rural Affairs/International ; Woo Jang-Choon Project (PJ01093904)//Rural Development Administration/International ; },
mesh = {Arabidopsis/*microbiology ; Archaea/*physiology ; Disease Resistance ; Pectobacterium carotovorum/*physiology ; Plant Development ; Plant Diseases/*microbiology ; Pseudomonas syringae/*physiology ; Salicylic Acid/metabolism ; Signal Transduction ; Soil Microbiology ; },
abstract = {Archaea have inhabited the earth for a long period of time and are ubiquitously distributed in diverse environments. However, few studies have focused on the interactions of archaea with other organisms, including eukaryotes such as plants, since it is difficult to cultivate sufficient numbers of archaeal cells for analysis. In this study, we investigated the interaction between soil archaea and Arabidopsis thaliana. We demonstrate for the first time that soil archaea promote plant growth and trigger induced systemic resistance (ISR) against the necrotrophic bacterium Pectobacterium carotovorum subsp. carotovorum SCC1 and biotrophic bacterium Pseudomonas syringae pv. tomato DC3000. Ammonia-oxidizing archaeon Nitrosocosmicus oleophilus MY3 cells clearly colonized the root surface of Arabidopsis plants, and increased resistance against both pathogenic species via the salicylic acid-independent signalling pathway. This mechanism of bacterial resistance resembles that underlying soil bacteria- and fungi-mediated ISR signalling. Additionally, volatile emissions from N. oleophilus MY3 were identified as major archaeal determinants that elicit ISR. Our results lay a foundation for archaea-plant interactions as a new field of research.},
}
@article {pmid30450139,
year = {2018},
author = {Najafi, A and Moradinasab, M and Seyedabadi, M and Haghighi, MA and Nabipour, I},
title = {First Molecular Identification of Symbiotic Archaea in a Sponge Collected from the Persian Gulf, Iran.},
journal = {The open microbiology journal},
volume = {12},
number = {},
pages = {323-332},
pmid = {30450139},
issn = {1874-2858},
abstract = {BACKGROUND: Marine sponges are associated with numerically vast and phylogenetically diverse microbial communities at different geographical locations. However, little is known about the archaeal diversity of sponges in the Persian Gulf. The present study was aimed to identify the symbiotic archaea with a sponge species gathered from the Persian Gulf, Iran.<br><br>METHODS: Sponge sample was collected from a depth of 3 m offshore Bushehr, Persian Gulf, Iran. Metagenomic DNA was extracted using a hexadecyl trimethyl ammonium bromide (CTAB) method. The COI mtDNA marker was used for molecular taxonomy identification of sponge sample. Also, symbiotic archaea were identified using the culture-independent analysis of the 16S rRNA gene and PCR- cloning.<br><br>RESULTS: In this study, analysis of multilocus DNA marker and morphological characteristics revealed that the sponge species belonged to Chondrilla australiensis isolate PG_BU4. PCR cloning and sequencing showed that all of the sequences of archaeal 16S rRNA gene libraries clustered into the uncultured archaeal group.<br><br>CONCLUSION: The present study is the first report of the presence of the genus of Chondrilla in the Persian Gulf. Traditional taxonomy methods, when used along with molecular techniques, could play a significant role in the accurate taxonomy of sponges. Also, the uncultured archaea may promise a potential source for bioactive compounds. Further functional studies are needed to explore the role of the sponge-associated uncultured archaea as a part of the marine symbiosis.},
}
@article {pmid30373756,
year = {2019},
author = {Peck, RF and Graham, SM and Gregory, AM},
title = {Species Widely Distributed in Halophilic Archaea Exhibit Opsin-Mediated Inhibition of Bacterioruberin Biosynthesis.},
journal = {Journal of bacteriology},
volume = {201},
number = {2},
pages = {},
pmid = {30373756},
issn = {1098-5530},
support = {P20 GM103423/GM/NIGMS NIH HHS/United States ; },
mesh = {Actinobacteria/chemistry ; Aerobiosis ; Anaerobiosis ; Carotenoids/*biosynthesis ; Enzyme Inhibitors/isolation &amp; purification/metabolism ; Gene Expression Regulation, Archaeal ; Halobacteriales/*drug effects/*metabolism ; Opsins/isolation &amp; purification/*metabolism ; },
abstract = {Halophilic Archaea are a distinctive pink color due to a carotenoid pigment called bacterioruberin. To sense or utilize light, many halophilic Archaea also produce rhodopsins, complexes of opsin proteins with a retinal prosthetic group. Both bacterioruberin and retinal are synthesized from isoprenoid precursors, with lycopene as the last shared intermediate. We previously described a regulatory mechanism by which Halobacterium salinarum bacterioopsin and Haloarcula vallismortis cruxopsin inhibit bacterioruberin synthesis catalyzed by lycopene elongase. In this work, we found that opsins in all three major Halobacteria clades inhibit bacterioruberin synthesis, suggesting that this regulatory mechanism existed in the common Halobacteria ancestor. Halophilic Archaea, which are generally heterotrophic and aerobic, likely evolved from an autotrophic, anaerobic methanogenic ancestor by acquiring many genes from Bacteria via lateral gene transfer. These bacterial "imports" include genes encoding opsins and lycopene elongases. To determine if opsins from Bacteria inhibit bacterioruberin synthesis, we tested bacterial opsins and found that an opsin from Curtobacterium, in the Actinobacteria phylum, inhibits bacterioruberin synthesis catalyzed by its own lycopene elongase, as well as that catalyzed by several archaeal enzymes. We also determined that the lycopene elongase from Halococcus salifodinae, a species from a family of Halobacteria lacking opsin homologs, retained the capacity to be inhibited by opsins. Together, our results indicate that opsin-mediated inhibition of bacterioruberin biosynthesis is a widely distributed mechanism found in both Archaea and Bacteria, possibly predating the divergence of the two domains. Further analysis may provide insight into the acquisition and evolution of the genes and their host species.IMPORTANCE All organisms use a variety of mechanisms to allocate limited resources to match their needs in their current environment. Here, we explore how halophilic microbes use a novel mechanism to allow efficient production of rhodopsin, a complex of an opsin protein and a retinal prosthetic group. We previously demonstrated that Halobacterium salinarum bacterioopsin directs available resources toward retinal by inhibiting synthesis of bacterioruberin, a molecule that shares precursors with retinal. In this work, we show that this mechanism can be carried out by proteins from halophilic Archaea that are not closely related to H. salinarum and those in at least one species of Bacteria Therefore, opsin-mediated inhibition of bacterioruberin synthesis may be a highly conserved, ancient regulatory mechanism.},
}
@article {pmid30370585,
year = {2019},
author = {Seth-Pasricha, M and Senn, S and Sanman, LE and Bogyo, M and Nanda, V and Bidle, KA and Bidle, KD},
title = {Catalytic linkage between caspase activity and proteostasis in Archaea.},
journal = {Environmental microbiology},
volume = {21},
number = {1},
pages = {286-298},
doi = {10.1111/1462-2920.14456},
pmid = {30370585},
issn = {1462-2920},
support = {3789//Gordon and Betty Moore Foundation/International ; },
mesh = {Adenosine Triphosphatases/metabolism ; Amino Acid Chloromethyl Ketones/pharmacology ; Caspase Inhibitors/pharmacology ; Caspases/*metabolism ; Enzyme Activation/drug effects ; Haloferax volcanii/drug effects/*enzymology/genetics ; Proteasome Endopeptidase Complex/metabolism ; Proteolysis ; Proteomics ; Proteostasis/drug effects/*physiology ; },
abstract = {The model haloarchaeon, Haloferax volcanii possess an extremely high, and highly specific, basal caspase activity in exponentially growing cells that closely resembles caspase-4. This activity is specifically inhibited by the pan-caspase inhibitor, z-VAD-FMK, and has no cross-reactivity with other known protease families. Although it is one of the dominant cellular proteolytic activities in exponentially growing H. volcanii cells, the interactive cellular roles remain unknown and the protein(s) responsible for this activity remain elusive. Here, biochemical purification and in situ trapping with caspase targeted covalent inhibitors combined with genome-enabled proteomics, structural analysis, targeted gene knockouts and treatment with canavanine demonstrated a catalytic linkage between caspase activity and thermosomes, proteasomes and cdc48b, a cell division protein and proteasomal degradation facilitating ATPase, as part of an 'interactase' of stress-related protein complexes with an established link to the unfolded protein response (UPR). Our findings provide novel cellular and biochemical context for the observed caspase activity in Archaea and add new insight to understanding the role of this activity, implicating their possible role in the establishment of protein stress and ER associated degradation pathways in Eukarya.},
}
@article {pmid30357005,
year = {2018},
author = {Harish, A},
title = {What is an archaeon and are the Archaea really unique?.},
journal = {PeerJ},
volume = {6},
number = {},
pages = {e5770},
pmid = {30357005},
issn = {2167-8359},
abstract = {The recognition of the group Archaea as a major branch of the tree of life (ToL) prompted a new view of the evolution of biodiversity. The genomic representation of archaeal biodiversity has since significantly increased. In addition, advances in phylogenetic modeling of multi-locus datasets have resolved many recalcitrant branches of the ToL. Despite the technical advances and an expanded taxonomic representation, two important aspects of the origins and evolution of the Archaea remain controversial, even as we celebrate the 40th anniversary of the monumental discovery. These issues concern (i) the uniqueness (monophyly) of the Archaea, and (ii) the evolutionary relationships of the Archaea to the Bacteria and the Eukarya; both of these are relevant to the deep structure of the ToL. To explore the causes for this persistent ambiguity, I examine multiple datasets and different phylogenetic approaches that support contradicting conclusions. I find that the uncertainty is primarily due to a scarcity of information in standard datasets-universal core-genes datasets-to reliably resolve the conflicts. These conflicts can be resolved efficiently by comparing patterns of variation in the distribution of functional genomic signatures, which are less diffused unlike patterns of primary sequence variation. Relatively lower heterogeneity in distribution patterns minimizes uncertainties and supports statistically robust phylogenetic inferences, especially of the earliest divergences of life. This case study further highlights the limitations of primary sequence data in resolving difficult phylogenetic problems, and raises questions about evolutionary inferences drawn from the analyses of sequence alignments of a small set of core genes. In particular, the findings of this study corroborate the growing consensus that reversible substitution mutations may not be optimal phylogenetic markers for resolving early divergences in the ToL, nor for determining the polarity of evolutionary transitions across the ToL.},
}
@article {pmid30343425,
year = {2018},
author = {Pornkulwat, P and Kurisu, F and Soonglerdsongpha, S and Banjongproo, P and Srithep, P and Limpiyakorn, T},
title = {Incorporation of [13]C-HCO3[-] by ammonia-oxidizing archaea and bacteria during ammonia oxidation of sludge from a municipal wastewater treatment plant.},
journal = {Applied microbiology and biotechnology},
volume = {102},
number = {24},
pages = {10767-10777},
doi = {10.1007/s00253-018-9436-0},
pmid = {30343425},
issn = {1432-0614},
support = {RSA5780036//Thailand Research Fund (TH)/ ; PHD/0103/2558//Thailand Research Fund/ ; },
mesh = {Ammonia/*metabolism ; Archaea/genetics/*metabolism ; Bacteria/genetics/*metabolism ; Bicarbonates/metabolism ; Carbon Isotopes/*metabolism ; DNA Primers ; Oxidation-Reduction ; Phylogeny ; Polymerase Chain Reaction ; Sewage ; Thailand ; Waste Disposal, Fluid/*methods ; },
abstract = {Ammonia-oxidizing archaea (AOA) have recently been proposed as potential players for ammonia removal in wastewater treatment plants (WWTPs). However, there is little evidence directly showing the contribution of AOA to ammonia oxidation in these engineered systems. In this study, DNA-stable isotope probing (DNA-SIP) with labeled [13]C-HCO3[-] was introduced to sludge from a municipal WWTP. Quantitative PCR demonstrated that AOA amoA genes outnumbered AOB amoA genes in this WWTP sludge. AOA amoA gene sequence analysis revealed that AOA present in this WWTP were specific to one subcluster within the group 1.1b Thaumarchaeota. When ammonia was supplied to DNA-SIP incubation, the DNA-SIP profiles demonstrated the incorporation of the [13]C into AOA and AOB. However, the [13]C was not found to be assimilated into both microorganisms in the incubation without ammonia. Specific primers were designed to target amoA genes of AOA belonging to the subcluster found in this WWTP. Applying the primers to DNA-SIP experiment revealed that AOA of this subcluter most likely utilized inorganic carbon during ammonia oxidation under the studied conditions.},
}
@article {pmid30342933,
year = {2018},
author = {Lemor, M and Kong, Z and Henry, E and Brizard, R and Laurent, S and Bossé, A and Henneke, G},
title = {Differential Activities of DNA Polymerases in Processing Ribonucleotides during DNA Synthesis in Archaea.},
journal = {Journal of molecular biology},
volume = {430},
number = {24},
pages = {4908-4924},
doi = {10.1016/j.jmb.2018.10.004},
pmid = {30342933},
issn = {1089-8638},
mesh = {Archaeal Proteins/metabolism ; DNA Replication ; DNA, Archaeal/*metabolism ; DNA-Directed DNA Polymerase/*metabolism ; Deoxyribonucleotides/metabolism ; Genomic Instability ; Ribonucleotides/*metabolism ; Thermococcales/enzymology/*genetics ; },
abstract = {Consistent with the fact that ribonucleotides (rNTPs) are in excess over deoxyribonucleotides (dNTPs) in vivo, recent findings indicate that replicative DNA polymerases (DNA Pols) are able to insert ribonucleotides (rNMPs) during DNA synthesis, raising crucial questions about the fidelity of DNA replication in both Bacteria and Eukarya. Here, we report that the level of rNTPs is 20-fold higher than that of dNTPs in Pyrococcus abyssi cells. Using dNTP and rNTP concentrations present in vivo, we recorded rNMP incorporation in a template-specific manner during in vitro synthesis, with the family-D DNA Pol (PolD) having the highest propensity compared with the family-B DNA Pol and the p41/p46 complex. We also showed that ribonucleotides accumulate at a relatively high frequency in the genome of wild-type Thermococcales cells, and this frequency significantly increases upon deletion of RNase HII, the major enzyme responsible for the removal of RNA from DNA. Because ribonucleotides remain in genomic DNA, we then analyzed the effects on polymerization activities by the three DNA Pols. Depending on the identity of the base and the sequence context, all three DNA Pols bypass rNMP-containing DNA templates with variable efficiency and nucleotide (mis)incorporation ability. Unexpectedly, we found that PolD correctly base-paired a single ribonucleotide opposite rNMP-containing DNA templates. An evolutionary scenario is discussed concerning rNMP incorporation into DNA and genome stability.},
}
@article {pmid30327333,
year = {2019},
author = {Huang, L and Ashraf, S and Lilley, DMJ},
title = {The role of RNA structure in translational regulation by L7Ae protein in archaea.},
journal = {RNA (New York, N.Y.)},
volume = {25},
number = {1},
pages = {60-69},
pmid = {30327333},
issn = {1469-9001},
support = {11722/CRUK_/Cancer Research UK/United Kingdom ; 18604/CRUK_/Cancer Research UK/United Kingdom ; B17092/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/E001777/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {5' Untranslated Regions ; Archaeal Proteins/*chemistry/genetics/*metabolism ; Archaeoglobus fulgidus/genetics/metabolism ; Base Sequence ; Binding Sites/genetics ; Crystallography, X-Ray ; Models, Molecular ; Nucleic Acid Conformation ; Protein Binding ; Protein Biosynthesis ; Protein Conformation ; RNA Stability ; RNA, Archaeal/*chemistry/genetics/*metabolism ; RNA, Messenger/chemistry/genetics/metabolism ; Ribosomal Proteins/*chemistry/genetics/*metabolism ; },
abstract = {A recent study has shown that archaeal L7Ae binds to a putative k-turn structure in the 5'-leader of the mRNA of its structural gene to regulate translation. To function as a regulator, the RNA should be unstructured in the absence of protein, but it should adopt a k-turn-containing stem-loop on binding L7Ae. Sequence analysis of UTR sequences indicates that their k-turn elements will be unable to fold in the absence of L7Ae, and we have demonstrated this experimentally in solution using FRET for the Archaeoglobus fulgidus sequence. We have solved the X-ray crystal structure of the complex of the A. fulgidus RNA bound to its cognate L7Ae protein. The RNA adopts a standard k-turn conformation that is specifically recognized by the L7Ae protein, so stabilizing the stem-loop. In-line probing of the natural-sequence UTR shows that the RNA is unstructured in the absence of L7Ae binding, but folds on binding the protein such that the ribosome binding site is occluded. Thus, L7Ae regulates its own translation by switching the conformation of the RNA to alter accessibility.},
}
@article {pmid30323263,
year = {2019},
author = {Rinke, C and Rubino, F and Messer, LF and Youssef, N and Parks, DH and Chuvochina, M and Brown, M and Jeffries, T and Tyson, GW and Seymour, JR and Hugenholtz, P},
title = {A phylogenomic and ecological analysis of the globally abundant Marine Group II archaea (Ca. Poseidoniales ord. nov.).},
journal = {The ISME journal},
volume = {13},
number = {3},
pages = {663-675},
pmid = {30323263},
issn = {1751-7370},
mesh = {Adaptation, Physiological ; Archaea/*genetics/isolation &amp; purification ; Biological Evolution ; Ecology ; *Gene Transfer, Horizontal ; Genome, Archaeal/*genetics ; *Metagenome ; Oceans and Seas ; Phylogeny ; Plankton/*genetics/isolation &amp; purification ; Rhodopsins, Microbial/*genetics ; Seawater ; },
abstract = {Marine Group II (MGII) archaea represent the most abundant planktonic archaeal group in ocean surface waters, but our understanding of the group has been limited by a lack of cultured representatives and few sequenced genomes. Here, we conducted a comparative phylogenomic analysis of 270 recently available MGII metagenome-assembled genomes (MAGs) to investigate their evolution and ecology. Based on a rank-normalised genome phylogeny, we propose that MGII is an order-level lineage for which we propose the name Candidatus Poseidoniales (after Gr. n. Poseidon, God of the sea), comprising the families Candidatus Poseidonaceae fam. nov. (formerly subgroup MGIIa) and Candidatus Thalassarchaeaceae fam. nov. (formerly subgroup MGIIb). Within these families, 21 genera could be resolved, many of which had distinct biogeographic ranges and inferred nutrient preferences. Phylogenetic analyses of key metabolic functions suggest that the ancestor of Ca. Poseidoniales was a surface water-dwelling photoheterotroph that evolved to occupy multiple related ecological niches based primarily on spectral tuning of proteorhodopsin genes. Interestingly, this adaptation appears to involve an overwrite mechanism whereby an existing single copy of the proteorhodopsin gene is replaced by a horizontally transferred copy, which in many instances should allow an abrupt change in light absorption capacity. Phototrophy was lost entirely from five Ca. Poseidoniales genera coinciding with their adaptation to deeper aphotic waters. We also report the first instances of nitrate reductase in two genera acquired via horizontal gene transfer (HGT), which was a potential adaptation to oxygen limitation. Additional metabolic traits differentiating families and genera include flagellar-based adhesion, transporters, and sugar, amino acid, and peptide degradation. Our results suggest that HGT has shaped the evolution of Ca. Poseidoniales to occupy a variety of ecological niches and to become the most successful archaeal lineage in ocean surface waters.},
}
@article {pmid30302054,
year = {2018},
author = {Yin, Z and Bi, X and Xu, C},
title = {Ammonia-Oxidizing Archaea (AOA) Play with Ammonia-Oxidizing Bacteria (AOB) in Nitrogen Removal from Wastewater.},
journal = {Archaea (Vancouver, B.C.)},
volume = {2018},
number = {},
pages = {8429145},
pmid = {30302054},
issn = {1472-3654},
mesh = {Ammonia/*metabolism ; Archaea/growth &amp; development/*metabolism ; Bacteria/growth &amp; development/*metabolism ; *Microbial Interactions ; Nitrogen/*metabolism ; Oxidation-Reduction ; Wastewater/*microbiology ; Water Purification/methods ; },
abstract = {An increase in the number of publications in recent years indicates that besides ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA) may play an important role in nitrogen removal from wastewater, gaining wide attention in the wastewater engineering field. This paper reviews the current knowledge on AOA and AOB involved in wastewater treatment systems and summarises the environmental factors affecting AOA and AOB. Current findings reveal that AOA have stronger environmental adaptability compared with AOB under extreme environmental conditions (such as low temperature and low oxygen level). However, there is still little information on the cooperation and competition relationship between AOA and AOB, and other microbes related to nitrogen removal, which needs further exploration. Furthermore, future studies are proposed to develop novel nitrogen removal processes dominated by AOA by parameter optimization.},
}
@article {pmid30294305,
year = {2018},
author = {Genderjahn, S and Alawi, M and Mangelsdorf, K and Horn, F and Wagner, D},
title = {Desiccation- and Saline-Tolerant Bacteria and Archaea in Kalahari Pan Sediments.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2082},
pmid = {30294305},
issn = {1664-302X},
abstract = {More than 41% of the Earth's land area is covered by permanent or seasonally arid dryland ecosystems. Global development and human activity have led to an increase in aridity, resulting in ecosystem degradation and desertification around the world. The objective of the present work was to investigate and compare the microbial community structure and geochemical characteristics of two geographically distinct saline pan sediments in the Kalahari Desert of southern Africa. Our data suggest that these microbial communities have been shaped by geochemical drivers, including water content, salinity, and the supply of organic matter. Using Illumina 16S rRNA gene sequencing, this study provides new insights into the diversity of bacteria and archaea in semi-arid, saline, and low-carbon environments. Many of the observed taxa are halophilic and adapted to water-limiting conditions. The analysis reveals a high relative abundance of halophilic archaea (primarily Halobacteria), and the bacterial diversity is marked by an abundance of Gemmatimonadetes and spore-forming Firmicutes. In the deeper, anoxic layers, candidate division MSBL1, and acetogenic bacteria (Acetothermia) are abundant. Together, the taxonomic information and geochemical data suggest that acetogenesis could be a prevalent form of metabolism in the deep layers of a saline pan.},
}
@article {pmid30291304,
year = {2018},
author = {Du Toit, A},
title = {Profilin(g) Asgard archaea.},
journal = {Nature reviews. Microbiology},
volume = {16},
number = {12},
pages = {717},
doi = {10.1038/s41579-018-0100-6},
pmid = {30291304},
issn = {1740-1534},
}
@article {pmid30283132,
year = {2018},
author = {Akıl, C and Robinson, RC},
title = {Genomes of Asgard archaea encode profilins that regulate actin.},
journal = {Nature},
volume = {562},
number = {7727},
pages = {439-443},
doi = {10.1038/s41586-018-0548-6},
pmid = {30283132},
issn = {1476-4687},
mesh = {Actin Cytoskeleton/metabolism ; Actins/chemistry/*metabolism ; Amino Acid Motifs ; Animals ; Archaea/cytology/*genetics/*metabolism ; Cell Movement ; Endocytosis ; Eukaryotic Cells/cytology/metabolism ; *Evolution, Molecular ; Genome, Archaeal/*genetics ; Humans ; Models, Molecular ; Peptides/chemistry/metabolism ; Phospholipids/metabolism/pharmacology ; Phylogeny ; Polymerization ; Profilins/chemistry/*genetics/*metabolism ; Protein Binding/drug effects ; Rabbits ; },
abstract = {The origin of the eukaryotic cell is unresolved[1,2]. Metagenomics sequencing has recently identified several potential eukaryotic gene homologues in Asgard archaea[3,4], consistent with the hypothesis that the eukaryotic cell evolved from within the Archaea domain. However, many of these eukaryotic-like sequences are highly divergent and the organisms have yet to be imaged or cultivated, which brings into question the extent to which these archaeal proteins represent functional equivalents of their eukaryotic counterparts. Here we show that Asgard archaea encode functional profilins and thereby establish that this archaeal superphylum has a regulated actin cytoskeleton, one of the hallmarks of the eukaryotic cell[5]. Loki profilin-1, Loki profilin-2 and Odin profilin adopt the typical profilin fold and are able to interact with rabbit actin-an interaction that involves proteins from species that diverged more than 1.2 billion years ago[6]. Biochemical experiments reveal that mammalian actin polymerizes in the presence of Asgard profilins; however, Loki, Odin and Heimdall profilins impede pointed-end elongation. These archaeal profilins also retard the spontaneous nucleation of actin filaments, an effect that is reduced in the presence of phospholipids. Asgard profilins do not interact with polyproline motifs and the profilin-polyproline interaction therefore probably evolved later in the Eukarya lineage. These results suggest that Asgard archaea possess a primordial, polar, profilin-regulated actin system, which may be localized to membranes owing to the sensitivity of Asgard profilins to phospholipids. Because Asgard archaea are also predicted to encode potential eukaryotic-like genes involved in membrane-trafficking and endocytosis[3,4], imaging is now necessary to elucidate whether these organisms are capable of generating eukaryotic-like membrane dynamics that are regulated by actin, such as are observed in eukaryotic cell movement, podosomes and endocytosis.},
}
@article {pmid30283097,
year = {2018},
author = {Ramezani, A and Nolin, TD and Barrows, IR and Serrano, MG and Buck, GA and Regunathan-Shenk, R and West, RE and Latham, PS and Amdur, R and Raj, DS},
title = {Gut Colonization with Methanogenic Archaea Lowers Plasma Trimethylamine N-oxide Concentrations in Apolipoprotein e-/- Mice.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {14752},
pmid = {30283097},
issn = {2045-2322},
support = {U01 DK099914/DK/NIDDK NIH HHS/United States ; U01 DK099924/DK/NIDDK NIH HHS/United States ; UL1 TR001876/TR/NCATS NIH HHS/United States ; },
mesh = {Administration, Oral ; Animals ; Aorta/metabolism/microbiology/pathology ; Apolipoproteins E/deficiency/*drug effects/genetics ; Atherosclerosis/microbiology/*prevention &amp; control ; Choline/administration &amp; dosage/metabolism ; Dietary Supplements ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*physiology ; Methane/metabolism ; Methanobrevibacter/growth &amp; development/*metabolism ; Methanosarcina/growth &amp; development/*metabolism ; Methylamines/administration &amp; dosage/*blood/metabolism ; Mice ; Mice, Inbred C57BL ; Mice, Knockout ; Microbial Consortia/physiology ; Plaque, Atherosclerotic/microbiology/*prevention &amp; control ; },
abstract = {A mechanistic link between trimethylamine N-oxide (TMAO) and atherogenesis has been reported. TMAO is generated enzymatically in the liver by the oxidation of trimethylamine (TMA), which is produced from dietary choline, carnitine and betaine by gut bacteria. It is known that certain members of methanogenic archaea (MA) could use methylated amines such as trimethylamine as growth substrates in culture. Therefore, we investigated the efficacy of gut colonization with MA on lowering plasma TMAO concentrations. Initially, we screened for the colonization potential and TMAO lowering efficacy of five MA species in C57BL/6 mice fed with high choline/TMA supplemented diet, and found out that all five species could colonize and lover plasma TMAO levels, although with different efficacies. The top performing MA, Methanobrevibacter smithii, Methanosarcina mazei, and Methanomicrococcus blatticola, were transplanted into Apoe[-/-] mice fed with high choline/TMA supplemented diet. Similar to C57BL/6 mice, following initial provision of the MA, there was progressive attrition of MA within fecal microbial communities post-transplantation during the initial 3 weeks of the study. In general, plasma TMAO concentrations decreased significantly in proportion to the level of MA colonization. In a subsequent experiment, use of antibiotics and repeated transplantation of Apoe[-/-] mice with M. smithii, led to high engraftment levels during the 9 weeks of the study, resulting in a sustained and significantly lower average plasma TMAO concentrations (18.2 ± 19.6 μM) compared to that in mock-transplanted control mice (120.8 ± 13.0 μM, p < 0.001). Compared to control Apoe[-/-] mice, M. smithii-colonized mice also had a 44% decrease in aortic plaque area (8,570 μm [95% CI 19587-151821] vs. 15,369 μm [95% CI [70058-237321], p = 0.34), and 52% reduction in the fat content in the atherosclerotic plaques (14,283 μm [95% CI 4,957-23,608] vs. 29,870 μm [95% CI 18,074-41,666], p = 0.10), although these differences did not reach significance. Gut colonization with M. smithii leads to a significant reduction in plasma TMAO levels, with a tendency for attenuation of atherosclerosis burden in Apoe[-/-] mice. The anti-atherogenic potential of MA should be further tested in adequately powered experiments.},
}
@article {pmid30278423,
year = {2019},
author = {Duan, P and Fan, C and Zhang, Q and Xiong, Z},
title = {Overdose fertilization induced ammonia-oxidizing archaea producing nitrous oxide in intensive vegetable fields.},
journal = {The Science of the total environment},
volume = {650},
number = {Pt 2},
pages = {1787-1794},
doi = {10.1016/j.scitotenv.2018.09.341},
pmid = {30278423},
issn = {1879-1026},
mesh = {Ammonia/*metabolism ; Archaea/*metabolism ; China ; Dose-Response Relationship, Drug ; *Fertilizers ; Nitrogen/*administration &amp; dosage ; Nitrous Oxide/*metabolism ; Oxidation-Reduction ; Seasons ; *Soil Microbiology ; Vegetables/growth &amp; development ; },
abstract = {Little is known about the effects of nitrogen (N) fertilization rates on ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) and their differential contribution to nitrous oxide (N2O) production, particularly in greenhouse based high N input vegetable soils. Six N treatments (N1, N2, N3, N4, N5 and N6 representing 0, 293, 587, 880, 1173 and 1760 kg N ha[-1] yr[-1], respectively) were continuously managed for three years in a typically intensified vegetable field in China. The aerobic incubation experiment involving these field-treated soils was designed to evaluate the relative contributions of AOA and AOB to N2O production by using acetylene or 1-octyne as inhibitors. The results showed that the soil pH and net nitrification rate gradually declined with increasing the fertilizer N application rates. The AOA were responsible for 44-71% of the N2O production with negligible N2O from AOB in urea unamended control soils. With urea amendment, the AOA were responsible for 48-53% of the N2O production in the excessively fertilized soils, namely the N5-N6 soils, while the AOB were responsible for 42-55% in the conventionally fertilized soils, namely the N1-N4 soils. Results indicated that overdose fertilization induced higher AOA-dependent N2O production than AOB, whereas urea supply led to higher AOB-dependent N2O production than AOA in conventionally fertilized soils. Additionally, a positive relationship existed between N2O production and NO2[-] accumulation during the incubation. Further mechanisms for NO2[-]-dependent N2O production in intensive vegetable soils therefore deserve urgent attention.},
}
@article {pmid30258074,
year = {2018},
author = {Cheung, MK and Wong, CK and Chu, KH and Kwan, HS},
title = {Community Structure, Dynamics and Interactions of Bacteria, Archaea and Fungi in Subtropical Coastal Wetland Sediments.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {14397},
pmid = {30258074},
issn = {2045-2322},
mesh = {Archaea/*growth &amp; development ; Ascomycota/*growth &amp; development ; Bacteria/*growth &amp; development ; Microbial Consortia/*physiology ; *Models, Biological ; *Tropical Climate ; *Wetlands ; },
abstract = {Bacteria, archaea and fungi play crucial roles in wetland biogeochemical processes. However, little is known about their community structure, dynamics and interactions in subtropical coastal wetlands. Here, we examined communities of the three kingdoms in mangrove and mudflat sediments of a subtropical coastal wetland using Ion Torrent amplicon sequencing and co-occurrence network analysis. Bacterial, archaeal and fungal communities comprised mainly of members from the phyla Proteobacteria and Bacteroidetes, Bathyarchaeota and Euryarchaeota, and Ascomycota, respectively. Species richness and Shannon diversity were highest in bacteria, followed by archaea and were lowest in fungi. Distinct spatiotemporal patterns were observed, with bacterial and fungal communities varying, to different extent, between wet and dry seasons and between mangrove and mudflat, and archaeal community remaining relatively stable between seasons and regions. Redundancy analysis revealed temperature as the major driver of the seasonal patterns of bacterial and fungal communities but also highlighted the importance of interkingdom biotic factors in shaping the community structure of all three kingdoms. Potential ecological interactions and putative keystone taxa were identified based on co-occurrence network analysis. These findings facilitate current understanding of the microbial ecology of subtropical coastal wetlands and provide a basis for better modelling of ecological processes in this important ecosystem.},
}
@article {pmid30254509,
year = {2018},
author = {Krzmarzick, MJ and Taylor, DK and Fu, X and McCutchan, AL},
title = {Diversity and Niche of Archaea in Bioremediation.},
journal = {Archaea (Vancouver, B.C.)},
volume = {2018},
number = {},
pages = {3194108},
pmid = {30254509},
issn = {1472-3654},
mesh = {Archaea/*growth &amp; development/*metabolism ; *Biodegradation, Environmental ; Environmental Pollutants/*metabolism ; Hydrocarbons/metabolism ; },
abstract = {Bioremediation is the use of microorganisms for the degradation or removal of contaminants. Most bioremediation research has focused on processes performed by the domain Bacteria; however, Archaea are known to play important roles in many situations. In extreme conditions, such as halophilic or acidophilic environments, Archaea are well suited for bioremediation. In other conditions, Archaea collaboratively work alongside Bacteria during biodegradation. In this review, the various roles that Archaea have in bioremediation is covered, including halophilic hydrocarbon degradation, acidophilic hydrocarbon degradation, hydrocarbon degradation in nonextreme environments such as soils and oceans, metal remediation, acid mine drainage, and dehalogenation. Research needs are addressed in these areas. Beyond bioremediation, these processes are important for wastewater treatment (particularly industrial wastewater treatment) and help in the understanding of the natural microbial ecology of several Archaea genera.},
}
@article {pmid30254323,
year = {2019},
author = {Lambert, S and Tragin, M and Lozano, JC and Ghiglione, JF and Vaulot, D and Bouget, FY and Galand, PE},
title = {Rhythmicity of coastal marine picoeukaryotes, bacteria and archaea despite irregular environmental perturbations.},
journal = {The ISME journal},
volume = {13},
number = {2},
pages = {388-401},
pmid = {30254323},
issn = {1751-7370},
mesh = {Archaea/classification/*genetics/physiology ; Bacteria/*classification/genetics ; Ecosystem ; Eukaryota/classification/*genetics ; Mediterranean Sea ; Phytoplankton/growth &amp; development ; Seasons ; Seawater/*microbiology ; },
abstract = {Seasonality in marine microorganisms has been classically observed in phytoplankton blooms, and more recently studied at the community level in prokaryotes, but rarely investigated at the scale of individual microbial taxa. Here we test if specific marine eukaryotic phytoplankton, bacterial and archaeal taxa display yearly rhythms at a coastal site impacted by irregular environmental perturbations. Our seven-year study in the Bay of Banyuls (North Western Mediterranean Sea) shows that despite some fluctuating environmental conditions, many microbial taxa displayed significant yearly rhythms. The robust rhythmicity was found in both autotrophs (picoeukaryotes and cyanobacteria) and heterotrophic prokaryotes. Sporadic meteorological events and irregular nutrient supplies did, however, trigger the appearance of less common non-rhythmic taxa. Among the environmental parameters that were measured, the main drivers of rhythmicity were temperature and day length. Seasonal autotrophs may thus be setting the pace for rhythmic heterotrophs. Similar environmental niches may be driving seasonality as well. The observed strong association between Micromonas and SAR11, which both need thiamine precursors for growth, could be a first indication that shared nutritional niches may explain some rhythmic patterns of co-occurrence.},
}
@article {pmid30254075,
year = {2018},
author = {Michael, AJ},
title = {Polyamine function in archaea and bacteria.},
journal = {The Journal of biological chemistry},
volume = {293},
number = {48},
pages = {18693-18701},
pmid = {30254075},
issn = {1083-351X},
mesh = {Archaea/chemistry/genetics/growth &amp; development/*metabolism ; Archaeal Proteins/genetics/metabolism ; Bacteria/chemistry/genetics/growth &amp; development/*metabolism ; Bacterial Proteins/genetics/metabolism ; Polyamines/chemistry/*metabolism ; },
abstract = {Most of the phylogenetic diversity of life is found in bacteria and archaea, and is reflected in the diverse metabolism and functions of bacterial and archaeal polyamines. The polyamine spermidine was probably present in the last universal common ancestor, and polyamines are known to be necessary for critical physiological functions in bacteria, such as growth, biofilm formation, and other surface behaviors, and production of natural products, such as siderophores. There is also phylogenetic diversity of function, indicated by the role of polyamines in planktonic growth of different species, ranging from absolutely essential to entirely dispensable. However, the cellular molecular mechanisms responsible for polyamine function in bacterial growth are almost entirely unknown. In contrast, the molecular mechanisms of essential polyamine functions in archaea are better understood: covalent modification by polyamines of translation factor aIF5A and the agmatine modification of tRNA[Ile] As with bacterial hyperthermophiles, archaeal thermophiles require long-chain and branched polyamines for growth at high temperatures. For bacterial species in which polyamines are essential for growth, it is still unknown whether the molecular mechanisms underpinning polyamine function involve covalent or noncovalent interactions. Understanding the cellular molecular mechanisms of polyamine function in bacterial growth and physiology remains one of the great challenges for future polyamine research.},
}
@article {pmid30250155,
year = {2018},
author = {Wolfe, JM and Fournier, GP},
title = {Reply to 'Molecular clocks provide little information to date methanogenic Archaea'.},
journal = {Nature ecology &amp; evolution},
volume = {2},
number = {11},
pages = {1678},
pmid = {30250155},
issn = {2397-334X},
mesh = {*Archaea ; *Soil Microbiology ; },
}
@article {pmid30250154,
year = {2018},
author = {Roger, AJ and Susko, E},
title = {Molecular clocks provide little information to date methanogenic Archaea.},
journal = {Nature ecology &amp; evolution},
volume = {2},
number = {11},
pages = {1676-1677},
pmid = {30250154},
issn = {2397-334X},
mesh = {Archaea/*genetics ; *Gene Transfer, Horizontal ; Phylogeny ; Soil Microbiology ; },
}
@article {pmid30245679,
year = {2018},
author = {Zaretsky, M and Roine, E and Eichler, J},
title = {Sialic Acid-Like Sugars in Archaea: Legionaminic Acid Biosynthesis in the Halophile Halorubrum sp. PV6.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2133},
pmid = {30245679},
issn = {1664-302X},
abstract = {N-glycosylation is a post-translational modification that occurs in all three domains. In Archaea, however, N-linked glycans present a degree of compositional diversity not observed in either Eukarya or Bacteria. As such, it is surprising that nonulosonic acids (NulOs), nine-carbon sugars that include sialic acids, pseudaminic acids, and legionaminic acids, are routinely detected as components of protein-linked glycans in Eukarya and Bacteria but not in Archaea. In the following, we report that the N-linked glycan attached to the S-layer glycoprotein of the haloarchaea Halorubrum sp. PV6 includes an N-formylated legionaminic acid. Analysis of the Halorubrum sp. PV6 genome led to the identification of sequences predicted to comprise the legionaminic acid biosynthesis pathway. The transcription of pathway genes was confirmed, as was the co-transcription of several of these genes. In addition, the activities of LegI, which catalyzes the condensation of 2,4-di-N-acetyl-6-deoxymannose and phosphoenolpyruvate to generate legionaminic acid, and LegF, which catalyzes the addition of cytidine monophosphate (CMP) to legionaminic acid, both heterologously expressed in Haloferax volcanii, were demonstrated. Further genome analysis predicts that the genes encoding enzymes of the legionaminic acid biosynthetic pathway are clustered together with sequences seemingly encoding components of the N-glycosylation pathway in this organism. In defining the first example of a legionaminic acid biosynthesis pathway in Archaea, the findings reported here expand our insight into archaeal N-glycosylation, an almost universal post-translational modification in this domain of life.},
}
@article {pmid30241308,
year = {2018},
author = {Maupin-Furlow, JA},
title = {Methionine Sulfoxide Reductases of Archaea.},
journal = {Antioxidants (Basel, Switzerland)},
volume = {7},
number = {10},
pages = {},
pmid = {30241308},
issn = {2076-3921},
support = {R01 GM057498/GM/NIGMS NIH HHS/United States ; NIH R01 GM57498/NH/NIH HHS/United States ; NSF 1642283//JM-F through the Bilateral NSF/BIO-BBSRC program/ ; DOE DE-FG02-05ER15650//the U.S. Department of Energy, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences and Biosciences, Physical Biosciences Program/ ; },
abstract = {Methionine sulfoxide reductases are found in all domains of life and are important in reversing the oxidative damage of the free and protein forms of methionine, a sulfur containing amino acid particularly sensitive to reactive oxygen species (ROS). Archaea are microbes of a domain of life distinct from bacteria and eukaryotes. Archaea are well known for their ability to withstand harsh environmental conditions that range from habitats of high ROS, such as hypersaline lakes of intense ultraviolet (UV) radiation and desiccation, to hydrothermal vents of low concentrations of dissolved oxygen at high temperature. Recent evidence reveals the methionine sulfoxide reductases of archaea function not only in the reduction of methionine sulfoxide but also in the ubiquitin-like modification of protein targets during oxidative stress, an association that appears evolutionarily conserved in eukaryotes. Here is reviewed methionine sulfoxide reductases and their distribution and function in archaea.},
}
@article {pmid30233557,
year = {2018},
author = {Eger, M and Graz, M and Riede, S and Breves, G},
title = {Application of Mootral[TM] Reduces Methane Production by Altering the Archaea Community in the Rumen Simulation Technique.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2094},
pmid = {30233557},
issn = {1664-302X},
abstract = {The reduction of methane emissions by ruminants is a highly desirable goal to mitigate greenhouse gas emissions. Various feed additives have already been tested for their ability to decrease methane production; however, practical use is often limited due to negative effects on rumen fermentation or high costs. Organosulphur compounds from garlic (Allium sativum) and flavonoids have been identified as promising plant-derived compounds which are able to reduce methane production. Here, we evaluated the effects of a combination of garlic powder and bitter orange (Citrus aurantium) extracts, Mootral, on ruminal methane production, ruminal fermentation and the community of methanogenic Archaea by using the rumen simulation technique as ex vivo model. The experiment consisted of an equilibration period of 7 days, an experimental period of 8 days and a withdrawal period of 4 days. During the experimental period three fermenters each were either treated as controls (CON), received a low dose of Mootral (LD), a high dose of Mootral (HD), or monensin (MON) as positive control. Application of Mootral strongly reduced the proportion of methane in the fermentation gas and the production rate of methane. Moreover, the experimental mixture induced a dose-dependent increase in the production rate of short chain fatty acids and in the molar proportion of butyrate. Some effects persisted during the withdrawal period. Both, single strand conformation polymorphism and Illumina MiSeq 16S rRNA amplicon sequencing indicated an archaeal community distinct from CON and MON samples in the LD and HD samples. Among archaeal families the percentage of Methanobacteriaceae was reduced during application of both doses of Mootral. Moreover, several significant differences were observed on OTU level among treatment groups and after withdrawal of the additives for LD and HD group. At day 14, 4 OTUs were positively correlated with methane production. In conclusion this mixture of garlic and citrus compounds appears to effectively reduce methane production by alteration of the archaeal community without exhibiting negative side effects on rumen fermentation.},
}
@article {pmid30223159,
year = {2018},
author = {Ren, L and Cai, C and Zhang, J and Yang, Y and Wu, G and Luo, L and Huang, H and Zhou, Y and Qin, P and Yu, M},
title = {Key environmental factors to variation of ammonia-oxidizing archaea community and potential ammonia oxidation rate during agricultural waste composting.},
journal = {Bioresource technology},
volume = {270},
number = {},
pages = {278-285},
doi = {10.1016/j.biortech.2018.09.042},
pmid = {30223159},
issn = {1873-2976},
mesh = {Agriculture ; Ammonia/*metabolism ; Archaea/genetics/*metabolism ; *Composting ; Oxidation-Reduction ; Phylogeny ; Soil ; Soil Microbiology ; },
abstract = {In this research, the abundance and structure of AOA amoA gene during agricultural waste composting were determined by quantitative PCR and sequencing techniques, respectively. Pairwise correlations between potential ammonia oxidation (PAO) rate, physicochemical parameters and the AOA abundance were evaluated using Pearson correlation coefficient. Relationships between these parameters, PAO rates and AOA community structure were evaluated by redundancy analysis. Results showed that 22 AOA gene OTUs were divided into the soil/sediment lineage by phylogenetic analyses. Significant positive correlations were obtained between AOA amoA gene abundance and moisture, ammonium, water soluble carbon (WSC) and organic matter (OM), respectively. Redundancy analysis showed OM, pH and nitrate significantly explained the AOA amoA gene structure. Pearson correlation revealed the PAO rate correlated positively to ammonium, AOA amoA gene abundance. These results indicated that AOA communities sense the fluctuations in surrounding environment, and ultimately react and influence the nitrogen transformation during agricultural waste composting.},
}
@article {pmid30212260,
year = {2019},
author = {Santoro, AE and Richter, RA and Dupont, CL},
title = {Planktonic Marine Archaea.},
journal = {Annual review of marine science},
volume = {11},
number = {},
pages = {131-158},
doi = {10.1146/annurev-marine-121916-063141},
pmid = {30212260},
issn = {1941-0611},
mesh = {Archaea/*physiology ; *Ecosystem ; Food Chain ; Plankton/*microbiology ; },
abstract = {Archaea are ubiquitous and abundant members of the marine plankton. Once thought of as rare organisms found in exotic extremes of temperature, pressure, or salinity, archaea are now known in nearly every marine environment. Though frequently referred to collectively, the planktonic archaea actually comprise four major phylogenetic groups, each with its own distinct physiology and ecology. Only one group-the marine Thaumarchaeota-has cultivated representatives, making marine archaea an attractive focus point for the latest developments in cultivation-independent molecular methods. Here, we review the ecology, physiology, and biogeochemical impact of the four archaeal groups using recent insights from cultures and large-scale environmental sequencing studies. We highlight key gaps in our knowledge about the ecological roles of marine archaea in carbon flow and food web interactions. We emphasize the incredible uncultivated diversity within each of the four groups, suggesting there is much more to be done.},
}
@article {pmid30207323,
year = {2018},
author = {Patching, SG},
title = {Recent developments in nucleobase cation symporter-1 (NCS1) family transport proteins from bacteria, archaea, fungi and plants.},
journal = {Journal of biosciences},
volume = {43},
number = {4},
pages = {797-815},
pmid = {30207323},
issn = {0973-7138},
support = {BB/C51725X/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/G020043/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Amino Acid Sequence/genetics ; Arabidopsis Proteins/*genetics ; Archaea/genetics ; Bacteria/genetics ; *Evolution, Molecular ; Fungi/genetics ; Microtubule-Associated Proteins/*genetics ; Nucleobase Transport Proteins/*genetics ; *Phylogeny ; Saccharomyces cerevisiae Proteins/*genetics ; Sequence Homology, Amino Acid ; Substrate Specificity ; },
abstract = {The nucleobase cation symporter-1 (NCS1) family of secondary active transport proteins comprises over 2500 sequenced members from bacteria, archaea, fungi and plants. NCS1 proteins use a proton or sodium gradient to drive inward cellular transport of purine and pyrimidine nucleobases and nucleosides, hydantoins and related compounds. The structural organization, substrate binding residues and molecular mechanism of NCS1 proteins are defined by crystal structures of sodium-coupled hydantoin transporter, Mhp1. Plant proteins are most closely related to bacterial/archaeal proteins and the distinct Fur-type and Fcy-type fungal proteins and plant proteins originated through independent horizontal transfers from prokaryotes. Analyses of 25 experimentally characterized proteins reveal high substrate specificity in bacterial proteins, distinct non-overlapping specificities in Fur-type and Fcy-type fungal proteins and broad specificity in plant proteins. Possible structural explanations are identified for differences in substrate specificity between bacterial proteins, whilst specificities of other proteins cannot be predicted by simple sequence comparisons. Specificity appears to be species specific and determined by combinations of effects dictated by multiple residues in the major substrate binding site and gating domains. This is an exploratory research review of evolutionary relationships, function and structural organization, molecular mechanism and origins of substrate specificity in NCS1 proteins and avenues of future direction.},
}
@article {pmid30199800,
year = {2018},
author = {Pan, KL and Gao, JF and Fan, XY and Li, DC and Dai, HH},
title = {The more important role of archaea than bacteria in nitrification of wastewater treatment plants in cold season despite their numerical relationships.},
journal = {Water research},
volume = {145},
number = {},
pages = {552-561},
doi = {10.1016/j.watres.2018.08.066},
pmid = {30199800},
issn = {1879-2448},
mesh = {Ammonia ; *Archaea ; Bacteria ; *Nitrification ; Oxidation-Reduction ; Phylogeny ; Seasons ; Soil Microbiology ; Wastewater ; },
abstract = {Nitrification failure of wastewater treatment plants (WWTPs) in cold season calls into investigations of the functional ammonia-oxidizing microorganisms (AOMs). In this study, we report the abundance of ammonia-oxidizing archaea (AOA), bacteria (AOB) and complete ammonia-oxidizing (comammox) Nitrospira in 23 municipal WWTPs in cold season, and explore the correlations between AOMs abundance and their relative contribution to nitrification. The copy numbers of AOA and AOB amoA gene ranged from 2.42 × 10[7] to 2.47 × 10[9] and 5.54 × 10[6] to 3.31 × 10[9] copies/g sludge, respectively. The abundance of amoA gene of Candidatus Nitrospira inopinata, an important strain of comammox Nitrospira, was stable with averaged abundance of 8.47 × 10[6] copies/g sludge. DNA-based stable isotope probing (DNA-SIP) assays were conducted with three typical WWTPs in which the abundance of AOA was lower than, similar to and higher than that of AOB, respectively. The results showed that considerable [13]C-assimilation by AOA was detected during active nitrification in all WWTPs, whereas just a much lesser extent of [13]C-incorporation by AOB and comammox Nitrospira was found in one WWTP. High-throughput sequencing with [13]C-labeled DNA also showed the higher reads abundance of AOA than AOB and comammox Nitrospira. Nitrososphaera viennensis was the dominant active AOA, while Nitrosomonas oligotropha and Nitrosomonas europaea were identified as active AOB. The results obtained suggest that AOA, rather than AOB and comammox Nitrospira, dominate ammonia oxidation in WWTPs in cold season despite the numerical relationships of AOMs.},
}
@article {pmid30194429,
year = {2019},
author = {Beulig, F and Røy, H and McGlynn, SE and Jørgensen, BB},
title = {Cryptic CH4 cycling in the sulfate-methane transition of marine sediments apparently mediated by ANME-1 archaea.},
journal = {The ISME journal},
volume = {13},
number = {2},
pages = {250-262},
pmid = {30194429},
issn = {1751-7370},
mesh = {Archaea/genetics/*metabolism ; Carbon Dioxide/metabolism ; Geologic Sediments/*chemistry/*microbiology ; Metagenome ; Methane/analysis/*metabolism ; Oceans and Seas ; Oxidation-Reduction ; Sulfates/analysis/*metabolism ; },
abstract = {Methane in the seabed is mostly oxidized to CO2 with sulfate as the oxidant before it reaches the overlying water column. This microbial oxidation takes place within the sulfate-methane transition (SMT), a sediment horizon where the downward diffusive flux of sulfate encounters an upward flux of methane. Across multiple sites in the Baltic Sea, we identified a systematic discrepancy between the opposing fluxes, such that more sulfate was consumed than expected from the 1:1 stoichiometry of methane oxidation with sulfate. The flux discrepancy was consistent with an oxidation of buried organic matter within the SMT, as corroborated by stable carbon isotope budgets. Detailed radiotracer experiments showed that up to 60% of the organic matter oxidation within the SMT first produced methane, which was concurrently oxidized to CO2 by sulfate reduction. This previously unrecognized "cryptic" methane cycling in the SMT is not discernible from geochemical profiles due to overall net methane consumption. Sedimentary gene pools suggested that nearly all potential methanogens within and beneath the SMT belonged to ANME-1 archaea, which are typically associated with anaerobic methane oxidation. Analysis of a metagenome-assembled genome suggests that predominant ANME-1 do indeed have the enzymatic potential to catalyze both methane production and consumption.},
}
@article {pmid30186275,
year = {2018},
author = {Ghuneim, LJ and Jones, DL and Golyshin, PN and Golyshina, OV},
title = {Nano-Sized and Filterable Bacteria and Archaea: Biodiversity and Function.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {1971},
pmid = {30186275},
issn = {1664-302X},
abstract = {Nano-sized and filterable microorganisms are thought to represent the smallest living organisms on earth and are characterized by their small size (50-400 nm) and their ability to physically pass through <0.45 μm pore size filters. They appear to be ubiquitous in the biosphere and are present at high abundance across a diverse range of habitats including oceans, rivers, soils, and subterranean bedrock. Small-sized organisms are detected by culture-independent and culture-dependent approaches, with most remaining uncultured and uncharacterized at both metabolic and taxonomic levels. Consequently, their significance in ecological roles remain largely unknown. Successful isolation, however, has been achieved for some species (e.g., Nanoarchaeum equitans and "Candidatus Pelagibacter ubique"). In many instances, small-sized organisms exhibit a significant genome reduction and loss of essential metabolic pathways required for a free-living lifestyle, making their survival reliant on other microbial community members. In these cases, the nano-sized prokaryotes can only be co-cultured with their 'hosts.' This paper analyses the recent data on small-sized microorganisms in the context of their taxonomic diversity and potential functions in the environment.},
}
@article {pmid30175688,
year = {2018},
author = {Ten-Caten, F and Vêncio, RZN and Lorenzetti, APR and Zaramela, LS and Santana, AC and Koide, T},
title = {Internal RNAs overlapping coding sequences can drive the production of alternative proteins in archaea.},
journal = {RNA biology},
volume = {15},
number = {8},
pages = {1119-1132},
pmid = {30175688},
issn = {1555-8584},
mesh = {*Alternative Splicing ; Archaeal Proteins/genetics/*metabolism ; Base Sequence ; Gene Expression Profiling ; *Genome, Archaeal ; Halobacterium salinarum/genetics/growth &amp; development/*metabolism ; High-Throughput Nucleotide Sequencing ; *Open Reading Frames ; RNA, Antisense/*genetics ; RNA, Archaeal/*genetics ; Transcription Initiation Site ; },
abstract = {Prokaryotic genomes show a high level of information compaction often with different molecules transcribed from the same locus. Although antisense RNAs have been relatively well studied, RNAs in the same strand, internal RNAs (intraRNAs), are still poorly understood. The question of how common is the translation of overlapping reading frames remains open. We address this question in the model archaeon Halobacterium salinarum. In the present work we used differential RNA-seq (dRNA-seq) in H. salinarum NRC-1 to locate intraRNA signals in subsets of internal transcription start sites (iTSS) and establish the open reading frames associated to them (intraORFs). Using C-terminally flagged proteins, we experimentally observed isoforms accurately predicted by intraRNA translation for kef1, acs3 and orc4 genes. We also recovered from the literature and mass spectrometry databases several instances of protein isoforms consistent with intraRNA translation such as the gas vesicle protein gene gvpC1. We found evidence for intraRNAs in horizontally transferred genes such as the chaperone dnaK and the aerobic respiration related cydA in both H. salinarum and Escherichia coli. Also, intraRNA translation evidence in H. salinarum, E. coli and yeast of a universal elongation factor (aEF-2, fusA and eEF-2) suggests that this is an ancient phenomenon present in all domains of life.},
}
@article {pmid30172418,
year = {2018},
author = {Liu, Y and Liu, J and Yao, P and Ge, T and Qiao, Y and Zhao, M and Zhang, XH},
title = {Distribution patterns of ammonia-oxidizing archaea and bacteria in sediments of the eastern China marginal seas.},
journal = {Systematic and applied microbiology},
volume = {41},
number = {6},
pages = {658-668},
doi = {10.1016/j.syapm.2018.08.008},
pmid = {30172418},
issn = {1618-0984},
mesh = {Ammonia/*metabolism ; Archaea/*classification/isolation &amp; purification/metabolism ; Bacteria/*classification/isolation &amp; purification/metabolism ; Geologic Sediments/*microbiology ; Nitrification ; *Oceans and Seas ; Oxidation-Reduction ; Oxidoreductases ; Oxygen/chemistry ; Phylogeny ; Seawater/chemistry/microbiology ; },
abstract = {Ammonia-oxidizing archaea (AOA) and bacteria (AOB) vary in their contribution to nitrification in different environments. The eastern China marginal seas (ECMS) are featured by complex river runoffs and ocean currents, forming different sediment patches. Here, via quantitative PCR and clone library analysis of the amoA genes, we showed that AOB were more abundant than AOA in ECMS sediments. The abundance, diversity and richness of AOA, but not AOB, were higher in the East China Sea (ECS) than in the Yellow Sea (YS) and Bohai Sea (BS). Nitrosopumilus (AOA) and Nitrosospira (AOB) were predominant lineages, but their abundances varied significantly between ECS, and BS and YS. This was mainly attributed to salinity and dissolved oxygen of the bottom water. The discovery of a high abundance of Nitrosophaera at estuarine sites suggested strong terrigenous influence exerted on the AOA community. In contrast, variations in ocean conditions played more important roles in structuring the AOB community, which was separated by bottom water dissolved oxygen into two groups: the south YS, and the north YS and BS. This study provides a comprehensive insight into the spatial distribution pattern of ammonia-oxidizing prokaryotes in ECMS sediments, laying a foundation for understanding their relative roles in nitrification.},
}
@article {pmid30160784,
year = {2018},
author = {Borsodi, AK and Anda, D and Makk, J and Krett, G and Dobosy, P and Büki, G and Erőss, A and Mádl-Szőnyi, J},
title = {Biofilm forming bacteria and archaea in thermal karst springs of Gellért Hill discharge area (Hungary).},
journal = {Journal of basic microbiology},
volume = {58},
number = {11},
pages = {928-937},
doi = {10.1002/jobm.201800138},
pmid = {30160784},
issn = {1521-4028},
support = {NK101356//Hungarian Scientific Research Fund (NKFI)/ ; },
mesh = {Archaea/classification/genetics/*physiology/ultrastructure ; Bacteria, Thermoduric/classification/genetics/*physiology/ultrastructure ; Biodiversity ; *Biofilms ; Chemoautotrophic Growth ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; Hot Springs/chemistry/*microbiology ; Hungary ; Microbial Consortia/genetics ; Microscopy, Electron, Scanning ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The Buda Thermal Karst System (BTKS) is an extensive active hypogenic cave system located beneath the residential area of the Hungarian capital. At the river Danube, several thermal springs discharge forming spring caves. To reveal and compare the morphological structure and prokaryotic diversity of reddish-brown biofilms developed on the carbonate rock surfaces of the springs, scanning electron microscopy (SEM), and molecular cloning were applied. Microbial networks formed by filamentous bacteria and other cells with mineral crystals embedded in extracellular polymeric substances were observed in the SEM images. Biofilms were dominated by prokaryotes belonging to phyla Proteobacteria, Chloroflexi and Nitrospirae (Bacteria) and Thaumarchaeota (Archaea) but their abundance showed differences according to the type of the host rock, geographic distance, and different water exchange. In addition, representatives of phyla Acidobacteria, Actinobacteria, Caldithrix, Cyanobacteria, Firmicutes Gemmatimonadetes, and several candidate divisions of Bacteria as well as Crenarchaeota and Euryarchaeota were detected in sample-dependent higher abundance. The results indicate that thermophilic, anaerobic sulfur-, sulfate-, nitrate-, and iron(III)-reducing chemoorganotrophic as well as sulfur-, ammonia-, and nitrite-oxidizing chemolithotrophic prokaryotes can interact in the studied biofilms adapted to the unique and extreme circumstances (e.g., aphotic and nearly anoxic conditions, oligotrophy, and radionuclide accumulation) in the thermal karst springs.},
}
@article {pmid30158917,
year = {2018},
author = {Fournier, GP and Poole, AM},
title = {A Briefly Argued Case That Asgard Archaea Are Part of the Eukaryote Tree.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {1896},
pmid = {30158917},
issn = {1664-302X},
abstract = {The recent discovery of the Lokiarchaeota and other members of the Asgard superphylum suggests that closer analysis of the cell biology and evolution of these groups may help shed light on the origin of the eukaryote cell. Asgard lineages often appear in molecular phylogenies as closely related to eukaryotes, and possess "Eukaryote Signature Proteins" coded by genes previously thought to be unique to eukaryotes. This phylogenetic affinity to eukaryotes has been widely interpreted as indicating that Asgard lineages are "eukaryote-like archaea," with eukaryotes evolving from within a paraphyletic Archaea. Guided by the established principles of systematics, we examine the potential implications of the monophyly of Asgard lineages and Eukarya. We show that a helpful parallel case is that of Synapsida, a group that includes modern mammals and their more "reptile-like" ancestors, united by shared derived characters that evolved in their common ancestor. While this group contains extinct members that share many similarities with modern reptiles and their extinct relatives, they are evolutionarily distinct from Sauropsida, the group which includes modern birds, reptiles, and all other amniotes. Similarly, Asgard lineages and eukaryotes are united by shared derived characters to the exclusion of all other groups. Consequently, the Asgard group is not only highly informative for our understanding of eukaryogenesis, but may be better understood as being early diverging members of a broader group including eukaryotes, for which we propose the name "Eukaryomorpha." Significantly, this means that the relationship between Eukarya and Asgard lineages cannot, on its own, resolve the debate over 2 vs. 3 Domains of life; instead, resolving this debate depends upon identifying the root of Archaea with respect to Bacteria.},
}
@article {pmid30158542,
year = {2018},
author = {Cavazzini, D and Grossi, G and Levati, E and Vallese, F and Montanini, B and Bolchi, A and Zanotti, G and Ottonello, S},
title = {Author Correction: A family of archaea-like carboxylesterases preferentially expressed in the symbiotic phase of the mycorrhizal fungus Tuber melanosporum.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {13173},
doi = {10.1038/s41598-018-29606-0},
pmid = {30158542},
issn = {2045-2322},
abstract = {A correction to this article has been published and is linked from the HTML and the PDF versions of this paper. The error has been fixed in the paper.},
}
@article {pmid30142055,
year = {2018},
author = {Dulmage, KA and Darnell, CL and Vreugdenhil, A and Schmid, AK},
title = {Copy number variation is associated with gene expression change in archaea.},
journal = {Microbial genomics},
volume = {4},
number = {9},
pages = {},
pmid = {30142055},
issn = {2057-5858},
mesh = {Chromosome Breakpoints ; Chromosome Deletion ; Chromosomes, Archaeal ; *DNA Copy Number Variations ; Gene Expression Profiling ; Gene Expression Regulation ; Halobacterium salinarum/*genetics/metabolism ; Interspersed Repetitive Sequences ; Oligonucleotide Array Sequence Analysis ; Plasmids/genetics ; *Transcriptome ; Workflow ; },
abstract = {Genomic instability, although frequently deleterious, is also an important mechanism for microbial adaptation to environmental change. Although widely studied in bacteria, in archaea the effect of genomic instability on organism phenotypes and fitness remains unclear. Here we use DNA segmentation methods to detect and quantify genome-wide copy number variation (CNV) in large compendia of high-throughput datasets in a model archaeal species, Halobacterium salinarum. CNV hotspots were identified throughout the genome. Some hotspots were strongly associated with changes in gene expression, suggesting a mechanism for phenotypic innovation. In contrast, CNV hotspots in other genomic loci left expression unchanged, suggesting buffering of certain phenotypes. The correspondence of CNVs with gene expression was validated with strain- and condition-matched transcriptomics and DNA quantification experiments at specific loci. Significant correlation of CNV hotspot locations with the positions of known insertion sequence (IS) elements suggested a mechanism for generating genomic instability. Given the efficient recombination capabilities in H. salinarum despite stability at the single nucleotide level, these results suggest that genomic plasticity mediated by IS element activity can provide a source of phenotypic innovation in extreme environments.},
}
@article {pmid30137299,
year = {2018},
author = {Pohlschroder, M and Albers, SV},
title = {Editorial: Editorial for thematic issue on Archaea.},
journal = {FEMS microbiology reviews},
volume = {42},
number = {6},
pages = {719-720},
doi = {10.1093/femsre/fuy032},
pmid = {30137299},
issn = {1574-6976},
mesh = {Archaea/*physiology ; Archaeal Proteins/metabolism ; Environmental Microbiology ; Genome, Archaeal/genetics ; },
}
@article {pmid30116037,
year = {2019},
author = {Hoshino, T and Inagaki, F},
title = {Abundance and distribution of Archaea in the subseafloor sedimentary biosphere.},
journal = {The ISME journal},
volume = {13},
number = {1},
pages = {227-231},
pmid = {30116037},
issn = {1751-7370},
mesh = {Archaea/*genetics/physiology ; Biomass ; DNA, Archaeal ; *Ecosystem ; Geologic Sediments/*microbiology ; Phylogeny ; Polymerase Chain Reaction ; RNA, Archaeal/genetics ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Subseafloor sedimentary environments harbor a remarkable number of microorganisms that constitute anaerobic and aerobic microbial ecosystems beneath the ocean margins and open-ocean gyres, respectively. Microbial biomass and diversity richness generally decrease with increasing sediment depth and burial time. However, there has been a long-standing debate over the contribution and distribution of Archaea in the subseafloor sedimentary biosphere. Here we show the global quantification of archaeal and bacterial 16S rRNA genes in 221 sediment core samples obtained from diverse oceanographic settings through scientific ocean drilling using microfluidic digital PCR. We estimated that archaeal cells constitute 37.3% of the total microbial cells (40.0% and 12.8% in the ocean margin and open-ocean sites, respectively), corresponding to 1.1 × 10[29] cells on Earth. In addition, the relative abundance of archaeal 16S rRNA genes generally decreased with the depth of water in the overlying sedimentary habitat, suggesting that Archaea may be more sensitive to nutrient quality and quantity supplied from the overlying ocean.},
}
@article {pmid30113887,
year = {2018},
author = {Grant, CR and Wan, J and Komeili, A},
title = {Organelle Formation in Bacteria and Archaea.},
journal = {Annual review of cell and developmental biology},
volume = {34},
number = {},
pages = {217-238},
doi = {10.1146/annurev-cellbio-100616-060908},
pmid = {30113887},
issn = {1530-8995},
support = {R01 GM084122/GM/NIGMS NIH HHS/United States ; R35 GM127114/GM/NIGMS NIH HHS/United States ; },
mesh = {Archaea/*genetics ; Bacteria/*genetics ; Cell Compartmentation/*genetics ; Cell Membrane/chemistry/genetics ; Lipids/chemistry/genetics ; Organelles/chemistry/*genetics ; },
abstract = {Uncovering the mechanisms that underlie the biogenesis and maintenance of eukaryotic organelles is a vibrant and essential area of biological research. In comparison, little attention has been paid to the process of compartmentalization in bacteria and archaea. This lack of attention is in part due to the common misconception that organelles are a unique evolutionary invention of the "complex" eukaryotic cell and are absent from the "primitive" bacterial and archaeal cells. Comparisons across the tree of life are further complicated by the nebulous criteria used to designate subcellular structures as organelles. Here, with the aid of a unified definition of a membrane-bounded organelle, we present some of the recent findings in the study of lipid-bounded organelles in bacteria and archaea.},
}
@article {pmid30105504,
year = {2019},
author = {Albright, MBN and Timalsina, B and Martiny, JBH and Dunbar, J},
title = {Comparative Genomics of Nitrogen Cycling Pathways in Bacteria and Archaea.},
journal = {Microbial ecology},
volume = {77},
number = {3},
pages = {597-606},
pmid = {30105504},
issn = {1432-184X},
support = {F260LANL2018//U.S. Department of Energy, Office of Science, Biological and Environmental Research Division/ ; Graduate Student Research (SCGSR) Fellowship//U.S. Department of Energy, Office of Science/ ; },
mesh = {Archaea/*genetics/metabolism ; Archaeal Proteins/*genetics/metabolism ; Bacteria/*genetics/metabolism ; Bacterial Proteins/*genetics/metabolism ; Ecosystem ; Genome, Archaeal ; Genome, Bacterial ; Genomics ; Nitrogen/*metabolism ; Nitrogen Cycle ; },
abstract = {Despite the explosion of metagenomic sequencing data, using -omics data to predict environmental biogeochemistry remains a challenge. One or a few genes (referred to as marker genes) in a metabolic pathway of interest in meta-omic data are typically used to represent the prevalence of a biogeochemical reaction. This approach often fails to demonstrate a consistent relationship between gene abundance and an ecosystem process rate. One reason this may occur is if a marker gene is not a good representative of a complete pathway. Here, we map the presence of 11 nitrogen (N)-cycling pathways in over 6000 complete bacterial and archaeal genomes using the Integrated Microbial Genomes database. Incomplete N-cycling pathways occurred in 39% of surveyed archaeal and bacterial species revealing a weakness in current marker-gene analyses. Furthermore, we found that most organisms have limited ability to utilize inorganic N in multiple oxidation states. This suggests that inter-organism exchange of inorganic N compounds is common, highlighting the importance of both community composition and spatial structure in determining the extent of recycling versus loss in an ecosystem.},
}
@article {pmid35542481,
year = {2018},
author = {Jiang, Q and Xing, D and Zhang, L and Sun, R and Zhang, J and Zhong, Y and Feng, Y and Ren, N},
title = {Interaction of bacteria and archaea in a microbial fuel cell with ITO anode.},
journal = {RSC advances},
volume = {8},
number = {50},
pages = {28487-28495},
pmid = {35542481},
issn = {2046-2069},
abstract = {A microbial fuel cell with an indium tin oxide (ITO) coated glass anode was used to study the mechanism of electricity generation and electron transfer of electrochemically active microbes (EAMs). A simple method of ITO anode pretreatment (pickling) was developed to improve the performance of the microbial fuel cell. After proper treatment, ITO-glass anodes maintained their conductivity with a slight increase in resistance. Using this pickling pretreatment, the ITO-glass microbial fuel cell with an anode area of only 8.3 cm[2], was successfully initiated and obtained a stable voltage and power output of 418.8 mW m[-2]. The electrode material with pretreatment showed optimal performance for the in situ study of EAMs. DNA was extracted from various parts of the reactor and the microbial communities were analyzed. The results indicated that the large proportion of methane-related microbes on the cathode of the MFC was one of the reasons for its high COD removal and low columbic efficiency. ITO glass is suitable as an anode material for the in situ study of EAMs, and shows potential for practical application.},
}
@article {pmid30071063,
year = {2018},
author = {Gorlas, A and Jacquemot, P and Guigner, JM and Gill, S and Forterre, P and Guyot, F},
title = {Greigite nanocrystals produced by hyperthermophilic archaea of Thermococcales order.},
journal = {PloS one},
volume = {13},
number = {8},
pages = {e0201549},
pmid = {30071063},
issn = {1932-6203},
support = {340440/ERC_/European Research Council/International ; },
mesh = {Carbon Dioxide/chemistry ; Catalysis ; Ecosystem ; Hot Temperature ; Hydrothermal Vents ; Iron/*chemistry ; Microscopy, Electron, Transmission ; Nanoparticles/*chemistry/metabolism ; Oxidation-Reduction ; Spectrometry, X-Ray Emission ; Sulfides/*chemistry ; Thermococcales/*metabolism ; },
abstract = {Interactions between hyperthermophilic archaea and minerals occur in hydrothermal deep-sea vents, one of the most extreme environments for life on Earth. These interactions occur in the internal pores and at surfaces of active hydrothermal chimneys. In this study, we show that, at 85°C, Thermococcales, the predominant hyperthermophilic microorganisms inhabiting hot parts of hydrothermal deep-sea vents, produce greigite nanocrystals (Fe3S4) on extracellular polymeric substances, and that an amorphous iron phosphate acts as a precursor phase. Greigite, although a minor component of chimneys, is a recognized catalyst for CO2 reduction thus implying that Thermococcales may influence the balance of CO2 in hydrothermal ecosystems. We propose that observation of greigite nanocrystals on extracellular polymeric substances could provide a signature of hyperthermophilic life in hydrothermal deep-sea vents.},
}
@article {pmid30062501,
year = {2018},
author = {Karray, F and Ben Abdallah, M and Kallel, N and Hamza, M and Fakhfakh, M and Sayadi, S},
title = {Extracellular hydrolytic enzymes produced by halophilic bacteria and archaea isolated from hypersaline lake.},
journal = {Molecular biology reports},
volume = {45},
number = {5},
pages = {1297-1309},
pmid = {30062501},
issn = {1573-4978},
mesh = {Archaea/classification/*enzymology/isolation &amp; purification ; Bacteria/classification/*enzymology/isolation &amp; purification ; Biodiversity ; Classification/methods ; Enzymes/analysis/classification ; Halobacteriales/classification/*enzymology/isolation &amp; purification ; Lakes ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Salinity ; Sequence Analysis, DNA ; Tunisia ; Water Microbiology ; },
abstract = {The screening of bacteria and archaea from Chott El Jerid, a hypersaline lake in the south of Tunisia, led to the isolation of 68 extremely halophilic prokaryotes growing in media with 15-25% of salt. Assessment of 68 partial 16S rRNA analyzed by amplified rDNA restriction analysis (ARDRA) revealed 15 different bacterial and archaeal taxonomic groups. Based on ARDRA results, phenotypic and hydrolytic activity tests, 20 archaeal and 6 bacterial isolates were selected for sequencing. The halophilic isolates were identified as members of the genera: Salicola, Bacillus, Halorubrum, Natrinema and Haloterrigena. Most of these isolates are able to produce hydrolytic enzymes such as amylase, protease, lipase, cellulase, xylanase, pectinase and some of them showed combined activities. Natrinema genus is an excellent candidate for lipase production. These results indicated that the extremely halophilic archaea and bacteria from Chott El Jerid are a potential source of hydrolytic enzymes and may possess commercial value.},
}
@article {pmid30060184,
year = {2018},
author = {Narrowe, AB and Spang, A and Stairs, CW and Caceres, EF and Baker, BJ and Miller, CS and Ettema, TJG},
title = {Complex Evolutionary History of Translation Elongation Factor 2 and Diphthamide Biosynthesis in Archaea and Parabasalids.},
journal = {Genome biology and evolution},
volume = {10},
number = {9},
pages = {2380-2393},
pmid = {30060184},
issn = {1759-6653},
support = {310039/ERC_/European Research Council/International ; },
mesh = {Archaea/*genetics/metabolism ; Biosynthetic Pathways ; Evolution, Molecular ; Genome, Archaeal ; Histidine/*analogs &amp; derivatives/genetics/metabolism ; Models, Molecular ; Parabasalidea/*genetics/metabolism ; Peptide Elongation Factor 2/*genetics/metabolism ; },
abstract = {Diphthamide is a modified histidine residue which is uniquely present in archaeal and eukaryotic elongation factor 2 (EF-2), an essential GTPase responsible for catalyzing the coordinated translocation of tRNA and mRNA through the ribosome. In part due to the role of diphthamide in maintaining translational fidelity, it was previously assumed that diphthamide biosynthesis genes (dph) are conserved across all eukaryotes and archaea. Here, comparative analysis of new and existing genomes reveals that some archaea (i.e., members of the Asgard superphylum, Geoarchaea, and Korarchaeota) and eukaryotes (i.e., parabasalids) lack dph. In addition, while EF-2 was thought to exist as a single copy in archaea, many of these dph-lacking archaeal genomes encode a second EF-2 paralog missing key residues required for diphthamide modification and for normal translocase function, perhaps suggesting functional divergence linked to loss of diphthamide biosynthesis. Interestingly, some Heimdallarchaeota previously suggested to be most closely related to the eukaryotic ancestor maintain dph genes and a single gene encoding canonical EF-2. Our findings reveal that the ability to produce diphthamide, once thought to be a universal feature in archaea and eukaryotes, has been lost multiple times during evolution, and suggest that anticipated compensatory mechanisms evolved independently.},
}
@article {pmid30054090,
year = {2019},
author = {Ma, M and Du, H and Sun, T and An, S and Yang, G and Wang, D},
title = {Characteristics of archaea and bacteria in rice rhizosphere along a mercury gradient.},
journal = {The Science of the total environment},
volume = {650},
number = {Pt 1},
pages = {1640-1651},
doi = {10.1016/j.scitotenv.2018.07.175},
pmid = {30054090},
issn = {1879-1026},
mesh = {*Archaea/classification/genetics ; *Bacteria/classification/genetics ; Biodiversity ; China ; *Environmental Monitoring ; Mercury/*analysis ; Methylmercury Compounds/analysis ; Mining ; Oryza/*microbiology ; RNA, Ribosomal, 16S/genetics ; *Rhizosphere ; Soil/chemistry ; *Soil Microbiology ; Soil Pollutants/analysis ; },
abstract = {Several strains of archaea have the ability to methylate or resist mercury (Hg), and the paddy field is regarded to be conducive to Hg methylation. However, our knowledge of Hg-methylating or Hg-resistant archaea in paddy soils is very limited so far. Therefore, the distribution of archaea and bacteria in the rhizosphere (RS) and bulk soil (BS) of the rice growing in Xiushan Hg-mining area of southwest China was investigated. Bacterial and archaeal 16S rRNA gene amplicon sequencing of the rice rhizosphere along the Hg gradient was conducted. THg concentrations in RS were significantly higher than that in BS at site S1 and S2, while MeHg concentrations in RS was always higher than that in BS, except S6. Bacterial species richness estimates were much higher than that in archaea. The bacterial α-diversity in high-Hg sites was significant higher than that in low-Hg sites based on ACE and Shannon indices. At the genus level, Thiobacillus, Xanthomonas, Defluviicoccus and Candidatus Nitrosoarchaeum were significantly more abundant in the rhizosphere of high-Hg sites, which meant that strains in these genera might play important roles in response to Hg stress. Hg-methylating archaea in the paddy field could potentially be affiliated to strains in Methanosarcina, but further evidence need to be found. The results provide reference to understand archaeal rhizosphere community along an Hg gradient paddy soils.},
}
@article {pmid30053578,
year = {2018},
author = {Smith-Moore, CM and Grunden, AM},
title = {Bacteria and archaea as the sources of traits for enhanced plant phenotypes.},
journal = {Biotechnology advances},
volume = {36},
number = {7},
pages = {1900-1916},
doi = {10.1016/j.biotechadv.2018.07.007},
pmid = {30053578},
issn = {1873-1899},
mesh = {Archaea/*genetics ; Bacteria/*genetics ; Carbon Cycle ; *Genetic Engineering ; Nitrogen/metabolism ; Phenotype ; Phosphates/metabolism ; Photosynthesis ; *Plant Development ; *Plant Physiological Phenomena ; Plants/genetics/*microbiology ; Plants, Genetically Modified ; Stress, Physiological ; },
abstract = {Rising global demand for food and population increases are driving the need for improved crop productivity over the next 30 years. Plants have inherent metabolic limitations on productivity such as inefficiencies in carbon fixation and sensitivity to environmental conditions. Bacteria and archaea inhabit some of the most inhospitable environments on the planet and possess unique metabolic pathways and genes to cope with these conditions. Microbial genes involved in carbon fixation, abiotic stress tolerance, and nutrient acquisition have been utilized in plants to enhance plant phenotypes by increasing yield, photosynthesis, and abiotic stress tolerance. Transgenic plants expressing bacterial and archaeal genes will be discussed along with emerging strategies and tools to increase plant growth and yield.},
}
@article {pmid30050524,
year = {2018},
author = {Kashyap, S and Sklute, EC and Dyar, MD and Holden, JF},
title = {Reduction and Morphological Transformation of Synthetic Nanophase Iron Oxide Minerals by Hyperthermophilic Archaea.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {1550},
pmid = {30050524},
issn = {1664-302X},
abstract = {Fe(III) (oxyhydr)oxides are electron acceptors for some hyperthermophilic archaea in mildly reducing geothermal environments. However, the kinds of iron oxides that can be used, growth rates, extent of iron reduction, and the morphological changes that occur to minerals are poorly understood. The hyperthermophilic iron-reducing crenarchaea Pyrodictium delaneyi and Pyrobaculum islandicum were grown separately on six different synthetic nanophase Fe(III) (oxyhydr)oxides. For both organisms, growth on ferrihydrite produced the highest growth rates and the largest amounts of Fe(II), although P. delaneyi produced four times more Fe(II) (25 mM) than P. islandicum (6 mM). Both organisms grew on lepidocrocite and akaganéite and produced 2 and 3 mM Fe(II). Modest growth occurred for both organisms on goethite, hematite, and maghemite where ≤1 mM Fe(II) was produced. The diameters of the spherical mineral end-products following P. delaneyi growth increased by 30 nm for ferrihydrite and 50-150 nm for lepidocrocite relative to heated abiotic controls. For akaganéite, spherical particle sizes were the same for P. delaneyi-reacted samples and heated abiotic controls, but the spherical particles were more numerous in the P. delaneyi samples. For P. islandicum, there was no increase in grain size for the mineral end-products following growth on ferrihydrite, lepidocrocite, or akaganéite relative to the heated abiotic controls. High-resolution transmission electron microscopy of lattice fringes and selected-area electron diffraction of the minerals produced by both organisms when grown on ferrihydrite showed that magnetite and/or possibly maghemite were the end-products while the heated abiotic controls only contained ferrihydrite. These results expand the current view of bioavailable Fe(III) (oxyhydr)oxides for reduction by hyperthermophilic archaea when presented as synthetic nanophase minerals. They show that growth and reduction rates are inversely correlated with the iron (oxyhydr)oxide crystallinity and that iron (oxyhydr)oxide mineral transformation takes different forms for these two organisms.},
}
@article {pmid30022612,
year = {2018},
author = {Heal, KR and Qin, W and Amin, SA and Devol, AH and Moffett, JW and Armbrust, EV and Stahl, DA and Ingalls, AE},
title = {Accumulation of NO2 -cobalamin in nutrient-stressed ammonia-oxidizing archaea and in the oxygen deficient zone of the eastern tropical North Pacific.},
journal = {Environmental microbiology reports},
volume = {10},
number = {4},
pages = {453-457},
doi = {10.1111/1758-2229.12664},
pmid = {30022612},
issn = {1758-2229},
mesh = {Ammonia/metabolism ; Archaea/*metabolism/physiology ; Bioreactors ; Copper/deficiency/metabolism ; Hypoxia ; Oxidation-Reduction ; Pacific Ocean ; Seawater/*chemistry ; *Stress, Physiological ; Tropical Climate ; Vitamin B 12/*analogs &amp; derivatives/analysis/chemistry/metabolism ; },
abstract = {Cobalamin (vitamin B12) is a precious resource in natural systems that is produced by select prokaryotes and required by a broad range of organisms. In this way, the production of cobalamin reinforces numerous microbial interdependencies. Here we report the accumulation of an unusual form of cobalamin, nitrocobalamin (NO2 -cobalamin), in a marine oxygen deficient zone (ODZ), isolates of ammonia-oxidizing archaea (AOA), and an anaerobic ammonium-oxidizing (anammox) bacteria enriched bioreactor. Low oxygen waters were enriched in NO2 -cobalamin, and AOA isolates experiencing ammonia or copper stress produced more NO2 -cobalamin, though there is wide strain-to-strain and batch-to-batch variability. NO2 -cobalamin has no known biochemical role. We hypothesize that AOA and anammox bacteria are a source of marine NO2 -cobalamin in the environment via a reactive nitrogen intermediate. These findings suggest connections between cobalamin forms and nitrogen transformations, physiological stress and ocean deoxygenation.},
}
@article {pmid30016225,
year = {2018},
author = {Aiewsakun, P and Adriaenssens, EM and Lavigne, R and Kropinski, AM and Simmonds, P},
title = {Evaluation of the genomic diversity of viruses infecting bacteria, archaea and eukaryotes using a common bioinformatic platform: steps towards a unified taxonomy.},
journal = {The Journal of general virology},
volume = {99},
number = {9},
pages = {1331-1343},
pmid = {30016225},
issn = {1465-2099},
support = {//Wellcome Trust/United Kingdom ; WT108418AIA//Wellcome Trust/United Kingdom ; },
mesh = {Archaea/virology ; Archaeal Viruses/*genetics ; Bacteria/virology ; Bacteriophages/*genetics ; Computational Biology/*methods ; Eukaryota/virology ; Genes, Viral ; *Genetic Variation ; *Genome, Viral ; Genomics ; Metagenomics ; Phylogeny ; Viruses/genetics ; },
abstract = {Genome Relationship Applied to Virus Taxonomy (GRAViTy) is a genetics-based tool that computes sequence relatedness between viruses. Composite generalized Jaccard (CGJ) distances combine measures of homology between encoded viral genes and similarities in genome organizational features (gene orders and orientations). This scoring framework effectively recapitulates the current, largely morphology and phenotypic-based, family-level classification of eukaryotic viruses. Eukaryotic virus families typically formed monophyletic groups with consistent CGJ distance cut-off dividing between and within family divergence ranges. In the current study, a parallel analysis of prokaryotic virus families revealed quite different sequence relationships, particularly those of tailed phage families (Siphoviridae, Myoviridae and Podoviridae), where members of the same family were generally far more divergent and often not detectably homologous to each other. Analysis of the 20 currently classified prokaryotic virus families indeed split them into 70 separate clusters of tailed phages genetically equivalent to family-level assignments of eukaryotic viruses. It further divided several bacterial (Sphaerolipoviridae, Tectiviridae) and archaeal (Lipothrixviridae) families. We also found that the subfamily-level groupings of tailed phages were generally more consistent with the family assignments of eukaryotic viruses, and this supports ongoing reclassifications, including Spounavirinae and Vi1virus taxa as new virus families. The current study applied a common benchmark with which to compare taxonomies of eukaryotic and prokaryotic viruses. The findings support the planned shift away from traditional morphology-based classifications of prokaryotic viruses towards a genome-based taxonomy. They demonstrate the feasibility of a unified taxonomy of viruses into which the vast body of metagenomic viral sequences may be consistently assigned.},
}
@article {pmid30010922,
year = {2018},
author = {van Tran, N and Muller, L and Ross, RL and Lestini, R and Létoquart, J and Ulryck, N and Limbach, PA and de Crécy-Lagard, V and Cianférani, S and Graille, M},
title = {Evolutionary insights into Trm112-methyltransferase holoenzymes involved in translation between archaea and eukaryotes.},
journal = {Nucleic acids research},
volume = {46},
number = {16},
pages = {8483-8499},
pmid = {30010922},
issn = {1362-4962},
support = {R01 GM070641/GM/NIGMS NIH HHS/United States ; R01 GM058843/GM/NIGMS NIH HHS/United States ; },
mesh = {Archaeal Proteins/*physiology ; Bacterial Proteins/genetics/*physiology ; Crystallography, X-Ray ; Datasets as Topic ; Enzyme Activation ; Eukaryotic Cells/enzymology ; Evolution, Molecular ; Haloferax volcanii/*enzymology ; Holoenzymes/physiology ; Immunoprecipitation ; Mass Spectrometry ; Methylation ; Models, Molecular ; Protein Binding ; Protein Conformation ; Protein Interaction Mapping ; Proteomics ; *RNA Processing, Post-Transcriptional ; Recombinant Proteins/metabolism ; Sequence Alignment ; Species Specificity ; tRNA Methyltransferases/deficiency/genetics/*physiology ; },
abstract = {Protein synthesis is a complex and highly coordinated process requiring many different protein factors as well as various types of nucleic acids. All translation machinery components require multiple maturation events to be functional. These include post-transcriptional and post-translational modification steps and methylations are the most frequent among these events. In eukaryotes, Trm112, a small protein (COG2835) conserved in all three domains of life, interacts and activates four methyltransferases (Bud23, Trm9, Trm11 and Mtq2) that target different components of the translation machinery (rRNA, tRNAs, release factors). To clarify the function of Trm112 in archaea, we have characterized functionally and structurally its interaction network using Haloferax volcanii as model system. This led us to unravel that methyltransferases are also privileged Trm112 partners in archaea and that this Trm112 network is much more complex than anticipated from eukaryotic studies. Interestingly, among the identified enzymes, some are functionally orthologous to eukaryotic Trm112 partners, emphasizing again the similarity between eukaryotic and archaeal translation machineries. Other partners display some similarities with bacterial methyltransferases, suggesting that Trm112 is a general partner for methyltransferases in all living organisms.},
}
@article {pmid30003649,
year = {2018},
author = {Aalto, SL and Saarenheimo, J and Mikkonen, A and Rissanen, AJ and Tiirola, M},
title = {Resistant ammonia-oxidizing archaea endure, but adapting ammonia-oxidizing bacteria thrive in boreal lake sediments receiving nutrient-rich effluents.},
journal = {Environmental microbiology},
volume = {20},
number = {10},
pages = {3616-3628},
pmid = {30003649},
issn = {1462-2920},
support = {286642310302//Biotieteiden ja Ymp&#xe4;rist&#xf6;n Tutkimuksen Toimikunta/International ; LIFE12 ENV/FI/597 (N-SINK)//European Commission/International ; 615146//European Research Council/International ; 286642//Academy of Finland/International ; 310302//Academy of Finland/International ; 260797//Academy of Finland/International ; },
mesh = {Ammonia/*metabolism ; Archaea/classification/genetics/isolation &amp; purification/*metabolism ; Bacteria/classification/genetics/isolation &amp; purification/*metabolism ; Betaproteobacteria/genetics ; Ecosystem ; Geologic Sediments/analysis/*microbiology ; Lakes/*microbiology ; Nitrification ; Nutrients/metabolism ; Oxidation-Reduction ; Phylogeny ; },
abstract = {Climate change along with anthropogenic activities changes biogeochemical conditions in lake ecosystems, modifying the sediment microbial communities. Wastewater effluents introduce nutrients and organic material but also novel microbes to lake ecosystems, simulating forthcoming increases in catchment loadings. In this work, we first used 16s rRNA gene sequencing to study how the overall sediment microbial community responds to wastewater in six boreal lakes. To examine forthcoming changes in the lake biogeochemistry, we focused on the ammonia-oxidizing archaea (AOA) and bacteria (AOB), and examined their functional and compositional community response to wastewater. Although we found the least diverse and least resistant prokaryotic communities from the most wastewater-influenced sediments, the community changed fast toward the natural composition with the diminishing influence of wastewater. Each lake hosted a unique resistant AOA community, while AOB communities were adapting, responding to environmental conditions as well as receiving new members from WWTPs. In general, AOB dominated in numbers in wastewater-influenced sediments, while the ratio between AOA and AOB increased when moving toward pristine conditions. Our results suggest that although future climate-change-driven increases in nutrient loading and microbial migration might significantly disrupt lake sediment microbiomes, they can promote nitrification through adapting and abundant AOB communities.},
}
@article {pmid29979671,
year = {2018},
author = {Bowers, RM and Kyrpides, NC and Stepanauskas, R and Harmon-Smith, M and Doud, D and Reddy, TBK and Schulz, F and Jarett, J and Rivers, AR and Eloe-Fadrosh, EA and Tringe, SG and Ivanova, NN and Copeland, A and Clum, A and Becraft, ED and Malmstrom, RR and Birren, B and Podar, M and Bork, P and Weinstock, GM and Garrity, GM and Dodsworth, JA and Yooseph, S and Sutton, G and Glöckner, FO and Gilbert, JA and Nelson, WC and Hallam, SJ and Jungbluth, SP and Ettema, TJG and Tighe, S and Konstantinidis, KT and Liu, WT and Baker, BJ and Rattei, T and Eisen, JA and Hedlund, B and McMahon, KD and Fierer, N and Knight, R and Finn, R and Cochrane, G and Karsch-Mizrachi, I and Tyson, GW and Rinke, C and , and Lapidus, A and Meyer, F and Yilmaz, P and Parks, DH and Eren, AM and Schriml, L and Banfield, JF and Hugenholtz, P and Woyke, T},
title = {Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.},
journal = {Nature biotechnology},
volume = {36},
number = {7},
pages = {660},
pmid = {29979671},
issn = {1546-1696},
}
@article {pmid29978909,
year = {2019},
author = {Yip, DZ and Veach, AM and Yang, ZK and Cregger, MA and Schadt, CW},
title = {Methanogenic Archaea dominate mature heartwood habitats of Eastern Cottonwood (Populus deltoides).},
journal = {The New phytologist},
volume = {222},
number = {1},
pages = {115-121},
doi = {10.1111/nph.15346},
pmid = {29978909},
issn = {1469-8137},
support = {DEAC05-00OR22725//US Department of Energy/International ; //Office of Science/International ; //Biological and Environmental Research/International ; },
mesh = {Archaea/*metabolism ; Bacteria/growth &amp; development ; Biodiversity ; *Ecosystem ; Methane/*metabolism ; Microbiota ; Populus/*microbiology ; Principal Component Analysis ; Wood/*microbiology ; },
abstract = {While recent reports demonstrate that the direct emission of methane from living tree trunks may be a significant terrestrial emission source, there has been debate whether tree emissions are due to transport from soils or produced in the wood environment itself. Reports of methanogens from wood of trees were prominent in the literature 40 years ago but have not been revisited with molecular ecology approaches. We examined communities associated with Populus deltoides using rRNA gene sequence analyses and how these vary with tree and wood properties. Our data indicate that wood environments are dominated by anaerobic microbiomes. Methanogens are prominent in heartwood (mean 34% relative abundance) compared to sapwood environments (13%), and dominant operational taxonomic units (OTUs) were classified as the Methanobacterium sp. Members of the Firmicutes phylum comprised 39% of total sequences and were in 42% greater abundance in sapwood over heartwood niches. Tree diameter was the strongest predictor of methanogen abundance, but wood moisture content and pH were also significant predictors of taxon abundance and overall community composition. Unlike microbiomes of the soil, rhizosphere and phyllosphere, wood associated communities are shaped by unique environmental conditions and may be prominent and overlooked sources of methane emissions in temperate forest systems.},
}
@article {pmid29978046,
year = {2018},
author = {Karimi, B and Terrat, S and Dequiedt, S and Saby, NPA and Horrigue, W and Lelièvre, M and Nowak, V and Jolivet, C and Arrouays, D and Wincker, P and Cruaud, C and Bispo, A and Maron, PA and Bouré, NCP and Ranjard, L},
title = {Biogeography of soil bacteria and archaea across France.},
journal = {Science advances},
volume = {4},
number = {7},
pages = {eaat1808},
pmid = {29978046},
issn = {2375-2548},
mesh = {Archaea/classification/*genetics ; Bacteria/classification/*genetics ; Biodiversity ; France ; Phylogeny ; RNA, Ribosomal, 16S/genetics/metabolism ; Soil/*chemistry ; *Soil Microbiology ; },
abstract = {Over the last two decades, a considerable effort has been made to decipher the biogeography of soil microbial communities as a whole, from small to broad scales. In contrast, few studies have focused on the taxonomic groups constituting these communities; thus, our knowledge of their ecological attributes and the drivers determining their composition and distribution is limited. We applied a pyrosequencing approach targeting 16S ribosomal RNA (rRNA) genes in soil DNA to a set of 2173 soil samples from France to reach a comprehensive understanding of the spatial distribution of bacteria and archaea and to identify the ecological processes and environmental drivers involved. Taxonomic assignment of the soil 16S rRNA sequences indicated the presence of 32 bacterial phyla or subphyla and 3 archaeal phyla. Twenty of these 35 phyla were cosmopolitan and abundant, with heterogeneous spatial distributions structured in patches ranging from a 43- to 260-km radius. The hierarchy of the main environmental drivers of phyla distribution was soil pH > land management > soil texture > soil nutrients > climate. At a lower taxonomic level, 47 dominant genera belonging to 12 phyla aggregated 62.1% of the sequences. We also showed that the phylum-level distribution can be determined largely by the distribution of the dominant genus or, alternatively, reflect the combined distribution of all of the phylum members. Together, our study demonstrated that soil bacteria and archaea present highly diverse biogeographical patterns on a nationwide scale and that studies based on intensive and systematic sampling on a wide spatial scale provide a promising contribution for elucidating soil biodiversity determinism.},
}
@article {pmid29946801,
year = {2018},
author = {Li, F and Xie, W and Yuan, Q and Luo, H and Li, P and Chen, T and Zhao, X and Wang, Z and Ma, H},
title = {Genome-scale metabolic model analysis indicates low energy production efficiency in marine ammonia-oxidizing archaea.},
journal = {AMB Express},
volume = {8},
number = {1},
pages = {106},
pmid = {29946801},
issn = {2191-0855},
support = {2015CB755704//National Key Basic Research Program of China/ ; 16YFXTsf00460//Major Research Plan of Tianjin/ ; 21390201//National Natural Science Foundation of China/ ; 21621004//National Natural Science Foundation of China/ ; 91428308//National Natural Science Foundation of China/ ; ZDRW-ZS-2016-3//Key Research Program of the Chinese Academy of Sciences/ ; 41306123//National Science Foundation for Young Scholars of China/ ; 2016YFA0601101//the State Key R&amp;D project of China/ ; },
abstract = {Marine ammonia-oxidizing archaea (AOA) play an important role in the global nitrogen cycle by obtaining energy for biomass production from CO2 via oxidation of ammonium. The isolation of Candidatus "Nitrosopumilus maritimus" strain SCM1, which represents the globally distributed AOA in the ocean, provided an opportunity for uncovering the contributions of those AOA to carbon and nitrogen cycles in ocean. Although several ammonia oxidation pathways have been proposed for SCM1, little is known about its ATP production efficiency. Here, based on the published genome of Nitrosopumilus maritimus SCM1, a genome-scale metabolic model named NmrFL413 was reconstructed. Based on the model NmrFL413, the estimated ATP/NH4[+] yield (0.149-0.276 ATP/NH4[+]) is tenfold lower than the calculated theoretical yield of the proposed ammonia oxidation pathways in marine AOA (1.5-1.75 ATP/NH4[+]), indicating a low energy production efficiency of SCM1. Our model also suggested the minor contribution of marine AOA to carbon cycle comparing with their significant contribution to nitrogen cycle in the ocean.},
}
@article {pmid29945179,
year = {2018},
author = {Straub, CT and Counts, JA and Nguyen, DMN and Wu, CH and Zeldes, BM and Crosby, JR and Conway, JM and Otten, JK and Lipscomb, GL and Schut, GJ and Adams, MWW and Kelly, RM},
title = {Biotechnology of extremely thermophilic archaea.},
journal = {FEMS microbiology reviews},
volume = {42},
number = {5},
pages = {543-578},
pmid = {29945179},
issn = {1574-6976},
support = {T32 GM008776/GM/NIGMS NIH HHS/United States ; },
mesh = {Archaea/genetics/*physiology ; Biotechnology/*trends ; *Hot Temperature ; Industrial Microbiology/trends ; Metabolic Engineering/*trends ; },
abstract = {Although the extremely thermophilic archaea (Topt ≥ 70°C) may be the most primitive extant forms of life, they have been studied to a limited extent relative to mesophilic microorganisms. Many of these organisms have unique biochemical and physiological characteristics with important biotechnological implications. These include methanogens that generate methane, fermentative anaerobes that produce hydrogen gas with high efficiency, and acidophiles that can mobilize base, precious and strategic metals from mineral ores. Extremely thermophilic archaea have also been a valuable source of thermoactive, thermostable biocatalysts, but their use as cellular systems has been limited because of the general lack of facile genetics tools. This situation has changed recently, however, thereby providing an important avenue for understanding their metabolic and physiological details and also opening up opportunities for metabolic engineering efforts. Along these lines, extremely thermophilic archaea have recently been engineered to produce a variety of alcohols and industrial chemicals, in some cases incorporating CO2 into the final product. There are barriers and challenges to these organisms reaching their full potential as industrial microorganisms but, if these can be overcome, a new dimension for biotechnology will be forthcoming that strategically exploits biology at high temperatures.},
}
@article {pmid29944192,
year = {2018},
author = {Staley, JT and Caetano-Anollés, G},
title = {Archaea-First and the Co-Evolutionary Diversification of Domains of Life.},
journal = {BioEssays : news and reviews in molecular, cellular and developmental biology},
volume = {40},
number = {8},
pages = {e1800036},
doi = {10.1002/bies.201800036},
pmid = {29944192},
issn = {1521-1878},
mesh = {Archaea/genetics/*physiology ; Archaeal Proteins/chemistry/genetics/metabolism ; Bacteria/cytology/genetics ; *Biological Evolution ; Cell Membrane/metabolism ; Cell Wall/chemistry/metabolism ; Eukaryota/cytology/genetics/*physiology ; Gene Transfer, Horizontal ; Genomics ; Methane/metabolism ; Phospholipids/metabolism ; Phylogeny ; Proteome ; },
abstract = {The origins and evolution of the Archaea, Bacteria, and Eukarya remain controversial. Phylogenomic-wide studies of molecular features that are evolutionarily conserved, such as protein structural domains, suggest Archaea is the first domain of life to diversify from a stem line of descent. This line embodies the last universal common ancestor of cellular life. Here, we propose that ancestors of Euryarchaeota co-evolved with those of Bacteria prior to the diversification of Eukarya. This co-evolutionary scenario is supported by comparative genomic and phylogenomic analyses of the distributions of fold families of domains in the proteomes of free-living organisms, which show horizontal gene recruitments and informational process homologies. It also benefits from the molecular study of cell physiologies responsible for membrane phospholipids, methanogenesis, methane oxidation, cell division, gas vesicles, and the cell wall. Our theory however challenges popular cell fusion and two-domain of life scenarios derived from sequence analysis, demanding phylogenetic reconciliation. Also see the video abstract here: https://youtu.be/9yVWn_Q9faY.},
}
@article {pmid29930548,
year = {2018},
author = {Wu, Y and Wu, P and Wang, B and Shao, ZQ},
title = {Genome-Wide Analysis Reveals Ancestral Lack of Seventeen Different tRNAs and Clade-Specific Loss of tRNA-CNNs in Archaea.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {1245},
pmid = {29930548},
issn = {1664-302X},
abstract = {Transfer RNA (tRNA) is a category of RNAs that specifically decode messenger RNAs (mRNAs) into proteins by recognizing a set of 61 codons commonly adopted by different life domains. The composition and abundance of tRNAs play critical roles in shaping codon usage and pairing bias, which subsequently modulate mRNA translation efficiency and accuracy. Over the past few decades, effort has been concentrated on evaluating the specificity and redundancy of different tRNA families. However, the mechanism and processes underlying tRNA evolution have only rarely been investigated. In this study, by surveying tRNA genes in 167 completely sequenced genomes, we systematically investigated the composition and evolution of tRNAs in Archaea from a phylogenetic perspective. Our data revealed that archaeal genomes are compact in both tRNA types and copy number. Generally, no more than 44 different types of tRNA are present in archaeal genomes to decode the 61 canonical codons, and most of them have only one gene copy per genome. Among them, tRNA-Met was significantly overrepresented, with an average of three copies per genome. In contrast, the tRNA-UAU and 16 tRNAs with A-starting anticodons (tRNA-ANNs) were rarely detected in all archaeal genomes. The conspicuous absence of these tRNAs across the archaeal phylogeny suggests they might have not been evolved in the common ancestor of Archaea, rather than have lost independently from different clades. Furthermore, widespread absence of tRNA-CNNs in the Methanococcales and Methanobacteriales genomes indicates convergent loss of these tRNAs in the two clades. This clade-specific tRNA loss may be attributing to the reductive evolution of their genomes. Our data suggest that the current tRNA profiles in Archaea are contributed not only by the ancestral tRNA composition, but also by differential maintenance and loss of redundant tRNAs.},
}
@article {pmid29916347,
year = {2018},
author = {Höfer, K and Jäschke, A},
title = {Epitranscriptomics: RNA Modifications in Bacteria and Archaea.},
journal = {Microbiology spectrum},
volume = {6},
number = {3},
pages = {},
doi = {10.1128/microbiolspec.RWR-0015-2017},
pmid = {29916347},
issn = {2165-0497},
mesh = {Archaea/*genetics/metabolism ; Bacteria/*genetics/metabolism ; Epigenesis, Genetic ; RNA Processing, Post-Transcriptional ; RNA Stability ; RNA, Archaeal/chemistry/*genetics/metabolism ; RNA, Bacterial/chemistry/*genetics/metabolism ; RNA, Transfer/chemistry/genetics/metabolism ; Transcriptome ; },
abstract = {The increasingly complex functionality of RNA is contrasted by its simple chemical composition. RNA is generally built from only four different nucleotides (adenine, guanine, cytosine, and uracil). To date, >160 chemical modifications are known to decorate RNA molecules and thereby alter their function or stability. Many RNA modifications are conserved throughout bacteria, archaea, and eukaryotes, while some are unique to each branch of life. Most known modifications occur at internal positions, while there is limited diversity at the termini. The dynamic nature of RNA modifications and newly discovered regulatory functions of some of these RNA modifications gave birth to a new field, now often referred to as "epitranscriptomics." This review highlights the major developments in this field and summarizes detection principles for internal as well as 5'-terminal mRNA modifications in prokaryotes and archaea to investigate their biological significance.},
}
@article {pmid29909833,
year = {2018},
author = {Ulrich, EC and Kamat, SS and Hove-Jensen, B and Zechel, DL},
title = {Methylphosphonic Acid Biosynthesis and Catabolism in Pelagic Archaea and Bacteria.},
journal = {Methods in enzymology},
volume = {605},
number = {},
pages = {351-426},
doi = {10.1016/bs.mie.2018.01.039},
pmid = {29909833},
issn = {1557-7988},
support = {P01 GM077596/GM/NIGMS NIH HHS/United States ; },
mesh = {Aquatic Organisms/*metabolism ; Archaea/*metabolism ; Archaeal Proteins/metabolism ; Bacteria/*metabolism ; Bacterial Proteins/metabolism ; Lyases/metabolism ; Methane/metabolism ; Oceans and Seas ; Organophosphorus Compounds/*metabolism ; Oxygenases/metabolism ; Phosphates/metabolism ; Seawater/microbiology ; },
abstract = {Inorganic phosphate is essential for all life forms, yet microbes in marine environments are in near constant deprivation of this important nutrient. Organophosphonic acids can serve as an alternative source of inorganic phosphate if microbes possess the appropriate biochemical pathways that allow cleavage of the stable carbon-phosphorus bond that defines this class of molecule. One prominent source of inorganic phosphate is methylphosphonic acid, which is found as a constituent of marine-dissolved organic matter. The cycle of biosynthesis and catabolism of methylphosphonic acid by marine microbes is the likely source of supersaturating levels of methane in shallow ocean waters. This review provides an overview of the rich biochemistry that has evolved to synthesize methylphosphonic acid and catabolize this molecule into Pi and methane, with an emphasis on the reactions catalyzed by methylphosphonic acid synthase MpnS and the carbon-phosphorus lyase system. The protocols and experiments that are described for MpnS and carbon-phosphorus lyase provide a foundation for studying the structures and mechanisms of these and related enzymes.},
}
@article {pmid29905870,
year = {2018},
author = {Rodriguez-R, LM and Gunturu, S and Harvey, WT and Rosselló-Mora, R and Tiedje, JM and Cole, JR and Konstantinidis, KT},
title = {The Microbial Genomes Atlas (MiGA) webserver: taxonomic and gene diversity analysis of Archaea and Bacteria at the whole genome level.},
journal = {Nucleic acids research},
volume = {46},
number = {W1},
pages = {W282-W288},
pmid = {29905870},
issn = {1362-4962},
mesh = {Classification ; Genetic Variation/genetics ; Genome, Archaeal/genetics ; Genome, Bacterial/genetics ; *Genomics ; *Internet ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; *Software ; },
abstract = {The small subunit ribosomal RNA gene (16S rRNA) has been successfully used to catalogue and study the diversity of prokaryotic species and communities but it offers limited resolution at the species and finer levels, and cannot represent the whole-genome diversity and fluidity. To overcome these limitations, we introduced the Microbial Genomes Atlas (MiGA), a webserver that allows the classification of an unknown query genomic sequence, complete or partial, against all taxonomically classified taxa with available genome sequences, as well as comparisons to other related genomes including uncultivated ones, based on the genome-aggregate Average Nucleotide and Amino Acid Identity (ANI/AAI) concepts. MiGA integrates best practices in sequence quality trimming and assembly and allows input to be raw reads or assemblies from isolate genomes, single-cell sequences, and metagenome-assembled genomes (MAGs). Further, MiGA can take as input hundreds of closely related genomes of the same or closely related species (a so-called 'Clade Project') to assess their gene content diversity and evolutionary relationships, and calculate important clade properties such as the pangenome and core gene sets. Therefore, MiGA is expected to facilitate a range of genome-based taxonomic and diversity studies, and quality assessment across environmental and clinical settings. MiGA is available at http://microbial-genomes.org/.},
}
@article {pmid29897479,
year = {2018},
author = {Feng, X and Sun, M and Han, W and Liang, YX and She, Q},
title = {A transcriptional factor B paralog functions as an activator to DNA damage-responsive expression in archaea.},
journal = {Nucleic acids research},
volume = {46},
number = {14},
pages = {7465},
doi = {10.1093/nar/gky302},
pmid = {29897479},
issn = {1362-4962},
}
@article {pmid29891388,
year = {2018},
author = {Marshall, A and Phillips, L and Longmore, A and Tang, C and Heidelberg, K and Mele, P},
title = {Primer selection influences abundance estimates of ammonia oxidizing archaea in coastal marine sediments.},
journal = {Marine environmental research},
volume = {140},
number = {},
pages = {90-95},
doi = {10.1016/j.marenvres.2018.06.001},
pmid = {29891388},
issn = {1879-0291},
mesh = {Ammonia/*metabolism ; Archaea/*physiology ; Archaeal Proteins ; Australia ; Biodiversity ; DNA, Archaeal ; DNA, Bacterial ; Geologic Sediments/chemistry/*microbiology ; Oxidation-Reduction ; Oxidoreductases ; Phylogeny ; Seawater ; Sequence Analysis, DNA ; Water Pollutants, Chemical/*metabolism ; },
abstract = {Quantification of the α-subunit of ammonia monooxygenase (amoA) through PCR is an established technique for estimating the abundance of ammonia oxidizing archaea (AOA) in environmental samples. This study quantified AOA with two established primer sets in 1 cm increments from the sediment surface (0-1 cm) to a depth of 10 cm at two locations within Port Phillip Bay (PPB), Australia. Primer choice had a significant effect on within sample estimates of AOA with copy numbers ranging from 10[2] to 10[4] copies per ng DNA. Variation in AOA abundance patterns with increasing sediment depth were site and primer specific. Sequence mismatches between the primer binding region of the isolated amoA sequences from PPB and Nitrosopumilus maritimus SCM1 were identified and may explain the high variation identified between primer estimates. Our results highlight the need for testing multiple primer pairs that target different regions of the AOA amoA sequence prior to large-scale marine sediment environmental studies.},
}
@article {pmid29888297,
year = {2018},
author = {Fu, X and Adams, Z and Maupin-Furlow, JA},
title = {In vitro Analysis of Ubiquitin-like Protein Modification in Archaea.},
journal = {Bio-protocol},
volume = {8},
number = {10},
pages = {},
pmid = {29888297},
issn = {2331-8325},
support = {R01 GM057498/GM/NIGMS NIH HHS/United States ; },
abstract = {The ubiquitin-like (Ubl) protein is widely distributed in Archaea and involved in many cellular pathways. A well-established method to reconstitute archaeal Ubl protein conjugation in vitro is important to better understand the process of archaeal Ubl protein modification. This protocol describes the in vitro reconstitution of Ubl protein modification and following analysis of this modification in Haloferax volcanii, a halophilic archaeon serving as the model organism.},
}
@article {pmid29879486,
year = {2018},
author = {McDougall, M and McEleney, K and Francisco, O and Trieu, B and Ogbomo, EK and Tomy, G and Stetefeld, J},
title = {Reductive power of the archaea right-handed coiled coil nanotube (RHCC-NT) and incorporation of mercury clusters inside protein cages.},
journal = {Journal of structural biology},
volume = {203},
number = {3},
pages = {281-287},
doi = {10.1016/j.jsb.2018.05.013},
pmid = {29879486},
issn = {1095-8657},
mesh = {Archaea/*chemistry ; Mercury ; Models, Molecular ; Nanotubes/*chemistry ; Protein Binding ; *Protein Conformation ; Protein Domains ; Protein Structure, Secondary ; Proteins/*chemistry/ultrastructure ; Static Electricity ; },
abstract = {Coiled coils are well described as powerful oligomerization motifs and exhibit a large diversity of functions, including gene regulation, cell division, membrane fusion and drug extrusion. The archaea S-layer originated right-handed coiled coil -RHCC-NT- is characterized by extreme stability and is free of cysteine and histidine moieties. In the current study, we have followed a multidisciplinary approach to investigate the capacity of RHCC-NT to bind a variety of ionic complex metal ions. At the outside of the RHCC-NT, one mercury ion forms an electrostatic interaction with the S-methyl moiety of the single methionine residue present in each coil. We demonstrate that RHCC-NT is reducing and incorporating metallic mercury in the large-sized interior cavities which are lined up along the tetrameric channel.},
}
@article {pmid29878182,
year = {2018},
author = {Sun, M and Feng, X and Liu, Z and Han, W and Liang, YX and She, Q},
title = {An Orc1/Cdc6 ortholog functions as a key regulator in the DNA damage response in Archaea.},
journal = {Nucleic acids research},
volume = {46},
number = {13},
pages = {6697-6711},
pmid = {29878182},
issn = {1362-4962},
mesh = {4-Nitroquinoline-1-oxide/toxicity ; Archaeal Proteins/genetics/metabolism/*physiology ; Cell Cycle ; Cell Cycle Proteins/genetics/metabolism/*physiology ; DNA Damage ; *DNA Repair ; DNA, Archaeal/chemistry ; Gene Deletion ; Gene Expression/drug effects ; Nucleotide Motifs ; Origin Recognition Complex/genetics/metabolism/*physiology ; Promoter Regions, Genetic ; Sulfolobus/drug effects/*genetics/metabolism ; },
abstract = {While bacteria and eukaryotes show distinct mechanisms of DNA damage response (DDR) regulation, investigation of ultraviolet (UV)-responsive expression in a few archaea did not yield any conclusive evidence for an archaeal DDR regulatory network. Nevertheless, expression of Orc1-2, an ortholog of the archaeal origin recognition complex 1/cell division control protein 6 (Orc1/Cdc6) superfamily proteins was strongly activated in Sulfolobus solfataricus and Sulfolobus acidocaldarius upon UV irradiation. Here, a series of experiments were conducted to investigate the possible functions of Orc1-2 in DNA damage repair in Sulfolobus islandicus. Study of DDR in Δorc1-2 revealed that Orc1-2 deficiency abolishes DNA damage-induced differential expression of a large number of genes and the mutant showed hypersensitivity to DNA damage treatment. Reporter gene and DNase I footprinting assays demonstrated that Orc1-2 interacts with a conserved hexanucleotide motif present in several DDR gene promoters and regulates their expression. Manipulation of orc1-2 expression by promoter substitution in this archaeon revealed that a high level of orc1-2 expression is essential but not sufficient to trigger DDR. Together, these results have placed Orc1-2 in the heart of the archaeal DDR regulation, and the resulting Orc1-2-centered regulatory circuit represents the first DDR network identified in Archaea, the third domain of life.},
}
@article {pmid29806626,
year = {2018},
author = {Mihara, T and Koyano, H and Hingamp, P and Grimsley, N and Goto, S and Ogata, H},
title = {Taxon Richness of "Megaviridae" Exceeds those of Bacteria and Archaea in the Ocean.},
journal = {Microbes and environments},
volume = {33},
number = {2},
pages = {162-171},
pmid = {29806626},
issn = {1347-4405},
mesh = {Archaea/*classification/genetics ; Bacteria/*classification/genetics ; *Biodiversity ; Databases, Genetic ; Evolution, Molecular ; Giant Viruses/*classification/genetics ; Metagenomics ; *Oceans and Seas ; *Phylogeny ; RNA Polymerase II/genetics ; },
abstract = {Since the discovery of the giant mimivirus, evolutionarily related viruses have been isolated or identified from various environments. Phylogenetic analyses of this group of viruses, tentatively referred to as the family "Megaviridae", suggest that it has an ancient origin that may predate the emergence of major eukaryotic lineages. Environmental genomics has since revealed that Megaviridae represents one of the most abundant and diverse groups of viruses in the ocean. In the present study, we compared the taxon richness and phylogenetic diversity of Megaviridae, Bacteria, and Archaea using DNA-dependent RNA polymerase as a common marker gene. By leveraging existing microbial metagenomic data, we found higher richness and phylogenetic diversity in this single viral family than in the two prokaryotic domains. We also obtained results showing that the evolutionary rate alone cannot account for the observed high diversity of Megaviridae lineages. These results suggest that the Megaviridae family has a deep co-evolutionary history with diverse marine protists since the early "Big-Bang" radiation of the eukaryotic tree of life.},
}
@article {pmid29797436,
year = {2018},
author = {Ramiro, FS and de Lira, E and Soares, G and Retamal-Valdes, B and Feres, M and Figueiredo, LC and Faveri, M},
title = {Effects of different periodontal treatments in changing the prevalence and levels of Archaea present in the subgingival biofilm of subjects with periodontitis: A secondary analysis from a randomized controlled clinical trial.},
journal = {International journal of dental hygiene},
volume = {16},
number = {4},
pages = {569-575},
doi = {10.1111/idh.12347},
pmid = {29797436},
issn = {1601-5037},
support = {2013/10139-6//S&#xe3;o Paulo Research Foundation (FAPESP, Brazil)/ ; 2012/23503-5//S&#xe3;o Paulo Research Foundation (FAPESP, Brazil)/ ; },
mesh = {Adult ; Amoxicillin/*administration &amp; dosage ; Archaea/*isolation &amp; purification ; *Biofilms ; Chronic Periodontitis/*microbiology/*therapy ; Combined Modality Therapy ; Dental Plaque/*microbiology ; *Dental Scaling ; Drug Therapy, Combination ; Female ; Gingiva/*microbiology ; Humans ; Male ; Metronidazole/*administration &amp; dosage ; Middle Aged ; *Root Planing ; Time Factors ; Treatment Outcome ; },
abstract = {OBJECTIVE: The aim of this randomized double-blind and placebo-controlled study was to assess if periodontal treatment with or without systemic antibiotic would change the mean level of Archaea.<br><br>METHODS: Fifty-nine (59) subjects were randomly assigned to receive scaling and root planing (SRP) alone or combined with metronidazole (MTZ; 400&#xa0;mg/TID) or either with MTZ and amoxicillin (AMX; 500&#xa0;mg/TID) for 14&#xa0;days. Clinical and microbiological examinations were performed at baseline and at 6&#xa0;months post-SRP. Six subgingival plaque samples per subject were analysed for the presence and levels of Archaea using quantitative polymerase chain reaction.<br><br>RESULTS: Scaling and root planing alone or combined with MTZ or MTZ&#xa0;+&#xa0;AMX significantly reduced the prevalence of subjects colonized by Archaea at 6&#xa0;months post-therapy, without significant differences among groups (P&#xa0;>&#xa0;.05). Both therapies led to a statistically significant decrease in the mean percentage of sites colonized by Archaea (P&#xa0;<&#xa0;.05). The MTZ and MTZ&#xa0;+&#xa0;AMX group had a significantly lower mean number of sites colonized by Archaea and lower levels of these micro-organisms at sites with probing depth &#x2265;5&#xa0;mm at 6&#xa0;months compared with SRP group (P&#xa0;<&#xa0;.05).<br><br>CONCLUSION: Periodontal treatments including adjunctive MTZ or MTZ&#xa0;+&#xa0;AMX are more effective than mechanical treatment alone in reducing the levels and prevalence of sites colonized by Archaea in subjects with chronic periodontitis.},
}
@article {pmid29795539,
year = {2018},
author = {Teske, A},
title = {Aerobic Archaea in iron-rich springs.},
journal = {Nature microbiology},
volume = {3},
number = {6},
pages = {646-647},
pmid = {29795539},
issn = {2058-5276},
mesh = {*Archaea ; Ferric Compounds ; *Hot Springs ; Iron ; },
}
@article {pmid29789313,
year = {2018},
author = {Pedraza-Pérez, Y and Cuevas-Vede, RA and Canto-Gómez, &#xc1;B and López-Pliego, L and Gutiérrez-Ríos, RM and Hernández-Lucas, I and Rubín-Linares, G and Martínez-Laguna, Y and López-Olguín, JF and Fuentes-Ramírez, LE},
title = {BLAST-XYPlot Viewer: A Tool for Performing BLAST in Whole-Genome Sequenced Bacteria/Archaea and Visualize Whole Results Simultaneously.},
journal = {G3 (Bethesda, Md.)},
volume = {8},
number = {7},
pages = {2167-2172},
pmid = {29789313},
issn = {2160-1836},
mesh = {Archaea/genetics ; Bacteria/genetics ; Computational Biology/*methods ; Databases, Genetic ; Genome, Archaeal ; Genome, Bacterial ; Genomics/methods ; *Software ; User-Computer Interface ; Whole Genome Sequencing ; },
abstract = {One of the most commonly used tools to compare protein or DNA sequences against databases is BLAST. We introduce a web tool that allows the performance of BLAST-searches of protein/DNA sequences in whole-genome sequenced bacteria/archaea, and displays a large amount of BLAST-results simultaneously. The circular bacterial replicons are projected as horizontal lines with fixed length of 360, representing the degrees of a circle. A coordinate system is created with length of the replicon along the x-axis and the number of replicon used on the y-axis. When a query sequence matches with a gene/protein of a particular replicon, the BLAST-results are depicted as an "x,y" position in a specially adapted plot. This tool allows the visualization of the results from the whole data to a particular gene/protein in real time with low computational resources.},
}
@article {pmid29788499,
year = {2018},
author = {Nawrocki, EP and Jones, TA and Eddy, SR},
title = {Group I introns are widespread in archaea.},
journal = {Nucleic acids research},
volume = {46},
number = {15},
pages = {7970-7976},
pmid = {29788499},
issn = {1362-4962},
support = {R01 HG009116/HG/NHGRI NIH HHS/United States ; },
mesh = {Archaea/classification/enzymology/*genetics ; Base Sequence ; Introns/*genetics ; Nucleic Acid Conformation ; Phylogeny ; RNA, Archaeal/chemistry/classification/*genetics ; RNA, Catalytic/chemistry/classification/*genetics ; Species Specificity ; },
abstract = {Group I catalytic introns have been found in bacterial, viral, organellar, and some eukaryotic genomes, but not in archaea. All known archaeal introns are bulge-helix-bulge (BHB) introns, with the exception of a few group II introns. It has been proposed that BHB introns arose from extinct group I intron ancestors, much like eukaryotic spliceosomal introns are thought to have descended from group II introns. However, group I introns have little sequence conservation, making them difficult to detect with standard sequence similarity searches. Taking advantage of recent improvements in a computational homology search method that accounts for both conserved sequence and RNA secondary structure, we have identified 39 group I introns in a wide range of archaeal phyla, including examples of group I introns and BHB introns in the same host gene.},
}
@article {pmid29771354,
year = {2018},
author = {Lui, LM and Uzilov, AV and Bernick, DL and Corredor, A and Lowe, TM and Dennis, PP},
title = {Methylation guide RNA evolution in archaea: structure, function and genomic organization of 110 C/D box sRNA families across six Pyrobaculum species.},
journal = {Nucleic acids research},
volume = {46},
number = {11},
pages = {5678-5691},
pmid = {29771354},
issn = {1362-4962},
support = {T32 GM070386/GM/NIGMS NIH HHS/United States ; },
mesh = {Archaeal Proteins/genetics ; Base Pair Mismatch ; *Evolution, Molecular ; Genes, Duplicate ; Genomics ; Methylation ; Multigene Family ; Pyrobaculum/*genetics ; RNA, Archaeal/chemistry/classification/*genetics/metabolism ; RNA, Ribosomal/metabolism ; RNA, Small Nucleolar/chemistry/classification/*genetics/metabolism ; RNA, Transfer/metabolism ; RNA, Untranslated/genetics ; Sequence Alignment ; },
abstract = {Archaeal homologs of eukaryotic C/D box small nucleolar RNAs (C/D box sRNAs) guide precise 2'-O-methyl modification of ribosomal and transfer RNAs. Although C/D box sRNA genes constitute one of the largest RNA gene families in archaeal thermophiles, most genomes have incomplete sRNA gene annotation because reliable, fully automated detection methods are not available. We expanded and curated a comprehensive gene set across six species of the crenarchaeal genus Pyrobaculum, particularly rich in C/D box sRNA genes. Using high-throughput small RNA sequencing, specialized computational searches and comparative genomics, we analyzed 526 Pyrobaculum C/D box sRNAs, organizing them into 110 families based on synteny and conservation of guide sequences which determine methylation targets. We examined gene duplications and rearrangements, including one family that has expanded in a pattern similar to retrotransposed repetitive elements in eukaryotes. New training data and inclusion of kink-turn secondary structural features enabled creation of an improved search model. Our analyses provide the most comprehensive, dynamic view of C/D box sRNA evolutionary history within a genus, in terms of modification function, feature plasticity, and gene mobility.},
}
@article {pmid29769540,
year = {2018},
author = {Xu, S and Cai, C and Guo, J and Lu, W and Yuan, Z and Hu, S},
title = {Different clusters of Candidatus 'Methanoperedens nitroreducens'-like archaea as revealed by high-throughput sequencing with new primers.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {7695},
pmid = {29769540},
issn = {2045-2322},
mesh = {Biodiversity ; DNA Primers/*chemistry ; DNA, Archaeal/*analysis/genetics ; Ecosystem ; High-Throughput Nucleotide Sequencing/*methods ; Methanosarcinales/*classification/*genetics ; Phylogeny ; },
abstract = {The newly discovered Candidatus 'Methanoperedens nitroreducens' (M. nitroreducens), mediating nitrate-dependent anaerobic oxidation of methane, is an important microorganism in linking carbon and nitrogen cycles. In order to explore the diversity of M. nitroreducens-like archaea in various environmental niches with advanced high-throughput sequencing, new primers based on alpha subunit of methyl-coenzyme M reductase gene were designed. The PCR results demonstrated that the new primers could effectively detect M. nitroreducens-like archaea from an enrichment culture dominated by M. nitroreducens as well as samples collected from a natural freshwater lake and a full-scale wastewater treatment plant (WWTP). By high-throughput sequencing, more than 30,000 M. nitroreducens-like sequences were obtained. Phylogenetic analysis of these sequences along with published sequences showed that M. nitroreducens-like archaea could be divided into three sub-branches (named as Group A, Group B and Group C in this study). Clear geographical difference was observed, with Group A and Group B dominating samples in Queensland (Australia) and in European ecosystems, respectively. Further quantitative PCR revealed that the M. nitroreducens-like archaea were more abundant in WWTP than the freshwater lake. The study provided a large number of sequences for M. nitroreducens-like archaeal communities, thus expanded our understanding on the ecological diversity of M. nitroreducens-like archaea.},
}
@article {pmid29757234,
year = {2018},
author = {Sinha, N and Kral, TA},
title = {Effect of UVC Radiation on Hydrated and Desiccated Cultures of Slightly Halophilic and Non-Halophilic Methanogenic Archaea: Implications for Life on Mars.},
journal = {Microorganisms},
volume = {6},
number = {2},
pages = {},
pmid = {29757234},
issn = {2076-2607},
abstract = {Methanogens have been considered models for life on Mars for many years. In order to survive any exposure at the surface of Mars, methanogens would have to endure Martian UVC radiation. In this research, we irradiated hydrated and desiccated cultures of slightly halophilic Methanococcus maripaludis and non-halophilic Methanobacterium formicicum for various time intervals with UVC (254 nm) radiation. The survivability of the methanogens was determined by measuring methane concentrations in the headspace gas samples of culture tubes after re-inoculation of the methanogens into their growth-supporting media following exposure to UVC radiation. Hydrated M. maripaludis survived 24 h of UVC exposure, while in a desiccated condition they endured for 16 h. M. formicicum also survived UVC radiation for 24 h in a liquid state; however, in a desiccated condition, the survivability of M. formicicum was only 12 h. Some of the components of the growth media could have served as shielding agents that protected cells from damage caused by exposure to ultraviolet radiation. Overall, these results suggest that limited exposure (12[-]24 h) to UVC radiation on the surface of Mars would not necessarily be a limiting factor for the survivability of M. maripaludis and M. formicicum.},
}
@article {pmid29753224,
year = {2018},
author = {Liu, X and Pan, J and Liu, Y and Li, M and Gu, JD},
title = {Diversity and distribution of Archaea in global estuarine ecosystems.},
journal = {The Science of the total environment},
volume = {637-638},
number = {},
pages = {349-358},
doi = {10.1016/j.scitotenv.2018.05.016},
pmid = {29753224},
issn = {1879-1026},
mesh = {Archaea/classification/*genetics/growth &amp; development ; Biodiversity ; DNA, Archaeal ; Ecosystem ; *Estuaries ; Phylogeny ; RNA, Ribosomal, 16S ; Sequence Analysis, DNA ; *Water Microbiology ; },
abstract = {Estuarine ecosystem is a unique geographical transitional zone between freshwater and seawater, harboring a wide range of microbial communities including Archaea. Although a large number of Archaea have been detected in such ecosystem, the global patterns in archaeal diversity and distribution are extremely scarce. To bridge this gap, we carried out a comprehensive survey of archaeal communities using ca. 4000 publicly available archaeal 16S rRNA gene sequences (>300 bp) collected from 24 estuaries in different latitude regions. These sequences were divided into 1450 operational taxonomic units (OTUs) at 97% identity, suggesting a high biodiversity that increased gradually from the high- to low-latitude estuaries. Phylogenetic analysis showed that estuarine ecosystem was a large biodiversity pool of Archaea that was mainly composed of 12 phyla. Among them, the predominant groups were Bathyarchaeota, Euryarchaeota and Thaumarchaeota. Interestingly, archaeal distribution demonstrated a geographical differentiation in that Thaumarchaeota was dominated in the low-latitude estuaries, Bathyarchaeota in the mid-latitude estuaries, and Euryarchaeota in the high-latitude estuaries, respectively. Furthermore, the majority of the most abundant 20 OTUs demonstrated an overrepresented or underrepresented distribution pattern in some specific estuaries or latitude regions while a few were evenly distributed throughout the estuaries. This pattern indicates a potential selectivity of geographical distribution. In addition, the analysis of environmental parameters suggested that latitude would be one of the major factors driving the distribution of archaeal communities in estuarine ecosystem. This study profiles a clear framework on the diversity and distribution of Archaea in the global estuarine ecosystem and explores the general environmental factors that influence these patterns. Our findings constitute an important part of the exploration of the global ecology of Archaea.},
}
@article {pmid29743201,
year = {2018},
author = {Taffner, J and Erlacher, A and Bragina, A and Berg, C and Moissl-Eichinger, C and Berg, G},
title = {What Is the Role of Archaea in Plants? New Insights from the Vegetation of Alpine Bogs.},
journal = {mSphere},
volume = {3},
number = {3},
pages = {},
pmid = {29743201},
issn = {2379-5042},
mesh = {Archaea/*growth &amp; development/*metabolism ; Ecosystem ; Plants/*microbiology ; *Symbiosis ; Wetlands ; },
abstract = {The Archaea represent a significant component of the plant microbiome, whereas their function is still unclear. Different plant species representing the natural vegetation of alpine bogs harbor a substantial archaeal community originating from five phyla, 60 genera, and 334 operational taxonomic units (OTUs). We identified a core archaeome for all bog plants and ecosystem-specific, so far unclassified Archaea In the metagenomic data set, Archaea were found to have the potential to interact with plants by (i) possible plant growth promotion through auxin biosynthesis, (ii) nutrient supply, and (iii) protection against abiotic (especially oxidative and osmotic) stress. The unexpectedly high degree of plant specificity supports plant-archaeon interactions. Moreover, functional signatures of Archaea reveal genetic capacity for the interplay with fungi and an important role in the carbon and nitrogen cycle: e.g., CO2 and N2 fixation. These facts reveal an important, yet unobserved role of the Archaea for plants as well as for the bog ecosystem.IMPORTANCEArchaea are still an underdetected and little-studied part of the plant microbiome. We provide first and novel insights into Archaea as a functional component of the plant microbiome obtained by metagenomic analyses. Archaea were found to have the potential to interact with plants by (i) plant growth promotion through auxin biosynthesis, (ii) nutrient supply, and (iii) protection against abiotic stress.},
}
@article {pmid29741625,
year = {2018},
author = {White, MF and Allers, T},
title = {DNA repair in the archaea-an emerging picture.},
journal = {FEMS microbiology reviews},
volume = {42},
number = {4},
pages = {514-526},
doi = {10.1093/femsre/fuy020},
pmid = {29741625},
issn = {1574-6976},
support = {//Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Archaea/*genetics ; *Biological Evolution ; DNA Repair/*physiology ; DNA, Archaeal/*genetics ; },
abstract = {There has long been a fascination in the DNA repair pathways of archaea, for two main reasons. Firstly, many archaea inhabit extreme environments where the rate of physical damage to DNA is accelerated. These archaea might reasonably be expected to have particularly robust or novel DNA repair pathways to cope with this. Secondly, the archaea have long been understood to be a lineage distinct from the bacteria, and to share a close relationship with the eukarya, particularly in their information processing systems. Recent discoveries suggest the eukarya arose from within the archaeal domain, and in particular from lineages related to the TACK superphylum and Lokiarchaea. Thus, archaeal DNA repair proteins and pathways can represent a useful model system. This review focuses on recent advances in our understanding of archaeal DNA repair processes including base excision repair, nucleotide excision repair, mismatch repair and double-strand break repair. These advances are discussed in the context of the emerging picture of the evolution and relationship of the three domains of life.},
}
@article {pmid29733685,
year = {2018},
author = {Rinta-Kanto, JM and Pehkonen, K and Sinkko, H and Tamminen, MV and Timonen, S},
title = {Archaea are prominent members of the prokaryotic communities colonizing common forest mushrooms.},
journal = {Canadian journal of microbiology},
volume = {64},
number = {10},
pages = {716-726},
doi = {10.1139/cjm-2018-0035},
pmid = {29733685},
issn = {1480-3275},
mesh = {*Agaricales ; Archaea/genetics/*isolation &amp; purification ; Bacteria/genetics/isolation &amp; purification ; *Forests ; RNA, Ribosomal, 16S/genetics ; },
abstract = {In this study, the abundance and composition of prokaryotic communities associated with the inner tissue of fruiting bodies of Suillus bovinus, Boletus pinophilus, Cantharellus cibarius, Agaricus arvensis, Lycoperdon perlatum, and Piptoporus betulinus were analyzed using culture-independent methods. Our findings indicate that archaea and bacteria colonize the internal tissues of all investigated specimens and that archaea are prominent members of the prokaryotic community. The ratio of archaeal 16S rRNA gene copy numbers to those of bacteria was >1 in the fruiting bodies of four out of six fungal species included in the study. The largest proportion of archaeal 16S rRNA gene sequences belonged to thaumarchaeotal classes Terrestrial group, Miscellaneous Crenarchaeotic Group (MCG), and Thermoplasmata. Bacterial communities showed characteristic compositions in each fungal species. Bacterial classes Gammaproteobacteria, Actinobacteria, Bacilli, and Clostridia were prominent among communities in fruiting body tissues. Bacterial populations in each fungal species had different characteristics. The results of this study imply that fruiting body tissues are an important habitat for abundant and diverse populations of archaea and bacteria.},
}
@article {pmid29720404,
year = {2018},
author = {Prakash, D and Walters, KA and Martinie, RJ and McCarver, AC and Kumar, AK and Lessner, DJ and Krebs, C and Golbeck, JH and Ferry, JG},
title = {Toward a mechanistic and physiological understanding of a ferredoxin:disulfide reductase from the domains Archaea and Bacteria.},
journal = {The Journal of biological chemistry},
volume = {293},
number = {24},
pages = {9198-9209},
pmid = {29720404},
issn = {1083-351X},
mesh = {Archaea/chemistry/*enzymology/metabolism ; Bacteria/chemistry/*enzymology/metabolism ; Catalytic Domain ; Disulfides/chemistry/*metabolism ; Electron Transport ; Ferredoxins/chemistry/*metabolism ; Iron-Sulfur Proteins/chemistry/*metabolism ; Methanosarcina/chemistry/*enzymology/metabolism ; Models, Molecular ; NADH, NADPH Oxidoreductases/chemistry/*metabolism ; Oxidation-Reduction ; Oxidoreductases/chemistry/*metabolism ; Spinacia oleracea/chemistry/enzymology/metabolism ; },
abstract = {Disulfide reductases reduce other proteins and are critically important for cellular redox signaling and homeostasis. Methanosarcina acetivorans is a methane-producing microbe from the domain Archaea that produces a ferredoxin:disulfide reductase (FDR) for which the crystal structure has been reported, yet its biochemical mechanism and physiological substrates are unknown. FDR and the extensively characterized plant-type ferredoxin:thioredoxin reductase (FTR) belong to a distinct class of disulfide reductases that contain a unique active-site [4Fe-4S] cluster. The results reported here support a mechanism for FDR similar to that reported for FTR with notable exceptions. Unlike FTR, FDR contains a rubredoxin [1Fe-0S] center postulated to mediate electron transfer from ferredoxin to the active-site [4Fe-4S] cluster. UV-visible, EPR, and Mössbauer spectroscopic data indicated that two-electron reduction of the active-site disulfide in FDR involves a one-electron-reduced [4Fe-4S][1+] intermediate previously hypothesized for FTR. Our results support a role for an active-site tyrosine in FDR that occupies the equivalent position of an essential histidine in the active site of FTR. Of note, one of seven Trxs encoded in the genome (Trx5) and methanoredoxin, a glutaredoxin-like enzyme from M. acetivorans, were reduced by FDR, advancing the physiological understanding of FDR's role in the redox metabolism of methanoarchaea. Finally, bioinformatics analyses show that FDR homologs are widespread in diverse microbes from the domain Bacteria.},
}
@article {pmid33525806,
year = {2017},
author = {Bowers, RM and Doud, DFR and Woyke, T},
title = {Analysis of single-cell genome sequences of bacteria and archaea.},
journal = {Emerging topics in life sciences},
volume = {1},
number = {3},
pages = {249-255},
pmid = {33525806},
issn = {2397-8554},
abstract = {Single-cell genome sequencing of individual archaeal and bacterial cells is a vital approach to decipher the genetic makeup of uncultured microorganisms. With this review, we describe single-cell genome analysis with a focus on the unique properties of single-cell sequence data and with emphasis on quality assessment and assurance.},
}
@article {pmid36659324,
year = {2017},
author = {Feng, Y and Dolfing, J and Guo, Z and Zhang, J and Zhang, G and Li, S and Lin, X},
title = {Chronosequencing methanogenic archaea in ancient Longji rice Terraces in China.},
journal = {Science bulletin},
volume = {62},
number = {12},
pages = {879-887},
doi = {10.1016/j.scib.2017.05.024},
pmid = {36659324},
issn = {2095-9281},
abstract = {Chronosequences of ancient rice terraces serve as an invaluable archive for reconstructions of historical human-environment interactions. Presently, however, these reconstructions are based on traditional soil physico-chemical properties. The microorganisms in palaeosols have been unexplored. We hypothesized that microbial information can be used as an additional proxy to complement and consolidate archaeological interpretations. To test this hypothesis, the palaeoenvironmental methanogenic archaeal DNA in Longji Terraces, one of the famous ancient terraces in China, dating back to the late Yuan Dynasty (CE 1361-1406), was chronosequenced by high-throughput sequencing. It was found that the methanogenic archaeal abundance, diversity and community composition were closely associated with the 630years of rice cultivation and in line with changes in multi-proxy data. Particularly, the centennial- and decadal-scale influences of known historical events, including social turbulences (The Taiping Rebellion, CE 1850-1865), palaeoclimate changes (the Little Ice Age) and recorded natural disasters (earthquakes and inundation), on ancient agricultural society were clearly echoed in the microbial archives as variations in alpha and beta diversity. This striking correlation suggests that the microorganisms archived in palaeosols can be quantitatively and qualitatively analyzed to provide an additional proxy, and palaeo-microbial information could be routinely incorporated in the toolkit for archaeological interpretation.},
}
@article {pmid31529916,
year = {2016},
author = {Titov, VN and Parchimovitch, RM},
title = {[The phylogenetic theory of general pathology. The becoming of function of at mitochondria at symbiosis of bacterial cells and archaea. Inconsistency of Randle cycle, regulation metabolism of fatty acids and glucose by insulin.].},
journal = {Klinicheskaia laboratornaia diagnostika},
volume = {61},
number = {7},
pages = {388-396},
doi = {10.18821/0860-2084-2016-61-7-388-396},
pmid = {31529916},
issn = {0869-2084},
abstract = {The implementation of Randle rule is not a cycle; fatty acids C4 - ketone bodies at interrelationships with glucose metabolite - pyruvate regulate production of mitochondria of acetyl-KoA by induction of substrate and its conversion in Krebs cycle, reactions of respiratory chain, oxidative phosphorylation and formation of ATP. In phylogenesis, the early substrate for formation of ATP by mitochondria is acetyl-KoA from C4 fatty acids 4; this is alternative A of induction by substrate adopted from archaea. The alternative B of induction in bacteria is based on synthesis of acetyl-KoA by mitohondria from pyruvate developed in cytosol from exogenous glucose. The insulin is late activator of absorption by glucose cells in phylogenesis; using induction by substrate, insulin inhibits absorption of fatty acids by cells and specifically activates absorption of glucose by them. The insulin activates absorption of glucose only by insulin-dependent cells by force of decreasing of "bioavailability" of fatty acids. These cells are preferred to be metabolize by mitochondria from times of archaea. The insulin, blocking lipolysis in insulin-dependent adipocytes "forces" mitochondria, instead of formation of acetyl-KoA from fatty acids, to produce it from pyruvate at activation of glycolysis and pyruvate-dehydrogenased complex. Under effect of insulin, mitochondria form acetyl-KoA and synthesize ATP from oleic mono-saturated fatty acids but not from palmitic saturated fatty acids. The kinetic parameters of second reaction and formation of ATP per unit of time (effectiveness) are much higher than in first reaction. The effectiveness of i9mplementation of alternative A in synthesis of ATP, kinetic parameters of production of acetyl-KoA in mitochondria in alternative A are more effective than in case of alternative B and metabolic conversion of glucose. The syndrome of resistance to insulin is, at the first place, pathology of metabolism of fatty acids and only in the second place metabolism of glucose. The incapacity of insulin to block lipolysis in the phylogenetically earlier visceral fatty cells is the basis of resistance.},
}
@article {pmid32214732,
year = {2010},
author = {Sun, J and Xu, Z and Hao, B},
title = {Whole-genome based Archaea phylogeny and taxonomy: A composition vector approach.},
journal = {Chinese science bulletin = Kexue tongbao},
volume = {55},
number = {22},
pages = {2323-2328},
pmid = {32214732},
issn = {1001-6538},
abstract = {The newly proposed alignment-free and parameter-free composition vector (CVtree) method has been successfully applied to infer phylogenetic relationship of viruses, chloroplasts, bacteria, and fungi from their whole-genome data. In this study we pay special attention to the phylogenetic positions of 56 Archaea genomes among which 7 species have not been listed either in Bergey's Manual of Systematic Bacteriology or in Taxonomic Outline of Bacteria and Archaea (TOBA). By inspecting the stable monophyletic branchings in CVTrees reconstructed from a total of 861 genomes (56 Archaea plus 797 Bacteria, using 8 Eukarya as outgroups) definite taxonomic assignments were proposed for these not-fully-classified species. Further development of Archaea taxonomy may verify the predicted phylogenetic results of the CVTree approach.},
}
@article {pmid29711416,
year = {1998},
author = {Geierstanger, BH and Prasch, T and Griesinger, C and Hartmann, G and Buurman, G and Thauer, RK},
title = {Catalytic Mechanism of the Metal-Free Hydrogenase from Methanogenic Archaea: Reversed Stereospecificity of the Catalytic and Noncatalytic Reaction.},
journal = {Angewandte Chemie (International ed. in English)},
volume = {37},
number = {23},
pages = {3300-3303},
doi = {10.1002/(SICI)1521-3773(19981217)37:23&lt;3300::AID-ANIE3300&gt;3.0.CO;2-A},
pmid = {29711416},
issn = {1521-3773},
abstract = {By activation of the hydrogen acceptor, the metal-free hydrogenase from methanogenic archaea catalyzes the reduction of methenyl tetrahydromethanopterin with H2 . According to NMR spectroscopic analysis of the conformation of the hydrogen acceptor in solution and of the stereospecificity of the catalyzed and noncatalyzed reaction, in the enzyme-catalyzed reaction the hydrogenation product is formed in a constraint conformation which relaxes upon dissociation from the enzyme. This exergonic conformational change could help to avoid product inhibition of the enzyme.},
}
@article {pmid29699482,
year = {2018},
author = {Mitić, NS and Malkov, SN and Kovačević, JJ and Pavlović-Lažetić, GM and Beljanski, MV},
title = {Structural disorder of plasmid-encoded proteins in Bacteria and Archaea.},
journal = {BMC bioinformatics},
volume = {19},
number = {1},
pages = {158},
pmid = {29699482},
issn = {1471-2105},
support = {174021//Ministry of Education, Science and Technological Development, Republic of Serbia/International ; },
mesh = {Archaea/*genetics ; Archaeal Proteins/*chemistry ; Bacteria/*genetics ; Bacterial Proteins/*chemistry ; Chromosomes, Archaeal/metabolism ; Chromosomes, Bacterial/metabolism ; Intrinsically Disordered Proteins/*chemistry ; Plasmids/*metabolism ; Proteome/metabolism ; Toxins, Biological/chemistry ; },
abstract = {BACKGROUND: In the last decade and a half it has been firmly established that a large number of proteins do not adopt a well-defined (ordered) structure under physiological conditions. Such intrinsically disordered proteins (IDPs) and intrinsically disordered (protein) regions (IDRs) are involved in essential cell processes through two basic mechanisms: the entropic chain mechanism which is responsible for rapid fluctuations among many alternative conformations, and molecular recognition via short recognition elements that bind to other molecules. IDPs possess a high adaptive potential and there is special interest in investigating their involvement in organism evolution.<br><br>RESULTS: We analyzed 2554 Bacterial and 139 Archaeal proteomes, with a total of 8,455,194 proteins for disorder content and its implications for adaptation of organisms, using three disorder predictors and three measures. Along with other findings, we revealed that for all three predictors and all three measures (1) Bacteria exhibit significantly more disorder than Archaea; (2) plasmid-encoded proteins contain considerably more IDRs than proteins encoded on chromosomes (or whole genomes) in both prokaryote superkingdoms; (3) plasmid proteins are significantly more disordered than chromosomal proteins only in the group of proteins with no COG category assigned; (4) antitoxin proteins in comparison to other proteins, are the most disordered (almost double) in both Bacterial and Archaeal proteomes; (5) plasmidal proteins are more disordered than chromosomal proteins in Bacterial antitoxins and toxin-unclassified proteins, but have almost the same disorder content in toxin proteins.<br><br>CONCLUSION: Our results suggest that while disorder content depends on genome and proteome characteristics, it is more influenced by functional engagements than by gene location (on chromosome or plasmid).},
}
@article {pmid29687586,
year = {2018},
author = {Meinhardt, KA and Stopnisek, N and Pannu, MW and Strand, SE and Fransen, SC and Casciotti, KL and Stahl, DA},
title = {Ammonia-oxidizing bacteria are the primary N2 O producers in an ammonia-oxidizing archaea dominated alkaline agricultural soil.},
journal = {Environmental microbiology},
volume = {20},
number = {6},
pages = {2195-2206},
doi = {10.1111/1462-2920.14246},
pmid = {29687586},
issn = {1462-2920},
support = {DE-SC0006869//Genomic Science and Technology for Energy and the Environment/International ; },
mesh = {Agriculture ; Ammonia/chemistry/*metabolism ; Archaea/*metabolism ; Bacteria/classification/*metabolism ; Fertilizers/analysis ; Nitrification ; Nitrogen ; Nitrous Oxide/*metabolism ; Oxidation-Reduction ; Soil/chemistry ; *Soil Microbiology ; },
abstract = {Most agricultural N2 O emissions are a consequence of microbial transformations of nitrogen (N) fertilizer, and mitigating increases in N2 O emission will depend on identifying microbial sources and variables influencing their activities. Here, using controlled microcosm and field studies, we found that synthetic N addition in any tested amount stimulated the production of N2 O from ammonia-oxidizing bacteria (AOB), but not archaea (AOA), from a bioenergy crop soil. The activities of these two populations were differentiated by N treatments, with abundance and activity of AOB increasing as nitrate and N2 O production increased. Moreover, as N2 O production increased, the isotopic composition of N2 O was consistent with an AOB source. Relative N2 O contributions by both populations were quantified using selective inhibitors and varying N availability. Complementary field analyses confirmed a positive correlation between N2 O flux and AOB abundance with N application. Collectively, our data indicate that AOB are the major N2 O producers, even with low N addition, and that better-metered N application, complemented by selective inhibitors, could reduce projected N2 O emissions from agricultural soils.},
}
@article {pmid29684598,
year = {2018},
author = {Aouad, M and Taib, N and Oudart, A and Lecocq, M and Gouy, M and Brochier-Armanet, C},
title = {Extreme halophilic archaea derive from two distinct methanogen Class II lineages.},
journal = {Molecular phylogenetics and evolution},
volume = {127},
number = {},
pages = {46-54},
doi = {10.1016/j.ympev.2018.04.011},
pmid = {29684598},
issn = {1095-9513},
mesh = {Bayes Theorem ; Conserved Sequence ; Euryarchaeota/*classification ; Genes, Archaeal ; Genomics ; *Phylogeny ; *Salinity ; },
abstract = {Phylogenetic analyses of conserved core genes have disentangled most of the ancient relationships in Archaea. However, some groups remain debated, like the DPANN, a deep-branching super-phylum composed of nanosized archaea with reduced genomes. Among these, the Nanohaloarchaea require high-salt concentrations for growth. Their discovery in 2012 was significant because they represent, together with Halobacteria (a Class belonging to Euryarchaeota), the only two described lineages of extreme halophilic archaea. The phylogenetic position of Nanohaloarchaea is highly debated, being alternatively proposed as the sister-lineage of Halobacteria or a member of the DPANN super-phylum. Pinpointing the phylogenetic position of extreme halophilic archaea is important to improve our knowledge of the deep evolutionary history of Archaea and the molecular adaptive processes and evolutionary paths that allowed their emergence. Using comparative genomic approaches, we identified 258 markers carrying a reliable phylogenetic signal. By combining strategies limiting the impact of biases on phylogenetic inference, we showed that Nanohaloarchaea and Halobacteria represent two independent lines that derived from two distinct but related methanogen Class II lineages. This implies that adaptation to high salinity emerged twice independently in Archaea and indicates that emergence of Nanohaloarchaea within DPANN in previous studies is likely the consequence of a tree reconstruction artifact, challenging the existence of this super-phylum.},
}
@article {pmid29684129,
year = {2018},
author = {Clouet-d'Orval, B and Batista, M and Bouvier, M and Quentin, Y and Fichant, G and Marchfelder, A and Maier, LK},
title = {Insights into RNA-processing pathways and associated RNA-degrading enzymes in Archaea.},
journal = {FEMS microbiology reviews},
volume = {42},
number = {5},
pages = {579-613},
doi = {10.1093/femsre/fuy016},
pmid = {29684129},
issn = {1574-6976},
mesh = {Archaea/*enzymology/metabolism ; Endoribonucleases/*metabolism ; Exoribonucleases/*metabolism ; RNA Processing, Post-Transcriptional/*physiology ; },
abstract = {RNA-processing pathways are at the centre of regulation of gene expression. All RNA transcripts undergo multiple maturation steps in addition to covalent chemical modifications to become functional in the cell. This includes destroying unnecessary or defective cellular RNAs. In Archaea, information on mechanisms by which RNA species reach their mature forms and associated RNA-modifying enzymes are still fragmentary. To date, most archaeal actors and pathways have been proposed in light of information gathered from Bacteria and Eukarya. In this context, this review provides a state of the art overview of archaeal endoribonucleases and exoribonucleases that cleave and trim RNA species and also of the key small archaeal proteins that bind RNAs. Furthermore, synthetic up-to-date views of processing and biogenesis pathways of archaeal transfer and ribosomal RNAs as well as of maturation of stable small non-coding RNAs such as CRISPR RNAs, small C/D and H/ACA box guide RNAs, and other emerging classes of small RNAs are described. Finally, prospective post-transcriptional mechanisms to control archaeal messenger RNA quality and quantity are discussed.},
}
@article {pmid29672703,
year = {2018},
author = {Keshri, V and Panda, A and Levasseur, A and Rolain, JM and Pontarotti, P and Raoult, D},
title = {Phylogenomic Analysis of β-Lactamase in Archaea and Bacteria Enables the Identification of Putative New Members.},
journal = {Genome biology and evolution},
volume = {10},
number = {4},
pages = {1106-1114},
pmid = {29672703},
issn = {1759-6653},
mesh = {Anti-Bacterial Agents/adverse effects/therapeutic use ; Archaea/enzymology ; Bacteria/enzymology ; Carbapenems/*biosynthesis/chemistry ; Humans ; Metagenomics ; *Phylogeny ; beta-Lactamases/*genetics ; beta-Lactams/*metabolism ; },
abstract = {β-lactamases are enzymes which are commonly produced by bacteria and which degrade the β-lactam ring of β-lactam antibiotics, namely penicillins, cephalosporins, carbapenems, and monobactams, and inactivate these antibiotics. We performed a rational and comprehensive investigation of β-lactamases in different biological databases. In this study, we constructed hidden Markov model profiles as well as the ancestral sequence of four classes of β-lactamases (A, B, C, and D), which were used to identify potential β-lactamases from environmental metagenomic (1206), human microbiome metagenomic (6417), human microbiome reference genome (1310), and NCBI's nonredundant databases (44101). Our analysis revealed the existence of putative β-lactamases in the metagenomic databases, which appeared to be similar to the four different molecular classes (A-D). This is the first report on the large-scale phylogenetic diversity of new members of β-lactamases, and our results revealed that metagenomic database dark-matter contains β-lactamase-like antibiotic resistance genes.},
}
@article {pmid29668953,
year = {2018},
author = {Ausiannikava, D and Mitchell, L and Marriott, H and Smith, V and Hawkins, M and Makarova, KS and Koonin, EV and Nieduszynski, CA and Allers, T},
title = {Evolution of Genome Architecture in Archaea: Spontaneous Generation of a New Chromosome in Haloferax volcanii.},
journal = {Molecular biology and evolution},
volume = {35},
number = {8},
pages = {1855-1868},
pmid = {29668953},
issn = {1537-1719},
support = {BB/K007211/2/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/M001393/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {*Biological Evolution ; *Chromosomes, Archaeal ; *Genome, Archaeal ; Haloferax volcanii/*genetics ; Replicon ; },
abstract = {The common ancestry of archaea and eukaryotes is evident in their genome architecture. All eukaryotic and several archaeal genomes consist of multiple chromosomes, each replicated from multiple origins. Three scenarios have been proposed for the evolution of this genome architecture: 1) mutational diversification of a multi-copy chromosome; 2) capture of a new chromosome by horizontal transfer; 3) acquisition of new origins and splitting into two replication-competent chromosomes. We report an example of the third scenario: the multi-origin chromosome of the archaeon Haloferax volcanii has split into two elements via homologous recombination. The newly generated elements are bona fide chromosomes, because each bears "chromosomal" replication origins, rRNA loci, and essential genes. The new chromosomes were stable during routine growth but additional genetic manipulation, which involves selective bottlenecks, provoked further rearrangements. To the best of our knowledge, rearrangement of a naturally evolved prokaryotic genome to generate two new chromosomes has not been described previously.},
}
@article {pmid29668558,
year = {2018},
author = {Brugère, JF and Ben Hania, W and Arnal, ME and Ribière, C and Ballet, N and Vandeckerkove, P and Ollivier, B and O'Toole, PW},
title = {Archaea: Microbial Candidates in Next-generation Probiotics Development.},
journal = {Journal of clinical gastroenterology},
volume = {52 Suppl 1, Proceedings from the 9th Probiotics, Prebiotics and New Foods, Nutraceuticals and Botanicals for Nutrition &amp; Human and Microbiota Health Meeting, held in Rome, Italy from September 10 to 12, 2017},
number = {},
pages = {S71-S73},
doi = {10.1097/MCG.0000000000001043},
pmid = {29668558},
issn = {1539-2031},
mesh = {Archaea/*growth &amp; development ; *Gastrointestinal Microbiome ; Humans ; Probiotics/*analysis ; },
abstract = {Pharmabiotics and probiotics in current use or under development belong to 2 of 3 domains of life, Eukarya (eg, yeasts) and Bacteria (eg, lactobacilli). Archaea constitute a third domain of life, and are currently not used as probiotics, despite several interesting features. This includes the absence of known pathogens in humans, animals, or plants and the existence of some archaea closely associated to humans in various microbiomes. We promote the concept that some specific archaea that naturally thrive in the human gut are potential next-generation probiotics that can be rationally selected on the basis of their metabolic phenotype not being encountered in other human gut microbes, neither Bacteria nor Eukarya. The example of the possible bioremediation of the proatherogenic compound trimethylamine into methane by archaeal microbes is described.},
}
@article {pmid29666365,
year = {2018},
author = {Alves, RJE and Minh, BQ and Urich, T and von Haeseler, A and Schleper, C},
title = {Unifying the global phylogeny and environmental distribution of ammonia-oxidising archaea based on amoA genes.},
journal = {Nature communications},
volume = {9},
number = {1},
pages = {1517},
pmid = {29666365},
issn = {2041-1723},
support = {P 25369/FWF_/Austrian Science Fund FWF/Austria ; },
mesh = {Ammonia/*metabolism ; Archaea/*genetics/metabolism ; *Biodiversity ; Evolution, Molecular ; Gene Frequency ; Nitrogen Cycle/genetics ; Oceans and Seas ; Oxidation-Reduction ; Oxidoreductases/*genetics ; Oxygenases/genetics ; *Phylogeny ; Soil Microbiology ; },
abstract = {Ammonia-oxidising archaea (AOA) are ubiquitous and abundant in nature and play a major role in nitrogen cycling. AOA have been studied intensively based on the amoA gene (encoding ammonia monooxygenase subunit A), making it the most sequenced functional marker gene. Here, based on extensive phylogenetic and meta-data analyses of 33,378 curated archaeal amoA sequences, we define a highly resolved taxonomy and uncover global environmental patterns that challenge many earlier generalisations. Particularly, we show: (i) the global frequency of AOA is extremely uneven, with few clades dominating AOA diversity in most ecosystems; (ii) characterised AOA do not represent most predominant clades in nature, including soils and oceans; (iii) the functional role of the most prevalent environmental AOA clade remains unclear; and (iv) AOA harbour molecular signatures that possibly reflect phenotypic traits. Our work synthesises information from a decade of research and provides the first integrative framework to study AOA in a global context.},
}
@article {pmid29656122,
year = {2018},
author = {Rother, M and Quitzke, V},
title = {Selenoprotein synthesis and regulation in Archaea.},
journal = {Biochimica et biophysica acta. General subjects},
volume = {1862},
number = {11},
pages = {2451-2462},
doi = {10.1016/j.bbagen.2018.04.008},
pmid = {29656122},
issn = {1872-8006},
abstract = {BACKGROUND: The major biological form of selenium is that of the co-translationally inserted amino acid selenocysteine (Sec). In Archaea, the majority of proteins containing Sec, selenoproteins, are involved in methanogenesis. However, the function of this residue is often not known because selenium-independent homologs of the selenoproteins can be employed, sometimes even in one organism.<br><br>SCOPE OF REVIEW: This review summarizes current knowledge about the selenoproteins of Archaea, the metabolic pathways where they are involved, and discusses the (potential) function of individual Sec residues. Also, what is known about the "archaeal" way of selenoprotein synthesis, and the regulatory mechanism leading to the replacement of the selenoproteins with selenium-independent homologs, will be presented. Where appropriate, similarities with (and differences to) the respective steps employed in the other two domains, Bacteria and Eukarya, will be emphasized.<br><br>MAJOR CONCLUSIONS: Genetic and biochemical studies guided by analysis of genome sequences of Sec-encoding archaea has revealed that the pathway of Sec synthesis in Archaea and Eukarya are principally identical and that Sec insertion in Eukarya probably evolved from an archaeal mechanism employed prior to the separation of the archaeal and eukaryal lines of decent.<br><br>GENERAL SIGNIFICANCE: In light of the emerging close phylogenetic relationship of Eukarya and Archaea, archaeal models may be highly valuable tools for unraveling "eukaryotic" principles in molecular and cell biology.},
}
@article {pmid29643403,
year = {2018},
author = {Wei, Z and Wang, J and Zhu, L and Wang, J and Zhu, G},
title = {Toxicity of enrofloxacin, copper and their interactions on soil microbial populations and ammonia-oxidizing archaea and bacteria.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {5828},
pmid = {29643403},
issn = {2045-2322},
mesh = {Ammonia/metabolism ; Anti-Bacterial Agents/*toxicity ; Archaea/*drug effects/enzymology/isolation &amp; purification ; Archaeal Proteins/metabolism ; Bacteria/*drug effects/enzymology/isolation &amp; purification ; Bacterial Proteins/metabolism ; Copper/toxicity ; Enrofloxacin/toxicity ; Environmental Pollution/adverse effects ; Metals, Heavy/*toxicity ; Oxidation-Reduction/drug effects ; Oxidoreductases/metabolism ; Soil/chemistry ; Soil Microbiology ; Soil Pollutants/*toxicity ; },
abstract = {Enrofloxacin (EFX) is one of the most frequently used broad-spectrum veterinary drugs, and copper (Cu) is a heavy metal that could easily bind to certain antibiotic molecules. Hence EFX and Cu were chosen as representatives of antibiotics and heavy metals to explore the abundance and variation of soil microbial populations with a plate-counting technique, as well as the copy numbers of amoA gene in ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) by quantitative PCR methods in Argosols samples. Treatments of applied EFX (0.05, 0.20, 0.80 mmol/kg), Cu (1.60 mmol/kg) and combined EFX and Cu (at molar ratios of 1:32,1:8,1:2) exhibited various effects on different soil microorganisms. The toxicity of combined EFX and Cu was more strongly expressed on both soil microbial populations and amoA gene (AOA and AOB) compared to the EFX treatment alone, in most cases, time and dose effects were observed. With respect to the amoA gene, the AOA-amoA gene was more abundant than the AOB-amoA gene, and the ratio ranged from ~8 to ~11. Moreover, the interaction types of EFX and Cu were more likely to be antagonistic (64.29%) than synergistic (35.71%) on soil abundance and function, which may be related to the incubation time and the ratio of EFX to Cu in the soil.},
}
@article {pmid29636434,
year = {2018},
author = {Gilmour, CC and Bullock, AL and McBurney, A and Podar, M and Elias, DA},
title = {Robust Mercury Methylation across Diverse Methanogenic Archaea.},
journal = {mBio},
volume = {9},
number = {2},
pages = {},
pmid = {29636434},
issn = {2150-7511},
support = {R01 ES024284/ES/NIEHS NIH HHS/United States ; },
mesh = {Archaea/genetics/*metabolism ; Culture Media/chemistry ; Cysteine/metabolism ; Genes, Archaeal ; Mercuric Chloride/*metabolism ; Methane/*metabolism ; Methylation ; Methylmercury Compounds/*metabolism ; Sulfides/metabolism ; },
abstract = {Methylmercury (MeHg) production was compared among nine cultured methanogenic archaea that contain hgcAB, a gene pair that codes for mercury (Hg) methylation. The methanogens tested produced MeHg at inherently different rates, even when normalized to growth rate and Hg availability. Eight of the nine tested were capable of MeHg production greater than that of spent- and uninoculated-medium controls during batch culture growth. Methanococcoides methylutens, an hgcAB[+] strain with a fused gene pair, was unable to produce more MeHg than controls. Maximal conversion of Hg to MeHg through a full batch culture growth cycle for each species (except M. methylutens) ranged from 2 to >50% of the added Hg(II) or between 0.2 and 17 pmol of MeHg/mg of protein. Three of the species produced >10% MeHg. The ability to produce MeHg was confirmed in several hgcAB[+] methanogens that had not previously been tested (Methanocella paludicola SANAE, Methanocorpusculum bavaricum, Methanofollis liminatans GKZPZ, and Methanosphaerula palustris E1-9c). Maximal methylation was observed at low sulfide concentrations (<100 μM) and in the presence of 0.5 to 5 mM cysteine. For M. hollandica, the addition of up to 5 mM cysteine enhanced MeHg production and cell growth in a concentration-dependent manner. As observed for bacterial Hg methylators, sulfide inhibited MeHg production. An initial evaluation of sulfide and thiol impacts on bioavailability showed methanogens responding to Hg complexation in the same way as do Deltaproteobacteria The mercury methylation rates of several methanogens rival those of the better-studied Hg-methylating sulfate- and iron-reducing DeltaproteobacteriaIMPORTANCEArchaea, specifically methanogenic organisms, play a role in mercury methylation in nature, but their global importance to MeHg production and the subsequent risk to ecosystems are not known. Methanogenesis has been linked to Hg methylation in several natural habitats where methylmercury production incurs risk to people and ecosystems, including rice paddies and permafrost. In this study, we confirm that most methanogens carrying the hgcAB gene pair are capable of Hg methylation. We found that methylation rates vary inherently among hgcAB[+] methanogens but that several species are capable of MeHg production at rates that rival those of the better-know Hg-methylating sulfate- and iron-reducing bacteria. Methanogens may need to be considered equally with sulfate and iron reducers in evaluations of MeHg production in nature.},
}
@article {pmid29631688,
year = {2018},
author = {Khallef, S and Lestini, R and Myllykallio, H and Houali, K},
title = {Isolation and identification of two extremely halophilic archaea from sebkhas in the Algerian Sahara.},
journal = {Cellular and molecular biology (Noisy-le-Grand, France)},
volume = {64},
number = {4},
pages = {83-91},
pmid = {29631688},
issn = {1165-158X},
mesh = {Africa, Northern ; Algeria ; DNA, Archaeal/*genetics ; Halobacteriaceae/classification/drug effects/genetics/*isolation &amp; purification ; Halorubrum/classification/drug effects/genetics/*isolation &amp; purification ; Hydrogen-Ion Concentration ; Lakes/*microbiology ; RNA, Ribosomal, 16S/*genetics ; Salinity ; Sequence Analysis, DNA ; Sodium Chloride/pharmacology ; },
abstract = {In Algeria, many salt lakes are to be found spread from southern Tunisia up to the Atlas Mountains in northern Algeria. Oum Eraneb and Ain El beida sebkhas (salt lakes), are located in the Algerian Sahara. The aim of this study was to explore the diversity of the halobacteria in this type of habitats. The physicochemical properties of these shallow saline environments were examined and compared with other hypersaline and marine ecosystems. Both sites were relatively alkaline with a pH around 8.57- 8.74 and rich in salt at 13% and 16% (w/v) salinity for Oum Eraneb and Ain El beida, respectively, with dominant ions of sodium and chloride. The microbial approach revealed the presence of two halophilic archaea, strains JCM13561 and A33T in both explored sebkhas. Growth occurred between 10 and 25% (w/v) NaCl and the isolates grow optimally at 20% (w/v) NaCl. The pH range for growth was 6 to 9.5 with an optimum at pH 7.5 for the first strain and 7 to 9.5 with an optimum pH at 8.5-9 for the second strain. On the basis of 16S rRNA gene sequence analysis, strains JCM13561 and A33T were most closely related to Halorubrum litoreum and Natronorubrum bangense (99% and 96% similarity, respectively).},
}
@article {pmid29625978,
year = {2018},
author = {McGlynn, SE and Chadwick, GL and O'Neill, A and Mackey, M and Thor, A and Deerinck, TJ and Ellisman, MH and Orphan, VJ},
title = {Subgroup Characteristics of Marine Methane-Oxidizing ANME-2 Archaea and Their Syntrophic Partners as Revealed by Integrated Multimodal Analytical Microscopy.},
journal = {Applied and environmental microbiology},
volume = {84},
number = {11},
pages = {},
pmid = {29625978},
issn = {1098-5336},
support = {P41 GM103412/GM/NIGMS NIH HHS/United States ; },
mesh = {Anaerobiosis ; Archaea/*classification/metabolism/*ultrastructure ; Deltaproteobacteria/metabolism/ultrastructure ; Geologic Sediments/microbiology ; In Situ Hybridization, Fluorescence ; Methane/*metabolism ; Microbial Consortia ; Microscopy, Electron ; Oxidation-Reduction ; Phylogeny ; *Symbiosis ; },
abstract = {Phylogenetically diverse environmental ANME archaea and sulfate-reducing bacteria cooperatively catalyze the anaerobic oxidation of methane oxidation (AOM) in multicelled consortia within methane seep environments. To better understand these cells and their symbiotic associations, we applied a suite of electron microscopy approaches, including correlative fluorescence in situ hybridization-electron microscopy (FISH-EM), transmission electron microscopy (TEM), and serial block face scanning electron microscopy (SBEM) three-dimensional (3D) reconstructions. FISH-EM of methane seep-derived consortia revealed phylogenetic variability in terms of cell morphology, ultrastructure, and storage granules. Representatives of the ANME-2b clade, but not other ANME-2 groups, contained polyphosphate-like granules, while some bacteria associated with ANME-2a/2c contained two distinct phases of iron mineral chains resembling magnetosomes. 3D segmentation of two ANME-2 consortium types revealed cellular volumes of ANME and their symbiotic partners that were larger than previous estimates based on light microscopy. Polyphosphate-like granule-containing ANME (tentatively termed ANME-2b) were larger than both ANME with no granules and partner bacteria. This cell type was observed with up to 4 granules per cell, and the volume of the cell was larger in proportion to the number of granules inside it, but the percentage of the cell occupied by these granules did not vary with granule number. These results illuminate distinctions between ANME-2 archaeal lineages and partnering bacterial populations that are apparently unified in their ability to perform anaerobic methane oxidation.IMPORTANCE Methane oxidation in anaerobic environments can be accomplished by a number of archaeal groups, some of which live in syntrophic relationships with bacteria in structured consortia. Little is known of the distinguishing characteristics of these groups. Here, we applied imaging approaches to better understand the properties of these cells. We found unexpected morphological, structural, and volume variability of these uncultured groups by correlating fluorescence labeling of cells with electron microscopy observables.},
}
@article {pmid29622618,
year = {2018},
author = {Poehlein, A and Heym, D and Quitzke, V and Fersch, J and Daniel, R and Rother, M},
title = {Complete Genome Sequence of the Methanococcus maripaludis Type Strain JJ (DSM 2067), a Model for Selenoprotein Synthesis in Archaea.},
journal = {Genome announcements},
volume = {6},
number = {14},
pages = {},
pmid = {29622618},
issn = {2169-8287},
abstract = {Methanococcus maripaludis type strain JJ (DSM 2067) is an important organism because it serves as a model for primary energy metabolism and hydrogenotrophic methanogenesis and is amenable to genetic manipulation. The complete genome (1.7 Mb) harbors 1,815 predicted protein-encoding genes, including 9 encoding selenoproteins.},
}
@article {pmid29618058,
year = {2018},
author = {Feng, X and Sun, M and Han, W and Liang, YX and She, Q},
title = {A transcriptional factor B paralog functions as an activator to DNA damage-responsive expression in archaea.},
journal = {Nucleic acids research},
volume = {46},
number = {14},
pages = {7085-7096},
pmid = {29618058},
issn = {1362-4962},
mesh = {4-Nitroquinoline-1-oxide/pharmacology ; Archaeal Proteins/biosynthesis/chemistry/genetics/*metabolism ; Crenarchaeota/genetics ; DNA Damage ; *DNA Repair ; Evolution, Molecular ; Gene Deletion ; Promoter Regions, Genetic ; Protein Domains ; Sulfolobus/cytology/drug effects/*genetics/metabolism ; Transcription Factors/biosynthesis/chemistry/genetics/*metabolism ; Transcriptional Activation ; },
abstract = {Previously it was shown that UV irradiation induces a strong upregulation of tfb3 coding for a paralog of the archaeal transcriptional factor B (TFB) in Sulfolobus solfataricus, a crenarchaea. To investigate the function of this gene in DNA damage response (DDR), tfb3 was inactivated by gene deletion in Sulfolobus islandicus and the resulting Δtfb3 was more sensitive to DNA damage agents than the original strain. Transcriptome analysis revealed that a large set of genes show TFB3-dependent activation, including genes of the ups operon and ced system. Furthermore, the TFB3 protein was found to be associated with DDR gene promoters and functional dissection of TFB3 showed that the conserved Zn-ribbon and coiled-coil motif are essential for the activation. Together, the results indicated that TFB3 activates the expression of DDR genes by interaction with other transcriptional factors at the promoter regions of DDR genes to facilitate the formation of transcription initiation complex. Strikingly, TFB3 and Ced systems are present in a wide range of crenarchaea, suggesting that the Ced system function as a primary DNA damage repair mechanism in Crenarchaeota. Our findings further suggest that TFB3 and the concurrent TFB1 form a TFB3-dependent DNA damage-responsive circuit with their target genes, which is evolutionarily conserved in the major lineage of Archaea.},
}
@article {pmid29596428,
year = {2018},
author = {Da Cunha, V and Gaia, M and Nasir, A and Forterre, P},
title = {Asgard archaea do not close the debate about the universal tree of life topology.},
journal = {PLoS genetics},
volume = {14},
number = {3},
pages = {e1007215},
pmid = {29596428},
issn = {1553-7404},
mesh = {*Archaea ; *Eukaryota ; Euryarchaeota ; Phylogeny ; Prokaryotic Cells ; },
}
@article {pmid29596421,
year = {2018},
author = {Spang, A and Eme, L and Saw, JH and Caceres, EF and Zaremba-Niedzwiedzka, K and Lombard, J and Guy, L and Ettema, TJG},
title = {Asgard archaea are the closest prokaryotic relatives of eukaryotes.},
journal = {PLoS genetics},
volume = {14},
number = {3},
pages = {e1007080},
pmid = {29596421},
issn = {1553-7404},
mesh = {Archaea/*genetics ; Eukaryota/*genetics ; Euryarchaeota ; Genome, Archaeal ; Prokaryotic Cells ; },
}
@article {pmid29595162,
year = {2018},
author = {Kiadehi, MSH and Amoozegar, MA and Asad, S and Siroosi, M},
title = {Exploring the potential of halophilic archaea for the decolorization of azo dyes.},
journal = {Water science and technology : a journal of the International Association on Water Pollution Research},
volume = {77},
number = {5-6},
pages = {1602-1611},
doi = {10.2166/wst.2018.040},
pmid = {29595162},
issn = {0273-1223},
mesh = {Archaea/*metabolism ; Azo Compounds/*chemistry/*metabolism ; Biodegradation, Environmental ; Carbon ; Coloring Agents/chemistry/metabolism ; Coordination Complexes/chemistry ; Naphthalenesulfonates/chemistry ; Nitrogen ; Sodium Chloride ; Textile Industry ; Waste Disposal, Fluid ; },
abstract = {Azo dyes are being extensively used in textile industries, so finding a proper solution to decolorize them is of high importance. In order to find azo dye decolorizing strains among haloarchaea, which are well known for their tolerance to harsh environmental conditions, fifteen haloarchaeal strains were screened. Halogeometricum sp. strain A and Haloferax sp. strain B with the highest decolorization ability (95% and 91% for Remazol black B; both about 60% for Acid blue 161, respectively) were selected for further studies. It was shown that both strains were able to grow and decolorize the dye in a medium containing up to 5 M NaCl, with optimum decolorization activity at 2.5-3.4 M, pH 7, and a wide temperature range between 30 to 45 °C. Moreover, both strains were able to tolerate and decolorize up to 1,000 mg l[-1] Remazol black B. Also, they were able to survive in 5,000 mg l[-1] of the dye after 20 days' incubation. Glucose and yeast extract were found to be the best carbon and nitrogen sources in the decolorization medium for both strains. This is the first report studying decolorization of azo dyes using halophilic archaea.},
}
@article {pmid29573609,
year = {2018},
author = {Pillot, G and Frouin, E and Pasero, E and Godfroy, A and Combet-Blanc, Y and Davidson, S and Liebgott, PP},
title = {Specific enrichment of hyperthermophilic electroactive Archaea from deep-sea hydrothermal vent on electrically conductive support.},
journal = {Bioresource technology},
volume = {259},
number = {},
pages = {304-311},
doi = {10.1016/j.biortech.2018.03.053},
pmid = {29573609},
issn = {1873-2976},
mesh = {*Archaea ; Atlantic Ocean ; Bacteria ; Electrolysis ; *Hydrothermal Vents ; Phylogeny ; RNA, Ribosomal, 16S ; Seawater ; },
abstract = {While more and more investigations are done to study hyperthermophilic exoelectrogenic communities from environments, none have been performed yet on deep-sea hydrothermal vent. Samples of black smoker chimney from Rainbow site on the Atlantic mid-oceanic ridge have been harvested for enriching exoelectrogens in microbial electrolysis cells under hyperthermophilic (80 °C) condition. Two enrichments were performed in a BioElectrochemical System specially designed: one from direct inoculation of crushed chimney and the other one from inoculation of a pre-cultivation on iron (III) oxide. In both experiments, a current production was observed from 2.4 A/m[2] to 5.8 A/m[2] with a set anode potential of -0.110 V vs Ag/AgCl. Taxonomic affiliation of the exoelectrogen communities obtained on the electrode exhibited a specific enrichment of Archaea belonging to Thermococcales and Archeoglobales orders, even when both inocula were dominated by Bacteria.},
}
@article {pmid29522733,
year = {2018},
author = {},
title = {Extreme Excitement about Archaea.},
journal = {Cell},
volume = {172},
number = {6},
pages = {1153-1154},
doi = {10.1016/j.cell.2018.02.038},
pmid = {29522733},
issn = {1097-4172},
}
@article {pmid29510582,
year = {2018},
author = {Gelsinger, DR and DiRuggiero, J},
title = {The Non-Coding Regulatory RNA Revolution in Archaea.},
journal = {Genes},
volume = {9},
number = {3},
pages = {},
pmid = {29510582},
issn = {2073-4425},
support = {T32 GM007231/GM/NIGMS NIH HHS/United States ; },
abstract = {Small non-coding RNAs (sRNAs) are ubiquitously found in the three domains of life playing large-scale roles in gene regulation, transposable element silencing and defense against foreign elements. While a substantial body of experimental work has been done to uncover function of sRNAs in Bacteria and Eukarya, the functional roles of sRNAs in Archaea are still poorly understood. Recently, high throughput studies using RNA-sequencing revealed that sRNAs are broadly expressed in the Archaea, comprising thousands of transcripts within the transcriptome during non-challenged and stressed conditions. Antisense sRNAs, which overlap a portion of a gene on the opposite strand (cis-acting), are the most abundantly expressed non-coding RNAs and they can be classified based on their binding patterns to mRNAs (3' untranslated region (UTR), 5' UTR, CDS-binding). These antisense sRNAs target many genes and pathways, suggesting extensive roles in gene regulation. Intergenic sRNAs are less abundantly expressed and their targets are difficult to find because of a lack of complete overlap between sRNAs and target mRNAs (trans-acting). While many sRNAs have been validated experimentally, a regulatory role has only been reported for very few of them. Further work is needed to elucidate sRNA-RNA binding mechanisms, the molecular determinants of sRNA-mediated regulation, whether protein components are involved and how sRNAs integrate with complex regulatory networks.},
}
@article {pmid29507381,
year = {2018},
author = {Burns, JA and Pittis, AA and Kim, E},
title = {Publisher Correction: Gene-based predictive models of trophic modes suggest Asgard archaea are not phagocytotic.},
journal = {Nature ecology &amp; evolution},
volume = {2},
number = {4},
pages = {751},
doi = {10.1038/s41559-018-0520-8},
pmid = {29507381},
issn = {2397-334X},
abstract = {In the version of this Article originally published, question marks appeared in Table 1; they should have been tick marks. This has now been corrected in all versions of the Article.},
}
@article {pmid29497404,
year = {2018},
author = {Liu, J and Yu, Z and Yao, Q and Sui, Y and Shi, Y and Chu, H and Tang, C and Franks, AE and Jin, J and Liu, X and Wang, G},
title = {Ammonia-Oxidizing Archaea Show More Distinct Biogeographic Distribution Patterns than Ammonia-Oxidizing Bacteria across the Black Soil Zone of Northeast China.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {171},
pmid = {29497404},
issn = {1664-302X},
abstract = {Black soils (Mollisols) of northeast China are highly productive and agriculturally important for food production. Ammonia-oxidizing microbes play an important role in N cycling in the black soils. However, the information related to the composition and distribution of ammonia-oxidizing microbes in the black soils has not yet been addressed. In this study, we used the amoA gene to quantify the abundance and community composition of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) across the black soil zone. The amoA abundance of AOA was remarkably larger than that of AOB, with ratios of AOA/AOB in the range from 3.1 to 91.0 across all soil samples. The abundance of AOA amoA was positively correlated with total soil C content (p < 0.001) but not with soil pH (p > 0.05). In contrast, the abundance of AOB amoA positively correlated with soil pH (p = 0.009) but not with total soil C. Alpha diversity of AOA did not correlate with any soil parameter, however, alpha diversity of AOB was affected by multiple soil factors, such as soil pH, total P, N, and C, available K content, and soil water content. Canonical correspondence analysis indicated that the AOA community was mainly affected by the sampling latitude, followed by soil pH, total P and C; while the AOB community was mainly determined by soil pH, as well as total P, C and N, water content, and sampling latitude, which highlighted that the AOA community was more geographically distributed in the black soil zone of northeast China than AOB community. In addition, the pairwise analyses showed that the potential nitrification rate (PNR) was not correlated with alpha diversity but weakly positively with the abundance of the AOA community (p = 0.048), whereas PNR significantly correlated positively with the richness (p = 0.003), diversity (p = 0.001) and abundance (p < 0.001) of the AOB community, which suggested that AOB community might make a greater contribution to nitrification than AOA community in the black soils when ammonium is readily available.},
}
@article {pmid29478661,
year = {2018},
author = {Ma, W and Sun, J and Li, Y and Lun, X and Shan, D and Nie, C and Liu, M},
title = {17α-Ethynylestradiol biodegradation in different river-based groundwater recharge modes with reclaimed water and degradation-associated community structure of bacteria and archaea.},
journal = {Journal of environmental sciences (China)},
volume = {64},
number = {},
pages = {51-61},
doi = {10.1016/j.jes.2016.11.022},
pmid = {29478661},
issn = {1001-0742},
mesh = {Archaea/physiology ; Bacteria/metabolism ; Ethinyl Estradiol/analysis/*metabolism ; Groundwater/chemistry/*microbiology ; Rivers/chemistry/*microbiology ; Water Microbiology ; Water Pollutants, Chemical/analysis/*metabolism ; },
abstract = {This study investigated 17α-ethynylestradiol (EE2) biodegradation process and primary metabolic pathways associated with community structures of microorganism during groundwater recharge using reclaimed water. The attenuation rate is 1.58 times higher in wetting and drying alternative recharge (WDAR) than in continual recharge (CR). The primary biotransformation pathways of EE2 in WDAR system began with the oxidation of C-17 on ring D to form a ketone group, and D-ring was subsequently hydroxylated and cleaved. In the CR system, the metabolic pathway changed from the oxidation of C-17 on ring D to hydroxylation of C-4 on ring A, and ring A or B subsequently cleaved; this transition was related to DO, and the microbial community structure. Four hundred fifty four pyrosequencing of 16s rRNA genes indicated that the bacterial communities in the upper layer of the WDAR system were more diverse than those found in the bottom layer of the CR system; this result was reversed for archaea. Unweighted UniFrac and taxonomic analyses were conducted to relate the change in bacterial community structure to the metabolic pathway. Microorganism community diversity and structure were related to the concentrations of dissolved oxygen, EE2 and its intermediates in the system. Five known bacterial classes and one known archaeal class, five major bacterial genera and one major archaeal genus might be involved in EE2 degradation. The findings of this study provide an understanding of EE2 biodegradation in groundwater recharge areas under different recharging modes and can facilitate the prediction of the fate of EE2 in underground aquifers.},
}
@article {pmid29472326,
year = {2018},
author = {Oger, PM},
title = {Complete Genome Sequences of 11 Type Species from the Thermococcus Genus of Hyperthermophilic and Piezophilic Archaea.},
journal = {Genome announcements},
volume = {6},
number = {8},
pages = {},
pmid = {29472326},
issn = {2169-8287},
abstract = {We report here the genome sequences of the type strains of the species Thermococcus barossii, T. celer, T. chitonophagus, T. gorgonarius, T. pacificus, T. peptonophilus, T. profundus, T. radiotolerans, T. siculi, and T. thioreducens, as well as the prototype of a possible type strain of a novel Thermococcus species, strain P6.},
}
@article {pmid29465796,
year = {2018},
author = {Abdul Halim, MF and Rodriguez, R and Stoltzfus, JD and Duggin, IG and Pohlschroder, M},
title = {Conserved residues are critical for Haloferax volcanii archaeosortase catalytic activity: Implications for convergent evolution of the catalytic mechanisms of non-homologous sortases from archaea and bacteria.},
journal = {Molecular microbiology},
volume = {108},
number = {3},
pages = {276-287},
doi = {10.1111/mmi.13935},
pmid = {29465796},
issn = {1365-2958},
support = {R25 GM071745/GM/NIGMS NIH HHS/United States ; },
mesh = {Amino Acid Sequence ; Aminoacyltransferases/genetics/*metabolism ; Archaea/genetics ; Archaeal Proteins/metabolism ; Arginine/metabolism ; Bacteria/genetics ; Bacterial Proteins/genetics/metabolism ; Biological Evolution ; Catalysis ; Catalytic Domain ; Conserved Sequence/genetics ; Cysteine/metabolism ; Cysteine Endopeptidases/genetics/*metabolism ; Evolution, Molecular ; Haloferax volcanii/*metabolism ; Histidine/metabolism ; Protein Processing, Post-Translational ; },
abstract = {Proper protein anchoring is key to the biogenesis of prokaryotic cell surfaces, dynamic, resilient structures that play crucial roles in various cell processes. A novel surface protein anchoring mechanism in Haloferax volcanii depends upon the peptidase archaeosortase A (ArtA) processing C-termini of substrates containing C-terminal tripartite structures and anchoring mature substrates to the cell membrane via intercalation of lipid-modified C-terminal amino acid residues. While this membrane protein lacks clear homology to soluble sortase transpeptidases of Gram-positive bacteria, which also process C-termini of substrates whose C-terminal tripartite structures resemble those of ArtA substrates, archaeosortases do contain conserved cysteine, arginine and arginine/histidine/asparagine residues, reminiscent of His-Cys-Arg residues of sortase catalytic sites. The study presented here shows that ArtA[WT] -GFP expressed in trans complements ΔartA growth and motility phenotypes, while alanine substitution mutants, Cys[173] (C173A), Arg[214] (R214A) or Arg[253] (R253A), and the serine substitution mutant for Cys[173] (C173S), fail to complement these phenotypes. Consistent with sortase active site replacement mutants, ArtA[C173A] -GFP, ArtA[C173S] -GFP and ArtA[R214A] -GFP cannot process substrates, while replacement of the third residue, ArtA[R253A] -GFP retains some processing activity. These findings support the view that similarities between certain aspects of the structures and functions of the sortases and archaeosortases are the result of convergent evolution.},
}
@article {pmid29459706,
year = {2018},
author = {Burns, JA and Pittis, AA and Kim, E},
title = {Gene-based predictive models of trophic modes suggest Asgard archaea are not phagocytotic.},
journal = {Nature ecology &amp; evolution},
volume = {2},
number = {4},
pages = {697-704},
doi = {10.1038/s41559-018-0477-7},
pmid = {29459706},
issn = {2397-334X},
mesh = {Archaea/classification/*physiology ; *Models, Genetic ; *Phagocytosis ; Phylogeny ; },
abstract = {With the current explosion of genomic data, there is a greater need to draw inference on phenotypic information based on DNA sequence alone. We considered complete genomes from 35 diverse eukaryotic lineages, and discovered sets of proteins predictive of trophic mode, including a set of 485 proteins that are enriched among phagocytotic eukaryotes (organisms that internalize large particles). Our model is also predictive of other aspects of trophic mode, including photosynthesis and the ability to synthesize a set of organic compounds needed for growth (prototrophy for those molecules). We applied our model to the Asgard archaea, a group of uncultured microorganisms that show close affinities to eukaryotes, to test whether the organisms are capable of phagocytosis, a phenotypic trait often considered a prerequisite for mitochondrial acquisition. Our analyses suggest that members of the Asgard archaea-despite having some eukaryote-specific protein families not found in other prokaryotes-do not use phagocytosis. Moreover, our data suggest that the process of phagocytosis arose from a combination of both archaeal and bacterial components, but also required additional eukaryote-specific innovations.},
}
@article {pmid29459337,
year = {2018},
author = {Yan, L and Wang, G and Ai, S and Huo, Z and Wang, Y and Gu, JD and Wang, W},
title = {Abundance of ammonia-oxidizing bacteria and archaea under different ventilation strategies during cattle manure composting.},
journal = {Journal of environmental management},
volume = {212},
number = {},
pages = {375-383},
doi = {10.1016/j.jenvman.2018.02.032},
pmid = {29459337},
issn = {1095-8630},
mesh = {Ammonia ; Animals ; Archaea/*growth &amp; development ; Bacteria/*growth &amp; development ; Cattle ; *Composting ; *Manure ; Oxidation-Reduction ; Phylogeny ; Soil Microbiology ; Ventilation ; },
abstract = {Composting of cattle manure was conducted under four ventilation strategies, i.e., no-aeration (A-00), continuous aeration (B-44), non-aeration for 14 d and then aeration for 42 d (C-04), aeration for 14 d and then no-aeration for 42 d (D-40). Physicochemical parameters and potential ammonia oxidation (PAO) indicated that continuous and intermittent ventilation provide favourable conditions for ammonia-oxidizing bacteria (AOB) and archaea (AOA) to oxidize ammonia. Quantitative PCR (qPCR) analysis showed AOB amoA gene abundance of all treatments on every sampling day ranged from 2.25 × 10[5] to 2.76 × 10[9]copies/g, was significantly lower than that of archaeal amoA gene from 2.71 × 10[8] to 9.05 × 10[11]copies/g. There was also a significantly positive relationship between PAO rates and AOB (r[2] ≥ 0.066, p < 0.05) and AOA (r[2] ≥ 0.300, p < 0.05) abundance. These data suggested that ammonia oxidation is driven by both AOA and AOB in cattle manure composting.},
}
@article {pmid29459210,
year = {2018},
author = {Araujo, ASF and Mendes, LW and Bezerra, WM and Nunes, LAPL and Lyra, MDCCP and Figueiredo, MDVB and Melo, VMM},
title = {Archaea diversity in vegetation gradients from the Brazilian Cerrado.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {49},
number = {3},
pages = {522-528},
pmid = {29459210},
issn = {1678-4405},
mesh = {Archaea/classification/genetics/growth &amp; development/*isolation &amp; purification ; Biodiversity ; Brazil ; Phylogeny ; Plant Development ; Plants/classification/*microbiology ; Soil/chemistry ; *Soil Microbiology ; },
abstract = {We used 16S rRNA sequencing to assess the archaeal communities across a gradient of Cerrado. The archaeal communities differed across the gradient. Crenarcheota was the most abundant phyla, with Nitrosphaerales and NRPJ as the predominant classes. Euryachaeota was also found across the Cerrado gradient, including the classes Metanocellales and Methanomassiliicoccaceae.},
}
@article {pmid29458865,
year = {2018},
author = {Menasria, T and Aguilera, M and Hocine, H and Benammar, L and Ayachi, A and Si Bachir, A and Dekak, A and Monteoliva-Sánchez, M},
title = {Diversity and bioprospecting of extremely halophilic archaea isolated from Algerian arid and semi-arid wetland ecosystems for halophilic-active hydrolytic enzymes.},
journal = {Microbiological research},
volume = {207},
number = {},
pages = {289-298},
doi = {10.1016/j.micres.2017.12.011},
pmid = {29458865},
issn = {1618-0623},
mesh = {Algeria ; Biodiversity ; Esterases/*genetics ; Halobacteriaceae/*classification/*enzymology/genetics/isolation &amp; purification ; Lakes/chemistry ; Peptide Hydrolases/*genetics ; RNA, Ribosomal, 16S/genetics ; Salinity ; Sodium Chloride/analysis ; Wetlands ; },
abstract = {The diversity of haloarchaea associated with different dry salt lakes in northeastern Algeria was investigated together with their potential of hydrolytic enzyme production. A total of 68 aerobic halophilic archaea were isolated from saline sediments. Based on the 16S rRNA gene sequencing, the isolates were assigned to seven phylotypes within the class Halobacteria, namely Haloarcula, Halococcus, Haloferax, Halogeometricum, Haloterrigena, Natrialba, and Natrinema. The results showed that Haloferax group was found to be dominant in all samples (30 isolates) (44%) with high diversity, followed by Halococcus spp. (13%) (9 isolates). All phylotypes are extreme halophiles and thermotolerant with the ability to grow at temperatures up to 48 °C. In addition, the screening for extracellular halophilic enzymes showed that 89.7% of the isolates were able to produce at least two types of the screened enzymes. The strains producing esterase, gelatinase, inulinase, cellulase and protease activities were the most diverse functional group. These data showed an abundant and diverse haloarchaeal community, detected in Algerian wetland ecosystems, presenting a promising source of molecules with important biotechnological applications.},
}
@article {pmid29456526,
year = {2018},
author = {He, H and Zhen, Y and Mi, T and Fu, L and Yu, Z},
title = {Ammonia-Oxidizing Archaea and Bacteria Differentially Contribute to Ammonia Oxidation in Sediments from Adjacent Waters of Rushan Bay, China.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {116},
pmid = {29456526},
issn = {1664-302X},
abstract = {Ammonia oxidation plays a significant role in the nitrogen cycle in marine sediments. Ammonia-oxidizing archaea (AOA) and bacteria (AOB) are the key contributors to ammonia oxidation, and their relative contribution to this process is one of the most important issues related to the nitrogen cycle in the ocean. In this study, the differential contributions of AOA and AOB to ammonia oxidation in surface sediments from adjacent waters of Rushan Bay were studied based on the ammonia monooxygenase (amoA) gene. Molecular biology techniques were used to analyze ammonia oxidizers' community characteristics, and potential nitrification incubation was applied to understand the ammonia oxidizers' community activity. The objective was to determine the community structure and activity of AOA and AOB in surface sediments from adjacent waters of Rushan Bay and to discuss the different contributions of AOA and AOB to ammonia oxidation during summer and winter seasons in the studied area. Pyrosequencing analysis revealed that the diversity of AOA was higher than that of AOB. The majority of AOA and AOB clustered into Nitrosopumilus and Nitrosospira, respectively, indicating that the Nitrosopumilus group and Nitrosospira groups may be more adaptable in studied sediments. The AOA community was closely correlated to temperature, salinity and ammonium concentration, whereas the AOB community showed a stronger correlation with temperature, chlorophyll-a content (chla) and nitrite concentration. qPCR results showed that both the abundance and the transcript abundance of AOA was consistently greater than that of AOB. AOA and AOB differentially contributed to ammonia oxidation in different seasons. AOB occupied the dominant position in mediating ammonia oxidation during summer, while AOA might play a dominant role in ammonia oxidation during winter.},
}
@article {pmid29446847,
year = {2018},
author = {Řezanka, T and Kolouchová, I and Gharwalová, L and Palyzová, A and Sigler, K},
title = {Lipidomic Analysis: From Archaea to Mammals.},
journal = {Lipids},
volume = {53},
number = {1},
pages = {5-25},
doi = {10.1002/lipd.12001},
pmid = {29446847},
issn = {1558-9307},
mesh = {Animals ; Archaea/chemistry/*genetics ; Chromatography, High Pressure Liquid ; Chromatography, Liquid ; Humans ; Lipid Metabolism/*genetics ; Lipids/chemistry/*genetics ; Mammals/genetics ; Metabolomics/*methods ; },
abstract = {Lipids are among the most important organic compounds found in all living cells, from primitive archaebacteria to flowering plants or mammalian cells. They form part of cell walls and constitute cell storage material. Their biosynthesis and metabolism play key roles in faraway topics such as biofuel production (third-generation biofuels produced by microorganisms, e.g. algae) and human diseases such as adrenoleukodystrophy, Zellweger syndrome, or Refsum disease. Current lipidomic analysis requires fast and accurate processing of samples and especially their characterization. Because the number of possible lipids and, more specifically, molecular species of lipids is of the order of hundreds to thousands, it is necessary to process huge amounts of data in a short time. There are two basic approaches to lipidomic analysis: shotgun and liquid chromatography-mass spectometry. Both methods have their pros and cons. This review deals with lipidomics not according to the type of ionization or the lipid classes analyzed but according to the types of samples (organisms) under study. Thus, it is divided into lipidomic analysis of archaebacteria, bacteria, yeast, fungi, algae, plants, and animals.},
}
@article {pmid29429071,
year = {2018},
author = {Huang, Z and Jiang, Y and Song, X and Hallerman, E and Peng, L and Dong, D and Ma, T and Zhai, J and Li, W},
title = {Ammonia-oxidizing bacteria and archaea within biofilters of a commercial recirculating marine aquaculture system.},
journal = {AMB Express},
volume = {8},
number = {1},
pages = {17},
pmid = {29429071},
issn = {2191-0855},
support = {31502212//National Natural Science Foundation of China/ ; },
abstract = {While biofilters are widely used to metabolize ammonia and other wastes in marine recirculating aquaculture systems, the ammonia-oxidizing bacterial and archaeal communities have not been characterized across a diversity of production systems. Using a metagenomics approach, we characterized the ammonia-oxidizing microbiological community of biofilters in a commercial recirculating marine aquaculture system producing hybrid grouper (Epinephelus lanceolatus × E. fuscoguttatus). Cloning and sequencing of the amoA gene showed that nitrifying bacteria included Nitrosomonas europea, N. stercoris, N. cryotolerans, N. eutropha, N. estuarii, eight strains of N. marina, and 15 strains not associated with described species. Nitrifying archaea included eight strains of Nitrosopumilus maritimus, N. koreensis, N. piranensis, N. adriaticus, undescribed congeners, and other undescribed archaea. The species composition of the bacterial and especially the archaeal communities was beyond that yet reported for aquaculture biofilters. While ammonia flux through the respective communities has yet to be estimated, the diverse environmental adaptations of the bacterial and archaeal communities suggest resilience of function under a range of environmental conditions.},
}
@article {pmid29406516,
year = {2018},
author = {Bowers, RM and Kyrpides, NC and Stepanauskas, R and Harmon-Smith, M and Doud, D and Reddy, TBK and Schulz, F and Jarett, J and Rivers, AR and Eloe-Fadrosh, EA and Tringe, SG and Ivanova, NN and Copeland, A and Clum, A and Becraft, ED and Malmstrom, RR and Birren, B and Podar, M and Bork, P and Weinstock, GM and Garrity, GM and Dodsworth, JA and Yooseph, S and Sutton, G and Glöckner, FO and Gilbert, JA and Nelson, WC and Hallam, SJ and Jungbluth, SP and Ettema, TJG and Tighe, S and Konstantinidis, KT and Liu, WT and Baker, BJ and Rattei, T and Eisen, JA and Hedlund, B and McMahon, KD and Fierer, N and Knight, R and Finn, R and Cochrane, G and Karsch-Mizrachi, I and Tyson, GW and Rinke, C and , and Lapidus, A and Meyer, F and Yilmaz, P and Parks, DH and Eren, AM and Schriml, L and Banfield, JF and Hugenholtz, P and Woyke, T},
title = {Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.},
journal = {Nature biotechnology},
volume = {36},
number = {2},
pages = {196},
pmid = {29406516},
issn = {1546-1696},
}
@article {pmid29401401,
year = {2018},
author = {Brzezińska-Błaszczyk, E and Pawłowska, E and Płoszaj, T and Witas, H and Godzik, U and Agier, J},
title = {Presence of archaea and selected bacteria in infected root canal systems.},
journal = {Canadian journal of microbiology},
volume = {64},
number = {5},
pages = {317-326},
doi = {10.1139/cjm-2017-0531},
pmid = {29401401},
issn = {1480-3275},
mesh = {Adult ; Archaea/*genetics ; Bacterial Infections/*microbiology ; Bacteroidaceae/*genetics ; DNA, Bacterial/genetics ; Dental Pulp Cavity/microbiology ; Dental Pulp Necrosis/*microbiology ; Female ; Humans ; Male ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Reverse Transcriptase Polymerase Chain Reaction ; Young Adult ; },
abstract = {Infections of the root canal have polymicrobial etiology. The main group of microflora in the infected pulp is bacteria. There is limited data that archaea may be present in infected pulp tissue. The aim of this study was to check the prevalence of archaea in necrotic root canal samples obtained from patients with primary or post-treatment infection. The prevalence of selected bacteria species (Prevotella intermedia, Porphyromonas gingivalis, Tannerella forsythia, Treponema denticola, Synergistes sp.) in necrotic samples was evaluated as well. Sixty-four samples from root canal were collected for DNA and RNA extraction. A PCR assay based on the 16S rRNA gene was used to determine the presence of archaea and selected bacteria. Of the 64 samples, 6 were analyzed by semiquantitative reverse transcription PCR to estimate expression profiles of 16S rRNA, and another 9 were selected for direct sequencing. Archaea were detected in 48.4% samples. Statistical analysis indicated a negative association in coexistence between archaea and Treponema denticola (P < 0.05; Pearson's χ[2] test). The main representative of the Archaea domain found in infected pulp tissue was Methanobrevibacter oralis. Archaea 16S rRNA gene expression was significantly lower than Synergistes sp., Porphyromonas gingivalis, and Tannerella forsythia (P < 0.05; Student's t test). Thus, it can be hypothesized that archaea may participate in the endodontic microbial community.},
}
@article {pmid29396546,
year = {2018},
author = {Gonzalez-Martinez, A and Sihvonen, M and Muñoz-Palazon, B and Rodriguez-Sanchez, A and Mikola, A and Vahala, R},
title = {Microbial ecology of full-scale wastewater treatment systems in the Polar Arctic Circle: Archaea, Bacteria and Fungi.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {2208},
pmid = {29396546},
issn = {2045-2322},
mesh = {Archaea/classification/genetics/*isolation &amp; purification ; Arctic Regions ; Bacteria/classification/genetics/*isolation &amp; purification ; Bioreactors/*microbiology ; *Biota ; Finland ; Fungi/classification/genetics/*isolation &amp; purification ; Metagenomics ; Real-Time Polymerase Chain Reaction ; Sequence Analysis, DNA ; Sewage/microbiology ; Wastewater/*microbiology ; Water Purification ; },
abstract = {Seven full-scale biological wastewater treatment systems located in the Polar Arctic Circle region in Finland were investigated to determine their Archaea, Bacteria and Fungi community structure, and their relationship with the operational conditions of the bioreactors by the means of quantitative PCR, massive parallel sequencing and multivariate redundancy analysis. The results showed dominance of Archaea and Bacteria members in the bioreactors. The activated sludge systems showed strong selection of Bacteria but not for Archaea and Fungi, as suggested by diversity analyses. Core OTUs in influent and bioreactors were classified as Methanobrevibacter, Methanosarcina, Terrestrial Group Thaumarchaeota and unclassified Euryarchaeota member for Archaea; Trichococcus, Leptotrichiaceae and Comamonadaceae family, and Methylorosula for Bacteria and Trichosporonaceae family for Fungi. All influents shared core OTUs in all domains, but in bioreactors this did not occur for Bacteria. Oligotype structure of core OTUs showed several ubiquitous Fungi oligotypes as dominant in sewage and bioreactors. Multivariate redundancy analyses showed that the majority of core OTUs were related to organic matter and nutrients removal. Also, there was evidence of competition among Archaea and Fungi core OTUs, while all Bacteria OTUs were positively correlated among them. The results obtained highlighted interesting features of extremely cold temperature bioreactors.},
}
@article {pmid29390107,
year = {2018},
author = {Seyler, LM and McGuinness, LR and Gilbert, JA and Biddle, JF and Gong, D and Kerkhof, LJ},
title = {Discerning autotrophy, mixotrophy and heterotrophy in marine TACK archaea from the North Atlantic.},
journal = {FEMS microbiology ecology},
volume = {94},
number = {3},
pages = {},
doi = {10.1093/femsec/fiy014},
pmid = {29390107},
issn = {1574-6941},
mesh = {Archaea/genetics/isolation &amp; purification/*metabolism ; Atlantic Ocean ; Autotrophic Processes ; Carbon/metabolism ; Carbon Cycle ; Heterotrophic Processes ; Phylogeny ; Seawater/*microbiology ; },
abstract = {DNA stable isotope probing (SIP) was used to track the uptake of organic and inorganic carbon sources for TACK archaea (Thaumarchaeota/Aigarchaeota/Crenarchaeota/Korarchaeota) on a cruise of opportunity in the North Atlantic. Due to water limitations, duplicate samples from the deep photic (60-115 m), the mesopelagic zones (local oxygen minimum; 215-835 m) and the bathypelagic zone (2085-2835 m) were amended with various combinations of 12C- or 13C-acetate/urea/bicarbonate to assess cellular carbon acquisition. The SIP results indicated the majority of TACK archaeal operational taxonomic units (OTUs) incorporated 13C from acetate and/or urea into newly synthesized DNA within 48 h. A small fraction (16%) of the OTUs, often representing the most dominant members of the archaeal community, were able to incorporate bicarbonate in addition to organic substrates. Only two TACK archaeal OTUs were found to incorporate bicarbonate but not urea or acetate. These results further demonstrate the utility of SIP to elucidate the metabolic capability of mesothermal archaea in distinct oceanic settings and suggest that TACK archaea play a role in organic carbon recycling in the mid-depth to deep ocean.},
}
@article {pmid29371667,
year = {2018},
author = {Li, M and Wei, G and Shi, W and Sun, Z and Li, H and Wang, X and Gao, Z},
title = {Distinct distribution patterns of ammonia-oxidizing archaea and bacteria in sediment and water column of the Yellow River estuary.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {1584},
pmid = {29371667},
issn = {2045-2322},
mesh = {Ammonia/*metabolism ; Ammonium Compounds/analysis ; Archaea/*classification/isolation &amp; purification/metabolism ; Bacteria/*classification/isolation &amp; purification/metabolism ; *Biota ; Carbon/analysis ; China ; *Estuaries ; Geologic Sediments/chemistry/*microbiology ; Oxidation-Reduction ; Rivers/*microbiology ; Water/chemistry ; },
abstract = {Ammonia oxidation is a critical process of estuarine nitrogen cycling involving ammonia-oxidizing archaea (AOA) and bacteria (AOB). However, the distribution patterns of ammonia-oxidizing microorganisms (AOMs) between different habitats in the same area remain unclear. The present study investigated the AOMs' abundance and community compositions in both sediment and water habitats of the Yellow River estuary. Quantitative PCR (qPCR) revealed that AOA showed significant higher abundance than AOB both in sediment and water samples. AOA and AOB abundance distribution trends were consistent in sediment but distinct in water along the sampling sites. Clone library-based analyses showed that AOA sequences were affiliated with Nitrososphaera, Nitrosopumilus and Nitrosotalea clusters. Generally, Nitrososphaera was predominant in sediment, while Nitrosopumilus and Nitrosotalea dominated in water column. AOB sequences were classified into genera Nitrosospira and Nitrosomonas, and Nitrosospira dominated in both habitats. Principal coordinate analysis (PCoA) also indicated AOA community structures exhibited significant differences between two habitats, while AOB were not. Ammonium and carbon contents were the potential key factors to influence AOMs' abundance and compositions in sediment, while no measured variables were determined to have major influences on communities in water habitat. These findings increase the understanding of the AOMs' distribution patterns in estuarine ecosystems.},
}
@article {pmid29357055,
year = {2017},
author = {Bell, SD},
title = {Initiation of DNA Replication in the Archaea.},
journal = {Advances in experimental medicine and biology},
volume = {1042},
number = {},
pages = {99-115},
doi = {10.1007/978-981-10-6955-0_5},
pmid = {29357055},
issn = {0065-2598},
mesh = {Archaea/*genetics/metabolism ; Archaeal Proteins/metabolism/physiology ; Chromosomes/metabolism ; DNA Replication/*physiology ; *Replication Origin/genetics ; },
abstract = {Organisms within the archaeal domain of life possess a simplified version of the eukaryotic DNA replication machinery. While some archaea possess a bacterial-like mode of DNA replication with single origins of replication per chromosome, the majority of species characterized to date possess chromosomes with multiple replication origins. Genetic, structural, and biochemical studies have revealed the nature of archaeal origin specification. Recent work has begun to shed light on the mechanisms of replication initiation in these organisms.},
}
@article {pmid29354356,
year = {2018},
author = {Singh, A and Singh, AK},
title = {Isolation, characterization and exploring biotechnological potential of halophilic archaea from salterns of western India.},
journal = {3 Biotech},
volume = {8},
number = {1},
pages = {45},
pmid = {29354356},
issn = {2190-572X},
abstract = {Thirteen halophilic archaea were isolated from Kandla and Bhayander salt pans. These isolates were grouped into three different genera Halobacterium, Haloferax and Haloarcula based on morphological and biochemical characterization, polar lipid analysis, Amplified 16S rDNA restriction analysis (ARDRA) and 16S rDNA sequence analysis. Biochemical characterization suggested the ability of isolates to produce protease, amylase and poly-hydroxybutyrate (PHB) indicating their biotechnological potential. The isolates were further screened for the amount of extracellular protease produced. Halobacterium sp. SP1(1) showed significant protease production compared to other isolates. Protease producing ability of the isolate was influenced by several factors such as NaCl concentration, type of protein source, metal ions and surfactants, and presence of amino acid supplements in the production medium. Soybean flour, FeCl3 and dicotylsulfosuccinate were found to increase protease production by 2.36, 1.54 and 1.26 folds, respectively compared to production in basal medium. Effect of organic solvents used in paints (n-decane, n-undecane and n-dodecane) was also investigated on protease production by the isolate. Protease production by Halobacterium sp. SP1(1) was enhanced by 1.2 folds in presence of n-decane compared to control. Furthermore, the ability of isolate to hydrolyse fish protein was investigated using three different edible fishes (Pomfret, Flat fish and Seer fish) as sole protein source. Pomfret was found to be a good protein source for protease production by the isolate. These results revealed that Halobacterium sp. SP1(1) may have potential for paint-based antifouling coating preparations and fish sauce preparation by virtue of its extracellular protease.},
}
@article {pmid29335805,
year = {2018},
author = {Oren, A and Hirschberg, J and Mann, V and Jehlička, J},
title = {Effects of nicotine on the biosynthesis of carotenoids in halophilic Archaea (class Halobacteria): an HPLC and Raman spectroscopy study.},
journal = {Extremophiles : life under extreme conditions},
volume = {22},
number = {3},
pages = {359-366},
pmid = {29335805},
issn = {1433-4909},
support = {2221/15//Israel Science Foundation/ ; 850/13//Israel Science Foundation/ ; 17-04270S//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/ ; },
mesh = {Carotenoids/analysis/*biosynthesis ; Euryarchaeota/chemistry/*drug effects/metabolism ; Nicotine/*pharmacology ; Nicotinic Agonists/*pharmacology ; },
abstract = {Nicotine has a profound influence on the carotenoid metabolism in halophilic Archaea of the class Halobacteria. In a study of Halobacterium salinarum, Haloarcula marismortui and Halorubrum sodomense, using different analytical techniques to monitor the production of different carotenoids as a function of the presence of nicotine, we showed that the formation of α-bacterioruberin was inhibited in all. In Hbt. salinarum, addition of nicotine led to a significant change in the color of the culture due to the accumulation of lycopene, in addition to the formation of bisanhydrobacterioruberin which does not differ in color from α-bacterioruberin. Very little or no lycopene was formed in Har. marismortui and in Hrr. sodomense; instead bisanhydrobacterioruberin was the only major carotenoid found in nicotine-amended cultures. The findings are discussed in the framework of the recently elucidated biochemical pathway for the formation of the different carotenoid pigments encountered in the Halobacteria.},
}
@article {pmid29329319,
year = {2018},
author = {Bader, M and Müller, K and Foerstendorf, H and Schmidt, M and Simmons, K and Swanson, JS and Reed, DT and Stumpf, T and Cherkouk, A},
title = {Comparative analysis of uranium bioassociation with halophilic bacteria and archaea.},
journal = {PloS one},
volume = {13},
number = {1},
pages = {e0190953},
pmid = {29329319},
issn = {1932-6203},
mesh = {Bacteria/classification/growth &amp; development/*metabolism ; Halobacterium/classification/growth &amp; development/*metabolism ; Microscopy, Electron, Scanning ; Phylogeny ; Radioactive Waste ; Spectrometry, X-Ray Emission ; Spectroscopy, Fourier Transform Infrared ; Uranium/*metabolism ; },
abstract = {Rock salt represents a potential host rock formation for the final disposal of radioactive waste. The interactions between indigenous microorganisms and radionuclides, e.g. uranium, need to be investigated to better predict the influence of microorganisms on the safety assessment of the repository. Hence, the association process of uranium with two microorganisms isolated from rock salt was comparatively studied. Brachybacterium sp. G1, which was isolated from the German salt dome Gorleben, and Halobacterium noricense DSM15987T, were selected as examples of a moderately halophilic bacterium and an extremely halophilic archaeon, respectively. The microorganisms exhibited completely different association behaviors with uranium. While a pure biosorption process took place with Brachybacterium sp. G1 cells, a multistage association process occurred with the archaeon. In addition to batch experiments, in situ attenuated total reflection Fourier-transform infrared spectroscopy was applied to characterize the U(VI) interaction process. Biosorption was identified as the dominating process for Brachybacterium sp. G1 with this method. Carboxylic functionalities are the dominant interacting groups for the bacterium, whereas phosphoryl groups are also involved in U(VI) association by the archaeon H. noricense.},
}
@article {pmid29322393,
year = {2018},
author = {Srithep, P and Pornkulwat, P and Limpiyakorn, T},
title = {Contribution of ammonia-oxidizing archaea and ammonia-oxidizing bacteria to ammonia oxidation in two nitrifying reactors.},
journal = {Environmental science and pollution research international},
volume = {25},
number = {9},
pages = {8676-8687},
pmid = {29322393},
issn = {1614-7499},
support = {RSA5780036//Thailand Research Fund (TH)/ ; },
mesh = {Ammonia/*analysis ; Archaea/genetics/*isolation &amp; purification ; Autotrophic Processes ; Betaproteobacteria/genetics/*isolation &amp; purification ; Bioreactors/*microbiology ; Oxidation-Reduction ; Phylogeny ; Sewage/microbiology ; Water Pollutants, Chemical/*analysis ; Water Purification/*methods ; },
abstract = {In this study, two laboratory nitrifying reactors (NRI and NRII), which were seeded by sludge from different sources and operated under different operating conditions, were found to possess distinct dominant ammonia-oxidizing microorganisms. Ammonia-oxidizing archaeal (AOA) amoA genes outnumbered ammonia-oxidizing bacterial (AOB) amoA genes in reactor NRI, while only AOB amoA genes were detectable in reactor NRII. The AOA amoA gene sequences retrieved from NRI were characterized within the Nitrososphaera sister cluster of the group 1.1b Thaumarchaeota. Two inhibitors for ammonia oxidation, allylthiourea (ATU) and 2-phenyl-4,4,5,5-tetramethylimidazoline-1-oxyl 3-oxide (PTIO), were applied individually and as a mixture to observe the ammonia-oxidizing activity of both microorganisms in the reactors' sludge. The results indicated that AOA and AOB jointly oxidized ammonia in NRI, while AOB played the main role in ammonia oxidation in NRII. DNA-stable isotope probing with labeled [13]C-HCO3[-] was performed on NRI sludge. Incorporation of [13]C into AOA and AOB implied that both microorganisms may perform autotrophy during ammonia oxidation. Taken together, the results from this study provide direct evidence demonstrating the contribution of AOA and AOB to ammonia oxidation in the nitrifying reactors.},
}
@article {pmid29268981,
year = {2018},
author = {Kelman, LM and Kelman, Z},
title = {Do Archaea Need an Origin of Replication?.},
journal = {Trends in microbiology},
volume = {26},
number = {3},
pages = {172-174},
pmid = {29268981},
issn = {1878-4380},
support = {9999-NIST/ImNIST/Intramural NIST DOC/United States ; },
mesh = {Archaea/*genetics/growth &amp; development/metabolism ; Archaeal Proteins/genetics/metabolism ; Chromosomes, Archaeal/genetics ; DNA Replication/genetics/physiology ; DNA, Archaeal/genetics ; Genes, Archaeal/*genetics ; Microbial Viability/genetics ; Replication Origin/*genetics/*physiology ; },
abstract = {Chromosomal DNA replication starts at a specific region called an origin of replication. Until recently, all organisms were thought to require origins to replicate their chromosomes. It was recently discovered that some archaeal species do not utilize origins of replication under laboratory growth conditions.},
}
@article {pmid29235710,
year = {2018},
author = {Xie, W and Luo, H and Murugapiran, SK and Dodsworth, JA and Chen, S and Sun, Y and Hedlund, BP and Wang, P and Fang, H and Deng, M and Zhang, CL},
title = {Localized high abundance of Marine Group II archaea in the subtropical Pearl River Estuary: implications for their niche adaptation.},
journal = {Environmental microbiology},
volume = {20},
number = {2},
pages = {734-754},
doi = {10.1111/1462-2920.14004},
pmid = {29235710},
issn = {1462-2920},
mesh = {Adaptation, Physiological/*physiology ; Archaea/classification/*genetics/isolation &amp; purification/*metabolism ; China ; Ecology ; Estuaries ; Metagenome/genetics ; Phylogeny ; Plankton/*growth &amp; development ; RNA, Ribosomal, 16S/genetics ; Rivers/*microbiology ; Salinity ; Seawater/microbiology ; },
abstract = {Marine Group II archaea are widely distributed in global oceans and dominate the total archaeal community within the upper euphotic zone of temperate waters. However, factors controlling the distribution of MGII are poorly delineated and the physiology and ecological functions of these still-uncultured organisms remain elusive. In this study, we investigated the planktonic MGII associated with particles and in free-living forms in the Pearl River Estuary (PRE) over a 10-month period. We detected high abundance of particle-associated MGII in PRE (up to ∼10[8] 16S rRNA gene copies/l), which was around 10-fold higher than the free-living MGII in the same region, and an order of magnitude higher than previously reported in other marine environments. 10‰ salinity appeared to be a threshold value for these MGII because MGII abundance decreased sharply below it. Above 10‰ salinity, the abundance of MGII on the particles was positively correlated with phototrophs and MGII in the surface water was negatively correlated with irradiance. However, the abundances of those free-living MGII showed positive correlations with salinity and temperature, suggesting the different physiological characteristics between particle-attached and free-living MGIIs. A nearly completely assembled metagenome, MGIIa_P, was recovered using metagenome binning methods. Compared with the other two MGII genomes from surface ocean, MGIIa_P contained higher proportions of glycoside hydrolases, indicating the ability of MGIIa_P to hydrolyse glycosidic bonds in complex sugars in PRE. MGIIa_P is the first assembled MGII metagenome containing a catalase gene, which might be involved in scavenging reactive oxygen species generated by the abundant phototrophs in the eutrophic PRE. Our study presented the widespread and high abundance of MGII in the water columns of PRE, and characterized the determinant abiotic factors affecting their distribution. Their association with heterotrophs, preference for particles and resourceful metabolic traits indicate MGII might play a significant role in metabolising organic matters in the PRE and other temperate estuarine systems.},
}
@article {pmid29222443,
year = {2018},
author = {Chen, LX and Méndez-García, C and Dombrowski, N and Servín-Garcidueñas, LE and Eloe-Fadrosh, EA and Fang, BZ and Luo, ZH and Tan, S and Zhi, XY and Hua, ZS and Martinez-Romero, E and Woyke, T and Huang, LN and Sánchez, J and Peláez, AI and Ferrer, M and Baker, BJ and Shu, WS},
title = {Metabolic versatility of small archaea Micrarchaeota and Parvarchaeota.},
journal = {The ISME journal},
volume = {12},
number = {3},
pages = {756-775},
pmid = {29222443},
issn = {1751-7370},
mesh = {Amino Acids/metabolism ; Archaea/classification/genetics/isolation &amp; purification/*metabolism ; Biodiversity ; Biological Evolution ; Carbon/metabolism ; Fresh Water/microbiology ; Genome, Archaeal ; Genomics ; Hot Springs/microbiology ; Iron/metabolism ; Nitrogen/metabolism ; Nitrogen Cycle ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Small acidophilic archaea belonging to Micrarchaeota and Parvarchaeota phyla are known to physically interact with some Thermoplasmatales members in nature. However, due to a lack of cultivation and limited genomes on hand, their biodiversity, metabolisms, and physiologies remain largely unresolved. Here, we obtained 39 genomes from acid mine drainage (AMD) and hot spring environments around the world. 16S rRNA gene based analyses revealed that Parvarchaeota were only detected in AMD and hot spring habitats, while Micrarchaeota were also detected in others including soil, peat, hypersaline mat, and freshwater, suggesting a considerable higher diversity and broader than expected habitat distribution for this phylum. Despite their small genomes (0.64-1.08 Mb), these archaea may contribute to carbon and nitrogen cycling by degrading multiple saccharides and proteins, and produce ATP via aerobic respiration and fermentation. Additionally, we identified several syntenic genes with homology to those involved in iron oxidation in six Parvarchaeota genomes, suggesting their potential role in iron cycling. However, both phyla lack biosynthetic pathways for amino acids and nucleotides, suggesting that they likely scavenge these biomolecules from the environment and/or other community members. Moreover, low-oxygen enrichments in laboratory confirmed our speculation that both phyla are microaerobic/anaerobic, based on several specific genes identified in them. Furthermore, phylogenetic analyses provide insights into the close evolutionary history of energy related functionalities between both phyla with Thermoplasmatales. These results expand our understanding of these elusive archaea by revealing their involvement in carbon, nitrogen, and iron cycling, and suggest their potential interactions with Thermoplasmatales on genomic scale.},
}
@article {pmid29218041,
year = {2017},
author = {Ito, M and Morino, M and Krulwich, TA},
title = {Mrp Antiporters Have Important Roles in Diverse Bacteria and Archaea.},
journal = {Frontiers in microbiology},
volume = {8},
number = {},
pages = {2325},
pmid = {29218041},
issn = {1664-302X},
support = {R01 GM028454/GM/NIGMS NIH HHS/United States ; },
abstract = {Mrp (Multiple resistance and pH) antiporter was identified as a gene complementing an alkaline-sensitive mutant strain of alkaliphilic Bacillus halodurans C-125 in 1990. At that time, there was no example of a multi-subunit type Na[+]/H[+] antiporter comprising six or seven hydrophobic proteins, and it was newly designated as the monovalent cation: proton antiporter-3 (CPA3) family in the classification of transporters. The Mrp antiporter is broadly distributed among bacteria and archaea, not only in alkaliphiles. Generally, all Mrp subunits, mrpA-G, are required for enzymatic activity. Two exceptions are Mrp from the archaea Methanosarcina acetivorans and the eubacteria Natranaerobius thermophilus, which are reported to sustain Na[+]/H[+] antiport activity with the MrpA subunit alone. Two large subunits of the Mrp antiporter, MrpA and MrpD, are homologous to membrane-embedded subunits of the respiratory chain complex I, NuoL, NuoM, and NuoN, and the small subunit MrpC has homology with NuoK. The functions of the Mrp antiporter include sodium tolerance and pH homeostasis in an alkaline environment, nitrogen fixation in Schizolobium meliloti, bile salt tolerance in Bacillus subtilis and Vibrio cholerae, arsenic oxidation in Agrobacterium tumefaciens, pathogenesis in Pseudomonas aeruginosa and Staphylococcus aureus, and the conversion of energy involved in metabolism and hydrogen production in archaea. In addition, some Mrp antiporters transport K[+] and Ca[2+] instead of Na[+], depending on the environmental conditions. Recently, the molecular structure of the respiratory chain complex I has been elucidated by others, and details of the mechanism by which it transports protons are being clarified. Based on this, several hypotheses concerning the substrate transport mechanism in the Mrp antiporter have been proposed. The MrpA and MrpD subunits, which are homologous to the proton transport subunit of complex I, are involved in the transport of protons and their coupling cations. Herein, we outline other recent findings on the Mrp antiporter.},
}
@article {pmid29208997,
year = {2017},
author = {Miot, J and Bernard, S and Bourreau, M and Guyot, F and Kish, A},
title = {Experimental maturation of Archaea encrusted by Fe-phosphates.},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {16984},
pmid = {29208997},
issn = {2045-2322},
mesh = {*Ferrous Compounds/chemistry ; *Fossils ; Hydrogen-Ion Concentration ; Microscopy, Electron, Transmission ; Minerals/chemistry ; *Phosphates/chemistry ; Sulfolobus acidocaldarius/growth &amp; development/*physiology/ultrastructure ; Temperature ; X-Ray Absorption Spectroscopy ; X-Ray Diffraction ; },
abstract = {Burial is generally detrimental to the preservation of biological signals. It has often been assumed that (bio)mineral-encrusted microorganisms are more resistant to burial-induced degradation than non-encrusted ones over geological timescales. For the present study, we submitted Sulfolobus acidocaldarius experimentally encrusted by amorphous Fe phosphates to constrained temperature conditions (150 °C) under pressure for 1 to 5 days, thereby simulating burial-induced processes. We document the molecular and mineralogical evolution of these assemblages down to the sub-micrometer scale using X-ray diffraction, scanning and transmission electron microscopies and synchrotron-based X-ray absorption near edge structure spectroscopy at the carbon K-edge. The present results demonstrate that the presence of Fe-phosphates enhances the chemical degradation of microbial organic matter. While Fe-phosphates remained amorphous in abiotic controls, crystalline lipscombite (Fe[II]xFe[III]3-x(PO4)2(OH)3-x) entrapping organic matter formed in the presence of S. acidocaldarius cells. Lipscombite textures (framboidal vs. bipyramidal) appeared only controlled by the initial level of encrustation of the cells, suggesting that the initial organic matter to mineral ratio influences the competition between nucleation and crystal growth. Altogether these results highlight the important interplay between minerals and organic matter during fossilization, which should be taken into account when interpreting the fossil record.},
}
@article {pmid29208747,
year = {2017},
author = {Makarova, KS and Galperin, MY and Koonin, EV},
title = {Proposed Role for KaiC-Like ATPases as Major Signal Transduction Hubs in Archaea.},
journal = {mBio},
volume = {8},
number = {6},
pages = {},
pmid = {29208747},
issn = {2150-7511},
mesh = {Adenosine Triphosphatases/*genetics ; Archaea/classification/*genetics/metabolism ; Archaeal Proteins/genetics/metabolism ; Bacterial Proteins/genetics ; Circadian Clocks ; Circadian Rhythm Signaling Peptides and Proteins/*genetics ; Cluster Analysis ; Cyanobacteria/genetics ; Databases, Genetic ; Gene Expression Regulation, Archaeal ; Genomics ; Membrane Transport Proteins ; Models, Genetic ; Multigene Family ; Protein Domains ; *Signal Transduction ; },
abstract = {All organisms must adapt to ever-changing environmental conditions and accordingly have evolved diverse signal transduction systems. In bacteria, the most abundant networks are built around the two-component signal transduction systems that include histidine kinases and receiver domains. In contrast, eukaryotic signal transduction is dominated by serine/threonine/tyrosine protein kinases. Both of these systems are also found in archaea, but they are not as common and diversified as their bacterial and eukaryotic counterparts, suggesting the possibility that archaea have evolved other, still uncharacterized signal transduction networks. Here we propose a role for KaiC family ATPases, known to be key components of the circadian clock in cyanobacteria, in archaeal signal transduction. The KaiC family is notably expanded in most archaeal genomes, and although most of these ATPases remain poorly characterized, members of the KaiC family have been shown to control archaellum assembly and have been found to be a stable component of the gas vesicle system in Halobacteria Computational analyses described here suggest that KaiC-like ATPases and their homologues with inactivated ATPase domains are involved in many other archaeal signal transduction pathways and comprise major hubs of complex regulatory networks. We predict numerous input and output domains that are linked to KaiC-like proteins, including putative homologues of eukaryotic DEATH domains that could function as adapters in archaeal signaling networks. We further address the relationships of the archaeal family of KaiC homologues to the bona fide KaiC of cyanobacteria and implications for the existence of a KaiC-based circadian clock apparatus in archaea.IMPORTANCE Little is currently known about signal transduction pathways in Archaea Recent studies indicate that KaiC-like ATPases, known as key components of the circadian clock apparatus in cyanobacteria, are involved in the regulation of archaellum assembly and, likely, type IV pili and the gas vesicle system in Archaea We performed comprehensive comparative genomic analyses of the KaiC family. A vast protein interaction network was revealed, with KaiC family proteins as hubs for numerous input and output components, many of which are shared with two-component signal transduction systems. Putative KaiC-based signal transduction systems are predicted to regulate the activities of membrane-associated complexes and individual proteins, such as signal recognition particle and membrane transporters, and also could be important for oxidative stress response regulation. KaiC-centered signal transduction networks are predicted to play major roles in archaeal physiology, and this work is expected to stimulate their experimental characterization.},
}
@article {pmid29198957,
year = {2018},
author = {Kazlauskas, D and Sezonov, G and Charpin, N and Venclovas, &#x10c; and Forterre, P and Krupovic, M},
title = {Novel Families of Archaeo-Eukaryotic Primases Associated with Mobile Genetic Elements of Bacteria and Archaea.},
journal = {Journal of molecular biology},
volume = {430},
number = {5},
pages = {737-750},
pmid = {29198957},
issn = {1089-8638},
support = {340440/ERC_/European Research Council/International ; },
mesh = {Amino Acid Sequence ; Archaea/*enzymology/*genetics ; Bacteria/enzymology/*genetics ; Catalytic Domain ; DNA Helicases/metabolism ; DNA Primase/classification/*metabolism ; DNA Replication ; Eukaryota/*enzymology/*genetics ; Evolution, Molecular ; Interspersed Repetitive Sequences ; Models, Molecular ; Protein Conformation ; Protein Domains ; Sequence Alignment ; Thermococcus/genetics ; },
abstract = {Cellular organisms in different domains of life employ structurally unrelated, non-homologous DNA primases for synthesis of a primer for DNA replication. Archaea and eukaryotes encode enzymes of the archaeo-eukaryotic primase (AEP) superfamily, whereas bacteria uniformly use primases of the DnaG family. However, AEP genes are widespread in bacterial genomes raising questions regarding their provenance and function. Here, using an archaeal primase-polymerase PolpTN2 encoded by pTN2 plasmid as a seed for sequence similarity searches, we recovered over 800 AEP homologs from bacteria belonging to 12 highly diverse phyla. These sequences formed a supergroup, PrimPol-PV1, and could be classified into five novel AEP families which are characterized by a conserved motif containing an arginine residue likely to be involved in nucleotide binding. Functional assays confirm the essentiality of this motif for catalytic activity of the PolpTN2 primase-polymerase. Further analyses showed that bacterial AEPs display a range of domain organizations and uncovered several candidates for novel families of helicases. Furthermore, sequence and structure comparisons suggest that PriCT-1 and PriCT-2 domains frequently fused to the AEP domains are related to each other as well as to the non-catalytic, large subunit of archaeal and eukaryotic primases, and to the recently discovered PriX subunit of archaeal primases. Finally, genomic neighborhood analysis indicates that the identified AEPs encoded in bacterial genomes are nearly exclusively associated with highly diverse integrated mobile genetic elements, including integrative conjugative plasmids and prophages.},
}
@article {pmid29194812,
year = {2018},
author = {Chaudhury, P and Quax, TEF and Albers, SV},
title = {Versatile cell surface structures of archaea.},
journal = {Molecular microbiology},
volume = {107},
number = {3},
pages = {298-311},
doi = {10.1111/mmi.13889},
pmid = {29194812},
issn = {1365-2958},
mesh = {Archaea/metabolism/*physiology ; Bacterial Adhesion/physiology ; Biofilms ; Fimbriae, Bacterial/*metabolism/physiology ; Membrane Proteins/metabolism ; Pili, Sex/physiology ; },
abstract = {Archaea are ubiquitously present in nature and colonize environments with broadly varying growth conditions. Several surface appendages support their colonization of new habitats. A hallmark of archaea seems to be the high abundance of type IV pili (T4P). However, some unique non T4 filaments are present in a number of archaeal species. Archaeal surface structures can mediate different processes such as cellular surface adhesion, DNA exchange, motility and biofilm formation and represent an initial attachment site for infecting viruses. In addition to the functionally characterized archaeal T4P, archaeal genomes encode a large number of T4P components that might form yet undiscovered surface structures with novel functions. In this review, we summarize recent advancement in structural and functional characterizations of known archaeal surface structures and highlight the diverse processes in which they play a role.},
}
@article {pmid29184545,
year = {2017},
author = {Yang, W and Wang, Y and Tago, K and Tokuda, S and Hayatsu, M},
title = {Comparison of the Effects of Phenylhydrazine Hydrochloride and Dicyandiamide on Ammonia-Oxidizing Bacteria and Archaea in Andosols.},
journal = {Frontiers in microbiology},
volume = {8},
number = {},
pages = {2226},
pmid = {29184545},
issn = {1664-302X},
abstract = {Dicyandiamide, a routinely used commercial nitrification inhibitor (NI), inhibits ammonia oxidation catalyzed by ammonia monooxygenase (AMO). Phenylhydrazine hydrochloride has shown considerable potential for the development of next-generation NIs targeting hydroxylamine dehydrogenase (HAO). The effects of the AMO inhibitor and the HAO inhibitor on ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) present in agricultural soils have not been compared thus far. In the present study, the effects of the two inhibitors on soil nitrification and the abundance of AOA and AOB as well as their community structure were investigated in a soil microcosm using quantitative polymerase chain reaction and pyrosequencing. The net nitrification rates and the growth of AOA and AOB in this soil microcosm were inhibited by both NIs. Both NIs had limited effect on the community structure of AOB and no effect on that of AOA in this soil microcosm. The effects of phenylhydrazine hydrochloride were similar to those of dicyandiamide. These results indicated that organohydrazine-based NIs have potential for the development of next-generation NIs targeting HAO in the future.},
}
@article {pmid29178818,
year = {2017},
author = {Martinez-Pastor, M and Tonner, PD and Darnell, CL and Schmid, AK},
title = {Transcriptional Regulation in Archaea: From Individual Genes to Global Regulatory Networks.},
journal = {Annual review of genetics},
volume = {51},
number = {},
pages = {143-170},
doi = {10.1146/annurev-genet-120116-023413},
pmid = {29178818},
issn = {1545-2948},
mesh = {Adaptation, Biological/genetics ; Archaea/*genetics/metabolism ; Archaeal Proteins/*genetics/metabolism ; Chromosome Mapping ; *Gene Expression Regulation, Archaeal ; *Gene Regulatory Networks ; Gene-Environment Interaction ; *Genome, Archaeal ; Metabolic Networks and Pathways/genetics ; Stress, Physiological/genetics ; Systems Biology/methods ; Transcription Factors/*genetics/metabolism ; *Transcription, Genetic ; },
abstract = {Archaea are major contributors to biogeochemical cycles, possess unique metabolic capabilities, and resist extreme stress. To regulate the expression of genes encoding these unique programs, archaeal cells use gene regulatory networks (GRNs) composed of transcription factor proteins and their target genes. Recent developments in genetics, genomics, and computational methods used with archaeal model organisms have enabled the mapping and prediction of global GRN structures. Experimental tests of these predictions have revealed the dynamical function of GRNs in response to environmental variation. Here, we review recent progress made in this area, from investigating the mechanisms of transcriptional regulation of individual genes to small-scale subnetworks and genome-wide global networks. At each level, archaeal GRNs consist of a hybrid of bacterial, eukaryotic, and uniquely archaeal mechanisms. We discuss this theme from the perspective of the role of individual transcription factors in genome-wide regulation, how these proteins interact to compile GRN topological structures, and how these topologies lead to emergent, high-level GRN functions. We conclude by discussing how systems biology approaches are a fruitful avenue for addressing remaining challenges, such as discovering gene function and the evolution of GRNs.},
}
@article {pmid29176585,
year = {2018},
author = {Eme, L and Spang, A and Lombard, J and Stairs, CW and Ettema, TJG},
title = {Archaea and the origin of eukaryotes.},
journal = {Nature reviews. Microbiology},
volume = {16},
number = {2},
pages = {120},
pmid = {29176585},
issn = {1740-1534},
abstract = {This corrects the article DOI: 10.1038/nrmicro.2017.133.},
}
@article {pmid29175107,
year = {2018},
author = {Krupovic, M and Cvirkaite-Krupovic, V and Iranzo, J and Prangishvili, D and Koonin, EV},
title = {Viruses of archaea: Structural, functional, environmental and evolutionary genomics.},
journal = {Virus research},
volume = {244},
number = {},
pages = {181-193},
pmid = {29175107},
issn = {1872-7492},
support = {Z01 LM000073-12//Intramural NIH HHS/United States ; },
mesh = {Aquatic Organisms/virology ; Archaea/*virology ; Archaeal Viruses/classification/*genetics/isolation &amp; purification/ultrastructure ; Evolution, Molecular ; Genetic Variation ; *Genome, Viral ; Interspersed Repetitive Sequences ; Metagenomics/*methods ; Microbial Interactions ; *Phylogeny ; Sequence Analysis, DNA ; Viral Proteins/*genetics ; Virion/genetics/ultrastructure ; },
abstract = {Viruses of archaea represent one of the most enigmatic parts of the virosphere. Most of the characterized archaeal viruses infect extremophilic hosts and display remarkable diversity of virion morphotypes, many of which have never been observed among viruses of bacteria or eukaryotes. The uniqueness of the virion morphologies is matched by the distinctiveness of the genomes of these viruses, with ∼75% of genes encoding unique proteins, refractory to functional annotation based on sequence analyses. In this review, we summarize the state-of-the-art knowledge on various aspects of archaeal virus genomics. First, we outline how structural and functional genomics efforts provided valuable insights into the functions of viral proteins and revealed intricate details of the archaeal virus-host interactions. We then highlight recent metagenomics studies, which provided a glimpse at the diversity of uncultivated viruses associated with the ubiquitous archaea in the oceans, including Thaumarchaeota, Marine Group II Euryarchaeota, and others. These findings, combined with the recent discovery that archaeal viruses mediate a rapid turnover of thaumarchaea in the deep sea ecosystems, illuminate the prominent role of these viruses in the biosphere. Finally, we discuss the origins and evolution of archaeal viruses and emphasize the evolutionary relationships between viruses and non-viral mobile genetic elements. Further exploration of the archaeal virus diversity as well as functional studies on diverse virus-host systems are bound to uncover novel, unexpected facets of the archaeal virome.},
}
@article {pmid29170214,
year = {2017},
author = {Pennisi, E},
title = {Survey of archaea in the body reveals other microbial guests.},
journal = {Science (New York, N.Y.)},
volume = {358},
number = {6366},
pages = {983},
doi = {10.1126/science.358.6366.983},
pmid = {29170214},
issn = {1095-9203},
mesh = {Constipation/microbiology ; Digestion ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/*microbiology ; Humans ; Lung/microbiology ; Methane/*biosynthesis ; Methanobrevibacter/*pathogenicity ; Nose/microbiology ; Skin/microbiology ; },
}
@article {pmid29138298,
year = {2017},
author = {Koskinen, K and Pausan, MR and Perras, AK and Beck, M and Bang, C and Mora, M and Schilhabel, A and Schmitz, R and Moissl-Eichinger, C},
title = {First Insights into the Diverse Human Archaeome: Specific Detection of Archaea in the Gastrointestinal Tract, Lung, and Nose and on Skin.},
journal = {mBio},
volume = {8},
number = {6},
pages = {},
pmid = {29138298},
issn = {2150-7511},
mesh = {Archaea/*classification/genetics/*isolation &amp; purification ; Gastrointestinal Tract/*microbiology ; Humans ; Lung/*microbiology ; Metagenomics/methods ; *Microbiota ; Nose/*microbiology ; Polymerase Chain Reaction/methods ; Skin/*microbiology ; },
abstract = {Human-associated archaea remain understudied in the field of microbiome research, although in particular methanogenic archaea were found to be regular commensals of the human gut, where they represent keystone species in metabolic processes. Knowledge on the abundance and diversity of human-associated archaea is extremely limited, and little is known about their function(s), their overall role in human health, or their association with parts of the human body other than the gastrointestinal tract and oral cavity. Currently, methodological issues impede the full assessment of the human archaeome, as bacteria-targeting protocols are unsuitable for characterization of the full spectrum of Archaea The goal of this study was to establish conservative protocols based on specifically archaea-targeting, PCR-based methods to retrieve first insights into the archaeomes of the human gastrointestinal tract, lung, nose, and skin. Detection of Archaea was highly dependent on primer selection and the sequence processing pipeline used. Our results enabled us to retrieve a novel picture of the human archaeome, as we found for the first time Methanobacterium and Woesearchaeota (DPANN superphylum) to be associated with the human gastrointestinal tract and the human lung, respectively. Similar to bacteria, human-associated archaeal communities were found to group biogeographically, forming (i) the thaumarchaeal skin landscape, (ii) the (methano)euryarchaeal gastrointestinal tract, (iii) a mixed skin-gastrointestinal tract landscape for the nose, and (iv) a woesearchaeal lung landscape. On the basis of the protocols we used, we were able to detect unexpectedly high diversity of archaea associated with different body parts.IMPORTANCE In summary, our study highlights the importance of the primers and data processing pipeline used to study the human archaeome. We were able to establish protocols that revealed the presence of previously undetected Archaea in all of the tissue samples investigated and to detect biogeographic patterns of the human archaeome in the gastrointestinal tract and on the skin and for the first time in the respiratory tract, i.e., the nose and lungs. Our results are a solid basis for further investigation of the human archaeome and, in the long term, discovery of the potential role of archaea in human health and disease.},
}
@article {pmid29138003,
year = {2018},
author = {Stancik, IA and Šestak, MS and Ji, B and Axelson-Fisk, M and Franjevic, D and Jers, C and Domazet-Lošo, T and Mijakovic, I},
title = {Serine/Threonine Protein Kinases from Bacteria, Archaea and Eukarya Share a Common Evolutionary Origin Deeply Rooted in the Tree of Life.},
journal = {Journal of molecular biology},
volume = {430},
number = {1},
pages = {27-32},
doi = {10.1016/j.jmb.2017.11.004},
pmid = {29138003},
issn = {1089-8638},
mesh = {Amino Acid Sequence ; Archaea/*genetics ; Bacteria/*genetics ; Eukaryota/*genetics ; Evolution, Molecular ; Protein Serine-Threonine Kinases/*genetics ; },
abstract = {The main family of serine/threonine/tyrosine protein kinases present in eukarya was defined and described by Hanks et al. in 1988 (Science, 241, 42-52). It was initially believed that these kinases do not exist in bacteria, but extensive genome sequencing revealed their existence in many bacteria. For historical reasons, the term "eukaryotic-type kinases" propagated in the literature to describe bacterial members of this protein family. Here, we argue that this term should be abandoned as a misnomer, and we provide several lines of evidence to support this claim. Our comprehensive phylostratigraphic analysis suggests that Hanks-type kinases present in eukarya, bacteria and archaea all share a common evolutionary origin in the lineage leading to the last universal common ancestor (LUCA). We found no evidence to suggest substantial horizontal transfer of genes encoding Hanks-type kinases from eukarya to bacteria. Moreover, our systematic structural comparison suggests that bacterial Hanks-type kinases resemble their eukaryal counterparts very closely, while their structures appear to be dissimilar from other kinase families of bacterial origin. This indicates that a convergent evolution scenario, by which bacterial kinases could have evolved a kinase domain similar to that of eukaryal Hanks-type kinases, is not very likely. Overall, our results strongly support a monophyletic origin of all Hanks-type kinases, and we therefore propose that this term should be adopted as a universal name for this protein family.},
}
@article {pmid29123229,
year = {2017},
author = {},
title = {A flourishing field: going back to the roots of the Archaea.},
journal = {Nature reviews. Microbiology},
volume = {15},
number = {12},
pages = {705},
pmid = {29123229},
issn = {1740-1534},
mesh = {Adaptation, Biological/*genetics ; Archaea/classification/*genetics/physiology/virology ; Bacteria/genetics ; *Biodiversity ; Ecology ; Eukaryota/genetics ; Gene Transfer, Horizontal ; *Genetic Speciation ; Genome, Archaeal/*genetics ; },
}
@article {pmid29123225,
year = {2017},
author = {Eme, L and Spang, A and Lombard, J and Stairs, CW and Ettema, TJG},
title = {Archaea and the origin of eukaryotes.},
journal = {Nature reviews. Microbiology},
volume = {15},
number = {12},
pages = {711-723},
pmid = {29123225},
issn = {1740-1534},
mesh = {Archaea/*genetics ; *Biological Evolution ; Eukaryota/*genetics ; Pharmacogenomic Variants ; },
abstract = {Woese and Fox's 1977 paper on the discovery of the Archaea triggered a revolution in the field of evolutionary biology by showing that life was divided into not only prokaryotes and eukaryotes. Rather, they revealed that prokaryotes comprise two distinct types of organisms, the Bacteria and the Archaea. In subsequent years, molecular phylogenetic analyses indicated that eukaryotes and the Archaea represent sister groups in the tree of life. During the genomic era, it became evident that eukaryotic cells possess a mixture of archaeal and bacterial features in addition to eukaryotic-specific features. Although it has been generally accepted for some time that mitochondria descend from endosymbiotic alphaproteobacteria, the precise evolutionary relationship between eukaryotes and archaea has continued to be a subject of debate. In this Review, we outline a brief history of the changing shape of the tree of life and examine how the recent discovery of a myriad of diverse archaeal lineages has changed our understanding of the evolutionary relationships between the three domains of life and the origin of eukaryotes. Furthermore, we revisit central questions regarding the process of eukaryogenesis and discuss what can currently be inferred about the evolutionary transition from the first to the last eukaryotic common ancestor.},
}
@article {pmid29118356,
year = {2017},
author = {Nordgård, ASR and Bergland, WH and Vadstein, O and Mironov, V and Bakke, R and Østgaard, K and Bakke, I},
title = {Anaerobic digestion of pig manure supernatant at high ammonia concentrations characterized by high abundances of Methanosaeta and non-euryarchaeotal archaea.},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {15077},
pmid = {29118356},
issn = {2045-2322},
mesh = {Ammonia/*metabolism ; Anaerobiosis ; Animals ; Archaea/classification/genetics/*metabolism ; Bioreactors/microbiology ; Genetic Variation ; Manure/*microbiology ; Methane/metabolism ; Methanosarcinaceae/classification/genetics/*metabolism ; Microbial Consortia/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sewage/microbiology ; Swine ; Temperature ; },
abstract = {We examined the effect of ammonium and temperature on methane production in high rate upflow anaerobic sludge bed reactors treating pig manure supernatant. We operated four reactors at two ammonium concentrations ('low' at 1.9, 'high' at 3.7 g L[-1], termed LA and HA reactors, respectively) and at variable temperatures over 358 days. Archaeal and bacterial communities were characterized by Illumina sequencing of 16S rRNA amplicons. Ammonium was a major selective factor for bacterial and archaeal community structure. After ~200 days of adaptation to high ammonium levels, acetate and propionate removal and methane production improved substantially in HA reactors. Aceticlastic Methanosaeta was abundant and positively correlated to methane yield in the HA reactors, whereas Methanosarcina was more abundant in LA reactors. Furthermore, a group of monophyletic OTUs that was related to Thaumarchaeota in phylogenetic analysis was highly abundant in the archaeal communities, particularly in the HA reactors. The most abundant bacterial OTU in LA reactors, representing Syntrophomonadaceae, was also positively correlated to methane yield in the HA reactors, indicating its importance in methane production under ammonia stress. In conclusion, efficient methane production, involving aceticlastic methanogenesis by Methanosaeta took place in the reactors at free ammonia concentrations as high as 1 g L[-1].},
}
@article {pmid29109713,
year = {2017},
author = {Xia, X and Guo, W and Liu, H},
title = {Basin Scale Variation on the Composition and Diversity of Archaea in the Pacific Ocean.},
journal = {Frontiers in microbiology},
volume = {8},
number = {},
pages = {2057},
pmid = {29109713},
issn = {1664-302X},
abstract = {The Archaea are a widely distributed group of prokaryotes that inhabit and thrive in many different environments. In the sea, they play key roles in various global biogeochemical processes. Here, in order to investigate the vertical profiles of archaeal community across a large geographic distance, the compositions of archaeal communities in seven seawater columns in the Pacific Ocean were investigated using high throughput 454 pyrosequencing of the 16S rRNA gene. The surface archaeal communities showed lower diversity and greater variability than those in the deeper layers. Two of the major archaeal phyla that displayed different depth preferences were Thaumarchaeota and Euryarchaeota. The majority of Thaumarchaeota belonged to Marine Group I (MGI), which had high relative abundance in deep water. In contrast, Euryarchaeota, which mainly consisted of Marine Group II (MGII) and III (MGIII), were dominant in the surface layer. Compared with MGI and MGII, MGIII were less abundant in seawater and generally absent from the surface water of the subarctic Pacific. In addition, niche separation in the MGI, MGII, and MGIII subgroups was also observed. For example, MGI.C and MGII.A (the major subgroups of MGI and MGII, respectively) displayed a strong negative correlation with each other. The highest level of archaeal diversity was found in the core of an oxygen minimum zone (OMZ) located off Costa Rica, which resulted from the co-occurrence of both anaerobic and aerobic archaea. For example, methanotrophic archaea ANME-2, methanogenic archaea and several sediment origin archaea, such as Marine Benthic Group A (MBGA) and Bathyarchaeota, were all detected at relatively high abundance in the OMZ. Together, our findings indicate that vertical heterogeneities along water columns and latitudinal differentiation in the surface waters are ubiquitous features of archaeal communities in the Pacific Ocean, and the OMZ off Costa Rica is an archaeal biodiversity hot-spot.},
}
@article {pmid29107227,
year = {2018},
author = {Wang, L and Li, Y and Niu, L and Zhang, W and Zhang, H and Wang, L and Wang, P},
title = {Response of ammonia oxidizing archaea and bacteria to decabromodiphenyl ether and copper contamination in river sediments.},
journal = {Chemosphere},
volume = {191},
number = {},
pages = {858-867},
doi = {10.1016/j.chemosphere.2017.10.067},
pmid = {29107227},
issn = {1879-1298},
mesh = {Ammonia/*metabolism ; Archaea/*metabolism ; Bacteria/*metabolism ; Copper/*metabolism ; Environmental Pollutants/analysis/*metabolism ; Geologic Sediments/*chemistry ; Halogenated Diphenyl Ethers/*analysis ; Metals, Heavy/metabolism ; Nitrogen Cycle ; Oxidation-Reduction ; Oxidoreductases/metabolism ; Rivers/*microbiology ; },
abstract = {Ammonia oxidation plays a fundamental role in river nitrogen cycling ecosystems, which is normally governed by both ammonia oxidizing archaea (AOA) and ammonia oxidizing bacteria (AOB). Co-contamination of typical emerging pollutant Polybrominated diphenyl ethers (PBDEs) and heavy metal on AOA and AOB communities in river sediments remains unknown. In this study, multiple analytical tools, including high-throughput pyrosequencing and real-time quantitative PCR (qPCR), were used to reveal the ammonia monooxygenase (AMO) activity, subunit alpha (amoA) gene abundance, and community structures of AOA and AOB in river sediments. It was found that the inhibition of AMO activities was increased with the increase of decabromodiphenyl ether (BDE 209, 1-100 mg kg[-1]) and copper (Cu, 50-500 mg kg[-1]) concentrations. Moreover, the synergic effects of BDE 209 and Cu resulted in a higher AMO activity reduction than the individual pollutant BDE 209. The AOA amoA copy number declined by 75.9% and 83.2% and AOB amoA gene abundance declined 82.8% and 90.0% at 20 and 100 mg kg[-1] BDE 209 with a 100 mg kg[-1] Cu co-contamination, respectively. The pyrosequencing results showed that both AOB and AOA community structures were altered, with a higher change of AOB than that of AOA. The results demonstrated that the AOB microbial community may be better adapted to BDE 209 and Cu pollution, while AOA might possess a greater capacity for stress resistance. Our study provides a better understanding of the ecotoxicological effects of heavy metal and micropollutant combined exposure on AOA and AOB in river sediments.},
}
@article {pmid29098760,
year = {2017},
author = {Herbold, CW and Lehtovirta-Morley, LE and Jung, MY and Jehmlich, N and Hausmann, B and Han, P and Loy, A and Pester, M and Sayavedra-Soto, LA and Rhee, SK and Prosser, JI and Nicol, GW and Wagner, M and Gubry-Rangin, C},
title = {Ammonia-oxidising archaea living at low pH: Insights from comparative genomics.},
journal = {Environmental microbiology},
volume = {19},
number = {12},
pages = {4939-4952},
pmid = {29098760},
issn = {1462-2920},
support = {294343/ERC_/European Research Council/International ; },
mesh = {Ammonia/*metabolism ; Base Sequence ; Biological Evolution ; DNA, Archaeal/genetics ; Euryarchaeota/*genetics/*metabolism ; Gene Transfer, Horizontal ; Genome, Archaeal/*genetics ; Genomics ; Nitrification/*physiology ; Oxidation-Reduction ; Phylogeny ; Proteomics ; Sequence Analysis, DNA ; Soil/chemistry ; Soil Microbiology ; },
abstract = {Obligate acidophilic members of the thaumarchaeotal genus Candidatus Nitrosotalea play an important role in nitrification in acidic soils, but their evolutionary and physiological adaptations to acidic environments are still poorly understood, with only a single member of this genus (Ca. N. devanaterra) having its genome sequenced. In this study, we sequenced the genomes of two additional cultured Ca. Nitrosotalea strains, extracted an almost complete Ca. Nitrosotalea metagenome-assembled genome from an acidic fen, and performed comparative genomics of the four Ca. Nitrosotalea genomes with 19 other archaeal ammonia oxidiser genomes. Average nucleotide and amino acid identities revealed that the four Ca. Nitrosotalea strains represent separate species within the genus. The four Ca. Nitrosotalea genomes contained a core set of 103 orthologous gene families absent from all other ammonia-oxidizing archaea and, for most of these gene families, expression could be demonstrated in laboratory culture or the environment via proteomic or metatranscriptomic analyses respectively. Phylogenetic analyses indicated that four of these core gene families were acquired by the Ca. Nitrosotalea common ancestor via horizontal gene transfer from acidophilic representatives of Euryarchaeota. We hypothesize that gene exchange with these acidophiles contributed to the competitive success of the Ca. Nitrosotalea lineage in acidic environments.},
}
@article {pmid29084543,
year = {2017},
author = {Lambrecht, J and Cichocki, N and Hübschmann, T and Koch, C and Harms, H and Müller, S},
title = {Flow cytometric quantification, sorting and sequencing of methanogenic archaea based on F420 autofluorescence.},
journal = {Microbial cell factories},
volume = {16},
number = {1},
pages = {180},
pmid = {29084543},
issn = {1475-2859},
mesh = {Archaea/cytology/genetics/*metabolism ; Archaeal Proteins/genetics/metabolism ; Benzothiazoles ; Biofuels ; Biomass ; Diamines ; Flow Cytometry ; Methane/*metabolism ; Microscopy, Fluorescence ; Organic Chemicals/chemistry ; Quinolines ; RNA, Ribosomal, 16S/chemistry/isolation &amp; purification/metabolism ; Sequence Analysis, DNA ; },
abstract = {BACKGROUND: The widely established production of CH4 from renewable biomass in industrial scale anaerobic reactors may play a major role in the future energy supply. It relies on methanogenic archaea as key organisms which represent the bottleneck in the process. The quantitative analysis of these organisms can help to maximize process performance, uncover disturbances before failure, and may ultimately lead to community-based process control schemes. Existing qPCR and fluorescence microscopy-based methods are very attractive but can be cost-intensive and laborious.<br><br>RESULTS: In this study we present an autofluorescence-based, flow cytometric method for the fast low-cost quantification of methanogenic archaea in complex microbial communities and crude substrates. The method was applied to a methanogenic enrichment culture (MEC) and digester samples (DS). The methanogenic archaea were quantified using the distinct fluorescence of their cofactor F420 in a range from 3.7&#xa0;&#xd7;&#xa0;10[8] (&#xb1;&#xa0;3.3&#xa0;&#xd7;&#xa0;10[6])&#xa0;cells&#xa0;mL[-1] and 1.8&#xa0;x&#xa0;10[9] (&#xb1;&#xa0;1.1&#xa0;&#xd7;&#xa0;10[8]) cells mL[-1]. We evaluated different fixation methods and tested the sample stability. Stable abundance and fluorescence intensity were recorded up to 26&#xa0;days during aerobic storage in PBS at 6&#xa0;&#xb0;C. The discrimination of the whole microbial community from the ubiquitous particle noise was facilitated by SYBR Green I staining and enabled calculation of relative abundances of methanogenic archaea of up to 9.64&#xa0;&#xb1;&#xa0;0.23% in the MEC and up to 4.43&#xa0;&#xb1;&#xa0;0.74% in the DS. The metaprofiling of the mcrA gene reinforced the results.<br><br>CONCLUSIONS: The presented method allows for fast and reliable quantification of methanogenic archaea in microbial communities under authentic digester conditions and can thus be useful for process monitoring and control in biogas digesters.},
}
@article {pmid29083035,
year = {2018},
author = {Laskar, F and Das Purkayastha, S and Sen, A and Bhattacharya, MK and Misra, BB},
title = {Diversity of methanogenic archaea in freshwater sediments of lacustrine ecosystems.},
journal = {Journal of basic microbiology},
volume = {58},
number = {2},
pages = {101-119},
doi = {10.1002/jobm.201700341},
pmid = {29083035},
issn = {1521-4028},
mesh = {Archaea/*classification/genetics/growth &amp; development/*metabolism ; *Biodiversity ; DNA, Archaeal/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Fresh Water/*microbiology ; Geologic Sediments/microbiology ; Lakes/microbiology ; Metagenomics/*methods ; Methane/*metabolism ; Microbiological Techniques/*methods ; Oxidoreductases/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; },
abstract = {About half of the global methane (CH4) emission is contributed by the methanogenic archaeal communities leading to a significant increase in global warming. This unprecedented situation has increased the ever growing necessity of evaluating the control measures for limiting CH4 emission to the atmosphere. Unfortunately, research endeavors on the diversity and functional interactions of methanogens are not extensive till date. We anticipate that the study of the diversity of methanogenic community is paramount for understanding the metabolic processes in freshwater lake ecosystems. Although there are several disadvantages of conventional culture-based methods for determining the diversity of methanogenic archaeal communities, in order to understand their ecological roles in natural environments it is required to culture the microbes. Recently different molecular techniques have been developed for determining the structure of methanogenic archaeal communities thriving in freshwater lake ecosystem. The two gene based cloning techniques required for this purpose are 16S rRNA and methyl coenzyme M reductase (mcrA) in addition to the recently developed metagenomics approaches and high throughput next generation sequencing efforts. This review discusses the various methods of culture-dependent and -independent measures of determining the diversity of methanogen communities in lake sediments in lieu of the different molecular approaches and inter-relationships of diversity of methanogenic archaea.},
}
@article {pmid29080506,
year = {2018},
author = {Chaari, M and Theochari, I and Papadimitriou, V and Xenakis, A and Ammar, E},
title = {Encapsulation of carotenoids extracted from halophilic Archaea in oil-in-water (O/W) micro- and nano-emulsions.},
journal = {Colloids and surfaces. B, Biointerfaces},
volume = {161},
number = {},
pages = {219-227},
doi = {10.1016/j.colsurfb.2017.10.042},
pmid = {29080506},
issn = {1873-4367},
mesh = {Archaea/*chemistry ; Carotenoids/*chemistry ; Cyclohexenes/chemistry ; Drug Delivery Systems/methods ; Electron Spin Resonance Spectroscopy ; Emulsions/*chemistry ; Glycerol/chemistry ; Limonene ; Nanostructures/*chemistry ; Octoxynol/chemistry ; Oils/*chemistry ; Polysorbates/chemistry ; Solubility ; Surface-Active Agents/chemistry ; Terpenes/chemistry ; Thermodynamics ; Water/*chemistry ; },
abstract = {Carotenoids extracted from halophilc Archaea have potential health benefits. Their poor water-solubility and low bioavailability is a challenge to their incorporation into foods. The aim of this work was the carotenoids encapsulation into two oil-in-water (O/W) dispersions, to increase their use as functional food applications. A nanoemulsion produced by high pressure homogenization and a spontaneously formed microemulsion were conceived. The limonene was the dispersed oil phase, and mixtures of Triton X-100/Tween-80 (3:1) as emulsifiers and of water/glycerol (2:1) as the continuous aqueous phase. The microemulsion monophasic area was determined through the pseudo-ternary phase diagram. Dynamic Light Scattering was used for the structural characterization of the nano- and micro-emulsions in the presence of the carotenoids. Moreover, the radical scavenging activity of the encapsulated carotenoids was examined by Electron Paramagnetic Resonance spectroscopy. The results confirmed the delivery systems design effectiveness to encapsulate and stabilize the carotenoids for food applications.},
}
@article {pmid29064676,
year = {2017},
author = {White, RH},
title = {Identification and Biosynthesis of 1-Mercaptoethanesulfonic Acid (1-MES), an Analogue of Coenzyme M, Found Widely in the Methanogenic Archaea.},
journal = {Biochemistry},
volume = {56},
number = {46},
pages = {6137-6144},
doi = {10.1021/acs.biochem.7b00971},
pmid = {29064676},
issn = {1520-4995},
mesh = {*Biosynthetic Pathways ; Ethylenes/metabolism ; Mesna/*analogs &amp; derivatives/*metabolism ; Methanococcus/enzymology/growth &amp; development/*metabolism ; Sulfides/metabolism ; Sulfonic Acids/metabolism ; },
abstract = {Here I report on the identification of 1-mercaptoethanesulfonic acid (1-MES), an analogue of 2-mercaptoethanesulfonic acid (coenzyme M, HSCoM). 1-MES and HSCoM were both present in the growth media of eight different methanogens at concentrations ranging from ∼1 to 100 μM. In an effort to determine a chemical origin of 1-MES, several plausible chemical routes were examined each assuming that HSCoM was the precursor. In all examined routes, no 1-MES was formed. However, 1-MES was formed when a solution of vinylsulfonic acid and sulfide were exposed to ultraviolet light. On the basis of these results, I conclude 1-MES is formed enzymatically. This was confirmed by growing a culture of Methanococcus maripaludis S2 in the presence of [1,1',2,2'-[2]H4]HSCoM and measuring the incorporation of deuterium into 1-MES. 1-MES incorporated three of the four deuteriums from the fed HSCoM. This result is consistent with the abstraction of a C-2 deuterium of the HSCoM, likely by a 5'-dAdoCH2[•] radical, followed by a radical rearrangement in which the sulfonic acid moves to position C-1, followed by abstraction of a H[•] likely from 5'-dAdoCH2D. At present, the reason for the production of 1-MES is not clear. This is the first report of the occurrence of 1-MES in Nature.},
}
@article {pmid29038844,
year = {2018},
author = {Hou, J and Cui, HL},
title = {In Vitro Antioxidant, Antihemolytic, and Anticancer Activity of the Carotenoids from Halophilic Archaea.},
journal = {Current microbiology},
volume = {75},
number = {3},
pages = {266-271},
pmid = {29038844},
issn = {1432-0991},
support = {31600002//National Natural Science Foundation of China/ ; 31370054//National Natural Science Foundation of China/ ; },
mesh = {Animals ; Antineoplastic Agents/chemistry/metabolism/*pharmacology ; Antioxidants/chemistry/metabolism/*pharmacology ; Carotenoids/chemistry/metabolism/*pharmacology ; Cell Line ; Cell Survival/drug effects ; Erythrocytes/drug effects ; Factor VIII/chemistry/metabolism/*pharmacology ; Halobacteriaceae/*chemistry/classification/metabolism ; Humans ; Mice ; Sodium Chloride/metabolism ; },
abstract = {Halophilic archaea represent a promising natural source of carotenoids. However, little information is available about the biological effects of carotenoids from halophilic archaea. In this study, the carotenoids produced by seven halophilic archaeal strains Halogeometricum rufum, Halogeometricum limi, Haladaptatus litoreus, Haloplanus vescus, Halopelagius inordinatus, Halogranum rubrum, and Haloferax volcanii were identified by ultraviolet/visible spectroscopy, thin-layer chromatography, and high-performance liquid chromatography-tandem mass spectrometry. The C50 carotenoids bacterioruberin and its derivatives monoanhydrobacterioruberin and bisanhydrobacterioruberin were found to be the predominant carotenoids. The antioxidant capacities of the carotenoids from these strains were significantly higher than β-carotene as determined by 1,1-diphenyl-2-picrylhydrazyl radical scavenging assay. The antihemolytic activities of these carotenoid extracts against H2O2-induced hemolysis in mouse erythrocytes were 3.9-6.3 times higher than β-carotene. A dose-dependent in vitro antiproliferative activity against HepG2 cells was observed for the extract from Hgm. limi, while that from Hpn. vescus exhibited a relatively high activity in a dose-independent manner. These results suggested that halophilic archaea could be considered as an alternative source of natural carotenoids with high antioxidant, antihemolytic, and anticancer activity.},
}
@article {pmid29037137,
year = {2017},
author = {Peng, S and Chu, Z and Lu, J and Li, D and Wang, Y and Yang, S and Zhang, Y},
title = {Heterologous Expression of Chaperones from Hyperthermophilic Archaea Inhibits Aminoglycoside-Induced Protein Misfolding in Escherichia coli.},
journal = {Biochemistry. Biokhimiia},
volume = {82},
number = {10},
pages = {1169-1175},
doi = {10.1134/S0006297917100091},
pmid = {29037137},
issn = {1608-3040},
mesh = {Chaperonin 10/genetics/metabolism ; Chaperonin 60/genetics/*metabolism ; Escherichia coli/*metabolism ; Membrane Potentials/drug effects ; Molecular Chaperones/genetics/metabolism ; Protein Folding/drug effects ; Pyrococcus furiosus/*metabolism ; Recombinant Proteins/biosynthesis/chemistry ; Streptomycin/pharmacology ; },
abstract = {Aminoglycoside antibiotics affect protein translation fidelity and lead to protein aggregation and an increase in intracellular oxidative stress level as well. The overexpression of the chaperonin GroEL/GroES system promotes short-term tolerance to aminoglycosides in Escherichia coli. Here, we demonstrated that the coexpression of prefoldin or Hsp60 originating from the hyperthermophilic archaeon Pyrococcus furiosus in E. coli cells can rescue cell growth and inhibit protein aggregation induced by streptomycin exposure. The results of our study show that hyperthermophilic chaperones endow E. coli with a higher tolerance to streptomycin than the GroEL/GroES system, and that they exert better effects on the reduction of intracellular protein misfolding, indicating that these chaperones have unique features and functions.},
}
@article {pmid29034851,
year = {2017},
author = {Qin, W and Heal, KR and Ramdasi, R and Kobelt, JN and Martens-Habbena, W and Bertagnolli, AD and Amin, SA and Walker, CB and Urakawa, H and Könneke, M and Devol, AH and Moffett, JW and Armbrust, EV and Jensen, GJ and Ingalls, AE and Stahl, DA},
title = {Nitrosopumilus maritimus gen. nov., sp. nov., Nitrosopumilus cobalaminigenes sp. nov., Nitrosopumilus oxyclinae sp. nov., and Nitrosopumilus ureiphilus sp. nov., four marine ammonia-oxidizing archaea of the phylum Thaumarchaeota.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {67},
number = {12},
pages = {5067-5079},
doi = {10.1099/ijsem.0.002416},
pmid = {29034851},
issn = {1466-5034},
mesh = {Ammonia/metabolism ; Archaea/*classification/genetics/isolation &amp; purification ; Base Composition ; DNA, Archaeal/genetics ; Estuaries ; Geologic Sediments/*microbiology ; Glyceryl Ethers/chemistry ; Oxidation-Reduction ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; Sequence Analysis, DNA ; Washington ; },
abstract = {Four mesophilic, neutrophilic, and aerobic marine ammonia-oxidizing archaea, designated strains SCM1[T], HCA1[T], HCE1[T] and PS0[T], were isolated from a tropical marine fish tank, dimly lit deep coastal waters, the lower euphotic zone of coastal waters, and near-surface sediment in the Puget Sound estuary, respectively. Cells are straight or slightly curved small rods, 0.15-0.26 µm in diameter and 0.50-1.59 µm in length. Motility was not observed, although strain PS0[T] possesses genes associated with archaeal flagella and chemotaxis, suggesting it may be motile under some conditions. Cell membranes consist of glycerol dibiphytanyl glycerol tetraether (GDGT) lipids, with crenarchaeol as the major component. Strain SCM1[T] displays a single surface layer (S-layer) with p6 symmetry, distinct from the p3-S-layer reported for the soil ammonia-oxidizing archaeon Nitrososphaera viennensis EN76[T]. Respiratory quinones consist of fully saturated and monounsaturated menaquinones with 6 isoprenoid units in the side chain. Cells obtain energy from ammonia oxidation and use carbon dioxide as carbon source; addition of an α-keto acid (α-ketoglutaric acid) was necessary to sustain growth of strains HCA1[T], HCE1[T], and PS0[T]. Strain PS0[T] uses urea as a source of ammonia for energy production and growth. All strains synthesize vitamin B1 (thiamine), B2 (riboflavin), B6 (pyridoxine), and B12 (cobalamin). Optimal growth occurs between 25 and 32 °C, between pH 6.8 and 7.3, and between 25 and 37 ‰ salinity. All strains have a low mol% G+C content of 33.0-34.2. Strains are related by 98 % or greater 16S rRNA gene sequence identity, sharing ~85 % 16S rRNA gene sequence identity with Nitrososphaera viennensis EN76[T]. All four isolates are well separated by phenotypic and genotypic characteristics and are here assigned to distinct species within the genus Nitrosopumilus gen. nov. Isolates SCM1[T] (=ATCC TSD-97[T] =NCIMB 15022[T]), HCA1[T] (=ATCC TSD-96[T]), HCE1[T] (=ATCC TSD-98[T]), and PS0[T] (=ATCC TSD-99[T]) are type strains of the species Nitrosopumilusmaritimus sp. nov., Nitrosopumilus cobalaminigenes sp. nov., Nitrosopumilus oxyclinae sp. nov., and Nitrosopumilus ureiphilus sp. nov., respectively. In addition, we propose the family Nitrosopumilaceae fam. nov. and the order Nitrosopumilales ord. nov. within the class Nitrososphaeria.},
}
@article {pmid29034077,
year = {2017},
author = {Danovaro, R and Rastelli, E and Corinaldesi, C and Tangherlini, M and Dell'Anno, A},
title = {Marine archaea and archaeal viruses under global change.},
journal = {F1000Research},
volume = {6},
number = {},
pages = {1241},
pmid = {29034077},
issn = {2046-1402},
abstract = {Global change is altering oceanic temperature, salinity, pH, and oxygen concentration, directly and indirectly influencing marine microbial food web structure and function. As microbes represent >90% of the ocean's biomass and are major drivers of biogeochemical cycles, understanding their responses to such changes is fundamental for predicting the consequences of global change on ecosystem functioning. Recent findings indicate that marine archaea and archaeal viruses are active and relevant components of marine microbial assemblages, far more abundant and diverse than was previously thought. Further research is urgently needed to better understand the impacts of global change on virus-archaea dynamics and how archaea and their viruses can interactively influence the ocean's feedbacks on global change.},
}
@article {pmid29033920,
year = {2017},
author = {Jones, DL and Baxter, BK},
title = {DNA Repair and Photoprotection: Mechanisms of Overcoming Environmental Ultraviolet Radiation Exposure in Halophilic Archaea.},
journal = {Frontiers in microbiology},
volume = {8},
number = {},
pages = {1882},
pmid = {29033920},
issn = {1664-302X},
abstract = {Halophilic archaea push the limits of life at several extremes. In particular, they are noted for their biochemical strategies in dealing with osmotic stress, low water activity and cycles of desiccation in their hypersaline environments. Another feature common to their habitats is intense ultraviolet (UV) radiation, which is a challenge that microorganisms must overcome. The consequences of high UV exposure include DNA lesions arising directly from bond rearrangement of adjacent bipyrimidines, or indirectly from oxidative damage, which may ultimately result in mutation and cell death. As such, these microorganisms have evolved a number of strategies to navigate the threat of DNA damage, which we differentiate into two categories: DNA repair and photoprotection. Photoprotection encompasses damage avoidance strategies that serve as a "first line of defense," and in halophilic archaea include pigmentation by carotenoids, mechanisms of oxidative damage avoidance, polyploidy, and genomic signatures that make DNA less susceptible to photodamage. Photolesions that do arise are addressed by a number of DNA repair mechanisms that halophilic archaea efficiently utilize, which include photoreactivation, nucleotide excision repair, base excision repair, and homologous recombination. This review seeks to place DNA damage, repair, and photoprotection in the context of halophilic archaea and the solar radiation of their hypersaline environments. We also provide new insight into the breadth of strategies and how they may work together to produce remarkable UV-resistance for these microorganisms.},
}
@article {pmid29033916,
year = {2017},
author = {Wang, S and Giller, K and Kreuzer, M and Ulbrich, SE and Braun, U and Schwarm, A},
title = {Contribution of Ruminal Fungi, Archaea, Protozoa, and Bacteria to the Methane Suppression Caused by Oilseed Supplemented Diets.},
journal = {Frontiers in microbiology},
volume = {8},
number = {},
pages = {1864},
pmid = {29033916},
issn = {1664-302X},
abstract = {Dietary lipids can suppress methane emission from ruminants, but effects are variable. Especially the role of bacteria, archaea, fungi and protozoa in mediating the lipid effects is unclear. In the present in vitro study, archaea, fungi and protozoa were selectively inhibited by specific agents. This was fully or almost fully successful for fungi and protozoa as well as archaeal activity as determined by the methyl-coenzyme M reductase alpha subunit gene. Five different microbial treatments were generated: rumen fluid being intact (I), without archaea (-A), without fungi (-F), without protozoa (-P) and with bacteria only (-AFP). A forage-concentrate diet given alone or supplemented with crushed full-fat oilseeds of either safflower (Carthamus tinctorius) or poppy (Papaver somniferum) or camelina (Camelina sativa) at 70 g oil kg[-1] diet dry matter was incubated. This added up to 20 treatments with six incubation runs per treatment. All oilseeds suppressed methane emission compared to the non-supplemented control. Compared to the non-supplemented control, -F decreased organic matter (OM) degradation, and short-chain fatty acid concentration was greater with camelina and safflower seeds. Methane suppression per OM digested in -F was greater with camelina seeds (-12 vs.-7% with I, P = 0.06), but smaller with poppy seeds (-4 vs. -8% with I, P = 0.03), and not affected with safflower seeds. With -P, camelina seeds decreased the acetate-to-propionate ratio and enhanced the methane suppression per gram dry matter (18 vs. 10% with I, P = 0.08). Hydrogen recovery was improved with -P in any oilseeds compared to non-supplemented control. No methane emission was detected with the -A and -AFP treatments. In conclusion, concerning methanogenesis, camelina seeds seem to exert effects only on archaea and bacteria. By contrast, with safflower and poppy seeds methane was obviously reduced mainly through the interaction with protozoa or archaea associated with protozoa. This demonstrated that the microbial groups differ in their contribution to the methane suppressing effect dependent on the source of lipid. These findings help to understand how lipid supplementation and microbial groups interact, and thus may assist in making this methane mitigation tool more efficient, but await confirmation in vivo.},
}
@article {pmid29029047,
year = {2017},
author = {Yang, S and Winkel, M and Wagner, D and Liebner, S},
title = {Community structure of rare methanogenic archaea: insight from a single functional group.},
journal = {FEMS microbiology ecology},
volume = {93},
number = {11},
pages = {},
pmid = {29029047},
issn = {1574-6941},
mesh = {Bacteria/*classification/genetics ; *Biodiversity ; DNA Restriction Enzymes/genetics ; Euryarchaeota/*classification/genetics ; Methane/*biosynthesis ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Soil Microbiology ; },
abstract = {The rare biosphere, the low abundant microbial populations, is suggested to be a conserved way of microbial life. Here we conducted a molecular survey of rare methanogenic archaea in the environment targeting the mcrA gene in order to test if general concepts associated with the structure of the rare bacterial biosphere also apply to single functional groups. Similar to what is known about rare bacterial communities, the contribution of rare methanogens to the alpha diversity is much larger than to Bray-Curtis measures. Moreover, a similar core group of methanogens harbored by the abundant and rare communities suggests similar sources and environmental controls of both groups. Among the communities of different levels of rarity, the conditionally rare methanogenic taxa largely account for the overall community dynamics of the rare biosphere and likely enter the dominant community under favorable environmental conditions. In addition, we observed a positive correlation between the alpha diversity and the production of methane when the rare taxa were taken into account. This supports the concept that increasing microbial biodiversity enhances ecological function. The composition and environmental associations of the rare methanogenic biosphere allow us to conclude that rarity is a conserved way also for single functional groups.},
}
@article {pmid28992595,
year = {2018},
author = {Yilmazel, YD and Zhu, X and Kim, KY and Holmes, DE and Logan, BE},
title = {Electrical current generation in microbial electrolysis cells by hyperthermophilic archaea Ferroglobus placidus and Geoglobus ahangari.},
journal = {Bioelectrochemistry (Amsterdam, Netherlands)},
volume = {119},
number = {},
pages = {142-149},
doi = {10.1016/j.bioelechem.2017.09.012},
pmid = {28992595},
issn = {1878-562X},
mesh = {Archaeoglobales/*chemistry/physiology ; Biofilms ; *Electric Conductivity ; *Electrolysis ; *Temperature ; },
abstract = {Few microorganisms have been examined for current generation under thermophilic (40-65°C) or hyperthermophilic temperatures (≥80°C) in microbial electrochemical systems. Two iron-reducing archaea from the family Archaeoglobaceae, Ferroglobus placidus and Geoglobus ahangari, showed electro-active behavior leading to current generation at hyperthermophilic temperatures in single-chamber microbial electrolysis cells (MECs). A current density (j) of 0.68±0.11A/m[2] was attained in F. placidus MECs at 85°C, and 0.57±0.10A/m[2] in G. ahangari MECs at 80°C, with an applied voltage of 0.7V. Cyclic voltammetry (CV) showed that both strains produced a sigmoidal catalytic wave, with a mid-point potential of -0.39V (vs. Ag/AgCl) for F. placidus and -0.37V for G. ahangari. The comparison of CVs using spent medium and turnover CVs, coupled with the detection of peaks at the same potentials in both turnover and non-turnover conditions, suggested that mediators were not used for electron transfer and that both archaea produced current through direct contact with the electrode. These two archaeal species, and other hyperthermophilic exoelectrogens, have the potential to broaden the applications of microbial electrochemical technologies for producing biofuels and other bioelectrochemical products under extreme environmental conditions.},
}
@article {pmid28992240,
year = {2017},
author = {Nakamura, T and Oshima, M and Yasuda, M and Shimamura, A and Morita, J and Uegaki, K},
title = {Alteration of molecular assembly of peroxiredoxins from hyperthermophilic archaea.},
journal = {Journal of biochemistry},
volume = {162},
number = {6},
pages = {415-422},
doi = {10.1093/jb/mvx045},
pmid = {28992240},
issn = {1756-2651},
mesh = {Aeropyrum/*chemistry ; Hydrogen Peroxide/pharmacology ; Models, Molecular ; Peroxiredoxins/*chemistry/genetics/metabolism ; Point Mutation/genetics ; Protein Conformation ; Pyrococcus horikoshii/chemistry ; },
abstract = {Peroxiredoxin from Pyrococcus horikoshii (PhPrx) is a decameric protein formed by ring-type assembly of five dimers. To engineer the quaternary structure of PhPrx, we created a mutant PhPrx (PhPrx6m) by introducing six point mutations designed to dissociate PhPrx into dimers. Although PhPrx6m was a dimer in solution, the six dimers assembled into a dodecamer following crystallization. In the crystal structure, PhPrx6m was overoxidized, and the peroxidatic cysteine was in sulfonic acid form and two cysteines in the C-terminal region were linked by an intramolecular disulfide bond. Thus, we characterized the wild-type PhPrx overoxidized by hydrogen peroxide (PhPrxPer). Analytical ultracentrifugation showed that PhPrxPer had a higher molecular mass in solution than PhPrx. This was confirmed by analysis of the crystal structure of PhPrxPer, which was found to form a ring-type dodecamer composed of six dimers. The monomeric structures of PhPrx6m and PhPrxPer differed from that of PhPrx in the relative orientation of two domains, reflecting the number of dimers in the ring-type assembly. Unlike PhPrx, homologous peroxiredoxin from Aeropyrum pernix (ApPrx) did not undergo hexameric association. This property can be explained by the stronger connection between the two domains in ApPrx due to its C-terminal extension relative to PhPrx.},
}
@article {pmid28975058,
year = {2017},
author = {Fuchsman, CA and Collins, RE and Rocap, G and Brazelton, WJ},
title = {Effect of the environment on horizontal gene transfer between bacteria and archaea.},
journal = {PeerJ},
volume = {5},
number = {},
pages = {e3865},
pmid = {28975058},
issn = {2167-8359},
abstract = {BACKGROUND: Horizontal gene transfer, the transfer and incorporation of genetic material between different species of organisms, has an important but poorly quantified role in the adaptation of microbes to their environment. Previous work has shown that genome size and the number of horizontally transferred genes are strongly correlated. Here we consider how genome size confuses the quantification of horizontal gene transfer because the number of genes an organism accumulates over time depends on its evolutionary history and ecological context (e.g., the nutrient regime for which it is adapted).<br><br>RESULTS: We investigated horizontal gene transfer between archaea and bacteria by first counting reciprocal BLAST hits among 448 bacterial and 57 archaeal genomes to find shared genes. Then we used the DarkHorse algorithm, a probability-based, lineage-weighted method (Podell &amp; Gaasterland, 2007), to identify potential horizontally transferred genes among these shared genes. By removing the effect of genome size in the bacteria, we have identified bacteria with unusually large numbers of shared genes with archaea for their genome size. Interestingly, archaea and bacteria that live in anaerobic and/or high temperature conditions are more likely to share unusually large numbers of genes. However, high salt was not found to significantly affect the numbers of shared genes. Numbers of shared (genome size-corrected, reciprocal BLAST hits) and transferred genes (identified by DarkHorse) were strongly correlated. Thus archaea and bacteria that live in anaerobic and/or high temperature conditions are more likely to share horizontally transferred genes. These horizontally transferred genes are over-represented by genes involved in energy conversion as well as the transport and metabolism of inorganic ions and amino acids.<br><br>CONCLUSIONS: Anaerobic and thermophilic bacteria share unusually large numbers of genes with archaea. This is mainly due to horizontal gene transfer of genes from the archaea to the bacteria. In general, these transfers are from archaea that live in similar oxygen and temperature conditions as the bacteria that receive the genes. Potential hotspots of horizontal gene transfer between archaea and bacteria include hot springs, marine sediments, and oil wells. Cold spots for horizontal transfer included dilute, aerobic, mesophilic environments such as marine and freshwater surface waters.},
}
@article {pmid28974619,
year = {2017},
author = {Skennerton, CT and Chourey, K and Iyer, R and Hettich, RL and Tyson, GW and Orphan, VJ},
title = {Erratum for Skennerton et al., "Methane-Fueled Syntrophy through Extracellular Electron Transfer: Uncovering the Genomic Traits Conserved within Diverse Bacterial Partners of Anaerobic Methanotrophic Archaea".},
journal = {mBio},
volume = {8},
number = {5},
pages = {},
doi = {10.1128/mBio.01561-17},
pmid = {28974619},
issn = {2150-7511},
}
@article {pmid28973467,
year = {2017},
author = {Martinez-Pastor, M and Lancaster, WA and Tonner, PD and Adams, MWW and Schmid, AK},
title = {A transcription network of interlocking positive feedback loops maintains intracellular iron balance in archaea.},
journal = {Nucleic acids research},
volume = {45},
number = {17},
pages = {9990-10001},
pmid = {28973467},
issn = {1362-4962},
mesh = {Archaeal Proteins/*genetics/metabolism ; DNA-Binding Proteins/genetics/metabolism ; *Feedback, Physiological ; *Gene Expression Regulation, Archaeal ; *Gene Regulatory Networks ; Halobacterium salinarum/*genetics/metabolism ; Homeostasis/genetics ; Iron/*metabolism ; Mutation ; Repressor Proteins/genetics/metabolism ; Transcription, Genetic ; },
abstract = {Iron is required for key metabolic processes but is toxic in excess. This circumstance forces organisms across the tree of life to tightly regulate iron homeostasis. In hypersaline lakes dominated by archaeal species, iron levels are extremely low and subject to environmental change; however, mechanisms regulating iron homeostasis in archaea remain unclear. In previous work, we demonstrated that two transcription factors (TFs), Idr1 and Idr2, collaboratively regulate aspects of iron homeostasis in the model species Halobacterium salinarum. Here we show that Idr1 and Idr2 are part of an extended regulatory network of four TFs of the bacterial DtxR family that maintains intracellular iron balance. We demonstrate that each TF directly regulates at least one of the other DtxR TFs at the level of transcription. Dynamical modeling revealed interlocking positive feedback loop architecture, which exhibits bistable or oscillatory network dynamics depending on iron availability. TF knockout mutant phenotypes are consistent with model predictions. Together, our results support that this network regulates iron homeostasis despite variation in extracellular iron levels, consistent with dynamical properties of interlocking feedback architecture in eukaryotes. These results suggest that archaea use bacterial-type TFs in a eukaryotic regulatory network topology to adapt to harsh environments.},
}
@article {pmid28973046,
year = {2017},
author = {Visone, V and Han, W and Perugino, G and Del Monaco, G and She, Q and Rossi, M and Valenti, A and Ciaramella, M},
title = {In vivo and in vitro protein imaging in thermophilic archaea by exploiting a novel protein tag.},
journal = {PloS one},
volume = {12},
number = {10},
pages = {e0185791},
pmid = {28973046},
issn = {1932-6203},
mesh = {Archaea/*metabolism ; Archaeal Proteins/*metabolism ; DNA Topoisomerases, Type I/metabolism ; Hot Temperature ; Sulfolobus/*metabolism ; Sulfolobus solfataricus/*metabolism ; },
abstract = {Protein imaging, allowing a wide variety of biological studies both in vitro and in vivo, is of great importance in modern biology. Protein and peptide tags fused to proteins of interest provide the opportunity to elucidate protein location and functions, detect protein-protein interactions, and measure protein activity and kinetics in living cells. Whereas several tags are suitable for protein imaging in mesophilic organisms, the application of this approach to microorganisms living at high temperature has lagged behind. Archaea provide an excellent and unique model for understanding basic cell biology mechanisms. Here, we present the development of a toolkit for protein imaging in the hyperthermophilic archaeon Sulfolobus islandicus. The system relies on a thermostable protein tag (H5) constructed by engineering the alkylguanine-DNA-alkyl-transferase protein of Sulfolobus solfataricus, which can be covalently labeled using a wide range of small molecules. As a suitable host, we constructed, by CRISPR-based genome-editing technology, a S. islandicus mutant strain deleted for the alkylguanine-DNA-alkyl-transferase gene (Δogt). Introduction of a plasmid-borne H5 gene in this strain led to production of a functional H5 protein, which was successfully labeled with appropriate fluorescent molecules and visualized in cell extracts as well as in Δogt live cells. H5 was fused to reverse gyrase, a peculiar thermophile-specific DNA topoisomerase endowed with positive supercoiling activity, and allowed visualization of the enzyme in living cells. To the best of our knowledge, this is the first report of in vivo imaging of any protein of a thermophilic archaeon, filling an important gap in available tools for cell biology studies in these organisms.},
}
@article {pmid28957503,
year = {2017},
author = {Bobay, LM and Ochman, H},
title = {Impact of Recombination on the Base Composition of Bacteria and Archaea.},
journal = {Molecular biology and evolution},
volume = {34},
number = {10},
pages = {2627-2636},
pmid = {28957503},
issn = {1537-1719},
support = {R01 GM108657/GM/NIGMS NIH HHS/United States ; R35 GM118038/GM/NIGMS NIH HHS/United States ; },
mesh = {Archaea/genetics ; Bacteria/genetics ; Base Composition/*genetics ; Computer Simulation ; Evolution, Molecular ; Gene Conversion ; Genome, Bacterial ; Mutation ; Phylogeny ; Recombination, Genetic/*genetics ; Selection, Genetic ; Sequence Analysis/methods ; },
abstract = {The mutational process in bacteria is biased toward A and T, and most species are GC-rich relative to the mutational input to their genome. It has been proposed that the shift in base composition is an adaptive process-that natural selection operates to increase GC-contents-and there is experimental evidence that bacterial strains with GC-rich versions of genes have higher growth rates than those strains with AT-rich versions expressing identical proteins. Alternatively, a nonadaptive process, GC-biased gene conversion (gBGC), could also increase the GC-content of DNA due to the mechanistic bias of gene conversion events during recombination. To determine what role recombination plays in the base composition of bacterial genomes, we compared the spectrum of nucleotide polymorphisms introduced by recombination in all microbial species represented by large numbers of sequenced strains. We found that recombinant alleles are consistently biased toward A and T, and that the magnitude of AT-bias introduced by recombination is similar to that of mutations. These results indicate that recombination alone, without the intervention of selection, is unlikely to counteract the AT-enrichment of bacterial genomes.},
}
@article {pmid28942710,
year = {2017},
author = {Yamauchi, N and Tanoue, R},
title = {Deuterium incorporation experiments from (3R)- and (3S)-[3-[2]H]leucine into characteristic isoprenoidal lipid-core of halophilic archaea suggests the involvement of isovaleryl-CoA dehydrogenase.},
journal = {Bioscience, biotechnology, and biochemistry},
volume = {81},
number = {11},
pages = {2062-2070},
doi = {10.1080/09168451.2017.1373588},
pmid = {28942710},
issn = {1347-6947},
mesh = {Deuterium/*chemistry ; Halobacterium salinarum/*metabolism ; Isovaleryl-CoA Dehydrogenase/*metabolism ; Leucine/*chemistry ; Lipid Metabolism ; Lipids/*chemistry ; Terpenes/*chemistry ; },
abstract = {The stereochemical reaction course for the two C-3 hydrogens of leucine to produce a characteristic isoprenoidal lipid in halophilic archaea was observed using incubation experiments with whole cell Halobacterium salinarum. Deuterium-labeled (3R)- and (3S)-[3-[2]H]leucine were freshly prepared as substrates from 2,3-epoxy-4-methyl-1-pentanol. Incorporation of deuterium from (3S)-[3-[2]H]leucine and loss of deuterium from (3R)-[3-[2]H]leucine in the lipid-core of H. salinarum was observed. Taken together with the results of our previous report, involving the incubation of chiral-labeled [5-[2]H]leucine, these results strongly suggested an involvement of isovaleryl-CoA dehydrogenase in leucine conversion to isoprenoid lipid in halophilic archaea. The stereochemical course of the reaction (anti-elimination) might have been the same as that previously reported for mammalian enzyme reactions. Thus, these results suggested that branched amino acids were metabolized to mevalonate in archaea in a manner similar to other organisms.},
}
@article {pmid28920507,
year = {2018},
author = {Sharma, A and Rani, S and Goel, M},
title = {Navigating the structure-function-evolutionary relationship of CsaA chaperone in archaea.},
journal = {Critical reviews in microbiology},
volume = {44},
number = {3},
pages = {274-289},
doi = {10.1080/1040841X.2017.1357535},
pmid = {28920507},
issn = {1549-7828},
mesh = {Archaea/chemistry/classification/genetics/*metabolism ; Archaeal Proteins/*chemistry/genetics/*metabolism ; *Evolution, Molecular ; Molecular Chaperones/*chemistry/genetics/*metabolism ; Phylogeny ; },
abstract = {CsaA is a protein involved in the post-translational translocation of proteins across the cytoplasmic membrane. It is considered to be a functional homolog of SecB which participates in the Sec-dependent translocation pathway in an analogous manner. CsaA has also been reported to act as a molecular chaperone, preventing aggregation of unfolded proteins. It is essentially a prokaryotic protein which is absent in eukaryotes, but found extensively in bacteria and earlier thought to be widely present in archaea. The study of phylogenetic distribution of CsaA among prokaryotes suggests that it is present only in few archaeal organisms, mainly species of Thermoplasmatales and Halobacteriales. Interestingly, the CsaA protein from these two archaeal orders cluster separately on the phylogenetic tree with CsaA from Gram-positive and Gram-negative bacteria. It, thus, appears that this protein might have been acquired in these archaeal organisms through independent horizontal gene transfer (HGT) events from different bacteria. In this review, we summarize the earlier biochemical, structural, and functional characterization studies of CsaA. We draw new insights into the evolutionary history of this protein through phylogenetic and structural comparison of bacterial CsaA with modelled archaeal CsaA from Picrophilus torridus and Natrialba magadii.},
}
@article {pmid28917104,
year = {2017},
author = {Lee, J and Shin, SG and Han, G and Koo, T and Hwang, S},
title = {Bacteria and archaea communities in full-scale thermophilic and mesophilic anaerobic digesters treating food wastewater: Key process parameters and microbial indicators of process instability.},
journal = {Bioresource technology},
volume = {245},
number = {Pt A},
pages = {689-697},
doi = {10.1016/j.biortech.2017.09.015},
pmid = {28917104},
issn = {1873-2976},
mesh = {Anaerobiosis ; *Archaea ; Bacteria ; Bioreactors ; Methane ; Sewage ; *Wastewater ; },
abstract = {In this study, four different mesophilic and thermophilic full-scale anaerobic digesters treating food wastewater (FWW) were monitored for 1-2years in order to investigate: 1) microbial communities underpinning anaerobic digestion of FWW, 2) significant factors shaping microbial community structures, and 3) potential microbial indicators of process instability. Twenty-seven bacterial genera were identified as abundant bacteria underpinning the anaerobic digestion of FWW. Methanosaeta harundinacea, M. concilii, Methanoculleus bourgensis, M. thermophilus, and Methanobacterium beijingense were revealed as dominant methanogens. Bacterial community structures were clearly differentiated by digesters; archaeal community structures of each digester were dominated by one or two methanogen species. Temperature, ammonia, propionate, Na[+], and acetate in the digester were significant factors shaping microbial community structures. The total microbial populations, microbial diversity, and specific bacteria genera showed potential as indicators of process instability in the anaerobic digestion of FWW.},
}
@article {pmid28910647,
year = {2017},
author = {Dai, X and Hu, C and Zhang, D and Dai, L and Duan, N},
title = {Impact of a high ammonia-ammonium-pH system on methane-producing archaea and sulfate-reducing bacteria in mesophilic anaerobic digestion.},
journal = {Bioresource technology},
volume = {245},
number = {Pt A},
pages = {598-605},
doi = {10.1016/j.biortech.2017.08.208},
pmid = {28910647},
issn = {1873-2976},
mesh = {*Ammonia ; Ammonium Compounds ; Anaerobiosis ; *Archaea ; Bacteria, Anaerobic ; Bioreactors ; *Methane ; Sulfates ; },
abstract = {A novel strategy for acclimation to ammonia stress was implemented by stimulating a high ammonia-ammonium-pH environment in a high-solid anaerobic digestion (AD) system in this study. Three semi-continuously stirred anaerobic reactors performed well over the whole study period under mesophilic conditions, especially in experimental group (R-2) when accommodated from acclimation period which the maximum total ammonia nitrogen (TAN) and free ammonia nitrogen (FAN) increased to 4921 and 2996mg/L, respectively. Moreover, when it accommodated the high ammonia-ammonium-pH system, the daily biogas production and methane content were similar to those in R-1 (the blank control to R-2), but the hydrogen sulfide (H2S) content lower than the blank control. Moreover, mechanistic studies showed that high ammonia stress enhanced the activity of coenzyme F420. The results of real-time fluorescent quantitative polymerase chain reaction (PCR) showed that ammonia stress decreased the abundance of sulfate-reducing bacteria and increased the abundance of methane-producing archaea.},
}
@article {pmid28905430,
year = {2017},
author = {McDougall, M and Francisco, O and Harder-Viddal, C and Roshko, R and Meier, M and Stetefeld, J},
title = {Archaea S-layer nanotube from a "black smoker" in complex with cyclo-octasulfur (S8) rings.},
journal = {Proteins},
volume = {85},
number = {12},
pages = {2209-2216},
doi = {10.1002/prot.25385},
pmid = {28905430},
issn = {1097-0134},
mesh = {Amino Acid Motifs ; Archaeal Proteins ; Crystallography, X-Ray ; Desulfurococcaceae/*chemistry/metabolism ; Escherichia coli/genetics/metabolism ; Gene Expression ; Hydrophobic and Hydrophilic Interactions ; Hydrothermal Vents ; Molecular Dynamics Simulation ; Nanotubes/*chemistry/ultrastructure ; Plasmids/chemistry/metabolism ; Protein Interaction Domains and Motifs ; Protein Structure, Secondary ; Recombinant Fusion Proteins/chemistry/genetics/metabolism ; Sulfur/*chemistry/metabolism ; Thermodynamics ; Water/*chemistry/metabolism ; },
abstract = {Elemental sulfur exists primarily as an S80 ring and serves as terminal electron acceptor for a variety of sulfur-fermenting bacteria. Hyperthermophilic archaea from black smoker vents are an exciting research tool to advance our knowledge of sulfur respiration under extreme conditions. Here, we use a hybrid method approach to demonstrate that the proteinaceous cavities of the S-layer nanotube of the hyperthermophilic archaeon Staphylothermus marinus act as a storage reservoir for cyclo-octasulfur S8. Fully atomistic molecular dynamics (MD) simulations were performed and the method of multiconfigurational thermodynamic integration was employed to compute the absolute free energy for transferring a ring of elemental sulfur S8 from an aqueous bath into the largest hydrophobic cavity of a fragment of archaeal tetrabrachion. Comparisons with earlier MD studies of the free energy of hydration as a function of water occupancy in the same cavity of archaeal tetrabrachion show that the sulfur ring is energetically favored over water.},
}
@article {pmid28885627,
year = {2018},
author = {Ino, K and Hernsdorf, AW and Konno, U and Kouduka, M and Yanagawa, K and Kato, S and Sunamura, M and Hirota, A and Togo, YS and Ito, K and Fukuda, A and Iwatsuki, T and Mizuno, T and Komatsu, DD and Tsunogai, U and Ishimura, T and Amano, Y and Thomas, BC and Banfield, JF and Suzuki, Y},
title = {Ecological and genomic profiling of anaerobic methane-oxidizing archaea in a deep granitic environment.},
journal = {The ISME journal},
volume = {12},
number = {1},
pages = {31-47},
pmid = {28885627},
issn = {1751-7370},
mesh = {Anaerobiosis ; Environment ; Genomics ; Groundwater/chemistry/*microbiology ; Methane/*metabolism ; Methanosarcinales/classification/*genetics/isolation &amp; purification/*metabolism ; Nitrates/metabolism ; Oxidation-Reduction ; Phylogeny ; Silicon Dioxide/*analysis/metabolism ; Sulfates/metabolism ; },
abstract = {Recent single-gene-based surveys of deep continental aquifers demonstrated the widespread occurrence of archaea related to Candidatus Methanoperedens nitroreducens (ANME-2d) known to mediate anaerobic oxidation of methane (AOM). However, it is unclear whether ANME-2d mediates AOM in the deep continental biosphere. In this study, we found the dominance of ANME-2d in groundwater enriched in sulfate and methane from a 300-m deep underground borehole in granitic rock. A near-complete genome of one representative species of the ANME-2d obtained from the underground borehole has most of functional genes required for AOM and assimilatory sulfate reduction. The genome of the subsurface ANME-2d is different from those of other members of ANME-2d by lacking functional genes encoding nitrate and nitrite reductases and multiheme cytochromes. In addition, the subsurface ANME-2d genome contains a membrane-bound NiFe hydrogenase gene putatively involved in respiratory H2 oxidation, which is different from those of other methanotrophic archaea. Short-term incubation of microbial cells collected from the granitic groundwater with [13]C-labeled methane also demonstrates that AOM is linked to microbial sulfate reduction. Given the prominence of granitic continental crust and sulfate and methane in terrestrial subsurface fluids, we conclude that AOM may be widespread in the deep continental biosphere.},
}
@article {pmid28880150,
year = {2017},
author = {Nayak, DD and Mahanta, N and Mitchell, DA and Metcalf, WW},
title = {Post-translational thioamidation of methyl-coenzyme M reductase, a key enzyme in methanogenic and methanotrophic Archaea.},
journal = {eLife},
volume = {6},
number = {},
pages = {},
pmid = {28880150},
issn = {2050-084X},
support = {R01 GM097142/GM/NIGMS NIH HHS/United States ; },
mesh = {Amides/*chemistry ; Archaea/*enzymology/growth &amp; development ; Binding Sites ; Catalysis ; Methane/*metabolism ; Oxidoreductases/*chemistry/*metabolism ; Phylogeny ; *Protein Processing, Post-Translational ; Sulfhydryl Compounds/*chemistry ; },
abstract = {Methyl-coenzyme M reductase (MCR), found in strictly anaerobic methanogenic and methanotrophic archaea, catalyzes the reversible production and consumption of the potent greenhouse gas methane. The α subunit of MCR (McrA) contains several unusual post-translational modifications, including a rare thioamidation of glycine. Based on the presumed function of homologous genes involved in the biosynthesis of thioviridamide, a thioamide-containing natural product, we hypothesized that the archaeal tfuA and ycaO genes would be responsible for post-translational installation of thioglycine into McrA. Mass spectrometric characterization of McrA from the methanogenic archaeon Methanosarcina acetivorans lacking tfuA and/or ycaO revealed the presence of glycine, rather than thioglycine, supporting this hypothesis. Phenotypic characterization of the ∆ycaO-tfuA mutant revealed a severe growth rate defect on substrates with low free energy yields and at elevated temperatures (39°C - 45°C). Our analyses support a role for thioglycine in stabilizing the protein secondary structure near the active site.},
}
@article {pmid28874471,
year = {2017},
author = {Fu, X and Adams, Z and Liu, R and Hepowit, NL and Wu, Y and Bowmann, CF and Moskovitz, J and Maupin-Furlow, JA},
title = {Methionine Sulfoxide Reductase A (MsrA) and Its Function in Ubiquitin-Like Protein Modification in Archaea.},
journal = {mBio},
volume = {8},
number = {5},
pages = {},
pmid = {28874471},
issn = {2150-7511},
support = {P20 GM103418/GM/NIGMS NIH HHS/United States ; P30 AG035982/AG/NIA NIH HHS/United States ; R01 GM057498/GM/NIGMS NIH HHS/United States ; },
mesh = {Archaea/*enzymology ; Chromatography, Liquid ; Dimethyl Sulfoxide/pharmacology ; Methionine/analogs &amp; derivatives/metabolism ; Methionine Sulfoxide Reductases/biosynthesis/*genetics/*metabolism ; Oxidants/pharmacology ; Oxidative Stress ; Protein Processing, Post-Translational ; Proteolysis ; Tandem Mass Spectrometry ; Ubiquitination ; Ubiquitins/chemistry/*metabolism ; },
abstract = {Methionine sulfoxide reductase A (MsrA) is an antioxidant enzyme found in all domains of life that catalyzes the reduction of methionine-S-sulfoxide (MSO) to methionine in proteins and free amino acids. We demonstrate that archaeal MsrA has a ubiquitin-like (Ubl) protein modification activity that is distinct from its stereospecific reduction of MSO residues. MsrA catalyzes this Ubl modification activity, with the Ubl-activating E1 UbaA, in the presence of the mild oxidant dimethyl sulfoxide (DMSO) and in the absence of reductant. In contrast, the MSO reductase activity of MsrA is inhibited by DMSO and requires reductant. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis reveals that MsrA-dependent Ubl conjugates are associated with DNA replication, protein remodeling, and oxidative stress and include the Ubl-modified MsrA, Orc3 (Orc1/Cdc6), and Cdc48d (Cdc48/p97 AAA+ ATPase). Overall, we found archaeal MsrA to have opposing MSO reductase and Ubl modifying activities that are associated with oxidative stress responses and controlled by exposure to mild oxidant.IMPORTANCE Proteins that are damaged by oxidative stress are often targeted for proteolysis by the ubiquitin-proteasome system (UPS). The mechanisms that control this response are poorly understood, especially under conditions of mild oxidative stress when protein damage is modest. Here, we discovered a novel function of archaeal MsrA in guiding the Ubl modification of target proteins in the presence of mild oxidant. This newly reported activity of MsrA is distinct from its stereospecific reduction of methionine-S-sulfoxide to methionine residues. Our results are significant steps forward, first, in elucidating a protein factor that guides Ubl modification in archaea, and second, in providing an insight into oxidative stress responses that can trigger Ubl modification in a cell.},
}
@article {pmid28853770,
year = {2016},
author = {Kozhevnikova, DA and Taranov, EA and Lebedinsky, AV and Bonch-Osmolovskaya, EA and Sokolova, TG},
title = {Hydrogenogenic and Sulfidogenic Growth of Thermococcus Archaea on Carbon Monoxide and Formate.},
journal = {Mikrobiologiia},
volume = {85},
number = {4},
pages = {381-392},
pmid = {28853770},
issn = {0026-3656},
mesh = {Aldehyde Oxidoreductases/genetics/*metabolism ; Atlantic Ocean ; Carbon Monoxide/*metabolism ; Formate Dehydrogenases/genetics/*metabolism ; Formates/*metabolism ; Gene Expression ; *Genome, Archaeal ; Hot Temperature ; Hydrogen/metabolism ; Hydrothermal Vents ; Kinetics ; Multienzyme Complexes/genetics/*metabolism ; Multigene Family ; Oxidation-Reduction ; Phylogeny ; Seawater ; Sulfur/metabolism ; Thermococcus/classification/genetics/*metabolism ; },
abstract = {Enrichment and pure cultures of hyperthermophilic archaea capable of anaerobic growth on one- carbon compounds (CO and/or formate) were obtained from deep-sea sites of hydrothermal activity at the Mid-Atlantic Ridge, Lau Basin, and Guaymas Basin. All isolates belonged to the T barophilus-T paralvi- .nellae group within the genus Thermococcus. In all cases available for analysis, the genomes of Thermococcus strains capable of growth by hydrogenogenic utilization of CO and/or formate contained clusters of genes en- coding energy-converting hydrogenase and either CO dehydrogenase or formate dehydrogenase and formate transporter. Apart from the previously known processes of hydrogenogenic oxidation of CO and formate, the oxidation of these substrates coupled to sulfur reduction was observed, processes previously unknown among archaea. The capacities for hydrogenogenic or sulfidogenic oxidation of CO and formate occurred in the studied strains in all possible combinations, which could only in part be explained by peculiarities of organi- zation of genetic determinants revealed in the genomes. Investigation of CO and formate consumption kinet- ics revealed that T barophilus strain Ch5 was able to grow at concentrations close to the environmental ones. Thus, it was shown that hyperthermophilic archaea from deep-sea hydrothermal vents are able to utilize one- carbon substrates of abiotic origin both in the presence of an electron acceptor (sulfur) and in its absence. These processes were probably of importance under the conditions of the early Earth biosphere.},
}
@article {pmid28841790,
year = {2017},
author = {Roy, D and McEvoy, J and Blonigen, M and Amundson, M and Khan, E},
title = {Seasonal variation and ex-situ nitrification activity of ammonia oxidizing archaea in biofilm based wastewater treatment processes.},
journal = {Bioresource technology},
volume = {244},
number = {Pt 1},
pages = {850-859},
doi = {10.1016/j.biortech.2017.08.060},
pmid = {28841790},
issn = {1873-2976},
mesh = {Ammonia ; *Archaea ; Bacteria ; Biofilms ; *Nitrification ; Oxidation-Reduction ; Phylogeny ; Seasons ; *Wastewater ; },
abstract = {The abundance of ammonia oxidizing archaea (AOA) and ammonia oxidizing bacteria (AOB) was investigated in full-scale two-stage trickling filters (TF) and moving bed bioreactor (MBBR) treating municipal wastewater. Biofilm samples were collected for 17months from nitrifying TF (NTF), biochemical oxygen demand TF (BTF), and MBBR media. The abundance of AOA and AOB was determined using a quantitative PCR approach targeting the ammonia monooxygenase subunit A gene of archaea and bacteria. AOA were dominant in the NTF and MBBR, while AOB dominated in the BTF. AOA and AOB were more abundant during warmer months, and AOA were detected in the BTF only during warmer months. In laboratory nitrification activity experiments, ammonia oxidation to nitrite decreased when AOA populations from the NTF and MBBR were inhibited, demonstrating that AOA contributed to nitrification. This study has shown that AOA outnumber AOB and contribute to ammonia oxidation in full-scale nitrifying biofilm processes.},
}
@article {pmid28840778,
year = {2017},
author = {Tomita, T},
title = {Structure, function, and regulation of enzymes involved in amino acid metabolism of bacteria and archaea.},
journal = {Bioscience, biotechnology, and biochemistry},
volume = {81},
number = {11},
pages = {2050-2061},
doi = {10.1080/09168451.2017.1365593},
pmid = {28840778},
issn = {1347-6947},
mesh = {Allosteric Regulation ; Amino Acids/*metabolism ; Animals ; Archaea/*enzymology/metabolism ; Bacteria/*enzymology/metabolism ; Glutamate Dehydrogenase/*chemistry/*metabolism ; Humans ; },
abstract = {Amino acids are essential components in all organisms because they are building blocks of proteins. They are also produced industrially and used for various purposes. For example, L-glutamate is used as the component of "umami" taste and lysine has been used as livestock feed. Recently, many kinds of amino acids have attracted attention as biological regulators and are used for a healthy life. Thus, to clarify the mechanism of how amino acids are biosynthesized and how they work as biological regulators will lead to further effective utilization of them. Here, I review the leucine-induced-allosteric activation of glutamate dehydrogenase (GDH) from Thermus thermophilus and the relationship with the allosteric regulation of GDH from mammals. Next, I describe structural insights into the efficient production of L-glutamate by GDH from an excellent L-glutamate producer, Corynebacterium glutamicum. Finally, I review the structural biology of lysine biosynthesis of thermophilic bacterium and archaea.},
}
@article {pmid28837073,
year = {2017},
author = {Yi, GS and Song, Y and Wang, WW and Chen, JN and Deng, W and Cao, W and Wang, FP and Xiao, X and Liu, XP},
title = {Two Archaeal RecJ Nucleases from Methanocaldococcus jannaschii Show Reverse Hydrolysis Polarity: Implication to Their Unique Function in Archaea.},
journal = {Genes},
volume = {8},
number = {9},
pages = {},
pmid = {28837073},
issn = {2073-4425},
abstract = {Bacterial nuclease RecJ, which exists in almost all bacterial species, specifically degrades single-stranded (ss) DNA in the 5' to 3' direction. Some archaeal phyla, except Crenarchaea, also encode RecJ homologs. Compared with bacterial RecJ, archaeal RecJ exhibits a largely different amino acid sequence and domain organization. Archaeal RecJs from Thermococcus kodakarensis and Pyrococcus furiosus show 5'→3' exonuclease activity on ssDNA. Interestingly, more than one RecJ exists in some Euryarchaeota classes, such as Methanomicrobia, Methanococci, Methanomicrobia, Methanobacteria, and Archaeoglobi. Here we report the biochemical characterization of two RecJs from Methanocaldococcus jannaschii, the long RecJ1 (MJ0977) and short RecJ2 (MJ0831) to understand their enzymatic properties. RecJ1 is a 5'→3' exonuclease with a preference to ssDNA; however, RecJ2 is a 3'→5' exonuclease with a preference to ssRNA. The 5' terminal phosphate promotes RecJ1 activity, but the 3' terminal phosphate inhibits RecJ2 nuclease. Go-Ichi-Ni-San (GINS) complex does not interact with two RecJs and does not promote their nuclease activities. Finally, we discuss the diversity, function, and molecular evolution of RecJ in archaeal taxonomy. Our analyses provide insight into the function and evolution of conserved archaeal RecJ/eukaryotic Cdc45 protein.},
}
@article {pmid28826642,
year = {2018},
author = {Moissl-Eichinger, C and Pausan, M and Taffner, J and Berg, G and Bang, C and Schmitz, RA},
title = {Archaea Are Interactive Components of Complex Microbiomes.},
journal = {Trends in microbiology},
volume = {26},
number = {1},
pages = {70-85},
doi = {10.1016/j.tim.2017.07.004},
pmid = {28826642},
issn = {1878-4380},
mesh = {Animals ; Archaea/classification/*physiology ; Biodiversity ; Biofilms ; Ecology ; Ecosystem ; Eukaryota ; Euryarchaeota ; Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology ; Halobacteriales ; Health ; Humans ; Microbial Consortia ; Microbial Interactions/*physiology ; Microbiota/*physiology ; Mouth/microbiology ; Phylogeny ; Plants/microbiology ; Ruminants/microbiology ; Soil Microbiology ; Symbiosis ; Viruses ; },
abstract = {Recent findings have shaken our picture of the biology of the archaea and revealed novel traits beyond archaeal extremophily and supposed 'primitiveness'. The archaea constitute a considerable fraction of the Earth's ecosystems, and their potential to shape their surroundings by a profound interaction with their biotic and abiotic environment has been recognized. Moreover, archaea have been identified as a substantial component, or even as keystone species, in complex microbiomes - in the environment or accompanying a holobiont. Species of the Euryarchaeota (methanogens, halophiles) and Thaumarchaeota, in particular, have the capacity to coexist in plant, animal, and human microbiomes, where syntrophy allows them to thrive under energy-deficiency stress. Due to methodological limitations, the archaeome remains mysterious, and many questions with respect to potential pathogenicity, function, and structural interactions with their host and other microorganisms remain.},
}
@article {pmid28826405,
year = {2017},
author = {Gilmore, SP and Henske, JK and Sexton, JA and Solomon, KV and Seppälä, S and Yoo, JI and Huyett, LM and Pressman, A and Cogan, JZ and Kivenson, V and Peng, X and Tan, Y and Valentine, DL and O'Malley, MA},
title = {Genomic analysis of methanogenic archaea reveals a shift towards energy conservation.},
journal = {BMC genomics},
volume = {18},
number = {1},
pages = {639},
pmid = {28826405},
issn = {1471-2164},
mesh = {Anaerobiosis ; Archaeal Proteins/metabolism ; Energy Metabolism/*genetics ; *Genomics ; Methane/*biosynthesis ; Methanobacterium/*genetics/*metabolism ; },
abstract = {BACKGROUND: The metabolism of archaeal methanogens drives methane release into the environment and is critical to understanding global carbon cycling. Methanogenesis operates at a very low reducing potential compared to other forms of respiration and is therefore critical to many anaerobic environments. Harnessing or altering methanogen metabolism has the potential to mitigate global warming and even be utilized for energy applications.<br><br>RESULTS: Here, we report draft genome sequences for the isolated methanogens Methanobacterium bryantii, Methanosarcina spelaei, Methanosphaera cuniculi, and Methanocorpusculum parvum. These anaerobic, methane-producing archaea represent a diverse set of isolates, capable of methylotrophic, acetoclastic, and hydrogenotrophic methanogenesis. Assembly and analysis of the genomes allowed for simple and rapid reconstruction of metabolism in the four methanogens. Comparison of the distribution of Clusters of Orthologous Groups (COG) proteins to a sample of genomes from the RefSeq database revealed a trend towards energy conservation in genome composition of all methanogens sequenced. Further analysis of the predicted membrane proteins and transporters distinguished differing energy conservation methods utilized during methanogenesis, such as chemiosmotic coupling in Msar. spelaei and electron bifurcation linked to chemiosmotic coupling in Mbac. bryantii and Msph. cuniculi.<br><br>CONCLUSIONS: Methanogens occupy a unique ecological niche, acting as the terminal electron acceptors in anaerobic environments, and their genomes display a significant shift towards energy conservation. The genome-enabled reconstructed metabolisms reported here have significance to diverse anaerobic communities and have led to proposed substrate utilization not previously reported in isolation, such as formate and methanol metabolism in Mbac. bryantii and CO2 metabolism in Msph. cuniculi. The newly proposed substrates establish an important foundation with which to decipher how methanogens behave in native communities, as CO2 and formate are common electron carriers in microbial communities.},
}
@article {pmid28812261,
year = {2017},
author = {Xuan, J and Yao, H and Feng, Y and Wang, J},
title = {Backbone and side-chain [1]H, [15]N and [13]C resonance assignments of two Sac10b family members Mvo10b and Mth10bTQQA from archaea.},
journal = {Biomolecular NMR assignments},
volume = {11},
number = {2},
pages = {269-273},
doi = {10.1007/s12104-017-9761-8},
pmid = {28812261},
issn = {1874-270X},
support = {31300635//National Natural Science Foundation of China/ ; 31670735//National Natural Science Foundation of China/ ; 30770434//National Natural Science Foundation of China/ ; },
mesh = {Archaeal Proteins/*chemistry ; DNA-Binding Proteins/*chemistry ; *Nuclear Magnetic Resonance, Biomolecular ; },
abstract = {The Sac10b family proteins, also named as Alba, are small, basic, nucleic acid-binding proteins widely distributed in archaea. They possess divergent physiological functions such as binding to both DNA and RNA with a high affinity and involving in genomic DNA compaction, RNA transactions and transcriptional regulations. The structures of many Sac10b family proteins from hyperthermophilic archaea have been reported, while those from thermophilic and mesophilic archaea are largely unknown. As was pointed out, the homologous members from thermophilic and mesophilic archaea may have functions different from the hyperthermophilic members. Therefore, comparison of these homologous members can provide biophysical and structural insight into the functional diversity and thermal adaptation mechanism. The present work mainly focused on the NMR study of two Sac10b family members, Mvo10b and Mth10b, from the mesophilic and thermophilic archaea, respectively. To overcome the difficulties caused by the oligomerization and conformation heterogeneity of Mth10b, a M13T/L17Q/I20Q/P56A mutant Mth10b (Mth10bTQQA) was constructed and used together with Mvo10b for multi-dimensional NMR experiments. The resonance assignments of Mvo10b and Mth10bTQQA are reported for further structural determination which is a basis for understanding the functional diversity and their thermal adaption mechanisms.},
}
@article {pmid28808742,
year = {2017},
author = {Wu, RN and Meng, H and Wang, YF and Lan, W and Gu, JD},
title = {A More Comprehensive Community of Ammonia-Oxidizing Archaea (AOA) Revealed by Genomic DNA and RNA Analyses of amoA Gene in Subtropical Acidic Forest Soils.},
journal = {Microbial ecology},
volume = {74},
number = {4},
pages = {910-922},
pmid = {28808742},
issn = {1432-184X},
mesh = {Ammonia/metabolism ; Archaea/classification/*physiology ; Archaeal Proteins/*analysis ; China ; Cunninghamia/growth &amp; development ; *Forestry ; Forests ; *Microbiota ; Oxidation-Reduction ; Phylogeny ; *Soil Microbiology ; },
abstract = {Ammonia-oxidizing bacteria (AOB) and archaea (AOA) are the main nitrifiers which are well studied in natural environments, and AOA frequently outnumber AOB by orders especially in acidic conditions, making AOA the most promising ammonia oxidizers. The phylogeny of AOA revealed in related studies, however, often varied and hardly reach a consensus on functional phylotypes. The objective of this study was to compare ammonia-oxidizing communities by amoA gene and transcript based on both genomic DNA and RNA in extremely acidic forest soils (pH <4.5). Our results support the numerical and functional dominance of AOA over AOB in acidic soils as bacterial amoA gene and transcript were both under detection limits and archaeal amoA, in contrast, were abundant and responded to the fluctuations of environmental factors. Organic matter from tree residues was proposed as the main source of microbial available nitrogen, and the potential co-precipitation of dissolved organic matter (DOM) with soluble Al[3+] species in acidic soil matrix may further restrict the amount of nitrogen sources required by AOB besides NH3/NH4[+] equilibrium. Although AOA were better adapted to oligotrophic environments, they were susceptible to the toxicity of exchangeable Al[3+]. Phylotypes affiliated to Nitrososphaera, Nitrososphaera sister group, and Nitrosotalea were detected by amoA gene and transcript. Nitrosotalea devantaerra and Nitrososphaera sister group were the major AOA. Compared to the genomic DNA data, higher relative abundances of Nitrososphaera and Nitrososphaera sister group were recognized in amoA transcript inferred AOA communities, where Nitrosotalea relative abundance was found lower, implying the functional activities of Nitrososphaera sister group and Nitrososphaera were easily underestimated and Nitrosotalea did not attribute proportionally to nitrification in extremely acidic soils. Further comparison of the different AOA community compositions and relative abundance of each phylotypes revealed by amoA genes and transcripts make it possible to identify the functional AOA species and assess their ecological role in extremely acidic soils.},
}
@article {pmid28798133,
year = {2017},
author = {Mattiroli, F and Bhattacharyya, S and Dyer, PN and White, AE and Sandman, K and Burkhart, BW and Byrne, KR and Lee, T and Ahn, NG and Santangelo, TJ and Reeve, JN and Luger, K},
title = {Structure of histone-based chromatin in Archaea.},
journal = {Science (New York, N.Y.)},
volume = {357},
number = {6351},
pages = {609-612},
pmid = {28798133},
issn = {1095-9203},
support = {R01 GM114594/GM/NIGMS NIH HHS/United States ; S10 RR026641/RR/NCRR NIH HHS/United States ; R01 GM053185/GM/NIGMS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; R01 GM067777/GM/NIGMS NIH HHS/United States ; R01 GM100329/GM/NIGMS NIH HHS/United States ; },
mesh = {Amino Acid Substitution ; Chromatin/chemistry/*ultrastructure ; Crystallography, X-Ray ; DNA, Archaeal/chemistry/ultrastructure ; Gene Expression Regulation, Archaeal ; Glycine/genetics ; Histones/chemistry/*ultrastructure ; Nucleosomes/chemistry/ultrastructure ; Protein Multimerization ; *Thermococcus/chemistry/genetics/growth &amp; development ; Transcription, Genetic ; },
abstract = {Small basic proteins present in most Archaea share a common ancestor with the eukaryotic core histones. We report the crystal structure of an archaeal histone-DNA complex. DNA wraps around an extended polymer, formed by archaeal histone homodimers, in a quasi-continuous superhelix with the same geometry as DNA in the eukaryotic nucleosome. Substitutions of a conserved glycine at the interface of adjacent protein layers destabilize archaeal chromatin, reduce growth rate, and impair transcription regulation, confirming the biological importance of the polymeric structure. Our data establish that the histone-based mechanism of DNA compaction predates the nucleosome, illuminating the origin of the nucleosome.},
}
@article {pmid28794466,
year = {2017},
author = {Cavazzini, D and Grossi, G and Levati, E and Vallese, F and Montanini, B and Bolchi, A and Zanotti, G and Ottonello, S},
title = {A family of archaea-like carboxylesterases preferentially expressed in the symbiotic phase of the mychorrizal fungus Tuber melanosporum.},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {7628},
pmid = {28794466},
issn = {2045-2322},
mesh = {Ascomycota/*enzymology/*physiology ; Carboxylic Ester Hydrolases/chemistry/genetics/*metabolism ; Catalytic Domain ; Enzyme Stability ; Hot Temperature ; Mycorrhizae/*enzymology/*physiology ; Protein Conformation ; Protein Folding ; Protein Multimerization ; Static Electricity ; Substrate Specificity ; *Symbiosis ; X-Ray Diffraction ; },
abstract = {An increasing number of esterases is being revealed by (meta) genomic sequencing projects, but few of them are functionally/structurally characterized, especially enzymes of fungal origin. Starting from a three-member gene family of secreted putative "lipases/esterases" preferentially expressed in the symbiotic phase of the mycorrhizal fungus Tuber melanosporum ("black truffle"), we show here that these enzymes (TmelEST1-3) are dimeric, heat-resistant carboxylesterases capable of hydrolyzing various short/medium chain p-nitrophenyl esters. TmelEST2 was the most active (kcat = 2302 s[-1] for p-nitrophenyl-butyrate) and thermally stable (T50 = 68.3 °C), while TmelEST3 was the only one displaying some activity on tertiary alcohol esters. X-ray diffraction analysis of TmelEST2 revealed a classical α/β hydrolase-fold structure, with a network of dimer-stabilizing intermolecular interactions typical of archaea esterases. The predicted structures of TmelEST1 and 3 are overall quite similar to that of TmelEST2 but with some important differences. Most notably, the much smaller volume of the substrate-binding pocket and the more acidic electrostatic surface profile of TmelEST1. This was also the only TmelEST capable of hydrolyzing feruloyl-esters, suggestinng a possible role in root cell-wall deconstruction during symbiosis establishment. In addition to their potential biotechnological interest, TmelESTs raise important questions regarding the evolutionary recruitment of archaea-like enzymes into mesophilic subterranean fungi such as truffles.},
}
@article {pmid28790990,
year = {2017},
author = {Chen, J and Nie, Y and Liu, W and Wang, Z and Shen, W},
title = {Ammonia-Oxidizing Archaea Are More Resistant Than Denitrifiers to Seasonal Precipitation Changes in an Acidic Subtropical Forest Soil.},
journal = {Frontiers in microbiology},
volume = {8},
number = {},
pages = {1384},
pmid = {28790990},
issn = {1664-302X},
abstract = {Seasonal precipitation changes are increasingly severe in subtropical areas. However, the responses of soil nitrogen (N) cycle and its associated functional microorganisms to such precipitation changes remain unclear. In this study, two projected precipitation patterns were manipulated: intensifying the dry-season drought (DD) and extending the dry-season duration (ED) but increasing the wet-season storms following the DD and ED treatment period. The effects of these two contrasting precipitation patterns on soil net N transformation rates and functional gene abundances were quantitatively assessed through a resistance index. Results showed that the resistance index of functional microbial abundance (-0.03 ± 0.08) was much lower than that of the net N transformation rate (0.55 ± 0.02) throughout the experiment, indicating that microbial abundance was more responsive to precipitation changes compared with the N transformation rate. Spring drought under the ED treatment significantly increased the abundances of both nitrifying (amoA) and denitrifying genes (nirK, nirS, and nosZ), while changes in these gene abundances overlapped largely with control treatment during droughts in the dry season. Interestingly, the resistance index of the ammonia-oxidizing archaea (AOA) amoA abundance was significantly higher than that of the denitrifying gene abundances, suggesting that AOA were more resistant to the precipitation changes. This was attributed to the stronger environmental adaptability and higher resource utilization efficiency of the AOA community, as indicated by the lack of correlations between AOA gene abundance and environmental factors [i.e., soil water content, ammonium (NH4[+]) and dissolved organic carbon concentrations] during the experiment.},
}
@article {pmid28787424,
year = {2017},
author = {Bowers, RM and Kyrpides, NC and Stepanauskas, R and Harmon-Smith, M and Doud, D and Reddy, TBK and Schulz, F and Jarett, J and Rivers, AR and Eloe-Fadrosh, EA and Tringe, SG and Ivanova, NN and Copeland, A and Clum, A and Becraft, ED and Malmstrom, RR and Birren, B and Podar, M and Bork, P and Weinstock, GM and Garrity, GM and Dodsworth, JA and Yooseph, S and Sutton, G and Glöckner, FO and Gilbert, JA and Nelson, WC and Hallam, SJ and Jungbluth, SP and Ettema, TJG and Tighe, S and Konstantinidis, KT and Liu, WT and Baker, BJ and Rattei, T and Eisen, JA and Hedlund, B and McMahon, KD and Fierer, N and Knight, R and Finn, R and Cochrane, G and Karsch-Mizrachi, I and Tyson, GW and Rinke, C and , and Lapidus, A and Meyer, F and Yilmaz, P and Parks, DH and Eren, AM and Schriml, L and Banfield, JF and Hugenholtz, P and Woyke, T},
title = {Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.},
journal = {Nature biotechnology},
volume = {35},
number = {8},
pages = {725-731},
pmid = {28787424},
issn = {1546-1696},
support = {310039/ERC_/European Research Council/International ; R01 AI123037/AI/NIAID NIH HHS/United States ; R01 DE024463/DE/NIDCR NIH HHS/United States ; R01 HG004857/HG/NHGRI NIH HHS/United States ; },
mesh = {Genome, Archaeal/*genetics ; Genome, Bacterial/genetics ; Genomics/*methods/standards ; Metagenomics/*methods/standards ; Sequence Analysis, DNA ; },
abstract = {We present two standards developed by the Genomic Standards Consortium (GSC) for reporting bacterial and archaeal genome sequences. Both are extensions of the Minimum Information about Any (x) Sequence (MIxS). The standards are the Minimum Information about a Single Amplified Genome (MISAG) and the Minimum Information about a Metagenome-Assembled Genome (MIMAG), including, but not limited to, assembly quality, and estimates of genome completeness and contamination. These standards can be used in combination with other GSC checklists, including the Minimum Information about a Genome Sequence (MIGS), Minimum Information about a Metagenomic Sequence (MIMS), and Minimum Information about a Marker Gene Sequence (MIMARKS). Community-wide adoption of MISAG and MIMAG will facilitate more robust comparative genomic analyses of bacterial and archaeal diversity.},
}
@article {pmid28784816,
year = {2017},
author = {Peck, RF and Pleşa, AM and Graham, SM and Angelini, DR and Shaw, EL},
title = {Opsin-Mediated Inhibition of Bacterioruberin Synthesis in Halophilic Archaea.},
journal = {Journal of bacteriology},
volume = {199},
number = {21},
pages = {},
pmid = {28784816},
issn = {1098-5530},
support = {P20 GM103423/GM/NIGMS NIH HHS/United States ; R15 GM094735/GM/NIGMS NIH HHS/United States ; },
mesh = {Archaea/*metabolism ; Bacteriorhodopsins/genetics/*metabolism ; Carotenoids/*biosynthesis ; Cloning, Molecular ; Colorimetry ; Gene Expression ; Haloarcula/enzymology/genetics ; Haloferax volcanii/genetics/*metabolism ; Recombinant Proteins/genetics/metabolism ; Retinaldehyde/metabolism ; },
abstract = {Halophilic archaea often inhabit environments with limited oxygen, and many produce ion-pumping rhodopsin complexes that allow them to maintain electrochemical gradients when aerobic respiration is inhibited. Rhodopsins require a protein, an opsin, and an organic cofactor, retinal. We previously demonstrated that in Halobacterium salinarum, bacterioopsin (BO), when not bound by retinal, inhibits the production of bacterioruberin, a biochemical pathway that shares intermediates with retinal biosynthesis. In this work, we used heterologous expression in a related halophilic archaeon, Haloferax volcanii, to demonstrate that BO is sufficient to inhibit bacterioruberin synthesis catalyzed by the H. salinarum lycopene elongase (Lye) enzyme. This inhibition was observed both in liquid culture and in a novel colorimetric assay to quantify bacterioruberin abundance based on the colony color. Addition of retinal to convert BO to the bacteriorhodopsin complex resulted in a partial rescue of bacterioruberin production. To explore if this regulatory mechanism occurs in other organisms, we expressed a Lye homolog and an opsin from Haloarcula vallismortis in H. volcaniiH. vallismortis cruxopsin-3 expression inhibited bacterioruberin synthesis catalyzed by H. vallismortis Lye but had no effect when bacterioruberin synthesis was catalyzed by H. salinarum or H. volcanii Lye. Conversely, H. salinarum BO did not inhibit H. vallismortis Lye activity. Together, our data suggest that opsin-mediated inhibition of Lye is potentially widespread and represents an elegant regulatory mechanism that allows organisms to efficiently utilize ion-pumping rhodopsins obtained through lateral gene transfer.IMPORTANCE Many enzymes are complexes of proteins and nonprotein organic molecules called cofactors. To ensure efficient formation of functional complexes, organisms must regulate the production of proteins and cofactors. To study this regulation, we used bacteriorhodopsin from the archaeon Halobacterium salinarum Bacteriorhodopsin consists of the bacterioopsin protein and a retinal cofactor. In this article, we further characterize a novel regulatory mechanism in which bacterioopsin promotes retinal production by inhibiting a reaction that consumes lycopene, a retinal precursor. By expressing H. salinarum genes in a different organism, Haloferax volcanii, we demonstrated that bacterioopsin alone is sufficient for this inhibition. We also found that an opsin from Haloarcula vallismortis has inhibitory activity, suggesting that this regulatory mechanism might be found in other organisms.},
}
@article {pmid28783564,
year = {2017},
author = {Barros, VG and Duda, RM and Vantini, JDS and Omori, WP and Ferro, MIT and Oliveira, RA},
title = {Improved methane production from sugarcane vinasse with filter cake in thermophilic UASB reactors, with predominance of Methanothermobacter and Methanosarcina archaea and Thermotogae bacteria.},
journal = {Bioresource technology},
volume = {244},
number = {Pt 1},
pages = {371-381},
doi = {10.1016/j.biortech.2017.07.106},
pmid = {28783564},
issn = {1873-2976},
mesh = {Anaerobiosis ; *Archaea ; Bacteria ; *Bioreactors ; *Methane ; *Methanobacteriaceae ; *Methanosarcina ; Saccharum ; },
abstract = {Biogas production from sugarcane vinasse has enormous economic, energy, and environmental management potential. However, methane production stability and biodigested vinasse quality remain key issues, requiring better nutrient and alkalinity availability, operational strategies, and knowledge of reactor microbiota. This study demonstrates increased methane production from vinasse through the use of sugarcane filter cake and improved effluent recirculation, with elevated organic loading rates (OLR) and good reactor stability. We used UASB reactors in a two-stage configuration, with OLRs up to 45gCODL[-1]d[-1], and obtained methane production as high as 3LL[-1]d[-1]. Quantitative PCR indicated balanced amounts of bacteria and archaea in the sludge (10[9]-10[10]copiesg[-1]VS), and of the predominant archaea orders, Methanobacteriales and Methanosarcinales (10[6]-10[8]copiesg[-1]VS). 16S rDNA sequencing also indicated the thermophilic Thermotogae as the most abundant class of bacteria in the sludge.},
}
@article {pmid28779290,
year = {2017},
author = {Vaksmaa, A and Guerrero-Cruz, S and van Alen, TA and Cremers, G and Ettwig, KF and Lüke, C and Jetten, MSM},
title = {Enrichment of anaerobic nitrate-dependent methanotrophic 'Candidatus Methanoperedens nitroreducens' archaea from an Italian paddy field soil.},
journal = {Applied microbiology and biotechnology},
volume = {101},
number = {18},
pages = {7075-7084},
pmid = {28779290},
issn = {1432-0614},
support = {VENI 863.13.007//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; SIAM 024002002//Gravitation grant SIAM/ ; NESSC 024001001//Gravitation grant NESSC/ ; AG 339880 Eco_MoM//European Research Council/International ; 13178//Stichting voor de Technische Wetenschappen/ ; },
mesh = {Anaerobiosis ; Archaea/genetics/growth &amp; development/*isolation &amp; purification/metabolism ; Bioreactors ; Genome, Archaeal/*genetics ; Methane/*metabolism ; Molecular Sequence Annotation ; Nitrates/*metabolism ; Nitrites/*metabolism ; Oxidation-Reduction ; Phylogeny ; Sequence Analysis, DNA ; Soil ; Wetlands ; },
abstract = {Paddy fields are a significant source of methane and contribute up to 20% of total methane emissions from wetland ecosystems. These inundated, anoxic soils featuring abundant nitrogen compounds and methane are an ideal niche for nitrate-dependent anaerobic methanotrophs. After 2 years of enrichment with a continuous supply of methane and nitrate as the sole electron donor and acceptor, a stable enrichment dominated by 'Candidatus Methanoperedens nitroreducens' archaea and 'Candidatus Methylomirabilis oxyfera' NC10 phylum bacteria was achieved. In this community, the methanotrophic archaea supplied the NC10 phylum bacteria with the necessary nitrite through nitrate reduction coupled to methane oxidation. The results of qPCR quantification of 16S ribosomal RNA (rRNA) gene copies, analysis of metagenomic 16S rRNA reads, and fluorescence in situ hybridization (FISH) correlated well and showed that after 2 years, 'Candidatus Methanoperedens nitroreducens' had the highest abundance of (2.2 ± 0.4 × 10[8]) 16S rRNA copies per milliliter and constituted approximately 22% of the total microbial community. Phylogenetic analysis showed that the 16S rRNA genes of the dominant microorganisms clustered with previously described 'Candidatus Methanoperedens nitroreducens ANME2D' (96% identity) and 'Candidatus Methylomirabilis oxyfera' (99% identity) strains. The pooled metagenomic sequences resulted in a high-quality draft genome assembly of 'Candidatus Methanoperedens nitroreducens Vercelli' that contained all key functional genes for the reverse methanogenesis pathway and nitrate reduction. The diagnostic mcrA gene was 96% similar to 'Candidatus Methanoperedens nitroreducens ANME2D' (WP_048089615.1) at the protein level. The 'Candidatus Methylomirabilis oxyfera' draft genome contained the marker genes pmoCAB, mdh, and nirS and putative NO dismutase genes. Whole-reactor anaerobic activity measurements with methane and nitrate revealed an average methane oxidation rate of 0.012 mmol/h/L, with cell-specific methane oxidation rates up to 0.57 fmol/cell/day for 'Candidatus Methanoperedens nitroreducens'. In summary, this study describes the first enrichment and draft genome of methanotrophic archaea from paddy field soil, where these organisms can contribute significantly to the mitigation of methane emissions.},
}
@article {pmid28777382,
year = {2017},
author = {Adam, PS and Borrel, G and Brochier-Armanet, C and Gribaldo, S},
title = {The growing tree of Archaea: new perspectives on their diversity, evolution and ecology.},
journal = {The ISME journal},
volume = {11},
number = {11},
pages = {2407-2425},
pmid = {28777382},
issn = {1751-7370},
mesh = {Archaea/*classification/genetics/*isolation &amp; purification ; *Biodiversity ; Ecology ; Genome, Archaeal ; Phylogeny ; },
abstract = {The Archaea occupy a key position in the Tree of Life, and are a major fraction of microbial diversity. Abundant in soils, ocean sediments and the water column, they have crucial roles in processes mediating global carbon and nutrient fluxes. Moreover, they represent an important component of the human microbiome, where their role in health and disease is still unclear. The development of culture-independent sequencing techniques has provided unprecedented access to genomic data from a large number of so far inaccessible archaeal lineages. This is revolutionizing our view of the diversity and metabolic potential of the Archaea in a wide variety of environments, an important step toward understanding their ecological role. The archaeal tree is being rapidly filled up with new branches constituting phyla, classes and orders, generating novel challenges for high-rank systematics, and providing key information for dissecting the origin of this domain, the evolutionary trajectories that have shaped its current diversity, and its relationships with Bacteria and Eukarya. The present picture is that of a huge diversity of the Archaea, which we are only starting to explore.},
}
@article {pmid28777072,
year = {2017},
author = {Rivera-Gómez, N and Martínez-Núñez, MA and Pastor, N and Rodriguez-Vazquez, K and Perez-Rueda, E},
title = {Dissecting the protein architecture of DNA-binding transcription factors in bacteria and archaea.},
journal = {Microbiology (Reading, England)},
volume = {163},
number = {8},
pages = {1167-1178},
doi = {10.1099/mic.0.000504},
pmid = {28777072},
issn = {1465-2080},
mesh = {Archaea/chemistry/classification/genetics/*metabolism ; Archaeal Proteins/chemistry/genetics/*metabolism ; Bacteria/chemistry/classification/genetics/*metabolism ; Bacterial Proteins/chemistry/genetics/*metabolism ; DNA-Binding Proteins/chemistry/genetics/*metabolism ; Dimerization ; Genome, Archaeal ; Genome, Bacterial ; Models, Molecular ; Phylogeny ; Protein Conformation ; Transcription Factors/chemistry/genetics/*metabolism ; },
abstract = {Gene regulation at the transcriptional level is a central process in all organisms where DNA-binding transcription factors play a fundamental role. This class of proteins binds specifically at DNA sequences, activating or repressing gene expression as a function of the cell's metabolic status, operator context and ligand-binding status, among other factors, through the DNA-binding domain (DBD). In addition, TFs may contain partner domains (PaDos), which are involved in ligand binding and protein-protein interactions. In this work, we systematically evaluated the distribution, abundance and domain organization of DNA-binding TFs in 799 non-redundant bacterial and archaeal genomes. We found that the distributions of the DBDs and their corresponding PaDos correlated with the size of the genome. We also identified specific combinations between the DBDs and their corresponding PaDos. Within each class of DBDs there are differences in the actual angle formed at the dimerization interface, responding to the presence/absence of ligands and/or crystallization conditions, setting the orientation of the resulting helices and wings facing the DNA. Our results highlight the importance of PaDos as central elements that enhance the diversity of regulatory functions in all bacterial and archaeal organisms, and our results also demonstrate the role of PaDos in sensing diverse signal compounds. The highly specific interactions between DBDs and PaDos observed in this work, together with our structural analysis highlighting the difficulty in predicting both inter-domain geometry and quaternary structure, suggest that these systems appeared once and evolved with diverse duplication events in all the analysed organisms.},
}
@article {pmid28776097,
year = {2017},
author = {Zhao, K and Kong, W and Khan, A and Liu, J and Guo, G and Muhanmmad, S and Zhang, X and Dong, X},
title = {Elevational diversity and distribution of ammonia-oxidizing archaea community in meadow soils on the Tibetan Plateau.},
journal = {Applied microbiology and biotechnology},
volume = {101},
number = {18},
pages = {7065-7074},
doi = {10.1007/s00253-017-8435-x},
pmid = {28776097},
issn = {1432-0614},
support = {XDB15010203//Chinese Academy of Sciences/ ; KZZD-EW-TZ-14//Chinese Academy of Sciences/ ; 41471054//National Natural Science Foundation of China/ ; 41401287//National Natural Science Foundation of China/ ; },
mesh = {Ammonia/*metabolism ; Archaea/*metabolism ; Grassland ; Nitrification ; Oxidation-Reduction ; Polymorphism, Restriction Fragment Length ; Soil ; Tibet ; },
abstract = {Unraveling elevational diversity patterns of plants and animals has long been attracting scientific interests. However, whether soil microorganisms exhibit similar elevational patterns remains largely less explored, especially for functional microbial communities, such as ammonia oxidizers. Here, we investigated the diversity and distribution pattern of ammonia-oxidizing archaea (AOA) in meadow soils along an elevation gradient from 4400 m to the grassline at 5100 m on the Tibetan Plateau using terminal restriction fragment length polymorphism (T-RFLP) and sequencing methods by targeting amoA gene. Increasing elevations led to lower soil temperature and pH, but higher nutrients and water content. The results showed that AOA diversity and evenness monotonically increased with elevation, while richness was relatively stable. The increase of diversity and evenness was attributed to the growth inhibition of warm-adapted AOA phylotypes by lower temperature and the growth facilitation of cold-adapted AOA phylotypes by richer nutrients at higher elevations. Low temperature thus played an important role in the AOA growth and niche separation. The AOA community variation was explained by the combined effect of all soil properties (32.6%), and 8.1% of the total variation was individually explained by soil pH. The total AOA abundance decreased, whereas soil potential nitrification rate (PNR) increased with increasing elevations. Soil PNR positively correlated with the abundance of cold-adapted AOA phylotypes. Our findings suggest that low temperature plays an important role in AOA elevational diversity pattern and niche separation, rising the negative effects of warming on AOA diversity and soil nitrification process in the Tibetan region.},
}
@article {pmid28769904,
year = {2017},
author = {Wen, X and Yang, S and Horn, F and Winkel, M and Wagner, D and Liebner, S},
title = {Global Biogeographic Analysis of Methanogenic Archaea Identifies Community-Shaping Environmental Factors of Natural Environments.},
journal = {Frontiers in microbiology},
volume = {8},
number = {},
pages = {1339},
pmid = {28769904},
issn = {1664-302X},
abstract = {Methanogenic archaea are important for the global greenhouse gas budget since they produce methane under anoxic conditions in numerous natural environments such as oceans, estuaries, soils, and lakes. Whether and how environmental change will propagate into methanogenic assemblages of natural environments remains largely unknown owing to a poor understanding of global distribution patterns and environmental drivers of this specific group of microorganisms. In this study, we performed a meta-analysis targeting the biogeographic patterns and environmental controls of methanogenic communities using 94 public mcrA gene datasets. We show a global pattern of methanogenic archaea that is more associated with habitat filtering than with geographical dispersal. We identify salinity as the control on methanogenic community composition at global scale whereas pH and temperature are the major controls in non-saline soils and lakes. The importance of salinity for structuring methanogenic community composition is also reflected in the biogeography of methanogenic lineages and the physiological properties of methanogenic isolates. Linking methanogenic alpha-diversity with reported values of methane emission identifies estuaries as the most diverse methanogenic habitats with, however, minor contribution to the global methane budget. With salinity, temperature and pH our study identifies environmental drivers of methanogenic community composition facing drastic changes in many natural environments at the moment. However, consequences of this for the production of methane remain elusive owing to a lack of studies that combine methane production rate with community analysis.},
}
@article {pmid28765217,
year = {2017},
author = {Daume, M and Uhl, M and Backofen, R and Randau, L},
title = {RIP-Seq Suggests Translational Regulation by L7Ae in Archaea.},
journal = {mBio},
volume = {8},
number = {4},
pages = {},
pmid = {28765217},
issn = {2150-7511},
mesh = {Archaeal Proteins/*genetics/metabolism ; Escherichia coli/genetics ; *Gene Expression Regulation, Archaeal ; Immunoprecipitation ; Protein Binding ; *Protein Biosynthesis ; RNA, Archaeal/chemistry/*genetics ; RNA, Untranslated/genetics ; RNA-Binding Proteins/genetics/metabolism ; Ribosomal Proteins/genetics ; *Sequence Analysis, RNA ; Sulfolobus acidocaldarius/*genetics/metabolism ; },
abstract = {L7Ae is a universal archaeal protein that recognizes and stabilizes kink-turn (k-turn) motifs in RNA substrates. These structural motifs are widespread in nature and are found in many functional RNA species, including ribosomal RNAs. Synthetic biology approaches utilize L7Ae/k-turn interactions to control gene expression in eukaryotes. Here, we present results of comprehensive RNA immunoprecipitation sequencing (RIP-Seq) analysis of genomically tagged L7Ae from the hyperthermophilic archaeon Sulfolobus acidocaldarius A large set of interacting noncoding RNAs was identified. In addition, several mRNAs, including the l7ae transcript, were found to contain k-turn motifs that facilitate L7Ae binding. In vivo studies showed that L7Ae autoregulates the translation of its mRNA by binding to a k-turn motif present in the 5' untranslated region (UTR). A green fluorescent protein (GFP) reporter system was established in Escherichia coli and verified conservation of L7Ae-mediated feedback regulation in Archaea Mobility shift assays confirmed binding to a k-turn in the transcript of nop5-fibrillarin, suggesting that the expression of all C/D box sRNP core proteins is regulated by L7Ae. These studies revealed that L7Ae-mediated gene regulation evolved in archaeal organisms, generating new tools for the modulation of synthetic gene circuits in bacteria.IMPORTANCE L7Ae is an essential archaeal protein that is known to structure ribosomal RNAs and small RNAs (sRNAs) by binding to their kink-turn motifs. Here, we utilized RIP-Seq methodology to achieve a first global analysis of RNA substrates for L7Ae. Several novel interactions with noncoding RNA molecules (e.g., with the universal signal recognition particle RNA) were discovered. In addition, L7Ae was found to bind to mRNAs, including its own transcript's 5' untranslated region. This feedback-loop control is conserved in most archaea and was incorporated into a reporter system that was utilized to control gene expression in bacteria. These results demonstrate that L7Ae-mediated gene regulation evolved originally in archaeal organisms. The feedback-controlled reporter gene system can easily be adapted for synthetic biology approaches that require strict gene expression control.},
}
@article {pmid28765215,
year = {2017},
author = {Skennerton, CT and Chourey, K and Iyer, R and Hettich, RL and Tyson, GW and Orphan, VJ},
title = {Methane-Fueled Syntrophy through Extracellular Electron Transfer: Uncovering the Genomic Traits Conserved within Diverse Bacterial Partners of Anaerobic Methanotrophic Archaea.},
journal = {mBio},
volume = {8},
number = {4},
pages = {},
pmid = {28765215},
issn = {2150-7511},
mesh = {Anaerobiosis ; Archaea/*genetics/*metabolism ; Bacteria/*genetics/*metabolism ; Electron Transport ; Genome, Archaeal ; Genome, Bacterial ; Geologic Sediments/microbiology ; Hydrogen/metabolism ; Metagenomics ; Methane/*metabolism ; Oxidation-Reduction ; Phylogeny ; Sulfates/metabolism ; },
abstract = {The anaerobic oxidation of methane by anaerobic methanotrophic (ANME) archaea in syntrophic partnership with deltaproteobacterial sulfate-reducing bacteria (SRB) is the primary mechanism for methane removal in ocean sediments. The mechanism of their syntrophy has been the subject of much research as traditional intermediate compounds, such as hydrogen and formate, failed to decouple the partners. Recent findings have indicated the potential for extracellular electron transfer from ANME archaea to SRB, though it is unclear how extracellular electrons are integrated into the metabolism of the SRB partner. We used metagenomics to reconstruct eight genomes from the globally distributed SEEP-SRB1 clade of ANME partner bacteria to determine what genomic features are required for syntrophy. The SEEP-SRB1 genomes contain large multiheme cytochromes that were not found in previously described free-living SRB and also lack periplasmic hydrogenases that may prevent an independent lifestyle without an extracellular source of electrons from ANME archaea. Metaproteomics revealed the expression of these cytochromes at in situ methane seep sediments from three sites along the Pacific coast of the United States. Phylogenetic analysis showed that these cytochromes appear to have been horizontally transferred from metal-respiring members of the Deltaproteobacteria such as Geobacter and may allow these syntrophic SRB to accept extracellular electrons in place of other chemical/organic electron donors.IMPORTANCE Some archaea, known as anaerobic methanotrophs, are capable of converting methane into carbon dioxide when they are growing syntopically with sulfate-reducing bacteria. This partnership is the primary mechanism for methane removal in ocean sediments; however, there is still much to learn about how this syntrophy works. Previous studies have failed to identify the metabolic intermediate, such as hydrogen or formate, that is passed between partners. However, recent analysis of methanotrophic archaea has suggested that the syntrophy is formed through direct electron transfer. In this research, we analyzed the genomes of multiple partner bacteria and showed that they also contain the genes necessary to perform extracellular electron transfer, which are absent in related bacteria that do not form syntrophic partnerships with anaerobic methanotrophs. This genomic evidence shows a possible mechanism for direct electron transfer from methanotrophic archaea into the metabolism of the partner bacteria.},
}
@article {pmid28755506,
year = {2017},
author = {Di Maiuta, N and Rüfenacht, A and Küenzi, P},
title = {Assessment of bacteria and archaea in metalworking fluids using massive parallel 16S rRNA gene tag sequencing.},
journal = {Letters in applied microbiology},
volume = {65},
number = {4},
pages = {266-273},
doi = {10.1111/lam.12782},
pmid = {28755506},
issn = {1472-765X},
mesh = {Azides/chemistry ; Disinfectants ; Fungi/*classification/genetics/isolation &amp; purification ; High-Throughput Nucleotide Sequencing ; Manufacturing and Industrial Facilities ; Methanobrevibacter/*classification/genetics/isolation &amp; purification ; Propidium/analogs &amp; derivatives/chemistry ; Pseudomonas/*classification/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; },
abstract = {UNLABELLED: Determination of the bacterial diversity in industry-based liquid in-use water-miscible metalworking fluid (MWF) samples was targeted by massive parallel multiplex DNA sequencing, either directly or upon pretreatment with propidium monoazide (PMA) that allows differentiation between intact and physically damaged cells. As MWFs provide a suitable basis of life for micro-organisms, the majority is preserved by biocides. 'Bio-concept' fluids on the other hand are bactericide free, which intentionally leads to substantial bacterial populations. Samples from both fluid types were chosen: A median of 51 operational taxonomic units at genera level (OTUs) were detected per sample, but only 13 were present at or above 1·0% of the total population in any PMA-treated sample analysed. As both fluid types were mainly dominated by Pseudomonas spp., we resolved this genus on the species level and found the Pseudomonas oleovorans/pseudoalcaligenes group to predominate. We also looked for archaea and detected Methanobrevibacter spp., albeit in <3% of all samples analysed.<br><br>Water-miscible metalworking fluids provide a suitable base of life for micro-organisms, mainly bacteria and fungi. Earlier publications suggested that the diversity is rather low, but these studies were largely based on heterotrophic plate counts. This might have resulted in underestimation of population density and microbial diversity as some organisms might just refuse to grow. This study used high-throughput sequencing in the absence and presence of propidium monoazide to explore bacterial and archaeal presence in metalworking fluids. We established that diversity is low and bacterial populations are dominated by the genus Pseudomonas spp.},
}
@article {pmid28741608,
year = {2017},
author = {Spang, A and Ettema, TJG},
title = {Archaeal evolution: The methanogenic roots of Archaea.},
journal = {Nature microbiology},
volume = {2},
number = {},
pages = {17109},
pmid = {28741608},
issn = {2058-5276},
mesh = {Archaea/*genetics ; Chemoautotrophic Growth ; DNA, Archaeal ; *Euryarchaeota ; },
}
@article {pmid28734066,
year = {2017},
author = {Varnava, KG and Ronimus, RS and Sarojini, V},
title = {A review on comparative mechanistic studies of antimicrobial peptides against archaea.},
journal = {Biotechnology and bioengineering},
volume = {114},
number = {11},
pages = {2457-2473},
doi = {10.1002/bit.26387},
pmid = {28734066},
issn = {1097-0290},
mesh = {Antimicrobial Cationic Peptides/*administration &amp; dosage ; Apoptosis/*drug effects/*physiology ; Archaea/cytology/*drug effects/*physiology ; Cell Survival/drug effects/physiology ; Dose-Response Relationship, Drug ; Microbial Sensitivity Tests/*methods ; Species Specificity ; },
abstract = {Archaea was until recently considered as a third domain of life in addition to bacteria and eukarya but recent studies support the existence of only two superphyla (bacteria and archaea). The fundamental differences between archaeal, bacterial, and eukaryal cells are probably the main reasons for the comparatively lower susceptibility of archaeal strains to current antimicrobial agents. The possible emerging pathogenicity of archaea and the role of archaeal methanogens in methane emissions, a potent greenhouse gas, has led many researchers to examine the sensitivity patterns of archaea and make attempts to find agents that have significant anti-archaeal activity. Even though antimicrobial peptides (AMPs) are well known with several published reviews concerning their mode of action against bacteria and eukarya, to our knowledge, to date no reviews are available that focus on the action of these peptides against archaea. Herein, we present a review on all the peptides that have been tested against archaea. In addition, in an attempt to shed more light on possible future work that needs to be performed we have included a brief overview of the chemical characteristics, spectrum of activity, and the known mechanism of action of each of these peptides against bacteria and/or fungi. We also discuss the nature of and key physiological differences between Archaea, Bacteria, and Eukarya that are relevant to the development of anti-archaeal peptides. Despite our relatively limited knowledge about archaea, available data suggest that AMPs have an even broader spectrum of activity than currently recognized.},
}
@article {pmid28713363,
year = {2017},
author = {Jing, H and Cheung, S and Xia, X and Suzuki, K and Nishioka, J and Liu, H},
title = {Geographic Distribution of Ammonia-Oxidizing Archaea along the Kuril Islands in the Western Subarctic Pacific.},
journal = {Frontiers in microbiology},
volume = {8},
number = {},
pages = {1247},
pmid = {28713363},
issn = {1664-302X},
abstract = {Community composition and abundance of ammonia-oxidizing archaea (AOA) in the ocean were affected by different physicochemical conditions, but their responses to physical barriers (such as a chain of islands) were largely unknown. In our study, geographic distribution of the AOA from the surface photic zone to the deep bathypelagic waters in the western subarctic Pacific adjacent to the Kuril Islands was investigated using pyrosequencing based on the ammonia monooxygenase subunit A (amoA) gene. Genotypes of clusters A and B dominated in the upper euphotic zone and the deep waters, respectively. Quantitative PCR assays revealed that the occurrence and ammonia-oxidizing activity of ammonia-oxidizing archaea (AOA) reached their maxima at the depth of 200 m, where a higher diversity and abundance of actively transcribed AOA was observed at the station located in the marginal sea exposed to more terrestrial input. Similar community composition of AOA observed at the two stations adjacent to the Kuril Islands maybe due to water exchange across the Bussol Strait. They distinct from the station located in the western subarctic gyre, where sub-cluster WCAII had a specific distribution in the surface water, and this sub-cluster seemed having a confined distribution in the western Pacific. Habitat-specific groupings of different WCB sub-clusters were observed reflecting the isolated microevolution existed in cluster WCB. The effect of the Kuril Islands on the phylogenetic composition of AOA between the Sea of Okhotsk and the western subarctic Pacific is not obvious, possibly because our sampling stations are near to the Bussol Strait, the main gateway through which water is exchanged between the Sea of Okhotsk and the Pacific. The vertical and horizontal distribution patterns of AOA communities among stations along the Kuril Islands were essentially determined by the in situ prevailing physicochemical gradients along the two dimensions.},
}
@article {pmid28710268,
year = {2017},
author = {Duszenko, N and Buan, NR},
title = {Physiological Evidence for Isopotential Tunneling in the Electron Transport Chain of Methane-Producing Archaea.},
journal = {Applied and environmental microbiology},
volume = {83},
number = {18},
pages = {},
pmid = {28710268},
issn = {1098-5336},
support = {P20 GM113126/GM/NIGMS NIH HHS/United States ; P20 RR017675/RR/NCRR NIH HHS/United States ; },
mesh = {Benzoquinones/metabolism ; Electron Transport ; Escherichia coli/genetics/growth &amp; development/metabolism ; Hydrogen/metabolism ; Methane/*metabolism ; Methanosarcina/genetics/growth &amp; development/*metabolism ; },
abstract = {Many, but not all, organisms use quinones to conserve energy in their electron transport chains. Fermentative bacteria and methane-producing archaea (methanogens) do not produce quinones but have devised other ways to generate ATP. Methanophenazine (MPh) is a unique membrane electron carrier found in Methanosarcina species that plays the same role as quinones in the electron transport chain. To extend the analogy between quinones and MPh, we compared the MPh pool sizes between two well-studied Methanosarcina species, Methanosarcina acetivorans C2A and Methanosarcina barkeri Fusaro, to the quinone pool size in the bacterium Escherichia coli We found the quantity of MPh per cell increases as cultures transition from exponential growth to stationary phase, and absolute quantities of MPh were 3-fold higher in M. acetivorans than in M. barkeri The concentration of MPh suggests the cell membrane of M. acetivorans, but not of M. barkeri, is electrically quantized as if it were a single conductive metal sheet and near optimal for rate of electron transport. Similarly, stationary (but not exponentially growing) E. coli cells also have electrically quantized membranes on the basis of quinone content. Consistent with our hypothesis, we demonstrated that the exogenous addition of phenazine increases the growth rate of M. barkeri three times that of M. acetivorans Our work suggests electron flux through MPh is naturally higher in M. acetivorans than in M. barkeri and that hydrogen cycling is less efficient at conserving energy than scalar proton translocation using MPh.IMPORTANCE Can we grow more from less? The ability to optimize and manipulate metabolic efficiency in cells is the difference between commercially viable and nonviable renewable technologies. Much can be learned from methane-producing archaea (methanogens) which evolved a successful metabolic lifestyle under extreme thermodynamic constraints. Methanogens use highly efficient electron transport systems and supramolecular complexes to optimize electron and carbon flow to control biomass synthesis and the production of methane. Worldwide, methanogens are used to generate renewable methane for heat, electricity, and transportation. Our observations suggest Methanosarcina acetivorans, but not Methanosarcina barkeri, has electrically quantized membranes. Escherichia coli, a model facultative anaerobe, has optimal electron transport at the stationary phase but not during exponential growth. This study also suggests the metabolic efficiency of bacteria and archaea can be improved using exogenously supplied lipophilic electron carriers. The enhancement of methanogen electron transport through methanophenazine has the potential to increase renewable methane production at an industrial scale.},
}
@article {pmid28681113,
year = {2017},
author = {Sheppard, C and Werner, F},
title = {Structure and mechanisms of viral transcription factors in archaea.},
journal = {Extremophiles : life under extreme conditions},
volume = {21},
number = {5},
pages = {829-838},
pmid = {28681113},
issn = {1433-4909},
mesh = {Archaeal Viruses/*genetics/metabolism ; Gene Expression Regulation, Viral ; Transcription Factors/chemistry/genetics/*metabolism ; Viral Proteins/chemistry/genetics/*metabolism ; },
abstract = {Virus-encoded transcription factors have been pivotal in exploring the molecular mechanisms and regulation of gene expression in bacteria and eukaryotes since the birth of molecular biology, while our understanding of viral transcription in archaea is still in its infancy. Archaeal viruses do not encode their own RNA polymerases (RNAPs) and are consequently entirely dependent on their hosts for gene expression; this is fundamentally different from many bacteriophages and requires alternative regulatory strategies. Archaeal viruses wield a repertoire of proteins to expropriate the host transcription machinery to their own benefit. In this short review we summarise our current understanding of gene-specific and global mechanisms that viruses employ to chiefly downregulate host transcription and enable the efficient and temporal expression of the viral transcriptome. Most of the experimentally characterised archaeo-viral transcription regulators possess either ribbon-helix-helix or Zn-finger motifs that allow them to engage with the DNA in a sequence-specific manner, altering the expression of a specific subset of genes. Recently a novel type of regulator was reported that directly binds to the RNAP and shuts down transcription of both host and viral genes in a global fashion.},
}
@article {pmid28680072,
year = {2017},
author = {Golyshina, OV and Toshchakov, SV and Makarova, KS and Gavrilov, SN and Korzhenkov, AA and La Cono, V and Arcadi, E and Nechitaylo, TY and Ferrer, M and Kublanov, IV and Wolf, YI and Yakimov, MM and Golyshin, PN},
title = {'ARMAN' archaea depend on association with euryarchaeal host in culture and in situ.},
journal = {Nature communications},
volume = {8},
number = {1},
pages = {60},
pmid = {28680072},
issn = {2041-1723},
support = {/ImNIH/Intramural NIH HHS/United States ; },
mesh = {Archaea/*classification/genetics/*physiology ; Gene Expression Regulation, Archaeal ; Genetic Variation ; Genome, Archaeal ; Microscopy, Fluorescence ; Phylogeny ; RNA, Archaeal/genetics ; RNA, Ribosomal, 16S/genetics ; Species Specificity ; },
abstract = {Intriguing, yet uncultured 'ARMAN'-like archaea are metabolically dependent on other members of the microbial community. It remains uncertain though which hosts they rely upon, and, because of the lack of complete genomes, to what extent. Here, we report the co-culturing of ARMAN-2-related organism, Mia14, with Cuniculiplasma divulgatum PM4 during the isolation of this strain from acidic streamer in Parys Mountain (Isle of Anglesey, UK). Mia14 is highly enriched in the binary culture (ca. 10% genomic reads) and its ungapped 0.95 Mbp genome points at severe voids in central metabolic pathways, indicating dependence on the host, C. divulgatum PM4. Analysis of C. divulgatum isolates from different sites and shotgun sequence data of Parys Mountain samples suggests an extensive genetic exchange between Mia14 and hosts in situ. Within the subset of organisms with high-quality genomic assemblies representing the 'DPANN' superphylum, the Mia14 lineage has had the largest gene flux, with dozens of genes gained that are implicated in the host interaction.In the absence of complete genomes, the metabolic capabilities of uncultured ARMAN-like archaea have been uncertain. Here, Golyshina et al. apply an enrichment culture technique and find that the ungapped genome of the ARMAN-like archaeon Mia14 has lost key metabolic pathways, suggesting dependence on the host archaeon Cuniculiplasma divulgatum.},
}
@article {pmid28677304,
year = {2017},
author = {Tolar, BB and Herrmann, J and Bargar, JR and van den Bedem, H and Wakatsuki, S and Francis, CA},
title = {Integrated structural biology and molecular ecology of N-cycling enzymes from ammonia-oxidizing archaea.},
journal = {Environmental microbiology reports},
volume = {9},
number = {5},
pages = {484-491},
doi = {10.1111/1758-2229.12567},
pmid = {28677304},
issn = {1758-2229},
mesh = {Ammonia/*metabolism ; Archaea/classification/enzymology/*genetics/*metabolism ; Enzymes/*chemistry/*metabolism ; Nitrite Reductases/chemistry/genetics/metabolism ; *Oxidation-Reduction ; Oxidoreductases/chemistry/genetics/metabolism ; Phylogeny ; Structure-Activity Relationship ; },
abstract = {Knowledge of the molecular ecology and environmental determinants of ammonia-oxidizing organisms is critical to understanding and predicting the global nitrogen (N) and carbon cycles, but an incomplete biochemical picture hinders in vitro studies of N-cycling enzymes. Although an integrative structural and dynamic characterization at the atomic scale would advance our understanding of function tremendously, structural knowledge of key N-cycling enzymes from ecologically relevant ammonia oxidizers is unfortunately extremely limited. Here, we discuss the challenges and opportunities for examining the ecology of ammonia-oxidizing organisms, particularly uncultivated Thaumarchaeota, through (meta)genome-driven structural biology of the enzymes ammonia monooxygenase (AMO) and nitrite reductase (NirK).},
}
@article {pmid28663746,
year = {2017},
author = {Liu, H and Zhang, CL and Yang, C and Chen, S and Cao, Z and Zhang, Z and Tian, J},
title = {Marine Group II Dominates Planktonic Archaea in Water Column of the Northeastern South China Sea.},
journal = {Frontiers in microbiology},
volume = {8},
number = {},
pages = {1098},
pmid = {28663746},
issn = {1664-302X},
abstract = {Temperature, nutrients, and salinity are among the important factors constraining the distribution and abundance of microorganisms in the ocean. Marine Group II (MGII) belonging to Euryarchaeota commonly dominates the planktonic archaeal community in shallow water and Marine Group I (MGI, now is called Thaumarchaeota) in deeper water in global oceans. Results of quantitative PCR (qPCR) and 454 sequencing in our study, however, showed the dominance of MGII in planktonic archaea throughout the water column of the northeastern South China Sea (SCS) that is characterized by strong water mixing. The abundance of ammonia-oxidizing archaea (AOA) representing the main group of Thaumarchaeota in deeper water in the northeastern SCS was significantly lower than in other oceanic regions. Phylogenetic analysis showed that the top operational taxonomic units (OTUs) of the MGII occurring predominantly below 200 m depth may be unique in the northeastern SCS based on the observation that they are distantly related to known sequences (identity ranging from 90-94%). The abundance of MGII was also significantly correlated with total bacteria in the whole column, which may indicate that MGII and bacteria may have similar physiological or biochemical properties or responses to environmental variation. This study provides valuable information about the dominance of MGII over AOA in both shallow and deep water in the northeastern SCS and highlights the need for comprehensive studies integrating physical, chemical, and microbial oceanography.},
}
@article {pmid28659382,
year = {2017},
author = {Staley, JT},
title = {Domain Cell Theory supports the independent evolution of the Eukarya, Bacteria and Archaea and the Nuclear Compartment Commonality hypothesis.},
journal = {Open biology},
volume = {7},
number = {6},
pages = {},
pmid = {28659382},
issn = {2046-2441},
mesh = {Archaea/*classification/cytology ; Bacteria/*classification/cytology ; *Biological Evolution ; *Cell Nucleus ; Eukaryota/*classification/cytology ; *Models, Theoretical ; Phylogeny ; },
abstract = {In 2015, the Royal Society of London held a meeting to discuss the various hypotheses regarding the origin of the Eukarya. Although not all participants supported a hypothesis, the proposals that did fit into two broad categories: one group favoured 'Prokaryotes First' hypotheses and another addressed 'Eukaryotes First' hypotheses. Those who proposed Prokaryotes First hypotheses advocated either a fusion event between a bacterium and an archaeon that produced the first eukaryote or the direct evolution of the Eukarya from the Archaea. The Eukaryotes First proponents posit that the eukaryotes evolved initially and then, by reductive evolution, produced the Bacteria and Archaea. No mention was made of another previously published hypothesis termed the Nuclear Compartment Commonality (NuCom) hypothesis, which proposed the evolution of the Eukarya and Bacteria from nucleated ancestors (Staley 2013 Astrobiol Outreach1, 105 (doi:10.4172/2332-2519.1000105)). Evidence from two studies indicates that the nucleated Planctomycetes-Verrucomicrobia-Chlamydia superphylum members are the most ancient Bacteria known (Brochier &amp; Philippe 2002 Nature417, 244 (doi:10.1038/417244a); Jun et al. 2010 Proc. Natl Acad. Sci. USA107, 133-138 (doi:10.1073/pnas.0913033107)). This review summarizes the evidence for the NuCom hypothesis and discusses how simple the NuCom hypothesis is in explaining eukaryote evolution relative to the other hypotheses. The philosophical importance of simplicity and its relationship to truth in hypotheses such as NuCom and Domain Cell Theory is presented. Domain Cell Theory is also proposed herein, which contends that each of the three cellular lineages of life, the Archaea, Bacteria and Eukarya domains, evolved independently, in support of the NuCom hypothesis. All other proposed hypotheses violate Domain Cell Theory because they posit the evolution of different cellular descendants from ancestral cellular types.},
}
@article {pmid28657885,
year = {2017},
author = {Koonin, EV and Makarova, KS and Wolf, YI},
title = {Evolutionary Genomics of Defense Systems in Archaea and Bacteria.},
journal = {Annual review of microbiology},
volume = {71},
number = {},
pages = {233-261},
pmid = {28657885},
issn = {1545-3251},
support = {Z01 LM000061-15//Intramural NIH HHS/United States ; Z01 LM000073-12//Intramural NIH HHS/United States ; },
mesh = {Archaea/*genetics/*virology ; Bacteria/*genetics/*virology ; CRISPR-Cas Systems ; DNA Restriction-Modification Enzymes ; *Evolution, Molecular ; Genome, Archaeal ; Genome, Bacterial ; Genomics ; *Host-Parasite Interactions ; },
abstract = {Evolution of bacteria and archaea involves an incessant arms race against an enormous diversity of genetic parasites. Accordingly, a substantial fraction of the genes in most bacteria and archaea are dedicated to antiparasite defense. The functions of these defense systems follow several distinct strategies, including innate immunity; adaptive immunity; and dormancy induction, or programmed cell death. Recent comparative genomic studies taking advantage of the expanding database of microbial genomes and metagenomes, combined with direct experiments, resulted in the discovery of several previously unknown defense systems, including innate immunity centered on Argonaute proteins, bacteriophage exclusion, and new types of CRISPR-Cas systems of adaptive immunity. Some general principles of function and evolution of defense systems are starting to crystallize, in particular, extensive gain and loss of defense genes during the evolution of prokaryotes; formation of genomic defense islands; evolutionary connections between mobile genetic elements and defense, whereby genes of mobile elements are repeatedly recruited for defense functions; the partially selfish and addictive behavior of the defense systems; and coupling between immunity and dormancy induction/programmed cell death.},
}
@article {pmid28655184,
year = {2017},
author = {Cranford, MT and Chu, AM and Baguley, JK and Bauer, RJ and Trakselis, MA},
title = {Characterization of a coupled DNA replication and translesion synthesis polymerase supraholoenzyme from archaea.},
journal = {Nucleic acids research},
volume = {45},
number = {14},
pages = {8329-8340},
pmid = {28655184},
issn = {1362-4962},
mesh = {Archaeal Proteins/chemistry/genetics/*metabolism ; Blotting, Western ; *DNA Repair ; *DNA Replication ; DNA, Archaeal/chemistry/genetics/metabolism ; DNA-Directed DNA Polymerase/chemistry/genetics/*metabolism ; Holoenzymes/chemistry/genetics/metabolism ; Kinetics ; Models, Molecular ; Nucleic Acid Conformation ; Proliferating Cell Nuclear Antigen/genetics/metabolism ; Protein Binding ; Protein Structure, Tertiary ; Spectrometry, Fluorescence ; Sulfolobus solfataricus/enzymology/genetics/metabolism ; },
abstract = {The ability of the replisome to seamlessly coordinate both high fidelity and translesion DNA synthesis requires a means to regulate recruitment and binding of enzymes from solution. Co-occupancy of multiple DNA polymerases within the replisome has been observed primarily in bacteria and is regulated by posttranslational modifications in eukaryotes, and both cases are coordinated by the processivity clamp. Because of the heterotrimeric nature of the PCNA clamp in some archaea, there is potential to occupy and regulate specific polymerases at defined subunits. In addition to specific PCNA and polymerase interactions (PIP site), we have now identified and characterized a novel protein contact between the Y-family DNA polymerase and the B-family replication polymerase (YB site) bound to PCNA and DNA from Sulfolobus solfataricus. These YB contacts are essential in forming and stabilizing a supraholoenzyme (SHE) complex on DNA, effectively increasing processivity of DNA synthesis. The SHE complex can not only coordinate polymerase exchange within the complex but also provides a mechanism for recruitment of polymerases from solution based on multiequilibrium processes. Our results provide evidence for an archaeal PCNA 'tool-belt' recruitment model of multienzyme function that can facilitate both high fidelity and translesion synthesis within the replisome during DNA replication.},
}
@article {pmid28647121,
year = {2017},
author = {Xu, J and Jia, Z and Lin, X and Feng, Y},
title = {DNA-based stable isotope probing identifies formate-metabolizing methanogenic archaea in paddy soil.},
journal = {Microbiological research},
volume = {202},
number = {},
pages = {36-42},
doi = {10.1016/j.micres.2017.05.004},
pmid = {28647121},
issn = {1618-0623},
mesh = {*Biodegradation, Environmental ; Carbon Isotopes ; China ; Cloning, Molecular ; DNA/chemistry ; *DNA Probes ; DNA, Archaeal ; Denaturing Gradient Gel Electrophoresis ; Euryarchaeota/classification/*genetics/*metabolism ; Formates/*metabolism ; Methane/biosynthesis ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Real-Time Polymerase Chain Reaction ; Soil ; Soil Microbiology ; },
abstract = {Paddy methane (CH4) production is biologically dominated by methanogenic archaea that metabolize a variety of organic and/or inorganic carbon sources. Though formate is easily dissimilated into H2/CO2, formate-metabolizing methanogenic archaea are distinct from CO2-utilizing methanogen taxa. The identity of formate-metabolizing methanogenic archaea in paddy soil remains elusive. In this investigation, molecular approaches based on stable isotope probing (SIP) technique were conducted to identify the formate-metabolizing methanogenic archaea in paddy soil. CH4 emission monitor, real-time quantitative PCR (qPCR) and Denaturing Gradient Gel Electrophoresis (DGGE) analyses consistently indicated that some methanogenic archaea metabolized [13]C-labeled formate in microcosm and accounted for a large portion of formate-metabolizing archaea in anoxic paddy soil. Phylogenetic identification further found that this guild was affiliated to Methanobacteriaceae. Taken together Methanobacteriaceae could be the dominant formate-metabolizing methanogenic archaea and play an important role in the CH4 production in paddy soil. These findings would extend the extant knowledge on paddy methanogenic archaea and microbial-driven paddy CH4 emission.},
}
@article {pmid28642547,
year = {2017},
author = {Moissl-Eichinger, C and Probst, AJ and Birarda, G and Auerbach, A and Koskinen, K and Wolf, P and Holman, HN},
title = {Human age and skin physiology shape diversity and abundance of Archaea on skin.},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {4039},
pmid = {28642547},
issn = {2045-2322},
mesh = {Age Factors ; Archaea/*classification/*genetics ; Biodiversity ; Female ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; *Microbiota ; Middle Aged ; Phylogeny ; RNA, Ribosomal, 16S ; Skin/*microbiology ; *Skin Physiological Phenomena ; Spectroscopy, Fourier Transform Infrared ; },
abstract = {The human skin microbiome acts as an important barrier protecting our body from pathogens and other environmental influences. Recent investigations have provided evidence that Archaea are a constant but highly variable component of the human skin microbiome, yet factors that determine their abundance changes are unknown. Here, we tested the hypothesis that the abundance of archaea on human skin is influenced by human age and skin physiology by quantitative PCR of 51 different skin samples taken from human subjects of various age. Our results reveal that archaea are more abundant in human subjects either older than 60 years or younger than 12 years as compared to middle-aged human subjects. These results, together with results obtained from spectroscopy analysis, allowed us gain first insights into a potential link of lower sebum levels and lipid content and thus reduced skin moisture with an increase in archaeal signatures. Amplicon sequencing of selected samples revealed the prevalence of specific eury- and mainly thaumarchaeal taxa, represented by a core archaeome of the human skin.},
}
@article {pmid28628615,
year = {2017},
author = {Cossu, M and Badel, C and Catchpole, R and Gadelle, D and Marguet, E and Barbe, V and Forterre, P and Oberto, J},
title = {Flipping chromosomes in deep-sea archaea.},
journal = {PLoS genetics},
volume = {13},
number = {6},
pages = {e1006847},
pmid = {28628615},
issn = {1553-7404},
mesh = {Chromosome Inversion/*genetics ; *Evolution, Molecular ; Genome, Archaeal ; Integrases/*genetics ; Interspersed Repetitive Sequences/genetics ; Plasmids/genetics ; Recombination, Genetic ; Thermococcales/*genetics ; },
abstract = {One of the major mechanisms driving the evolution of all organisms is genomic rearrangement. In hyperthermophilic Archaea of the order Thermococcales, large chromosomal inversions occur so frequently that even closely related genomes are difficult to align. Clearly not resulting from the native homologous recombination machinery, the causative agent of these inversions has remained elusive. We present a model in which genomic inversions are catalyzed by the integrase enzyme encoded by a family of mobile genetic elements. We characterized the integrase from Thermococcus nautili plasmid pTN3 and showed that besides canonical site-specific reactions, it catalyzes low sequence specificity recombination reactions with the same outcome as homologous recombination events on DNA segments as short as 104bp both in vitro and in vivo, in contrast to other known tyrosine recombinases. Through serial culturing, we showed that the integrase-mediated divergence of T. nautili strains occurs at an astonishing rate, with at least four large-scale genomic inversions appearing within 60 generations. Our results and the ubiquitous distribution of pTN3-like integrated elements suggest that a major mechanism of evolution of an entire order of Archaea results from the activity of a selfish mobile genetic element.},
}
@article {pmid28628315,
year = {2017},
author = {Dokainish, HM and Simard, DJ and Gauld, JW},
title = {A Pseudohypervalent Sulfur Intermediate as an Oxidative Protective Mechanism in the Archaea Peroxiredoxin Enzyme ApTPx.},
journal = {The journal of physical chemistry. B},
volume = {121},
number = {27},
pages = {6570-6579},
doi = {10.1021/acs.jpcb.7b04671},
pmid = {28628315},
issn = {1520-5207},
mesh = {Archaea/*enzymology ; Molecular Dynamics Simulation ; Oxidation-Reduction ; Peroxiredoxins/chemistry/*metabolism ; *Quantum Theory ; Sulfur/chemistry/*metabolism ; },
abstract = {Peroxiredoxins (Prxs) are a ubiquitous class of enzymes that have central roles in a number of important physiological processes. Using a multiscale computational approach, we have investigated the mechanism by which the active-site cysteine (Cys50) in the typical 2-Cys Prx from Archaea (ApTPx) is oxidized by H2O2 to sulfenic acid. In addition, its further oxidation to give a sulfinic acid and its possible alternate intramolecular reaction to form an experimentally proposed hypervalent sulfurane were examined. Oxidation of Cys50 by H2O2 to give the sulfenic acid intermediate occurs in one step with a barrier of 82.1 kJ mol[-1]. A two-step pathway is proposed with a very low barrier of 16.5 kJ mol[-1] by which it can subsequently react with an adjacent histidyl (His42) to form the pseudohypervalent sulfurane. This pathway also involves an adjacent aspartyl (Asp45), which helps alternate the protonation state of His42. The sulfurane's Cys50S···NδHis42 interaction was characterized using QTAIM, NCI, and NBO analyses and found to be a noncovalent interaction. Notably, this bond helps orient the Cys50SOH moiety such that it is less susceptible to oxidation by H2O2 to sulfinic acid. Significantly, sulfurane formation is energetically favored to further H2O2 oxidation of Cys50SOH to a sulfinic acid, providing a mechanism by which the active-site Cys50 is protected against overoxidation.},
}
@article {pmid28625421,
year = {2017},
author = {Gaglione, R and Pirone, L and Farina, B and Fusco, S and Smaldone, G and Aulitto, M and Dell'Olmo, E and Roscetto, E and Del Gatto, A and Fattorusso, R and Notomista, E and Zaccaro, L and Arciello, A and Pedone, E and Contursi, P},
title = {Insights into the anticancer properties of the first antimicrobial peptide from Archaea.},
journal = {Biochimica et biophysica acta. General subjects},
volume = {1861},
number = {9},
pages = {2155-2164},
doi = {10.1016/j.bbagen.2017.06.009},
pmid = {28625421},
issn = {0304-4165},
mesh = {Animals ; Antimicrobial Cationic Peptides/chemistry/*pharmacology ; Antineoplastic Agents/chemistry/*pharmacology ; BALB 3T3 Cells ; Cell Death/drug effects ; Cell Membrane/drug effects ; Circular Dichroism ; Humans ; Mice ; Nuclear Magnetic Resonance, Biomolecular ; Protein Conformation ; Sulfolobus/*chemistry ; },
abstract = {BACKGROUND: The peptide VLL-28, identified in the sequence of an archaeal protein, the transcription factor Stf76 from Sulfolobus islandicus, was previously identified and characterized as an antimicrobial peptide, possessing a broad-spectrum antibacterial activity.<br><br>METHODS: Through a combined approach of NMR and Circular Dichroism spectroscopy, Dynamic Light Scattering, confocal microscopy and cell viability assays, the interaction of VLL-28 with the membranes of both parental and malignant cell lines has been characterized and peptide mechanism of action has been studied.<br><br>RESULTS: It is here demonstrated that VLL-28 selectively exerts cytotoxic activity against murine and human tumor cells. By means of structural methodologies, VLL-28 interaction with the membranes has been proven and the binding residues have been identified. Confocal microscopy data show that VLL-28 is internalized only into tumor cells. Finally, it is shown that cell death is mainly caused by a time-dependent activation of apoptotic pathways.<br><br>CONCLUSIONS: VLL-28, deriving from the archaeal kingdom, is here found to be endowed with selective cytotoxic activity towards both murine and human cancer cells and consequently can be classified as an ACP.<br><br>GENERAL SIGNIFICANCE: VLL-28 represents the first ACP identified in an archaeal microorganism, exerting a trans-kingdom activity.},
}
@article {pmid28587211,
year = {2017},
author = {Karayanni, H and Meziti, A and Spatharis, S and Genitsaris, S and Courties, C and Kormas, KA},
title = {Changes in Microbial (Bacteria and Archaea) Plankton Community Structure after Artificial Dispersal in Grazer-Free Microcosms.},
journal = {Microorganisms},
volume = {5},
number = {2},
pages = {},
pmid = {28587211},
issn = {2076-2607},
abstract = {Microbes are considered to have a global distribution due to their high dispersal capabilities. However, our knowledge of the way geographically distant microbial communities assemble after dispersal in a new environment is limited. In this study, we examined whether communities would converge because similar taxa would be selected under the same environmental conditions, or would diverge because of initial community composition, after artificial dispersal. To this aim, a microcosm experiment was performed, in which the temporal changes in the composition and diversity of different prokaryoplankton assemblages from three distant geographic coastal areas (Banyuls-sur-Mer in northwest Mediterranean Sea, Pagasitikos Gulf in northeast Mediterranean and Woods Hole, MA, USA in the northwest Atlantic), were studied. Diversity was investigated using amplicon pyrosequencing of the V1-V3 hypervariable regions of the 16S rRNA. The three assemblages were grown separately in particle free and autoclaved Banyuls-sur-mer seawater at 18 °C in the dark. We found that the variability of prokaryoplankton community diversity (expressed as richness, evenness and dominance) as well as the composition were driven by patterns observed in Bacteria. Regarding community composition, similarities were found between treatments at family level. However, at the OTU level microbial communities from the three different original locations diverge rather than converge during incubation. It is suggested that slight differences in the composition of the initial prokaryoplankton communities, resulted in separate clusters the following days even when growth took place under identical abiotic conditions.},
}
@article {pmid28585938,
year = {2017},
author = {Borrel, G and McCann, A and Deane, J and Neto, MC and Lynch, DB and Brugère, JF and O'Toole, PW},
title = {Genomics and metagenomics of trimethylamine-utilizing Archaea in the human gut microbiome.},
journal = {The ISME journal},
volume = {11},
number = {9},
pages = {2059-2074},
pmid = {28585938},
issn = {1751-7370},
mesh = {Aged ; Aged, 80 and over ; Animals ; Archaea/classification/*genetics/isolation &amp; purification/*metabolism ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology ; Genomics ; Humans ; Male ; Metagenome ; Metagenomics ; Methylamines/*metabolism ; Microbiota ; Phylogeny ; },
abstract = {The biological significance of Archaea in the human gut microbiota is largely unclear. We recently reported genomic and biochemical analyses of the Methanomassiliicoccales, a novel order of methanogenic Archaea dwelling in soil and the animal digestive tract. We now show that these Methanomassiliicoccales are present in published microbiome data sets from eight countries. They are represented by five Operational Taxonomic Units present in at least four cohorts and phylogenetically distributed into two clades. Genes for utilizing trimethylamine (TMA), a bacterial precursor to an atherosclerogenic human metabolite, were present in four of the six novel Methanomassiliicoccales genomes assembled from ELDERMET metagenomes. In addition to increased microbiota TMA production capacity in long-term residential care subjects, abundance of TMA-utilizing Methanomassiliicoccales correlated positively with bacterial gene count for TMA production and negatively with fecal TMA concentrations. The two large Methanomassiliicoccales clades have opposite correlations with host health status in the ELDERMET cohort and putative distinct genomic signatures for gut adaptation.},
}
@article {pmid28570690,
year = {2017},
author = {Majhi, MC and Behera, AK and Kulshreshtha, NM and Mahmooduzafar, D and Kumar, R and Kumar, A},
title = {Correction: ExtremeDB: A Unified Web Repository of Extremophilic Archaea and Bacteria.},
journal = {PloS one},
volume = {12},
number = {6},
pages = {e0179119},
pmid = {28570690},
issn = {1932-6203},
abstract = {[This corrects the article DOI: 10.1371/journal.pone.0063083.].},
}
@article {pmid28546547,
year = {2017},
author = {Chen, X and Andersen, TJ and Morono, Y and Inagaki, F and Jørgensen, BB and Lever, MA},
title = {Bioturbation as a key driver behind the dominance of Bacteria over Archaea in near-surface sediment.},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {2400},
pmid = {28546547},
issn = {2045-2322},
mesh = {Archaea/*classification ; Bacteria/*classification ; *Biodiversity ; DNA, Archaeal ; DNA, Bacterial ; Geologic Sediments/*microbiology ; Phylogeny ; Phylogeography ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The factors controlling the relative abundances of Archaea and Bacteria in marine sediments are poorly understood. We determined depth distributions of archaeal and bacterial 16S rRNA genes by quantitative PCR at eight stations in Aarhus Bay, Denmark. Bacterial outnumber archaeal genes 10-60-fold in uppermost sediments that are irrigated and mixed by macrofauna. This bioturbation is indicated by visual observations of sediment color and faunal tracks, by porewater profiles of dissolved inorganic carbon and sulfate, and by distributions of unsupported [210]Pb and [137]Cs. Below the depth of bioturbation, the relative abundances of archaeal genes increase, accounting for one third of 16S rRNA genes in the sulfate zone, and half of 16S rRNA genes in the sulfate-methane transition zone and methane zone. Phylogenetic analyses reveal a strong shift in bacterial and archaeal community structure from bioturbated sediments to underlying layers. Stable isotopic analyses on organic matter and porewater geochemical gradients suggest that macrofauna mediate bacterial dominance and affect microbial community structure in bioturbated sediment by introducing fresh organic matter and high-energy electron acceptors from overlying seawater. Below the zone of bioturbation, organic matter content and the presence of sulfate exert key influences on bacterial and archaeal abundances and overall microbial community structure.},
}
@article {pmid28523826,
year = {2017},
author = {Zheng, L and Zhao, X and Zhu, G and Yang, W and Xia, C and Xu, T},
title = {Occurrence and abundance of ammonia-oxidizing archaea and bacteria from the surface to below the water table, in deep soil, and their contributions to nitrification.},
journal = {MicrobiologyOpen},
volume = {6},
number = {4},
pages = {},
pmid = {28523826},
issn = {2045-8827},
mesh = {Ammonia/*metabolism ; Archaea/*classification/genetics/isolation &amp; purification/metabolism ; Bacteria/*classification/genetics/isolation &amp; purification/metabolism ; Bacterial Load ; *Biodiversity ; China ; Groundwater ; Lakes/*microbiology ; Nitrification ; Oxidation-Reduction ; Phylogeny ; Real-Time Polymerase Chain Reaction ; Sequence Analysis, DNA ; *Soil Microbiology ; Switzerland ; },
abstract = {Using molecular biology methods (qualitative and quantitative PCR), we determined the occurrence and abundance of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) from a dry inland soil in Basel, Switzerland, and from the riparian zone of Baiyangdian Lake, China. We also determined the contributions of these microorganisms to ammonia oxidization at different depths based on the nitrification rate. The number of archaeal amoA genes (the key functional gene in AOA) was larger than the number of bacterial amoA genes in each sample, suggesting a dominant role for the AOA amoA gene in environments with a low ammonium concentration. In Baiyangdian Lake, the number of archaeal amoA genes was highest at 6 m and lowest at 12 m from the land-water interface in the soil (at depths from 40 to 60 cm), close to the groundwater, which suggests that AOA become more competitive in environments with a low dissolved oxygen content and are promoted by low pH. The nitrification rate was significantly negatively correlated with depth in the Baiyangdian Lake soil and significantly positively correlated with the number of AOB amoA genes at this site, 6 m from the water.},
}
@article {pmid28520982,
year = {2017},
author = {Qi, L and Yue, L and Feng, D and Qi, F and Li, J and Dong, X},
title = {Genome-wide mRNA processing in methanogenic archaea reveals post-transcriptional regulation of ribosomal protein synthesis.},
journal = {Nucleic acids research},
volume = {45},
number = {12},
pages = {7285-7298},
pmid = {28520982},
issn = {1362-4962},
support = {R21 DE024235/DE/NIDCR NIH HHS/United States ; },
mesh = {Archaeal Proteins/*genetics/metabolism ; Base Sequence ; Cloning, Molecular ; Escherichia coli/genetics/metabolism ; Gene Expression ; *Genome, Archaeal ; Methanococcus/*genetics/metabolism ; Methanosarcinaceae/*genetics/metabolism ; Nucleic Acid Conformation ; Peptide Chain Initiation, Translational ; Protein Isoforms/genetics/metabolism ; *RNA Processing, Post-Transcriptional ; RNA, Messenger/chemistry/*genetics/metabolism ; Recombinant Proteins/genetics/metabolism ; Ribosomal Proteins/*genetics/metabolism ; },
abstract = {Unlike stable RNAs that require processing for maturation, prokaryotic cellular mRNAs generally follow an 'all-or-none' pattern. Herein, we used a 5΄ monophosphate transcript sequencing (5΄P-seq) that specifically captured the 5΄-end of processed transcripts and mapped the genome-wide RNA processing sites (PSSs) in a methanogenic archaeon. Following statistical analysis and stringent filtration, we identified 1429 PSSs, among which 23.5% and 5.4% were located in 5΄ untranslated region (uPSS) and intergenic region (iPSS), respectively. A predominant uridine downstream PSSs served as a processing signature. Remarkably, 5΄P-seq detected overrepresented uPSS and iPSS in the polycistronic operons encoding ribosomal proteins, and the majority upstream and proximal ribosome binding sites, suggesting a regulatory role of processing on translation initiation. The processed transcripts showed increased stability and translation efficiency. Particularly, processing within the tricistronic transcript of rplA-rplJ-rplL enhanced the translation of rplL, which can provide a driving force for the 1:4 stoichiometry of L10 to L12 in the ribosome. Growth-associated mRNA processing intensities were also correlated with the cellular ribosomal protein levels, thereby suggesting that mRNA processing is involved in tuning growth-dependent ribosome synthesis. In conclusion, our findings suggest that mRNA processing-mediated post-transcriptional regulation is a potential mechanism of ribosomal protein synthesis and stoichiometry.},
}
@article {pmid28515720,
year = {2017},
author = {Rajput, A and Kumar, M},
title = {Computational Exploration of Putative LuxR Solos in Archaea and Their Functional Implications in Quorum Sensing.},
journal = {Frontiers in microbiology},
volume = {8},
number = {},
pages = {798},
pmid = {28515720},
issn = {1664-302X},
abstract = {LuxR solos are unexplored in Archaea, despite their vital role in the bacterial regulatory network. They assist bacteria in perceiving acyl homoserine lactones (AHLs) and/or non-AHLs signaling molecules for establishing intraspecies, interspecies, and interkingdom communication. In this study, we explored the potential LuxR solos of Archaea from InterPro v62.0 meta-database employing taxonomic, probable function, distribution, and evolutionary aspects to decipher their role in quorum sensing (QS). Our bioinformatics analyses showed that putative LuxR solos of Archaea shared few conserved domains with bacterial LuxR despite having less similarity within proteins. Functional characterization revealed their ability to bind various AHLs and/or non-AHLs signaling molecules that involve in QS cascades alike bacteria. Further, the phylogenetic study indicates that Archaeal LuxR solos (with less substitution per site) evolved divergently from bacteria and share distant homology along with instances of horizontal gene transfer. Moreover, Archaea possessing putative LuxR solos, exhibit the correlation between taxonomy and ecological niche despite being the inhabitant of diverse habitats like halophilic, thermophilic, barophilic, methanogenic, and chemolithotrophic. Therefore, this study would shed light in deciphering the role of the putative LuxR solos of Archaea to adapt varied habitats via multilevel communication with other organisms using QS.},
}
@article {pmid28512451,
year = {2017},
author = {Wampach, L and Heintz-Buschart, A and Hogan, A and Muller, EEL and Narayanasamy, S and Laczny, CC and Hugerth, LW and Bindl, L and Bottu, J and Andersson, AF and de Beaufort, C and Wilmes, P},
title = {Colonization and Succession within the Human Gut Microbiome by Archaea, Bacteria, and Microeukaryotes during the First Year of Life.},
journal = {Frontiers in microbiology},
volume = {8},
number = {},
pages = {738},
pmid = {28512451},
issn = {1664-302X},
abstract = {Perturbations to the colonization process of the human gastrointestinal tract have been suggested to result in adverse health effects later in life. Although much research has been performed on bacterial colonization and succession, much less is known about the other two domains of life, archaea, and eukaryotes. Here we describe colonization and succession by bacteria, archaea and microeukaryotes during the first year of life (samples collected around days 1, 3, 5, 28, 150, and 365) within the gastrointestinal tract of infants delivered either vaginally or by cesarean section and using a combination of quantitative real-time PCR as well as 16S and 18S rRNA gene amplicon sequencing. Sequences from organisms belonging to all three domains of life were detectable in all of the collected meconium samples. The microeukaryotic community composition fluctuated strongly over time and early diversification was delayed in infants receiving formula milk. Cesarean section-delivered (CSD) infants experienced a delay in colonization and succession, which was observed for all three domains of life. Shifts in prokaryotic succession in CSD infants compared to vaginally delivered (VD) infants were apparent as early as days 3 and 5, which were characterized by increased relative abundances of the genera Streptococcus and Staphylococcus, and a decrease in relative abundance for the genera Bifidobacterium and Bacteroides. Generally, a depletion in Bacteroidetes was detected as early as day 5 postpartum in CSD infants, causing a significantly increased Firmicutes/Bacteroidetes ratio between days 5 and 150 when compared to VD infants. Although the delivery mode appeared to have the strongest influence on differences between the infants, other factors such as a younger gestational age or maternal antibiotics intake likely contributed to the observed patterns as well. Our findings complement previous observations of a delay in colonization and succession of CSD infants, which affects not only bacteria but also archaea and microeukaryotes. This further highlights the need for resolving bacterial, archaeal, and microeukaryotic dynamics in future longitudinal studies of microbial colonization and succession within the neonatal gastrointestinal tract.},
}
@article {pmid28502981,
year = {2017},
author = {Wagner, A and Whitaker, RJ and Krause, DJ and Heilers, JH and van Wolferen, M and van der Does, C and Albers, SV},
title = {Mechanisms of gene flow in archaea.},
journal = {Nature reviews. Microbiology},
volume = {15},
number = {8},
pages = {492-501},
pmid = {28502981},
issn = {1740-1534},
mesh = {Archaea/*genetics ; Evolution, Molecular ; *Gene Flow ; Gene Transfer, Horizontal ; Genes, Bacterial ; *Genome, Archaeal ; Genomics ; },
abstract = {Archaea are diverse, ecologically important, single-celled microorganisms. They have unique functions and features, such as methanogenesis and the composition of their cell envelope, although many characteristics are shared with the other domains of life, either through ancestry or through promiscuous horizontal gene transfer. The exchange of genetic material is a major driving force for genome evolution across the tree of life and has a role in archaeal speciation, adaptation and maintenance of diversity. In this Review, we discuss our current knowledge of archaeal mechanisms of DNA transfer and highlight the role of gene transfer in archaeal evolution.},
}
@article {pmid28500534,
year = {2017},
author = {Aylett, CHS and Duggin, IG},
title = {The Tubulin Superfamily in Archaea.},
journal = {Sub-cellular biochemistry},
volume = {84},
number = {},
pages = {393-417},
doi = {10.1007/978-3-319-53047-5_14},
pmid = {28500534},
issn = {0306-0225},
mesh = {Archaea/*metabolism ; Archaeal Proteins/*metabolism ; Tubulin/*classification/*metabolism ; },
abstract = {In comparison with bacteria and eukaryotes, the large and diverse group of microorganisms known as archaea possess a great diversity of cytoskeletal proteins, including members of the tubulin superfamily. Many species contain FtsZ, CetZ and even possible tubulins; however, some major taxonomic groups do not contain any member of the tubulin superfamily. Studies using the model archaeon, Halferax volcanii have recently been instrumental in defining the fundamental roles of FtsZ and CetZ in archaeal cell division and cell shape regulation. Structural studies of archaeal tubulin superfamily proteins provide a definitive contribution to the cytoskeletal field, showing which protein-types must have developed prior to the divergence of archaea and eukaryotes. Several regions of the globular core domain - the "signature" motifs - combine in the 3D structure of the common molecular fold to form the GTP-binding site. They are the most conserved sequence elements and provide the primary basis for identification of new superfamily members through homology searches. The currently well-characterised proteins also all share a common mechanism of GTP-dependent polymerisation, in which GTP molecules are sandwiched between successive subunits that are arranged in a head-to-tail manner. However, some poorly-characterised archaeal protein families retain only some of the signature motifs and are unlikely to be capable of dynamic polymerisation, since the promotion of depolymerisation by hydrolysis to GDP depends on contributions from both subunits that sandwich the nucleotide in the polymer.},
}
@article {pmid28493148,
year = {2017},
author = {Antranikian, G and Suleiman, M and Schäfers, C and Adams, MWW and Bartolucci, S and Blamey, JM and Birkeland, NK and Bonch-Osmolovskaya, E and da Costa, MS and Cowan, D and Danson, M and Forterre, P and Kelly, R and Ishino, Y and Littlechild, J and Moracci, M and Noll, K and Oshima, T and Robb, F and Rossi, M and Santos, H and Schönheit, P and Sterner, R and Thauer, R and Thomm, M and Wiegel, J and Stetter, KO},
title = {Diversity of bacteria and archaea from two shallow marine hydrothermal vents from Vulcano Island.},
journal = {Extremophiles : life under extreme conditions},
volume = {21},
number = {4},
pages = {733-742},
pmid = {28493148},
issn = {1433-4909},
mesh = {Archaea/*classification/genetics ; Bacteria/*classification/genetics ; Hydrothermal Vents/*microbiology ; Italy ; *Marine Biology ; RNA, Ribosomal, 16S/genetics ; },
abstract = {To obtain new insights into community compositions of hyperthermophilic microorganisms, defined as having optimal growth temperatures of 80 °C and above, sediment and water samples were taken from two shallow marine hydrothermal vents (I and II) with temperatures of 100 °C at Vulcano Island, Italy. A combinatorial approach of denaturant gradient gel electrophoresis (DGGE) and metagenomic sequencing was used for microbial community analyses of the samples. In addition, enrichment cultures, growing anaerobically on selected polysaccharides such as starch and cellulose, were also analyzed by the combinatorial approach. Our results showed a high abundance of hyperthermophilic archaea, especially in sample II, and a comparable diverse archaeal community composition in both samples. In particular, the strains of the hyperthermophilic anaerobic genera Staphylothermus and Thermococcus, and strains of the aerobic hyperthermophilic genus Aeropyrum, were abundant. Regarding the bacterial community, ε-Proteobacteria, especially the genera Sulfurimonas and Sulfurovum, were highly abundant. The microbial diversity of the enrichment cultures changed significantly by showing a high dominance of archaea, particularly the genera Thermococcus and Palaeococcus, depending on the carbon source and the selected temperature.},
}
@article {pmid28489329,
year = {2017},
author = {Dassen, S and Cortois, R and Martens, H and de Hollander, M and Kowalchuk, GA and van der Putten, WH and De Deyn, GB},
title = {Differential responses of soil bacteria, fungi, archaea and protists to plant species richness and plant functional group identity.},
journal = {Molecular ecology},
volume = {26},
number = {15},
pages = {4085-4098},
doi = {10.1111/mec.14175},
pmid = {28489329},
issn = {1365-294X},
mesh = {Archaea/classification ; Bacteria/classification ; *Biodiversity ; *Ecosystem ; Fungi/classification ; Germany ; Mycorrhizae/classification ; Plants/*classification ; *Soil Microbiology ; },
abstract = {Plants are known to influence belowground microbial community structure along their roots, but the impacts of plant species richness and plant functional group (FG) identity on microbial communities in the bulk soil are still not well understood. Here, we used 454-pyrosequencing to analyse the soil microbial community composition in a long-term biodiversity experiment at Jena, Germany. We examined responses of bacteria, fungi, archaea, and protists to plant species richness (communities varying from 1 to 60 sown species) and plant FG identity (grasses, legumes, small herbs, tall herbs) in bulk soil. We hypothesized that plant species richness and FG identity would alter microbial community composition and have a positive impact on microbial species richness. Plant species richness had a marginal positive effect on the richness of fungi, but we observed no such effect on bacteria, archaea and protists. Plant species richness also did not have a large impact on microbial community composition. Rather, abiotic soil properties partially explained the community composition of bacteria, fungi, arbuscular mycorrhizal fungi (AMF), archaea and protists. Plant FG richness did not impact microbial community composition; however, plant FG identity was more effective. Bacterial richness was highest in legume plots and lowest in small herb plots, and AMF and archaeal community composition in legume plant communities was distinct from that in communities composed of other plant FGs. We conclude that soil microbial community composition in bulk soil is influenced more by changes in plant FG composition and abiotic soil properties, than by changes in plant species richness per se.},
}
@article {pmid28487430,
year = {2017},
author = {Mukai, T and Crnković, A and Umehara, T and Ivanova, NN and Kyrpides, NC and Söll, D},
title = {RNA-Dependent Cysteine Biosynthesis in Bacteria and Archaea.},
journal = {mBio},
volume = {8},
number = {3},
pages = {},
pmid = {28487430},
issn = {2150-7511},
support = {R01 GM022854/GM/NIGMS NIH HHS/United States ; R35 GM122560/GM/NIGMS NIH HHS/United States ; },
mesh = {Amino Acyl-tRNA Synthetases/metabolism ; Archaea/*genetics/metabolism ; Archaeal Proteins/genetics/metabolism ; Bacteria/*genetics/metabolism ; Computational Biology ; Crystallography, X-Ray ; Cysteine/*biosynthesis ; Genetic Code ; Genome, Archaeal ; Genome, Bacterial ; Phosphoserine/metabolism ; Protein Binding ; Protein Biosynthesis ; RNA, Archaeal/*metabolism ; RNA, Bacterial/*metabolism ; RNA, Transfer, Amino Acyl/*metabolism ; RNA, Transfer, Cys/*metabolism ; Sulfur/metabolism ; },
abstract = {The diversity of the genetic code systems used by microbes on earth is yet to be elucidated. It is known that certain methanogenic archaea employ an alternative system for cysteine (Cys) biosynthesis and encoding; tRNA[Cys] is first acylated with phosphoserine (Sep) by O-phosphoseryl-tRNA synthetase (SepRS) and then converted to Cys-tRNA[Cys] by Sep-tRNA:Cys-tRNA synthase (SepCysS). In this study, we searched all genomic and metagenomic protein sequence data in the Integrated Microbial Genomes (IMG) system and at the NCBI to reveal new clades of SepRS and SepCysS proteins belonging to diverse archaea in the four major groups (DPANN, Euryarchaeota, TACK, and Asgard) and two groups of bacteria ("Candidatus Parcubacteria" and Chloroflexi). Bacterial SepRS and SepCysS charged bacterial tRNA[Cys] species with cysteine in vitro Homologs of SepCysE, a scaffold protein facilitating SepRS⋅SepCysS complex assembly in Euryarchaeota class I methanogens, are found in a few groups of TACK and Asgard archaea, whereas the C-terminally truncated homologs exist fused or genetically coupled with diverse SepCysS species. Investigation of the selenocysteine (Sec)- and pyrrolysine (Pyl)-utilizing traits in SepRS-utilizing archaea and bacteria revealed that the archaea carrying full-length SepCysE employ Sec and that SepRS is often found in Pyl-utilizing archaea and Chloroflexi bacteria. We discuss possible contributions of the SepRS-SepCysS system for sulfur assimilation, methanogenesis, and other metabolic processes requiring large amounts of iron-sulfur enzymes or Pyl-containing enzymes.IMPORTANCE Comprehensive analyses of all genomic and metagenomic protein sequence data in public databases revealed the distribution and evolution of an alternative cysteine-encoding system in diverse archaea and bacteria. The finding that the SepRS-SepCysS-SepCysE- and the selenocysteine-encoding systems are shared by the Euryarchaeota class I methanogens, the Crenarchaeota AK8/W8A-19 group, and an Asgard archaeon suggests that ancient archaea may have used both systems. In contrast, bacteria may have obtained the SepRS-SepCysS system from archaea. The SepRS-SepCysS system sometimes coexists with a pyrrolysine-encoding system in both archaea and bacteria. Our results provide additional bioinformatic evidence for the contribution of the SepRS-SepCysS system for sulfur assimilation and diverse metabolisms which require vast amounts of iron-sulfur enzymes and proteins. Among these biological activities, methanogenesis, methylamine metabolism, and organohalide respiration may have local and global effects on earth. Taken together, uncultured bacteria and archaea provide an expanded record of the evolution of the genetic code.},
}
@article {pmid28480883,
year = {2017},
author = {Zweerink, S and Kallnik, V and Ninck, S and Nickel, S and Verheyen, J and Blum, M and Wagner, A and Feldmann, I and Sickmann, A and Albers, SV and Bräsen, C and Kaschani, F and Siebers, B and Kaiser, M},
title = {Activity-based protein profiling as a robust method for enzyme identification and screening in extremophilic Archaea.},
journal = {Nature communications},
volume = {8},
number = {},
pages = {15352},
pmid = {28480883},
issn = {2041-1723},
mesh = {Archaeal Proteins/*metabolism ; Extremophiles/*metabolism ; Hydrolases/*metabolism ; Mass Spectrometry ; Proteomics/*methods ; Reproducibility of Results ; Serine/metabolism ; },
abstract = {Archaea are characterized by a unique life style in often environmental extremes but their thorough investigation is currently hampered by a limited set of suitable in vivo research methodologies. Here, we demonstrate that in vivo activity-based protein profiling (ABPP) may be used to sensitively detect either native or heterogeneously expressed active enzymes in living archaea even under these extreme conditions. In combination with the development of a genetically engineered archaeal screening strain, ABPP can furthermore be used in functional enzyme screenings from (meta)genome samples. We anticipate that our ABPP approach may therefore find application in basic archaeal research but also in the discovery of novel enzymes from (meta)genome libraries.},
}
@article {pmid28480138,
year = {2017},
author = {Bolduc, B and Jang, HB and Doulcier, G and You, ZQ and Roux, S and Sullivan, MB},
title = {vConTACT: an iVirus tool to classify double-stranded DNA viruses that infect Archaea and Bacteria.},
journal = {PeerJ},
volume = {5},
number = {},
pages = {e3243},
pmid = {28480138},
issn = {2167-8359},
abstract = {Taxonomic classification of archaeal and bacterial viruses is challenging, yet also fundamental for developing a predictive understanding of microbial ecosystems. Recent identification of hundreds of thousands of new viral genomes and genome fragments, whose hosts remain unknown, requires a paradigm shift away from traditional classification approaches and towards the use of genomes for taxonomy. Here we revisited the use of genomes and their protein content as a means for developing a viral taxonomy for bacterial and archaeal viruses. A network-based analytic was evaluated and benchmarked against authority-accepted taxonomic assignments and found to be largely concordant. Exceptions were manually examined and found to represent areas of viral genome 'sequence space' that are under-sampled or prone to excessive genetic exchange. While both cases are poorly resolved by genome-based taxonomic approaches, the former will improve as viral sequence space is better sampled and the latter are uncommon. Finally, given the largely robust taxonomic capabilities of this approach, we sought to enable researchers to easily and systematically classify new viruses. Thus, we established a tool, vConTACT, as an app at iVirus, where it operates as a fast, highly scalable, user-friendly app within the free and powerful CyVerse cyberinfrastructure.},
}
@article {pmid28464532,
year = {2017},
author = {Sogin, EM and Putnam, HM and Nelson, CE and Anderson, P and Gates, RD},
title = {Correspondence of coral holobiont metabolome with symbiotic bacteria, archaea and Symbiodinium communities.},
journal = {Environmental microbiology reports},
volume = {9},
number = {3},
pages = {310-315},
doi = {10.1111/1758-2229.12541},
pmid = {28464532},
issn = {1758-2229},
mesh = {Alveolata/*growth &amp; development/metabolism ; Animals ; Anthozoa/*microbiology/*parasitology ; Archaea/classification/*growth &amp; development/metabolism ; Biodiversity ; Coral Reefs ; Gammaproteobacteria/*growth &amp; development/metabolism ; Metabolome/physiology ; Symbiosis/*physiology ; Vibrionaceae/*growth &amp; development/metabolism ; },
abstract = {Microbial symbiotic partners, such as those associated with Scleractinian corals, mediate biochemical transformations that influence host performance and survival. While evidence suggests microbial community composition partly accounts for differences in coral physiology, how these symbionts affect metabolic pathways remains underexplored. We aimed to assess functional implications of variation among coral-associated microbial partners in hospite. To this end, we characterized and compared metabolomic profiles and microbial community composition from nine reef-building coral species. These data demonstrate metabolite profiles and microbial communities are species-specific and are correlated to one another. Using Porites spp. as a case study, we present evidence that the relative abundance of different sub-clades of Symbiodinium and bacterial/archaeal families are linked to positive and negative metabolomic signatures. Our data suggest that while some microbial partners benefit the union, others are more opportunistic with potential detriment to the host. Consequently, coral partner choice likely influences cellular metabolic activities and, therefore, holobiont nutrition.},
}
@article {pmid28446901,
year = {2017},
author = {Weber, HS and Habicht, KS and Thamdrup, B},
title = {Anaerobic Methanotrophic Archaea of the ANME-2d Cluster Are Active in a Low-sulfate, Iron-rich Freshwater Sediment.},
journal = {Frontiers in microbiology},
volume = {8},
number = {},
pages = {619},
pmid = {28446901},
issn = {1664-302X},
abstract = {ANaerobic MEthanotrophic (ANME) archaea remove the greenhouse gas methane from anoxic environments and diminish its flux to the atmosphere. High methane removal efficiencies are well documented in marine environments, whereas anaerobic oxidation of methane (AOM) was only recently indicated as an important methane sink in freshwater systems. Freshwater AOM-mediating microorganisms lack taxonomic identification and only little is known about metabolic adaptions to prevailing biogeochemical conditions. One of the first study sites providing information about AOM activity in freshwater sediment is Lake Ørn, a low-sulfate, iron-rich Danish lake. With the aim to identify freshwater AOM-mediating archaea, we incubated AOM-active anoxic, nitrate-free freshwater sediment from Lake Ørn with [13]C-labeled methane ([13]CCH4) and [13]C-labeled bicarbonate ([13]CDIC) and followed the assimilation of [13]C into RNA by stable isotope probing. While AOM was active, [13]CCH4 and probably also [13]CDIC were incorporated into uncultured archaea of the Methanosarcinales-related cluster ANME-2d, whereas other known ANME lineages were not detected. This finding strongly suggests that ANME-2d archaea perform AOM coupled to sulfate and/or iron reduction and may have the capability of mixed assimilation of CH4 and DIC. ANME-2d archaea may thus play an important role in controlling methane emissions from nitrate-depleted and low-sulfate freshwater systems.},
}
@article {pmid28425930,
year = {2017},
author = {Zhang, Y and Kouril, T and Snoep, JL and Siebers, B and Barberis, M and Westerhoff, HV},
title = {The Peculiar Glycolytic Pathway in Hyperthermophylic Archaea: Understanding Its Whims by Experimentation In Silico.},
journal = {International journal of molecular sciences},
volume = {18},
number = {4},
pages = {},
pmid = {28425930},
issn = {1422-0067},
mesh = {Adenosine Triphosphate/metabolism ; Computer Simulation ; Glyceraldehyde 3-Phosphate/metabolism ; Glyceraldehyde-3-Phosphate Dehydrogenases/metabolism ; *Glycolysis ; *Hot Temperature ; Kinetics ; Metabolic Networks and Pathways ; *Models, Biological ; Saccharomyces cerevisiae/metabolism ; Sulfolobus solfataricus/*metabolism ; Systems Biology ; },
abstract = {Mathematical models are key to systems biology where they typically describe the topology and dynamics of biological networks, listing biochemical entities and their relationships with one another. Some (hyper)thermophilic Archaea contain an enzyme, called non-phosphorylating glyceraldehyde-3-phosphate dehydrogenase (GAPN), which catalyzes the direct oxidation of glyceraldehyde-3-phosphate to 3-phosphoglycerate omitting adenosine 5'-triphosphate (ATP) formation by substrate-level-phosphorylation via phosphoglycerate kinase. In this study we formulate three hypotheses that could explain functionally why GAPN exists in these Archaea, and then construct and use mathematical models to test these three hypotheses. We used kinetic parameters of enzymes of Sulfolobus solfataricus (S. solfataricus) which is a thermo-acidophilic archaeon that grows optimally between 60 and 90 °C and between pH 2 and 4. For comparison, we used a model of Saccharomyces cerevisiae (S. cerevisiae), an organism that can live at moderate temperatures. We find that both the first hypothesis, i.e., that the glyceraldehyde-3-phosphate dehydrogenase (GAPDH) plus phosphoglycerate kinase (PGK) route (the alternative to GAPN) is thermodynamically too much uphill and the third hypothesis, i.e., that GAPDH plus PGK are required to carry the flux in the gluconeogenic direction, are correct. The second hypothesis, i.e., that the GAPDH plus PGK route delivers less than the 1 ATP per pyruvate that is delivered by the GAPN route, is only correct when GAPDH reaction has a high rate and 1,3-bis-phosphoglycerate (BPG) spontaneously degrades to 3PG at a high rate.},
}
@article {pmid28424284,
year = {2017},
author = {Liu, Y and Ishino, S and Ishino, Y and Pehau-Arnaudet, G and Krupovic, M and Prangishvili, D},
title = {A Novel Type of Polyhedral Viruses Infecting Hyperthermophilic Archaea.},
journal = {Journal of virology},
volume = {91},
number = {13},
pages = {},
pmid = {28424284},
issn = {1098-5514},
mesh = {DNA Viruses/*classification/genetics/*isolation &amp; purification/ultrastructure ; Gene Order ; Genome, Viral ; Microscopy, Electron ; Open Reading Frames ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Sulfolobus/*virology ; Viral Proteins/genetics ; *Viral Structures ; Virion/chemistry/ultrastructure ; },
abstract = {Encapsidation of genetic material into polyhedral particles is one of the most common structural solutions employed by viruses infecting hosts in all three domains of life. Here, we describe a new virus of hyperthermophilic archaea, Sulfolobus polyhedral virus 1 (SPV1), which condenses its circular double-stranded DNA genome in a manner not previously observed for other known viruses. The genome complexed with virion proteins is wound up sinusoidally into a spherical coil which is surrounded by an envelope and further encased by an outer polyhedral capsid apparently composed of the 20-kDa virion protein. Lipids selectively acquired from the pool of host lipids are integral constituents of the virion. None of the major virion proteins of SPV1 show similarity to structural proteins of known viruses. However, minor structural proteins, which are predicted to mediate host recognition, are shared with other hyperthermophilic archaeal viruses infecting members of the order Sulfolobales The SPV1 genome consists of 20,222 bp and contains 45 open reading frames, only one-fifth of which could be functionally annotated.IMPORTANCE Viruses infecting hyperthermophilic archaea display a remarkable morphological diversity, often presenting architectural solutions not employed by known viruses of bacteria and eukaryotes. Here we present the isolation and characterization of Sulfolobus polyhedral virus 1, which condenses its genome into a unique spherical coil. Due to the original genomic and architectural features of SPV1, the virus should be considered a representative of a new viral family, "Portogloboviridae."},
}
@article {pmid28420220,
year = {2017},
author = {Michel, CJ},
title = {The Maximal C[3] Self-Complementary Trinucleotide Circular Code X in Genes of Bacteria, Archaea, Eukaryotes, Plasmids and Viruses.},
journal = {Life (Basel, Switzerland)},
volume = {7},
number = {2},
pages = {},
pmid = {28420220},
issn = {2075-1729},
abstract = {In 1996, a set X of 20 trinucleotides was identified in genes of both prokaryotes and eukaryotes which has on average the highest occurrence in reading frame compared to its two shifted frames. Furthermore, this set X has an interesting mathematical property as X is a maximal C 3 self-complementary trinucleotide circular code. In 2015, by quantifying the inspection approach used in 1996, the circular code X was confirmed in the genes of bacteria and eukaryotes and was also identified in the genes of plasmids and viruses. The method was based on the preferential occurrence of trinucleotides among the three frames at the gene population level. We extend here this definition at the gene level. This new statistical approach considers all the genes, i.e., of large and small lengths, with the same weight for searching the circular code X . As a consequence, the concept of circular code, in particular the reading frame retrieval, is directly associated to each gene. At the gene level, the circular code X is strengthened in the genes of bacteria, eukaryotes, plasmids, and viruses, and is now also identified in the genes of archaea. The genes of mitochondria and chloroplasts contain a subset of the circular code X . Finally, by studying viral genes, the circular code X was found in DNA genomes, RNA genomes, double-stranded genomes, and single-stranded genomes.},
}
@article {pmid28409190,
year = {2017},
author = {Salah Ud-Din, AIM and Roujeinikova, A},
title = {Methyl-accepting chemotaxis proteins: a core sensing element in prokaryotes and archaea.},
journal = {Cellular and molecular life sciences : CMLS},
volume = {74},
number = {18},
pages = {3293-3303},
pmid = {28409190},
issn = {1420-9071},
mesh = {Archaea/classification/*metabolism ; Chemotaxis ; Membrane Proteins/chemistry/metabolism ; Methyl-Accepting Chemotaxis Proteins/chemistry/*metabolism ; Prokaryotic Cells/classification/*metabolism ; Protein Domains ; Signal Transduction ; Structure-Activity Relationship ; },
abstract = {Chemotaxis is the directed motility by means of which microbes sense chemical cues and relocate towards more favorable environments. Methyl-accepting chemotaxis proteins (MCPs) are the most common receptors in bacteria and archaea. They are arranged as trimers of dimers that, in turn, form hexagonal arrays in the cytoplasmic membrane or in the cytoplasm. Several different classes of MCPs have been identified according to their ligand binding region and membrane topology. MCPs have been further classified based on the length and sequence conservation of their cytoplasmic domains. Clusters of membrane-embedded MCPs often localize to the poles of the cell, whereas cytoplasmic MCPs can be targeted to the poles or distributed throughout the cell body. MCPs play an important role in cell survival, pathogenesis, and biodegradation. Bacterial adaptation to diverse environmental conditions promotes diversity among the MCPs. This review summarizes structure, classification, and structure-activity relationship of the known MCP receptors, with a brief overview of the signal transduction mechanisms in bacteria and archaea.},
}
@article {pmid28402397,
year = {2017},
author = {Peay, KG and von Sperber, C and Cardarelli, E and Toju, H and Francis, CA and Chadwick, OA and Vitousek, PM},
title = {Convergence and contrast in the community structure of Bacteria, Fungi and Archaea along a tropical elevation-climate gradient.},
journal = {FEMS microbiology ecology},
volume = {93},
number = {5},
pages = {},
doi = {10.1093/femsec/fix045},
pmid = {28402397},
issn = {1574-6941},
mesh = {Ammonia/analysis ; Archaea/*classification/genetics ; Bacteria/*classification/genetics ; Biodiversity ; Carbon/analysis ; Fungi/*classification/genetics ; High-Throughput Nucleotide Sequencing ; Microbial Consortia/*physiology ; Nitrogen/analysis ; Phosphorus/analysis ; Soil/*chemistry ; Soil Microbiology ; Tropical Climate ; },
abstract = {Changes in species richness along climatological gradients have been instrumental in developing theories about the general drivers of biodiversity. Previous studies on microbial communities along climate gradients on mountainsides have revealed positive, negative and neutral richness trends. We examined changes in richness and composition of Fungi, Bacteria and Archaea in soil along a 50-1000 m elevation, 280-3280 mm/yr precipitation gradient in Hawai'i. Soil properties and their drivers are exceptionally well understood along this gradient. All three microbial groups responded strongly to the gradient, with community ordinations being similar along axes of environmental conditions (pH, rainfall) and resource availability (nitrogen, phosphorus). However, the form of the richness-climate relationship varied between Fungi (positive linear), Bacteria (unimodal) and Archaea (negative linear). These differences were related to resource-ecology and limiting conditions for each group, with fungal richness increasing most strongly with soil carbon, ammonia-oxidizing Archaea increasing with nitrogen mineralization rate, and Bacteria increasing with both carbon and pH. Reponses to the gradient became increasingly variable at finer taxonomic scales and within any taxonomic group most individual OTUs occurred in narrow climate-elevation ranges. These results show that microbial responses to climate gradients are heterogeneous due to complexity of underlying environmental changes and the diverse ecologies of microbial taxa.},
}
@article {pmid28397816,
year = {2017},
author = {Wong, HL and Visscher, PT and White, RA and Smith, DL and Patterson, MM and Burns, BP},
title = {Dynamics of archaea at fine spatial scales in Shark Bay mat microbiomes.},
journal = {Scientific reports},
volume = {7},
number = {},
pages = {46160},
pmid = {28397816},
issn = {2045-2322},
mesh = {Archaea/*physiology ; Australia ; Bays/*microbiology ; Biodiversity ; Methane/biosynthesis ; Microbial Interactions ; *Microbiota ; },
abstract = {The role of archaea in microbial mats is poorly understood. Delineating the spatial distribution of archaea with mat depth will enable resolution of putative niches in these systems. In the present study, high throughput amplicon sequencing was undertaken in conjunction with analysis of key biogeochemical properties of two mats (smooth and pustular) from Shark Bay, Australia. One-way analysis of similarity tests indicated the archaeal community structures of smooth and pustular mats were significantly different (global R = 1, p = 0.1%). Smooth mats possessed higher archaeal diversity, dominated by Parvarchaeota. The methanogenic community in smooth mats was dominated by hydrogenotrophic Methanomicrobiales, as well as methylotrophic Methanosarcinales, Methanococcales, Methanobacteriales and Methanomassiliicoccaceae. Pustular mats were enriched with Halobacteria and Parvarchaeota. Key metabolisms (bacterial and archaeal) were measured, and the rates of oxygen production/consumption and sulfate reduction were up to four times higher in smooth than in pustular mats. Methane production peaked in the oxic layers and was up to seven-fold higher in smooth than pustular mats. The finding of an abundance of anaerobic methanogens enriched at the surface where oxygen levels were highest, coupled with peak methane production in the oxic zone, suggests putative surface anoxic niches in these microbial mats.},
}
@article {pmid28391963,
year = {2017},
author = {Gophna, U and Allers, T and Marchfelder, A},
title = {Finally, Archaea Get Their CRISPR-Cas Toolbox.},
journal = {Trends in microbiology},
volume = {25},
number = {6},
pages = {430-432},
doi = {10.1016/j.tim.2017.03.009},
pmid = {28391963},
issn = {1878-4380},
mesh = {Archaea/*genetics ; Archaeal Proteins/genetics ; Bacterial Proteins/genetics ; CRISPR-Cas Systems/*genetics ; Clustered Regularly Interspaced Short Palindromic Repeats/*genetics ; DNA End-Joining Repair/genetics ; Gene Deletion ; Gene Editing ; Gene Targeting ; Genes, Archaeal ; Homologous Recombination/genetics ; Methanosarcina/genetics ; RNA, Guide, CRISPR-Cas Systems ; },
abstract = {The majority of archaea encode CRISPR-Cas systems but only a few CRISPR-Cas-based genetic tools have been developed for organisms from this domain. Nayak and Metcalf have harnessed a bacterial Cas9 protein for genome editing in Methanosarcina acetivorans, enabling efficient gene deletion and replacement.},
}
@article {pmid28388930,
year = {2017},
author = {Wurzbacher, C and Fuchs, A and Attermeyer, K and Frindte, K and Grossart, HP and Hupfer, M and Casper, P and Monaghan, MT},
title = {Shifts among Eukaryota, Bacteria, and Archaea define the vertical organization of a lake sediment.},
journal = {Microbiome},
volume = {5},
number = {1},
pages = {41},
pmid = {28388930},
issn = {2049-2618},
mesh = {Archaea/*classification/genetics/isolation &amp; purification ; Bacteria/*classification/genetics/isolation &amp; purification ; Ecosystem ; Eukaryota/*classification/genetics/isolation &amp; purification ; Geologic Sediments/*microbiology/*parasitology ; Germany ; Lakes/*microbiology/*parasitology ; Microbiota/genetics ; Water Microbiology ; },
abstract = {BACKGROUND: Lake sediments harbor diverse microbial communities that cycle carbon and nutrients while being constantly colonized and potentially buried by organic matter sinking from the water column. The interaction of activity and burial remained largely unexplored in aquatic sediments. We aimed to relate taxonomic composition to sediment biogeochemical parameters, test whether community turnover with depth resulted from taxonomic replacement or from richness effects, and to provide a basic model for the vertical community structure in sediments.<br><br>METHODS: We analyzed four replicate sediment cores taken from 30-m depth in oligo-mesotrophic Lake Stechlin in northern Germany. Each 30-cm core spanned ca. 170 years of sediment accumulation according to [137]Cs dating and was sectioned into layers 1-4 cm thick. We examined a full suite of biogeochemical parameters and used DNA metabarcoding to examine community composition of microbial Archaea, Bacteria, and Eukaryota.<br><br>RESULTS: Community &#x3b2;-diversity indicated nearly complete turnover within the uppermost 30 cm. We observed a pronounced shift from Eukaryota- and Bacteria-dominated upper layers (<5 cm) to Bacteria-dominated intermediate layers (5-14 cm) and to deep layers (>14 cm) dominated by enigmatic Archaea that typically occur in deep-sea sediments. Taxonomic replacement was the prevalent mechanism in structuring the community composition and was linked to parameters indicative of microbial activity (e.g., CO2 and CH4 concentration, bacterial protein production). Richness loss played a lesser role but was linked to conservative parameters (e.g., C, N, P) indicative of past conditions.<br><br>CONCLUSIONS: By including all three domains, we were able to directly link the exponential decay of eukaryotes with the active sediment microbial community. The dominance of Archaea in deeper layers confirms earlier findings from marine systems and establishes freshwater sediments as a potential low-energy environment, similar to deep sea sediments. We propose a general model of sediment structure and function based on microbial characteristics and burial processes. An upper "replacement horizon" is dominated by rapid taxonomic turnover with depth, high microbial activity, and biotic interactions. A lower "depauperate horizon" is characterized by low taxonomic richness, more stable "low-energy" conditions, and a dominance of enigmatic Archaea.},
}
@article {pmid28373277,
year = {2017},
author = {Heider, MR and Burkhart, BW and Santangelo, TJ and Gardner, AF},
title = {Defining the RNaseH2 enzyme-initiated ribonucleotide excision repair pathway in Archaea.},
journal = {The Journal of biological chemistry},
volume = {292},
number = {21},
pages = {8835-8845},
pmid = {28373277},
issn = {1083-351X},
support = {R01 GM100329/GM/NIGMS NIH HHS/United States ; },
mesh = {Archaeal Proteins/genetics/*metabolism ; *DNA Breaks, Single-Stranded ; DNA Ligases/genetics/metabolism ; DNA Polymerase beta/genetics/metabolism ; DNA Repair/*physiology ; DNA, Archaeal/genetics/*metabolism ; Ribonuclease H/genetics/*metabolism ; Thermococcus/genetics/*metabolism ; },
abstract = {Incorporation of ribonucleotides during DNA replication has severe consequences for genome stability. Although eukaryotes possess a number of redundancies for initiating and completing repair of misincorporated ribonucleotides, archaea such as Thermococcus rely only upon RNaseH2 to initiate the pathway. Because Thermococcus DNA polymerases incorporate as many as 1,000 ribonucleotides per genome, RNaseH2 must be efficient at recognizing and nicking at embedded ribonucleotides to ensure genome integrity. Here, we show that ribonucleotides are incorporated by the hyperthermophilic archaeon Thermococcus kodakarensis both in vitro and in vivo and a robust ribonucleotide excision repair pathway is critical to keeping incorporation levels low in wild-type cells. Using pre-steady-state and steady-state kinetics experiments, we also show that archaeal RNaseH2 rapidly cleaves at embedded ribonucleotides (200-450 s[-1]), but exhibits an ∼1,000-fold slower turnover rate (0.06-0.17 s[-1]), suggesting a potential role for RNaseH2 in protecting or marking nicked sites for further processing. We found that following RNaseH2 cleavage, the combined activities of polymerase B (PolB), flap endonuclease (Fen1), and DNA ligase are required to complete ribonucleotide processing. PolB formed a ribonucleotide-containing flap by strand displacement synthesis that was cleaved by Fen1, and DNA ligase sealed the nick for complete repair. Our study reveals conservation of the overall mechanism of ribonucleotide excision repair across domains of life. The lack of redundancies in ribonucleotide repair in archaea perhaps suggests a more ancestral form of ribonucleotide excision repair compared with the eukaryotic pathway.},
}
@article {pmid28368387,
year = {2017},
author = {Paul, BG and Burstein, D and Castelle, CJ and Handa, S and Arambula, D and Czornyj, E and Thomas, BC and Ghosh, P and Miller, JF and Banfield, JF and Valentine, DL},
title = {Retroelement-guided protein diversification abounds in vast lineages of Bacteria and Archaea.},
journal = {Nature microbiology},
volume = {2},
number = {},
pages = {17045},
pmid = {28368387},
issn = {2058-5276},
support = {R01 AI096838/AI/NIAID NIH HHS/United States ; },
mesh = {Archaea/classification/*genetics/metabolism ; Archaeal Proteins/*genetics ; Bacteria/classification/*genetics/metabolism ; Bacterial Proteins/*genetics ; *Evolution, Molecular ; Genome, Archaeal ; Genome, Bacterial ; Genomics ; Nanoarchaeota/genetics/metabolism ; Phylogeny ; RNA-Directed DNA Polymerase/genetics ; Retroelements/*genetics ; },
abstract = {Major radiations of enigmatic Bacteria and Archaea with large inventories of uncharacterized proteins are a striking feature of the Tree of Life[1-5]. The processes that led to functional diversity in these lineages, which may contribute to a host-dependent lifestyle, are poorly understood. Here, we show that diversity-generating retroelements (DGRs), which guide site-specific protein hypervariability[6-8], are prominent features of genomically reduced organisms from the bacterial candidate phyla radiation (CPR) and as yet uncultivated phyla belonging to the DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota and Nanohaloarchaea) archaeal superphylum. From reconstructed genomes we have defined monophyletic bacterial and archaeal DGR lineages that expand the known DGR range by 120% and reveal a history of horizontal retroelement transfer. Retroelement-guided diversification is further shown to be active in current CPR and DPANN populations, with an assortment of protein targets potentially involved in attachment, defence and regulation. Based on observations of DGR abundance, function and evolutionary history, we find that targeted protein diversification is a pronounced trait of CPR and DPANN phyla compared to other bacterial and archaeal phyla. This diversification mechanism may provide CPR and DPANN organisms with a versatile tool that could be used for adaptation to a dynamic, host-dependent existence.},
}
@article {pmid28360898,
year = {2017},
author = {Wang, J and Kan, J and Zhang, X and Xia, Z and Zhang, X and Qian, G and Miao, Y and Leng, X and Sun, J},
title = {Archaea Dominate the Ammonia-Oxidizing Community in Deep-Sea Sediments of the Eastern Indian Ocean-from the Equator to the Bay of Bengal.},
journal = {Frontiers in microbiology},
volume = {8},
number = {},
pages = {415},
pmid = {28360898},
issn = {1664-302X},
abstract = {Ammonia-oxidizing Archaea (AOA) and ammonia-oxidizing Bacteria (AOB) oxidize ammonia to nitrite, and therefore play essential roles in nitrification and global nitrogen cycling. To better understand the population structure and the distribution of AOA and AOB in the deep Eastern Indian Ocean (EIO), nine surface sediment samples (>3,300 m depth) were collected during the inter-monsoon Spring 2013. One sediment sample from the South China Sea (SCS; 2,510 m) was also included for comparison. The community composition, species richness, and diversity were characterized by clone libraries (total 1,238 clones), and higher diversity of archaeal amoA genes than bacterial amoA genes was observed in all analyzed samples. Real time qPCR analysis also demonstrated higher abundances (gene copy numbers) of archaeal amoA genes than bacterial amoA genes, and the ratios of AOA/AOB ranged from 1.42 to 8.49 among sites. In addition, unique and distinct clades were found in both reconstructed AOA and AOB phylogeny, suggesting the presence of niche-specific ammonia-oxidizing microorganisms in the EIO. The distribution pattern of both archaeal and bacterial amoA genes revealed by NMDS (non-metric multidimensional scaling) showed a distinct geographic separation of the sample from the SCS and most of the samples from the EIO following nitrogen gradients. Higher abundance and diversity of archaeal amoA genes indicated that AOA may play a more important role than AOB in the deep Indian Ocean. Environmental parameters shaping the distribution pattern of AOA were different from that of AOB, indicating distinct metabolic characteristics and/or adaptation mechanisms between AOA and AOB in the EIO, especially in deep-sea environments.},
}
@article {pmid28350393,
year = {2017},
author = {Hernsdorf, AW and Amano, Y and Miyakawa, K and Ise, K and Suzuki, Y and Anantharaman, K and Probst, A and Burstein, D and Thomas, BC and Banfield, JF},
title = {Potential for microbial H2 and metal transformations associated with novel bacteria and archaea in deep terrestrial subsurface sediments.},
journal = {The ISME journal},
volume = {11},
number = {8},
pages = {1915-1929},
pmid = {28350393},
issn = {1751-7370},
mesh = {Archaea/*metabolism ; Bacteria/*metabolism ; Carbon/metabolism ; Hydrogen/chemistry/*metabolism ; Hydrogenase ; Metals/chemistry/*metabolism ; Methane/metabolism ; Nitrogen/metabolism ; Oxidation-Reduction ; Radioactive Waste ; Soil/*chemistry ; Soil Microbiology ; Sulfur/metabolism ; Waste Disposal Facilities ; },
abstract = {Geological sequestration in deep underground repositories is the prevailing proposed route for radioactive waste disposal. After the disposal of radioactive waste in the subsurface, H2 may be produced by corrosion of steel and, ultimately, radionuclides will be exposed to the surrounding environment. To evaluate the potential for microbial activities to impact disposal systems, we explored the microbial community structure and metabolic functions of a sediment-hosted ecosystem at the Horonobe Underground Research Laboratory, Hokkaido, Japan. Overall, we found that the ecosystem hosted organisms from diverse lineages, including many from the phyla that lack isolated representatives. The majority of organisms can metabolize H2, often via oxidative [NiFe] hydrogenases or electron-bifurcating [FeFe] hydrogenases that enable ferredoxin-based pathways, including the ion motive Rnf complex. Many organisms implicated in H2 metabolism are also predicted to catalyze carbon, nitrogen, iron and sulfur transformations. Notably, iron-based metabolism is predicted in a novel lineage of Actinobacteria and in a putative methane-oxidizing ANME-2d archaeon. We infer an ecological model that links microorganisms to sediment-derived resources and predict potential impacts of microbial activity on H2 consumption and retardation of radionuclide migration.},
}
@article {pmid28344572,
year = {2017},
author = {van de Pol, JA and van Best, N and Mbakwa, CA and Thijs, C and Savelkoul, PH and Arts, IC and Hornef, MW and Mommers, M and Penders, J},
title = {Gut Colonization by Methanogenic Archaea Is Associated with Organic Dairy Consumption in Children.},
journal = {Frontiers in microbiology},
volume = {8},
number = {},
pages = {355},
pmid = {28344572},
issn = {1664-302X},
abstract = {The gut microbiota represents a complex and diverse ecosystem with a profound impact on human health, promoting immune maturation, and host metabolism as well as colonization resistance. Important members that have often been disregarded are the methanogenic archaea. Methanogenic archaea reduce hydrogen levels via the production of methane, thereby stimulating food fermentation by saccharolytic bacteria. On the other hand, colonization by archaea has been suggested to promote a number of gastrointestinal and metabolic diseases such as colorectal cancer, inflammatory bowel disease, and obesity. Archaea have been shown to be absent during infancy while omnipresent in school-aged children, suggesting that colonization may result from environmental exposure during childhood. The factors that determine the acquisition of methanogenic archaea, however, have remained undefined. Therefore, we aimed to explore determinants associated with the acquisition of the two main gastrointestinal archaeal species, Methanobrevibacter smithii and Methanosphaera stadtmanae, in children. Within the context of the KOALA Birth Cohort Study, fecal samples from 472 children aged 6-10 years were analyzed for the abundance of M. smithii and M. stadtmanae using qPCR. Environmental factors such as diet, lifestyle, hygiene, child rearing, and medication were recorded by repeated questionnaires. The relationship between these determinants and the presence and abundance of archaea was analyzed by logistic and linear regression respectively. Three hundred and sixty-nine out of the 472 children (78.2%) were colonized by M. smithii, and 39 out of the 472 children (8.3%) by M. stadtmanae. The consumption of organic yogurt (odds ratio: 4.25, CI95: 1.51; 11.95) and the consumption of organic milk (odds ratio: 5.58, CI95: 1.83; 17.01) were positively associated with the presence of M. smithii. We subsequently screened raw milk, processed milk, and yogurt samples for methanogens. We identified milk products as possible source for M. smithii, but not M. stadtmanae. In conclusion, M. smithii seems present in milk products and their consumption may determine archaeal gut colonization in children. For the first time, a large variety of determinants have been explored in association with gut colonization by methanogenic archaea. Although more information is needed to confirm and unravel the mechanisms in detail, it provides new insights on microbial colonization processes in early life.},
}
@article {pmid28340330,
year = {2017},
author = {Blombach, F and Grohmann, D},
title = {Same same but different: The evolution of TBP in archaea and their eukaryotic offspring.},
journal = {Transcription},
volume = {8},
number = {3},
pages = {162-168},
pmid = {28340330},
issn = {2154-1272},
mesh = {*Archaea/genetics/metabolism ; *Archaeal Proteins/genetics/metabolism ; DNA, Archaeal/genetics/metabolism ; DNA-Directed RNA Polymerases/genetics/metabolism ; *Evolution, Molecular ; Promoter Regions, Genetic/physiology ; *Transcription Factor TFIIB/metabolism ; },
abstract = {Transcription factors TBP and TF(II)B assemble with RNA polymerase at the promoter DNA forming the initiation complex. Despite a high degree of conservation, the molecular binding mechanisms of archaeal and eukaryotic TBP and TF(II)B differ significantly. Based on recent biophysical data, we speculate how the mechanisms co-evolved with transcription regulation and TBP multiplicity.},
}
@article {pmid28330764,
year = {2017},
author = {Eichler, J and Guan, Z},
title = {Lipid sugar carriers at the extremes: The phosphodolichols Archaea use in N-glycosylation.},
journal = {Biochimica et biophysica acta. Molecular and cell biology of lipids},
volume = {1862},
number = {6},
pages = {589-599},
pmid = {28330764},
issn = {1388-1981},
support = {R01 EY023666/EY/NEI NIH HHS/United States ; R01 GM120594/GM/NIGMS NIH HHS/United States ; U54 GM069338/GM/NIGMS NIH HHS/United States ; },
mesh = {Archaea/genetics/*metabolism ; Carbohydrates/genetics ; Dolichol Phosphates/genetics/*metabolism ; Glycosylation ; },
abstract = {N-glycosylation, a post-translational modification whereby glycans are covalently linked to select Asn residues of target proteins, occurs in all three domains of life. Across evolution, the N-linked glycans are initially assembled on phosphorylated cytoplasmically-oriented polyisoprenoids, with polyprenol (mainly C55 undecaprenol) fulfilling this role in Bacteria and dolichol assuming this function in Eukarya and Archaea. The eukaryal and archaeal versions of dolichol can, however, be distinguished on the basis of their length, degree of saturation and by other traits. As is true for many facets of their biology, Archaea, best known in their capacity as extremophiles, present unique approaches for synthesizing phosphodolichols. At the same time, general insight into the assembly and processing of glycan-bearing phosphodolichols has come from studies of the archaeal enzymes responsible. In this review, these and other aspects of archaeal phosphodolichol biology are addressed.},
}
@article {pmid28321126,
year = {2017},
author = {Lazar, CS and Baker, BJ and Seitz, KW and Teske, AP},
title = {Genomic reconstruction of multiple lineages of uncultured benthic archaea suggests distinct biogeochemical roles and ecological niches.},
journal = {The ISME journal},
volume = {11},
number = {4},
pages = {1058},
doi = {10.1038/ismej.2017.8},
pmid = {28321126},
issn = {1751-7370},
}
@article {pmid28321009,
year = {2017},
author = {McGlynn, SE},
title = {Energy Metabolism during Anaerobic Methane Oxidation in ANME Archaea.},
journal = {Microbes and environments},
volume = {32},
number = {1},
pages = {5-13},
pmid = {28321009},
issn = {1347-4405},
mesh = {Anaerobiosis ; Archaea/*metabolism ; *Energy Metabolism ; Metabolic Networks and Pathways ; Methane/*metabolism ; Oxidation-Reduction ; },
abstract = {Anaerobic methane oxidation in archaea is often presented to operate via a pathway of "reverse methanogenesis". However, if the cumulative reactions of a methanogen are run in reverse there is no apparent way to conserve energy. Recent findings suggest that chemiosmotic coupling enzymes known from their use in methylotrophic and acetoclastic methanogens-in addition to unique terminal reductases-biochemically facilitate energy conservation during complete CH4 oxidation to CO2. The apparent enzyme modularity of these organisms highlights how microbes can arrange their energy metabolisms to accommodate diverse chemical potentials in various ecological niches, even in the extreme case of utilizing "reverse" thermodynamic potentials.},
}
@article {pmid28286499,
year = {2017},
author = {Knüppel, R and Kuttenberger, C and Ferreira-Cerca, S},
title = {Toward Time-Resolved Analysis of RNA Metabolism in Archaea Using 4-Thiouracil.},
journal = {Frontiers in microbiology},
volume = {8},
number = {},
pages = {286},
pmid = {28286499},
issn = {1664-302X},
abstract = {Archaea are widespread organisms colonizing almost every habitat on Earth. However, the molecular biology of archaea still remains relatively uncharacterized. RNA metabolism is a central cellular process, which has been extensively analyzed in both bacteria and eukarya. In contrast, analysis of RNA metabolism dynamic in archaea has been limited to date. To facilitate analysis of the RNA metabolism dynamic at a system-wide scale in archaea, we have established non-radioactive pulse labeling of RNA, using the nucleotide analog 4-thiouracil (4TU) in two commonly used model archaea: the halophile Euryarchaeota Haloferax volcanii, and the thermo-acidophile Crenarchaeota Sulfolobus acidocaldarius. In this work, we show that 4TU pulse labeling can be efficiently performed in these two organisms in a dose- and time-dependent manner. In addition, our results suggest that uracil prototrophy had no critical impact on the overall 4TU incorporation in RNA molecules. Accordingly, our work suggests that 4TU incorporation can be widely performed in archaea, thereby expanding the molecular toolkit to analyze archaeal gene expression network dynamic in unprecedented detail.},
}
@article {pmid28270994,
year = {2017},
author = {Qi, X and Carberry, DM and Cai, C and Hu, S and Yuan, Z and Dunlop, HR and Guo, J},
title = {Optical sorting and cultivation of denitrifying anaerobic methane oxidation archaea.},
journal = {Biomedical optics express},
volume = {8},
number = {2},
pages = {934-942},
pmid = {28270994},
issn = {2156-7085},
abstract = {Denitrifying anaerobic methane oxidizing (DAMO) microorganisms play an important role in the global carbon and nitrogen cycles as they are able to mediate methane oxidation using nitrite/nitrate under anoxic conditions. However, the physiological properties of DAMO microorganisms remain poorly understood, partially since the organisms are difficult to isolate or cultivate in pure culture and partially because of their long cultivation time. In this study, DAMO cell sorting has been conducted by integrating optical tweezers within enclosed microfluidic chips. This integrated cell sorting method has high purity, low infection rates, and causes no discernable harm to cell viability. The purity of the sorted cells was controlled by the microfluidic chip structure design and operation, while the cell viability was verified by imaging the cultured DAMO archaea after 420 days.},
}
@article {pmid28261173,
year = {2017},
author = {Bhute, SS and Suryavanshi, MV and Joshi, SM and Yajnik, CS and Shouche, YS and Ghaskadbi, SS},
title = {Gut Microbial Diversity Assessment of Indian Type-2-Diabetics Reveals Alterations in Eubacteria, Archaea, and Eukaryotes.},
journal = {Frontiers in microbiology},
volume = {8},
number = {},
pages = {214},
pmid = {28261173},
issn = {1664-302X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {Diabetes in India has distinct genetic, nutritional, developmental and socio-economic aspects; owing to the fact that changes in gut microbiota are associated with diabetes, we employed semiconductor-based sequencing to characterize gut microbiota of diabetic subjects from this region. We suggest consolidated dysbiosis of eubacterial, archaeal and eukaryotic components in the gut microbiota of newly diagnosed (New-DMs) and long-standing diabetic subjects (Known-DMs) compared to healthy subjects (NGTs). Increased abundance of phylum Firmicutes (p = 0.010) and Operational Taxonomic Units (OTUs) of Lactobacillus (p < 0.01) were observed in Known-DMs subjects along with the concomitant graded decrease in butyrate-producing bacterial families like Ruminococcaceae and Lachnospiraceae. Eukaryotes and fungi were the least affected components in these subjects but archaea, except Methanobrevibacter were significantly decreased in them. The two dominant archaea viz. Methanobrevibacater and Methanosphaera followed opposite trends in abundance from NGTs to Known-DMs subjects. There was a substantial reduction in eubacteria, with a noticeable decrease in Bacteroidetes phylum (p = 0.098) and an increased abundance of fungi in New-DMs subjects. Likewise, opportunistic fungal pathogens such as Aspergillus, Candida were found to be enriched in New-DMs subjects. Analysis of eubacterial interaction network revealed disease-state specific patterns of ecological interactions, suggesting the distinct behavior of individual components of eubacteria in response to the disease. PERMANOVA test indicated that the eubacterial component was associated with diabetes-related risk factors like high triglyceride (p = 0.05), low HDL (p = 0.03), and waist-to-hip ratio (p = 0.02). Metagenomic imputation of eubacteria depict deficiencies of various essential functions such as carbohydrate metabolism, amino acid metabolism etc. in New-DMs subjects. Results presented here shows that in diabetes, microbial dysbiosis may not be just limited to eubacteria. Due to the inter-linked metabolic interactions among the eubacteria, archaea and eukarya in the gut, it may extend into other two domains leading to trans-domain dysbiosis in microbiota. Our results thus contribute to and expand the identification of biomarkers in diabetes.},
}
@article {pmid28249694,
year = {2017},
author = {Rosselló-Móra, R and Trujillo, ME and Sutcliffe, IC},
title = {Introducing a Digital Protologue: A timely move towards a database-driven systematics of Archaea and Bacteria.},
journal = {Systematic and applied microbiology},
volume = {40},
number = {3},
pages = {121-122},
doi = {10.1016/j.syapm.2017.02.001},
pmid = {28249694},
issn = {1618-0984},
mesh = {Archaea/*classification ; Bacteria/*classification ; *Databases, Factual ; Phylogeny ; },
}
@article {pmid28249125,
year = {2017},
author = {He, Y and Hu, W and Ma, D and Lan, H and Yang, Y and Gao, Y},
title = {Abundance and diversity of ammonia-oxidizing archaea and bacteria in the rhizosphere soil of three plants in the Ebinur Lake wetland.},
journal = {Canadian journal of microbiology},
volume = {63},
number = {7},
pages = {573-582},
doi = {10.1139/cjm-2016-0492},
pmid = {28249125},
issn = {1480-3275},
mesh = {Amaranthaceae ; Ammonia/*metabolism ; Archaea/*genetics/isolation &amp; purification/metabolism ; Asteraceae ; Bacteria/*genetics/isolation &amp; purification/metabolism ; Biodiversity ; China ; DNA, Ribosomal/chemistry/genetics ; Ecosystem ; Lakes ; Oxidation-Reduction ; Phylogeny ; Poaceae ; Rhizosphere ; Sequence Analysis, DNA ; Soil/chemistry ; *Soil Microbiology ; Wetlands ; },
abstract = {Ammonia oxidation is carried out by ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA). The Ebinur Lake wetland is the best example of a temperate arid zone wetland ecosystem in China. Soil samples were collected from rhizosphere and non-rhizosphere soil containing Halocnemum strobilaceum (samples H and H'), Phragmites australis (samples R and R'), and Karelinia caspia (samples K and K') to study the relationship between environmental factors and the community structure of AOB and AOA. Phylogenetic analysis showed that the AOA sequences belonged to the Nitrosopumilus and Nitrososphaera clusters. AOB were grouped into Nitrosospira sp. and Nitrosomonas sp. Quantitative polymerase chain reaction results showed that the AOA abundance ranged from 2.09 × 10[4] to 2.94 × 10[5] gene copies/g soil. The highest number of AOA was detected in sample K, followed by samples R and H. AOB abundance varied between 2.91 × 10[5] and 1.05 × 10[6] gene copies/g soil, which was higher than that of AOA. Redundancy analysis indicated that electrical conductivity, pH, and NH4[+]-N might influence the community structure of AOA and AOB. AOB might play a more crucial role than AOA in ammonia oxidation based on AOB's higher diversity and abundance in the Ebinur Lake wetland in Xinjiang.},
}
@article {pmid28229970,
year = {2017},
author = {Rani, SB and Balamurugan, R and Ramakrishna, BS},
title = {Molecular analysis of the human faecal archaea in a southern Indian population.},
journal = {Journal of biosciences},
volume = {42},
number = {1},
pages = {113-119},
pmid = {28229970},
issn = {0973-7138},
mesh = {Adolescent ; Adult ; Age Factors ; Aged ; Archaea/classification/*genetics/isolation &amp; purification ; Child ; Child, Preschool ; Feces/*microbiology ; Female ; Gastrointestinal Microbiome/*genetics ; Humans ; India ; Infant ; Infant, Newborn ; Male ; Methanobrevibacter/classification/*genetics/isolation &amp; purification ; Middle Aged ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Archaea are an important constituent of the human gut microbiota, but there is no information on human gut archaea in an Indian population. In this study, faecal samples were obtained from different age groups (neonatal babies, preschool children, school-going children, adolescents, adults and elderly) of a southern Indian population, and from a tribal population also resident in southern India). 16S rRNA gene sequences specific to Archaea were amplified from pooled faecal DNA in each group, sequenced, and aligned against the NCBI database. Of the 806 adequate sequences in the study, most aligned with 22 known sequences. There were 9 novel sequences in the present study. All sequences were deposited in the GenBank nucleotide sequence database with the following accession numbers: KF607113 - KF607918. Methanobrevibacter was the most prevalent genus among all the age groups accounting for 98% in neonates, 96% in post-weaning, and 100% each in preschool, school and adult population. In the elderly, Methanobrevibacter accounted for 96% and in tribal adults, 99% of the clones belonged to Methanobrevibacter genus. Other genera detected included Caldisphaera, Halobaculum, Methanosphaeraand Thermogymnomonas. Methanobrevibacter smithii predominated in all age groups, accounting for 749 (92.9%) of the 806 sequences. Archaea can be found in the faeces of southern Indian residents immediately after birth. Methanobrevibacter smithii was the dominant faecal archeon in all age groups, with other genera being found at the extremes of age.},
}
@article {pmid28221378,
year = {2017},
author = {Leriche, G and Cifelli, JL and Sibucao, KC and Patterson, JP and Koyanagi, T and Gianneschi, NC and Yang, J},
title = {Characterization of drug encapsulation and retention in archaea-inspired tetraether liposomes.},
journal = {Organic &amp; biomolecular chemistry},
volume = {15},
number = {10},
pages = {2157-2162},
doi = {10.1039/c6ob02832b},
pmid = {28221378},
issn = {1477-0539},
mesh = {Antineoplastic Agents/*analysis/*chemistry ; Archaea/*chemistry ; *Drug Compounding ; Humans ; KB Cells ; Lipids/chemistry ; Liposomes/chemical synthesis/*chemistry ; },
abstract = {The passive leakage of small molecules across membranes is a major limitation of liposomal drug formulations. Here, we evaluate the leakage of 3 clinically used chemotherapeutic agents (cytarabine, methotrexate and vincristine) encapsulated in liposomes comprised of a synthetic, archaea-inspired, membrane-spanning tetraether lipid. Liposomes comprised of the pure tetraether lipid exhibited superior retention of both a neutrally and positively charged drug (up to an ∼9-fold decrease in the rate of drug leakage) compared to liposomes formed from a commercial diacyl lipid, while exhibiting a similar retention of a negatively charged drug that did not appreciably leak from either type of liposome. We also demonstrate that liposomes made of the archaea-inspired lipid can be used for the delivery of encapsulated small molecules into living cells.},
}
@article {pmid28211189,
year = {2017},
author = {Qin, W and Meinhardt, KA and Moffett, JW and Devol, AH and Virginia Armbrust, E and Ingalls, AE and Stahl, DA},
title = {Influence of oxygen availability on the activities of ammonia-oxidizing archaea.},
journal = {Environmental microbiology reports},
volume = {9},
number = {3},
pages = {250-256},
doi = {10.1111/1758-2229.12525},
pmid = {28211189},
issn = {1758-2229},
mesh = {Ammonia/*metabolism ; Anaerobiosis/*physiology ; Archaea/growth &amp; development/*metabolism ; Hydrogen Peroxide/pharmacology ; Nitrous Oxide/*metabolism ; Oceans and Seas ; Oxidation-Reduction ; Oxygen/*metabolism ; },
abstract = {Recent studies point to the importance of oxygen (O2) in controlling the distribution and activity of marine ammonia-oxidizing archaea (AOA), one of the most abundant prokaryotes in the ocean. The AOA are associated with regions of low O2 tension in oceanic oxygen minimum zones (OMZs), and O2 availability is suggested to influence their production of the ozone-depleting greenhouse gas nitrous oxide (N2 O). We show that marine AOA available in pure culture sustain high ammonia oxidation activity at low μM O2 concentrations, characteristic of suboxic regions of OMZs (<10 µM O2), and that atmospheric concentrations of O2 may inhibit the growth of some environmental populations. We quantify the increasing N2 O production by marine AOA with decreasing O2 tensions, consistent with the plausibility of an AOA contribution to the accumulation of N2 O at the oxic-anoxic redox boundaries of OMZs. Variable sensitivity to peroxide also suggests that endogenous or exogenous reactive oxygen species are of importance in determining the environmental distribution of some populations.},
}
@article {pmid28194147,
year = {2017},
author = {Bartelme, RP and McLellan, SL and Newton, RJ},
title = {Freshwater Recirculating Aquaculture System Operations Drive Biofilter Bacterial Community Shifts around a Stable Nitrifying Consortium of Ammonia-Oxidizing Archaea and Comammox Nitrospira.},
journal = {Frontiers in microbiology},
volume = {8},
number = {},
pages = {101},
pmid = {28194147},
issn = {1664-302X},
abstract = {Recirculating aquaculture systems (RAS) are unique engineered ecosystems that minimize environmental perturbation by reducing nutrient pollution discharge. RAS typically employ a biofilter to control ammonia levels produced as a byproduct of fish protein catabolism. Nitrosomonas (ammonia-oxidizing), Nitrospira, and Nitrobacter (nitrite-oxidizing) species are thought to be the primary nitrifiers present in RAS biofilters. We explored this assertion by characterizing the biofilter bacterial and archaeal community of a commercial scale freshwater RAS that has been in operation for >15 years. We found the biofilter community harbored a diverse array of bacterial taxa (>1000 genus-level taxon assignments) dominated by Chitinophagaceae (~12%) and Acidobacteria (~9%). The bacterial community exhibited significant composition shifts with changes in biofilter depth and in conjunction with operational changes across a fish rearing cycle. Archaea also were abundant, and were comprised solely of a low diversity assemblage of Thaumarchaeota (>95%), thought to be ammonia-oxidizing archaea (AOA) from the presence of AOA ammonia monooxygenase genes. Nitrosomonas were present at all depths and time points. However, their abundance was >3 orders of magnitude less than AOA and exhibited significant depth-time variability not observed for AOA. Phylogenetic analysis of the nitrite oxidoreductase beta subunit (nxrB) gene indicated two distinct Nitrospira populations were present, while Nitrobacter were not detected. Subsequent identification of Nitrospira ammonia monooxygenase alpha subunit genes in conjunction with the phylogenetic placement and quantification of the nxrB genotypes suggests complete ammonia-oxidizing (comammox) and nitrite-oxidizing Nitrospira populations co-exist with relatively equivalent and stable abundances in this system. It appears RAS biofilters harbor complex microbial communities whose composition can be affected directly by typical system operations while supporting multiple ammonia oxidation lifestyles within the nitrifying consortium.},
}
@article {pmid28191504,
year = {2017},
author = {Ma, B and Dai, Z and Wang, H and Dsouza, M and Liu, X and He, Y and Wu, J and Rodrigues, JL and Gilbert, JA and Brookes, PC and Xu, J},
title = {Distinct Biogeographic Patterns for Archaea, Bacteria, and Fungi along the Vegetation Gradient at the Continental Scale in Eastern China.},
journal = {mSystems},
volume = {2},
number = {1},
pages = {},
pmid = {28191504},
issn = {2379-5077},
abstract = {The natural forest ecosystem in Eastern China, from tropical forest to boreal forest, has declined due to cropland development during the last 300 years, yet little is known about the historical biogeographic patterns and driving processes for the major domains of microorganisms along this continental-scale natural vegetation gradient. We predicted the biogeographic patterns of soil archaeal, bacterial, and fungal communities across 110 natural forest sites along a transect across four vegetation zones in Eastern China. The distance decay relationships demonstrated the distinct biogeographic patterns of archaeal, bacterial, and fungal communities. While historical processes mainly influenced bacterial community variations, spatially autocorrelated environmental variables mainly influenced the fungal community. Archaea did not display a distance decay pattern along the vegetation gradient. Bacterial community diversity and structure were correlated with the ratio of acid oxalate-soluble Fe to free Fe oxides (Feo/Fed ratio). Fungal community diversity and structure were influenced by dissolved organic carbon (DOC) and free aluminum (Ald), respectively. The role of these environmental variables was confirmed by the correlations between dominant operational taxonomic units (OTUs) and edaphic variables. However, most of the dominant OTUs were not correlated with the major driving variables for the entire communities. These results demonstrate that soil archaea, bacteria, and fungi have different biogeographic patterns and driving processes along this continental-scale natural vegetation gradient, implying different community assembly mechanisms and ecological functions for archaea, bacteria, and fungi in soil ecosystems. IMPORTANCE Understanding biogeographic patterns is a precursor to improving our knowledge of the function of microbiomes and to predicting ecosystem responses to environmental change. Using natural forest soil samples from 110 locations, this study is one of the largest attempts to comprehensively understand the different patterns of soil archaeal, bacterial, and fungal biogeography at the continental scale in eastern China. These patterns in natural forest sites could ascertain reliable soil microbial biogeographic patterns by eliminating anthropogenic influences. This information provides guidelines for monitoring the belowground ecosystem's decline and restoration. Meanwhile, the deviations in the soil microbial communities from corresponding natural forest states indicate the extent of degradation of the soil ecosystem. Moreover, given the association between vegetation type and the microbial community, this information could be used to predict the long-term response of the underground ecosystem to the vegetation distribution caused by global climate change.},
}
@article {pmid28188879,
year = {2017},
author = {Jin, D and Kang, K and Wang, H and Wang, Z and Xue, B and Wang, L and Xu, F and Peng, Q},
title = {Effects of dietary supplementation of active dried yeast on fecal methanogenic archaea diversity in dairy cows.},
journal = {Anaerobe},
volume = {44},
number = {},
pages = {78-86},
doi = {10.1016/j.anaerobe.2017.02.007},
pmid = {28188879},
issn = {1095-8274},
mesh = {Animals ; Archaea/classification/genetics/*isolation &amp; purification/metabolism ; *Biodiversity ; Cattle ; Diet/*methods ; *Dietary Supplements ; Feces/*microbiology ; High-Throughput Nucleotide Sequencing ; Methane/*metabolism ; Real-Time Polymerase Chain Reaction ; Yeast, Dried/*administration &amp; dosage ; },
abstract = {This study aimed to investigate the effects of dietary supplementation of different dosages of active dried yeast (ADY) on the fecal methanogenic archaea community of dairy cattle. Twelve multiparous, healthy, mid-lactating Holstein dairy cows (body weight: 584 ± 23.2 kg, milk produced: 26.3 ± 1.22 kg/d) were randomly assigned to one of three treatments (control, ADY2, and ADY4) according to body weight with four replicates per treatment. Cows in the control group were fed conventional rations without ADY supplementation, while cows in the ADY2 and ADY4 group were fed rations supplemented with ADY at 2 or 4 g/d/head. Real-time PCR analysis showed the populations of total methanogens in the feces were significantly decreased (P < 0.05) in the ADY4 group compared with control. High-throughput sequencing technology was applied to examine the differences in methanogenic archaea diversity in the feces of the three treatment groups. A total of 155,609 sequences were recovered (a mean of 12,967 sequences per sample) from the twelve fecal samples, which consisted of a number of operational taxonomic units (OTUs) ranging from 1451 to 1,733, were assigned to two phyla, four classes, five orders, five families and six genera. Bioinformatic analyses illustrated that the natural fecal archaeal community of the control group was predominated by Methanobrevibacter (86.9% of the total sequence reads) and Methanocorpusculum (10.4%), while the relative abundance of the remaining four genera were below 1% with Methanosphaera comprising 0.8%, Thermoplasma composing 0.4%, and the relative abundance of Candidatus Nitrososphaera and Halalkalicoccus being close to zero. At the genus level, the relative abundances of Methanocorpusculum and Thermoplasma were increased (P < 0.05) with increasing dosage of ADY. Conversely, the predominant methanogen genus Methanobrevibacter was decreased with ADY dosage (P < 0.05). Dietary supplementation of ADY had no significant effect (P > 0.05) on the abundances of genera unclassified, Candidatus Nitrososphaera, and Halalkalicoccus. In conclusion, supplementation of ADY to the rations of dairy cattle could alter the population sizes and composition of fecal methanogenic archaea in the feces of dairy cattle. The decrease in Methanobrevibacter happened with a commensurate increase in the genera Methanocorpusculum and Thermoplasma.},
}
@article {pmid28177649,
year = {2017},
author = {Thomas, L and Ram, H and Singh, VP},
title = {Evolutionary Relationships and Taxa-Specific Conserved Signature Indels Among Cellulases of Archaea, Bacteria, and Eukarya.},
journal = {Journal of computational biology : a journal of computational molecular cell biology},
volume = {24},
number = {10},
pages = {1029-1042},
doi = {10.1089/cmb.2016.0161},
pmid = {28177649},
issn = {1557-8666},
mesh = {Archaea/classification/*enzymology/genetics ; Bacteria/classification/*enzymology/genetics ; Cellulases/*genetics ; Eukaryota/classification/*enzymology/genetics ; *Evolution, Molecular ; *INDEL Mutation ; Phylogeny ; Substrate Specificity ; },
abstract = {The cellulases from different cellulolytic organisms have evolutionary relationships, which range from single-celled prokaryotes to the complex eukaryotes of the living world. This in silico analysis revealed the presence of a conserved cellulase domain along with evolutionary relationships among cellulases from several species of Archaea, Bacteria, and Eukarya. The amino acid sequences of cellulases from Archaea and Bacteria showed closer identity with their domain or phylum members that provided insights into convergent and divergent evolution of cellulases from other enzymes with different substrate specificities. Evolutionary relatedness was also observed in phylogenetic trees among a number of cellulase sequences of diverse taxa. In cellulases, propensity for alanine, glycine, leucine, serine, and threonine was high, but low for cysteine, histidine, and methionine. Catalytic aspartic acid had a higher propensity than glutamic acid, and both were involved in regular expression patterns. Characteristic group and multigroup-specific conserved signature indels located in the catalytic domains of cellulases were observed that further clarified evolutionary relationships. These indels can be distinctive molecular tools for understanding phylogeny and identification of unknown cellulolytic species of common evolutionary descent in different environments.},
}
@article {pmid28174314,
year = {2017},
author = {Yan, Z and Wang, M and Ferry, JG},
title = {A Ferredoxin- and F420H2-Dependent, Electron-Bifurcating, Heterodisulfide Reductase with Homologs in the Domains Bacteria and Archaea.},
journal = {mBio},
volume = {8},
number = {1},
pages = {},
pmid = {28174314},
issn = {2150-7511},
mesh = {Anaerobiosis ; Electron Transport ; Escherichia coli/genetics/*metabolism ; Ferredoxins/*metabolism ; Gene Expression ; Methane/metabolism ; Methanosarcina/*enzymology/genetics ; Oxidation-Reduction ; Oxidoreductases/*genetics/*metabolism ; Riboflavin/*analogs &amp; derivatives/metabolism ; Sequence Homology ; },
abstract = {UNLABELLED: Heterodisulfide reductases (Hdr) of the HdrABC class are ancient enzymes and a component of the anaerobic core belonging to the prokaryotic common ancestor. The ancient origin is consistent with the widespread occurrence of genes encoding putative HdrABC homologs in metabolically diverse prokaryotes predicting diverse physiological functions; however, only one HdrABC has been characterized and that was from a narrow metabolic group of obligate CO2-reducing methanogenic anaerobes (methanogens) from the domain Archaea Here we report the biochemical characterization of an HdrABC homolog (HdrA2B2C2) from the acetate-utilizing methanogen Methanosarcina acetivorans with unusual properties structurally and functionally distinct from the only other HdrABC characterized. Homologs of the HdrA2B2C2 archetype are present in phylogenetically and metabolically diverse species from the domains Bacteria and Archaea The expression of the individual HdrA2, HdrB2, and HdrB2C2 enzymes in Escherichia coli, and reconstitution of an active HdrA2B2C2 complex, revealed an intersubunit electron transport pathway dependent on ferredoxin or coenzyme F420 (F420H2) as an electron donor. Remarkably, HdrA2B2C2 couples the previously unknown endergonic oxidation of F420H2 and reduction of ferredoxin with the exergonic oxidation of F420H2 and reduction of the heterodisulfide of coenzyme M and coenzyme B (CoMS-SCoB). The unique electron bifurcation predicts a role for HdrA2B2C2 in Fe(III)-dependent anaerobic methane oxidation (ANME) by M. acetivorans and uncultured species from ANME environments. HdrA2B2C2, ubiquitous in acetotrophic methanogens, was shown to participate in electron transfer during acetotrophic growth of M. acetivorans and proposed to be essential for growth in the environment when acetate is limiting.<br><br>IMPORTANCE: Discovery of the archetype HdrA2B2C2 heterodisulfide reductase with categorically unique properties extends the understanding of this ancient family beyond CO2-reducing methanogens to include diverse prokaryotes from the domains Bacteria and Archaea The unprecedented coenzyme F420-dependent electron bifurcation, an emerging fundamental principle of energy conservation, predicts a role for HdrA2B2C2 in diverse metabolisms, including anaerobic CH4-oxidizing pathways. The results document an electron transport role for HdrA2B2C2 in acetate-utilizing methanogens responsible for at least two-thirds of the methane produced in Earth's biosphere. The previously unavailable heterologous production of individual subunits and the reconstitution of HdrA2B2C2 with activity have provided an understanding of intersubunit electron transfer in the HdrABC class and a platform for investigating the principles of electron bifurcation.},
}
@article {pmid28168565,
year = {2017},
author = {Rosselló-Móra, R and Trujillo, ME and Sutcliffe, IC},
title = {Introducing a digital protologue: a timely move towards a database-driven systematics of archaea and bacteria.},
journal = {Antonie van Leeuwenhoek},
volume = {110},
number = {4},
pages = {455-456},
doi = {10.1007/s10482-017-0841-7},
pmid = {28168565},
issn = {1572-9699},
mesh = {Archaea/*classification/genetics ; Bacteria/*classification/genetics ; Classification/*methods ; Databases as Topic ; Phylogeny ; },
}
@article {pmid28154498,
year = {2017},
author = {Timmers, PH and Welte, CU and Koehorst, JJ and Plugge, CM and Jetten, MS and Stams, AJ},
title = {Reverse Methanogenesis and Respiration in Methanotrophic Archaea.},
journal = {Archaea (Vancouver, B.C.)},
volume = {2017},
number = {},
pages = {1654237},
pmid = {28154498},
issn = {1472-3654},
mesh = {Anaerobiosis ; Archaea/*metabolism ; Methane/*metabolism ; Oxidation-Reduction ; },
abstract = {Anaerobic oxidation of methane (AOM) is catalyzed by anaerobic methane-oxidizing archaea (ANME) via a reverse and modified methanogenesis pathway. Methanogens can also reverse the methanogenesis pathway to oxidize methane, but only during net methane production (i.e., "trace methane oxidation"). In turn, ANME can produce methane, but only during net methane oxidation (i.e., enzymatic back flux). Net AOM is exergonic when coupled to an external electron acceptor such as sulfate (ANME-1, ANME-2abc, and ANME-3), nitrate (ANME-2d), or metal (oxides). In this review, the reversibility of the methanogenesis pathway and essential differences between ANME and methanogens are described by combining published information with domain based (meta)genome comparison of archaeal methanotrophs and selected archaea. These differences include abundances and special structure of methyl coenzyme M reductase and of multiheme cytochromes and the presence of menaquinones or methanophenazines. ANME-2a and ANME-2d can use electron acceptors other than sulfate or nitrate for AOM, respectively. Environmental studies suggest that ANME-2d are also involved in sulfate-dependent AOM. ANME-1 seem to use a different mechanism for disposal of electrons and possibly are less versatile in electron acceptors use than ANME-2. Future research will shed light on the molecular basis of reversal of the methanogenic pathway and electron transfer in different ANME types.},
}
@article {pmid28146124,
year = {2017},
author = {Ausiannikava, D and Allers, T},
title = {Diversity of DNA Replication in the Archaea.},
journal = {Genes},
volume = {8},
number = {2},
pages = {},
pmid = {28146124},
issn = {2073-4425},
abstract = {DNA replication is arguably the most fundamental biological process. On account of their shared evolutionary ancestry, the replication machinery found in archaea is similar to that found in eukaryotes. DNA replication is initiated at origins and is highly conserved in eukaryotes, but our limited understanding of archaea has uncovered a wide diversity of replication initiation mechanisms. Archaeal origins are sequence-based, as in bacteria, but are bound by initiator proteins that share homology with the eukaryotic origin recognition complex subunit Orc1 and helicase loader Cdc6). Unlike bacteria, archaea may have multiple origins per chromosome and multiple Orc1/Cdc6 initiator proteins. There is no consensus on how these archaeal origins are recognised- some are bound by a single Orc1/Cdc6 protein while others require a multi- Orc1/Cdc6 complex. Many archaeal genomes consist of multiple parts-the main chromosome plus several megaplasmids-and in polyploid species these parts are present in multiple copies. This poses a challenge to the regulation of DNA replication. However, one archaeal species (Haloferax volcanii) can survive without replication origins; instead, it uses homologous recombination as an alternative mechanism of initiation. This diversity in DNA replication initiation is all the more remarkable for having been discovered in only three groups of archaea where in vivo studies are possible.},
}
@article {pmid28140393,
year = {2017},
author = {Mamet, SD and Lamb, EG and Piper, CL and Winsley, T and Siciliano, SD},
title = {Archaea and bacteria mediate the effects of native species root loss on fungi during plant invasion.},
journal = {The ISME journal},
volume = {11},
number = {5},
pages = {1261-1275},
pmid = {28140393},
issn = {1751-7370},
mesh = {Archaea/classification/*isolation &amp; purification ; Bacteria/classification/*isolation &amp; purification ; Biodiversity ; Bromus/microbiology ; Fungi/classification/*isolation &amp; purification ; Introduced Species ; Microbial Interactions ; Plant Roots/*microbiology ; *Soil Microbiology ; },
abstract = {Although invasive plants can drive ecosystem change, little is known about the directional nature of belowground interactions between invasive plants, native roots, bacteria, archaea and fungi. We used detailed bioinformatics and a recently developed root assay on soils collected in fescue grassland along a gradient of smooth brome (Bromus inermis Leyss) invasion to examine the links between smooth brome shoot litter and root, archaea, bacteria and fungal communities. We examined (1) aboveground versus belowground influences of smooth brome on soil microbial communities, (2) the importance of direct versus microbe-mediated impacts of plants on soil fungal communities, and (3) the web of roots, shoots, archaea, bacteria and fungi interactions across the A and B soil horizons in invaded and non-invaded sites. Archaea and bacteria influenced fungal composition, but not vice versa, as indicated by redundancy analyses. Co-inertia analyses suggested that bacterial-fungal variance was driven primarily by 12 bacterial operational taxonomic units (OTUs). Brome increased bacterial diversity via smooth brome litter in the A horizon and roots in the B horizon, which then reduced fungal diversity. Archaea increased abundance of several bacterial OTUs, and the key bacterial OTUs mediated changes in the fungi's response to invasion. Overall, native root diversity loss and bacterial mediation were more important drivers of fungal composition than were the direct effects of increases in smooth brome. Critically, native plant species displacement and root loss appeared to be the most important driver of fungal composition during invasion. This causal web likely gives rise to the plant-fungi feedbacks, which are an essential factor determining plant diversity in invaded grassland ecosystems.},
}
@article {pmid28133437,
year = {2017},
author = {Thor, S and Peterson, JR and Luthey-Schulten, Z},
title = {Genome-Scale Metabolic Modeling of Archaea Lends Insight into Diversity of Metabolic Function.},
journal = {Archaea (Vancouver, B.C.)},
volume = {2017},
number = {},
pages = {9763848},
pmid = {28133437},
issn = {1472-3654},
mesh = {Computational Biology ; Euryarchaeota/*metabolism ; *Metabolic Networks and Pathways ; *Models, Biological ; },
abstract = {Decades of biochemical, bioinformatic, and sequencing data are currently being systematically compiled into genome-scale metabolic reconstructions (GEMs). Such reconstructions are knowledge-bases useful for engineering, modeling, and comparative analysis. Here we review the fifteen GEMs of archaeal species that have been constructed to date. They represent primarily members of the Euryarchaeota with three-quarters comprising representative of methanogens. Unlike other reviews on GEMs, we specially focus on archaea. We briefly review the GEM construction process and the genealogy of the archaeal models. The major insights gained during the construction of these models are then reviewed with specific focus on novel metabolic pathway predictions and growth characteristics. Metabolic pathway usage is discussed in the context of the composition of each organism's biomass and their specific energy and growth requirements. We show how the metabolic models can be used to study the evolution of metabolism in archaea. Conservation of particular metabolic pathways can be studied by comparing reactions using the genes associated with their enzymes. This demonstrates the utility of GEMs to evolutionary studies, far beyond their original purpose of metabolic modeling; however, much needs to be done before archaeal models are as extensively complete as those for bacteria.},
}
@article {pmid28115203,
year = {2017},
author = {Michel, CJ},
title = {WITHDRAWN: The maximal C[3] self-complementary trinucleotide circular code X in genes of bacteria, archaea, eukaryotes, plasmids and viruses.},
journal = {Journal of theoretical biology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jtbi.2017.01.028},
pmid = {28115203},
issn = {1095-8541},
}
@article {pmid28104666,
year = {2017},
author = {Buongiorno, J and Turner, S and Webster, G and Asai, M and Shumaker, AK and Roy, T and Weightman, A and Schippers, A and Lloyd, KG},
title = {Interlaboratory quantification of Bacteria and Archaea in deeply buried sediments of the Baltic Sea (IODP Expedition 347).},
journal = {FEMS microbiology ecology},
volume = {93},
number = {3},
pages = {},
doi = {10.1093/femsec/fix007},
pmid = {28104666},
issn = {1574-6941},
mesh = {Archaea/*genetics/growth &amp; development ; Bacteria/*genetics/growth &amp; development ; *Colony Count, Microbial ; DNA Primers ; Expeditions ; Geologic Sediments/*microbiology ; In Situ Hybridization, Fluorescence/methods ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; *Water Microbiology ; },
abstract = {Two common quantification methods for subseafloor microorganisms are catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH) and quantitative PCR (qPCR). Using these methods, we quantified Bacteria and Archaea in Baltic Sea basin sediments (IODP Exp. 347) down to 90 mbsf, testing the following hypotheses in an interlaboratory comparison: (1) proteinase K permeabilization of archaeal cell walls increases CARD-FISH accuracy and (2) qPCR varies by more than an order of magnitude between laboratories using similar protocols. CARD-FISH counts did not differ between permeabilization treatments, demonstrating that proteinase K did not increase accuracy of CARD-FISH counts. However, 91% of these counts were below the quantification limit of 1.3 × 107 cells cm-3. For qPCR, data varied between laboratories, but were largely within the same order of magnitude if the same primers were used, with 88% of samples being above the quantification limit. Copy number values were elevated by preparing a sediment slurry before DNA extraction: 3.88 × 106-2.34 × 109 16S rRNA gene copies cm-3 vs. 1.39 × 107-1.87 × 109 total cells cm-3. By qPCR, Bacteria were more abundant than Archaea, although they usually were within the same order of magnitude. Overall, qPCR is more sensitive than CARD-FISH, but both require optimization to consistently achieve both precision and accuracy.},
}
@article {pmid28085154,
year = {2017},
author = {Lazar, CS and Baker, BJ and Seitz, KW and Teske, AP},
title = {Genomic reconstruction of multiple lineages of uncultured benthic archaea suggests distinct biogeochemical roles and ecological niches.},
journal = {The ISME journal},
volume = {11},
number = {5},
pages = {1118-1129},
pmid = {28085154},
issn = {1751-7370},
support = {247153/ERC_/European Research Council/International ; },
mesh = {Acetyl Coenzyme A/metabolism ; Archaea/classification/*genetics/isolation &amp; purification/metabolism ; Carbon Cycle ; Ecosystem ; Estuaries ; *Genome, Archaeal ; Genomics ; Geologic Sediments/*microbiology ; Phylogeny ; Rivers ; },
abstract = {Genomic bins belonging to multiple archaeal lineages were recovered from distinct redox regimes in sediments of the White Oak River estuary. The reconstructed archaeal genomes were identified as belonging to the rice cluster subgroups III and V (RC-III, RC-V), the Marine Benthic Group D (MBG-D), and a newly described archaeal class, the Theionarchaea. The metabolic capabilities of these uncultured archaea were inferred and indicated a common capability for extracellular protein degradation, supplemented by other pathways. The multiple genomic bins within the MBG-D archaea shared a nearly complete reductive acetyl-CoA pathway suggesting acetogenic capabilities. In contrast, the RC-III metabolism appeared centered on the degradation of detrital proteins and production of H2, whereas the RC-V archaea lacked capabilities for protein degradation and uptake, and appeared to be specialized on carbohydrate fermentation. The Theionarchaea appeared as complex metabolic hybrids; encoding a complete tricarboxylic acid cycle permitting carbon (acetyl-CoA) oxidation, together with a complete reductive acetyl-CoA pathway and sulfur reduction by a sulfhydrogenase. The differentiated inferred capabilities of these uncultured archaeal lineages indicated lineage-specific linkages with the nitrogen, carbon and sulfur cycles. The predicted metabolisms of these archaea suggest preferences for distinct geochemical niches within the estuarine sedimentary environment.},
}
@article {pmid28082747,
year = {2017},
author = {Kono, T and Mehrotra, S and Endo, C and Kizu, N and Matusda, M and Kimura, H and Mizohata, E and Inoue, T and Hasunuma, T and Yokota, A and Matsumura, H and Ashida, H},
title = {A RuBisCO-mediated carbon metabolic pathway in methanogenic archaea.},
journal = {Nature communications},
volume = {8},
number = {},
pages = {14007},
pmid = {28082747},
issn = {2041-1723},
mesh = {Archaeal Proteins/chemistry/genetics/*metabolism ; Carbon/metabolism ; Euryarchaeota/classification/*enzymology/genetics/metabolism ; Metabolic Networks and Pathways ; Phosphotransferases (Alcohol Group Acceptor)/chemistry/genetics/metabolism ; Photosynthesis ; Phylogeny ; Ribulose-Bisphosphate Carboxylase/chemistry/genetics/*metabolism ; },
abstract = {Two enzymes are considered to be unique to the photosynthetic Calvin-Benson cycle: ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO), responsible for CO2 fixation, and phosphoribulokinase (PRK). Some archaea possess bona fide RuBisCOs, despite not being photosynthetic organisms, but are thought to lack PRK. Here we demonstrate the existence in methanogenic archaea of a carbon metabolic pathway involving RuBisCO and PRK, which we term 'reductive hexulose-phosphate' (RHP) pathway. These archaea possess both RuBisCO and a catalytically active PRK whose crystal structure resembles that of photosynthetic bacterial PRK. Capillary electrophoresis-mass spectrometric analysis of metabolites reveals that the RHP pathway, which differs from the Calvin-Benson cycle only in a few steps, is active in vivo. Our work highlights evolutionary and functional links between RuBisCO-mediated carbon metabolic pathways in methanogenic archaea and photosynthetic organisms. Whether the RHP pathway allows for autotrophy (that is, growth exclusively with CO2 as carbon source) remains unknown.},
}
@article {pmid28077874,
year = {2017},
author = {Zaremba-Niedzwiedzka, K and Caceres, EF and Saw, JH and Bäckström, D and Juzokaite, L and Vancaester, E and Seitz, KW and Anantharaman, K and Starnawski, P and Kjeldsen, KU and Stott, MB and Nunoura, T and Banfield, JF and Schramm, A and Baker, BJ and Spang, A and Ettema, TJ},
title = {Asgard archaea illuminate the origin of eukaryotic cellular complexity.},
journal = {Nature},
volume = {541},
number = {7637},
pages = {353-358},
pmid = {28077874},
issn = {1476-4687},
mesh = {Archaea/classification/*cytology/*genetics ; Archaeal Proteins/genetics/metabolism ; Biological Transport/genetics ; COP-Coated Vesicles/metabolism ; Eukaryota/classification/*cytology/genetics ; Eukaryotic Cells/classification/*cytology/metabolism ; *Evolution, Molecular ; Genome, Archaeal/*genetics ; Metagenomics ; *Models, Biological ; *Phylogeny ; },
abstract = {The origin and cellular complexity of eukaryotes represent a major enigma in biology. Current data support scenarios in which an archaeal host cell and an alphaproteobacterial (mitochondrial) endosymbiont merged together, resulting in the first eukaryotic cell. The host cell is related to Lokiarchaeota, an archaeal phylum with many eukaryotic features. The emergence of the structural complexity that characterizes eukaryotic cells remains unclear. Here we describe the 'Asgard' superphylum, a group of uncultivated archaea that, as well as Lokiarchaeota, includes Thor-, Odin- and Heimdallarchaeota. Asgard archaea affiliate with eukaryotes in phylogenomic analyses, and their genomes are enriched for proteins formerly considered specific to eukaryotes. Notably, thorarchaeal genomes encode several homologues of eukaryotic membrane-trafficking machinery components, including Sec23/24 and TRAPP domains. Furthermore, we identify thorarchaeal proteins with similar features to eukaryotic coat proteins involved in vesicle biogenesis. Our results expand the known repertoire of 'eukaryote-specific' proteins in Archaea, indicating that the archaeal host cell already contained many key components that govern eukaryotic cellular complexity.},
}
@article {pmid28073944,
year = {2017},
author = {Rodionova, IA and Vetting, MW and Li, X and Almo, SC and Osterman, AL and Rodionov, DA},
title = {A novel bifunctional transcriptional regulator of riboflavin metabolism in Archaea.},
journal = {Nucleic acids research},
volume = {45},
number = {7},
pages = {3785-3799},
pmid = {28073944},
issn = {1362-4962},
support = {P30 CA030199/CA/NCI NIH HHS/United States ; },
mesh = {Archaea/enzymology/*genetics/metabolism ; Archaeal Proteins/chemistry/*metabolism ; DNA, Archaeal/chemistry/metabolism ; Evolution, Molecular ; Genome, Archaeal ; Operator Regions, Genetic ; Phosphotransferases (Alcohol Group Acceptor)/chemistry/*metabolism ; Protein Domains ; Regulon ; Riboflavin/*metabolism ; Transcription Factors/chemistry/*metabolism ; },
abstract = {Riboflavin (vitamin B2) is the precursor of flavin mononucleotide (FMN) and flavin adenine dinucleotide, which are essential coenzymes in all free-living organisms. Riboflavin biosynthesis in many Bacteria but not in Archaea is controlled by FMN-responsive riboswitches. We identified a novel bifunctional riboflavin kinase/regulator (RbkR), which controls riboflavin biosynthesis and transport genes in major lineages of Crenarchaeota, Euryarchaeota and Thaumarchaeota. RbkR proteins are composed of the riboflavin kinase domain and a DNA-binding winged helix-turn-helix-like domain. Using comparative genomics, we predicted RbkR operator sites and reconstructed RbkR regulons in 94 archaeal genomes. While the identified RbkR operators showed significant variability between archaeal lineages, the conserved core of RbkR regulons includes riboflavin biosynthesis genes, known/predicted vitamin uptake transporters and the rbkR gene. The DNA motifs and CTP-dependent riboflavin kinase activity of two RbkR proteins were experimentally validated in vitro. The DNA binding activity of RbkR was stimulated by CTP and suppressed by FMN, a product of riboflavin kinase. The crystallographic structure of RbkR from Thermoplasma acidophilum was determined in complex with CTP and its DNA operator revealing key residues for operator and ligand recognition. Overall, this study contributes to our understanding of metabolic and regulatory networks for vitamin homeostasis in Archaea.},
}
@article {pmid28070167,
year = {2016},
author = {Ma, Y and Liu, F and Kong, Z and Yin, J and Kou, W and Wu, L and Ge, G},
title = {The Distribution Pattern of Sediment Archaea Community of the Poyang Lake, the Largest Freshwater Lake in China.},
journal = {Archaea (Vancouver, B.C.)},
volume = {2016},
number = {},
pages = {9278929},
pmid = {28070167},
issn = {1472-3654},
mesh = {Archaea/*classification/genetics ; *Biota ; China ; Cluster Analysis ; DNA, Archaeal/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Fresh Water/*microbiology ; Geologic Sediments/*microbiology ; Lakes/*microbiology ; Phylogeography ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Spatial Analysis ; },
abstract = {Archaea plays an important role in the global geobiochemical circulation of various environments. However, much less is known about the ecological role of archaea in freshwater lake sediments. Thus, investigating the structure and diversity of archaea community is vital to understand the metabolic processes in freshwater lake ecosystems. In this study, sediment physicochemical properties were combined with the results from 16S rRNA clone library-sequencing to examine the sediment archaea diversity and the environmental factors driving the sediment archaea community structures. Seven sites were chosen from Poyang Lake, including two sites from the main lake body and five sites from the inflow river estuaries. Our results revealed high diverse archaea community in the sediment of Poyang Lake, including Bathyarchaeota (45.5%), Euryarchaeota (43.1%), Woesearchaeota (3.6%), Pacearchaeota (1.7%), Thaumarchaeota (1.4%), suspended Lokiarchaeota (0.7%), Aigarchaeota (0.2%), and Unclassified Archaea (3.8%). The archaea community compositions differed among sites, and sediment property had considerable influence on archaea community structures and distribution, especially total organic carbon (TOC) and metal lead (Pb) (p < 0.05). This study provides primary profile of sediment archaea distribution in freshwater lakes and helps to deepen our understanding of lake sediment microbes.},
}
@article {pmid28053595,
year = {2016},
author = {Prunetti, L and Graf, M and Blaby, IK and Peil, L and Makkay, AM and Starosta, AL and Papke, RT and Oshima, T and Wilson, DN and de Crécy-Lagard, V},
title = {Deciphering the Translation Initiation Factor 5A Modification Pathway in Halophilic Archaea.},
journal = {Archaea (Vancouver, B.C.)},
volume = {2016},
number = {},
pages = {7316725},
pmid = {28053595},
issn = {1472-3654},
support = {R01 GM070641/GM/NIGMS NIH HHS/United States ; },
mesh = {Archaeal Proteins/*metabolism ; Chromatography, Liquid ; Haloferax volcanii/*enzymology/*metabolism ; Lysine/*analogs &amp; derivatives/metabolism ; Peptide Initiation Factors/*metabolism ; *Protein Processing, Post-Translational ; Tandem Mass Spectrometry ; },
abstract = {Translation initiation factor 5A (IF5A) is essential and highly conserved in Eukarya (eIF5A) and Archaea (aIF5A). The activity of IF5A requires hypusine, a posttranslational modification synthesized in Eukarya from the polyamine precursor spermidine. Intracellular polyamine analyses revealed that agmatine and cadaverine were the main polyamines produced in Haloferax volcanii in minimal medium, raising the question of how hypusine is synthesized in this halophilic Archaea. Metabolic reconstruction led to a tentative picture of polyamine metabolism and aIF5A modification in Hfx. volcanii that was experimentally tested. Analysis of aIF5A from Hfx. volcanii by LC-MS/MS revealed it was exclusively deoxyhypusinylated. Genetic studies confirmed the role of the predicted arginine decarboxylase gene (HVO_1958) in agmatine synthesis. The agmatinase-like gene (HVO_2299) was found to be essential, consistent with a role in aIF5A modification predicted by physical clustering evidence. Recombinant deoxyhypusine synthase (DHS) from S. cerevisiae was shown to transfer 4-aminobutyl moiety from spermidine to aIF5A from Hfx. volcanii in vitro. However, at least under conditions tested, this transfer was not observed with the Hfx. volcanii DHS. Furthermore, the growth of Hfx. volcanii was not inhibited by the classical DHS inhibitor GC7. We propose a model of deoxyhypusine synthesis in Hfx. volcanii that differs from the canonical eukaryotic pathway, paving the way for further studies.},
}
@article {pmid28029780,
year = {2017},
author = {Srivastava, SS and Jamkhindikar, AA and Raman, R and Jobby, MK and Chadalawada, S and Sankaranarayanan, R and Sharma, Y},
title = {A Transition Metal-Binding, Trimeric βγ-Crystallin from Methane-Producing Thermophilic Archaea, Methanosaeta thermophila.},
journal = {Biochemistry},
volume = {56},
number = {9},
pages = {1299-1310},
doi = {10.1021/acs.biochem.6b00985},
pmid = {28029780},
issn = {1520-4995},
mesh = {Archaea/*metabolism ; Methane/biosynthesis ; Models, Molecular ; *Protein Multimerization ; Protein Structure, Quaternary ; Temperature ; Transition Elements/*metabolism ; beta-Crystallins/*chemistry/*metabolism ; gamma-Crystallins/*chemistry/*metabolism ; },
abstract = {βγ-Crystallins are important constituents of the vertebrate eye lens, whereas in microbes, they are prevalent as Ca[2+]-binding proteins. In archaea, βγ-crystallins are conspicuously confined to two methanogens, viz., Methanosaeta and Methanosarcina. One of these, i.e., M-crystallin from Methanosarcina acetivorans, has been shown to be a typical Ca[2+]-binding βγ-crystallin. Here, with the aid of a high-resolution crystal structure and isothermal titration calorimetry, we report that "Methallin", a βγ-crystallin from Methanosaeta thermophila, is a trimeric, transition metal-binding protein. It binds Fe, Ni, Co, or Zn ion with nanomolar affinity, which is consistent even at 55 °C, the optimal temperature for the methanogen's growth. At the center of the protein trimer, the metal ion is coordinated by six histidines, two from each protomer, leading to an octahedral geometry. Small-angle X-ray scattering analysis confirms that the trimer seen in the crystal lattice is a biological assembly; this assembly dissociates to monomers upon removal of the metal ion. The introduction of two histidines (S17H/S19H) into a homologous βγ-crystallin, Clostrillin, allows it to bind nickel at the introduced site, though with micromolar affinity. However, because of the lack of a compatible interface, nickel binding could not induce trimerization, affirming that Methallin is a naturally occurring trimer for high-affinity transition metal binding. While βγ-crystallins are known to bind Ca[2+] and form homodimers and oligomers, the transition metal-binding, trimeric Methallin is a new paradigm for βγ-crystallins. The distinct features of Methallin, such as nickel or iron binding, are also possible imprints of biogeochemical changes during the period of its origin.},
}
@article {pmid28018603,
year = {2017},
author = {Khelaifia, S and Caputo, A and Djossou, F and Raoult, D},
title = {Draft genome sequence of a human-associated isolate of Haloferax alexandrinus strain Arc-hr, an extremely halophilic archaea.},
journal = {New microbes and new infections},
volume = {15},
number = {},
pages = {44-45},
pmid = {28018603},
issn = {2052-2975},
abstract = {We report the draft genome sequence of Haloferax alexandrinus strain Arc-hr (CSUR P798), isolated from the human gut of a 10-year-old Amazonian individual. Its 3 893 626 bp genome exhibits a 66.00% GC content. The genome of the strain Arc-hr contains 37 genes identified as ORFans, seven genes associated to halocin and 11 genes associated with polyketide synthases or nonribosomal peptide synthetases.},
}
@article {pmid27998783,
year = {2017},
author = {Ding, J and Lu, YZ and Fu, L and Ding, ZW and Mu, Y and Cheng, SH and Zeng, RJ},
title = {Decoupling of DAMO archaea from DAMO bacteria in a methane-driven microbial fuel cell.},
journal = {Water research},
volume = {110},
number = {},
pages = {112-119},
doi = {10.1016/j.watres.2016.12.006},
pmid = {27998783},
issn = {1879-2448},
mesh = {Anaerobiosis ; Archaea/*genetics ; Bacteria/metabolism ; Bioelectric Energy Sources ; In Situ Hybridization, Fluorescence ; Methane/metabolism ; Methylococcaceae/*metabolism ; Oxidation-Reduction ; },
abstract = {Anaerobic oxidation of methane (AOM) contributes significantly to the global methane sink. Previously, studies of anaerobic methanotrophic (ANME) archaea have been limited as they have not been separable from their bacterial partners during the AOM process because of their dependence on the bacteria. A microbial fuel cell (MFC) is a device capable of directly transforming chemical energy to electrical energy via electrochemical reactions involving biochemical pathways. In this study, decoupling of denitrifying anaerobic methane oxidation (DAMO) archaea and DAMO bacteria was investigated in an microbial fuel cell (MFC) using methane as the fuel. The DAMO fuel cell worked successfully but demonstrated weak electrogenic capability with around 25 mV production. After 45 days' enrichment, the sequencing and fluorescence in situ hybridization results showed the DAMO archaea percentage had increased from 26.96% (inoculum) to 65.77% (electrode biofilm), while the DAMO bacteria percentage decreased from 24.39% to 2.07%. Moreover, the amount of ANME-2d had doubled in the electrode biofilm compared with the inoculum. The sequencing results also showed substantial enrichment of the Ignavibacterium and Geobacter genera. The roles of Ignavibacterium and Geobacter in the MFC system need to be further investigated. Nevertheless, these results illustrate that an MFC device may provide a possible approach to separate DAMO archaea from DAMO bacteria.},
}
@article {pmid27996979,
year = {2017},
author = {Taylor, AE and Giguere, AT and Zoebelein, CM and Myrold, DD and Bottomley, PJ},
title = {Modeling of soil nitrification responses to temperature reveals thermodynamic differences between ammonia-oxidizing activity of archaea and bacteria.},
journal = {The ISME journal},
volume = {11},
number = {4},
pages = {896-908},
pmid = {27996979},
issn = {1751-7370},
mesh = {Ammonia/chemistry/*metabolism ; Archaea/classification/*metabolism ; Bacteria/classification/*metabolism ; Nitrification ; Oregon ; Oxidation-Reduction ; Soil/*chemistry ; *Soil Microbiology ; Temperature ; },
abstract = {Soil nitrification potential (NP) activities of ammonia-oxidizing archaea and bacteria (AOA and AOB, respectively) were evaluated across a temperature gradient (4-42 °C) imposed upon eight soils from four different sites in Oregon and modeled with both the macromolecular rate theory and the square root growth models to quantify the thermodynamic responses. There were significant differences in response by the dominant AOA and AOB contributing to the NPs. The optimal temperatures (Topt) for AOA- and AOB-supported NPs were significantly different (P<0.001), with AOA having Topt>12 °C greater than AOB. The change in heat capacity associated with the temperature dependence of nitrification (ΔCP[‡]) was correlated with Topt across the eight soils, and the ΔCP[‡] of AOB activity was significantly more negative than that of AOA activity (P<0.01). Model results predicted, and confirmatory experiments showed, a significantly lower minimum temperature (Tmin) and different, albeit very similar, maximum temperature (Tmax) values for AOB than for AOA activity. The results also suggested that there may be different forms of AOA AMO that are active over different temperature ranges with different Tmin, but no evidence of multiple Tmin values within the AOB. Fundamental differences in temperature-influenced properties of nitrification driven by AOA and AOB provides support for the idea that the biochemical processes associated with NH3 oxidation in AOA and AOB differ thermodynamically from each other, and that also might account for the difficulties encountered in attempting to model the response of nitrification to temperature change in soil environments.},
}
@article {pmid27984824,
year = {2017},
author = {Moukhtar, M and Chaar, W and Abdel-Razzak, Z and Khalil, M and Taha, S and Chamieh, H},
title = {ARCPHdb: A comprehensive protein database for SF1 and SF2 helicase from archaea.},
journal = {Computers in biology and medicine},
volume = {80},
number = {},
pages = {185-189},
doi = {10.1016/j.compbiomed.2016.12.004},
pmid = {27984824},
issn = {1879-0534},
mesh = {Archaea ; *Archaeal Proteins ; *Computational Biology ; Database Management Systems ; *Databases, Protein ; *RNA Helicases ; User-Computer Interface ; },
abstract = {PURPOSE: Superfamily 1 and Superfamily 2 helicases, two of the largest helicase protein families, play vital roles in many biological processes including replication, transcription and translation. Study of helicase proteins in the model microorganisms of archaea have largely contributed to the understanding of their function, architecture and assembly. Based on a large phylogenomics approach, we have identified and classified all SF1 and SF2 protein families in ninety five sequenced archaea genomes. Here we developed an online webserver linked to a specialized protein database named ARCPHdb to provide access for SF1 and SF2 helicase families from archaea.<br><br>METHODS: ARCPHdb was implemented using MySQL relational database. Web interfaces were developed using Netbeans. Data were stored according to UniProt accession numbers, NCBI Ref Seq ID, PDB IDs and Entrez Databases.<br><br>RESULTS: A user-friendly interactive web interface has been developed to browse, search and download archaeal helicase protein sequences, their available 3D structure models, and related documentation available in the literature provided by ARCPHdb. The database provides direct links to matching external databases.<br><br>CONCLUSIONS: The ARCPHdb is the first online database to compile all protein information on SF1 and SF2 helicase from archaea in one platform. This database provides essential resource information for all researchers interested in the field.},
}
@article {pmid27976411,
year = {2017},
author = {Paul, SS and Dey, A and Baro, D and Punia, BS},
title = {Comparative community structure of archaea in rumen of buffaloes and cattle.},
journal = {Journal of the science of food and agriculture},
volume = {97},
number = {10},
pages = {3284-3293},
doi = {10.1002/jsfa.8177},
pmid = {27976411},
issn = {1097-0010},
mesh = {Animals ; Archaea/classification/genetics/growth &amp; development/*isolation &amp; purification ; Buffaloes/*microbiology ; Cattle/*microbiology ; *Gastrointestinal Microbiome ; Phylogeny ; Rumen/*microbiology ; },
abstract = {BACKGROUND: Detailed knowledge of the community structure of methanogens is essential for amelioration of methane emission from livestock species. Several studies have indicated that predominant methanogens of buffalo rumen are different from those in cattle. However, predominant genera of methanogens reported by individual studies varied primarily because of limited scope of sampling, sequencing of limited number of sequences and potential PCR bias in individual studies. In this study, the collective comparative diversity of methanogenic archaea in the rumen of cattle and buffaloes was examined by performing a meta-analysis of all the 16S rRNA (rrn) sequences deposited in GenBank.<br><br>RESULTS: Ruminal methanogen sequences of buffalo were clustered into 900 species-level operational taxonomic units (OTUs), and ruminal methanogen sequences of cattle were clustered into 1522 species level OTUs. The number of species-level OTUs shared between cattle and buffaloes was 229 (10.4% of all OTUs), comprising 1746 sequences (27% of the total 6447 sequences). According to taxonomic classification by three different classifiers, Methanobrevibacter was found to be the most predominant genus both in cattle (69-71% of sequences) as well as buffaloes (65.1-68.9% of sequences). Percentage of Methanomicrobium was much higher (P&#x2009;<&#x2009;0.05) in the case of buffalo (18%) than that of cattle (4.5%). On the other hand, percentages of Methanosphaera- and Methanomassiliicoccus-like methanogens were much higher (P&#x2009;<&#x2009;0.05) in cattle than in buffaloes.<br><br>CONCLUSION: This study indicated that there is a substantial difference in community structure of ruminal methanogens of cattle and buffaloes. The study has also indicated that the percent of species-level operational taxonomic units shared between cattle and buffalo is very low, and thus host species-specific methane mitigation strategies need to be developed for cattle and buffaloes. &#xa9; 2016 Society of Chemical Industry.},
}
@article {pmid27966672,
year = {2016},
author = {Golyshina, OV and Kublanov, IV and Tran, H and Korzhenkov, AA and Lünsdorf, H and Nechitaylo, TY and Gavrilov, SN and Toshchakov, SV and Golyshin, PN},
title = {Biology of archaea from a novel family Cuniculiplasmataceae (Thermoplasmata) ubiquitous in hyperacidic environments.},
journal = {Scientific reports},
volume = {6},
number = {},
pages = {39034},
pmid = {27966672},
issn = {2045-2322},
support = {BB/M029085/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Acids/*chemistry ; Archaeal Proteins/genetics/metabolism ; California ; *Ecosystem ; Euryarchaeota/classification/*genetics/metabolism ; Genome, Archaeal/*genetics ; Genomics/methods ; Geography ; Hydrogen-Ion Concentration ; Microscopy, Electron ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Spain ; Thermoplasmales/*genetics/metabolism/ultrastructure ; United Kingdom ; },
abstract = {The order Thermoplasmatales (Euryarchaeota) is represented by the most acidophilic organisms known so far that are poorly amenable to cultivation. Earlier culture-independent studies in Iron Mountain (California) pointed at an abundant archaeal group, dubbed 'G-plasma'. We examined the genomes and physiology of two cultured representatives of a Family Cuniculiplasmataceae, recently isolated from acidic (pH 1-1.5) sites in Spain and UK that are 16S rRNA gene sequence-identical with 'G-plasma'. Organisms had largest genomes among Thermoplasmatales (1.87-1.94 Mbp), that shared 98.7-98.8% average nucleotide identities between themselves and 'G-plasma' and exhibited a high genome conservation even within their genomic islands, despite their remote geographical localisations. Facultatively anaerobic heterotrophs, they possess an ancestral form of A-type terminal oxygen reductase from a distinct parental clade. The lack of complete pathways for biosynthesis of histidine, valine, leucine, isoleucine, lysine and proline pre-determines the reliance on external sources of amino acids and hence the lifestyle of these organisms as scavengers of proteinaceous compounds from surrounding microbial community members. In contrast to earlier metagenomics-based assumptions, isolates were S-layer-deficient, non-motile, non-methylotrophic and devoid of iron-oxidation despite the abundance of methylotrophy substrates and ferrous iron in situ, which underlines the essentiality of experimental validation of bioinformatic predictions.},
}
@article {pmid27920295,
year = {2017},
author = {Rodionov, DA and Leyn, SA and Li, X and Rodionova, IA},
title = {A Novel Transcriptional Regulator Related to Thiamine Phosphate Synthase Controls Thiamine Metabolism Genes in Archaea.},
journal = {Journal of bacteriology},
volume = {199},
number = {4},
pages = {},
pmid = {27920295},
issn = {1098-5530},
mesh = {Alkyl and Aryl Transferases/genetics/*metabolism ; Archaea/*enzymology/genetics/metabolism ; Computational Biology ; Gene Expression Regulation, Archaeal/*physiology ; Gene Expression Regulation, Enzymologic/*physiology ; Genome, Archaeal/genetics ; Genomics ; Thiamine/*metabolism ; Thiamine Pyrophosphate/*metabolism ; },
abstract = {UNLABELLED: Thiamine (vitamin B1) is a precursor of thiamine pyrophosphate (TPP), an essential coenzyme in the central metabolism of all living organisms. Bacterial thiamine biosynthesis and salvage genes are controlled at the RNA level by TPP-responsive riboswitches. In Archaea, TPP riboswitches are restricted to the Thermoplasmatales order. Mechanisms of transcriptional control of thiamine genes in other archaeal lineages remain unknown. Using the comparative genomics approach, we identified a novel family of transcriptional regulators (named ThiR) controlling thiamine biosynthesis and transport genes in diverse lineages in the Crenarchaeota phylum as well as in the Halobacteria and Thermococci classes of the Euryarchaeota ThiR regulators are composed of an N-terminal DNA-binding domain and a C-terminal ligand-binding domain, which is similar to the archaeal thiamine phosphate synthase ThiN. By using comparative genomics, we predicted ThiR-binding DNA motifs and reconstructed ThiR regulons in 67 genomes representing all above-mentioned lineages. The predicted ThiR-binding motifs are characterized by palindromic symmetry with several distinct lineage-specific consensus sequences. In addition to thiamine biosynthesis genes, the reconstructed ThiR regulons include various transporters for thiamine and its precursors. Bioinformatics predictions were experimentally validated by in vitro DNA-binding assays with the recombinant ThiR protein from the hyperthermophilic archaeon Metallosphaera yellowstonensis MK1. Thiamine phosphate and, to some extent, TPP and hydroxyethylthiazole phosphate were required for the binding of ThiR to its DNA targets, suggesting that ThiR is derepressed by limitation of thiamine phosphates. The thiamine phosphate-binding residues previously identified in ThiN are highly conserved in ThiR regulators, suggesting a conserved mechanism for effector recognition.<br><br>IMPORTANCE: Thiamine pyrophosphate is a cofactor for many essential enzymes for glucose and energy metabolism. Thiamine or vitamin B1 biosynthesis and its transcriptional regulation in Archaea are poorly understood. We applied the comparative genomics approach to identify a novel family of regulators for the transcriptional control of thiamine metabolism genes in Archaea and reconstructed the respective regulons. The predicted ThiR regulons in archaeal genomes control the majority of thiamine biosynthesis genes. The reconstructed regulon content suggests that numerous uptake transporters for thiamine and/or its precursors are encoded in archaeal genomes. The ThiR regulon was experimentally validated by DNA-binding assays with Metallosphaera spp. These discoveries contribute to our understanding of metabolic and regulatory networks involved in vitamin homeostasis in diverse lineages of Archaea.},
}
@article {pmid27919704,
year = {2017},
author = {Kurt-Kızıldoğan, A and Abanoz, B and Okay, S},
title = {Global transcriptome analysis of Halolamina sp. to decipher the salt tolerance in extremely halophilic archaea.},
journal = {Gene},
volume = {601},
number = {},
pages = {56-64},
doi = {10.1016/j.gene.2016.11.042},
pmid = {27919704},
issn = {1879-0038},
mesh = {Archaeal Proteins/genetics/metabolism ; Gene Expression Profiling ; Gene Expression Regulation, Archaeal ; Genome, Archaeal ; Halobacteriales/*genetics/isolation &amp; purification/*metabolism ; RNA, Archaeal/genetics ; Salinity ; Salt Tolerance/*genetics ; Sequence Analysis, RNA ; Transcriptome ; },
abstract = {Extremely halophilic archaea survive in the hypersaline environments such as salt lakes or salt mines. Therefore, these microorganisms are good sources to investigate the molecular mechanisms underlying the tolerance to high salt concentrations. In this study, a global transcriptome analysis was conducted in an extremely halophilic archaeon, Halolamina sp. YKT1, isolated from a salt mine in Turkey. A comparative RNA-seq analysis was performed using YKT1 isolate grown either at 2.7M NaCl or 5.5M NaCl concentrations. A total of 2149 genes were predicted to be up-regulated and 1638 genes were down-regulated in the presence of 5.5M NaCl. The salt tolerance of Halolamina sp. YKT1 involves the up-regulation of genes related with membrane transporters, CRISPR-Cas systems, osmoprotectant solutes, oxidative stress proteins, and iron metabolism. On the other hand, the genes encoding the proteins involved in DNA replication, transcription, translation, mismatch and nucleotide excision repair were down-regulated. The RNA-seq data were verified for seven up-regulated genes as well as six down-regulated genes via qRT-PCR analysis. This comprehensive transcriptome analysis showed that the halophilic archaeon canalizes its energy towards keeping the intracellular osmotic balance minimizing the production of nucleic acids and peptides.},
}
@article {pmid27879020,
year = {2017},
author = {Kuhn, A and Kiefer, D},
title = {Membrane protein insertase YidC in bacteria and archaea.},
journal = {Molecular microbiology},
volume = {103},
number = {4},
pages = {590-594},
doi = {10.1111/mmi.13586},
pmid = {27879020},
issn = {1365-2958},
mesh = {Cell Membrane/metabolism ; Escherichia coli/genetics/*metabolism ; Escherichia coli Proteins/genetics/*metabolism ; *Hydrophobic and Hydrophilic Interactions ; Membrane Transport Proteins/genetics/*metabolism ; Methanocaldococcus/genetics/*metabolism ; SEC Translocation Channels/genetics ; },
abstract = {The insertion of proteins into the prokaryotic plasma membrane is catalyzed by translocases and insertases. On one hand, the Sec translocase operates as a transmembrane channel that can open laterally to first bind and then release the hydrophobic segments of a substrate protein into the lipid bilayer. On the other hand, YidC insertases interact with their substrates in a groove-like structure at an amphiphilic protein-lipid interface thus allowing the transmembrane segments of the substrate to slide into the lipid bilayer. The recently published high-resolution structures of YidC provide new mechanistic insights of how transmembrane proteins achieve the transition from an aqueous environment in the cytoplasm to the hydrophobic lipid bilayer environment of the membrane.},
}
@article {pmid27864137,
year = {2017},
author = {Bharathi, M and Chellapandi, P},
title = {Intergenomic evolution and metabolic cross-talk between rumen and thermophilic autotrophic methanogenic archaea.},
journal = {Molecular phylogenetics and evolution},
volume = {107},
number = {},
pages = {293-304},
doi = {10.1016/j.ympev.2016.11.008},
pmid = {27864137},
issn = {1095-9513},
mesh = {Animals ; Archaea/*genetics ; *Autotrophic Processes ; DNA Replication/genetics ; *Evolution, Molecular ; Genetic Markers ; Genetic Variation ; *Genome, Archaeal ; Metabolic Networks and Pathways/genetics ; Methane/*metabolism ; Methanobacteriaceae/genetics ; Phylogeny ; Rumen/*microbiology ; Synteny ; },
abstract = {Methanobrevibacter ruminantium M1 (MRU) is a rumen methanogenic archaean that can be able to utilize formate and CO2/H2 as growth substrates. Extensive analysis on the evolutionary genomic contexts considered herein to unravel its intergenomic relationship and metabolic adjustment acquired from the genomic content of Methanothermobacter thermautotrophicus ΔH. We demonstrated its intergenomic distance, genome function, synteny homologs and gene families, origin of replication, and methanogenesis to reveal the evolutionary relationships between Methanobrevibacter and Methanothermobacter. Comparison of the phylogenetic and metabolic markers was suggested for its archaeal metabolic core lineage that might have evolved from Methanothermobacter. Orthologous genes involved in its hydrogenotrophic methanogenesis might be acquired from intergenomic ancestry of Methanothermobacter via Methanobacterium formicicum. Formate dehydrogenase (fdhAB) coding gene cluster and carbon monoxide dehydrogenase (cooF) coding gene might have evolved from duplication events within Methanobrevibacter-Methanothermobacter lineage, and fdhCD gene cluster acquired from bacterial origins. Genome-wide metabolic survey found the existence of four novel pathways viz. l-tyrosine catabolism, mevalonate pathway II, acyl-carrier protein metabolism II and glutathione redox reactions II in MRU. Finding of these pathways suggested that MRU has shown a metabolic potential to tolerate molecular oxygen, antimicrobial metabolite biosynthesis and atypical lipid composition in cell wall, which was acquainted by metabolic cross-talk with mammalian bacterial origins. We conclude that coevolution of genomic contents between Methanobrevibacter and Methanothermobacter provides a clue to understand the metabolic adaptation of MRU in the rumen at different environmental niches.},
}
@article {pmid27852927,
year = {2016},
author = {Urbonavičius, J and Rutkienė, R and Lopato, A and Tauraitė, D and Stankevičiūtė, J and Aučynaitė, A and Kaliniene, L and van Tilbeurgh, H and Meškys, R},
title = {Evolution of tRNAPhe:imG2 methyltransferases involved in the biosynthesis of wyosine derivatives in Archaea.},
journal = {RNA (New York, N.Y.)},
volume = {22},
number = {12},
pages = {1871-1883},
pmid = {27852927},
issn = {1469-9001},
mesh = {Amino Acid Sequence ; Archaea/*metabolism ; Guanosine/*analogs &amp; derivatives/biosynthesis ; Methyltransferases/chemistry/*metabolism ; RNA, Transfer, Phe/chemistry/*metabolism ; Sequence Homology, Amino Acid ; },
abstract = {Tricyclic wyosine derivatives are found at position 37 of eukaryotic and archaeal tRNA[Phe] In Archaea, the intermediate imG-14 is targeted by three different enzymes that catalyze the formation of yW-86, imG, and imG2. We have suggested previously that a peculiar methyltransferase (aTrm5a/Taw22) likely catalyzes two distinct reactions: N[1]-methylation of guanosine to yield m[1]G; and C[7]-methylation of imG-14 to yield imG2. Here we show that the recombinant aTrm5a/Taw22-like enzymes from both Pyrococcus abyssi and Nanoarchaeum equitans indeed possess such dual specificity. We also show that substitutions of individual conservative amino acids of P. abyssi Taw22 (P260N, E173A, and R174A) have a differential effect on the formation of m[1]G/imG2, while replacement of R134, F165, E213, and P262 with alanine abolishes the formation of both derivatives of G37. We further demonstrate that aTrm5a-type enzyme SSO2439 from Sulfolobus solfataricus, which has no N[1]-methyltransferase activity, exhibits C[7]-methyltransferase activity, thereby producing imG2 from imG-14. We thus suggest renaming such aTrm5a methyltransferases as Taw21 to distinguish between monofunctional and bifunctional aTrm5a enzymes.},
}
@article {pmid27846569,
year = {2016},
author = {Zheng, K and Ngo, PD and Owens, VL and Yang, XP and Mansoorabadi, SO},
title = {The biosynthetic pathway of coenzyme F430 in methanogenic and methanotrophic archaea.},
journal = {Science (New York, N.Y.)},
volume = {354},
number = {6310},
pages = {339-342},
doi = {10.1126/science.aag2947},
pmid = {27846569},
issn = {1095-9203},
mesh = {Amides/metabolism ; Archaeal Proteins/genetics/*metabolism ; Biosynthetic Pathways ; Genes, Archaeal ; Genetic Loci ; Genomics ; Metalloporphyrins/genetics/*metabolism ; Methane/*metabolism ; Methanosarcina/*enzymology/genetics ; Nickel/metabolism ; Oxidoreductases/genetics/*metabolism ; Uroporphyrins/*metabolism ; },
abstract = {Methyl-coenzyme M reductase (MCR) is the key enzyme of methanogenesis and anaerobic methane oxidation. The activity of MCR is dependent on the unique nickel-containing tetrapyrrole known as coenzyme F430. We used comparative genomics to identify the coenzyme F430 biosynthesis (cfb) genes and characterized the encoded enzymes from Methanosarcina acetivorans C2A. The pathway involves nickelochelation by a nickel-specific chelatase, followed by amidation to form Ni-sirohydrochlorin a,c-diamide. Next, a primitive homolog of nitrogenase mediates a six-electron reduction and γ-lactamization reaction before a Mur ligase homolog forms the six-membered carbocyclic ring in the final step of the pathway. These data show that coenzyme F430 can be synthesized from sirohydrochlorin using Cfb enzymes produced heterologously in a nonmethanogen host and identify several targets for inhibitors of biological methane formation.},
}
@article {pmid27829818,
year = {2016},
author = {Rodrigues, T and Belmok, A and Catão, E and Kyaw, CM},
title = {Archaea in Natural and Impacted Brazilian Environments.},
journal = {Archaea (Vancouver, B.C.)},
volume = {2016},
number = {},
pages = {1259608},
pmid = {27829818},
issn = {1472-3654},
mesh = {Archaea/*classification/*isolation &amp; purification ; *Biodiversity ; Brazil ; *Environmental Microbiology ; },
abstract = {In recent years, archaeal diversity surveys have received increasing attention. Brazil is a country known for its natural diversity and variety of biomes, which makes it an interesting sampling site for such studies. However, archaeal communities in natural and impacted Brazilian environments have only recently been investigated. In this review, based on a search on the PubMed database on the last week of April 2016, we present and discuss the results obtained in the 51 studies retrieved, focusing on archaeal communities in water, sediments, and soils of different Brazilian environments. We concluded that, in spite of its vast territory and biomes, the number of publications focusing on archaeal detection and/or characterization in Brazil is still incipient, indicating that these environments still represent a great potential to be explored.},
}
@article {pmid27815273,
year = {2017},
author = {Ballen-Segura, M and Felip, M and Catalan, J},
title = {Some Mixotrophic Flagellate Species Selectively Graze on Archaea.},
journal = {Applied and environmental microbiology},
volume = {83},
number = {2},
pages = {},
pmid = {27815273},
issn = {1098-5336},
mesh = {*Archaea ; *Bacteria ; Chrysophyta/*physiology ; Cryptophyta/*physiology ; *Food Chain ; In Situ Hybridization, Fluorescence ; Lakes/microbiology ; Plankton/*physiology ; Spain ; },
abstract = {UNLABELLED: Many phototrophic flagellates ingest prokaryotes. This mixotrophic trait becomes a critical aspect of the microbial loop in planktonic food webs because of the typical high abundance of these flagellates. Our knowledge of their selective feeding upon different groups of prokaryotes, particularly under field conditions, is still quite limited. In this study, we investigated the feeding behavior of three species (Rhodomonas sp., Cryptomonas ovata, and Dinobryon cylindricum) via their food vacuole content in field populations of a high mountain lake. We used the catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH) protocol with probes specific for the domain Archaea and three groups of Eubacteria: Betaproteobacteria, Actinobacteria, and Cytophaga-Flavobacteria of Bacteroidetes Our results provide field evidence that contrasting selective feeding exists between coexisting mixotrophic flagellates under the same environmental conditions and that some prokaryotic groups may be preferentially impacted by phagotrophic pressure in aquatic microbial food webs. In our study, Archaea were the preferred prey, chiefly in the case of Rhodomonas sp., which rarely fed on any other prokaryotic group. In general, prey selection did not relate to prey size among the grazed groups. However, Actinobacteria, which were clearly avoided, mostly showed a size of <0.5 μm, markedly smaller than cells from the other groups.<br><br>IMPORTANCE: That mixotrophic flagellates are not randomly feeding in the main prokaryotic groups under field conditions is a pioneer finding in species-specific behavior that paves the way for future studies according to this new paradigm. The particular case that Archaea were preferentially affected in the situation studied shows that phagotrophic pressure cannot be disregarded when considering the distribution of this group in freshwater oligotrophic systems.},
}
@article {pmid27810876,
year = {2017},
author = {Miragoli, F and Federici, S and Ferrari, S and Minuti, A and Rebecchi, A and Bruzzese, E and Buccigrossi, V and Guarino, A and Callegari, ML},
title = {Impact of cystic fibrosis disease on archaea and bacteria composition of gut microbiota.},
journal = {FEMS microbiology ecology},
volume = {93},
number = {2},
pages = {},
pmid = {27810876},
issn = {1574-6941},
mesh = {Adolescent ; Adult ; Archaea/classification/genetics ; Bacteria/classification/genetics ; *Biodiversity ; Child ; Colon ; Cystic Fibrosis/*microbiology ; Euryarchaeota/genetics ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Intestines/*microbiology/physiopathology ; Male ; Microbiota/genetics ; Real-Time Polymerase Chain Reaction ; Young Adult ; },
abstract = {Cystic fibrosis is often associated with intestinal inflammation due to several factors, including altered gut microbiota composition. In this study, we analyzed the fecal microbiota among patients with cystic fibrosis of 10-22 years of age, and compared the findings with age-matched healthy subjects. The participating patients included 14 homozygotes and 14 heterozygotes with the delF508 mutation, and 2 heterozygotes presenting non-delF508 mutations. We used PCR-DGGE and qPCR to analyze the presence of bacteria, archaea and sulfate-reducing bacteria. Overall, our findings confirmed disruption of the cystic fibrosis gut microbiota. Principal component analysis of the qPCR data revealed no differences between homozygotes and heterozygotes, while both groups were distinct from healthy subjects who showed higher biodiversity. Archaea were under the detection limit in all homozygotes subjects, whereas methanogens were detected in 62% of both cystic fibrosis heterozygotes and healthy subjects. Our qPCR results revealed a low frequency of sulfate-reducing bacteria in the homozygote (13%) and heterozygote (13%) patients with cystic fibrosis compared with healthy subjects (87.5%). This is a pioneer study showing that patients with cystic fibrosis exhibit significant reduction of H2-consuming microorganisms, which could increase hydrogen accumulation in the colon and the expulsion of this gas through non-microbial routes.},
}
@article {pmid27795311,
year = {2017},
author = {Rodrigues, MV and Borges, N and Santos, H},
title = {Glycerol Phosphate Cytidylyltransferase Stereospecificity Is Key to Understanding the Distinct Stereochemical Compositions of Glycerophosphoinositol in Bacteria and Archaea.},
journal = {Applied and environmental microbiology},
volume = {83},
number = {1},
pages = {},
pmid = {27795311},
issn = {1098-5336},
mesh = {Archaeoglobus/*enzymology/genetics/metabolism ; Bacteria/*enzymology/genetics/metabolism ; Cytidine Triphosphate/chemistry/*metabolism ; Glycerol/metabolism ; Inositol Phosphates/*chemistry/metabolism ; Magnetic Resonance Spectroscopy ; Molecular Conformation ; Nucleotidyltransferases/chemistry/*metabolism ; Recombinant Proteins/metabolism ; Stereoisomerism ; Substrate Specificity ; },
abstract = {UNLABELLED: Glycerophosphoinositol (GPI) is a compatible solute present in a few hyperthermophiles. Interestingly, different GPI stereoisomers accumulate in Bacteria and Archaea, and the basis for this domain-dependent specificity was investigated herein. The archaeon Archaeoglobus fulgidus and the bacterium Aquifex aeolicus were used as model organisms. The synthesis of GPI involves glycerol phosphate cytidylyltransferase (GCT), which catalyzes the production of CDP-glycerol from CTP and glycerol phosphate, and di-myo-inositol phosphate-phosphate synthase (DIPPS), catalyzing the formation of phosphorylated GPI from CDP-glycerol and l-myo-inositol 1-phosphate. DIPPS of A. fulgidus recognized the two CDP-glycerol stereoisomers similarly. This feature and the ability of [31]P nuclear magnetic resonance (NMR) to distinguish the GPI diastereomers provided a means to study the stereospecificity of GCTs. The AF1418 gene and genes aq_185 and aq_1368 are annotated as putative GCT genes in the genomes of A. fulgidus and Aq. aeolicus, respectively. The functions of these genes were determined by assaying the activity of the respective recombinant proteins: AQ1368 and AQ185 are GCTs, while AF1418 has flavin adenine dinucleotide (FAD) synthetase activity. AQ185 is absolutely specific for sn-glycerol 3-phosphate, while AQ1368 recognizes the two enantiomers but has a 2:1 preference for sn-glycerol 3-phosphate. In contrast, the partially purified A. fulgidus GCT uses sn-glycerol 1-phosphate preferentially (4:1). Significantly, the predominant GPI stereoforms found in the bacterium and the archaeon reflect the distinct stereospecificities of the respective GCTs: i.e., A. fulgidus accumulates predominantly sn-glycero-1-phospho-3-l-myo-inositol, while Aq. aeolicus accumulates sn-glycero-3-phospho-3-l-myo-inositol.<br><br>IMPORTANCE: Compatible solutes of hyperthermophiles show high efficacy in thermal protection of proteins in comparison with solutes typical of mesophiles; therefore, they are potentially useful in several biotechnological applications. Glycerophosphoinositol (GPI) is synthesized from CDP-glycerol and l-myo-inositol 1-phosphate in a few hyperthermophiles. In this study, the molecular configuration of the GPI stereoisomers accumulated by members of the Bacteria and Archaea was established. The stereospecificity of glycerol phosphate cytidylyltransferase (GCT), the enzyme catalyzing the synthesis of CDP-glycerol, is crucial to the stereochemistry of GPI. However, the stereospecific properties of GCTs have not been investigated thus far. We devised a method to characterize GCT stereospecificity which does not require sn-glycerol 1-phosphate, a commercially unavailable substrate. This led us to understand the biochemical basis for the distinct GPI stereoisomer composition observed in archaea and bacteria.},
}
@article {pmid27749816,
year = {2016},
author = {Laso-Pérez, R and Wegener, G and Knittel, K and Widdel, F and Harding, KJ and Krukenberg, V and Meier, DV and Richter, M and Tegetmeyer, HE and Riedel, D and Richnow, HH and Adrian, L and Reemtsma, T and Lechtenfeld, OJ and Musat, F},
title = {Thermophilic archaea activate butane via alkyl-coenzyme M formation.},
journal = {Nature},
volume = {539},
number = {7629},
pages = {396-401},
pmid = {27749816},
issn = {1476-4687},
mesh = {Alkylation ; Anaerobiosis ; Archaea/genetics/*metabolism ; Archaeal Proteins/chemistry/genetics/metabolism ; Biocatalysis ; Butanes/*metabolism ; Evolution, Molecular ; Mesna/*chemistry/*metabolism ; Oxidation-Reduction ; Sulfates/metabolism ; Temperature ; },
abstract = {The anaerobic formation and oxidation of methane involve unique enzymatic mechanisms and cofactors, all of which are believed to be specific for C1-compounds. Here we show that an anaerobic thermophilic enrichment culture composed of dense consortia of archaea and bacteria apparently uses partly similar pathways to oxidize the C4 hydrocarbon butane. The archaea, proposed genus 'Candidatus Syntrophoarchaeum', show the characteristic autofluorescence of methanogens, and contain highly expressed genes encoding enzymes similar to methyl-coenzyme M reductase. We detect butyl-coenzyme M, indicating archaeal butane activation analogous to the first step in anaerobic methane oxidation. In addition, Ca. Syntrophoarchaeum expresses the genes encoding β-oxidation enzymes, carbon monoxide dehydrogenase and reversible C1 methanogenesis enzymes. This allows for the complete oxidation of butane. Reducing equivalents are seemingly channelled to HotSeep-1, a thermophilic sulfate-reducing partner bacterium known from the anaerobic oxidation of methane. Genes encoding 16S rRNA and methyl-coenzyme M reductase similar to those identifying Ca. Syntrophoarchaeum were repeatedly retrieved from marine subsurface sediments, suggesting that the presented activation mechanism is naturally widespread in the anaerobic oxidation of short-chain hydrocarbons.},
}
@article {pmid27791189,
year = {2016},
author = {Liu, Y and Vinyard, DJ and Reesbeck, ME and Suzuki, T and Manakongtreecheep, K and Holland, PL and Brudvig, GW and Söll, D},
title = {A [3Fe-4S] cluster is required for tRNA thiolation in archaea and eukaryotes.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {113},
number = {45},
pages = {12703-12708},
pmid = {27791189},
issn = {1091-6490},
support = {R01 GM022854/GM/NIGMS NIH HHS/United States ; R01 GM065313/GM/NIGMS NIH HHS/United States ; R37 GM022854/GM/NIGMS NIH HHS/United States ; UL1 TR001863/TR/NCATS NIH HHS/United States ; },
abstract = {The sulfur-containing nucleosides in transfer RNA (tRNAs) are present in all three domains of life; they have critical functions for accurate and efficient translation, such as tRNA structure stabilization and proper codon recognition. The tRNA modification enzymes ThiI (in bacteria and archaea) and Ncs6 (in archaea and eukaryotic cytosols) catalyze the formation of 4-thiouridine (s[4]U) and 2-thiouridine (s[2]U), respectively. The ThiI homologs were proposed to transfer sulfur via cysteine persulfide enzyme adducts, whereas the reaction mechanism of Ncs6 remains unknown. Here we show that ThiI from the archaeon Methanococcus maripaludis contains a [3Fe-4S] cluster that is essential for its tRNA thiolation activity. Furthermore, the archaeal and eukaryotic Ncs6 homologs as well as phosphoseryl-tRNA (Sep-tRNA):Cys-tRNA synthase (SepCysS), which catalyzes the Sep-tRNA to Cys-tRNA conversion in methanogens, also possess a [3Fe-4S] cluster similar to the methanogenic archaeal ThiI. These results suggest that the diverse tRNA thiolation processes in archaea and eukaryotic cytosols share a common mechanism dependent on a [3Fe-4S] cluster for sulfur transfer.},
}
@article {pmid27791118,
year = {2016},
author = {Ettwig, KF and Zhu, B and Speth, D and Keltjens, JT and Jetten, MSM and Kartal, B},
title = {Archaea catalyze iron-dependent anaerobic oxidation of methane.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {113},
number = {45},
pages = {12792-12796},
pmid = {27791118},
issn = {1091-6490},
support = {339880/ERC_/European Research Council/International ; },
abstract = {Anaerobic oxidation of methane (AOM) is crucial for controlling the emission of this potent greenhouse gas to the atmosphere. Nitrite-, nitrate-, and sulfate-dependent methane oxidation is well-documented, but AOM coupled to the reduction of oxidized metals has so far been demonstrated only in environmental samples. Here, using a freshwater enrichment culture, we show that archaea of the order Methanosarcinales, related to "Candidatus Methanoperedens nitroreducens," couple the reduction of environmentally relevant forms of Fe[3+] and Mn[4+] to the oxidation of methane. We obtained an enrichment culture of these archaea under anaerobic, nitrate-reducing conditions with a continuous supply of methane. Via batch incubations using [[13]C]methane, we demonstrated that soluble ferric iron (Fe[3+], as Fe-citrate) and nanoparticulate forms of Fe[3+] and Mn[4+] supported methane-oxidizing activity. CO2 and ferrous iron (Fe[2+]) were produced in stoichiometric amounts. Our study connects the previous finding of iron-dependent AOM to microorganisms detected in numerous habitats worldwide. Consequently, it enables a better understanding of the interaction between the biogeochemical cycles of iron and methane.},
}
@article {pmid27137126,
year = {2016},
author = {Wrighton, KC and Castelle, CJ and Varaljay, VA and Satagopan, S and Brown, CT and Wilkins, MJ and Thomas, BC and Sharon, I and Williams, KH and Tabita, FR and Banfield, JF},
title = {RubisCO of a nucleoside pathway known from Archaea is found in diverse uncultivated phyla in bacteria.},
journal = {The ISME journal},
volume = {10},
number = {11},
pages = {2702-2714},
pmid = {27137126},
issn = {1751-7370},
support = {R01 GM095742/GM/NIGMS NIH HHS/United States ; },
mesh = {Archaea/genetics/growth &amp; development/isolation &amp; purification/*metabolism ; Archaeal Proteins/genetics/*metabolism ; Bacteria/genetics/growth &amp; development/isolation &amp; purification/*metabolism ; Bacterial Proteins/genetics/metabolism ; Fermentation ; Metagenomics ; Molecular Sequence Data ; Nucleosides/*metabolism ; Phylogeny ; Ribulose-Bisphosphate Carboxylase/genetics ; },
abstract = {Metagenomic studies recently uncovered form II/III RubisCO genes, originally thought to only occur in archaea, from uncultivated bacteria of the candidate phyla radiation (CPR). There are no isolated CPR bacteria and these organisms are predicted to have limited metabolic capacities. Here we expand the known diversity of RubisCO from CPR lineages. We report a form of RubisCO, distantly similar to the archaeal form III RubisCO, in some CPR bacteria from the Parcubacteria (OD1), WS6 and Microgenomates (OP11) phyla. In addition, we significantly expand the Peregrinibacteria (PER) II/III RubisCO diversity and report the first II/III RubisCO sequences from the Microgenomates and WS6 phyla. To provide a metabolic context for these RubisCOs, we reconstructed near-complete (>93%) PER genomes and the first closed genome for a WS6 bacterium, for which we propose the phylum name Dojkabacteria. Genomic and bioinformatic analyses suggest that the CPR RubisCOs function in a nucleoside pathway similar to that proposed in Archaea. Detection of form II/III RubisCO and nucleoside metabolism gene transcripts from a PER supports the operation of this pathway in situ. We demonstrate that the PER form II/III RubisCO is catalytically active, fixing CO2 to physiologically complement phototrophic growth in a bacterial photoautotrophic RubisCO deletion strain. We propose that the identification of these RubisCOs across a radiation of obligately fermentative, small-celled organisms hints at a widespread, simple metabolic platform in which ribose may be a prominent currency.},
}
@article {pmid27771364,
year = {2016},
author = {Loder, AJ and Han, Y and Hawkins, AB and Lian, H and Lipscomb, GL and Schut, GJ and Keller, MW and Adams, MWW and Kelly, RM},
title = {Reaction kinetic analysis of the 3-hydroxypropionate/4-hydroxybutyrate CO2 fixation cycle in extremely thermoacidophilic archaea.},
journal = {Metabolic engineering},
volume = {38},
number = {},
pages = {446-463},
pmid = {27771364},
issn = {1096-7184},
support = {T32 GM008776/GM/NIGMS NIH HHS/United States ; },
mesh = {Archaea/metabolism ; Carbon Dioxide/*metabolism ; Extremophiles/metabolism ; Hydroxybutyrates/*metabolism ; Kinetics ; Lactic Acid/*analogs &amp; derivatives/metabolism ; Metabolic Clearance Rate ; Metabolic Flux Analysis/*methods ; Metabolic Networks and Pathways/*physiology ; *Models, Biological ; Signal Transduction/physiology ; Sulfolobaceae/*metabolism ; },
abstract = {The 3-hydroxypropionate/4-hydroxybutyrate (3HP/4HB) cycle fixes CO2 in extremely thermoacidophilic archaea and holds promise for metabolic engineering because of its thermostability and potentially rapid pathway kinetics. A reaction kinetics model was developed to examine the biological and biotechnological attributes of the 3HP/4HB cycle as it operates in Metallosphaera sedula, based on previous information as well as on kinetic parameters determined here for recombinant versions of five of the cycle enzymes (malonyl-CoA/succinyl-CoA reductase, 3-hydroxypropionyl-CoA synthetase, 3-hydroxypropionyl-CoA dehydratase, acryloyl-CoA reductase, and succinic semialdehyde reductase). The model correctly predicted previously observed features of the cycle: the 35-65% split of carbon flux through the acetyl-CoA and succinate branches, the high abundance and relative ratio of acetyl-CoA/propionyl-CoA carboxylase (ACC) and MCR, and the significance of ACC and hydroxybutyryl-CoA synthetase (HBCS) as regulated control points for the cycle. The model was then used to assess metabolic engineering strategies for incorporating CO2 into chemical intermediates and products of biotechnological importance: acetyl-CoA, succinate, and 3-hydroxypropionate.},
}
@article {pmid27771305,
year = {2016},
author = {Walter, ME and Ortiz, A and Sondgeroth, C and Sindt, NM and Duszenko, N and Catlett, JL and Zhou, Y and Valloppilly, S and Anderson, C and Fernando, S and Buan, NR},
title = {High-throughput mutation, selection, and phenotype screening of mutant methanogenic archaea.},
journal = {Journal of microbiological methods},
volume = {131},
number = {},
pages = {113-121},
doi = {10.1016/j.mimet.2016.10.010},
pmid = {27771305},
issn = {1872-8359},
mesh = {Acetates/metabolism ; Archaea/*genetics/*isolation &amp; purification/metabolism/*radiation effects ; DNA, Archaeal/genetics/radiation effects ; Genes, Archaeal ; High-Throughput Screening Assays/*methods ; Methane/metabolism ; Methanol/metabolism ; Methanosarcina/genetics/growth &amp; development/radiation effects ; Methyltransferases/genetics ; Microbial Viability/radiation effects ; Mutagenesis/radiation effects ; *Phenotype ; Point Mutation/*radiation effects ; *Ultraviolet Rays ; },
abstract = {Bacterial and archaeal genomes can contain 30% or more hypothetical genes with no predicted function. Phylogenetically deep-branching microbes, such as methane-producing archaea (methanogens), contain up to 50% genes with unknown function. In order to formulate hypotheses about the function of hypothetical gene functions in the strict anaerobe, Methanosarcina acetivorans, we have developed high-throughput anaerobic techniques to UV mutagenize, screen, and select for mutant strains in 96-well plates. Using these approaches we have isolated 10 mutant strains that exhibit a variety of physiological changes including increased or decreased growth rate relative to the parent strain when cells use methanol and/or acetate as carbon and energy sources. This method provides an avenue for the first step in identifying new gene functions: associating a genetic mutation with a reproducible phenotype. Mutations in bona fide methanogenesis genes such as corrinoid methyltransferases and proton-translocating F420H2:methanophenazine oxidoreductase (Fpo) were also generated, opening the door to in vivo functional complementation experiments. Irradiation-based mutagenesis such as from ultraviolet (UV) light, combined with modern genome sequencing, is a useful procedure to discern systems-level gene function in prokaryote taxa that can be axenically cultured but which may be resistant to chemical mutagens.},
}
@article {pmid27752237,
year = {2016},
author = {Sarcinelli, C and Fiorentino, G and Pizzo, E and Bartolucci, S and Limauro, D},
title = {Discovering Antioxidant Molecules in the Archaea Domain: Peroxiredoxin Bcp1 from Sulfolobus solfataricus Protects H9c2 Cardiomyoblasts from Oxidative Stress.},
journal = {Archaea (Vancouver, B.C.)},
volume = {2016},
number = {},
pages = {7424870},
pmid = {27752237},
issn = {1472-3654},
mesh = {Animals ; Antioxidants/*isolation &amp; purification/*metabolism ; Apoptosis ; Cell Line ; Hydrogen Peroxide/metabolism/toxicity ; Hydrogen-Ion Concentration ; Myocytes, Cardiac/*drug effects/physiology ; Oxidation-Reduction ; *Oxidative Stress ; Peroxiredoxins/genetics/*isolation &amp; purification/*metabolism ; Rats ; Sulfolobus solfataricus/*enzymology/genetics ; Temperature ; },
abstract = {Peroxiredoxins (Prxs) are ubiquitous thiol peroxidases that are involved in the reduction of peroxides. It has been reported that prokaryotic Prxs generally show greater structural robustness than their eukaryotic counterparts, making them less prone to inactivation by overoxidation. This difference has inspired the search for new antioxidants from prokaryotic sources that can be used as possible therapeutic biodrugs. Bacterioferritin comigratory proteins (Bcps) of the hyperthermophilic archaeon Sulfolobus solfataricus that belong to the Prx family have recently been characterized. One of these proteins, Bcp1, was chosen to determine its antioxidant effects in H9c2 rat cardiomyoblast cells. Bcp1 activity was measured in vitro under physiological temperature and pH conditions that are typical of mammalian cells; the yeast thioredoxin reductase (yTrxR)/thioredoxin (yTrx) reducing system was used to evaluate enzyme activity. A TAT-Bcp1 fusion protein was constructed to allow its internalization and verify the effect of Bcp1 on H9c2 rat cardiomyoblasts subjected to oxidative stress. The results reveal that TAT-Bcp1 is not cytotoxic and inhibits H2O2-induced apoptosis in H9c2 cells by reducing the H2O2 content inside these cells.},
}
@article {pmid27729650,
year = {2016},
author = {Du Toit, A},
title = {Archaeal genomics: Divergent methanogenic archaea.},
journal = {Nature reviews. Microbiology},
volume = {14},
number = {11},
pages = {667},
pmid = {27729650},
issn = {1740-1534},
}
@article {pmid27725793,
year = {2016},
author = {Esquivel-Elizondo, S and Parameswaran, P and Delgado, AG and Maldonado, J and Rittmann, BE and Krajmalnik-Brown, R},
title = {Archaea and Bacteria Acclimate to High Total Ammonia in a Methanogenic Reactor Treating Swine Waste.},
journal = {Archaea (Vancouver, B.C.)},
volume = {2016},
number = {},
pages = {4089684},
pmid = {27725793},
issn = {1472-3654},
mesh = {Ammonia/*metabolism ; Anaerobiosis ; Animals ; Archaea/*classification/genetics/growth &amp; development/*metabolism ; Bacteria/*classification/genetics/growth &amp; development/*metabolism ; Biological Oxygen Demand Analysis ; Bioreactors/*microbiology ; *Biota ; Culture Media/chemistry ; Manure ; Real-Time Polymerase Chain Reaction ; Swine ; },
abstract = {Inhibition by ammonium at concentrations above 1000 mgN/L is known to harm the methanogenesis phase of anaerobic digestion. We anaerobically digested swine waste and achieved steady state COD-removal efficiency of around 52% with no fatty-acid or H2 accumulation. As the anaerobic microbial community adapted to the gradual increase of total ammonia-N (NH3-N) from 890 ± 295 to 2040 ± 30 mg/L, the Bacterial and Archaeal communities became less diverse. Phylotypes most closely related to hydrogenotrophic Methanoculleus (36.4%) and Methanobrevibacter (11.6%), along with acetoclastic Methanosaeta (29.3%), became the most abundant Archaeal sequences during acclimation. This was accompanied by a sharp increase in the relative abundances of phylotypes most closely related to acetogens and fatty-acid producers (Clostridium, Coprococcus, and Sphaerochaeta) and syntrophic fatty-acid Bacteria (Syntrophomonas, Clostridium, Clostridiaceae species, and Cloacamonaceae species) that have metabolic capabilities for butyrate and propionate fermentation, as well as for reverse acetogenesis. Our results provide evidence countering a prevailing theory that acetoclastic methanogens are selectively inhibited when the total ammonia-N concentration is greater than ~1000 mgN/L. Instead, acetoclastic and hydrogenotrophic methanogens coexisted in the presence of total ammonia-N of ~2000 mgN/L by establishing syntrophic relationships with fatty-acid fermenters, as well as homoacetogens able to carry out forward and reverse acetogenesis.},
}
@article {pmid27720988,
year = {2016},
author = {Ciragan, A and Aranko, AS and Tascon, I and Iwaï, H},
title = {Salt-inducible Protein Splicing in cis and trans by Inteins from Extremely Halophilic Archaea as a Novel Protein-Engineering Tool.},
journal = {Journal of molecular biology},
volume = {428},
number = {23},
pages = {4573-4588},
doi = {10.1016/j.jmb.2016.10.006},
pmid = {27720988},
issn = {1089-8638},
mesh = {Bacterial Proteins/metabolism ; Enzyme Activators/*metabolism ; Halobacteriales/*enzymology/metabolism ; *Inteins ; Isotope Labeling/methods ; Membrane Proteins/metabolism ; Protein Engineering/*methods ; *Protein Splicing ; Salts/*metabolism ; },
abstract = {Intervening protein sequences (inteins) from extremely halophilic haloarchaea can be inactive under low salinity but could be activated by increasing the salt content to a specific concentration for each intein. The halo-obligatory inteins confer high solubility under both low and high salinity conditions. We showed the broad utility of salt-dependent protein splicing in cis and trans by demonstrating backbone cyclization, self-cleavage for purification, and scarless protein ligation for segmental isotopic labeling. Artificially split MCM2 intein derived from Halorhabdus utahensis remained highly soluble and was capable of protein trans-splicing with excellent ligation kinetics by reassembly under high salinity conditions. Importantly, the MCM2 intein has the active site residue of Ser at the +1 position, which remains in the ligated product, instead of Cys as found in many other efficient split inteins. Since Ser is more abundant than Cys in proteins, the novel split intein could widen the applications of segmental labeling in protein NMR spectroscopy and traceless protein ligation by exploiting a Ser residue in the native sequences as the +1 position of the MCM2 intein. The split halo-obligatory intein was successfully used to demonstrate the utility in NMR investigation of intact proteins by producing segmentally isotope-labeled intact TonB protein from Helicobacter pylori.},
}
@article {pmid27687996,
year = {2016},
author = {Cerrillo, M and Morey, L and Viñas, M and Bonmatí, A},
title = {Assessment of active methanogenic archaea in a methanol-fed upflow anaerobic sludge blanket reactor.},
journal = {Applied microbiology and biotechnology},
volume = {100},
number = {23},
pages = {10137-10146},
doi = {10.1007/s00253-016-7862-4},
pmid = {27687996},
issn = {1432-0614},
mesh = {Acetates/metabolism ; Anaerobiosis ; Archaea/*classification/genetics/*metabolism ; Bioreactors/*microbiology ; DNA, Ribosomal/chemistry/genetics ; High-Throughput Nucleotide Sequencing ; Hydrogen/metabolism ; Methane/*metabolism ; Methanol/*metabolism ; Oxidoreductases/genetics ; RNA, Ribosomal, 16S/genetics ; Real-Time Polymerase Chain Reaction ; Sequence Analysis, DNA ; Sewage/*microbiology ; },
abstract = {Methanogenic archaea enrichment of a granular sludge was undertaken in an upflow anaerobic sludge blanket (UASB) reactor fed with methanol in order to enrich methylotrophic and hydrogenotrophic methanogenic populations. A microbial community assessment, in terms of microbial composition and activity-throughout the different stages of the feeding process with methanol and acetate-was performed using specific methanogenic activity (SMA) assays, quantitative real-time polymerase chain reaction (qPCR), and high-throughput sequencing of 16S ribosomal RNA (rRNA) genes from DNA and complementary DNA (cDNA). Distinct methanogenic enrichment was revealed by qPCR of mcrA gene in the methanol-fed community, being two orders of magnitude higher with respect to the initial inoculum, achieving a final mcrA/16S rRNA ratio of 0.25. High-throughput sequencing analysis revealed that the resulting methanogenic population was mainly composed by methylotrophic archaea (Methanomethylovorans and Methanolobus genus), being also highly active according to the RNA-based assessment. SMA confirmed that the methylotrophic pathway, with a direct conversion of methanol to CH4, was the main step of methanol degradation in the UASB. The biomass from the UASB, enriched in methanogenic archaea, may bear great potential as additional inoculum for bioreactors to carry out biogas production and other related processes.},
}
@article {pmid27683365,
year = {2016},
author = {Gulbudak, H and Weitz, JS},
title = {A touch of sleep: biophysical model of contact-mediated dormancy of archaea by viruses.},
journal = {Proceedings. Biological sciences},
volume = {283},
number = {1839},
pages = {},
pmid = {27683365},
issn = {1471-2954},
abstract = {The canonical view of the interactions between viruses and their microbial hosts presumes that changes in host and virus fate requires the initiation of infection of a host by a virus. Infection may lead to the death of the host cell and release of viruses, to the elimination of the viral genome through cellular defence mechanisms or the integration of the viral genome with the host as a chromosomal or extrachromosomal element. Here, we revisit this canonical view, inspired by recent experimental findings in which the majority of target host cells can be induced into a dormant state when exposed to either active or deactivated viruses, even when viruses are present at low relative titre. We propose that both the qualitative phenomena and the quantitative timescales of dormancy induction are consistent with the hypothesis that cellular physiology can be altered by contact on the surface of host cells rather than strictly by infection In order to test this hypothesis, we develop and study a biophysical model of contact-mediated dynamics involving virus particles and target cells. We show how virus particles can catalyse cellular transformations among many cells, even if they ultimately infect only one (or none). We also find that population-scale dormancy is robust to variation in the representation of model dynamics, including cell growth, death and recovery.},
}
@article {pmid27681926,
year = {2016},
author = {Lauer, A and Sørensen, KB and Teske, A},
title = {Phylogenetic Characterization of Marine Benthic Archaea in Organic-Poor Sediments of the Eastern Equatorial Pacific Ocean (ODP Site 1225).},
journal = {Microorganisms},
volume = {4},
number = {3},
pages = {},
pmid = {27681926},
issn = {2076-2607},
abstract = {Sequencing surveys of microbial communities in marine subsurface sediments have focused on organic-rich, continental margins; the database for organic-lean deep-sea sediments from mid-ocean regions is underdeveloped. The archaeal community in subsurface sediments of ODP Site 1225 in the eastern equatorial Pacific (3760 m water depth; 1.1 and 7.8 m sediment depth) was analyzed by PCR, cloning and sequencing, and by denaturant gradient gel electrophoresis (DGGE) of 16S rRNA genes. Three uncultured archaeal lineages with different depth distributions were found: Marine Group I (MG-I) within the Thaumarchaeota, its sister lineage Marine Benthic Group A (MBG-A), the phylum-level archaeal lineage Marine Benthic Group B (also known as Deep-Sea Archaeal Group or Lokiarchaeota), and the Deep-Sea Euryarchaeotal Group 3. The MG-I phylotypes included representatives of sediment clusters that are distinct from the pelagic members of this phylum. On the scale from fully oxidized, extremely organic carbon-depleted sediments (for example, those the South Pacific Gyre) to fully reduced, organic carbon-rich marine subsurface sediments (such as those of the Peru Margin), Ocean Drilling Program (ODP) Site 1225 falls into the non-extreme organic carbon-lean category, and harbors archaeal communities from both ends of the spectrum.},
}
@article {pmid27679621,
year = {2016},
author = {Zu, Q and Zhong, L and Deng, Y and Shi, Y and Wang, B and Jia, Z and Lin, X and Feng, Y},
title = {Geographical Distribution of Methanogenic Archaea in Nine Representative Paddy Soils in China.},
journal = {Frontiers in microbiology},
volume = {7},
number = {},
pages = {1447},
pmid = {27679621},
issn = {1664-302X},
abstract = {Paddy field methanogenic archaea are responsible for methane (CH4) production and contribute significantly to climate change. The information regarding the spatial variations in the abundance, the diversity and the composition of such ecologically important microbes, however, is quite limited at large scale. In this investigation, we studied the abundance, alpha diversity and geographical distribution of methanogenic archaeal communities in nine representative paddy sites, along a large latitudinal gradient in China, using pyrosequencing and real-time quantitative PCR. It is found that all paddy soils harbor constant methanogenic archaeal constituents, which is dominated by family Methanocellaceae (37.3%), Methanobacteriaceae (22.1%), Methanosaetaceae (17.2%), and Methanosarcinaceae (9.8%). Methanogenic archaeal abundance is primarily influenced by soil C (R = 0.612, P = 0.001) and N (R = 0.673, P = 0.001) contents, as well as alpha diversity by soil pH (PD: R = -0.552, P = 0.006; Chao1: R = -0.615, P = 0.002). Further exploration revealed that both spatial distance (R = 0.3469, P = 0.001, partial mental test) and soil chemical variables mainly about soil C and N (R = 0.2847, P = 0.001) are the two major factors affecting methanogenic archaeal community composition distribution in paddy soils. This finding will allow us to develop a better picture of the biogeographic ranges of these ecologically important microbes and get deeper insights into their ecology.},
}
@article {pmid27679616,
year = {2016},
author = {Chistoserdova, L},
title = {Wide Distribution of Genes for Tetrahydromethanopterin/Methanofuran-Linked C1 Transfer Reactions Argues for Their Presence in the Common Ancestor of Bacteria and Archaea.},
journal = {Frontiers in microbiology},
volume = {7},
number = {},
pages = {1425},
pmid = {27679616},
issn = {1664-302X},
}
@article {pmid27679615,
year = {2016},
author = {Thombre, RS and Shinde, V and Thaiparambil, E and Zende, S and Mehta, S},
title = {Antimicrobial Activity and Mechanism of Inhibition of Silver Nanoparticles against Extreme Halophilic Archaea.},
journal = {Frontiers in microbiology},
volume = {7},
number = {},
pages = {1424},
pmid = {27679615},
issn = {1664-302X},
abstract = {Haloarchaea are salt-loving halophilic microorganisms that inhabit marine environments, sea water, salterns, and lakes. The resistance of haloarchaea to physical extremities that challenge organismic survival is ubiquitous. Metal and antibiotic resistance of haloarchaea has been on an upsurge due to the exposure of these organisms to metal sinks and drug resistance genes augmented in their natural habitats due to anthropogenic activities and environmental pollution. The efficacy of silver nanoparticles (SNPs) as a potent and broad spectrum inhibitory agent is known, however, there are no reports on the inhibitory activity of SNPs against haloarchaea. In the present study, we have investigated the antimicrobial potentials of SNPs synthesized using aqueous leaf extract of Cinnamomum tamala against antibiotic resistant haloarchaeal isolates Haloferax prahovense RR8, Haloferax lucentense RR15, Haloarcula argentinensis RR10 and Haloarcula tradensis RR13. The synthesized SNPs were characterized by UV-Vis spectroscopy, scanning electron microscopy, energy dispersive X-ray spectroscopy, dynamic light scattering, X-ray diffraction and Fourier transform infrared spectroscopy. The SNPs demonstrated potent antimicrobial activity against the haloarchaea with a minimum inhibitory concentration of 300-400 μg/ml. Growth kinetics of haloarchaea in the presence of SNPs was studied by employing the Baranyi mathematical model for microbial growth using the DMFit curve fitting program. The C. tamala SNPs also demonstrated cytotoxic activity against human lung adenocarcinoma epithelial cell line (A540) and human breast adenocarcinoma cell line (MCF-7). The mechanism of inhibition of haloarchaea by the SNPs was investigated. The plausible mechanism proposed is the alterations and disruption of haloarchaeal membrane permeability by turbulence, inhibition of respiratory dehydrogenases and lipid peroxidation causing cellular and DNA damage resulting in cell death.},
}
@article {pmid27670118,
year = {2016},
author = {Dar, D and Prasse, D and Schmitz, RA and Sorek, R},
title = {Widespread formation of alternative 3' UTR isoforms via transcription termination in archaea.},
journal = {Nature microbiology},
volume = {1},
number = {10},
pages = {16143},
pmid = {27670118},
issn = {2058-5276},
mesh = {*3' Untranslated Regions ; Archaea/*genetics ; Archaeal Proteins/genetics ; Gene Expression Profiling ; *Gene Expression Regulation, Archaeal ; Genes, Archaeal ; RNA Isoforms/*genetics ; RNA, Archaeal/*genetics ; RNA, Untranslated ; *Transcription Termination, Genetic ; },
abstract = {Transcription termination sets the 3' end boundaries of RNAs and plays key roles in gene regulation. Although termination has been well studied in bacteria, the signals that mediate termination in archaea remain poorly understood. Here, we applied term-seq to comprehensively map RNA 3' termini, with single-base precision, in two phylogenetically distant archaea: Methanosarcina mazei and Sulfolobus acidocaldarius. Comparison of RNA 3' ends across hundreds of genes revealed the sequence composition of transcriptional terminators in each organism, highlighting both common and divergent characteristics between the different archaeal phyla. We find that, in contrast to bacteria, a considerable portion of archaeal genes are controlled by multiple consecutive terminators, generating several alternative 3' untranslated region isoforms for >30% of the genes. These alternative isoforms often present marked length differences, implying that archaea can employ regulation via alternative 3' untranslated regions, similar to eukaryotes. Although most of the terminators are intergenic, we discover numerous cases in which termination of one gene occurs within the coding region of a downstream gene, implying that leaky termination may tune inter-transcript stoichiometry in multi-gene operons. These results provide the first high-throughput maps of transcriptional terminators in archaea and point to an evolutionary path linking bacterial and eukaryal non-coding regulatory strategies.},
}
@article {pmid27652169,
year = {2016},
author = {Watanabe, K and Kohzu, A and Suda, W and Yamamura, S and Takamatsu, T and Takenaka, A and Koshikawa, MK and Hayashi, S and Watanabe, M},
title = {Microbial nitrification in throughfall of a Japanese cedar associated with archaea from the tree canopy.},
journal = {SpringerPlus},
volume = {5},
number = {1},
pages = {1596},
pmid = {27652169},
issn = {2193-1801},
abstract = {To investigate the nitrification potential of phyllospheric microbes, we incubated throughfall samples collected under the canopies of Japanese cedar (Cryptomeria japonica) and analyzed the transformation of inorganic nitrogen in the samples. Nitrate concentration increased in the unfiltered throughfall after 4 weeks of incubation, but remained nearly constant in the filtered samples (pore size: 0.2 and 0.4 µm). In the unfiltered samples, δ(18)O and δ(15)N values of nitrate decreased during incubation. In addition, archaeal ammonia monooxygenase subunit A (amoA) genes, which participate in the oxidation of ammonia, were found in the throughfall samples, although betaproteobacterial amoA genes were not detected. The amoA genes recovered from the leaf surface of C. japonica were also from archaea. Conversely, nitrate production, decreased isotope ratios of nitrate, and the presence of amoA genes was not observed in rainfall samples collected from an open area. Thus, the microbial nitrification that occurred in the incubated throughfall is likely due to ammonia-oxidizing archaea that were washed off the tree canopy by precipitation.},
}
@article {pmid27642845,
year = {2016},
author = {Umu, SU and Poole, AM and Dobson, RC and Gardner, PP},
title = {Avoidance of stochastic RNA interactions can be harnessed to control protein expression levels in bacteria and archaea.},
journal = {eLife},
volume = {5},
number = {},
pages = {},
pmid = {27642845},
issn = {2050-084X},
mesh = {Archaea/*genetics/*metabolism ; Bacteria/*genetics/*metabolism ; Genes, Reporter ; Green Fluorescent Proteins/analysis/genetics ; *Protein Biosynthesis ; RNA, Messenger/*metabolism ; RNA, Untranslated/*metabolism ; },
abstract = {A critical assumption of gene expression analysis is that mRNA abundances broadly correlate with protein abundance, but these two are often imperfectly correlated. Some of the discrepancy can be accounted for by two important mRNA features: codon usage and mRNA secondary structure. We present a new global factor, called mRNA:ncRNA avoidance, and provide evidence that avoidance increases translational efficiency. We also demonstrate a strong selection for the avoidance of stochastic mRNA:ncRNA interactions across prokaryotes, and that these have a greater impact on protein abundance than mRNA structure or codon usage. By generating synonymously variant green fluorescent protein (GFP) mRNAs with different potential for mRNA:ncRNA interactions, we demonstrate that GFP levels correlate well with interaction avoidance. Therefore, taking stochastic mRNA:ncRNA interactions into account enables precise modulation of protein abundance.},
}
@article {pmid27624130,
year = {2016},
author = {Quemin, ER and Chlanda, P and Sachse, M and Forterre, P and Prangishvili, D and Krupovic, M},
title = {Eukaryotic-Like Virus Budding in Archaea.},
journal = {mBio},
volume = {7},
number = {5},
pages = {},
pmid = {27624130},
issn = {2150-7511},
mesh = {Archaea/ultrastructure/*virology ; Electron Microscope Tomography ; Fuselloviridae/*physiology/ultrastructure ; *Virus Release ; },
abstract = {UNLABELLED: Similar to many eukaryotic viruses (and unlike bacteriophages), viruses infecting archaea are often encased in lipid-containing envelopes. However, the mechanisms of their morphogenesis and egress remain unexplored. Here, we used dual-axis electron tomography (ET) to characterize the morphogenesis of Sulfolobus spindle-shaped virus 1 (SSV1), the prototype of the family Fuselloviridae and representative of the most abundant archaea-specific group of viruses. Our results show that SSV1 assembly and egress are concomitant and occur at the cellular cytoplasmic membrane via a process highly reminiscent of the budding of enveloped viruses that infect eukaryotes. The viral nucleoprotein complexes are extruded in the form of previously unknown rod-shaped intermediate structures which have an envelope continuous with the host membrane. Further maturation into characteristic spindle-shaped virions takes place while virions remain attached to the cell surface. Our data also revealed the formation of constricted ring-like structures which resemble the budding necks observed prior to the ESCRT machinery-mediated membrane scission during egress of various enveloped viruses of eukaryotes. Collectively, we provide evidence that archaeal spindle-shaped viruses contain a lipid envelope acquired upon budding of the viral nucleoprotein complex through the host cytoplasmic membrane. The proposed model bears a clear resemblance to the egress strategy employed by enveloped eukaryotic viruses and raises important questions as to how the archaeal single-layered membrane composed of tetraether lipids can undergo scission.<br><br>IMPORTANCE: The replication of enveloped viruses has been extensively studied in eukaryotes but has remained unexplored for enveloped viruses infecting Archaea Here, we provide a sequential view on the assembly and egress of SSV1, a prototypic archaeal virus. The observed process is highly similar to the budding of eukaryotic enveloped viruses, including human immunodeficiency virus, influenza virus, and Ebola virus. The present study is the first to characterize such a phenomenon in archeal cells, showing that membrane budding is not an exclusive feature of eukaryotic viruses. Our results provide significant insights into the biogenesis and architecture of unique, spindle-shaped virions that infect archaea. Furthermore, our findings open doors for future inquiries into (i) the evolution of the virus budding process, (ii) mechanistic details of virus-mediated membrane scission in Archaea, and (iii) elucidation of virus- and host-encoded molecular players responsible for archaeal membrane and surface remodeling.},
}
@article {pmid27598206,
year = {2016},
author = {Jones, DL and Baxter, BK},
title = {Bipyrimidine Signatures as a Photoprotective Genome Strategy in G + C-rich Halophilic Archaea.},
journal = {Life (Basel, Switzerland)},
volume = {6},
number = {3},
pages = {},
pmid = {27598206},
issn = {2075-1729},
abstract = {Halophilic archaea experience high levels of ultraviolet (UV) light in their environments and demonstrate resistance to UV irradiation. DNA repair systems and carotenoids provide UV protection but do not account for the high resistance observed. Herein, we consider genomic signatures as an additional photoprotective strategy. The predominant forms of UV-induced DNA damage are cyclobutane pyrimidine dimers, most notoriously thymine dimers (T^Ts), which form at adjacent Ts. We tested whether the high G + C content seen in halophilic archaea serves a photoprotective function through limiting T nucleotides, and thus T^T lesions. However, this speculation overlooks the other bipyrimidine sequences, all of which capable of forming photolesions to varying degrees. Therefore, we designed a program to determine the frequencies of the four bipyrimidine pairs (5' to 3': TT, TC, CT, and CC) within genomes of halophilic archaea and four other randomized sample groups for comparison. The outputs for each sampled genome were weighted by the intrinsic photoreactivities of each dinucleotide pair. Statistical methods were employed to investigate intergroup differences. Our findings indicate that the UV-resistance seen in halophilic archaea can be attributed in part to a genomic strategy: high G + C content and the resulting bipyrimidine signature reduces the genomic photoreactivity.},
}
@article {pmid27596731,
year = {2016},
author = {Zhang, X and Tang, Y and Shi, Y and He, N and Wen, X and Yu, Q and Zheng, C and Sun, X and Qiu, W},
title = {Responses of soil hydrolytic enzymes, ammonia-oxidizing bacteria and archaea to nitrogen applications in a temperate grassland in Inner Mongolia.},
journal = {Scientific reports},
volume = {6},
number = {},
pages = {32791},
pmid = {27596731},
issn = {2045-2322},
mesh = {Ammonia/*metabolism ; Archaea/*metabolism ; Bacteria/*metabolism ; China ; Ecosystem ; Fertilizers/microbiology ; Grassland ; Hydrolysis ; Nitrification/physiology ; Nitrogen/*metabolism ; Oxidation-Reduction ; Soil ; Soil Microbiology ; },
abstract = {We used a seven-year urea gradient applied field experiment to investigate the effects of nitrogen (N) applications on soil N hydrolytic enzyme activity and ammonia-oxidizing microbial abundance in a typical steppe ecosystem in Inner Mongolia. The results showed that N additions inhibited the soil N-related hydrolytic enzyme activities, especially in 392 kg N ha(-1)yr(-1) treatment. As N additions increased, the amoA gene copy ratios of ammonia-oxidizing archaea (AOA) to ammonia-oxidizing bacteria (AOB) decreased from 1.13 to 0.65. Pearson correlation analysis showed that the AOA gene copies were negatively related with NH4(+)-N content. However, the AOB gene copies were positively correlated with NO3(-)-N content. Moderate N application rates (56-224 kg N ha(-1)yr(-1)) accompanied by P additions are beneficial to maintaining the abundance of AOB, as opposed to the inhibition of highest N application rate (392 kg N ha(-1)yr(-1)) on the abundance of AOB. This study suggests that the abundance of AOB and AOA would not decrease unless N applications exceed 224 kg N ha(-1)yr(-1) in temperate grasslands in Inner Mongolia.},
}
@article {pmid27582505,
year = {2016},
author = {Pergolizzi, G and Wagner, GK and Bowater, RP},
title = {Biochemical and Structural Characterisation of DNA Ligases from Bacteria and Archaea.},
journal = {Bioscience reports},
volume = {36},
number = {5},
pages = {00391},
pmid = {27582505},
issn = {1573-4935},
abstract = {DNA ligases are enzymes that seal breaks in the backbones of DNA, leading to them being essential for the survival of all organisms. DNA ligases have been studied from many different types of cells and organisms and shown to have diverse sizes and sequences, with well conserved specific sequences that are required for enzymatic activity. A significant number of DNA ligases have been isolated or prepared in recombinant forms and, here, we review their biochemical and structural characterisation. All DNA ligases contain an essential lysine that transfers an adenylate group from a co-factor to the 5'-phosphate of the DNA end that will ultimately be joined to the 3'-hydroxyl of the neighbouring DNA strand. The essential DNA ligases in bacteria use nicotinamide adenine dinucleotide (β -NAD[+]) as their co-factor whereas those that are essential in other cells use adenosine-5'-triphosphate (ATP) as their co-factor. This observation suggests that the essential bacterial enzyme could be targeted by novel antibiotics and the complex molecular structure of β -NAD[+] affords multiple opportunities for chemical modification. Several recent studies have synthesised novel derivatives and their biological activity against a range of DNA ligases has been evaluated as inhibitors for drug discovery and/or non-natural substrates for biochemical applications. Here, we review the recent advances that herald new opportunities to alter the biochemical activities of these important enzymes. The recent development of modified derivatives of nucleotides highlights that the continued combination of structural, biochemical and biophysical techniques will be useful in targeting these essential cellular enzymes.},
}
@article {pmid29251473,
year = {2016},
author = {Dong, L and Meng, Y and Wang, J and Sun, G},
title = {Effects of Transgenic Bt+CpTI cotton on the abundance and diversity of rhizosphere ammonia oxidizing bacteria and archaea.},
journal = {Journal of environmental biology},
volume = {37},
number = {5},
pages = {881-888},
pmid = {29251473},
issn = {0254-8704},
mesh = {Ammonia/*metabolism ; Archaea/classification/*metabolism ; Bacteria/classification/*metabolism ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; Gossypium/*genetics ; Oxidation-Reduction ; Plant Roots ; Plants, Genetically Modified ; Soil ; *Soil Microbiology ; },
abstract = {Genetically modified crops (GMCs) hold great promise for improving agricultural output, but at the same time present challenges in terms of environmental safety assessment. Ammonia oxidizers, including ammonia oxidizing bacteria (AOB) and archaea (AOA), are very important functional microbial groups in nitrogen cycle. The abundance and diversity of AOA and AOB in the rhizosphere of genetically modified cotton (SGK321) and non-GM cotton (SY321) across growth stages were investigated using real time quantitative PCR (qPCR) and terminal restriction fragment length polymorphism (T-RFLP). Results showed that cotton genotype had a significant effect on the change in abundance of AOA and AOB, as indicated by amoA copy number. Variations in AOB abundance in rhizosphere of SY321 differed from those in SGK321. The number of AOB in the rhizosphere of SY321 fluctuated considerably: It dramatically decreased from 1.2?106 copies g-1 dry soil to 3?105 copies g-1 dry soil during the flowering stage and then increased to 1.1?106 copies g-1 and 1.5?106 copies g-1 at the belling and boll opening stages, respectively. However, abundance of AOB in the rhizosphere of SGK321 was relatively stable during all the stages of growth. The effect of SGK321 and SY321 on AOA number was quite similar to that of AOB: AOA abundance in SGK321 increased smoothly from 1.0 ?105 copies g-1 dry soil to 1.4?106 copies g-1 dry soil during growth, but that in SY321 fluctuated. Correspondence analysis (CA), canonical CA (CCA), and partial CCA (pCCA) of T-RFLP profiles of AOA and AOB showed that AOB community changed across growth stages in both cotton genotypes, and cotton genotype was the most important factor affecting the AOA community. In conclusion, the current findings indicated no adverse effect of GM cotton on functional microorganisms.},
}
@article {pmid27572439,
year = {2016},
author = {Needham, DM and Fuhrman, JA},
title = {Pronounced daily succession of phytoplankton, archaea and bacteria following a spring bloom.},
journal = {Nature microbiology},
volume = {1},
number = {},
pages = {16005},
pmid = {27572439},
issn = {2058-5276},
mesh = {Archaea/classification/genetics/*growth &amp; development ; Bacteria/classification/genetics/*growth &amp; development ; California ; Cluster Analysis ; DNA, Ribosomal/chemistry/genetics ; Eukaryota/classification/genetics/*growth &amp; development ; Phylogeny ; Phytoplankton/classification/genetics/*growth &amp; development ; RNA, Archaeal/genetics ; RNA, Bacterial/genetics ; RNA, Protozoan/genetics ; RNA, Ribosomal, 16S/genetics ; Seasons ; Seawater/*microbiology ; Sequence Analysis, DNA ; },
abstract = {Marine phytoplankton perform approximately half of global carbon fixation, with their blooms contributing disproportionately to carbon sequestration(1), and most phytoplankton production is ultimately consumed by heterotrophic prokaryotes(2). Therefore, phytoplankton and heterotrophic community dynamics are important in modelling carbon cycling and the impacts of global change(3). In a typical bloom, diatoms dominate initially, transitioning over several weeks to smaller and motile phytoplankton(4). Here, we show unexpected, rapid community variation from daily rRNA analysis of phytoplankton and prokaryotic community members following a bloom off southern California. Analysis of phytoplankton chloroplast 16S rRNA demonstrated ten different dominant phytoplankton over 18 days alone, including four taxa with animal toxin-producing strains. The dominant diatoms, flagellates and picophytoplankton varied dramatically in carbon export potential. Dominant prokaryotes also varied rapidly. Euryarchaea briefly became the most abundant organism, peaking over a few days to account for about 40% of prokaryotes. Phytoplankton and prokaryotic communities correlated better with each other than with environmental parameters. Extending beyond the traditional view of blooms being controlled primarily by physics and inorganic nutrients, these dynamics imply highly heterogeneous, continually changing conditions over time and/or space and suggest that interactions among microorganisms are critical in controlling plankton diversity, dynamics and fates.},
}
@article {pmid27572167,
year = {2016},
author = {Baker, BJ and Saw, JH and Lind, AE and Lazar, CS and Hinrichs, KU and Teske, AP and Ettema, TJ},
title = {Genomic inference of the metabolism of cosmopolitan subsurface Archaea, Hadesarchaea.},
journal = {Nature microbiology},
volume = {1},
number = {},
pages = {16002},
pmid = {27572167},
issn = {2058-5276},
mesh = {Ammonia/metabolism ; Archaea/classification/*genetics/*metabolism ; Carbon Monoxide/metabolism ; *Environmental Microbiology ; Estuaries ; Hot Springs ; Hydrogen/metabolism ; Metabolic Networks and Pathways/*genetics ; Nitrites/metabolism ; Oxidation-Reduction ; *Phylogeny ; Sequence Analysis, DNA ; },
abstract = {The subsurface biosphere is largely unexplored and contains a broad diversity of uncultured microbes(1). Despite being one of the few prokaryotic lineages that is cosmopolitan in both the terrestrial and marine subsurface(2-4), the physiological and ecological roles of SAGMEG (South-African Gold Mine Miscellaneous Euryarchaeal Group) Archaea are unknown. Here, we report the metabolic capabilities of this enigmatic group as inferred from genomic reconstructions. Four high-quality (63-90% complete) genomes were obtained from White Oak River estuary and Yellowstone National Park hot spring sediment metagenomes. Phylogenomic analyses place SAGMEG Archaea as a deeply rooting sister clade of the Thermococci, leading us to propose the name Hadesarchaea for this new Archaeal class. With an estimated genome size of around 1.5 Mbp, the genomes of Hadesarchaea are distinctly streamlined, yet metabolically versatile. They share several physiological mechanisms with strict anaerobic Euryarchaeota. Several metabolic characteristics make them successful in the subsurface, including genes involved in CO and H2 oxidation (or H2 production), with potential coupling to nitrite reduction to ammonia (DNRA). This first glimpse into the metabolic capabilities of these cosmopolitan Archaea suggests they are mediating key geochemical processes and are specialized for survival in the subsurface biosphere.},
}
@article {pmid27561235,
year = {2017},
author = {Zhu, Y and Sun, Y and Wang, C and Li, F},
title = {Impact of dietary fibre:starch ratio in shaping caecal archaea revealed in rabbits.},
journal = {Journal of animal physiology and animal nutrition},
volume = {101},
number = {4},
pages = {635-640},
doi = {10.1111/jpn.12585},
pmid = {27561235},
issn = {1439-0396},
mesh = {Animal Feed/analysis ; Animal Nutritional Physiological Phenomena ; Animals ; Archaea/genetics/*physiology ; Cecum/*microbiology ; Diet/veterinary ; Dietary Carbohydrates/analysis/*metabolism ; Dietary Fiber/analysis/*metabolism ; *Rabbits ; },
abstract = {In rabbits, many studies have investigated the effect of diet, including the fibre intake, on caecal microbiota; however, there are no direct measurements of the influence of diets with different dietary fibre-to-starch ratios and the archaeal community composition in the caecum. We used 16S rDNA sequencing to investigate the impact of different dietary neutral detergent fibre (NDF)-to-starch ratios (1.0-2.3) on the caecal archaeal community in rabbits. The results revealed that the archaeal community from all experimental rabbits was relatively less complex than intestinal bacterial community. High-throughput 16S rDNA sequencing of the gut archaea indicated that the rabbit caecum was inhabited by Methanobrevibacter and Methanosphaera species, and therefore is possibly dominated by two species of archaea. Here, we compared the effect of different diets on the archaeal community in the rabbit caecum and found no significant differences in the diversity and abundance of caecal archaeal community of rabbits that were fed diets with different dietary fibre-to-starch ratios. Therefore, we suggest that the contribution of host-derived substrates to caecal archaea constitution is insignificant.},
}
@article {pmid27507826,
year = {2016},
author = {Fu, X and Liu, R and Sanchez, I and Silva-Sanchez, C and Hepowit, NL and Cao, S and Chen, S and Maupin-Furlow, J},
title = {Erratum for Fu et al., Ubiquitin-Like Proteasome System Represents a Eukaryotic-Like Pathway for Targeted Proteolysis in Archaea.},
journal = {mBio},
volume = {7},
number = {4},
pages = {},
doi = {10.1128/mBio.01192-16},
pmid = {27507826},
issn = {2150-7511},
}
@article {pmid27459543,
year = {2016},
author = {Hepowit, NL and de Vera, IM and Cao, S and Fu, X and Wu, Y and Uthandi, S and Chavarria, NE and Englert, M and Su, D and Sӧll, D and Kojetin, DJ and Maupin-Furlow, JA},
title = {Mechanistic insight into protein modification and sulfur mobilization activities of noncanonical E1 and associated ubiquitin-like proteins of Archaea.},
journal = {The FEBS journal},
volume = {283},
number = {19},
pages = {3567-3586},
pmid = {27459543},
issn = {1742-4658},
support = {R01 GM022854/GM/NIGMS NIH HHS/United States ; R01 GM057498/GM/NIGMS NIH HHS/United States ; R37 GM022854/GM/NIGMS NIH HHS/United States ; },
mesh = {Adenosine Triphosphate/metabolism ; Archaeal Proteins/*chemistry/*metabolism ; Cysteine/physiology ; Haloferax volcanii/enzymology ; Ligands ; Models, Molecular ; Protein Binding ; Protein Domains ; Small Ubiquitin-Related Modifier Proteins/chemistry/*metabolism ; Sulfhydryl Compounds/metabolism ; Sulfur/*metabolism ; Thermodynamics ; Ubiquitin-Activating Enzymes/*chemistry/*metabolism ; Ubiquitination ; },
abstract = {Here we provide the first detailed biochemical study of a noncanonical E1-like enzyme with broad specificity for cognate ubiquitin-like (Ubl) proteins that mediates Ubl protein modification and sulfur mobilization to form molybdopterin and thiolated tRNA. Isothermal titration calorimetry and in vivo analyses proved useful in discovering that environmental conditions, ATP binding, and Ubl type controlled the mechanism of association of the Ubl protein with its cognate E1-like enzyme (SAMP and UbaA of the archaeon Haloferax volcanii, respectively). Further analysis revealed that ATP hydrolysis triggered the formation of thioester and peptide bonds within the Ubl:E1-like complex. Importantly, the thioester was an apparent precursor to Ubl protein modification but not sulfur mobilization. Comparative modeling to MoeB/ThiF guided the discovery of key residues within the adenylation domain of UbaA that were needed to bind ATP as well as residues that were specifically needed to catalyze the downstream reactions of sulfur mobilization and/or Ubl protein modification. UbaA was also found to be Ubl-automodified at lysine residues required for early (ATP binding) and late (sulfur mobilization) stages of enzyme activity revealing multiple layers of autoregulation. Cysteine residues, distinct from the canonical E1 'active site' cysteine, were found important in UbaA function supporting a model that this noncanonical E1 is structurally flexible in its active site to allow Ubl~adenylate, Ubl~E1-like thioester and cysteine persulfide(s) intermediates to form.},
}
@article {pmid27450111,
year = {2016},
author = {Barillà, D},
title = {Driving Apart and Segregating Genomes in Archaea.},
journal = {Trends in microbiology},
volume = {24},
number = {12},
pages = {957-967},
pmid = {27450111},
issn = {1878-4380},
support = {BB/F012004/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Archaea/*genetics ; Archaeal Proteins/*genetics ; Bacteria/genetics ; Cell Cycle/genetics ; Conserved Sequence ; DNA/genetics/metabolism ; DNA Replication ; Eukaryotic Cells ; *Genome, Archaeal ; Plasmids/genetics ; },
abstract = {Genome segregation is a fundamental biological process in organisms from all domains of life. How this stage of the cell cycle unfolds in Eukarya has been clearly defined and considerable progress has been made to unravel chromosome partition in Bacteria. The picture is still elusive in Archaea. The lineages of this domain exhibit different cell-cycle lifestyles and wide-ranging chromosome copy numbers, fluctuating from 1 up to 55. This plurality of patterns suggests that a variety of mechanisms might underpin disentangling and delivery of DNA molecules to daughter cells. Here I describe recent developments in archaeal genome maintenance, including investigations of novel genome segregation machines that point to unforeseen bacterial and eukaryotic connections.},
}
@article {pmid27408734,
year = {2016},
author = {Khelaifia, S and Raoult, D},
title = {Haloferax massiliensis sp. nov., the first human-associated halophilic archaea.},
journal = {New microbes and new infections},
volume = {12},
number = {},
pages = {96-98},
pmid = {27408734},
issn = {2052-2975},
abstract = {We report the main characteristics of Haloferax massiliensis strain Arc-Hr(T) (= CSUR P974) isolated from stool specimen of a 22-year-old Amazonian obese female patient.},
}
@article {pmid27388368,
year = {2016},
author = {Kambura, AK and Mwirichia, RK and Kasili, RW and Karanja, EN and Makonde, HM and Boga, HI},
title = {Bacteria and Archaea diversity within the hot springs of Lake Magadi and Little Magadi in Kenya.},
journal = {BMC microbiology},
volume = {16},
number = {1},
pages = {136},
pmid = {27388368},
issn = {1471-2180},
mesh = {Archaea/*classification/genetics/isolation &amp; purification ; Bacteria/*classification/genetics/isolation &amp; purification ; Biodiversity ; Classification ; DNA, Archaeal/analysis ; DNA, Bacterial/analysis ; Geologic Sediments ; Hot Springs/*microbiology ; Kenya ; Lakes/chemistry/*microbiology ; Phylogeny ; Sequence Analysis, DNA ; *Water Microbiology ; },
abstract = {BACKGROUND: Lake Magadi and little Magadi are hypersaline, alkaline lakes situated in the southern part of Kenyan Rift Valley. Solutes are supplied mainly by a series of alkaline hot springs with temperatures as high as 86 °C. Previous culture-dependent and culture-independent studies have revealed diverse groups of microorganisms thriving under these conditions. Previous culture independent studies were based on the analysis of 16S rDNA but were done on less saline lakes. For the first time, this study combined illumina sequencing and analysis of amplicons of both total community rDNA and 16S rRNA cDNA to determine the diversity and community structure of bacteria and archaea within 3 hot springs of L. Magadi and little Magadi.<br><br>METHODS: Water, wet sediments and microbial mats were collected from springs in the main lake at a temperature of 45.1&#xa0;&#xb0;C and from Little Magadi "Nasikie eng'ida" (temperature of 81&#xa0;&#xb0;C and 83.6&#xa0;&#xb0;C). Total community DNA and RNA were extracted from samples using phenol-chloroform and Trizol RNA extraction protocols respectively. The 16S rRNA gene variable region (V4 - V7) of the extracted DNA and RNA were amplified and library construction performed following Illumina sequencing protocol. Sequences were analyzed done using QIIME while calculation of Bray-Curtis dissimilarities between datasets, hierarchical clustering, Non Metric Dimensional Scaling (NMDS) redundancy analysis (RDA) and diversity indices were carried out using the R programming language and the Vegan package.<br><br>RESULTS: Three thousand four hundred twenty-six and one thousand nine hundred thirteen OTUs were recovered from 16S rDNA and 16S rRNA cDNA respectively. Uncultured diversity accounted for 89.35&#xa0;% 16S rDNA and 87.61&#xa0;% 16S rRNA cDNA reads. The most abundant phyla in both the 16S rDNA and 16S rRNA cDNA datasets included: Proteobacteria (8.33-50&#xa0;%), Firmicutes 3.52-28.92&#xa0;%, Bacteroidetes (3.45-26.44&#xa0;%), Actinobacteria (0.98-28.57&#xa0;%) and Euryarchaeota (3.55-34.48&#xa0;%) in all samples. NMDS analyses of taxonomic composition clustered the taxa into three groups according to sample types (i.e. wet sediments, mats and water samples) with evident overlap of clusters between wet sediments and microbial mats from the three sample types in both DNA and cDNA datasets. The hot spring (45.1&#xa0;&#xb0;C) contained less diverse populations compared to those in Little Magadi (81-83&#xa0;&#xb0;C).<br><br>CONCLUSION: There were significant differences in microbial community structure at 95&#xa0;% level of confidence for both total diversity (P value, 0.009) based on 16S rDNA analysis and active microbial diversity (P value, 0.01) based on 16S rRNA cDNA analysis, within the three hot springs. Differences in microbial composition and structure were observed as a function of sample type and temperature, with wet sediments harboring the highest diversity.},
}
@article {pmid27388200,
year = {2016},
author = {Castro, C and Zhang, R and Liu, J and Bellenberg, S and Neu, TR and Donati, E and Sand, W and Vera, M},
title = {Biofilm formation and interspecies interactions in mixed cultures of thermo-acidophilic archaea Acidianus spp. and Sulfolobus metallicus.},
journal = {Research in microbiology},
volume = {167},
number = {7},
pages = {604-612},
doi = {10.1016/j.resmic.2016.06.005},
pmid = {27388200},
issn = {1769-7123},
mesh = {Acidianus/*physiology ; Bacterial Adhesion ; Biofilms/*growth &amp; development ; *Environmental Microbiology ; Iron/metabolism ; *Microbial Interactions ; Microscopy, Confocal ; Sulfides/metabolism ; Sulfolobus/*physiology ; Sulfur/metabolism ; },
abstract = {The understanding of biofilm formation by bioleaching microorganisms is of great importance for influencing mineral dissolution rates and to prevent acid mine drainage (AMD). Thermo-acidophilic archaea such as Acidianus, Sulfolobus and Metallosphaera are of special interest due to their ability to perform leaching at high temperatures, thereby enhancing leaching rates. In this work, leaching experiments and visualization by microscopy of cell attachment and biofilm formation patterns of the crenarchaeotes Sulfolobus metallicus DSM 6482(T) and the Acidianus isolates DSM 29038 and DSM 29099 in pure and mixed cultures on sulfur or pyrite were studied. Confocal laser scanning microscopy (CLSM) combined with fluorescent dyes as well as fluorescently labeled lectins were used to visualize different components (e.g. DNA, proteins or glycoconjugates) of the aforementioned species. The data indicate that cell attachment and the subsequently formed biofilms were species- and substrate-dependent. Pyrite leaching experiments coupled with pre-colonization and further inoculation with a second species suggest that both species may negatively influence each other during pyrite leaching with respect to initial attachment and pyrite dissolution rates. In addition, the investigation of binary biofilms on pyrite showed that both species were heterogeneously distributed on pyrite surfaces in the form of individual cells or microcolonies. Physical contact between the two species seems to occur, as revealed by specific lectins able to specifically bind single species within mixed cultures.},
}
@article {pmid27386507,
year = {2016},
author = {Danovaro, R and Molari, M and Corinaldesi, C and Dell'Anno, A},
title = {Macroecological drivers of archaea and bacteria in benthic deep-sea ecosystems.},
journal = {Science advances},
volume = {2},
number = {4},
pages = {e1500961},
pmid = {27386507},
issn = {2375-2548},
mesh = {Archaea/*growth &amp; development ; Bacteria/*growth &amp; development ; Biodiversity ; Biomass ; Climate Change ; *Ecosystem ; Geologic Sediments ; Seawater/microbiology ; Temperature ; },
abstract = {Bacteria and archaea dominate the biomass of benthic deep-sea ecosystems at all latitudes, playing a crucial role in global biogeochemical cycles, but their macroscale patterns and macroecological drivers are still largely unknown. We show the results of the most extensive field study conducted so far to investigate patterns and drivers of the distribution and structure of benthic prokaryote assemblages from 228 samples collected at latitudes comprising 34°N to 79°N, and from ca. 400- to 5570-m depth. We provide evidence that, in deep-sea ecosystems, benthic bacterial and archaeal abundances significantly increase from middle to high latitudes, with patterns more pronounced for archaea, and particularly for Marine Group I Thaumarchaeota. Our results also reveal that different microbial components show varying sensitivities to changes in temperature conditions and food supply. We conclude that climate change will primarily affect deep-sea benthic archaea, with important consequences on global biogeochemical cycles, particularly at high latitudes.},
}
@article {pmid27376057,
year = {2016},
author = {Régnier, M and Chassignet, P},
title = {Accurate Prediction of the Statistics of Repetitions in Random Sequences: A Case Study in Archaea Genomes.},
journal = {Frontiers in bioengineering and biotechnology},
volume = {4},
number = {},
pages = {35},
pmid = {27376057},
issn = {2296-4185},
abstract = {Repetitive patterns in genomic sequences have a great biological significance and also algorithmic implications. Analytic combinatorics allow to derive formula for the expected length of repetitions in a random sequence. Asymptotic results, which generalize previous works on a binary alphabet, are easily computable. Simulations on random sequences show their accuracy. As an application, the sample case of Archaea genomes illustrates how biological sequences may differ from random sequences.},
}
@article {pmid27356769,
year = {2016},
author = {Xue, C and Zhang, X and Zhu, C and Zhao, J and Zhu, P and Peng, C and Ling, N and Shen, Q},
title = {Quantitative and compositional responses of ammonia-oxidizing archaea and bacteria to long-term field fertilization.},
journal = {Scientific reports},
volume = {6},
number = {},
pages = {28981},
pmid = {27356769},
issn = {2045-2322},
mesh = {Agriculture/*methods ; Ammonia/*metabolism ; Archaea/*classification/genetics/isolation &amp; purification/metabolism ; Bacteria/*classification/genetics/isolation &amp; purification/metabolism ; Biota/*drug effects ; Fertilizers/statistics &amp; numerical data ; Genes, Archaeal ; Genes, Bacterial ; Oxidation-Reduction ; Sequence Analysis, DNA ; *Soil Microbiology ; },
abstract = {Archaeal (AOA) and bacterial (AOB) ammonia-oxidizer responses to long-term field fertilization in a Mollisol soil were assessed through pyrosequencing of amoA genes. Long-term fertilization treatments including chemical fertilizer (NPK), NPK plus manure (NPKM), and no fertilization over 23 years altered soil properties resulting in significant shifts in AOA and AOB community composition and abundance. NPK exhibited a strong influence on AOA and AOB composition while the addition of manure neutralized the community change induced by NPK. NPK also led to significant soil acidification and enrichment of Nitrosotalea. Nitrosospira cluster 9 and 3c were the most abundant AOB populations with opposing responses to fertilization treatments. NPKM had the largest abundance of ammonia-oxidizers and highest potential nitrification activity (PNA), suggesting high N loss potential due to a doubling of nutrient input compared to NPK. PNA was strongly correlated to AOA and AOB community composition indicating that both were important in ammonium oxidization in this Mollisol soil. Total N and organic C were the most important factors driving shifts in AOA and AOB community composition. The AOA community was strongly correlated to the activities of all sugar hydrolysis associated soil enzymes and was more responsive to C and N input than AOB.},
}
@article {pmid27339136,
year = {2016},
author = {Kim, JG and Park, SJ and Sinninghe Damsté, JS and Schouten, S and Rijpstra, WI and Jung, MY and Kim, SJ and Gwak, JH and Hong, H and Si, OJ and Lee, S and Madsen, EL and Rhee, SK},
title = {Hydrogen peroxide detoxification is a key mechanism for growth of ammonia-oxidizing archaea.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {113},
number = {28},
pages = {7888-7893},
pmid = {27339136},
issn = {1091-6490},
mesh = {Ammonia/*metabolism ; Archaea/isolation &amp; purification/*physiology ; Genome, Bacterial ; Hydrogen Peroxide/*metabolism ; Nitrification ; Oxidation-Reduction ; Peroxidase/metabolism ; },
abstract = {Ammonia-oxidizing archaea (AOA), that is, members of the Thaumarchaeota phylum, occur ubiquitously in the environment and are of major significance for global nitrogen cycling. However, controls on cell growth and organic carbon assimilation by AOA are poorly understood. We isolated an ammonia-oxidizing archaeon (designated strain DDS1) from seawater and used this organism to study the physiology of ammonia oxidation. These findings were confirmed using four additional Thaumarchaeota strains from both marine and terrestrial habitats. Ammonia oxidation by strain DDS1 was enhanced in coculture with other bacteria, as well as in artificial seawater media supplemented with α-keto acids (e.g., pyruvate, oxaloacetate). α-Keto acid-enhanced activity of AOA has previously been interpreted as evidence of mixotrophy. However, assays for heterotrophic growth indicated that incorporation of pyruvate into archaeal membrane lipids was negligible. Lipid carbon atoms were, instead, derived from dissolved inorganic carbon, indicating strict autotrophic growth. α-Keto acids spontaneously detoxify H2O2 via a nonenzymatic decarboxylation reaction, suggesting a role of α-keto acids as H2O2 scavengers. Indeed, agents that also scavenge H2O2, such as dimethylthiourea and catalase, replaced the α-keto acid requirement, enhancing growth of strain DDS1. In fact, in the absence of α-keto acids, strain DDS1 and other AOA isolates were shown to endogenously produce H2O2 (up to ∼4.5 μM), which was inhibitory to growth. Genomic analyses indicated catalase genes are largely absent in the AOA. Our results indicate that AOA broadly feature strict autotrophic nutrition and implicate H2O2 as an important factor determining the activity, evolution, and community ecology of AOA ecotypes.},
}
@article {pmid27290727,
year = {2016},
author = {Shlaifer, I and Turnbull, JL},
title = {Characterization of two key enzymes for aromatic amino acid biosynthesis in symbiotic archaea.},
journal = {Extremophiles : life under extreme conditions},
volume = {20},
number = {4},
pages = {503-514},
pmid = {27290727},
issn = {1433-4909},
mesh = {Amino Acids, Aromatic/biosynthesis ; Archaeal Proteins/chemistry/genetics/*metabolism ; Chorismate Mutase/chemistry/genetics/*metabolism ; Desulfurococcaceae/*enzymology/physiology ; Enzyme Stability ; Hot Temperature ; Nanoarchaeota/*enzymology/physiology ; Nitrosamines/metabolism ; Prephenate Dehydratase/chemistry/genetics/*metabolism ; Prephenate Dehydrogenase/chemistry/genetics/*metabolism ; Substrate Specificity ; Symbiosis ; },
abstract = {Biosynthesis of L-tyrosine (L-Tyr) and L-phenylalanine (L-Phe) is directed by the interplay of three enzymes. Chorismate mutase (CM) catalyzes the rearrangement of chorismate to prephenate, which can be either converted to hydroxyphenylpyruvate by prephenate dehydrogenase (PD) or to phenylpyruvate by prephenate dehydratase (PDT). This work reports the first characterization of a trifunctional PD-CM-PDT from the smallest hyperthermophilic archaeon Nanoarchaeum equitans and a bifunctional CM-PD from its host, the crenarchaeon Ignicoccus hospitalis. Hexa-histidine tagged proteins were expressed in Escherichia coli and purified by affinity chromatography. Specific activities determined for the trifunctional enzyme were 21, 80, and 30 U/mg for CM, PD, and PDT, respectively, and 47 and 21 U/mg for bifunctional CM and PD, respectively. Unlike most PDs, these two archaeal enzymes were insensitive to regulation by L-Tyr and preferred NADP(+) to NAD(+) as a cofactor. Both the enzymes were highly thermally stable and exhibited maximal activity at 90 °C. N. equitans PDT was feedback inhibited by L-Phe (Ki = 0.8 µM) in a non-competitive fashion consistent with L-Phe's combination at a site separate from that of prephenate. Our results suggest that PD from the unique symbiotic archaeal pair encompass a distinct subfamily of prephenate dehydrogenases with regard to their regulation and co-substrate specificity.},
}
@article {pmid27279625,
year = {2016},
author = {Voica, DM and Bartha, L and Banciu, HL and Oren, A},
title = {Heavy metal resistance in halophilic Bacteria and Archaea.},
journal = {FEMS microbiology letters},
volume = {363},
number = {14},
pages = {},
doi = {10.1093/femsle/fnw146},
pmid = {27279625},
issn = {1574-6968},
mesh = {*Adaptation, Biological ; Archaea/classification/*physiology ; Bacteria/classification/drug effects/genetics/*metabolism ; *Bacterial Physiological Phenomena/drug effects ; Biodegradation, Environmental ; Biological Transport ; Cell Membrane/metabolism ; Inactivation, Metabolic ; Metals, Heavy/*metabolism/pharmacology ; Prokaryotic Cells/physiology ; Salinity ; },
abstract = {Heavy metals are dense chemicals with dual biological role as micronutrients and intoxicants. A few hypersaline environmental systems are naturally enriched with heavy metals, while most metal-contaminated sites are a consequence of human activities. Numerous halotolerant and moderately halophilic Bacteria possess metal tolerance, whereas a few archaeal counterparts share similar features. The main mechanisms underlying heavy metal resistance in halophilic Bacteria and Archaea include extracellular metal sequestration by biopolymers, metal efflux mediated by specific transporters and enzymatic detoxification. Biotransformation of metals by halophiles has implications both for trace metal turnover in natural saline ecosystems and for development of novel bioremediation strategies.},
}
@article {pmid27268252,
year = {2016},
author = {Michael, AJ},
title = {Polyamines in Eukaryotes, Bacteria, and Archaea.},
journal = {The Journal of biological chemistry},
volume = {291},
number = {29},
pages = {14896-14903},
pmid = {27268252},
issn = {1083-351X},
mesh = {Archaea/*metabolism ; Bacteria/*metabolism ; Biosynthetic Pathways ; Eukaryota/*metabolism ; Gene Transfer, Horizontal/genetics ; Polyamines/*metabolism ; },
abstract = {Polyamines are primordial polycations found in most cells and perform different functions in different organisms. Although polyamines are mainly known for their essential roles in cell growth and proliferation, their functions range from a critical role in cellular translation in eukaryotes and archaea, to bacterial biofilm formation and specialized roles in natural product biosynthesis. At first glance, the diversity of polyamine structures in different organisms appears chaotic; however, biosynthetic flexibility and evolutionary and ecological processes largely explain this heterogeneity. In this review, I discuss the biosynthetic, evolutionary, and physiological processes that constrain or expand polyamine structural and functional diversity.},
}
@article {pmid27242149,
year = {2016},
author = {Quadri, I and Hassani, II and l'Haridon, S and Chalopin, M and Hacène, H and Jebbar, M},
title = {Characterization and antimicrobial potential of extremely halophilic archaea isolated from hypersaline environments of the Algerian Sahara.},
journal = {Microbiological research},
volume = {186-187},
number = {},
pages = {119-131},
doi = {10.1016/j.micres.2016.04.003},
pmid = {27242149},
issn = {1618-0623},
mesh = {Africa, Northern ; Algeria ; Anti-Infective Agents/*metabolism ; Archaea/classification/genetics/*isolation &amp; purification/*metabolism ; Bacterial Typing Techniques ; Cluster Analysis ; DNA, Archaeal/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; *Environmental Microbiology ; Enzymes/metabolism ; Peptides/genetics/metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; },
abstract = {Halophilic archaea were isolated from different chotts and sebkha, dry salt lakes and salt flat respectively, of the Algerian Sahara and characterized using phenotypic and phylogenetic approaches. From 102 extremely halophilic strains isolated, forty three were selected and studied. These strains were also screened for their antagonistic potential and the production of hydrolytic enzymes. Sequencing of the 16S rRNA genes and phylogenetic analysis allowed the identification of 10 archaeal genera within the class Halobacteria: Natrinema (13 strains), Natrialba (12 strains), Haloarcula (4 strains), Halopiger (4 strains), Haloterrigena (3 strains), Halorubrum (2 strains), Halostagnicola (2 strains), Natronococcus, Halogeometricum and Haloferax (1 strain each). The most common producers of antimicrobial compounds belong to the genus Natrinema while the most hydrolytic isolates, with combined production of several enzymes, belong to the genus Natrialba. The strain affiliated to Halopiger djelfamassilliensis was found to produce some substances of interest (halocins, anti-Candida, enzymes). After partial purification and characterization of one of the strains Natrinema gari QI1, we found similarities between the antimicrobial compound and the halocin C8. Therefore, the gene encoding halocin C8 was amplified and sequenced.},
}
@article {pmid27234458,
year = {2016},
author = {Mojica, FJ and Rodriguez-Valera, F},
title = {The discovery of CRISPR in archaea and bacteria.},
journal = {The FEBS journal},
volume = {283},
number = {17},
pages = {3162-3169},
doi = {10.1111/febs.13766},
pmid = {27234458},
issn = {1742-4658},
mesh = {Archaea/*genetics ; Bacteria/*genetics ; *CRISPR-Cas Systems ; Genome, Archaeal ; Genome, Bacterial ; Genomics ; },
abstract = {CRISPR-Cas are self-/nonself-discriminating systems found in prokaryotic cells. They represent a remarkable example of molecular memory that is hereditarily transmitted. Their discovery can be considered as one of the first fruits of the systematic exploration of prokaryotic genomes. Although this genomic feature was serendipitously discovered in molecular biology studies, it was the availability of multiple complete genomes that shed light about their role as a genetic immune system. Here we tell the story of how this discovery originated and was slowly and painstakingly advanced to the point of understating the biological role of what initially was just an odd genomic feature.},
}
@article {pmid27199977,
year = {2016},
author = {Makarova, KS and Koonin, EV and Albers, SV},
title = {Diversity and Evolution of Type IV pili Systems in Archaea.},
journal = {Frontiers in microbiology},
volume = {7},
number = {},
pages = {667},
pmid = {27199977},
issn = {1664-302X},
support = {311523/ERC_/European Research Council/International ; },
abstract = {Many surface structures in archaea including various types of pili and the archaellum (archaeal flagellum) are homologous to bacterial type IV pili systems (T4P). The T4P consist of multiple proteins, often with poorly conserved sequences, complicating their identification in sequenced genomes. Here we report a comprehensive census of T4P encoded in archaeal genomes using sensitive methods for protein sequence comparison. This analysis confidently identifies as T4P components about 5000 archaeal gene products, 56% of which are currently annotated as hypothetical in public databases. Combining results of this analysis with a comprehensive comparison of genomic neighborhoods of the T4P, we present models of organization of 10 most abundant variants of archaeal T4P. In addition to the differentiation between major and minor pilins, these models include extra components, such as S-layer proteins, adhesins and other membrane and intracellular proteins. For most of these systems, dedicated major pilin families are identified including numerous stand alone major pilin genes of the PilA family. Evidence is presented that secretion ATPases of the T4P and cognate TadC proteins can interact with different pilin sets. Modular evolution of T4P results in combinatorial variability of these systems. Potential regulatory or modulating proteins for the T4P are identified including KaiC family ATPases, vWA domain-containing proteins and the associated MoxR/GvpN ATPase, TFIIB homologs and multiple unrelated transcription regulators some of which are associated specific T4P. Phylogenomic analysis suggests that at least one T4P system was present in the last common ancestor of the extant archaea. Multiple cases of horizontal transfer and lineage-specific duplication of T4P loci were detected. Generally, the T4P of the archaeal TACK superphylum are more diverse and evolve notably faster than those of euryarchaea. The abundance and enormous diversity of T4P in hyperthermophilic archaea present a major enigma. Apparently, fundamental aspects of the biology of hyperthermophiles remain to be elucidated.},
}
@article {pmid27194687,
year = {2016},
author = {Garrity, GM},
title = {A New Genomics-Driven Taxonomy of Bacteria and Archaea: Are We There Yet?.},
journal = {Journal of clinical microbiology},
volume = {54},
number = {8},
pages = {1956-1963},
pmid = {27194687},
issn = {1098-660X},
mesh = {Archaea/*classification/*genetics ; Bacteria/*classification/*genetics ; Classification/*methods ; Genomics/*methods ; Humans ; },
abstract = {Taxonomy is often criticized for being too conservative and too slow and having limited relevance because it has not taken into consideration the latest methods and findings. Yet the cumulative work product of its practitioners underpins contemporary microbiology and serves as a principal means of shaping and referencing knowledge. Using methods drawn from the field of exploratory data analysis, this minireview examines the current state of the field as it transitions from a taxonomy based on 16S rRNA gene sequences to one based on whole-genome sequences and tests the validity of some commonly held beliefs.},
}
@article {pmid27190215,
year = {2016},
author = {Fu, X and Liu, R and Sanchez, I and Silva-Sanchez, C and Hepowit, NL and Cao, S and Chen, S and Maupin-Furlow, J},
title = {Ubiquitin-Like Proteasome System Represents a Eukaryotic-Like Pathway for Targeted Proteolysis in Archaea.},
journal = {mBio},
volume = {7},
number = {3},
pages = {},
pmid = {27190215},
issn = {2150-7511},
support = {R01 GM057498/GM/NIGMS NIH HHS/United States ; },
mesh = {Adenosine Triphosphatases/metabolism ; Archaea/*genetics/*metabolism ; Archaeal Proteins/chemistry/genetics/*metabolism ; Cytoplasm/chemistry/*metabolism ; Mutation ; Proteasome Endopeptidase Complex/chemistry/genetics/*metabolism ; Proteolysis ; TATA-Box Binding Protein/*metabolism ; Ubiquitin/genetics/*metabolism ; },
abstract = {UNLABELLED: The molecular mechanisms of targeted proteolysis in archaea are poorly understood, yet they may have deep evolutionary roots shared with the ubiquitin-proteasome system of eukaryotic cells. Here, we demonstrate in archaea that TBP2, a TATA-binding protein (TBP) modified by ubiquitin-like isopeptide bonds, is phosphorylated and targeted for degradation by proteasomes. Rapid turnover of TBP2 required the functions of UbaA (the E1/MoeB/ThiF homolog of archaea), AAA ATPases (Cdc48/p97 and Rpt types), a type 2 JAB1/MPN/MOV34 metalloenzyme (JAMM/MPN+) homolog (JAMM2), and 20S proteasomes. The ubiquitin-like protein modifier small archaeal modifier protein 2 (SAMP2) stimulated the degradation of TBP2, but SAMP2 itself was not degraded. Analysis of the TBP2 fractions that were not modified by ubiquitin-like linkages revealed that TBP2 had multiple N termini, including Met1-Ser2, Ser2, and Met1-Ser2(p) [where (p) represents phosphorylation]. The evidence suggested that the Met1-Ser2(p) form accumulated in cells that were unable to degrade TBP2. We propose a model in archaea in which the attachment of ubiquitin-like tags can target proteins for degradation by proteasomes and be controlled by N-terminal degrons. In support of a proteolytic mechanism that is energy dependent and recycles the ubiquitin-like protein tags, we find that a network of AAA ATPases and a JAMM/MPN+ metalloprotease are required, in addition to 20S proteasomes, for controlled intracellular proteolysis.<br><br>IMPORTANCE: This study advances the fundamental knowledge of signal-guided proteolysis in archaea and sheds light on components that are related to the ubiquitin-proteasome system of eukaryotes. In archaea, the ubiquitin-like proteasome system is found to require function of an E1/MoeB/ThiF homolog, a type 2 JAMM/MPN+ metalloprotease, and a network of AAA ATPases for the targeted destruction of proteins. We provide evidence that the attachment of the ubiquitin-like protein is controlled by an N-terminal degron and stimulates proteasome-mediated proteolysis.},
}
@article {pmid27155047,
year = {2016},
author = {Srivastava, A and Gogoi, P and Deka, B and Goswami, S and Kanaujia, SP},
title = {In silico analysis of 5'-UTRs highlights the prevalence of Shine-Dalgarno and leaderless-dependent mechanisms of translation initiation in bacteria and archaea, respectively.},
journal = {Journal of theoretical biology},
volume = {402},
number = {},
pages = {54-61},
doi = {10.1016/j.jtbi.2016.05.005},
pmid = {27155047},
issn = {1095-8541},
mesh = {5' Untranslated Regions/*genetics ; Archaea/*genetics ; Bacteria/*genetics ; Base Composition/genetics ; Base Sequence ; Codon, Initiator/genetics ; *Computer Simulation ; Genes, Archaeal ; Genes, Bacterial ; Genome Size ; Peptide Chain Initiation, Translational/*genetics ; Prokaryotic Cells ; },
abstract = {In prokaryotes, a heterogeneous set of protein translation initiation mechanisms such as Shine-Dalgarno (SD) sequence-dependent, SD sequence-independent or ribosomal protein S1 mediated and leaderless transcript-dependent exists. To estimate the distribution of coding sequences employing a particular translation initiation mechanism, a total of 107 prokaryotic genomes were analysed using in silico approaches. Analysis of 5'-untranslated regions (UTRs) of genes reveals the existence of three types of mRNAs described as transcripts with and without SD motif and leaderless transcripts. Our results indicate that although all the three types of translation initiation mechanisms are widespread among prokaryotes, the number of SD-dependent genes in bacteria is higher than that of archaea. In contrast, archaea contain a significantly higher number of leaderless genes than SD-led genes. The correlation analysis between genome size and SD-led &amp; leaderless genes suggests that the SD-led genes are decreasing (increasing) with genome size in bacteria (archaea). However, the leaderless genes are increasing (decreasing) in bacteria (archaea) with genome size. Moreover, an analysis of the start-codon biasness confirms that among ATG, GTG and TTG codons, ATG is indeed the most preferred codon at the translation initiation site in most of the coding sequences. In leaderless genes, however, the codons GTG and TTG are also observed at the translation initiation site in some species contradicting earlier studies which suggested the usage of only ATG codon. Henceforth, the conventional mechanism of translation initiation cannot be generalized as an exclusive way of initiating the process of protein biosynthesis in prokaryotes.},
}
@article {pmid27142341,
year = {2016},
author = {Koyanagi, T and Leriche, G and Yep, A and Onofrei, D and Holland, GP and Mayer, M and Yang, J},
title = {Effect of Headgroups on Small-Ion Permeability across Archaea-Inspired Tetraether Lipid Membranes.},
journal = {Chemistry (Weinheim an der Bergstrasse, Germany)},
volume = {22},
number = {24},
pages = {8074-8077},
doi = {10.1002/chem.201601326},
pmid = {27142341},
issn = {1521-3765},
mesh = {Archaea/*metabolism ; Diglycerides/chemistry ; Dynamic Light Scattering ; Fluoresceins/chemistry/metabolism ; Ions/chemistry/metabolism ; Liposomes/chemistry/metabolism ; Membrane Lipids/chemical synthesis/chemistry/*metabolism ; Phosphatidylcholines ; Spectroscopy, Fourier Transform Infrared ; X-Ray Diffraction ; },
abstract = {This paper examines the effects of four different polar headgroups on small-ion membrane permeability from liposomes comprised of Archaea-inspired glycerolmonoalkyl glycerol tetraether (GMGT) lipids. We found that the membrane-leakage rate across GMGT lipid membranes varied by a factor of ≤1.6 as a function of headgroup structure. However, the leakage rates of small ions across membranes comprised of commercial bilayer-forming 1-palmitoyl-2-oleoyl-sn-glycerol (PO) lipids varied by as much as 32-fold within the same series of headgroups. These results demonstrate that membrane leakage from GMGT lipids is less influenced by headgroup structure, making it possible to tailor the structure of the polar headgroups on GMGT lipids while retaining predictable leakage properties of membranes comprised of these tethered lipids.},
}
@article {pmid27137495,
year = {2016},
author = {Gehring, AM and Walker, JE and Santangelo, TJ},
title = {Transcription Regulation in Archaea.},
journal = {Journal of bacteriology},
volume = {198},
number = {14},
pages = {1906-1917},
pmid = {27137495},
issn = {1098-5530},
support = {R01 GM100329/GM/NIGMS NIH HHS/United States ; },
mesh = {Archaea/*genetics/metabolism ; Archaeal Proteins/*genetics/metabolism ; *Gene Expression Regulation, Archaeal ; *Transcription, Genetic ; },
abstract = {The known diversity of metabolic strategies and physiological adaptations of archaeal species to extreme environments is extraordinary. Accurate and responsive mechanisms to ensure that gene expression patterns match the needs of the cell necessitate regulatory strategies that control the activities and output of the archaeal transcription apparatus. Archaea are reliant on a single RNA polymerase for all transcription, and many of the known regulatory mechanisms employed for archaeal transcription mimic strategies also employed for eukaryotic and bacterial species. Novel mechanisms of transcription regulation have become apparent by increasingly sophisticated in vivo and in vitro investigations of archaeal species. This review emphasizes recent progress in understanding archaeal transcription regulatory mechanisms and highlights insights gained from studies of the influence of archaeal chromatin on transcription.},
}
@article {pmid27127195,
year = {2016},
author = {Rinta-Kanto, JM and Sinkko, H and Rajala, T and Al-Soud, WA and Sørensen, SJ and Tamminen, MV and Timonen, S},
title = {Natural decay process affects the abundance and community structure of Bacteria and Archaea in Picea abies logs.},
journal = {FEMS microbiology ecology},
volume = {92},
number = {7},
pages = {},
doi = {10.1093/femsec/fiw087},
pmid = {27127195},
issn = {1574-6941},
mesh = {Archaea/classification/genetics/*isolation &amp; purification ; Bacteria/classification/genetics/*isolation &amp; purification ; Biota ; Finland ; Fungi/classification/genetics/isolation &amp; purification ; Picea/*microbiology ; Wood/*microbiology ; },
abstract = {Prokaryotes colonize decaying wood and contribute to the degradation process, but the dynamics of prokaryotic communities during wood decay is still poorly understood. We studied the abundance and community composition of Bacteria and Archaea inhabiting naturally decaying Picea abies logs and tested the hypothesis that the variations in archaeal and bacterial abundances and community composition are coupled with environmental parameters related to the decay process. The data set comprises >500 logs at different decay stages from five geographical locations in south and central Finland. The results show that Bacteria and Archaea are an integral and dynamic component of decaying wood biota. The abundances of bacterial and archaeal 16S rRNA genes increase as wood decay progresses. Changes in bacterial community composition are clearly linked to the loss of density of wood, while specific fungal-bacterial interactions may also affect the distribution of bacterial taxa in decaying wood. Thaumarchaeota were prominent members of the archaeal populations colonizing decaying wood, providing further evidence of the versatility and cosmopolitan nature of this phylum in the environment. The composition and dynamics of the prokaryotic community suggest that they are an active component of biota that are involved in processing substrates in decaying wood material.},
}
@article {pmid27114874,
year = {2016},
author = {Trembath-Reichert, E and Case, DH and Orphan, VJ},
title = {Characterization of microbial associations with methanotrophic archaea and sulfate-reducing bacteria through statistical comparison of nested Magneto-FISH enrichments.},
journal = {PeerJ},
volume = {4},
number = {},
pages = {e1913},
pmid = {27114874},
issn = {2167-8359},
support = {T32 GM007616/GM/NIGMS NIH HHS/United States ; },
abstract = {Methane seep systems along continental margins host diverse and dynamic microbial assemblages, sustained in large part through the microbially mediated process of sulfate-coupled Anaerobic Oxidation of Methane (AOM). This methanotrophic metabolism has been linked to consortia of anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria (SRB). These two groups are the focus of numerous studies; however, less is known about the wide diversity of other seep associated microorganisms. We selected a hierarchical set of FISH probes targeting a range of Deltaproteobacteria diversity. Using the Magneto-FISH enrichment technique, we then magnetically captured CARD-FISH hybridized cells and their physically associated microorganisms from a methane seep sediment incubation. DNA from nested Magneto-FISH experiments was analyzed using Illumina tag 16S rRNA gene sequencing (iTag). Enrichment success and potential bias with iTag was evaluated in the context of full-length 16S rRNA gene clone libraries, CARD-FISH, functional gene clone libraries, and iTag mock communities. We determined commonly used Earth Microbiome Project (EMP) iTAG primers introduced bias in some common methane seep microbial taxa that reduced the ability to directly compare OTU relative abundances within a sample, but comparison of relative abundances between samples (in nearly all cases) and whole community-based analyses were robust. The iTag dataset was subjected to statistical co-occurrence measures of the most abundant OTUs to determine which taxa in this dataset were most correlated across all samples. Many non-canonical microbial partnerships were statistically significant in our co-occurrence network analysis, most of which were not recovered with conventional clone library sequencing, demonstrating the utility of combining Magneto-FISH and iTag sequencing methods for hypothesis generation of associations within complex microbial communities. Network analysis pointed to many co-occurrences containing putatively heterotrophic, candidate phyla such as OD1, Atribacteria, MBG-B, and Hyd24-12 and the potential for complex sulfur cycling involving Epsilon-, Delta-, and Gammaproteobacteria in methane seep ecosystems.},
}
@article {pmid27113140,
year = {2016},
author = {Feng, G and Sun, W and Zhang, F and Karthik, L and Li, Z},
title = {Inhabitancy of active Nitrosopumilus-like ammonia-oxidizing archaea and Nitrospira nitrite-oxidizing bacteria in the sponge Theonella swinhoei.},
journal = {Scientific reports},
volume = {6},
number = {},
pages = {24966},
pmid = {27113140},
issn = {2045-2322},
mesh = {Animals ; Archaea/classification/enzymology/genetics/*metabolism ; Archaeal Proteins/genetics/metabolism ; Bacteria/classification/enzymology/genetics/*metabolism ; Bacterial Proteins/genetics/metabolism ; Gene Expression Profiling/methods ; Nitrite Reductases/*genetics ; Nitrites/*metabolism ; Oxidoreductases/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/analysis ; Sequence Analysis, DNA/methods ; Sequence Analysis, RNA/methods ; Theonella/genetics/*microbiology ; },
abstract = {Nitrification directly contributes to the ammonia removal in sponges, and it plays an indispensable role in sponge-mediated nitrogen cycle. Previous studies have demonstrated genomic evidences of nitrifying lineages in the sponge Theonella swinhoei. However, little is known about the transcriptional activity of nitrifying community in this sponge. In this study, combined DNA- and transcript-based analyses were performed to reveal the composition and transcriptional activity of the nitrifiers in T. swinhoei from the South China Sea. Transcriptional activity of ammonia-oxidizing archaea (AOA) and nitrite-oxidizing bacteria (NOB) in this sponge were confirmed by targeting their nitrifying genes,16S rRNA genes and their transcripts. Phylogenetic analysis coupled with RDP rRNA classification indicated that archaeal 16S rRNA genes, amoA (the subunit of ammonia monooxygenase) genes and their transcripts were closely related to Nitrosopumilus-like AOA; whereas nitrifying bacterial 16S rRNA genes, nxrB (the subunit of nitrite oxidoreductase) genes and their transcripts were closely related to Nitrospira NOB. Quantitative assessment demonstrated relative higher abundances of nitrifying genes and transcripts of Nitrosopumilus-like AOA than those of Nitrospira NOB in this sponge. This study illustrated the transcriptional potentials of Nitrosopumilus-like archaea and Nitrospira bacteria that would predominantly contribute to the nitrification functionality in the South China Sea T. swinhoei.},
}
@article {pmid27112361,
year = {2017},
author = {Villanueva, L and Schouten, S and Damsté, JS},
title = {Phylogenomic analysis of lipid biosynthetic genes of Archaea shed light on the 'lipid divide'.},
journal = {Environmental microbiology},
volume = {19},
number = {1},
pages = {54-69},
doi = {10.1111/1462-2920.13361},
pmid = {27112361},
issn = {1462-2920},
mesh = {Archaea/genetics/*metabolism ; Bacteria/genetics/*metabolism ; Biological Evolution ; Butadienes/*metabolism ; Cell Membrane/*metabolism ; Fatty Acids/*metabolism ; Genome, Archaeal ; Glycerophosphates/*metabolism ; Hemiterpenes/*metabolism ; Membrane Lipids/chemistry/*metabolism ; Pentanes/*metabolism ; Terpenes ; },
abstract = {The lipid membrane is one of the most characteristic traits distinguishing the three domains of life. Membrane lipids of Bacteria and Eukarya are composed of fatty acids linked to glycerol-3-phosphate (G3P) via ester bonds, while those of Archaea possess isoprene-based alkyl chains linked by ether linkages to glycerol-1-phosphate (G1P), resulting in the opposite stereochemistry of the glycerol phosphate backbone. This 'lipid divide' has raised questions on the evolution of microbial life since eukaryotes are thought to have evolved from the Archaea, requiring a radical change in membrane composition. Here, we searched for homologs of enzymes involved in membrane lipid and fatty acid synthesis in a wide variety of archaeal genomes and performed phylogenomic analyses. We found that two uncultured archaeal groups, i.e. marine euryarchaeota group II/III and 'Lokiarchaeota', recently discovered descendants of the archaeal ancestor leading to eukaryotes, lack the gene to synthesize G1P and, consequently, the capacity to synthesize archaeal membrane lipids. However, our analyses reveal their genetic capacity to synthesize G3P-based 'chimeric lipids' with either two ether-bound isoprenoidal chains or with an ester-bound fatty acid instead of an ether-bound isoprenoid. These archaea may reflect the 'archaea-to-eukaryote' membrane transition stage which have led to the current 'lipid divide'.},
}
@article {pmid27109114,
year = {2016},
author = {Yang, Y and Li, N and Zhao, Q and Yang, M and Wu, Z and Xie, S and Liu, Y},
title = {Ammonia-oxidizing archaea and bacteria in water columns and sediments of a highly eutrophic plateau freshwater lake.},
journal = {Environmental science and pollution research international},
volume = {23},
number = {15},
pages = {15358-15369},
pmid = {27109114},
issn = {1614-7499},
mesh = {Ammonia/analysis ; Archaea/enzymology/genetics ; Archaeal Proteins/genetics ; Bacteria/enzymology/genetics ; Bacterial Proteins/genetics ; China ; Eutrophication ; Geologic Sediments/*microbiology ; Lakes/*microbiology ; Nitrogen Cycle ; Oxidation-Reduction ; Oxidoreductases/genetics ; Phylogeny ; Seasons ; *Water Microbiology ; Water Pollutants, Chemical/analysis ; },
abstract = {Both ammonia-oxidizing archaea (AOA) and bacteria (AOB) can play important roles in the microbial oxidation of ammonia nitrogen in freshwater lake, but information on spatiotemporal variation in water column and sediment community structure is still limited. Additionally, the drivers of the differences between sediment and water assemblages are still unclear. The present study investigated the variation of AOA and AOB communities in both water columns and sediments of eutrophic freshwater Dianchi Lake. The abundance, diversity, and structure of both planktonic and sediment ammonia-oxidizing microorganisms in Dianchi Lake showed the evident changes with sampling site and time. In both water columns and sediments, AOB amoA gene generally outnumbered AOA, and the AOB/AOA ratio was much higher in summer than in autumn. The total AOA amoA abundance was relatively great in autumn, while sediment AOB was relatively abundant in summer. Sediment AOA amoA abundance was likely correlated with ammonia nitrogen (rs = 0.963). The AOB/AOA ratio in lake sediment was positively correlated with total phosphorus (rs = 0.835), while pH, dissolved organic carbon, and ammonia nitrogen might be the key driving forces for the AOB/AOA ratio in lake water. Sediment AOA and AOB diversity was correlated with nitrate nitrogen (rs = -0.786) and total organic carbon (rs = 0.769), respectively, while planktonic AOB diversity was correlated with ammonia nitrogen (rs = 0.854). Surface water and sediment in the same location had a distinctively different microbial community structure. In addition, sediment AOB community structure was influenced by total phosphorus, while total phosphorus might be a key determinant of planktonic AOB community structure.},
}
@article {pmid27098176,
year = {2016},
author = {Pakpour, S and Scott, JA and Turvey, SE and Brook, JR and Takaro, TK and Sears, MR and Klironomos, J},
title = {Presence of Archaea in the Indoor Environment and Their Relationships with Housing Characteristics.},
journal = {Microbial ecology},
volume = {72},
number = {2},
pages = {305-312},
pmid = {27098176},
issn = {1432-184X},
mesh = {Archaea/classification/*isolation &amp; purification ; DNA, Archaeal/genetics ; *Environmental Microbiology ; *Housing ; Humans ; Microbiota ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; },
abstract = {Archaea are widespread and abundant in soils, oceans, or human and animal gastrointestinal (GI) tracts. However, very little is known about the presence of Archaea in indoor environments and factors that can regulate their abundances. Using a quantitative PCR approach, and targeting the archaeal and bacterial 16S rRNA genes in floor dust samples, we found that Archaea are a common part of the indoor microbiota, 5.01 ± 0.14 (log 16S rRNA gene copies/g dust, mean ± SE) in bedrooms and 5.58 ± 0.13 in common rooms, such as living rooms. Their abundance, however, was lower than bacteria: 9.20 ± 0.32 and 9.17 ± 0.32 in bedrooms and common rooms, respectively. In addition, by measuring a broad array of environmental factors, we obtained preliminary insights into how the abundance of total archaeal 16S rRNA gene copies in indoor environment would be associated with building characteristics and occupants' activities. Based on the results, Archaea are not equally distributed within houses, and the areas with greater input of outdoor microbiome and higher traffic and material heterogeneity tend to have a higher abundance of Archaea. Nevertheless, more research is needed to better understand causes and consequences of this microbial group in indoor environments.},
}
@article {pmid27094186,
year = {2016},
author = {Zhang, FQ and Pan, W and Gu, JD and Xu, B and Zhang, WH and Zhu, BZ and Wang, YX and Wang, YF},
title = {Dominance of ammonia-oxidizing archaea community induced by land use change from Masson pine to eucalypt plantation in subtropical China.},
journal = {Applied microbiology and biotechnology},
volume = {100},
number = {15},
pages = {6859-6869},
doi = {10.1007/s00253-016-7506-8},
pmid = {27094186},
issn = {1432-0614},
mesh = {Agriculture ; Ammonia/*metabolism ; Archaea/genetics/*metabolism ; Biodiversity ; China ; *Eucalyptus ; Forests ; Nitrification ; Oxidation-Reduction ; *Pinus ; Soil/chemistry ; *Soil Microbiology ; },
abstract = {A considerable proportion of Masson pine forests have been converted into eucalypt plantations in the last 30 years in Guangdong Province, subtropical China, for economic reasons, which may affect the ammonia-oxidizing archaea (AOA) community and the process of ammonia transformation. In order to determine the effects of forest conversion on AOA community, AOA communities in a Masson pine (Pinus massoniana) plantation and a eucalypt (Eucalyptus urophylla) plantation, which was converted from the Masson pine, were compared. Results showed that the land use change from the Masson pine to the eucalypt plantation decreased soil nutrient levels. A significant decrease of the potential nitrification rates (PNR) was also observed after the forest conversion (p < 5 %, n = 6). AOA were the only ammonia oxidizers in both plantations (no ammonia-oxidizing bacteria were detected). The detected AOA are affiliated with the genera Nitrosotalea and Nitrososphaera. A decrease of AOA abundance and an increase of the diversity were evident with the plantation conversion in the surface layer. AOA amoA gene diversity was negatively correlated with organic C and total N, respectively (p < 0.05, n = 12). AOA amoA gene abundance was negatively correlated with NH4 (+) and available P, respectively (p < 0.05, n = 12). However, AOA abundance was positively correlated with PNR, but not significantly (p < 0.05, n = 6), indicating AOA community change was only a partial reason for the decrease of PNR.},
}
@article {pmid27088618,
year = {2016},
author = {Stantial, N and Dumpe, J and Pietrosimone, K and Baltazar, F and Crowley, DJ},
title = {Transcription-coupled repair of UV damage in the halophilic archaea.},
journal = {DNA repair},
volume = {41},
number = {},
pages = {63-68},
doi = {10.1016/j.dnarep.2016.03.007},
pmid = {27088618},
issn = {1568-7856},
mesh = {Archaeal Proteins/genetics/metabolism ; *DNA Damage ; DNA Repair/drug effects/genetics/*radiation effects ; Fructose/pharmacology ; Halobacterium/drug effects/*genetics/radiation effects ; Haloferax/drug effects/*genetics/radiation effects ; Operon/genetics ; Transcription, Genetic/drug effects/*radiation effects ; Ultraviolet Rays/*adverse effects ; },
abstract = {Transcription-coupled repair (TCR) is a subpathway of nucleotide excision repair (NER) in which excision repair proteins are targeted to RNA polymerase-arresting lesions located in the transcribed strand of active genes. TCR has been documented in a variety of bacterial and eukaryotic organisms but has yet to be observed in the Archaea. We used Halobacterium sp. NRC-1 and Haloferax volcanii to determine if TCR occurs in the halophilic archaea. Following UV irradiation of exponentially growing cultures, we quantified the rate of repair of cyclobutane pyrimidine dimers in the two strands of the rpoB2B1A1A2 and the trpDFEG operons of Halobacterium sp. NRC-1 and the pts operon of H. volcanii through the use of a Southern blot assay and strand-specific probes. TCR was observed in all three operons and was dependent on the NER gene uvrA in Halobacterium sp. NRC-1, but not in H. volcanii. The halophilic archaea likely employ a novel mechanism for TCR in which an as yet unknown coupling factor recognizes the arrested archaeal RNA polymerase complex and recruits certain NER proteins to complete the process.},
}
@article {pmid27037935,
year = {2016},
author = {Sher, Y and Ronen, Z and Nejidat, A},
title = {Differential response of ammonia-oxidizing archaea and bacteria to the wetting of salty arid soil.},
journal = {Journal of basic microbiology},
volume = {56},
number = {8},
pages = {900-906},
doi = {10.1002/jobm.201600035},
pmid = {27037935},
issn = {1521-4028},
mesh = {Ammonia/*metabolism ; Archaea/genetics/*metabolism ; Bacteria/genetics/*metabolism ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; Desert Climate ; Ecosystem ; Nitrification ; Oxidation-Reduction ; Oxidoreductases/genetics/*metabolism ; Soil/chemistry ; *Soil Microbiology ; Water ; },
abstract = {Ammonia-oxidizing archaea and bacteria (AOA, AOB) catalyze the first and rate-limiting step of nitrification. To examine their differential responses to the wetting of dry and salty arid soil, AOA and AOB amoA genes (encoding subunit A of the ammonia monooxygenase) and transcripts were enumerated in dry (summer) and wet (after the first rainfall) soil under the canopy of halophytic shrubs and between the shrubs. AOA and AOB were more abundant under shrub canopies than between shrubs in both the dry and wetted soil. Soil wetting caused a significant decrease in AOB abundance under the canopy and an increase of AOA between the shrubs. The abundance of the archaeal amoA gene transcript was similar for both the wet and dry soil, and the transcript-to-gene ratios were < 1 independent of niche or water content. In contrast, the bacterial amoA transcript-to-gene ratios were between 78 and 514. The lowest ratio was in dry soil under the canopy and the highest in the soil between the shrubs. The results suggest that the AOA are more resilient to stress conditions and maintain a basic activity in arid ecosystems, while the AOB are more responsive to changes in the biotic and abiotic conditions.},
}
@article {pmid27037624,
year = {2016},
author = {Wang, C and Uversky, VN and Kurgan, L},
title = {Disordered nucleiome: Abundance of intrinsic disorder in the DNA- and RNA-binding proteins in 1121 species from Eukaryota, Bacteria and Archaea.},
journal = {Proteomics},
volume = {16},
number = {10},
pages = {1486-1498},
doi = {10.1002/pmic.201500177},
pmid = {27037624},
issn = {1615-9861},
mesh = {Archaeal Proteins/chemistry ; Bacterial Proteins/chemistry ; Binding Sites ; Computational Biology ; DNA-Binding Proteins/*chemistry ; Intrinsically Disordered Proteins/*chemistry ; Molecular Sequence Annotation ; Protein Domains ; Proteome/*chemistry ; },
abstract = {Intrinsically disordered proteins (IDPs) are abundant in various proteomes, where they play numerous important roles and complement biological activities of ordered proteins. Among functions assigned to IDPs are interactions with nucleic acids. However, often, such assignments are made based on the guilty-by-association principle. The validity of the extension of these correlations to all nucleic acid binding proteins has never been analyzed on a large scale across all domains of life. To fill this gap, we perform a comprehensive computational analysis of the abundance of intrinsic disorder and intrinsically disordered domains in nucleiomes (∼548 000 nucleic acid binding proteins) of 1121 species from Archaea, Bacteria and Eukaryota. Nucleiome is a whole complement of proteins involved in interactions with nucleic acids. We show that relative to other proteins in the corresponding proteomes, the DNA-binding proteins have significantly increased disorder content and are significantly enriched in disordered domains in Eukaryotes but not in Archaea and Bacteria. The RNA-binding proteins are significantly enriched in the disordered domains in Bacteria, Archaea and Eukaryota, while the overall abundance of disorder in these proteins is significantly increased in Bacteria, Archaea, animals and fungi. The high abundance of disorder in nucleiomes supports the notion that the nucleic acid binding proteins often require intrinsic disorder for their functions and regulation.},
}
@article {pmid27034425,
year = {2016},
author = {Surkont, J and Pereira-Leal, JB},
title = {Are There Rab GTPases in Archaea?.},
journal = {Molecular biology and evolution},
volume = {33},
number = {7},
pages = {1833-1842},
pmid = {27034425},
issn = {1537-1719},
mesh = {Archaea/*enzymology/genetics/metabolism ; Biological Evolution ; Eukaryotic Cells/metabolism ; Evolution, Molecular ; Guanine Nucleotide Dissociation Inhibitors/genetics/metabolism ; Phylogeny ; Protein Binding ; Protein Transport ; Sequence Analysis, Protein/methods ; rab GTP-Binding Proteins/genetics/*metabolism ; },
abstract = {A complex endomembrane system is one of the hallmarks of Eukaryotes. Vesicle trafficking between compartments is controlled by a diverse protein repertoire, including Rab GTPases. These small GTP-binding proteins contribute identity and specificity to the system, and by working as molecular switches, trigger multiple events in vesicle budding, transport, and fusion. A diverse collection of Rab GTPases already existed in the ancestral Eukaryote, yet, it is unclear how such elaborate repertoire emerged. A novel archaeal phylum, the Lokiarchaeota, revealed that several eukaryotic-like protein systems, including small GTPases, are present in Archaea. Here, we test the hypothesis that the Rab family of small GTPases predates the origin of Eukaryotes. Our bioinformatic pipeline detected multiple putative Rab-like proteins in several archaeal species. Our analyses revealed the presence and strict conservation of sequence features that distinguish eukaryotic Rabs from other small GTPases (Rab family motifs), mapping to the same regions in the structure as in eukaryotic Rabs. These mediate Rab-specific interactions with regulators of the REP/GDI (Rab Escort Protein/GDP dissociation Inhibitor) family. Sensitive structure-based methods further revealed the existence of REP/GDI-like genes in Archaea, involved in isoprenyl metabolism. Our analysis supports a scenario where Rabs differentiated into an independent family in Archaea, interacting with proteins involved in membrane biogenesis. These results further support the archaeal nature of the eukaryotic ancestor and provide a new insight into the intermediate stages and the evolutionary path toward the complex membrane-associated signaling circuits that characterize the Ras superfamily of small GTPases, and specifically Rab proteins.},
}
@article {pmid27022996,
year = {2016},
author = {Hoedt, EC and Cuív, P&#xd3; and Evans, PN and Smith, WJ and McSweeney, CS and Denman, SE and Morrison, M},
title = {Differences down-under: alcohol-fueled methanogenesis by archaea present in Australian macropodids.},
journal = {The ISME journal},
volume = {10},
number = {10},
pages = {2376-2388},
pmid = {27022996},
issn = {1751-7370},
mesh = {Alcohols/*metabolism ; Animals ; Archaea/classification/genetics/*isolation &amp; purification/*metabolism ; Australia ; Base Composition ; *Gastrointestinal Microbiome ; Hydrogen/metabolism ; Macropodidae/*microbiology ; Methane/*metabolism ; Stomach/microbiology ; },
abstract = {The Australian macropodids (kangaroos and wallabies) possess a distinctive foregut microbiota that contributes to their reduced methane emissions. However, methanogenic archaea are present within the macropodid foregut, although there is scant understanding of these microbes. Here, an isolate taxonomically assigned to the Methanosphaera genus (Methanosphaera sp. WGK6) was recovered from the anterior sacciform forestomach contents of a Western grey kangaroo (Macropus fuliginosus). Like the human gut isolate Methanosphaera stadtmanae DSMZ 3091(T), strain WGK6 is a methylotroph with no capacity for autotrophic growth. In contrast, though with the human isolate, strain WGK6 was found to utilize ethanol to support growth, but principally as a source of reducing power. Both the WGK6 and DSMZ 3091(T) genomes are very similar in terms of their size, synteny and G:C content. However, the WGK6 genome was found to encode contiguous genes encoding putative alcohol and aldehyde dehydrogenases, which are absent from the DSMZ 3091(T) genome. Interestingly, homologs of these genes are present in the genomes for several other members of the Methanobacteriales. In WGK6, these genes are cotranscribed under both growth conditions, and we propose the two genes provide a plausible explanation for the ability of WGK6 to utilize ethanol for methanol reduction to methane. Furthermore, our in vitro studies suggest that ethanol supports a greater cell yield per mol of methane formed compared to hydrogen-dependent growth. Taken together, this expansion in metabolic versatility can explain the persistence of these archaea in the kangaroo foregut, and their abundance in these 'low-methane-emitting' herbivores.},
}
@article {pmid27012006,
year = {2015},
author = {Li, H and Huang, FY and Su, JQ and Hong, YW and Yu, S},
title = {[Distribution and Diversity of Ammonium-oxidizing Archaea and Ammonium-oxidizing Bacteria in Surface Sediments of Oujiang River].},
journal = {Huan jing ke xue= Huanjing kexue},
volume = {36},
number = {12},
pages = {4659-4666},
pmid = {27012006},
issn = {0250-3301},
mesh = {Ammonia ; Ammonium Compounds/*metabolism ; Archaea/*classification/metabolism ; Bacteria/*classification/metabolism ; Denaturing Gradient Gel Electrophoresis ; Geologic Sediments/*microbiology ; Oxidation-Reduction ; Phylogeny ; Rivers/*microbiology ; },
abstract = {Ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) play important roles in the biogeochemical nitrogen cycle. Rivers are important ecosystems containing a large number of functional microbes in nitrogen cycle. In this study, denaturing gradient gel electrophoresis (DGGE) and real-time quantitative PCR (qPCR) technology were used to analyze the distribution and diversity of AOA and AOB in sediments from Oujiang. The results showed that the AOA community structure was similar among various sites, while the AOB community structure was significantly different, in which all detected AOB sequences were classified into Nitrosospira and Nitrosomonas, and 90% affiliated to Nitrosospira. The community composition of AOA was influenced by NH4[+] and TS, in addition, the AOB composition was affected by NH4[+], EC, pH, NO3[-], TC and TN. Total sulfur (TS) and electrical conductivity (EC) were the major factors influencing the diversity of AOA and AOB, respectively. AOA abundance was significantly higher than that of AOB. EC, NH4[+]-N and NO3[-]-N were the main environmental factors affecting the abundance of AOA and AOB. This study indicated that the community composition and diversity of AOA and AOB were significantly influenced by environmental factors, and AOA might be dominant drivers in the ammonia oxidation process in Oujiang surface sediment.},
}
@article {pmid27010920,
year = {2016},
author = {Tanabe, AS and Toju, H},
title = {Correction: Two New Computational Methods for Universal DNA Barcoding: A Benchmark Using Barcode Sequences of Bacteria, Archaea, Animals, Fungi, and Land Plants.},
journal = {PloS one},
volume = {11},
number = {3},
pages = {e0152242},
pmid = {27010920},
issn = {1932-6203},
}
@article {pmid27010812,
year = {2016},
author = {Khelaifia, S and Lagier, JC and Nkamga, VD and Guilhot, E and Drancourt, M and Raoult, D},
title = {Aerobic culture of methanogenic archaea without an external source of hydrogen.},
journal = {European journal of clinical microbiology &amp; infectious diseases : official publication of the European Society of Clinical Microbiology},
volume = {35},
number = {6},
pages = {985-991},
pmid = {27010812},
issn = {1435-4373},
mesh = {Aerobiosis ; Anti-Bacterial Agents/pharmacology ; Antioxidants/metabolism ; Archaea/drug effects/*growth &amp; development/*metabolism ; Carbon/metabolism ; Culture Media ; Humans ; Hydrogen/*metabolism ; Methane/*biosynthesis ; Methanobacteriaceae/metabolism ; },
abstract = {Culturing methanogenic archaea is fastidious, expensive, and requires an external source of hydrogen and carbon dioxide. Until now, these microorganisms have only been cultivated under strictly anaerobic conditions. We previously developed a single versatile culture medium containing sugars and anti-oxydants for cultivating all human known methanogens. Performing aerobic cultures in the presence of Bacteroides thetaiotaomicron, which produces hydrogen, allows for cultivation of Methanobrevibacter smithii which itself produces methane. To obtain colonies, we cultivated M. smithii in an agar plate in the upper part of a double chamber flask with a liquid culture of B. thetaiotaomicron in the lower compartment. We subsequently cultured four other methanogenic species for the first time and successfully isolated 13 strains of M. smithii and nine strains of Methanobrevibacter oralis from 100 stools and 45 oral samples. This procedure allows aerobic isolation and antibiotic susceptibility testing. This changes the ability to routinely study methanogens, which have been neglected in clinical microbiology laboratories and may be useful for biogas production.},
}
@article {pmid27002962,
year = {2016},
author = {Reitschuler, C and Hofmann, K and Illmer, P},
title = {Abundances, diversity and seasonality of (non-extremophilic) Archaea in Alpine freshwaters.},
journal = {Antonie van Leeuwenhoek},
volume = {109},
number = {6},
pages = {855-868},
doi = {10.1007/s10482-016-0685-6},
pmid = {27002962},
issn = {1572-9699},
mesh = {Ammonia/metabolism ; Archaea/*classification/genetics/metabolism/*physiology ; Austria ; Bacteria/classification ; Biodiversity ; DNA, Archaeal/genetics ; Denaturing Gradient Gel Electrophoresis/methods ; Ecology ; Euryarchaeota/classification/genetics ; Extremophiles/*classification/genetics/metabolism/*physiology ; Fresh Water/*microbiology ; Fungi/classification ; Lakes/microbiology ; Real-Time Polymerase Chain Reaction/methods ; Reproducibility of Results ; Rivers/microbiology ; Seasons ; },
abstract = {The objectives of this study were to assess abundances and community compositions of Archaea within a heterogeneous set of freshwater systems in the Austrian Alps. Seasonal changes and geographical differences within Archaea, considering abiotic and biotic factors (e.g. temperature, pH, total organic carbon (TOC), NH4 (+), bacteria, fungi), were analysed in this context. Water samples were collected from 8 lakes, 10 creeks and the river Inn in 2014. Qualitative-quantitative data were derived via a comprehensive set of (quantitative) PCR assays and PCR-DGGE (denaturing gradient gel electrophoresis) based methodology, which was evaluated concerning specificity and reliability either previously or in this study. QPCR-derived archaeal abundances reached values of 10(3) copies mL(-1) on average, with a peak in winter-spring ('Cold Peak'), and covered 0-15 % (average: 1 %) of the microbial populations. This peak correlated with significantly raised TOC and low NH4 (+) levels during the cold seasons. Stagnant waters showed significantly higher archaeal abundances and diversities than flowing ones. Among methanogens, Methanosarcinales were the most common order. PCR-DGGE data showed that the archaeal communities were site-specific and could function as an ecological marker, in contrast to the more heterogeneous and unsteady bacterial and fungal community. This is attributable to the highly heterogeneous community of methanogenic Archaea (MA, Euryarchaeota), while only two species, Nitrosopumilus maritimus and Ca. Nitrososphaera gargensis, were found to be the ubiquitous representatives of ammonia-oxidizing Archaea (AOA, Thaumarchaeota) in Alpine freshwaters. This work emphasises the diversity, distribution and seasonality of non-extremophilic Archaea in Alpine freshwaters, with a first insight into their ecophysiological potential.},
}
@article {pmid27001046,
year = {2016},
author = {Ishino, S and Nishi, Y and Oda, S and Uemori, T and Sagara, T and Takatsu, N and Yamagami, T and Shirai, T and Ishino, Y},
title = {Identification of a mismatch-specific endonuclease in hyperthermophilic Archaea.},
journal = {Nucleic acids research},
volume = {44},
number = {7},
pages = {2977-2986},
pmid = {27001046},
issn = {1362-4962},
mesh = {Archaeal Proteins/genetics/isolation &amp; purification/*metabolism ; *Base Pair Mismatch ; DNA Cleavage ; Endodeoxyribonucleases/genetics/isolation &amp; purification/*metabolism ; Hot Temperature ; Mutation ; Proliferating Cell Nuclear Antigen/metabolism ; Pyrococcus furiosus/enzymology ; Recombinant Proteins/isolation &amp; purification/metabolism ; Substrate Specificity ; Thermococcus/*enzymology ; },
abstract = {The common mismatch repair system processed by MutS and MutL and their homologs was identified in Bacteria and Eukarya. However, no evidence of a functional MutS/L homolog has been reported for archaeal organisms, and it is not known whether the mismatch repair system is conserved in Archaea. Here, we describe an endonuclease that cleaves double-stranded DNA containing a mismatched base pair, from the hyperthermophilic archaeon Pyrococcus furiosus The corresponding gene revealed that the activity originates from PF0012, and we named this enzyme Endonuclease MS (EndoMS) as the mismatch-specific Endonuclease. The sequence similarity suggested that EndoMS is the ortholog of NucS isolated from Pyrococcus abyssi, published previously. Biochemical characterizations of the EndoMS homolog from Thermococcus kodakarensis clearly showed that EndoMS specifically cleaves both strands of double-stranded DNA into 5'-protruding forms, with the mismatched base pair in the central position. EndoMS cleaves G/T, G/G, T/T, T/C and A/G mismatches, with a more preference for G/T, G/G and T/T, but has very little or no effect on C/C, A/C and A/A mismatches. The discovery of this endonuclease suggests the existence of a novel mismatch repair process, initiated by the double-strand break generated by the EndoMS endonuclease, in Archaea and some Bacteria.},
}
@article {pmid26973602,
year = {2016},
author = {Kan, J and Clingenpeel, S and Dow, CL and McDermott, TR and Macur, RE and Inskeep, WP and Nealson, KH},
title = {Geochemistry and Mixing Drive the Spatial Distribution of Free-Living Archaea and Bacteria in Yellowstone Lake.},
journal = {Frontiers in microbiology},
volume = {7},
number = {},
pages = {210},
pmid = {26973602},
issn = {1664-302X},
abstract = {Yellowstone Lake, the largest subalpine lake in the United States, harbors great novelty and diversity of Bacteria and Archaea. Size-fractionated water samples (0.1-0.8, 0.8-3.0, and 3.0-20 μm) were collected from surface photic zone, deep mixing zone, and vent fluids at different locations in the lake by using a remotely operated vehicle (ROV). Quantification with real-time PCR indicated that Bacteria dominated free-living microorganisms with Bacteria/Archaea ratios ranging from 4037:1 (surface water) to 25:1 (vent water). Microbial population structures (both Bacteria and Archaea) were assessed using 454-FLX sequencing with a total of 662,302 pyrosequencing reads for V1 and V2 regions of 16S rRNA genes. Non-metric multidimensional scaling (NMDS) analyses indicated that strong spatial distribution patterns existed from surface to deep vents for free-living Archaea and Bacteria in the lake. Along with pH, major vent-associated geochemical constituents including CH4, CO2, H2, DIC (dissolved inorganic carbon), DOC (dissolved organic carbon), SO4 (2-), O2 and metals were likely the major drivers for microbial population structures, however, mixing events occurring in the lake also impacted the distribution patterns. Distinct Bacteria and Archaea were present among size fractions, and bigger size fractions included particle-associated microbes (> 3 μm) and contained higher predicted operational taxonomic unit richness and microbial diversities (genus level) than free-living ones (<0.8 μm). Our study represents the first attempt at addressing the spatial distribution of Bacteria and Archaea in Yellowstone Lake, and our results highlight the variable contribution of Archaea and Bacteria to the hydrogeochemical-relevant metabolism of hydrogen, carbon, nitrogen, and sulfur.},
}
@article {pmid26971439,
year = {2017},
author = {Hink, L and Nicol, GW and Prosser, JI},
title = {Archaea produce lower yields of N2 O than bacteria during aerobic ammonia oxidation in soil.},
journal = {Environmental microbiology},
volume = {19},
number = {12},
pages = {4829-4837},
doi = {10.1111/1462-2920.13282},
pmid = {26971439},
issn = {1462-2920},
mesh = {Agriculture ; Alkynes/pharmacology ; Ammonia/*metabolism ; Archaea/growth &amp; development/*metabolism ; Bacteria/growth &amp; development/*metabolism ; Denitrification ; Fertilizers/analysis ; Global Warming ; Nitrification ; Nitrogen Cycle ; Nitrous Oxide/*metabolism ; Oxidation-Reduction ; Soil ; Soil Microbiology ; },
abstract = {Nitrogen fertilisation of agricultural soil contributes significantly to emissions of the potent greenhouse gas nitrous oxide (N2 O), which is generated during denitrification and, in oxic soils, mainly by ammonia oxidisers. Although laboratory cultures of ammonia oxidising bacteria (AOB) and archaea (AOA) produce N2 O, their relative activities in soil are unknown. This work tested the hypothesis that AOB dominate ammonia oxidation and N2 O production under conditions of high inorganic ammonia (NH3) input, but result mainly from the activity of AOA when NH3 is derived from mineralisation. 1-octyne, a recently discovered inhibitor of AOB, was used to distinguish N2 O production resulting from archaeal and bacterial ammonia oxidation in soil microcosms, and specifically inhibited AOB growth, activity and N2 O production. In unamended soils, ammonia oxidation and N2 O production were lower and resulted mainly from ammonia oxidation by AOA. The AOA N2 O yield relative to nitrite produced was half that of AOB, likely due to additional enzymatic mechanisms in the latter, but ammonia oxidation and N2 O production were directly linked in all treatments. Relative contributions of AOA and AOB to N2 O production, therefore, reflect their respective contributions to ammonia oxidation. These results suggest potential mitigation strategies for N2 O emissions from fertilised agricultural soils.},
}
@article {pmid26961528,
year = {2016},
author = {Song, H and Che, Z and Cao, W and Huang, T and Wang, J and Dong, Z},
title = {Changing roles of ammonia-oxidizing bacteria and archaea in a continuously acidifying soil caused by over-fertilization with nitrogen.},
journal = {Environmental science and pollution research international},
volume = {23},
number = {12},
pages = {11964-11974},
pmid = {26961528},
issn = {1614-7499},
mesh = {Ammonia/chemistry ; Archaea/genetics ; Bacteria/genetics ; Betaproteobacteria/genetics ; Fertilizers ; Hydrogen-Ion Concentration ; Microbial Consortia/*drug effects ; *Nitrification ; Nitrogen/chemistry/*pharmacology ; Oxidation-Reduction ; Phylogeny ; Real-Time Polymerase Chain Reaction ; Soil/*chemistry ; *Soil Microbiology ; },
abstract = {Nitrification coupled with nitrate leaching contributes to soil acidification. However, little is known about the effect of soil acidification on nitrification, especially on ammonia oxidation that is the rate-limiting step of nitrification and performed by ammonia-oxidizing bacteria (AOB) and archaea (AOA). Serious soil acidification occurs in Chinese greenhouses due to the overuse of N-fertilizer. In the present study, greenhouse soils with 1, 3, 5, 7, and 9 years of vegetable cultivation showed a consistent pH decline (i.e., 7.0, 6.3, 5.6, 4.9, and 4.3). Across the pH gradient, we analyzed the community structure and abundance of AOB and AOA by pyrosequencing and real-time PCR techniques, respectively. The recovered nitrification potential (RNP) method was used to determine relative contributions of AOA and AOB to nitrification potential. The results revealed that soil acidification shaped the community structures of AOA and AOB. In acidifying soil, soil pH, NH3 concentration, and DOC content were critical factors shaping ammonia oxidizer community structure. AOB abundance, but not AOA, was strongly influenced by soil acidification. When soil pH was below 5.0, AOA rather than AOB were responsible for almost all of the RNP. However, when soil pH ranged from 5.6 to 7.0, AOB were the major contributors to RNP. The group I.1a-associatied AOA had more relative abundance in low pH (pH<6.3), whereas group I.1b tended to prefer neutral pH. Clusters 2, 10, and 12 in AOB were more abundant in acidic soil (pH <5.6), while Nitrosomonas-like lineage and unclassified lineage 3 were prevailing in neutral soil and slightly acidic soil (pH, 6.0-6.5), respectively. These results suggested that soil acidification had a profound impact on ammonia oxidation and more specific lineages in AOB occupying different pH-associated niches required further investigation.},
}
@article {pmid26960319,
year = {2016},
author = {Zhang, Y and Chen, L and Sun, R and Dai, T and Tian, J and Zheng, W and Wen, D},
title = {Population and diversity of ammonia-oxidizing archaea and bacteria in a pollutants' receiving area in Hangzhou Bay.},
journal = {Applied microbiology and biotechnology},
volume = {100},
number = {13},
pages = {6035-6045},
doi = {10.1007/s00253-016-7421-z},
pmid = {26960319},
issn = {1432-0614},
mesh = {Ammonia/*metabolism ; Archaea/classification/genetics/*isolation &amp; purification/metabolism ; Bacteria/classification/genetics/*isolation &amp; purification/metabolism ; Bays/analysis/*microbiology ; *Biodiversity ; China ; Geologic Sediments/chemistry/microbiology ; Oxidation-Reduction ; Phylogeny ; Water Pollution, Chemical/analysis ; },
abstract = {The community structure of ammonia-oxidizing microorganisms is sensitive to various environmental factors, including pollutions. In this study, real-time PCR and 454 pyrosequencing were adopted to investigate the population and diversity of ammonia-oxidizing archaea (AOA) and bacteria (AOB) temporally and spatially in the sediments of an industrial effluent receiving area in the Qiantang River's estuary, Hangzhou Bay. The abundances of AOA and AOB amoA genes fluctuated in 10(5)-10(7) gene copies per gram of sediment; the ratio of AOA amoA/AOB amoA ranged in 0.39-5.52. The AOA amoA/archaeal 16S rRNA, AOB amoA/bacterial 16S rRNA, and AOA amoA/AOB amoA were found to positively correlate with NH4 (+)-N concentration of the seawater. Nitrosopumilus cluster and Nitrosomonas-like cluster were the dominant AOA and AOB, respectively. The community structures of both AOA and AOB in the sediments exhibited significant seasonal differences rather than spatial changes in the effluent receiving area. The phylogenetic distribution of AOB in this area was consistent with the wastewater treatment plants (WWTPs) discharging the effluent but differed from the Qiantang River and other estuaries, which might be an outcome of long-term effluent discharge.},
}
@article {pmid26953597,
year = {2016},
author = {Orsi, WD and Smith, JM and Liu, S and Liu, Z and Sakamoto, CM and Wilken, S and Poirier, C and Richards, TA and Keeling, PJ and Worden, AZ and Santoro, AE},
title = {Diverse, uncultivated bacteria and archaea underlying the cycling of dissolved protein in the ocean.},
journal = {The ISME journal},
volume = {10},
number = {9},
pages = {2158-2173},
pmid = {26953597},
issn = {1751-7370},
mesh = {Archaea/genetics/*metabolism ; Bacteria/genetics/*metabolism ; California ; Carbon/*metabolism ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Nitrogen/*metabolism ; Oceans and Seas ; Phytoplankton/genetics/*metabolism ; Proteins/*metabolism ; },
abstract = {Dissolved organic nitrogen (DON) supports a significant amount of heterotrophic production in the ocean. Yet, to date, the identity and diversity of microbial groups that transform DON are not well understood. To better understand the organisms responsible for transforming high molecular weight (HMW)-DON in the upper ocean, isotopically labeled protein extract from Micromonas pusilla, a eukaryotic member of the resident phytoplankton community, was added as substrate to euphotic zone water from the central California Current system. Carbon and nitrogen remineralization rates from the added proteins ranged from 0.002 to 0.35 μmol C l(-1) per day and 0.03 to 0.27 nmol N l(-1) per day. DNA stable-isotope probing (DNA-SIP) coupled with high-throughput sequencing of 16S rRNA genes linked the activity of 77 uncultivated free-living and particle-associated bacterial and archaeal taxa to the utilization of Micromonas protein extract. The high-throughput DNA-SIP method was sensitive in detecting isotopic assimilation by individual operational taxonomic units (OTUs), as substrate assimilation was observed after only 24 h. Many uncultivated free-living microbial taxa are newly implicated in the cycling of dissolved proteins affiliated with the Verrucomicrobia, Planctomycetes, Actinobacteria and Marine Group II (MGII) Euryarchaeota. In addition, a particle-associated community actively cycling DON was discovered, dominated by uncultivated organisms affiliated with MGII, Flavobacteria, Planctomycetes, Verrucomicrobia and Bdellovibrionaceae. The number of taxa assimilating protein correlated with genomic representation of TonB-dependent receptor (TBDR)-encoding genes, suggesting a possible role of TBDR in utilization of dissolved proteins by marine microbes. Our results significantly expand the known microbial diversity mediating the cycling of dissolved proteins in the ocean.},
}
@article {pmid26950522,
year = {2016},
author = {Zhu, C and Wakeham, SG and Elling, FJ and Basse, A and Mollenhauer, G and Versteegh, GJ and Könneke, M and Hinrichs, KU},
title = {Stratification of archaeal membrane lipids in the ocean and implications for adaptation and chemotaxonomy of planktonic archaea.},
journal = {Environmental microbiology},
volume = {18},
number = {12},
pages = {4324-4336},
doi = {10.1111/1462-2920.13289},
pmid = {26950522},
issn = {1462-2920},
mesh = {Adaptation, Physiological ; Archaea/classification/isolation &amp; purification/*metabolism ; Cell Membrane/chemistry/metabolism ; Ecology ; *Lipid Metabolism ; Lipids/chemistry ; Membrane Lipids/chemistry/*metabolism ; Oceans and Seas ; Oxygen/metabolism ; Plankton/classification/isolation &amp; purification/*metabolism ; Seawater/chemistry/*microbiology ; },
abstract = {Membrane lipids of marine planktonic archaea have provided unique insights into archaeal ecology and paleoceanography. However, past studies of archaeal lipids in suspended particulate matter (SPM) and sediments mainly focused on a small class of fully saturated glycerol dibiphytanyl glycerol tetraether (GDGT) homologues identified decades ago. The apparent low structural diversity of GDGTs is in strong contrast to the high diversity of metabolism and taxonomy among planktonic archaea. Furthermore, adaptation of archaeal lipids in the deep ocean remains poorly constrained. We report the archaeal lipidome in SPM from diverse oceanic regimes. We extend the known inventory of planktonic archaeal lipids to include numerous unsaturated archaeal ether lipids (uns-AELs). We further reveal (i) different thermal regulations and polar headgroup compositions of membrane lipids between the epipelagic (≤ 100 m) and deep (>100 m) populations of archaea, (ii) stratification of unsaturated GDGTs with varying redox conditions, and (iii) enrichment of tetra-unsaturated archaeol and fully saturated GDGTs in epipelagic and deep oxygenated waters, respectively. Such stratified lipid patterns are consistent with the typical distribution of archaeal phylotypes in marine environments. We, thus, provide an ecological context for GDGT-based paleoclimatology and bring about the potential use of uns-AELs as biomarkers for planktonic Euryarchaeota.},
}
@article {pmid26950321,
year = {2016},
author = {Utturkar, SM and Huber, H and Leptihn, S and Loh, B and Brown, SD and Stetter, KO and Podar, M},
title = {Draft Genome Sequence of Pyrodictium occultum PL19T, a Marine Hyperthermophilic Species of Archaea That Grows Optimally at 105°C.},
journal = {Genome announcements},
volume = {4},
number = {1},
pages = {},
pmid = {26950321},
issn = {2169-8287},
abstract = {We report here the draft genome sequence of Pyrodictium occultum PL19(T), a marine hyperthermophilic archaeon. The genome provides insights into molecular and cellular adaptation mechanisms to life in extreme environments and the evolution of early organisms on Earth.},
}
@article {pmid26946536,
year = {2016},
author = {Sauder, LA and Ross, AA and Neufeld, JD},
title = {Nitric oxide scavengers differentially inhibit ammonia oxidation in ammonia-oxidizing archaea and bacteria.},
journal = {FEMS microbiology letters},
volume = {363},
number = {7},
pages = {},
doi = {10.1093/femsle/fnw052},
pmid = {26946536},
issn = {1574-6968},
mesh = {Ammonia/antagonists &amp; inhibitors/*metabolism ; Archaea/*drug effects/*metabolism ; Bacteria/*drug effects/*metabolism ; Benzenesulfonates/pharmacology ; Benzoates/pharmacology ; Betaproteobacteria/drug effects/metabolism ; Caffeic Acids/pharmacology ; Chromans/pharmacology ; Curcumin/pharmacology ; Imidazoles/pharmacology ; Nitric Oxide/*metabolism ; Nitrification ; Nitrosomonas europaea/drug effects/metabolism ; Oxidation-Reduction/drug effects ; Phylogeny ; *Soil Microbiology ; },
abstract = {Differential inhibitors are important for measuring the relative contributions of microbial groups, such as ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA), to biogeochemical processes in environmental samples. In particular, 2-phenyl-4,4,5,5-tetramethylimidazoline-1-oxyl 3-oxide (PTIO) represents a nitric oxide scavenger used for the specific inhibition of AOA, implicating nitric oxide as an intermediate of thaumarchaeotal ammonia oxidation. This study investigated four alternative nitric oxide scavengers for their ability to differentially inhibit AOA and AOB in comparison to PTIO. Caffeic acid, curcumin, methylene blue hydrate and trolox were tested onNitrosopumilus maritimus, two unpublished AOA representatives (AOA-6f and AOA-G6) as well as the AOB representative Nitrosomonas europaea All four scavengers inhibited ammonia oxidation by AOA at lower concentrations than for AOB. In particular, differential inhibition of AOA and AOB by caffeic acid (100 μM) and methylene blue hydrate (3 μM) was comparable to carboxy-PTIO (100 μM) in pure and enrichment culture incubations. However, when added to aquarium sponge biofilm microcosms, both scavengers were unable to inhibit ammonia oxidation consistently, likely due to degradation of the inhibitors themselves. This study provides evidence that a variety of nitric oxide scavengers result in differential inhibition of ammonia oxidation in AOA and AOB, and provides support to the proposed role of nitric oxide as a key intermediate in the thaumarchaeotal ammonia oxidation pathway.},
}
@article {pmid26925607,
year = {2016},
author = {Graziadei, A and Masiewicz, P and Lapinaite, A and Carlomagno, T},
title = {Archaea box C/D enzymes methylate two distinct substrate rRNA sequences with different efficiency.},
journal = {RNA (New York, N.Y.)},
volume = {22},
number = {5},
pages = {764-772},
pmid = {26925607},
issn = {1469-9001},
mesh = {Archaea/*enzymology ; Enzymes/*metabolism ; Methylation ; Mutation ; Nucleic Acid Conformation ; RNA, Ribosomal/chemistry/*genetics ; },
abstract = {RNA modifications confer complexity to the 4-nucleotide polymer; nevertheless, their exact function is mostly unknown. rRNA 2'-O-ribose methylation concentrates to ribosome functional sites and is important for ribosome biogenesis. The methyl group is transferred to rRNA by the box C/D RNPs: The rRNA sequence to be methylated is recognized by a complementary sequence on the guide RNA, which is part of the enzyme. In contrast to their eukaryotic homologs, archaeal box C/D enzymes can be assembled in vitro and are used to study the mechanism of 2'-O-ribose methylation. In Archaea, each guide RNA directs methylation to two distinct rRNA sequences, posing the question whether this dual architecture of the enzyme has a regulatory role. Here we use methylation assays and low-resolution structural analysis with small-angle X-ray scattering to study the methylation reaction guided by the sR26 guide RNA fromPyrococcus furiosus We find that the methylation efficacy at sites D and D' differ substantially, with substrate D' turning over more efficiently than substrate D. This observation correlates well with structural data: The scattering profile of the box C/D RNP half-loaded with substrate D' is similar to that of the holo complex, which has the highest activity. Unexpectedly, the guide RNA secondary structure is not responsible for the functional difference at the D and D' sites. Instead, this difference is recapitulated by the nature of the first base pair of the guide-substrate duplex. We suggest that substrate turnover may occur through a zip mechanism that initiates at the 5'-end of the product.},
}
@article {pmid26914534,
year = {2016},
author = {Crits-Christoph, A and Gelsinger, DR and Ma, B and Wierzchos, J and Ravel, J and Davila, A and Casero, MC and DiRuggiero, J},
title = {Functional interactions of archaea, bacteria and viruses in a hypersaline endolithic community.},
journal = {Environmental microbiology},
volume = {18},
number = {6},
pages = {2064-2077},
doi = {10.1111/1462-2920.13259},
pmid = {26914534},
issn = {1462-2920},
mesh = {Archaea/genetics ; Archaeal Proteins/chemistry ; Bacteria/genetics/*isolation &amp; purification ; Cyanobacteria/genetics/isolation &amp; purification/virology ; *Desert Climate ; Ecosystem ; Euryarchaeota/genetics/*isolation &amp; purification/virology ; Genome, Viral ; Isoelectric Point ; Metagenome ; Microbial Consortia ; Microbial Interactions ; Phylogeny ; *Salinity ; Viruses/genetics/*isolation &amp; purification ; },
abstract = {Halite endoliths in the Atacama Desert represent one of the most extreme ecosystems on Earth. Cultivation-independent methods were used to examine the functional adaptations of the microbial consortia inhabiting halite nodules. The community was dominated by haloarchaea and functional analysis attributed most of the autotrophic CO2 fixation to one unique cyanobacterium. The assembled 1.1 Mbp genome of a novel nanohaloarchaeon, Candidatus Nanopetramus SG9, revealed a photoheterotrophic life style and a low median isoelectric point (pI) for all predicted proteins, suggesting a 'salt-in' strategy for osmotic balance. Predicted proteins of the algae identified in the community also had pI distributions similar to 'salt-in' strategists. The Nanopetramus genome contained a unique CRISPR/Cas system with a spacer that matched a partial viral genome from the metagenome. A combination of reference-independent methods identified over 30 complete or near complete viral or proviral genomes with diverse genome structure, genome size, gene content and hosts. Putative hosts included Halobacteriaceae, Nanohaloarchaea and Cyanobacteria. Despite the dependence of the halite community on deliquescence for liquid water availability, this study exposed an ecosystem spanning three phylogenetic domains, containing a large diversity of viruses and predominance of a 'salt-in' strategy to balance the high osmotic pressure of the environment.},
}
@article {pmid26886233,
year = {2016},
author = {MacNeill, SA},
title = {PCNA-binding proteins in the archaea: novel functionality beyond the conserved core.},
journal = {Current genetics},
volume = {62},
number = {3},
pages = {527-532},
pmid = {26886233},
issn = {1432-0983},
mesh = {Archaea/genetics/*metabolism ; Carrier Proteins/chemistry/*metabolism ; DNA Repair ; DNA Replication ; Proliferating Cell Nuclear Antigen/chemistry/*metabolism ; Protein Binding ; Protein Interaction Domains and Motifs ; Protein Interaction Mapping ; Protein Multimerization ; },
abstract = {Sliding clamps play an essential role in coordinating protein activity in DNA metabolism in all three domains of life. In eukaryotes and archaea, the sliding clamp is PCNA (proliferating cell nuclear antigen). Across the diversity of the archaea PCNA interacts with a highly conserved set of proteins with key roles in DNA replication and repair, including DNA polymerases B and D, replication factor C, the Fen1 nuclease and RNAseH2, but this core set of factors is likely to represent a fraction of the PCNA interactome only. Here, I review three recently characterised non-core archaeal PCNA-binding proteins NusS, NreA/NreB and TIP, highlighting what is known of their interactions with PCNA and their functions in vivo and in vitro. Gaining a detailed understanding of the non-core PCNA interactome will provide significant insights into key aspects of chromosome biology in divergent archaeal lineages.},
}
@article {pmid26884161,
year = {2016},
author = {Rensen, EI and Mochizuki, T and Quemin, E and Schouten, S and Krupovic, M and Prangishvili, D},
title = {A virus of hyperthermophilic archaea with a unique architecture among DNA viruses.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {113},
number = {9},
pages = {2478-2483},
pmid = {26884161},
issn = {1091-6490},
mesh = {Archaea/*virology ; DNA Viruses/*classification/genetics/ultrastructure ; Genome, Viral ; Host-Pathogen Interactions ; Microscopy, Electron, Transmission ; },
abstract = {Viruses package their genetic material in diverse ways. Most known strategies include encapsulation of nucleic acids into spherical or filamentous virions with icosahedral or helical symmetry, respectively. Filamentous viruses with dsDNA genomes are currently associated exclusively with Archaea. Here, we describe a filamentous hyperthermophilic archaeal virus, Pyrobaculum filamentous virus 1 (PFV1), with a type of virion organization not previously observed in DNA viruses. The PFV1 virion, 400 ± 20 × 32 ± 3 nm, contains an envelope and an inner core consisting of two structural units: a rod-shaped helical nucleocapsid formed of two 14-kDa major virion proteins and a nucleocapsid-encompassing protein sheath composed of a single major virion protein of 18 kDa. The virion organization of PFV1 is superficially similar to that of negative-sense RNA viruses of the family Filoviridae, including Ebola virus and Marburg virus. The linear dsDNA of PFV1 carries 17,714 bp, including 60-bp-long terminal inverted repeats, and contains 39 predicted ORFs, most of which do not show similarities to sequences in public databases. PFV1 is a lytic virus that completely disrupts the host cell membrane at the end of the infection cycle.},
}
@article {pmid26879980,
year = {2016},
author = {Gerrity, S and Clifford, E and Kennelly, C and Collins, G},
title = {Ammonia oxidizing bacteria and archaea in horizontal flow biofilm reactors treating ammonia-contaminated air at 10 °C.},
journal = {Journal of industrial microbiology &amp; biotechnology},
volume = {43},
number = {5},
pages = {651-661},
pmid = {26879980},
issn = {1476-5535},
mesh = {Air/*analysis ; Ammonia/*isolation &amp; purification/*metabolism ; Archaea/*metabolism ; Bacteria/*metabolism ; *Biofilms ; *Bioreactors ; Feasibility Studies ; Nitrates/metabolism ; *Nitrification ; Nitrites/metabolism ; Oxidation-Reduction ; *Temperature ; },
abstract = {The objective of this study was to demonstrate the feasibility of novel, Horizontal Flow Biofilm Reactor (HFBR) technology for the treatment of ammonia (NH3)-contaminated airstreams. Three laboratory-scale HFBRs were used for remediation of an NH3-containing airstream at 10 °C during a 90-d trial to test the efficacy of low-temperature treatment. Average ammonia removal efficiencies of 99.7 % were achieved at maximum loading rates of 4.8 g NH3 m(3) h(-1). Biological nitrification of ammonia to nitrite (NO2 (-)) and nitrate (NO3 (-)) was mediated by nitrifying bacterial and archaeal biofilm populations. Ammonia-oxidising bacteria (AOB) were significantly more abundant than ammonia-oxidising archaea (AOA) vertically at each of seven sampling zones along the vertical HFBRs. Nitrosomonas and Nitrosospira, were the two most dominant bacterial genera detected in the HFBRs, while an uncultured archaeal clone dominated the AOA community. The bacterial community composition across the three HFBRs was highly conserved, although variations occurred between HFBR zones and were driven by physicochemical variables. The study demonstrates the feasibility of HFBRs for the treatment of ammonia-contaminated airstreams at low temperatures; identifies key nitrifying microorganisms driving the removal process; and provides insights for process optimisation and control. The findings are significant for industrial applications of gas oxidation technology in temperate climates.},
}
@article {pmid26834709,
year = {2015},
author = {Lu, S and Liu, X and Ma, Z and Liu, Q and Wu, Z and Zeng, X and Shi, X and Gu, Z},
title = {Vertical Segregation and Phylogenetic Characterization of Ammonia-Oxidizing Bacteria and Archaea in the Sediment of a Freshwater Aquaculture Pond.},
journal = {Frontiers in microbiology},
volume = {6},
number = {},
pages = {1539},
pmid = {26834709},
issn = {1664-302X},
abstract = {Pond aquaculture is the major freshwater aquaculture method in China. Ammonia-oxidizing communities inhabiting pond sediments play an important role in controlling culture water quality. However, the distribution and activities of ammonia-oxidizing microbial communities along sediment profiles are poorly understood in this specific environment. Vertical variations in the abundance, transcription, potential ammonia oxidizing rate, and community composition of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) in sediment samples (0-50 cm depth) collected from a freshwater aquaculture pond were investigated. The concentrations of the AOA amoA gene were higher than those of the AOB by an order of magnitude, which suggested that AOA, as opposed to AOB, were the numerically predominant ammonia-oxidizing organisms in the surface sediment. This could be attributed to the fact that AOA are more resistant to low levels of dissolved oxygen. However, the concentrations of the AOB amoA mRNA were higher than those of the AOA by 2.5- to 39.9-fold in surface sediments (0-10 cm depth), which suggests that the oxidation of ammonia was mainly performed by AOB in the surface sediments, and by AOA in the deeper sediments, where only AOA could be detected. Clone libraries of AOA and AOB amoA sequences indicated that the diversity of AOA and AOB decreased with increasing depth. The AOB community consisted of two groups: the Nitrosospira and Nitrosomonas clusters, and Nitrosomonas were predominant in the freshwater pond sediment. All AOA amoA gene sequences in the 0-2 cm deep sediment were grouped into the Nitrososphaera cluster, while other AOA sequences in deeper sediments (10-15 and 20-25 cm depths) were grouped into the Nitrosopumilus cluster.},
}
@article {pmid26769275,
year = {2016},
author = {Taha, and Siddiqui, KS and Campanaro, S and Najnin, T and Deshpande, N and Williams, TJ and Aldrich-Wright, J and Wilkins, M and Curmi, PM and Cavicchioli, R},
title = {Single TRAM domain RNA-binding proteins in Archaea: functional insight from Ctr3 from the Antarctic methanogen Methanococcoides burtonii.},
journal = {Environmental microbiology},
volume = {18},
number = {9},
pages = {2810-2824},
doi = {10.1111/1462-2920.13229},
pmid = {26769275},
issn = {1462-2920},
mesh = {Antarctic Regions ; Archaeal Proteins/*chemistry/genetics/metabolism ; Cold Temperature ; Methanosarcinaceae/*genetics ; RNA, Archaeal/*chemistry/metabolism ; RNA, Ribosomal, 5S/chemistry/metabolism ; RNA, Transfer/chemistry/metabolism ; RNA-Binding Proteins/*chemistry/genetics/metabolism ; },
abstract = {TRAM domain proteins present in Archaea and Bacteria have a β-barrel shape with anti-parallel β-sheets that form a nucleic acid binding surface; a structure also present in cold shock proteins (Csps). Aside from protein structures, experimental data defining the function of TRAM domains is lacking. Here, we explore the possible functional properties of a single TRAM domain protein, Ctr3 (cold-responsive TRAM domain protein 3) from the Antarctic archaeon Methanococcoides burtonii that has increased abundance during low temperature growth. Ribonucleic acid (RNA) bound by Ctr3 in vitro was determined using RNA-seq. Ctr3-bound M. burtonii RNA with a preference for transfer (t)RNA and 5S ribosomal RNA, and a potential binding motif was identified. In tRNA, the motif represented the C loop; a region that is conserved in tRNA from all domains of life and appears to be solvent exposed, potentially providing access for Ctr3 to bind. Ctr3 and Csps are structurally similar and are both inferred to function in low temperature translation. The broad representation of single TRAM domain proteins within Archaea compared with their apparent absence in Bacteria, and scarcity of Csps in Archaea but prevalence in Bacteria, suggests they represent distinct evolutionary lineages of functionally equivalent RNA-binding proteins.},
}
@article {pmid26750123,
year = {2016},
author = {Calegari-Santos, R and Diogo, RA and Fontana, JD and Bonfim, TM},
title = {Carotenoid Production by Halophilic Archaea Under Different Culture Conditions.},
journal = {Current microbiology},
volume = {72},
number = {5},
pages = {641-651},
pmid = {26750123},
issn = {1432-0991},
mesh = {Archaea/genetics/*metabolism ; Carotenoids/*biosynthesis ; Culture Media/chemistry/*metabolism ; Sodium Chloride/metabolism ; },
abstract = {Carotenoids are pigments that may be used as colorants and antioxidants in food, pharmaceutical, and cosmetic industries. Since they also benefit human health, great efforts have been undertaken to search for natural sources of carotenoids, including microbial ones. The optimization of culture conditions to increase carotenoid yield is one of the strategies used to minimize the high cost of carotenoid production by microorganisms. Halophilic archaea are capable of producing carotenoids according to culture conditions. Their main carotenoid is bacterioruberin with 50 carbon atoms. In fact, the carotenoid has important biological functions since it acts as cell membrane reinforcement and it protects the microorganism against DNA damaging agents. Moreover, carotenoid extracts from halophilic archaea have shown high antioxidant capacity. Therefore, current review summarizes the effect of different culture conditions such as salt and carbon source concentrations in the medium, light incidence, and oxygen tension on carotenoid production by halophilic archaea and the strategies such as optimization methodology and two-stage cultivation already used to increase the carotenoid yield of these microorganisms.},
}
@article {pmid26745984,
year = {2016},
author = {Yan, S and Wu, G},
title = {Analysis on evolutionary relationship of amylases from archaea, bacteria and eukaryota.},
journal = {World journal of microbiology &amp; biotechnology},
volume = {32},
number = {2},
pages = {24},
pmid = {26745984},
issn = {1573-0972},
mesh = {Amino Acid Sequence ; Amylases/classification/*genetics/metabolism ; Archaea/*enzymology/genetics ; Bacteria/*enzymology/genetics ; Data Interpretation, Statistical ; Eukaryota/*enzymology/genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genetic Engineering ; Genetic Variation ; Molecular Sequence Data ; *Phylogeny ; Sequence Alignment ; },
abstract = {Amylase is one of the earliest characterized enzymes and has many applications in clinical and industrial settings. In biotechnological industries, the amylase activity is enhanced through modifying amylase structure and through cloning and expressing targeted amylases in different species. It is important to understand how engineered amylases can survive from generation to generation. This study used phylogenetic and statistical approaches to explore general patterns of amylases evolution, including 3118 α-amylases and 280 β-amylases from archaea, eukaryota and bacteria with fully documented taxonomic lineage. First, the phylogenetic tree was created to analyze the evolution of amylases with focus on individual amylases used in biofuel industry. Second, the average pairwise p-distance was computed for each kingdom, phylum, class, order, family and genus, and its diversity implies multi-time and multi-clan evolution. Finally, the variance was further partitioned into inter-clan variance and intra-clan variance for each taxonomic group, and they represent horizontal and vertical gene transfer. Theoretically, the results show a full picture on the evolution of amylases in manners of vertical and horizontal gene transfer, and multi-time and multi-clan evolution as well. Practically, this study provides the information on the surviving chance of desired amylase in a given taxonomic group, which may potentially enhance the successful rate of cloning and expression of amylase gene in different species.},
}
@article {pmid26733968,
year = {2015},
author = {Arshad, A and Speth, DR and de Graaf, RM and Op den Camp, HJ and Jetten, MS and Welte, CU},
title = {A Metagenomics-Based Metabolic Model of Nitrate-Dependent Anaerobic Oxidation of Methane by Methanoperedens-Like Archaea.},
journal = {Frontiers in microbiology},
volume = {6},
number = {},
pages = {1423},
pmid = {26733968},
issn = {1664-302X},
abstract = {Methane oxidation is an important process to mitigate the emission of the greenhouse gas methane and further exacerbating of climate forcing. Both aerobic and anaerobic microorganisms have been reported to catalyze methane oxidation with only a few possible electron acceptors. Recently, new microorganisms were identified that could couple the oxidation of methane to nitrate or nitrite reduction. Here we investigated such an enrichment culture at the (meta) genomic level to establish a metabolic model of nitrate-driven anaerobic oxidation of methane (nitrate-AOM). Nitrate-AOM is catalyzed by an archaeon closely related to (reverse) methanogens that belongs to the ANME-2d clade, tentatively named Methanoperedens nitroreducens. Methane may be activated by methyl-CoM reductase and subsequently undergo full oxidation to carbon dioxide via reverse methanogenesis. All enzymes of this pathway were present and expressed in the investigated culture. The genome of the archaeal enrichment culture encoded a variety of enzymes involved in an electron transport chain similar to those found in Methanosarcina species with additional features not previously found in methane-converting archaea. Nitrate reduction to nitrite seems to be located in the pseudoperiplasm and may be catalyzed by an unusual Nar-like protein complex. A small part of the resulting nitrite is reduced to ammonium which may be catalyzed by a Nrf-type nitrite reductase. One of the key questions is how electrons from cytoplasmically located reverse methanogenesis reach the nitrate reductase in the pseudoperiplasm. Electron transport in M. nitroreducens probably involves cofactor F420 in the cytoplasm, quinones in the cytoplasmic membrane and cytochrome c in the pseudoperiplasm. The membrane-bound electron transport chain includes F420H2 dehydrogenase and an unusual Rieske/cytochrome b complex. Based on genome and transcriptome studies a tentative model of how central energy metabolism of nitrate-AOM could work is presented and discussed.},
}
@article {pmid28330329,
year = {2016},
author = {Dubey, G and Kollah, B and Gour, VK and Shukla, AK and Mohanty, SR},
title = {Diversity of bacteria and archaea in the rhizosphere of bioenergy crop Jatropha curcas.},
journal = {3 Biotech},
volume = {6},
number = {2},
pages = {257},
pmid = {28330329},
issn = {2190-572X},
abstract = {Plant-microbial interaction in rhizosphere plays vital role in shaping plant's growth and ecosystem function. Most of the rhizospheric microbial diversity studies are restricted to bacteria. In natural ecosystem, archaea also constitutes a major component of the microbial population. However, their diversity is less known compared to bacteria. Experiments were carried out to examine diversity of bacteria and archaea in the rhizosphere of bioenergy crop Jatropha curcas (J. curcas). Samples were collected from three locations varying widely in the soil physico-chemical properties. Diversity was estimated by terminal restriction fragment length polymorphism (TRFLP) targeting 16S rRNA gene of bacteria and archaea. Fifteen bacterial and 17 archaeal terminal restriction fragments (TRFs) were retrieved from J. curcas rhizosphere. Bacterial indicative TRFs were Actinobacteria, Firmicutes, Acidobacteria, Verrumicrobiaceae, and Chlroflexi. Major archaeal TRFs were crenarchaeota, and euryarchaeota. In case of bacteria, relative fluorescence was low for TRF160 and high for TRF51, TRF 420. Similarly, for archaea relative fluorescence of TRF 218, and TRF 282 was low and high for TRF 278, TRF468 and TRF93. Principal component analysis (PCA) of bacterial TRFs designated PC 1 with 46.83% of variation and PC2 with 31.07% variation. Archaeal TRFs designated 90.94% of variation by PC1 and 9.05% by PC2. Simpson index varied from 0.530 to 0.880 and Shannon index from 1.462 to 3.139 for bacteria. For archaea, Simpson index varied from 0.855 to 0.897 and Shannon index varied from 3.027 to 3.155. Study concluded that rhizosphere of J. curcas constituted of diverse set of both bacteria and archaea, which might have promising plant growth promoting activities.},
}
@article {pmid26711582,
year = {2016},
author = {Ortiz-Alvarez, R and Casamayor, EO},
title = {High occurrence of Pacearchaeota and Woesearchaeota (Archaea superphylum DPANN) in the surface waters of oligotrophic high-altitude lakes.},
journal = {Environmental microbiology reports},
volume = {8},
number = {2},
pages = {210-217},
doi = {10.1111/1758-2229.12370},
pmid = {26711582},
issn = {1758-2229},
mesh = {Bacteria/classification/genetics/isolation &amp; purification ; *Biota ; Cluster Analysis ; DNA, Archaeal/chemistry/genetics ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Euryarchaeota/*classification/genetics/*isolation &amp; purification ; Lakes/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Spain ; },
abstract = {We carried out a regional survey on the archaea composition from surface waters of > 300 high-altitude Pyrenean lakes (average altitude 2300 m, pH range 4.4-10.1) by 16S rRNA gene tag sequencing. Relative Archaea abundances ranged between 0% and 6.3% of total prokaryotes amplicons in the polymerase chain reaction (PCR) mixture, and we detected 769 operational taxonomic units (OTUs; grouped at 97% identity) that split into 13 different lineages, with altitude and pH having a significant effect on the community composition. Woesearchaeota and Pacearchaeota (formerly Euryarchaeota DHVEG-6 cluster) dominated the data set (83% of total OTUS), showed a high occurrence (presence in c. 75% of the lakes) and had relative abundances significantly and positively correlated with the phylogenetic diversity of bacterial communities. Micrarchaeota-Diapherotrites (formerly Euryarchaeota MEG cluster), Methanomicrobia, Thermoplasmata and ammonia-oxidizing thaumarchaeota (AOA) showed relative abundances between 1% and 3% and occurrences between 14% and 26%. Minor lineages were SM1K20, Aenigmarchaeota (formerly Euryarchaeota DSEG cluster), Methanobacteria, Bathyarchaeota and SCG. Environmental preferences substantially differed among lineages, with Aenigmarchaeota and Methanomicrobia having the largest habitat breadth, and Thermoplasmata, AOA and Micrarchaeota having the smallest. Pacearchaeota and Woesearchaeota had been mostly reported from saline habitats and sediments, but surface waters of oligotrophic alpine lakes are suitable environments for such ecologically spread and genetically diverse archaeal lineages.},
}
@article {pmid26695717,
year = {2016},
author = {Koyanagi, T and Leriche, G and Onofrei, D and Holland, GP and Mayer, M and Yang, J},
title = {Cyclohexane Rings Reduce Membrane Permeability to Small Ions in Archaea-Inspired Tetraether Lipids.},
journal = {Angewandte Chemie (International ed. in English)},
volume = {55},
number = {5},
pages = {1890-1893},
doi = {10.1002/anie.201510445},
pmid = {26695717},
issn = {1521-3773},
mesh = {Archaea/*chemistry ; *Cell Membrane Permeability ; Cyclohexanes/*chemistry ; Ions ; Lipids/*chemistry ; },
abstract = {Extremophile archaeal organisms overcome problems of membrane permeability by producing lipids with structural elements that putatively improve membrane integrity compared to lipids from other life forms. Herein, we describe a series of lipids that mimic some key structural features of archaeal lipids, such as: 1) single tethering of lipid tails to create fully transmembrane tetraether lipids and 2) the incorporation of small rings into these tethered segments. We found that membranes formed from pure tetraether lipids leaked small ions at a rate that was about two orders of magnitude slower than common bilayer-forming lipids. Incorporation of cyclopentane rings into the tetraether lipids did not affect membrane leakage, whereas a cyclohexane ring reduced leakage by an additional 40 %. These results show that mimicking certain structural features of natural archaeal lipids results in improved membrane integrity, which may help overcome limitations of many current lipid-based technologies.},
}
@article {pmid26661751,
year = {2016},
author = {Sipos, AJ and Urakawa, H},
title = {Differential responses of nitrifying archaea and bacteria to methylene blue toxicity.},
journal = {Letters in applied microbiology},
volume = {62},
number = {2},
pages = {199-206},
doi = {10.1111/lam.12534},
pmid = {26661751},
issn = {1472-765X},
mesh = {Ammonia/metabolism ; Animals ; Aquaculture ; Archaea/*drug effects/metabolism ; Bacteria/*drug effects/metabolism ; Methylene Blue/*pharmacology ; Microbial Sensitivity Tests ; Nitrification/*drug effects ; Oxidation-Reduction ; },
abstract = {UNLABELLED: Methylene blue, a heterocyclic aromatic chemical compound used to treat fish diseases in the ornamental fish aquaculture industry, is believed to impair nitrification as a side effect. However, very little is known about the toxicity of methylene blue to nitrifying micro-organisms. Here, we report the susceptibility of six bacterial and one archaeal ammonia-oxidizing micro-organisms to methylene blue within the range of 10 ppb to 10 ppm. Remarkably high susceptibility was observed in the archaeal species Nitrosopumilus maritimus compared to the bacterial species. Ammonia oxidation by Nitrosopumilus maritimus was inhibited 65% by 10 ppb of methylene blue. Of the bacterial species examined, Nitrosococcus oceani was the most resistant to methylene blue toxicity. For similar inhibition of Nitrosococcus oceani (75% inhibition), one thousand times more methylene blue (10 ppm) was needed. The examination of single cell viability on Nitrosomonas marina demonstrated that methylene blue is lethal to the cells rather than reducing their single cell ammonia oxidation activity. The level of susceptibility to methylene blue was related to the cell volume, intracytoplasmic membrane arrangement and the evolutionary lineage of nitrifying micro-organisms. Our findings are relevant for effectively using methylene blue in various aquaculture settings by helping minimize its impact on nitrifiers during the treatment of fish diseases. In the future, resistant nitrifiers such as Nitrosococcus oceani may be purposely added to aquaculture systems to maintain nitrification activity during treatments with methylene blue.<br><br>The susceptibility of six bacterial and one archaeal nitrifying micro-organisms to methylene blue was tested. Remarkably high susceptibility was observed in the archaeal species compared to the bacterial species. The level of resistance to methylene blue was related to the cell volume, cytomembrane system and the taxonomic position of the nitrifying micro-organisms. This may be significant in the design and management of engineered nitrification systems and the stability of the nitrification process in various ecosystems if these systems are exposed to harmful chemicals or toxins.},
}
@article {pmid26634977,
year = {2015},
author = {Knappy, C and Barillà, D and Chong, J and Hodgson, D and Morgan, H and Suleman, M and Tan, C and Yao, P and Keely, B},
title = {Mono-, di- and trimethylated homologues of isoprenoid tetraether lipid cores in archaea and environmental samples: mass spectrometric identification and significance.},
journal = {Journal of mass spectrometry : JMS},
volume = {50},
number = {12},
pages = {1420-1432},
doi = {10.1002/jms.3709},
pmid = {26634977},
issn = {1096-9888},
support = {BB/F003099/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Archaea/*chemistry ; Chromatography, Liquid ; Diglycerides/*chemistry ; Methylation ; Tandem Mass Spectrometry ; Terpenes/*chemistry ; },
abstract = {Higher homologues of widely reported C(86) isoprenoid diglycerol tetraether lipid cores, containing 0-6 cyclopentyl rings, have been identified in (hyper)thermophilic archaea, representing up to 21% of total tetraether lipids in the cells. Liquid chromatography-tandem mass spectrometry confirms that the additional carbon atoms in the C(87-88) homologues are located in the etherified chains. Structures identified include dialkyl and monoalkyl ('H-shaped') tetraethers containing C(40-42) or C(81-82) hydrocarbons, respectively, many representing novel compounds. Gas chromatography-mass spectrometric analysis of hydrocarbons released from the lipid cores by ether cleavage suggests that the C(40) chains are biphytanes and the C(41) chains 13-methylbiphytanes. Multiple isomers, having different chain combinations, were recognised among the dialkyl lipids. Methylated tetraethers are produced by Methanothermobacter thermautotrophicus in varying proportions depending on growth conditions, suggesting that methylation may be an adaptive mechanism to regulate cellular function. The detection of methylated lipids in Pyrobaculum sp. AQ1.S2 and Sulfolobus acidocaldarius represents the first reported occurrences in Crenarchaeota. Soils and aquatic sediments from geographically distinct mesotemperate environments that were screened for homologues contained monomethylated tetraethers, with di- and trimethylated structures being detected occasionally. The structural diversity and range of occurrences of the C(87-89) tetraethers highlight their potential as complementary biomarkers for archaea in natural environments.},
}
@article {pmid26626057,
year = {2016},
author = {Gan, XH and Zhang, FQ and Gu, JD and Guo, YD and Li, ZQ and Zhang, WQ and Xu, XY and Zhou, Y and Wen, XY and Xie, GG and Wang, YF},
title = {Differential distribution patterns of ammonia-oxidizing archaea and bacteria in acidic soils of Nanling National Nature Reserve forests in subtropical China.},
journal = {Antonie van Leeuwenhoek},
volume = {109},
number = {2},
pages = {237-251},
doi = {10.1007/s10482-015-0627-8},
pmid = {26626057},
issn = {1572-9699},
mesh = {Ammonia/*metabolism ; Archaea/classification/genetics/*isolation &amp; purification/*metabolism ; Bacteria/classification/genetics/*isolation &amp; purification/*metabolism ; China ; Conservation of Natural Resources ; Molecular Sequence Data ; Oxidation-Reduction ; Phylogeny ; Soil/chemistry ; *Soil Microbiology ; },
abstract = {In addition to ammonia-oxidizing bacteria (AOB) the more recently discovered ammonia-oxidizing archaea (AOA) can also oxidize ammonia, but little is known about AOA community structure and abundance in subtropical forest soils. In this study, both AOA and AOB were investigated with molecular techniques in eight types of forests at surface soils (0-2 cm) and deep layers (18-20 cm) in Nanling National Nature Reserve in subtropical China. The results showed that the forest soils, all acidic (pH 4.24-5.10), harbored a wide range of AOA phylotypes, including the genera Nitrosotalea, Nitrososphaera, and another 6 clusters, one of which was reported for the first time. For AOB, only members of Nitrosospira were retrieved. Moreover, the abundance of the ammonia monooxygenase gene (amoA) from AOA dominated over AOB in most soil samples (13/16). Soil depth, rather than forest type, was an important factor shaping the community structure of AOA and AOB. The distribution patterns of AOA and AOB in soil layers were reversed: AOA diversity and abundances in the deep layers were higher than those in the surface layers; on the contrary, AOB diversity and abundances in the deep layers were lower than those in the surface layers. Interestingly, the diversity of AOA was positively correlated with pH, but negatively correlated with organic carbon, total nitrogen and total phosphorus, and the abundance of AOA was negatively correlated with available phosphorus. Our results demonstrated that AOA and AOB were differentially distributed in acidic soils in subtropical forests and affected differently by soil characteristics.},
}
@article {pmid26602691,
year = {2016},
author = {Peabody, MA and Laird, MR and Vlasschaert, C and Lo, R and Brinkman, FS},
title = {PSORTdb: expanding the bacteria and archaea protein subcellular localization database to better reflect diversity in cell envelope structures.},
journal = {Nucleic acids research},
volume = {44},
number = {D1},
pages = {D663-8},
pmid = {26602691},
issn = {1362-4962},
mesh = {Archaeal Proteins/analysis/*genetics ; Bacterial Proteins/analysis/*genetics ; Cell Membrane/chemistry ; Cell Wall/chemistry ; *Databases, Protein ; Genome, Archaeal ; Genome, Bacterial ; Membrane Proteins/analysis/*genetics ; },
abstract = {Protein subcellular localization (SCL) is important for understanding protein function, genome annotation, and has practical applications such as identification of potential vaccine components or diagnostic/drug targets. PSORTdb (http://db.psort.org) comprises manually curated SCLs for proteins which have been experimentally verified (ePSORTdb), as well as pre-computed SCL predictions for deduced proteomes from bacterial and archaeal complete genomes available from NCBI (cPSORTdb). We now report PSORTdb 3.0. It features improvements increasing user-friendliness, and further expands both ePSORTdb and cPSORTdb with a focus on improving protein SCL data in cases where it is most difficult-proteins associated with non-classical Gram-positive/Gram-negative/Gram-variable cell envelopes. ePSORTdb data curation was expanded, including adding in additional cell envelope localizations, and incorporating markers for cPSORTdb to automatically computationally identify if new genomes to be analysed fall into certain atypical cell envelope categories (i.e. Deinococcus-Thermus, Thermotogae, Corynebacteriales/Corynebacterineae, including Mycobacteria). The number of predicted proteins in cPSORTdb has increased from 3,700,000 when PSORTdb 2.0 was released to over 13,000,000 currently. PSORTdb 3.0 will be of wider use to researchers studying a greater diversity of monoderm or diderm microbes, including medically, agriculturally and industrially important species that have non-classical outer membranes or other cell envelope features.},
}
@article {pmid26592025,
year = {2015},
author = {Gao, JF and Li, T and Zhang, SJ and Fan, XY and Pan, KL and Ma, Q and Yuan, YL},
title = {[Abundance and Community Composition of Ammonia-Oxidizing Archaea in Two Completely Autotrophic Nitrogen Removal over Nitrite Systems].},
journal = {Huan jing ke xue= Huanjing kexue},
volume = {36},
number = {8},
pages = {2939-2946},
pmid = {26592025},
issn = {0250-3301},
mesh = {Ammonia/analysis ; Archaea/*classification ; *Denitrification ; Nitrification ; Nitrites/*analysis ; Nitrogen/*analysis ; Oxidation-Reduction ; Sewage ; Waste Disposal, Fluid ; *Wastewater ; },
abstract = {Ammonia oxidation is the first and rate-limiting step of nitrification, which was thought to be only performed by ammonia-oxidizing bacteria (AOB). In recent years, ammonia-oxidizing archaea (AOA) was also confirmed to take part in ammonia oxidation. The diversity and abundance of AOA have been investigated in various environments, however, little is known regarding the AOA in the completely autotrophic nitrogen removal over nitrite (CANON) wastewater treatment process. In this study, the abundance and diversity of AOA were investigated in the biofilm and flocculent activated sludge collected in a lab-scale (L) CANON system and a pilot-scale (P) CANON systems, respectively. The quantitative real time PCR (qPCR) was applied to investigate the abundance of AOA and the diversity of AOA was determined by polymerase chain reaction (PCR), cloning and sequencing. The qPCR results showed that the average abundance of AOA amoA gene of L and P was 2.42 x 10(6) copies x g(-1) dry sludge and 6.51 x 10(6) copies x g(-1) dry sludge, respectively. The abundance of AOA in biofilm was 10.1-14.1 times higher than that in flocculent activated sludge. For P system, the abundance of AOA in flocculent activated sludge was 1.8 times higher than that in biofilm. The results indicated that the abundance of AOA might be affected by different sludge morphology. The diversity of AOA in P system was extremely limited, only one OTU was observed, which was classified into Nitrosopumilus subcluster 5.2. The diversity of AOA in L system was higher, eight OTUs were observed, which were classified into five genera: Nitrososphaera subcluster 9, subcluster 8.1, subcluster 4.1, subcluster 1.1 and Nitrosopumilus subcluster 5.2. The diversity and abundance of AOA were different in CANON systems with different sludge morphology. AOA may play an important role in ammonia oxidation in CANON system.},
}
@article {pmid26585514,
year = {2015},
author = {Palecek, JJ and Gruber, S},
title = {Kite Proteins: a Superfamily of SMC/Kleisin Partners Conserved Across Bacteria, Archaea, and Eukaryotes.},
journal = {Structure (London, England : 1993)},
volume = {23},
number = {12},
pages = {2183-2190},
doi = {10.1016/j.str.2015.10.004},
pmid = {26585514},
issn = {1878-4186},
mesh = {Amino Acid Sequence ; Archaeal Proteins/*chemistry/genetics/metabolism ; Bacterial Proteins/*chemistry/genetics/metabolism ; Cell Cycle Proteins/*chemistry/genetics/metabolism ; Conserved Sequence ; Kinesins/chemistry/metabolism ; Molecular Sequence Data ; },
abstract = {SMC/kleisin complexes form elongated annular structures, which are critical for chromosome segregation, genome maintenance, and the regulation of gene expression. We describe marked structural similarities between bacterial and eukaryotic SMC/kleisin partner proteins (designated here as "kite" proteins for kleisin interacting tandem winged-helix (WH) elements of SMC complexes). Kite proteins are integral parts of all prokaryotic SMC complexes and Smc5/6 but not cohesin and condensin. They are made up of tandem WH domains, form homo- or heterodimers via their amino-terminal WH domain, and they associate with the central part of a kleisin subunit. In placental mammals, the kite subunit NSE3 gave rise to several (>60) kite-related proteins, named MAGE, many of which encode tumor- and testis-specific antigens. Based on architectural rather than sequence similarity, we propose an adapted model for the evolution of the SMC protein complexes and discuss potential functional similarities between bacterial Smc/ScpAB and eukaryotic Smc5/6.},
}
@article {pmid26573375,
year = {2015},
author = {Li, M and Baker, BJ and Anantharaman, K and Jain, S and Breier, JA and Dick, GJ},
title = {Genomic and transcriptomic evidence for scavenging of diverse organic compounds by widespread deep-sea archaea.},
journal = {Nature communications},
volume = {6},
number = {},
pages = {8933},
pmid = {26573375},
issn = {2041-1723},
mesh = {Archaea/*genetics/metabolism ; Carbohydrate Metabolism/*genetics ; Carbohydrates ; Carbon/*metabolism ; Carbon Cycle/*genetics ; Caribbean Region ; Fatty Acids/*metabolism ; Gene Expression Profiling ; Genomics ; Hydrothermal Vents/*microbiology ; Lipid Metabolism/*genetics ; Lipids ; Oceans and Seas ; Proteins/*metabolism ; Seawater/microbiology ; },
abstract = {Microbial activity is one of the most important processes to mediate the flux of organic carbon from the ocean surface to the seafloor. However, little is known about the microorganisms that underpin this key step of the global carbon cycle in the deep oceans. Here we present genomic and transcriptomic evidence that five ubiquitous archaeal groups actively use proteins, carbohydrates, fatty acids and lipids as sources of carbon and energy at depths ranging from 800 to 4,950 m in hydrothermal vent plumes and pelagic background seawater across three different ocean basins. Genome-enabled metabolic reconstructions and gene expression patterns show that these marine archaea are motile heterotrophs with extensive mechanisms for scavenging organic matter. Our results shed light on the ecological and physiological properties of ubiquitous marine archaea and highlight their versatile metabolic strategies in deep oceans that might play a critical role in global carbon cycling.},
}
@article {pmid26565069,
year = {2015},
author = {Chen, J and Zhang, H and Liu, W and Lian, J and Ye, W and Shen, W},
title = {Spatial distribution patterns of ammonia-oxidizing archaea abundance in subtropical forests at early and late successional stages.},
journal = {Scientific reports},
volume = {5},
number = {},
pages = {16587},
pmid = {26565069},
issn = {2045-2322},
mesh = {Ammonia/*metabolism ; Archaea/*physiology ; Bacteria/growth &amp; development/metabolism ; Ecosystem ; Forests ; Oxidation-Reduction ; Oxides/*metabolism ; Phylogeny ; Soil ; Soil Microbiology ; },
abstract = {Characterizing the spatial distribution patterns of soil microorganisms is helpful in understanding the biogeochemical processes they perform, but has been less studied relative to those of macroorganisms. In this study, we investigated and compared the spatially explicit distribution patterns of ammonia-oxidizing archaea (AOA) abundance and the influential factors between an early (ES) and a late successional (LS) subtropical forest stand. The average AOA abundance, vegetational attributes, and soil nutrient contents were mostly greater in the LS than the ES stand (P = 0.085 or smaller), but their spatial variations were more pronounced in the ES than the LS stand. The spatial distribution patches of AOA abundance were smaller and more irregular in the ES stand (patch size <50 m) than in the LS stand (patch size about 120 m). Edaphic and vegetational variables contributed more to the spatial variations of AOA abundance for the ES (9.3%) stand than for LS stand, whereas spatial variables (MEMs) were the main contributors (62%) for the LS stand. These results suggest that environmental filtering likely influence the spatial distribution of AOA abundance at early successional stage more than that at late successional stage, while spatial dispersal is dominant at late successional stage.},
}
@article {pmid26559904,
year = {2016},
author = {Gottlieb, K and Wacher, V and Sliman, J and Pimentel, M},
title = {Review article: inhibition of methanogenic archaea by statins as a targeted management strategy for constipation and related disorders.},
journal = {Alimentary pharmacology &amp; therapeutics},
volume = {43},
number = {2},
pages = {197-212},
pmid = {26559904},
issn = {1365-2036},
mesh = {Archaea/metabolism ; Constipation/*drug therapy/microbiology ; Humans ; Hydroxymethylglutaryl-CoA Reductase Inhibitors/*pharmacology ; Irritable Bowel Syndrome/drug therapy/microbiology ; Male ; Methane/*metabolism ; },
abstract = {BACKGROUND: Observational studies show a strong association between delayed intestinal transit and the production of methane. Experimental data suggest a direct inhibitory activity of methane on the colonic and ileal smooth muscle and a possible role for methane as a gasotransmitter. Archaea are the only confirmed biological sources of methane in nature and Methanobrevibacter smithii is the predominant methanogen in the human intestine.<br><br>AIM: To review the biosynthesis and composition of archaeal cell membranes, archaeal methanogenesis and the mechanism of action of statins in this context.<br><br>METHODS: Narrative review of the literature.<br><br>RESULTS: Statins can inhibit archaeal cell membrane biosynthesis without affecting bacterial numbers as demonstrated in livestock and humans. This opens the possibility of a therapeutic intervention that targets a specific aetiological factor of constipation while protecting the intestinal microbiome. While it is generally believed that statins inhibit methane production via their effect on cell membrane biosynthesis, mediated by inhibition of the HMG-CoA reductase, there is accumulating evidence for an alternative or additional mechanism of action where statins inhibit methanogenesis directly. It appears that this other mechanism may predominate when the lactone form of statins, particularly lovastatin lactone, is administered.<br><br>CONCLUSIONS: Clinical development appears promising. A phase 2 clinical trial is currently in progress that evaluates the effect of lovastatin lactone on methanogenesis and symptoms in patients with irritable bowel syndrome with constipation. The review concludes with an outlook for the future and subsequent work that needs to be done.},
}
@article {pmid26557034,
year = {2015},
author = {Efenberger, M and Agier, J and Pawłowska, E and Brzezińska-Błaszczyk, E},
title = {Archaea prevalence in inflamed pulp tissues.},
journal = {Central-European journal of immunology},
volume = {40},
number = {2},
pages = {194-200},
pmid = {26557034},
issn = {1426-3912},
abstract = {Archaea have been detected in several ecological niches of the human body such as the large intestine, skin, vagina as well as the oral cavity. At present, archaea are recognized as nonpathogenic microorganisms. However, some data indicate that they may be involved in the etiopathogenesis of several diseases, including intestinal diseases as well as oral diseases: periodontitis, peri-implantitis and endodontitis. In this study, on the basis of 16S rRNA gene sequence analysis, we examined whether archaea might be present in inflamed pulp tissues and contribute to the development of endodontic infection. In comparison, we also determined selected bacterial species associated with endodontitis. We detected archaea in 85% of infected endodontic samples. In addition, Prevotella intermedia, Porphyromonas gingivalis, Tannerella forsythia and Treponema denticola were present in inflamed pulp tissue samples and Treponema denticola occurred with the highest frequency (70%). Further analysis revealed the presence of methanogenic archaea in analyzed samples. Direct sequencing of archaeal 16S rRNA gene PCR products indicated the occurrence of methanogenic archaea in inflamed pulp tissues; phylogenetically most similar were Methanobrevibacter oralis and Methanobrevibacter smithii. Therefore, our results show that methanogenic archaea are present in inflamed pulp tissues and may participate in the development of endodontic infection.},
}
@article {pmid26554846,
year = {2015},
author = {Kristensen, DM and Saeed, U and Frishman, D and Koonin, EV},
title = {A census of α-helical membrane proteins in double-stranded DNA viruses infecting bacteria and archaea.},
journal = {BMC bioinformatics},
volume = {16},
number = {},
pages = {380},
pmid = {26554846},
issn = {1471-2105},
support = {//Intramural NIH HHS/United States ; },
mesh = {Archaea/*metabolism/virology ; Archaeal Viruses/isolation &amp; purification/*metabolism ; Bacteria/*metabolism/virology ; DNA Viruses/isolation &amp; purification/*metabolism ; Host-Pathogen Interactions ; Membrane Proteins/chemistry/*metabolism ; Viral Proteins/*metabolism ; Virion/*physiology ; Virus Integration ; },
abstract = {BACKGROUND: Viruses are the most abundant and genetically diverse biological entities on earth, yet the repertoire of viral proteins remains poorly explored. As the number of sequenced virus genomes grows into the thousands, and the number of viral proteins into the hundreds of thousands, we report a systematic computational analysis of the point of first-contact between viruses and their hosts, namely viral transmembrane (TM) proteins.<br><br>RESULTS: The complement of &#x3b1;-helical TM proteins in double-stranded DNA viruses infecting bacteria and archaea reveals large-scale trends that differ from those of their hosts. Viruses typically encode a substantially lower fraction of TM proteins than archaea or bacteria, with the notable exception of viruses with virions containing a lipid component such as a lipid envelope, internal lipid core, or inner membrane vesicle. Compared to bacteriophages, archaeal viruses are substantially enriched in membrane proteins. However, this feature is not always stable throughout the evolution of a viral lineage; for example, TM proteins are not part of the common heritage shared between Lipothrixviridae and Rudiviridae. In contrast to bacteria and archaea, viruses almost completely lack proteins with complicated membrane topologies composed of more than 4 TM segments, with the few detected exceptions being obvious cases of relatively recent horizontal transfer from the host.<br><br>CONCLUSIONS: The dramatic differences between the membrane proteomes of cells and viruses stem from the fact that viruses do not depend on essential membranes for energy transformation, ion homeostasis, nutrient transport and signaling.},
}
@article {pmid26543273,
year = {2015},
author = {Chu, YJ and Lee, JY and Shin, SR and Kim, GJ},
title = {A Method for Cell Culture and Maintenance of Ammonia-Oxidizing Archaea in Agar Stab.},
journal = {Indian journal of microbiology},
volume = {55},
number = {4},
pages = {460-463},
pmid = {26543273},
issn = {0046-8991},
abstract = {Ammonia oxidizing archaea (AOA) are predominantly found and closely linked with geochemical cycling of nitrogen in non-extreme habitats. However, these strains have mainly been investigated using liquid cultures of enriched cells. Here, we provide an agar stab as a simple and reliable means of cultivating and maintaining AOA.},
}
@article {pmid26528260,
year = {2015},
author = {Zhang, CL and Xie, W and Martin-Cuadrado, AB and Rodriguez-Valera, F},
title = {Marine Group II Archaea, potentially important players in the global ocean carbon cycle.},
journal = {Frontiers in microbiology},
volume = {6},
number = {},
pages = {1108},
pmid = {26528260},
issn = {1664-302X},
abstract = {Marine Group (MG) I (currently known as Thaumarchaeota) and MG II Archaea were first reported over two decades ago. While significant progress has been made on MG I microbiology and ecology, the progress on MG II has been noticeably slower. The common understanding is that while MG I mainly function as chemolithoautotrophs and occur predominantly in the deep ocean, MG II reside mostly in the photic zone and live heterotrophically. Studies to date have shown that MG II are abundant in the marine aquatic environment and display great seasonal and spatial variation and phylogenetic diversity. They also show unique patterns of organic carbon degradation and their energy requirements may be augmented by light in the photic zone. However, no pure culture of MG II has been obtained and thus their precise ecological role remains elusive.},
}
@article {pmid26522086,
year = {2015},
author = {Zhou, L and Wang, S and Zou, Y and Xia, C and Zhu, G},
title = {Species, Abundance and Function of Ammonia-oxidizing Archaea in Inland Waters across China.},
journal = {Scientific reports},
volume = {5},
number = {},
pages = {15969},
pmid = {26522086},
issn = {2045-2322},
mesh = {Ammonia ; Archaea/*genetics/*physiology ; Bacteria/genetics ; China ; Ecosystem ; Nitrification/genetics/physiology ; Nitrogen Cycle/genetics/physiology ; Oxidation-Reduction ; Phylogeny ; Soil Microbiology ; Temperature ; Water/metabolism ; },
abstract = {Ammonia oxidation is the first step in nitrification and was thought to be performed solely by specialized bacteria. The discovery of ammonia-oxidizing archaea (AOA) changed this view. We examined the large scale and spatio-temporal occurrence, abundance and role of AOA throughout Chinese inland waters (n = 28). Molecular survey showed that AOA was ubiquitous in inland waters. The existence of AOA in extreme acidic, alkaline, hot, cold, eutrophic and oligotrophic environments expanded the tolerance limits of AOA, especially their known temperature tolerance to -25 °C, and substrate load to 42.04 mM. There were spatio-temporal divergences of AOA community structure in inland waters, and the diversity of AOA in inland water ecosystems was high with 34 observed species-level operational taxonomic units (OTUs; based on a 15% cutoff) distributed widely in group I.1b, I.1a, and I.1a-associated. The abundance of AOA was quite high (8.5 × 10(4) to 8.5 × 10(9) copies g(-1)), and AOA outnumbered ammonia-oxidizing bacteria (AOB) in the inland waters where little human activities were involved. On the whole AOB predominate the ammonia oxidation rate over AOA in inland water ecosystems, and AOA play an indispensable role in global nitrogen cycle considering that AOA occupy a broader habitat range than AOB, especially in extreme environments.},
}
@article {pmid26504428,
year = {2015},
author = {Charlesworth, JC and Burns, BP},
title = {Untapped Resources: Biotechnological Potential of Peptides and Secondary Metabolites in Archaea.},
journal = {Archaea (Vancouver, B.C.)},
volume = {2015},
number = {},
pages = {282035},
pmid = {26504428},
issn = {1472-3654},
mesh = {Archaea/*chemistry/metabolism ; Biological Products/*isolation &amp; purification/*metabolism ; Biotechnology/methods ; Food-Processing Industry/methods ; Peptides/isolation &amp; purification/metabolism ; Technology, Pharmaceutical/methods ; },
abstract = {Archaea are an understudied domain of life often found in "extreme" environments in terms of temperature, salinity, and a range of other factors. Archaeal proteins, such as a wide range of enzymes, have adapted to function under these extreme conditions, providing biotechnology with interesting activities to exploit. In addition to producing structural and enzymatic proteins, archaea also produce a range of small peptide molecules (such as archaeocins) and other novel secondary metabolites such as those putatively involved in cell communication (acyl homoserine lactones), which can be exploited for biotechnological purposes. Due to the wide array of metabolites produced there is a great deal of biotechnological potential from antimicrobials such as diketopiperazines and archaeocins, as well as roles in the cosmetics and food industry. In this review we will discuss the diversity of small molecules, both peptide and nonpeptide, produced by archaea and their potential biotechnological applications.},
}
@article {pmid26499486,
year = {2015},
author = {Serrano, P and Hermelink, A and Lasch, P and de Vera, JP and König, N and Burckhardt, O and Wagner, D},
title = {Confocal Raman microspectroscopy reveals a convergence of the chemical composition in methanogenic archaea from a Siberian permafrost-affected soil.},
journal = {FEMS microbiology ecology},
volume = {91},
number = {12},
pages = {},
doi = {10.1093/femsec/fiv126},
pmid = {26499486},
issn = {1574-6941},
mesh = {Cold Temperature ; DNA Restriction Enzymes/*genetics ; Desiccation ; Euryarchaeota/*chemistry/genetics/*isolation &amp; purification ; Methane/*biosynthesis ; Microscopy, Confocal ; Molecular Typing ; Osmotic Pressure/physiology ; Permafrost/chemistry/*microbiology ; Phylogeny ; Radiation Tolerance/physiology ; Siberia ; Soil Microbiology ; Spectrum Analysis, Raman ; },
abstract = {Methanogenic archaea are widespread anaerobic microorganisms responsible for the production of biogenic methane. Several new species of psychrotolerant methanogenic archaea were recently isolated from a permafrost-affected soil in the Lena Delta (Siberia, Russia), showing an exceptional resistance against desiccation, osmotic stress, low temperatures, starvation, UV and ionizing radiation when compared to methanogens from non-permafrost environments. To gain a deeper insight into the differences observed in their resistance, we described the chemical composition of methanogenic strains from permafrost and non-permafrost environments using confocal Raman microspectroscopy (CRM). CRM is a powerful tool for microbial identification and provides fingerprint-like information about the chemical composition of the cells. Our results show that the chemical composition of methanogens from permafrost-affected soils presents a high homology and is remarkably different from strains inhabiting non-permafrost environments. In addition, we performed a phylogenetic reconstruction of the studied strains based on the functional gene mcrA to prove the different evolutionary relationship of the permafrost strains. We conclude that the permafrost methanogenic strains show a convergent chemical composition regardless of their genotype. This fact is likely to be the consequence of a complex adaptive process to the Siberian permafrost environment and might be the reason underlying their resistant nature.},
}
@article {pmid26490622,
year = {2015},
author = {Wegener, G and Krukenberg, V and Riedel, D and Tegetmeyer, HE and Boetius, A},
title = {Intercellular wiring enables electron transfer between methanotrophic archaea and bacteria.},
journal = {Nature},
volume = {526},
number = {7574},
pages = {587-590},
doi = {10.1038/nature15733},
pmid = {26490622},
issn = {1476-4687},
mesh = {Anaerobiosis ; Archaea/*metabolism ; Bacteria/*metabolism ; Cytochromes/metabolism ; Electron Transport ; Fimbriae, Bacterial/metabolism ; Geologic Sediments/microbiology ; Heme/metabolism ; Hydrogen/metabolism ; Hydrothermal Vents/microbiology ; Methane/*metabolism ; Microbiota/physiology ; Molecular Sequence Data ; Oceans and Seas ; Sulfates/metabolism ; Symbiosis ; Temperature ; },
abstract = {The anaerobic oxidation of methane (AOM) with sulfate controls the emission of the greenhouse gas methane from the ocean floor. In marine sediments, AOM is performed by dual-species consortia of anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria (SRB) inhabiting the methane-sulfate transition zone. The biochemical pathways and biological adaptations enabling this globally relevant process are not fully understood. Here we study the syntrophic interaction in thermophilic AOM (TAOM) between ANME-1 archaea and their consortium partner SRB HotSeep-1 (ref. 6) at 60 °C to test the hypothesis of a direct interspecies exchange of electrons. The activity of TAOM consortia was compared to the first ANME-free culture of an AOM partner bacterium that grows using hydrogen as the sole electron donor. The thermophilic ANME-1 do not produce sufficient hydrogen to sustain the observed growth of the HotSeep-1 partner. Enhancing the growth of the HotSeep-1 partner by hydrogen addition represses methane oxidation and the metabolic activity of ANME-1. Further supporting the hypothesis of direct electron transfer between the partners, we observe that under TAOM conditions, both ANME and the HotSeep-1 bacteria overexpress genes for extracellular cytochrome production and form cell-to-cell connections that resemble the nanowire structures responsible for interspecies electron transfer between syntrophic consortia of Geobacter. HotSeep-1 highly expresses genes for pili production only during consortial growth using methane, and the nanowire-like structures are absent in HotSeep-1 cells isolated with hydrogen. These observations suggest that direct electron transfer is a principal mechanism in TAOM, which may also explain the enigmatic functioning and specificity of other methanotrophic ANME-SRB consortia.},
}
@article {pmid26477689,
year = {2016},
author = {Cacciapuoti, G and Bagarolo, ML and Martino, E and Scafuri, B and Marabotti, A and Porcelli, M},
title = {Efficient Fludarabine-Activating PNP From Archaea as a Guidance for Redesign the Active Site of E. Coli PNP.},
journal = {Journal of cellular biochemistry},
volume = {117},
number = {5},
pages = {1126-1135},
doi = {10.1002/jcb.25396},
pmid = {26477689},
issn = {1097-4644},
mesh = {Adenosine/chemistry/metabolism ; Arabinonucleosides/chemistry/metabolism ; Archaeal Proteins/chemistry/*metabolism ; Binding, Competitive ; Biocatalysis ; Catalytic Domain ; Crystallography, X-Ray ; Escherichia coli Proteins/chemistry/*metabolism ; Isoenzymes/chemistry/metabolism ; Kinetics ; Models, Molecular ; Molecular Structure ; Protein Binding ; Protein Domains ; Purine-Nucleoside Phosphorylase/chemistry/*metabolism ; Substrate Specificity ; Sulfolobus solfataricus/*enzymology ; Vidarabine/*analogs &amp; derivatives/chemistry/metabolism ; },
abstract = {The combination of the gene of purine nucleoside phosphorylase (PNP) from Escherichia coli and fludarabine represents one of the most promising systems in the gene therapy of solid tumors. The use of fludarabine in gene therapy is limited by the lack of an enzyme that is able to efficiently activate this prodrug which, consequently, has to be administered in high doses that cause serious side effects. In an attempt to identify enzymes with a better catalytic efficiency than E. coli PNP towards fludarabine to be used as a guidance on how to improve the activity of the bacterial enzyme, we have selected 5'-deoxy-5'-methylthioadenosine phosphorylase (SsMTAP) and 5'-deoxy-5'-methylthioadenosine phosphorylase II (SsMTAPII), two PNPs isolated from the hyperthermophilic archaeon Sulfolobus solfataricus. Substrate specificity and catalytic efficiency of SsMTAP and SsMTAPII for fludarabine were analyzed by kinetic studies and compared with E. coli PNP. SsMTAP and SsMTAPII share with E. coli PNP a comparable low affinity for the arabinonucleoside but are better catalysts of fludarabine cleavage with k(cat)/K(m) values that are 12.8-fold and 6-fold higher, respectively, than those reported for the bacterial enzyme. A computational analysis of the interactions of fludarabine in the active sites of E. coli PNP, SsMTAP, and SsMTAPII allowed to identify the crucial residues involved in the binding with this substrate, and provided structural information to improve the catalytic efficiency of E. coli PNP by enzyme redesign.},
}
@article {pmid26472620,
year = {2016},
author = {Elling, FJ and Becker, KW and Könneke, M and Schröder, JM and Kellermann, MY and Thomm, M and Hinrichs, KU},
title = {Respiratory quinones in Archaea: phylogenetic distribution and application as biomarkers in the marine environment.},
journal = {Environmental microbiology},
volume = {18},
number = {2},
pages = {692-707},
doi = {10.1111/1462-2920.13086},
pmid = {26472620},
issn = {1462-2920},
mesh = {Archaea/*classification/genetics/*metabolism ; Bacteria/metabolism ; Biomarkers/metabolism ; Biomass ; Black Sea ; Ecology ; Gene Transfer, Horizontal ; Membrane Lipids/metabolism ; Oxidation-Reduction ; Phylogeny ; Quinones/*chemistry ; Terpenes/*chemistry ; },
abstract = {The distribution of respiratory quinone electron carriers among cultivated organisms provides clues on both the taxonomy of their producers and the redox processes these are mediating. Our study of the quinone inventories of 25 archaeal species belonging to the phyla Eury-, Cren- and Thaumarchaeota facilitates their use as chemotaxonomic markers for ecologically important archaeal clades. Saturated and monounsaturated menaquinones with six isoprenoid units forming the alkyl chain may serve as chemotaxonomic markers for Thaumarchaeota. Other diagnostic biomarkers are thiophene-bearing quinones for Sulfolobales and methanophenazines as functional quinone analogues of the Methanosarcinales. The ubiquity of saturated menaquinones in the Archaea in comparison to Bacteria suggests that these compounds may represent an ancestral and diagnostic feature of the Archaea. Overlap between quinone compositions of distinct thermophilic and halophilic archaea and bacteria may indicate lateral gene transfer. The biomarker potential of thaumarchaeal quinones was exemplarily demonstrated on a water column profile of the Black Sea. Both, thaumarchaeal quinones and membrane lipids showed similar distributions with maxima at the chemocline. Quinone distributions indicate that Thaumarchaeota dominate respiratory activity at a narrow interval in the chemocline, while they contribute only 9% to the microbial biomass at this depth, as determined by membrane lipid analysis.},
}
@article {pmid26463999,
year = {2016},
author = {Niu, J and Kasuga, I and Kurisu, F and Furumai, H and Shigeeda, T and Takahashi, K},
title = {Abundance and diversity of ammonia-oxidizing archaea and bacteria on granular activated carbon and their fates during drinking water purification process.},
journal = {Applied microbiology and biotechnology},
volume = {100},
number = {2},
pages = {729-742},
doi = {10.1007/s00253-015-6969-3},
pmid = {26463999},
issn = {1432-0614},
mesh = {Ammonia/*metabolism ; Archaea/classification/*genetics/isolation &amp; purification/*metabolism ; Bacteria/classification/*genetics/isolation &amp; purification/*metabolism ; Charcoal ; Drinking Water/analysis/*microbiology ; Genetic Variation ; Microbial Consortia/genetics/physiology ; Nitrification ; Oxidation-Reduction ; Phylogeny ; Seasons ; Tokyo ; Water Purification ; },
abstract = {Ammonia is a precursor to trichloramine, which causes an undesirable chlorinous odor. Granular activated carbon (GAC) filtration is used to biologically oxidize ammonia during drinking water purification; however, little information is available regarding the abundance and diversity of ammonia-oxidizing archaea (AOA) and bacteria (AOB) associated with GAC. In addition, their sources and fates in water purification process remain unknown. In this study, six GAC samples were collected from five full-scale drinking water purification plants in Tokyo during summer and winter, and the abundance and community structure of AOA and AOB associated with GAC were studied in these two seasons. In summer, archaeal and bacterial amoA genes on GACs were present at 3.7 × 10(5)-3.9 × 10(8) gene copies/g-dry and 4.5 × 10(6)-4.2 × 10(8) gene copies/g-dry, respectively. In winter, archaeal amoA genes remained at the same level, while bacterial amoA genes decreased significantly for all GACs. No differences were observed in the community diversity of AOA and AOB from summer to winter. Phylogenetic analysis revealed high AOA diversity in group I.1a and group I.1b in raw water. Terminal-restriction fragment length polymorphism analysis of processed water samples revealed that AOA diversity decreased dramatically to only two OTUs in group I.1a after ozonation, which were identical to those detected on GAC. It suggests that ozonation plays an important role in determining AOA diversity on GAC. Further study on the cell-specific activity of AOA and AOB is necessary to understand their contributions to in situ nitrification performance.},
}
@article {pmid26456193,
year = {2016},
author = {Chamieh, H and Ibrahim, H and Kozah, J},
title = {Genome-wide identification of SF1 and SF2 helicases from archaea.},
journal = {Gene},
volume = {576},
number = {1 Pt 2},
pages = {214-228},
doi = {10.1016/j.gene.2015.10.007},
pmid = {26456193},
issn = {1879-0038},
mesh = {Amino Acid Motifs ; Amino Acid Sequence ; Archaeal Proteins/*chemistry/*genetics/metabolism ; Conserved Sequence ; DNA Helicases/*chemistry/*genetics/metabolism ; DNA Repair/physiology ; DNA-Binding Proteins/chemistry/genetics ; Escherichia coli Proteins/chemistry/genetics ; Genome, Archaeal ; Humans ; *Phylogeny ; Protein Structure, Tertiary ; RNA Splicing Factors ; Transcription Factors/chemistry/genetics ; },
abstract = {Archaea microorganisms have long been used as model organisms for the study of protein molecular machines. Archaeal proteins are particularly appealing to study since archaea, even though prokaryotic, possess eukaryotic-like cellular processes. Super Family I (SF1) and Super Family II (SF2) helicase families have been studied in many model organisms, little is known about their presence and distribution in archaea. We performed an exhaustive search of homologs of SF1 and SF2 helicase proteins in 95 complete archaeal genomes. In the present study, we identified the complete sets of SF1 and SF2 helicases in archaea. Comparative analysis between archaea, human and the bacteria E. coli SF1 and SF2 helicases, resulted in the identification of seven helicase families conserved among representatives of the domains of life. This analysis suggests that these helicase families are highly conserved throughout evolution. We highlight the conserved motifs of each family and characteristic domains of the detected families. Distribution of SF1/SF2 families show that Ski2-like, Lhr, Sfth and Rad3-like helicases are ubiquitous among archaeal genomes while the other families are specific to certain archaeal groups. We also report the presence of a novel SF2 helicase specific to archaea domain named Archaea Specific Helicase (ASH). Phylogenetic analysis indicated that ASH has evolved in Euryarchaeota and is evolutionary related to the Ski2-like family with specific characteristic domains. Our study provides the first exhaustive analysis of SF1 and SF2 helicases from archaea. It expands the variety of SF1 and SF2 archaeal helicases known to exist to date and provides a starting point for new biochemical and genetic studies needed to validate their biological functions.},
}
@article {pmid26450358,
year = {2015},
author = {Dong, J and Ding, L and Wang, X and Chi, Z and Lei, J},
title = {Erratum to: Vertical Profiles of Community Abundance and Diversity of Anaerobic Methanotrophic Archaea (ANME) and Bacteria in a Simple Waste Landfill in North China.},
journal = {Applied biochemistry and biotechnology},
volume = {177},
number = {6},
pages = {1394},
doi = {10.1007/s12010-015-1885-7},
pmid = {26450358},
issn = {1559-0291},
}
@article {pmid26441877,
year = {2015},
author = {Sorokin, DY and Toshchakov, SV and Kolganova, TV and Kublanov, IV},
title = {Halo(natrono)archaea isolated from hypersaline lakes utilize cellulose and chitin as growth substrates.},
journal = {Frontiers in microbiology},
volume = {6},
number = {},
pages = {942},
pmid = {26441877},
issn = {1664-302X},
abstract = {Until recently, extremely halophilic euryarchaeota were considered mostly as aerobic heterotrophs utilizing simple organic compounds as growth substrates. Almost nothing is known on the ability of these prokaryotes to utilize complex polysaccharides, such as cellulose, xylan, and chitin. Although few haloarchaeal cellulases and chitinases were recently characterized, the analysis of currently available haloarchaeal genomes deciphered numerous genes-encoding glycosidases of various families including endoglucanases and chitinases. However, all these haloarchaea were isolated and cultivated on simple substrates and their ability to grow on polysaccharides in situ or in vitro is unknown. This study examines several halo(natrono)archaeal strains from geographically distant hypersaline lakes for the ability to grow on insoluble polymers as a sole growth substrate in salt-saturated mineral media. Some of them belonged to known taxa, while other represented novel phylogenetic lineages within the class Halobacteria. All isolates produced extracellular extremely salt-tolerant cellulases or chitinases, either cell-free or cell-bound. Obtained results demonstrate a presence of diverse populations of haloarchaeal cellulo/chitinotrophs in hypersaline habitats indicating that euryarchaea participate in aerobic mineralization of recalcitrant organic polymers in salt-saturated environments.},
}
@article {pmid26441844,
year = {2015},
author = {Borgonie, G and Linage-Alvarez, B and Ojo, A and Shivambu, S and Kuloyo, O and Cason, ED and Maphanga, S and Vermeulen, JG and Litthauer, D and Ralston, CD and Onstott, TC and Sherwood-Lollar, B and Van Heerden, E},
title = {Deep subsurface mine stalactites trap endemic fissure fluid Archaea, Bacteria, and Nematoda possibly originating from ancient seas.},
journal = {Frontiers in microbiology},
volume = {6},
number = {},
pages = {833},
pmid = {26441844},
issn = {1664-302X},
abstract = {Stalactites (CaCO3 and salt) from water seeps are frequently encountered in ceilings of mine tunnels whenever they intersect water-bearing faults or fractures. To determine whether stalactites could be mineralized traps for indigenous fracture water microorganisms, we analyzed stalactites collected from three different mines ranging in depth from 1.3 to 3.1 km. During sampling in Beatrix gold mine (1.4 km beneath the surface), central South Africa, CaCO3 stalactites growing on the mine tunnel ceiling were collected and observed, in two cases, to contain a living obligate brackish water/marine nematode species, Monhystrella parvella. After sterilization of the outer surface, mineral layers were physically removed from the outside to the interior, and DNA extracted. Based upon 16S and 18S rRNA gene sequencing, Archaea, Bacteria, and Eukarya in different combinations were detected for each layer. Using CT scan and electron microscopy the inner structure of CaCO3 and salt stalactites were analyzed. CaCO3 stalactites show a complex pattern of lamellae carrying bacterially precipitated mineral structures. Nematoda were clearly identified between these layers confirming that bacteria and nematodes live inside the stalactites and not only in the central straw. Salt stalactites exhibit a more uniform internal structure. Surprisingly, several Bacteria showing highest sequence identities to marine species were identified. This, together with the observation that the nematode M. parvella recovered from Beatrix gold mine stalactite can only survive in a salty environment makes the origin of the deep subsurface colonization enigmatic. The possibility of a Permian origin of fracture fluids is discussed. Our results indicate stalactites are suitable for biodiversity recovery and act as natural traps for microorganisms in the fissure water long after the water that formed the stalactite stopped flowing.},
}
@article {pmid26439345,
year = {2015},
author = {Eme, L and Doolittle, WF},
title = {Archaea.},
journal = {Current biology : CB},
volume = {25},
number = {19},
pages = {R851-5},
doi = {10.1016/j.cub.2015.05.025},
pmid = {26439345},
issn = {1879-0445},
mesh = {Adaptation, Biological ; Archaea/*classification/genetics/physiology ; Bacteria/*classification/genetics ; Bacterial Physiological Phenomena ; *Biological Evolution ; Eukaryota/*classification/genetics/physiology ; History, 20th Century ; History, 21st Century ; Microbiology/*history ; Phylogeny ; },
abstract = {A headline on the front page of the New York Times for November 3, 1977, read "Scientists Discover a Way of Life That Predates Higher Organisms". The accompanying article described a spectacular claim by Carl Woese and George Fox to have discovered a third form of life, a new 'domain' that we now call Archaea. It's not that these microbes were unknown before, nor was it the case that their peculiarities had gone completely unnoticed. Indeed, Ralph Wolfe, in the same department at the University of Illinois as Woese, had already discovered how it was that methanogens (uniquely on the planet) make methane, and the bizarre adaptations that allow extremely halophilic archaea (then called halobacteria) and thermoacidophiles to live in the extreme environments where they do were already under investigation in many labs. But what Woese and Fox had found was that these organisms were related to each other not just in their 'extremophily' but also phylogenetically. And, most surprisingly, they were only remotely related to the rest of the prokaryotes, which we now call the domain Bacteria (Figure 1).},
}
@article {pmid26411976,
year = {2015},
author = {Bai, L and Xie, T and Hu, Q and Deng, C and Zheng, R and Chen, W},
title = {Genome-wide comparison of ferritin family from Archaea, Bacteria, Eukarya, and Viruses: its distribution, characteristic motif, and phylogenetic relationship.},
journal = {Die Naturwissenschaften},
volume = {102},
number = {9-10},
pages = {64},
pmid = {26411976},
issn = {1432-1904},
mesh = {Amino Acid Motifs ; Animals ; *Archaea/classification/genetics ; *Bacteria/classification/genetics ; *Eukaryota/classification/genetics ; Evolution, Molecular ; Ferritins/*genetics ; Genome/*genetics ; *Phylogeny ; *Viruses/classification/genetics ; },
abstract = {Ferritins are highly conserved proteins that are widely distributed in various species from archaea to humans. The ubiquitous characteristic of these proteins reflects the pivotal contribution of ferritins to the safe storage and timely delivery of iron to achieve iron homeostasis. This study investigated the ferritin genes in 248 genomes from various species, including viruses, archaea, bacteria, and eukarya. The distribution comparison suggests that mammals and eudicots possess abundant ferritin genes, whereas fungi contain very few ferritin genes. Archaea and bacteria show considerable numbers of ferritin genes. Generally, prokaryotes possess three types of ferritin (the typical ferritin, bacterioferritin, and DNA-binding protein from starved cell), whereas eukaryotes have various subunit types of ferritin, thereby indicating the individuation of the ferritin family during evolution. The characteristic motif analysis of ferritins suggested that all key residues specifying the unique structural motifs of ferritin are highly conserved across three domains of life. Meanwhile, the characteristic motifs were also distinguishable between ferritin groups, especially phytoferritins, which show a plant-specific motif. The phylogenetic analyses show that ferritins within the same subfamily or subunits are generally clustered together. The phylogenetic relationships among ferritin members suggest that both gene duplication and horizontal transfer contribute to the wide variety of ferritins, and their possible evolutionary scenario was also proposed. The results contribute to a better understanding of the distribution, characteristic motif, and evolutionary relationship of the ferritin family.},
}
@article {pmid26403496,
year = {2015},
author = {Prangishvili, D and Gribaldo, S and Franzetti, B and Forterre, P},
title = {Special section on Molecular biology of Archaea.},
journal = {Biochimie},
volume = {118},
number = {},
pages = {253},
doi = {10.1016/j.biochi.2015.09.020},
pmid = {26403496},
issn = {1638-6183},
mesh = {Archaea/*genetics ; Phylogeny ; },
}
@article {pmid26394860,
year = {2016},
author = {Ding, J and Fu, L and Ding, ZW and Lu, YZ and Cheng, SH and Zeng, RJ},
title = {Environmental evaluation of coexistence of denitrifying anaerobic methane-oxidizing archaea and bacteria in a paddy field.},
journal = {Applied microbiology and biotechnology},
volume = {100},
number = {1},
pages = {439-446},
doi = {10.1007/s00253-015-6986-2},
pmid = {26394860},
issn = {1432-0614},
mesh = {Anaerobiosis ; Archaea/classification/*growth &amp; development/isolation &amp; purification/*metabolism ; Bacteria/classification/*growth &amp; development/isolation &amp; purification/*metabolism ; Biota ; Denitrification ; High-Throughput Nucleotide Sequencing ; Methane/*metabolism ; Nitrates/*metabolism ; Oxidation-Reduction ; Sequence Analysis, DNA ; *Soil Microbiology ; },
abstract = {The nitrate-dependent denitrifying anaerobic methane oxidation (DAMO) process, which is metabolized together by anaerobic methanotrophic archaea and NC10 phylum bacteria, is expected to be important for the global carbon and nitrogen cycles. However, there are little studies about the existence of this process and the functional microbes in environments. Therefore, the coexistence of DAMO archaea and bacteria in a paddy field was evaluated in this study. Next-generation sequencing showed that the two orders, Methanosarcinales and Nitrospirales, to which DAMO archaea and DAMO bacteria belong, were detected in the four soil samples. Then the in vitro experiments demonstrated both of nitrite- and nitrate-dependent DAMO activities, which confirmed the coexistence of DAMO archaea and DAMO bacteria. It was the first report about the coexistence of DAMO archaea and bacteria in a paddy field. Furthermore, anammox bacteria were detected in two of the four samples. The in vitro experiments did not show anammox activity in the initial period but showed low anammox activity after 20 days' enrichment. These results implicated that anammox bacteria may coexist with DAMO microorganisms in this field, but at a very low percentage.},
}
@article {pmid26369647,
year = {2015},
author = {Martin del Campo, M and Camacho, RM and Mateos-Díaz, JC and Müller-Santos, M and Córdova, J and Rodríguez, JA},
title = {Solid-state fermentation as a potential technique for esterase/lipase production by halophilic archaea.},
journal = {Extremophiles : life under extreme conditions},
volume = {19},
number = {6},
pages = {1121-1132},
pmid = {26369647},
issn = {1433-4909},
mesh = {Archaeal Proteins/genetics/*metabolism ; Biomass ; Esterases/genetics/*metabolism ; *Fermentation ; Halobacteriaceae/*enzymology/growth &amp; development/metabolism ; Industrial Microbiology/*methods ; Lipase/genetics/*metabolism ; },
abstract = {Halophilic archaea are extremophiles, adapted to high-salt environments, showing a big biotechnological potential as enzyme, lipids and pigments producers. Four inert supports (perlite, vermiculite, polyurethane foam and glass fiber) were employed for solid-state fermentation (SSF) of the halophilic archaeon Natronococcus sp. TC6 to investigate biomass and esterase production. A very low esterase activity and high water activity were observed when perlite, vermiculite and polyurethane were used as supports. When glass fiber was employed, an important moisture loss was observed (8.6%). Moreover, moisture retention was improved by mixing polyurethane and glass fiber, resulting in maximal biomass and esterase production. Three halophilic archaea: Natronococcus sp. TC6, Halobacterium sp. NRC-1 and Haloarcula marismortui were cultured by submerged fermentation (SmF) and by SSF; an improvement of 1.3- to 6.2-fold was observed in the biomass and esterase production when SSF was used. Growth was not homogeneous in the mixture, but was predominant in the glass fiber thus was probably because the glass fiber provides a holder to the cells, while the polyurethane acts as an impregnation medium reservoir. To the best of our knowledge, this work is the first report on haloarchaea cultivation by SSF aiming biomass and esterase/lipase activity production.},
}
@article {pmid26346219,
year = {2015},
author = {Bhattacharyya, A and Majumder, NS and Basak, P and Mukherji, S and Roy, D and Nag, S and Haldar, A and Chattopadhyay, D and Mitra, S and Bhattacharyya, M and Ghosh, A},
title = {Diversity and Distribution of Archaea in the Mangrove Sediment of Sundarbans.},
journal = {Archaea (Vancouver, B.C.)},
volume = {2015},
number = {},
pages = {968582},
pmid = {26346219},
issn = {1472-3654},
mesh = {Archaea/*classification/genetics/*isolation &amp; purification ; *Biodiversity ; Cluster Analysis ; DNA, Archaeal/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; *Environmental Microbiology ; India ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Tropical Climate ; *Wetlands ; },
abstract = {Mangroves are among the most diverse and productive coastal ecosystems in the tropical and subtropical regions. Environmental conditions particular to this biome make mangroves hotspots for microbial diversity, and the resident microbial communities play essential roles in maintenance of the ecosystem. Recently, there has been increasing interest to understand the composition and contribution of microorganisms in mangroves. In the present study, we have analyzed the diversity and distribution of archaea in the tropical mangrove sediments of Sundarbans using 16S rRNA gene amplicon sequencing. The extraction of DNA from sediment samples and the direct application of 16S rRNA gene amplicon sequencing resulted in approximately 142 Mb of data from three distinct mangrove areas (Godkhali, Bonnie camp, and Dhulibhashani). The taxonomic analysis revealed the dominance of phyla Euryarchaeota and Thaumarchaeota (Marine Group I) within our dataset. The distribution of different archaeal taxa and respective statistical analysis (SIMPER, NMDS) revealed a clear community shift along the sampling stations. The sampling stations (Godkhali and Bonnie camp) with history of higher hydrocarbon/oil pollution showed different archaeal community pattern (dominated by haloarchaea) compared to station (Dhulibhashani) with nearly pristine environment (dominated by methanogens). It is indicated that sediment archaeal community patterns were influenced by environmental conditions.},
}
@article {pmid26339125,
year = {2015},
author = {Wagner, AO and Praeg, N and Reitschuler, C and Illmer, P},
title = {Effect of DNA extraction procedure, repeated extraction and ethidium monoazide (EMA)/propidium monoazide (PMA) treatment on overall DNA yield and impact on microbial fingerprints for bacteria, fungi and archaea in a reference soil.},
journal = {Applied soil ecology : a section of Agriculture, Ecosystems &amp; Environment},
volume = {93},
number = {},
pages = {56-64},
pmid = {26339125},
issn = {0929-1393},
support = {P 22815/FWF_/Austrian Science Fund FWF/Austria ; },
abstract = {Different DNA extraction protocols were evaluated on a reference soil. A wide difference was found in the total extractable DNA as derived from different extraction protocols. Concerning the DNA yield phenol-chloroform-isomyl alcohol extraction resulted in high DNA yield but also in a remarkable co-extraction of contaminants making PCR from undiluted DNA extracts impossible. By comparison of two different extraction kits, the Macherey&amp;Nagel SoilExtract II kit resulted in the highest DNA yields when buffer SL1 and the enhancer solution were applied. The enhancer solution not only significantly increased the DNA yield but also the amount of co-extracted contaminates, whereas additional disintegration strategies did not. Although a three times repeated DNA extraction increased the total amount of extracted DNA, microbial fingerprints were merely affected. However, with the 5th extraction this changed. A reduction of total DGGE band numbers was observed for archaea and fungi, whereas for bacteria the diversity increased. The application of ethidium monoazide (EMA) or propidium monoazide (PMA) treatment aiming on the selective removal of soil DNA derived from cells lacking cell wall integrity resulted in a significant reduction of total extracted DNA, however, the hypothesized effect on microbial fingerprints failed to appear indicating the need for further investigations.},
}
@article {pmid26323767,
year = {2015},
author = {Akanni, WA and Siu-Ting, K and Creevey, CJ and McInerney, JO and Wilkinson, M and Foster, PG and Pisani, D},
title = {Horizontal gene flow from Eubacteria to Archaebacteria and what it means for our understanding of eukaryogenesis.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {370},
number = {1678},
pages = {20140337},
pmid = {26323767},
issn = {1471-2970},
support = {BB/G024707/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/K007440//BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Bacteria/*genetics ; *Biological Evolution ; *Gene Flow ; Genome, Bacterial ; Models, Genetic ; },
abstract = {The origin of the eukaryotic cell is considered one of the major evolutionary transitions in the history of life. Current evidence strongly supports a scenario of eukaryotic origin in which two prokaryotes, an archaebacterial host and an α-proteobacterium (the free-living ancestor of the mitochondrion), entered a stable symbiotic relationship. The establishment of this relationship was associated with a process of chimerization, whereby a large number of genes from the α-proteobacterial symbiont were transferred to the host nucleus. A general framework allowing the conceptualization of eukaryogenesis from a genomic perspective has long been lacking. Recent studies suggest that the origins of several archaebacterial phyla were coincident with massive imports of eubacterial genes. Although this does not indicate that these phyla originated through the same process that led to the origin of Eukaryota, it suggests that Archaebacteria might have had a general propensity to integrate into their genomes large amounts of eubacterial DNA. We suggest that this propensity provides a framework in which eukaryogenesis can be understood and studied in the light of archaebacterial ecology. We applied a recently developed supertree method to a genomic dataset composed of 392 eubacterial and 51 archaebacterial genera to test whether large numbers of genes flowing from Eubacteria are indeed coincident with the origin of major archaebacterial clades. In addition, we identified two potential large-scale transfers of uncertain directionality at the base of the archaebacterial tree. Our results are consistent with previous findings and seem to indicate that eubacterial gene imports (particularly from δ-Proteobacteria, Clostridia and Actinobacteria) were an important factor in archaebacterial history. Archaebacteria seem to have long relied on Eubacteria as a source of genetic diversity, and while the precise mechanism that allowed these imports is unknown, we suggest that our results support the view that processes comparable to those through which eukaryotes emerged might have been common in archaebacterial history.},
}
@article {pmid26323764,
year = {2015},
author = {Koonin, EV},
title = {Origin of eukaryotes from within archaea, archaeal eukaryome and bursts of gene gain: eukaryogenesis just made easier?.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {370},
number = {1678},
pages = {20140333},
pmid = {26323764},
issn = {1471-2970},
mesh = {Archaea/*genetics ; *Biological Evolution ; Eukaryota/genetics ; *Eukaryotic Cells ; *Genome, Archaeal ; },
abstract = {The origin of eukaryotes is a fundamental, forbidding evolutionary puzzle. Comparative genomic analysis clearly shows that the last eukaryotic common ancestor (LECA) possessed most of the signature complex features of modern eukaryotic cells, in particular the mitochondria, the endomembrane system including the nucleus, an advanced cytoskeleton and the ubiquitin network. Numerous duplications of ancestral genes, e.g. DNA polymerases, RNA polymerases and proteasome subunits, also can be traced back to the LECA. Thus, the LECA was not a primitive organism and its emergence must have resulted from extensive evolution towards cellular complexity. However, the scenario of eukaryogenesis, and in particular the relationship between endosymbiosis and the origin of eukaryotes, is far from being clear. Four recent developments provide new clues to the likely routes of eukaryogenesis. First, evolutionary reconstructions suggest complex ancestors for most of the major groups of archaea, with the subsequent evolution dominated by gene loss. Second, homologues of signature eukaryotic proteins, such as actin and tubulin that form the core of the cytoskeleton or the ubiquitin system, have been detected in diverse archaea. The discovery of this 'dispersed eukaryome' implies that the archaeal ancestor of eukaryotes was a complex cell that might have been capable of a primitive form of phagocytosis and thus conducive to endosymbiont capture. Third, phylogenomic analyses converge on the origin of most eukaryotic genes of archaeal descent from within the archaeal evolutionary tree, specifically, the TACK superphylum. Fourth, evidence has been presented that the origin of the major archaeal phyla involved massive acquisition of bacterial genes. Taken together, these findings make the symbiogenetic scenario for the origin of eukaryotes considerably more plausible and the origin of the organizational complexity of eukaryotic cells more readily explainable than they appeared until recently.},
}
@article {pmid26320243,
year = {2015},
author = {Acosta, S and Carela, M and Garcia-Gonzalez, A and Gines, M and Vicens, L and Cruet, R and Massey, SE},
title = {DNA Repair Is Associated with Information Content in Bacteria, Archaea, and DNA Viruses.},
journal = {The Journal of heredity},
volume = {106},
number = {5},
pages = {644-659},
doi = {10.1093/jhered/esv055},
pmid = {26320243},
issn = {1465-7333},
mesh = {Archaea/genetics ; Bacteria/*genetics ; Base Composition ; Cluster Analysis ; *DNA Repair ; DNA Viruses/genetics ; *Evolution, Molecular ; Genes, Archaeal ; *Genes, Bacterial ; Genes, Viral ; Genome, Bacterial ; Mutation Rate ; Phylogeny ; Proteome ; },
abstract = {The concept of a "proteomic constraint" proposes that DNA repair capacity is positively correlated with the information content of a genome, which can be approximated to the size of the proteome (P). This in turn implies that DNA repair genes are more likely to be present in genomes with larger values of P. This stands in contrast to the common assumption that informational genes have a core function and so are evenly distributed across organisms. We examined the presence/absence of 18 DNA repair genes in bacterial genomes. A positive relationship between gene presence and P was observed for 17 genes in the total dataset, and 16 genes when only nonintracellular bacteria were examined. A marked reduction of DNA repair genes was observed in intracellular bacteria, consistent with their reduced value of P. We also examined archaeal and DNA virus genomes, and show that the presence of DNA repair genes is likewise related to a larger value of P. In addition, the products of the bacterial genes mutY, vsr, and ndk, involved in the correction of GC/AT mutations, are strongly associated with reduced genome GC content. We therefore propose that a reduction in information content leads to a loss of DNA repair genes and indirectly to a reduction in genome GC content in bacteria by exposure to the underlying AT mutation bias. The reduction in P may also indirectly lead to the increase in substitution rates observed in intracellular bacteria via loss of DNA repair genes.},
}
@article {pmid26300291,
year = {2015},
author = {Ding, J and Ding, ZW and Fu, L and Lu, YZ and Cheng, SH and Zeng, RJ},
title = {New primers for detecting and quantifying denitrifying anaerobic methane oxidation archaea in different ecological niches.},
journal = {Applied microbiology and biotechnology},
volume = {99},
number = {22},
pages = {9805-9812},
doi = {10.1007/s00253-015-6893-6},
pmid = {26300291},
issn = {1432-0614},
mesh = {Anaerobiosis ; Archaea/classification/*genetics/*isolation &amp; purification ; DNA Primers/*genetics ; DNA, Archaeal/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Methane/*metabolism ; Oxidation-Reduction ; Polymerase Chain Reaction/*methods ; RNA, Ribosomal, 16S/genetics ; Real-Time Polymerase Chain Reaction/methods ; Sensitivity and Specificity ; *Water Microbiology ; },
abstract = {The significance of ANME-2d in methane sink in the environment has been overlooked, and there was no any study evaluating the distribution of ANME-2d in the environment. New primers were thus needed to be designed for following research. In this paper, a pair of primers (DP397F and DP569R) was designed to quantify ANME-2d. The specificity and amplification efficiency of this primer pair were acceptable. PCR amplification of another pair of primers (DP142F and DP779R) generated a single, bright targeted band from the enrichment sample, but yielded faint, multiple bands from the environmental samples. Nested PCR was conducted using the primers DP142F/DP779R in the first round and DP142F/DP569R in the second round, which generated a bright targeted band. Further phylogenetic analysis showed that these targeted bands were ANME-2d-related sequences. Real-time PCR showed that the copies of the 16s ribosomal RNA gene of ANME-2d in these samples ranged from 3.72 × 10(4) to 2.30 × 10(5) copies μg(-1) DNA, indicating that the percentage of ANME-2d was greatest in a polluted river sample and least in a rice paddy sample. These results demonstrate that the newly developed real-time PCR primers could sufficiently quantify ANME-2d and that nested PCR with an appropriate combination of the new primers could successfully detect ANME-2d in environmental samples; the latter finding suggests that ANME-2d may spread in environments.},
}
@article {pmid26296935,
year = {2015},
author = {Wagner, EGH and Romby, P},
title = {Small RNAs in bacteria and archaea: who they are, what they do, and how they do it.},
journal = {Advances in genetics},
volume = {90},
number = {},
pages = {133-208},
doi = {10.1016/bs.adgen.2015.05.001},
pmid = {26296935},
issn = {0065-2660},
mesh = {Archaea/*genetics ; Bacteria/*genetics ; Gene Expression Regulation ; Host Factor 1 Protein/metabolism ; RNA, Archaeal/metabolism ; RNA, Bacterial/metabolism ; RNA, Small Untranslated/*metabolism ; },
abstract = {Small RNAs are ubiquitously present regulators in all kingdoms of life. Most bacterial and archaeal small RNAs (sRNAs) act by antisense mechanisms on multiple target mRNAs, thereby globally affecting essentially any conceivable trait-stress responses, adaptive metabolic changes, virulence etc. The sRNAs display many distinct mechanisms of action, most of them through effects on target mRNA translation and/or stability, and helper proteins like Hfq often play key roles. Recent data highlight the interplay between posttranscriptional control by sRNAs and transcription factor-mediated transcriptional control, and cross talk through mutual regulation of regulators. Based on the properties that distinguish sRNA-type from transcription factors-type control, we begin to glimpse why sRNAs have evolved as a second, essential layer of gene regulation. This review will discuss the prevalence of sRNAs, who they are, what biological roles they play, and how they carry out their functions.},
}
@article {pmid26284058,
year = {2015},
author = {Kumar, S and Indugu, N and Vecchiarelli, B and Pitta, DW},
title = {Associative patterns among anaerobic fungi, methanogenic archaea, and bacterial communities in response to changes in diet and age in the rumen of dairy cows.},
journal = {Frontiers in microbiology},
volume = {6},
number = {},
pages = {781},
pmid = {26284058},
issn = {1664-302X},
abstract = {The rumen microbiome represents a complex microbial genetic web where bacteria, anaerobic rumen fungi (ARF), protozoa and archaea work in harmony contributing to the health and productivity of ruminants. We hypothesized that the rumen microbiome shifts as the dairy cow advances in lactations and these microbial changes may contribute to differences in productivity between primiparous (first lactation) and multiparous (≥second lactation) cows. To this end, we investigated shifts in the ruminal ARF and methanogenic communities in both primiparous (n = 5) and multiparous (n = 5) cows as they transitioned from a high forage to a high grain diet upon initiation of lactation. A total of 20 rumen samples were extracted for genomic DNA, amplified using archaeal and fungal specific primers, sequenced on a 454 platform and analyzed using QIIME. Community comparisons (Bray-Curtis index) revealed the effect of diet (P < 0.01) on ARF composition, while archaeal communities differed between primiparous and multiparous cows (P < 0.05). Among ARF, several lineages were unclassified, however, phylum Neocallimastigomycota showed the presence of three known genera. Abundance of Cyllamyces and Caecomyces shifted with diet, whereas Orpinomyces was influenced by both diet and age. Methanobrevibacter constituted the most dominant archaeal genus across all samples. Co-occurrence analysis incorporating taxa from bacteria, ARF and archaea revealed syntrophic interactions both within and between microbial domains in response to change in diet as well as age of dairy cows. Notably, these interactions were numerous and complex in multiparous cows, supporting our hypothesis that the rumen microbiome also matures with age to sustain the growing metabolic needs of the host. This study provides a broader picture of the ARF and methanogenic populations in the rumen of dairy cows and their co-occurrence implicates specific relationships between different microbial domains in response to diet and age.},
}
@article {pmid26284036,
year = {2015},
author = {Spaans, SK and Weusthuis, RA and van der Oost, J and Kengen, SW},
title = {NADPH-generating systems in bacteria and archaea.},
journal = {Frontiers in microbiology},
volume = {6},
number = {},
pages = {742},
pmid = {26284036},
issn = {1664-302X},
abstract = {Reduced nicotinamide adenine dinucleotide phosphate (NADPH) is an essential electron donor in all organisms. It provides the reducing power that drives numerous anabolic reactions, including those responsible for the biosynthesis of all major cell components and many products in biotechnology. The efficient synthesis of many of these products, however, is limited by the rate of NADPH regeneration. Hence, a thorough understanding of the reactions involved in the generation of NADPH is required to increase its turnover through rational strain improvement. Traditionally, the main engineering targets for increasing NADPH availability have included the dehydrogenase reactions of the oxidative pentose phosphate pathway and the isocitrate dehydrogenase step of the tricarboxylic acid (TCA) cycle. However, the importance of alternative NADPH-generating reactions has recently become evident. In the current review, the major canonical and non-canonical reactions involved in the production and regeneration of NADPH in prokaryotes are described, and their key enzymes are discussed. In addition, an overview of how different enzymes have been applied to increase NADPH availability and thereby enhance productivity is provided.},
}
@article {pmid26248160,
year = {2015},
author = {Scharko, NK and Schütte, UM and Berke, AE and Banina, L and Peel, HR and Donaldson, MA and Hemmerich, C and White, JR and Raff, JD},
title = {Combined Flux Chamber and Genomics Approach Links Nitrous Acid Emissions to Ammonia Oxidizing Bacteria and Archaea in Urban and Agricultural Soil.},
journal = {Environmental science &amp; technology},
volume = {49},
number = {23},
pages = {13825-13834},
doi = {10.1021/acs.est.5b00838},
pmid = {26248160},
issn = {1520-5851},
mesh = {Agriculture ; Ammonia/*metabolism ; Archaea/genetics/*metabolism ; Atmosphere/chemistry ; Betaproteobacteria/genetics/metabolism ; Genomics/methods ; Indiana ; Microbial Consortia/*genetics/physiology ; Nitrification ; Nitrogen Isotopes/analysis ; *Nitrous Acid/metabolism ; Oxidation-Reduction ; RNA, Ribosomal, 16S/genetics ; Soil/chemistry ; *Soil Microbiology ; Urbanization ; },
abstract = {Nitrous acid (HONO) is a photochemical source of hydroxyl radical and nitric oxide in the atmosphere that stems from abiotic and biogenic processes, including the activity of ammonia-oxidizing soil microbes. HONO fluxes were measured from agricultural and urban soil in mesocosm studies aimed at characterizing biogenic sources and linking them to indigenous microbial consortia. Fluxes of HONO from agricultural and urban soil were suppressed by addition of a nitrification inhibitor and enhanced by amendment with ammonium (NH4(+)), with peaks at 19 and 8 ng m(-2) s(-1), respectively. In addition, both agricultural and urban soils were observed to convert (15)NH4(+) to HO(15)NO. Genomic surveys of soil samples revealed that 1.5-6% of total expressed 16S rRNA sequences detected belonged to known ammonia oxidizing bacteria and archaea. Peak fluxes of HONO were directly related to the abundance of ammonia-oxidizer sequences, which in turn depended on soil pH. Peak HONO fluxes under fertilized conditions are comparable in magnitude to fluxes reported during field campaigns. The results suggest that biogenic HONO emissions will be important in soil environments that exhibit high nitrification rates (e.g., agricultural soil) although the widespread occurrence of ammonia oxidizers implies that biogenic HONO emissions are also possible in the urban and remote environment.},
}
@article {pmid26235787,
year = {2015},
author = {Barnhart, EP and McClure, MA and Johnson, K and Cleveland, S and Hunt, KA and Fields, MW},
title = {Potential Role of Acetyl-CoA Synthetase (acs) and Malate Dehydrogenase (mae) in the Evolution of the Acetate Switch in Bacteria and Archaea.},
journal = {Scientific reports},
volume = {5},
number = {},
pages = {12498},
pmid = {26235787},
issn = {2045-2322},
mesh = {Acetate Kinase/chemistry/metabolism ; Acetate-CoA Ligase/chemistry/genetics/*metabolism ; Acetates/*metabolism ; Amino Acid Motifs ; Amino Acid Sequence ; Archaeal Proteins/*chemistry/genetics/metabolism ; Bacterial Proteins/*chemistry/genetics/metabolism ; *Biological Evolution ; Conserved Sequence ; Evolution, Molecular ; Halobacteriales/enzymology/genetics ; Malate Dehydrogenase/chemistry/genetics/*metabolism ; Methanosarcina/genetics/metabolism ; Phosphate Acetyltransferase/chemistry/metabolism ; Phylogeny ; Substrate Specificity ; },
abstract = {Although many Archaea have AMP-Acs (acetyl-coenzyme A synthetase) and ADP-Acs, the extant methanogenic genus Methanosarcina is the only identified Archaeal genus that can utilize acetate via acetate kinase (Ack) and phosphotransacetylase (Pta). Despite the importance of ack as the potential urkinase in the ASKHA phosphotransferase superfamily, an origin hypothesis does not exist for the acetate kinase in Bacteria, Archaea, or Eukarya. Here we demonstrate that Archaeal AMP-Acs and ADP-Acs contain paralogous ATPase motifs previously identified in Ack, which demonstrate a novel relation between these proteins in Archaea. The identification of ATPase motif conservation and resulting structural features in AMP- and ADP-acetyl-CoA synthetase proteins in this study expand the ASKHA superfamily to include acetyl-CoA synthetase. Additional phylogenetic analysis showed that Pta and MaeB sequences had a common ancestor, and that the Pta lineage within the halophilc archaea was an ancestral lineage. These results suggested that divergence of a duplicated maeB within an ancient halophilic, archaeal lineage formed a putative pta ancestor. These results provide a potential scenario for the establishment of the Ack/Pta pathway and provide novel insight into the evolution of acetate metabolism for all three domains of life.},
}
@article {pmid26226005,
year = {2015},
author = {Stan-Lotter, H and Fendrihan, S},
title = {Halophilic Archaea: Life with Desiccation, Radiation and Oligotrophy over Geological Times.},
journal = {Life (Basel, Switzerland)},
volume = {5},
number = {3},
pages = {1487-1496},
pmid = {26226005},
issn = {2075-1729},
abstract = {Halophilic archaebacteria (Haloarchaea) can survive extreme desiccation, starvation and radiation, sometimes apparently for millions of years. Several of the strategies that are involved appear specific for Haloarchaea (for example, the formation of halomucin, survival in fluid inclusions of halite), and some are known from other prokaryotes (dwarfing of cells, reduction of ATP). Several newly-discovered haloarchaeal strategies that were inferred to possibly promote long-term survival-halomucin, polyploidy, usage of DNA as a phosphate storage polymer, production of spherical dormant stages-remain to be characterized in detail. More information on potential strategies is desirable, since evidence for the presence of halite on Mars and on several moons in the solar system increased interest in halophiles with respect to the search for extraterrestrial life. This review deals in particular with novel findings and hypotheses on haloarchaeal long-term survival.},
}
@article {pmid26217762,
year = {2015},
author = {Cerletti, M and Paggi, RA and Ramallo Guevara, C and Poetsch, A and De Castro, RE},
title = {Data in support of global role of the membrane protease LonB in Archaea: Potential protease targets revealed by quantitative proteome analysis of a lonB mutant in Haloferax volcanii.},
journal = {Data in brief},
volume = {4},
number = {},
pages = {50-53},
pmid = {26217762},
issn = {2352-3409},
abstract = {This data article provides information in support of the research article "Global role of the membrane protease LonB in Archaea: Potential protease targets revealed by quantitative proteome analysis of a lonB mutant in Haloferax volcanii" [1]. The proteome composition of a wt and a LonB protease mutant strain (suboptimal expression) in the archaeon Haloferax volcanii was assessed by a quantitative shotgun proteomic approach. Membrane and cytosol fractions of H. volcanii strains were examined at two different growth stages (exponential and stationary phase). Data is supplied in the present article. This study represents the first proteome examination of a Lon-deficient cell of the Archaea Domain.},
}
@article {pmid26211960,
year = {2015},
author = {Anupama, VN and Prajeesh, PV and Anju, S and Priya, P and Krishnakumar, B},
title = {Diversity of bacteria, archaea and protozoa in a perchlorate treating bioreactor.},
journal = {Microbiological research},
volume = {177},
number = {},
pages = {8-14},
doi = {10.1016/j.micres.2015.04.011},
pmid = {26211960},
issn = {1618-0623},
mesh = {Acetates/metabolism ; Archaea/*classification/genetics ; Bacteria/*classification/genetics ; Bioreactors/*microbiology ; *Biota ; Biotransformation ; Denaturing Gradient Gel Electrophoresis ; In Situ Hybridization, Fluorescence ; Microscopy ; Molecular Sequence Data ; Oxidation-Reduction ; Perchlorates/*metabolism ; Phylogeny ; Sequence Analysis, DNA ; Volvocida/*classification/genetics ; },
abstract = {A microbial consortium reducing high level of perchlorate was developed and in a fed batch bioreactor using acetate as substrate perchlorate was reduced at 0.25 g/g vss. day. Under stable performance, the microbial community structure of the reactor was analyzed through molecular and phenotypic methods. The diversity of bacteria and archaea were analyzed through whole cell Fluorescence In-Situ Hybridization (FISH) and PCR-Denaturing Gradient Gel Electrophoresis (DGGE), whereas higher trophic community was analyzed phenotypically. FISH analysis revealed the presence of alpha, beta, gamma and delta proteobacteria in the sludge, dominated by beta proteobacteria (68.7%). DGGE analysis of bacteria revealed the presence of a single known perchlorate reducing bacterium-Dechloromonas, nitrate reducers like Thaeura and Azoarcus and a number of other genera so far not reported as perchlorate or nitrate reducing. The archaea community was represented by an acetoclastic methanogen, Methanosaeta harundinacea. We have also observed the presence of an acetate consuming flagellate, Polytomella sp. in significant number in the reactor. Archaea and protozoa community in perchlorate treating bioreactor is reported first time in this study and point out further the significance of non perchlorate reducing but acetate scavenging microbial groups in acetate fed perchlorate treating reactors.},
}
@article {pmid26194817,
year = {2016},
author = {Huynh, HT and Verneau, J and Levasseur, A and Drancourt, M and Aboudharam, G},
title = {Bacteria and archaea paleomicrobiology of the dental calculus: a review.},
journal = {Molecular oral microbiology},
volume = {31},
number = {3},
pages = {234-242},
doi = {10.1111/omi.12118},
pmid = {26194817},
issn = {2041-1014},
mesh = {Adult ; Archaea/genetics/*isolation &amp; purification ; Bacteria/genetics/*isolation &amp; purification ; Bacteroidetes/genetics/isolation &amp; purification ; Dental Calculus/*history/microbiology/virology ; Diet/history ; Fusobacterium/genetics/isolation &amp; purification ; History, Ancient ; Humans ; Immunohistochemistry ; Isotope Labeling ; Microbiota ; Paleodontology ; Phylogeny ; Proteobacteria/genetics/isolation &amp; purification ; Streptococcus mutans/genetics ; },
abstract = {Dental calculus, a material observed in the majority of adults worldwide, emerged as a source for correlating paleomicrobiology with human health and diet. This mini review of 48 articles on the paleomicrobiology of dental calculus over 7550 years discloses a secular core microbiota comprising nine bacterial phyla - Firmicutes, Actinobacteria, Proteobacteria, Bacteroidetes, TM7, Synergistetes, Chloroflexi, Fusobacteria, Spirochetes - and one archaeal phylum Euryarchaeota; and some accessory microbiota that appear and disappear according to time frame. The diet residues and oral microbes, including bacteria, archaea, viruses and fungi, consisting of harmless organisms and pathogens associated with local and systemic infections have been found trapped in ancient dental calculus by morphological approaches, immunolabeling techniques, isotope analyses, fluorescent in situ hybridization, DNA-based approaches, and protein-based approaches. These observations led to correlation of paleomicrobiology, particularly Streptococcus mutans and archaea, with past human health and diet.},
}
@article {pmid26174392,
year = {2015},
author = {Oger, PM},
title = {Homeoviscous Adaptation of Membranes in Archaea.},
journal = {Sub-cellular biochemistry},
volume = {72},
number = {},
pages = {383-403},
doi = {10.1007/978-94-017-9918-8_19},
pmid = {26174392},
issn = {0306-0225},
mesh = {*Adaptation, Physiological ; Archaea/*physiology ; Cell Membrane/chemistry ; Membrane Lipids/chemistry ; Molecular Structure ; *Viscosity ; },
abstract = {Because membranes play a central role in regulating fluxes inward and outward from the cells, maintaining the appropriate structure of the membrane is crucial to maintain cellular integrity and functions. Microbes often face contrasted and fluctuating environmental conditions, to which they need to adapt or die. Membrane adaptation is achieved by a modification of the membrane lipid composition, a strategy termed homeoviscous adaptation. Homeoviscous adaptation in archaea involves strategies similar to that observed in bacteria and eucarya, such as the regulation of lipid chain length or saturation levels, as well as strategies specific to archaea, such as the regulation of the number of cycles along the isoprenoid chains or the regulation of the ratio between mono and bipolar lipids. Although not described yet described in hyperthermophilic bacteria, it is possible that these two strategies also apply to these latter organisms.},
}
@article {pmid26172994,
year = {2015},
author = {Chen, Z and Wu, W and Shao, X and Li, L and Guo, Y and Ding, G},
title = {Shifts in Abundance and Diversity of Soil Ammonia-Oxidizing Bacteria and Archaea Associated with Land Restoration in a Semi-Arid Ecosystem.},
journal = {PloS one},
volume = {10},
number = {7},
pages = {e0132879},
pmid = {26172994},
issn = {1932-6203},
mesh = {Agriculture ; Ammonia/*metabolism ; Archaea/*genetics ; Bacteria/*genetics ; Biodiversity ; Caragana/growth &amp; development ; China ; Droughts ; Ecosystem ; Environmental Restoration and Remediation/*methods ; Lolium/growth &amp; development ; Nitrification/genetics ; Nitrogen/metabolism ; Nitrogen Cycle/genetics ; Oxidation-Reduction ; Polymorphism, Restriction Fragment Length/genetics ; Soil ; Soil Microbiology ; },
abstract = {The Grain to Green Project (GGP) is an unprecedented land restoration action in China. The project converted large areas (ca 10 million ha) of steep-sloped/degraded farmland and barren land into forest and grassland resulting in ecological benefits such as a reduction in severe soil erosion. It may also affect soil microorganisms involved in ammonia oxidization, which is a key step in the global nitrogen cycle. The methods for restoration that are typically adopted in semi-arid regions include abandoning farmland and growing drought tolerant grass (Lolium perenne L.) or shrubs (Caragana korshinskii Kom.). In the present study, the effects of these methods on the abundance and diversity of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) were evaluated via quantitative real-time PCR, terminal restriction fragment length polymorphism and clone library analysis of amoA genes. Comparisons were made between soil samples from three restored lands and the adjacent farmland in Inner Mongolia. Both the abundance and community composition of AOB were significantly different between the restored lands and the adjacent control. Significantly lower nitrification activity was observed for the restored land. Clone library analysis revealed that all AOB amoA gene sequences were affiliated with Nitrosospira. Abundance of the populations that were associated with Nitrosospira sp. Nv6 which had possibly adapted to high concentrations of inorganic nitrogen, decreased on the restored land. Only a slight difference in the AOB communities was observed between the restored land with and without the shrub (Caragana korshinskii Kom.). A minor effect of land restoration on AOA was observed. In summary, land restoration negatively affected the abundance of AOB and soil nitrification activities, suggesting the potential role of GGP in the leaching of nitrates, and in the emission of N2O in related terrestrial ecosystems.},
}
@article {pmid26161079,
year = {2015},
author = {Lee, HJ and Jeong, SE and Kim, PJ and Madsen, EL and Jeon, CO},
title = {High resolution depth distribution of Bacteria, Archaea, methanotrophs, and methanogens in the bulk and rhizosphere soils of a flooded rice paddy.},
journal = {Frontiers in microbiology},
volume = {6},
number = {},
pages = {639},
pmid = {26161079},
issn = {1664-302X},
abstract = {The communities and abundances of methanotrophs and methanogens, along with the oxygen, methane, and total organic carbon (TOC) concentrations, were investigated along a depth gradient in a flooded rice paddy. Broad patterns in vertical profiles of oxygen, methane, TOC, and microbial abundances were similar in the bulk and rhizosphere soils, though methane and TOC concentrations and 16S rRNA gene copies were clearly higher in the rhizosphere soil than in the bulk soil. Oxygen concentrations decreased sharply to below detection limits at 8 mm depth. Pyrosequencing of 16S rRNA genes showed that bacterial and archaeal communities varied according to the oxic, oxic-anoxic, and anoxic zones, indicating that oxygen is a determining factor for the distribution of bacterial and archaeal communities. Aerobic methanotrophs were maximally observed near the oxic-anoxic interface, while methane, TOC, and methanogens were highest in the rhizosphere soil at 30-200 mm depth, suggesting that methane is produced mainly from organic carbon derived from rice plants and is metabolized aerobically. The relative abundances of type I methanotrophs such as Methylococcus, Methylomonas, and Methylocaldum decreased more drastically than those of type II methanotrophs (such as Methylocystis and Methylosinus) with increasing depth. Methanosaeta and Methanoregula were predominant methanogens at all depths, and the relative abundances of Methanosaeta, Methanoregula, and Methanosphaerula, and GOM_Arc_I increased with increasing depth. Based on contrasts between absolute abundances of methanogens and methanotrophs at depths sampled across rhizosphere and bulk soils (especially millimeter-scale slices at the surface), we have identified populations of methanogens (Methanosaeta, Methanoregula, Methanocella, Methanobacterium, and Methanosphaerula), and methanotrophs (Methylosarcina, Methylococcus, Methylosinus, and unclassified Methylocystaceae) that are likely physiologically active in situ.},
}
@article {pmid26146487,
year = {2015},
author = {Grogan, DW},
title = {Understanding DNA Repair in Hyperthermophilic Archaea: Persistent Gaps and Other Reasons to Focus on the Fork.},
journal = {Archaea (Vancouver, B.C.)},
volume = {2015},
number = {},
pages = {942605},
pmid = {26146487},
issn = {1472-3654},
mesh = {Archaea/genetics/*physiology/*radiation effects ; DNA Damage ; *DNA Repair ; DNA Repair Enzymes/genetics/metabolism ; DNA, Archaeal/radiation effects ; Hot Temperature ; },
abstract = {Although hyperthermophilic archaea arguably have a great need for efficient DNA repair, they lack members of several DNA repair protein families broadly conserved among bacteria and eukaryotes. Conversely, the putative DNA repair genes that do occur in these archaea often do not generate the expected phenotype when deleted. The prospect that hyperthermophilic archaea have some unique strategies for coping with DNA damage and replication errors has intellectual and technological appeal, but resolving this question will require alternative coping mechanisms to be proposed and tested experimentally. This review evaluates a combination of four enigmatic properties that distinguishes the hyperthermophilic archaea from all other organisms: DNA polymerase stalling at dU, apparent lack of conventional NER, lack of MutSL homologs, and apparent essentiality of homologous recombination proteins. Hypothetical damage-coping strategies that could explain this set of properties may provide new starting points for efforts to define how archaea differ from conventional models of DNA repair and replication fidelity.},
}
@article {pmid26125682,
year = {2015},
author = {Tschitschko, B and Williams, TJ and Allen, MA and Páez-Espino, D and Kyrpides, N and Zhong, L and Raftery, MJ and Cavicchioli, R},
title = {Antarctic archaea-virus interactions: metaproteome-led analysis of invasion, evasion and adaptation.},
journal = {The ISME journal},
volume = {9},
number = {9},
pages = {2094-2107},
pmid = {26125682},
issn = {1751-7370},
mesh = {Acclimatization ; Antarctic Regions ; Archaea/genetics/virology ; Archaeal Viruses/*genetics ; CRISPR-Cas Systems ; Capsid Proteins/physiology ; Cell Membrane/metabolism ; Ecosystem ; Genetic Variation ; Lakes/*microbiology/*virology ; Metagenome ; Metagenomics ; Phenotype ; Proteomics ; Viruses/genetics ; *Water Microbiology ; },
abstract = {Despite knowledge that viruses are abundant in natural ecosystems, there is limited understanding of which viruses infect which hosts, and how both hosts and viruses respond to those interactions-interactions that ultimately shape community structure and dynamics. In Deep Lake, Antarctica, intergenera gene exchange occurs rampantly within the low complexity, haloarchaea-dominated community, strongly balanced by distinctions in niche adaptation which maintain sympatric speciation. By performing metaproteomics for the first time on haloarchaea, genomic variation of S-layer, archaella and other cell surface proteins was linked to mechanisms of infection evasion. CRISPR defense systems were found to be active, with haloarchaea responding to at least eight distinct types of viruses, including those infecting between genera. The role of BREX systems in defending against viruses was also examined. Although evasion and defense were evident, both hosts and viruses also may benefit from viruses carrying and expressing host genes, thereby potentially enhancing genetic variation and phenotypic differences within populations. The data point to a complex inter-play leading to a dynamic optimization of host-virus interactions. This comprehensive overview was achieved only through the integration of results from metaproteomics, genomics and metagenomics.},
}
@article {pmid26125322,
year = {2015},
author = {Zhang, Y and Tian, Z and Liu, M and Shi, ZJ and Hale, L and Zhou, J and Yang, M},
title = {High Concentrations of the Antibiotic Spiramycin in Wastewater Lead to High Abundance of Ammonia-Oxidizing Archaea in Nitrifying Populations.},
journal = {Environmental science &amp; technology},
volume = {49},
number = {15},
pages = {9124-9132},
doi = {10.1021/acs.est.5b01293},
pmid = {26125322},
issn = {1520-5851},
mesh = {Ammonia/*metabolism ; Anti-Bacterial Agents/*analysis ; Archaea/genetics/*metabolism ; Bacteria/genetics/metabolism ; Genes, Archaeal ; Genetic Variation ; *Nitrification ; Nitrogen Cycle ; Oxidation-Reduction ; Phylogeny ; Real-Time Polymerase Chain Reaction ; Sequence Analysis, DNA ; Sewage/microbiology ; Spiramycin/*analysis ; Wastewater/*chemistry/microbiology ; Water Pollutants, Chemical/*analysis ; Water Quality ; },
abstract = {To evaluate the potential effects of antibiotics on ammonia-oxidizing microbes, multiple tools including quantitative PCR (qPCR), 454-pyrosequencing, and a high-throughput functional gene array (GeoChip) were used to reveal the distribution of ammonia-oxidizing archaea (AOA) and archaeal amoA (Arch-amoA) genes in three wastewater treatment systems receiving spiramycin or oxytetracycline production wastewaters. The qPCR results revealed that the copy number ratios of Arch-amoA to ammonia-oxidizing bacteria (AOB) amoA genes were the highest in the spiramycin full-scale (5.30) and pilot-scale systems (1.49 × 10(-1)), followed by the oxytetracycline system (4.90 × 10(-4)), with no Arch-amoA genes detected in the control systems treating sewage or inosine production wastewater. The pyrosequencing result showed that the relative abundance of AOA affiliated with Thaumarchaeota accounted for 78.5-99.6% of total archaea in the two spiramycin systems, which was in accordance with the qPCR results. Mantel test based on GeoChip data showed that Arch-amoA gene signal intensity correlated with the presence of spiramycin (P < 0.05). Antibiotics explained 25.8% of variations in amoA functional gene structures by variance partitioning analysis. This study revealed the selection of AOA in the presence of high concentrations of spiramycin in activated sludge systems.},
}
@article {pmid26103451,
year = {2015},
author = {Paul, SS and Deb, SM and Dey, A and Somvanshi, SP and Singh, D and Rathore, R and Stiverson, J},
title = {16S rDNA analysis of archaea indicates dominance of Methanobacterium and high abundance of Methanomassiliicoccaceae in rumen of Nili-Ravi buffalo.},
journal = {Anaerobe},
volume = {35},
number = {Pt B},
pages = {3-10},
doi = {10.1016/j.anaerobe.2015.06.002},
pmid = {26103451},
issn = {1095-8274},
mesh = {Animals ; Archaea/*classification/genetics/*isolation &amp; purification ; *Biota ; Buffaloes/*microbiology ; Cluster Analysis ; DNA, Archaeal/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Male ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Rumen/*microbiology ; Sequence Analysis, DNA ; },
abstract = {The molecular diversity of rumen methanogens was investigated using 16S rDNA gene library prepared from the rumen contents of Nili-Ravi buffaloes. Microbial genomic DNA was isolated from four adult male fistulated buffaloes and PCR conditions were set up using specific primers. Amplified product was cloned into a suitable vector, and the inserts of positive clones were sequenced. A total of 142 clones were examined, and the analysis revealed 46 species level (0.01 distance) operational taxonomic units (OTUs). Twenty six OTUs comprising 89 clones (63% of the total clones) were taxonomically assigned to Methanobacterium genus and the majority of them had highest percent identity with Methanobacterium flexile among cultured methanogens. Five OTUs comprising 27 clones (19% of total clones) were taxonomically assigned to Methanomicrobium genus and these clones showed highest sequence identity with Methanomicrobium mobile. Only two OTUs comprising 6 clones (4% of total clones) were assigned to Methanobrevibacter genus. A total of 17 clones belonging to 10 species level OTUs showed highest percent identity (ranging from 85 to 95%) with Methanomassilicoccus luminyensis and were taxonomically classified as Methanomassiliicocaceae. Out of the 142 rDNA clones, 112 clones, which constitute 79% of the total clones representing 42 OTUs, had less than 98.5% sequence identity with any of the cultured strains of methanogens and represent novel species of methanogens. This study has revealed the largest assortment of hydrogenotrophic methanogen phylotypes ever identified from the rumen of Nili-Ravi buffaloes. The study indicates that Methanobacterium is the most dominant methanogen in the rumen of Nili-Ravi buffalo. This is also the first report on the presence of methanogens phylogenetically close to M. luminyensis, an H2 dependent methylotrophic methanogen, in the rumen of buffaloes at such a high level of abundance.},
}
@article {pmid26099334,
year = {2015},
author = {Liu, S and Hu, B and He, Z and Zhang, B and Tian, G and Zheng, P and Fang, F},
title = {Ammonia-oxidizing archaea have better adaptability in oxygenated/hypoxic alternant conditions compared to ammonia-oxidizing bacteria.},
journal = {Applied microbiology and biotechnology},
volume = {99},
number = {20},
pages = {8587-8596},
doi = {10.1007/s00253-015-6750-7},
pmid = {26099334},
issn = {1432-0614},
mesh = {Adaptation, Biological ; Aerobiosis ; Ammonia/*metabolism ; Anaerobiosis ; Archaea/*classification/*genetics/metabolism ; Bacteria/*classification/*genetics/metabolism ; Cluster Analysis ; DNA, Archaeal/chemistry/genetics ; DNA, Bacterial/chemistry/genetics ; *Genetic Variation ; Molecular Sequence Data ; Oxidation-Reduction ; Phylogeny ; Real-Time Polymerase Chain Reaction ; Sequence Analysis, DNA ; *Soil Microbiology ; },
abstract = {Ammonia oxidation is performed by both ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). Few studies compared the adaptability of AOA and AOB for oxygenated/hypoxic alternant conditions in water-level-fluctuating zones. Here, using qPCR and 454 high-throughput sequencing of functional amoA genes of AOA and AOB, we examined the changes of abundances, diversities, and community structures of AOA and AOB in periodically flooded soils compared to the non-flooded soils in Three Gorges Reservoir. The increased AOA operational taxonomic unit (OTU) numbers and the higher ratios of abundance (AOA:AOB) in the periodically flooded soils suggested AOA have better adaptability for oxygenated/hypoxic alternant conditions in the water-level-fluctuating zones in the Three Gorges Reservoir and probably responsible for the ammonia oxidation there. Canonical correspondence analysis (CCA) showed that oxidation-reduction potential (ORP) had the most significant effect on the community distribution of AOA (p < 0.01). Pearson analysis also indicated that ORP was the most important factor influencing the abundances and diversities of ammonia-oxidizing microbes. ORP was significantly negatively correlated with AOA OTU numbers (p < 0.05), ratio of OTU numbers (AOA:AOB) (p < 0.01), and ratio of amoA gene abundances (AOA:AOB) (p < 0.05). ORP was also significantly positively correlated with AOB abundance (p < 0.05).},
}
@article {pmid26098850,
year = {2015},
author = {Chang, MM and Imperiali, B and Eichler, J and Guan, Z},
title = {N-Linked Glycans Are Assembled on Highly Reduced Dolichol Phosphate Carriers in the Hyperthermophilic Archaea Pyrococcus furiosus.},
journal = {PloS one},
volume = {10},
number = {6},
pages = {e0130482},
pmid = {26098850},
issn = {1932-6203},
support = {R01 GM039334/GM/NIGMS NIH HHS/United States ; U54 GM069338/GM/NIGMS NIH HHS/United States ; GM-069338/GM/NIGMS NIH HHS/United States ; GM-039334/GM/NIGMS NIH HHS/United States ; },
mesh = {Archaea/*metabolism ; Butadienes/metabolism ; Dolichol Phosphates/*metabolism ; Dolichols/*metabolism ; Glycosylation ; Hemiterpenes/metabolism ; Oligosaccharides/metabolism ; Pentanes/metabolism ; Phosphate Transport Proteins/*metabolism ; Polysaccharides/*metabolism ; Pyrococcus furiosus/*metabolism ; },
abstract = {In all three domains of life, N-glycosylation begins with the assembly of glycans on phosphorylated polyisoprenoid carriers. Like eukaryotes, archaea also utilize phosphorylated dolichol for this role, yet whereas the assembled oligosaccharide is transferred to target proteins from dolichol pyrophosphate in eukaryotes, archaeal N-linked glycans characterized to date are derived from a dolichol monophosphate carrier, apart from a single example. In this study, glycan-charged dolichol phosphate from the hyperthermophile Pyrococcus furiosus was identified and structurally characterized. Normal and reverse phase liquid chromatography-electrospray ionization mass spectrometry revealed the existence of dolichol phosphate charged with the heptasaccharide recently described in in vitro studies of N-glycosylation on this species. As with other described archaeal dolichol phosphates, the α- and ω-terminal isoprene subunits of the P. furiosus lipid are saturated, in contrast to eukaryal phosphodolichols that present only a saturated α-position isoprene subunit. Interestingly, an additional 1-4 of the 12-14 isoprene subunits comprising P. furiosus dolichol phosphate are saturated, making this lipid not only the longest archaeal dolichol phosphate described to date but also the most highly saturated.},
}
@article {pmid26097504,
year = {2015},
author = {Abendroth, C and Vilanova, C and Günther, T and Luschnig, O and Porcar, M},
title = {Eubacteria and archaea communities in seven mesophile anaerobic digester plants in Germany.},
journal = {Biotechnology for biofuels},
volume = {8},
number = {},
pages = {87},
pmid = {26097504},
issn = {1754-6834},
abstract = {BACKGROUND: Only a fraction of the microbial species used for anaerobic digestion in biogas production plants are methanogenic archaea. We have analyzed the taxonomic profiles of eubacteria and archaea, a set of chemical key parameters, and biogas production in samples from nine production plants in seven facilities in Thuringia, Germany, including co-digesters, leach-bed, and sewage sludge treatment plants. Reactors were sampled twice, at a 1-week interval, and three biological replicates were taken in each case.<br><br>RESULTS: A complex taxonomic composition was found for both eubacteria and archaea, both of which strongly correlated with digester type. Plant-degrading Firmicutes as well as Bacteroidetes dominated eubacteria profiles in high biogas-producing co-digesters; whereas Bacteroidetes and Spirochaetes were the major phyla in leach-bed and sewage sludge digesters. Methanoculleus was the dominant archaea genus in co-digesters, whereas Methanosarcina and Methanosaeta were the most abundant methanogens in leachate from leach-bed and sewage sludge digesters, respectively.<br><br>CONCLUSIONS: This is one of the most comprehensive characterizations of the microbial communities of biogas-producing facilities. Bacterial profiles exhibited very low variation within replicates, including those of semi-solid samples; and, in general, low variation in time. However, facility type correlated closely with the bacterial profile: each of the three reactor types exhibited a characteristic eubacteria and archaea profile. Digesters operated with solid feedstock, and high biogas production correlated with abundance of plant degraders (Firmicutes) and biofilm-forming methanogens (Methanoculleus spp.). By contrast, low biogas-producing sewage sludge treatment digesters correlated with high titers of volatile fatty acid-adapted Methanosaeta spp.},
}
@article {pmid26085149,
year = {2015},
author = {Hochstein, R and Bollschweiler, D and Engelhardt, H and Lawrence, CM and Young, M},
title = {Large Tailed Spindle Viruses of Archaea: a New Way of Doing Viral Business.},
journal = {Journal of virology},
volume = {89},
number = {18},
pages = {9146-9149},
pmid = {26085149},
issn = {1098-5514},
mesh = {Archaea/*virology ; Archaeal Viruses/chemistry/*physiology ; Capsid Proteins/chemistry/*physiology ; Genes, Viral/*physiology ; },
abstract = {Viruses of Archaea continue to surprise us. Archaeal viruses have revealed new morphologies, protein folds, and gene content. This is especially true for large spindle viruses, which infect only Archaea. We present a comparison of particle morphologies, major coat protein structures, and gene content among the five characterized large spindle viruses to elucidate defining characteristics. Structural similarities and a core set of genes support the grouping of the large spindle viruses into a new superfamily.},
}
@article {pmid26084810,
year = {2015},
author = {Grazziotin, AL and Vidal, NM and Venancio, TM},
title = {Uncovering major genomic features of essential genes in Bacteria and a methanogenic Archaea.},
journal = {The FEBS journal},
volume = {282},
number = {17},
pages = {3395-3411},
pmid = {26084810},
issn = {1742-4658},
support = {ZIA LM594244-08//Intramural NIH HHS/United States ; },
mesh = {Archaea/genetics ; Biological Evolution ; Burkholderia pseudomallei/genetics ; Escherichia coli/genetics ; *Gene Expression Regulation, Archaeal ; *Gene Expression Regulation, Bacterial ; Gene Regulatory Networks ; *Genes, Essential ; *Genome, Archaeal ; *Genome, Bacterial ; Molecular Sequence Annotation ; Mycobacterium tuberculosis/genetics ; Streptococcus/genetics ; },
abstract = {Identification of essential genes is critical to understanding the physiology of a species, proposing novel drug targets and uncovering minimal gene sets required for life. Although essential gene sets of several organisms have been determined using large-scale mutagenesis techniques, systematic studies addressing their conservation, genomic context and functions remain scant. Here we integrate 17 essential gene sets from genome-wide in vitro screenings and three gene collections required for growth in vivo, encompassing 15 Bacteria and one Archaea. We refine and generalize important theories proposed using Escherichia coli. Essential genes are typically monogenic and more conserved than nonessential genes. Genes required in vivo are less conserved than those essential in vitro, suggesting that more divergent strategies are deployed when the organism is stressed by the host immune system and unstable nutrient availability. We identified essential analogous pathways that would probably be missed by orthology-based essentiality prediction strategies. For example, Streptococcus sanguinis carries horizontally transferred isoprenoid biosynthesis genes that are widespread in Archaea. Genes specifically essential in Mycobacterium tuberculosis and Burkholderia pseudomallei are reported as potential drug targets. Moreover, essential genes are not only preferentially located in operons, but also occupy the first position therein, supporting the influence of their regulatory regions in driving transcription of whole operons. Finally, these important genomic features are shared between Bacteria and at least one Archaea, suggesting that high order properties of gene essentiality and genome architecture were probably present in the last universal common ancestor or evolved independently in the prokaryotic domains.},
}
@article {pmid26075362,
year = {2015},
author = {López-García, P and Zivanovic, Y and Deschamps, P and Moreira, D},
title = {Bacterial gene import and mesophilic adaptation in archaea.},
journal = {Nature reviews. Microbiology},
volume = {13},
number = {7},
pages = {447-456},
pmid = {26075362},
issn = {1740-1534},
support = {322669/ERC_/European Research Council/International ; },
mesh = {Adaptation, Biological ; Archaea/*classification/*genetics/physiology ; *Evolution, Molecular ; Phylogeny ; Temperature ; },
abstract = {It is widely believed that the archaeal ancestor was hyperthermophilic, but during archaeal evolution, several lineages - including haloarchaea and their sister methanogens, the Thaumarchaeota, and the uncultured Marine Group II and Marine Group III Euryarchaeota (MGII/III) - independently adapted to lower temperatures. Recent phylogenomic studies suggest that the ancestors of these lineages were recipients of massive horizontal gene transfer from bacteria. Many of the acquired genes, which are often involved in metabolism and cell envelope biogenesis, were convergently acquired by distant mesophilic archaea. In this Opinion article, we explore the intriguing hypothesis that the import of these bacterial genes was crucial for the adaptation of archaea to mesophilic lifestyles.},
}
@article {pmid26074892,
year = {2015},
author = {Ozuolmez, D and Na, H and Lever, MA and Kjeldsen, KU and Jørgensen, BB and Plugge, CM},
title = {Methanogenic archaea and sulfate reducing bacteria co-cultured on acetate: teamwork or coexistence?.},
journal = {Frontiers in microbiology},
volume = {6},
number = {},
pages = {492},
pmid = {26074892},
issn = {1664-302X},
abstract = {Acetate is a major product of fermentation processes and an important substrate for sulfate reducing bacteria and methanogenic archaea. Most studies on acetate catabolism by sulfate reducers and methanogens have used pure cultures. Less is known about acetate conversion by mixed pure cultures and the interactions between both groups. We tested interspecies hydrogen transfer and coexistence between marine methanogens and sulfate reducers using mixed pure cultures of two types of microorganisms. First, Desulfovibrio vulgaris subsp. vulgaris (DSM 1744), a hydrogenotrophic sulfate reducer, was cocultured together with the obligate aceticlastic methanogen Methanosaeta concilii using acetate as carbon and energy source. Next, Methanococcus maripaludis S2, an obligate H2- and formate-utilizing methanogen, was used as a partner organism to M. concilii in the presence of acetate. Finally, we performed a coexistence experiment between M. concilii and an acetotrophic sulfate reducer Desulfobacter latus AcSR2. Our results showed that D. vulgaris was able to reduce sulfate and grow from hydrogen leaked by M. concilii. In the other coculture, M. maripaludis was sustained by hydrogen leaked by M. concilii as revealed by qPCR. The growth of the two aceticlastic microbes indicated co-existence rather than competition. Altogether, our results indicate that H2 leaking from M. concilii could be used by efficient H2-scavengers. This metabolic trait, revealed from coculture studies, brings new insight to the metabolic flexibility of methanogens and sulfate reducers residing in marine environments in response to changing environmental conditions and community compositions. Using dedicated physiological studies we were able to unravel the occurrence of less obvious interactions between marine methanogens and sulfate-reducing bacteria.},
}
@article {pmid26068860,
year = {2015},
author = {Ferry, JG},
title = {Acetate Metabolism in Anaerobes from the Domain Archaea.},
journal = {Life (Basel, Switzerland)},
volume = {5},
number = {2},
pages = {1454-1471},
pmid = {26068860},
issn = {2075-1729},
support = {R01 GM044661/GM/NIGMS NIH HHS/United States ; },
abstract = {Acetate and acetyl-CoA play fundamental roles in all of biology, including anaerobic prokaryotes from the domains Bacteria and Archaea, which compose an estimated quarter of all living protoplasm in Earth's biosphere. Anaerobes from the domain Archaea contribute to the global carbon cycle by metabolizing acetate as a growth substrate or product. They are components of anaerobic microbial food chains converting complex organic matter to methane, and many fix CO2 into cell material via synthesis of acetyl-CoA. They are found in a diversity of ecological habitats ranging from the digestive tracts of insects to deep-sea hydrothermal vents, and synthesize a plethora of novel enzymes with biotechnological potential. Ecological investigations suggest that still more acetate-metabolizing species with novel properties await discovery.},
}
@article {pmid26066650,
year = {2015},
author = {Lurie-Weinberger, MN and Gophna, U},
title = {Archaea in and on the Human Body: Health Implications and Future Directions.},
journal = {PLoS pathogens},
volume = {11},
number = {6},
pages = {e1004833},
pmid = {26066650},
issn = {1553-7374},
mesh = {*Archaea ; Humans ; *Microbiota ; },
}
@article {pmid26054421,
year = {2015},
author = {Clouet-d'Orval, B and Phung, DK and Langendijk-Genevaux, PS and Quentin, Y},
title = {Universal RNA-degrading enzymes in Archaea: Prevalence, activities and functions of β-CASP ribonucleases.},
journal = {Biochimie},
volume = {118},
number = {},
pages = {278-285},
doi = {10.1016/j.biochi.2015.05.021},
pmid = {26054421},
issn = {1638-6183},
mesh = {Archaea/*enzymology/*genetics ; Archaeal Proteins/*metabolism ; RNA Stability/*physiology ; Ribonucleases/*metabolism ; },
abstract = {β-CASP ribonucleases are widespread in all three domains of life. They catalyse both 5'-3' exoribonucleolytic RNA trimming and/or endoribonucleolytic RNA cleavage using a unique active site coordinated by two zinc ions. These fascinating enzymes have a key role in 3' end processing in Eukarya and in RNA decay and ribosomal RNA maturation in Bacteria. The recent recognition of β-CASP ribonucleases as major players in Archaea is an important contribution towards identifying RNA-degrading enzymes in the third domain of life. Three β-CASP orthologous groups, aCPSF1, aCPSF2, aCPSF1b, are closely related to the eukaryal CPSF73 termination factor and one, aRNase J, is ortholog of the bacterial RNase J. The endo- and 5'-3' exoribonucleolytic activities carried by archaeal β-CASP enzymes are strictly conserved throughout archaeal phylogeny suggesting essential roles in maturation and/or degradation of RNA. The recent progress in understanding the prevalence, activities and functions of archaeal β-CASP ribonucleases is the focus of this review. The current status of our understanding of RNA processing pathways in Archaea is covered in light of this new knowledge on β-CASP ribonucleases.},
}
@article {pmid26053257,
year = {2015},
author = {Banning, NC and Maccarone, LD and Fisk, LM and Murphy, DV},
title = {Ammonia-oxidising bacteria not archaea dominate nitrification activity in semi-arid agricultural soil.},
journal = {Scientific reports},
volume = {5},
number = {},
pages = {11146},
pmid = {26053257},
issn = {2045-2322},
mesh = {Agriculture ; Ammonia/*metabolism ; Archaea/enzymology/genetics/*metabolism ; Bacteria/enzymology/genetics/*metabolism ; Ecosystem ; Nitrification/*physiology ; Nitrogen/metabolism ; Nitrogen Cycle ; Oxidation-Reduction ; Oxidoreductases/genetics/*metabolism ; RNA, Ribosomal, 16S/genetics ; Soil/chemistry ; Soil Microbiology ; },
abstract = {Ammonia-oxidising archaea (AOA) and bacteria (AOB) are responsible for the rate limiting step in nitrification; a key nitrogen (N) loss pathway in agricultural systems. Dominance of AOA relative to AOB in the amoA gene pool has been reported in many ecosystems, although their relative contributions to nitrification activity are less clear. Here we examined the distribution of AOA and AOB with depth in semi-arid agricultural soils in which soil organic matter content or pH had been altered, and related their distribution to gross nitrification rates. Soil depth had a significant effect on gene abundances, irrespective of management history. Contrary to reports of AOA dominance in soils elsewhere, AOA gene copy numbers were four-fold lower than AOB in the surface (0-10 cm). AOA gene abundance increased with depth while AOB decreased, and sub-soil abundances were approximately equal (10-90 cm). The depth profile of total archaea did not mirror that of AOA, indicating the likely presence of archaea without nitrification capacity in the surface. Gross nitrification rates declined significantly with depth and were positively correlated to AOB but negatively correlated to AOA gene abundances. We conclude that AOB are most likely responsible for regulating nitrification in these semi-arid soils.},
}
@article {pmid26029183,
year = {2015},
author = {Kletzin, A and Heimerl, T and Flechsler, J and van Niftrik, L and Rachel, R and Klingl, A},
title = {Cytochromes c in Archaea: distribution, maturation, cell architecture, and the special case of Ignicoccus hospitalis.},
journal = {Frontiers in microbiology},
volume = {6},
number = {},
pages = {439},
pmid = {26029183},
issn = {1664-302X},
abstract = {Cytochromes c (Cytc) are widespread electron transfer proteins and important enzymes in the global nitrogen and sulfur cycles. The distribution of Cytc in more than 300 archaeal proteomes deduced from sequence was analyzed with computational methods including pattern and similarity searches, secondary and tertiary structure prediction. Two hundred and fifty-eight predicted Cytc (with single, double, or multiple heme c attachment sites) were found in some but not all species of the Desulfurococcales, Thermoproteales, Archaeoglobales, Methanosarcinales, Halobacteriales, and in two single-cell genome sequences of the Thermoplasmatales, all of them Cren- or Euryarchaeota. Other archaeal phyla including the Thaumarchaeota are so far free of these proteins. The archaeal Cytc sequences were bundled into 54 clusters of mutual similarity, some of which were specific for Archaea while others had homologs in the Bacteria. The cytochrome c maturation system I (CCM) was the only one found. The highest number and variability of Cytc were present in those species with known or predicted metal oxidation and/or reduction capabilities. Paradoxical findings were made in the haloarchaea: several Cytc had been purified biochemically but corresponding proteins were not found in the proteomes. The results are discussed with emphasis on cell morphologies and envelopes and especially for double-membraned Archaea-like Ignicoccus hospitalis. A comparison is made with compartmentalized bacteria such as the Planctomycetes of the Anammox group with a focus on the putative localization and roles of the Cytc and other electron transport proteins.},
}
@article {pmid26014885,
year = {2015},
author = {Guillén-Navarro, K and Herrera-López, D and López-Chávez, MY and Cancino-Gómez, M and Reyes-Reyes, AL},
title = {Assessment of methods to recover DNA from bacteria, fungi and archaea in complex environmental samples.},
journal = {Folia microbiologica},
volume = {60},
number = {6},
pages = {551-558},
pmid = {26014885},
issn = {1874-9356},
mesh = {Archaea/genetics/*isolation &amp; purification ; Bacteria/genetics/*isolation &amp; purification ; Chemistry Techniques, Analytical/*methods ; DNA, Archaeal/genetics/*isolation &amp; purification ; DNA, Bacterial/genetics/*isolation &amp; purification ; DNA, Fungal/genetics/*isolation &amp; purification ; Environmental Microbiology ; Fungi/genetics/*isolation &amp; purification ; Polymerase Chain Reaction ; },
abstract = {DNA extraction from environmental samples is a critical step for metagenomic analysis to study microbial communities, including those considered uncultivable. Nevertheless, obtaining good quality DNA in sufficient quantities for downstream methodologies is not always possible, and it depends on the complexity and stability of each ecosystem, which could be more problematic for samples from tropical regions because those ecosystems are less stable and more complex. Three laboratory methods for the extraction of nucleic acids from samples representing unstable (decaying coffee pulp and mangrove sediments) and relatively stable (compost and soil) environments were tested. The results were compared with those obtained using two commercial DNA extraction kits. The quality of the extracted DNA was evaluated by PCR amplification to verify the recovery of bacterial, archaeal, and fungal genetic material. The laboratory method that gave the best results used a lysis procedure combining physical, chemical, and enzymatic steps.},
}
@article {pmid26013483,
year = {2015},
author = {Gao, L and Imanaka, T and Fujiwara, S},
title = {A Mutant Chaperonin That Is Functional at Lower Temperatures Enables Hyperthermophilic Archaea To Grow under Cold-Stress Conditions.},
journal = {Journal of bacteriology},
volume = {197},
number = {16},
pages = {2642-2652},
pmid = {26013483},
issn = {1098-5530},
mesh = {Adenosine Triphosphatases/metabolism ; Archaeal Proteins/genetics/*metabolism ; *Cold Temperature ; DNA, Archaeal/genetics ; *Gene Expression Regulation, Archaeal ; Hot Temperature ; Molecular Chaperones/genetics/*metabolism ; Mutation ; Plasmids/genetics ; Sequence Alignment ; Thermococcus/*genetics/metabolism ; },
abstract = {UNLABELLED: Thermococcus kodakarensis grows optimally at 85°C and possesses two chaperonins, cold-inducible CpkA and heat-inducible CpkB, which are involved in adaptation to low and high temperatures, respectively. The two chaperonins share a high sequence identity (77%), except in their C-terminal regions. CpkA, which contains tandem repeats of a GGM motif, shows its highest ATPase activity at 60°C to 70°C, whereas CpkB shows its highest activity at temperatures higher than 90°C. To clarify the effects of changes in ATPase activity on chaperonin function at lower temperatures, various CpkA variants were constructed by introducing single point mutations into the C-terminal region. A CpkA variant in which Glu530 was replaced with Gly (CpkA-E530G) showed increased ATPase activity, with its highest activity at 50°C. The efficacy of the CpkA variants against denatured indole-3-glycerol-phosphate synthase of T. kodakarensis (TrpCTk), which is a CpkA target, was then examined in vitro. CpkA-E530G was more effective than wild-type CpkA at facilitating the refolding of chemically unfolded TrpCTk at 50°C. The effect of cpkA-E530G on cell growth was then examined by introducing cpkA-E530G into the genome of T. kodakarensis KU216 (pyrF). The mutant strain, DA4 (pyrF cpkA-E530G), grew as well as the parental KU216 strain at 60°C. In contrast, DA4 grew more vigorously than KU216 at 50°C. These results suggested that the CpkA-E530G mutation prevented cold denaturation of proteins under cold-stress conditions, thereby enabling cells to grow in cooler environments. Thus, a single base pair substitution in a chaperonin gene allows cells to grow vigorously in a new environment.<br><br>IMPORTANCE: Thermococcus kodakarensis possesses two group II chaperonins, cold-inducible CpkA and heat-inducible CpkB, which are involved in adaptation to low and high temperatures, respectively. CpkA might act as an "adaptive allele" to adapt to cooler environments. In this study, we compared the last 20 amino acids within the C termini of the chaperonins and found a clear correlation between the CpkA-type chaperonin gene copy number and growth temperature. Furthermore, we introduced single mutations into the CpkA C-terminal region to clarify its role in cold adaptation, and we showed that a single base substitution allowed the organism to adapt to a lower temperature. The present data suggest that hyperthermophiles have evolved by obtaining mutations in chaperonins that allow them to adapt to a colder environment.},
}
@article {pmid26010867,
year = {2015},
author = {Cao, S and Hepowit, N and Maupin-Furlow, JA},
title = {Ubiquitin-Like Protein SAMP1 and JAMM/MPN+ Metalloprotease HvJAMM1 Constitute a System for Reversible Regulation of Metabolic Enzyme Activity in Archaea.},
journal = {PloS one},
volume = {10},
number = {5},
pages = {e0128399},
pmid = {26010867},
issn = {1932-6203},
support = {R01 GM057498/GM/NIGMS NIH HHS/United States ; R01 GM57498/GM/NIGMS NIH HHS/United States ; },
mesh = {Archaeal Proteins/metabolism ; Catalytic Domain ; Enzyme Activation ; Haloferax volcanii/chemistry/*metabolism ; Metalloproteases/*metabolism ; Models, Molecular ; Protein Processing, Post-Translational ; Proteolysis ; Sulfurtransferases/*metabolism ; Ubiquitins/chemistry/*metabolism ; },
abstract = {Ubiquitin/ubiquitin-like (Ub/Ubl) proteins are involved in diverse cellular processes by their covalent linkage to protein substrates. Here, we provide evidence for a post-translational modification system that regulates enzyme activity which is composed of an archaeal Ubl protein (SAMP1) and a JAMM/MPN+ metalloprotease (HvJAMM1). Molybdopterin (MPT) synthase activity was found to be inhibited by covalent linkage of SAMP1 to the large subunit (MoaE) of MPT synthase. HvJAMM1 was shown to cleave the covalently linked inactive form of SAMP1-MoaE to the free functional individual SAMP1 and MoaE subunits of MPT synthase, suggesting reactivation of MPT synthase by this metalloprotease. Overall, this study provides new insight into the broad idea that Ub/Ubl modification is a post-translational process that can directly and reversibly regulate the activity of metabolic enzymes. In particular, we show that Ub/Ubl linkages on the active site residues of an enzyme (MPT synthase) can inhibit its catalytic activity and that the enzyme can be reactivated through cleavage by a JAMM/MPN+ metalloprotease.},
}
@article {pmid25997109,
year = {2015},
author = {French, E and Bollmann, A},
title = {Freshwater Ammonia-Oxidizing Archaea Retain amoA mRNA and 16S rRNA during Ammonia Starvation.},
journal = {Life (Basel, Switzerland)},
volume = {5},
number = {2},
pages = {1396-1404},
pmid = {25997109},
issn = {2075-1729},
abstract = {In their natural habitats, microorganisms are often exposed to periods of starvation if their substrates for energy generation or other nutrients are limiting. Many microorganisms have developed strategies to adapt to fluctuating nutrients and long-term starvation. In the environment, ammonia oxidizers have to compete with many different organisms for ammonium and are often exposed to long periods of ammonium starvation. We investigated the effect of ammonium starvation on ammonia-oxidizing archaea (AOA) and bacteria (AOB) enriched from freshwater lake sediments. Both AOA and AOB were able to recover even after almost two months of starvation; however, the recovery time differed. AOA and AOB retained their 16S rRNA (ribosomes) throughout the complete starvation period. The AOA retained also a small portion of the mRNA of the ammonia monooxygenase subunit A (amoA) for the complete starvation period. However, after 10 days, no amoA mRNA was detected anymore in the AOB. These results indicate that AOA and AOB are able to survive longer periods of starvation, but might utilize different strategies.},
}
@article {pmid25984733,
year = {2015},
author = {Probst, AJ and Moissl-Eichinger, C},
title = {"Altiarchaeales": uncultivated archaea from the subsurface.},
journal = {Life (Basel, Switzerland)},
volume = {5},
number = {2},
pages = {1381-1395},
pmid = {25984733},
issn = {2075-1729},
abstract = {Due to the limited cultivability of the vast majority of microorganisms, researchers have applied environmental genomics and other state-of-the-art technologies to gain insights into the biology of uncultivated Archaea and bacteria in their natural biotope. In this review, we summarize the scientific findings on a recently proposed order-level lineage of uncultivated Archaea called Altiarchaeales, which includes "Candidatus Altiarchaeum hamiconexum" as the most well-described representative. Ca. A. hamiconexum possesses a complex biology: thriving strictly anaerobically, this microorganism is capable of forming highly-pure biofilms, connecting the cells by extraordinary cell surface appendages (the "hami") and has other highly unusual traits, such as a double-membrane-based cell wall. Indicated by genomic information from different biotopes, the Altiarchaeales seem to proliferate in deep, anoxic groundwater of Earth's crust bearing a potentially very important function: carbon fixation. Although their net carbon fixation rate has not yet been determined, they appear as highly abundant organisms in their biotopes and may thus represent an important primary producer in the subsurface. In sum, the research over more than a decade on Ca. A. hamiconexum has revealed many interesting features of its lifestyle, its genomic information, metabolism and ultrastructure, making this archaeon one of the best-studied uncultivated Archaea in the literature.},
}
@article {pmid25976837,
year = {2015},
author = {Darnell, CL and Schmid, AK},
title = {Systems biology approaches to defining transcription regulatory networks in halophilic archaea.},
journal = {Methods (San Diego, Calif.)},
volume = {86},
number = {},
pages = {102-114},
doi = {10.1016/j.ymeth.2015.04.034},
pmid = {25976837},
issn = {1095-9130},
mesh = {Archaea/*genetics ; Computational Biology/methods ; Gene Regulatory Networks ; Genome, Archaeal ; Halobacterium salinarum ; *Systems Biology ; Transcription Factors/*genetics ; *Transcription, Genetic ; },
abstract = {To survive complex and changing environmental conditions, microorganisms use gene regulatory networks (GRNs) composed of interacting regulatory transcription factors (TFs) to control the timing and magnitude of gene expression. Genome-wide datasets; such as transcriptomics and protein-DNA interactions; and experiments such as high throughput growth curves; facilitate the construction of GRNs and provide insight into TF interactions occurring under stress. Systems biology approaches integrate these datasets into models of GRN architecture as well as statistical and/or dynamical models to understand the function of networks occurring in cells. Previously, these types of studies have focused on traditional model organisms (e.g. Escherichia coli, yeast). However, recent advances in archaeal genetics and other tools have enabled a systems approach to understanding GRNs in these relatively less studied archaeal model organisms. In this report, we outline a systems biology workflow for generating and integrating data focusing on the TF regulator. We discuss experimental design, outline the process of data collection, and provide the tools required to produce high confidence regulons for the TFs of interest. We provide a case study as an example of this workflow, describing the construction of a GRN centered on multi-TF coordinate control of gene expression governing the oxidative stress response in the hypersaline-adapted archaeon Halobacterium salinarum.},
}
@article {pmid25964353,
year = {2015},
author = {Raymann, K and Brochier-Armanet, C and Gribaldo, S},
title = {The two-domain tree of life is linked to a new root for the Archaea.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {112},
number = {21},
pages = {6670-6675},
pmid = {25964353},
issn = {1091-6490},
mesh = {Archaea/*classification/*genetics ; Bacteria/classification/genetics ; Bayes Theorem ; *Biological Evolution ; Databases, Genetic ; Eukaryota/classification/genetics ; Euryarchaeota/classification/genetics ; Evolution, Molecular ; Genetic Markers ; Genetic Speciation ; Genome, Archaeal ; Genome, Bacterial ; Models, Biological ; Phylogeny ; },
abstract = {One of the most fundamental questions in evolutionary biology is the origin of the lineage leading to eukaryotes. Recent phylogenomic analyses have indicated an emergence of eukaryotes from within the radiation of modern Archaea and specifically from a group comprising Thaumarchaeota/"Aigarchaeota" (candidate phylum)/Crenarchaeota/Korarchaeota (TACK). Despite their major implications, these studies were all based on the reconstruction of universal trees and left the exact placement of eukaryotes with respect to the TACK lineage unclear. Here we have applied an original two-step approach that involves the separate analysis of markers shared between Archaea and eukaryotes and between Archaea and Bacteria. This strategy allowed us to use a larger number of markers and greater taxonomic coverage, obtain high-quality alignments, and alleviate tree reconstruction artifacts potentially introduced when analyzing the three domains simultaneously. Our results robustly indicate a sister relationship of eukaryotes with the TACK superphylum that is strongly associated with a distinct root of the Archaea that lies within the Euryarchaeota, challenging the traditional topology of the archaeal tree. Therefore, if we are to embrace an archaeal origin for eukaryotes, our view of the evolution of the third domain of life will have to be profoundly reconsidered, as will many areas of investigation aimed at inferring ancestral characteristics of early life and Earth.},
}
@article {pmid25947248,
year = {2015},
author = {Zhang, J and Dai, Y and Wang, Y and Wu, Z and Xie, S and Liu, Y},
title = {Distribution of ammonia-oxidizing archaea and bacteria in plateau soils across different land use types.},
journal = {Applied microbiology and biotechnology},
volume = {99},
number = {16},
pages = {6899-6909},
doi = {10.1007/s00253-015-6625-y},
pmid = {25947248},
issn = {1432-0614},
mesh = {Ammonia/*metabolism ; Archaea/*classification/*metabolism ; Bacteria/*classification/*metabolism ; *Biota ; Carbon/analysis ; Chemical Phenomena ; China ; DNA, Archaeal/chemistry/genetics ; DNA, Bacterial/chemistry/genetics ; Molecular Sequence Data ; Nitrates/analysis ; Nitrification ; Nitrogen/analysis ; Oxidation-Reduction ; Real-Time Polymerase Chain Reaction ; Sequence Analysis, DNA ; Soil/chemistry ; *Soil Microbiology ; },
abstract = {Ammonia oxidation is known to be performed by both ammonia-oxidizing archaea (AOA) and bacteria (AOB), although their relative significance to nitrification process in soil ecosystems remains controversial. The distribution of AOA and AOB in plateau soils with different land use types and the influential factors remains unclear. The present study investigated the abundance and structure of AOA and AOB communities in upland soils adjacent to Erhai Lake in the Yunnan Plateau (China). Quantitative PCR assays indicated a large variation in the community size of AOA and AOB communities, with the numerical dominance of AOA over AOB in most of soils. Clone library analysis illustrated a marked shift in the structure of soil AOA and AOB communities. A high abundance of Nitrososphaera- and Nitrosotalea-like AOA was observed, while Nitrosospira-like species predominated in AOB. AOA and AOB abundance was positively influenced by total nitrogen and moisture content, respectively. Moreover, moisture content might be a key determinant of AOA community composition, while C/N and nitrate nitrogen played an important role in shaping AOB community composition. However, further efforts will be necessary in order to elucidate the links between soil AOA and AOB and land use.},
}
@article {pmid25945739,
year = {2015},
author = {Spang, A and Saw, JH and Jørgensen, SL and Zaremba-Niedzwiedzka, K and Martijn, J and Lind, AE and van Eijk, R and Schleper, C and Guy, L and Ettema, TJG},
title = {Complex archaea that bridge the gap between prokaryotes and eukaryotes.},
journal = {Nature},
volume = {521},
number = {7551},
pages = {173-179},
pmid = {25945739},
issn = {1476-4687},
support = {310039/ERC_/European Research Council/International ; },
mesh = {Actin Cytoskeleton/metabolism ; Actins/genetics/metabolism ; Archaea/*classification/genetics/metabolism ; Arctic Regions ; Endosomal Sorting Complexes Required for Transport/genetics/metabolism ; Eukaryota/*classification/genetics/metabolism ; Eukaryotic Cells/classification/metabolism ; *Evolution, Molecular ; Hydrothermal Vents/*microbiology ; Metagenome/genetics ; Molecular Sequence Data ; Monomeric GTP-Binding Proteins/genetics/metabolism ; *Phylogeny ; Prokaryotic Cells/*classification ; Proteome/genetics/isolation &amp; purification/metabolism ; },
abstract = {The origin of the eukaryotic cell remains one of the most contentious puzzles in modern biology. Recent studies have provided support for the emergence of the eukaryotic host cell from within the archaeal domain of life, but the identity and nature of the putative archaeal ancestor remain a subject of debate. Here we describe the discovery of 'Lokiarchaeota', a novel candidate archaeal phylum, which forms a monophyletic group with eukaryotes in phylogenomic analyses, and whose genomes encode an expanded repertoire of eukaryotic signature proteins that are suggestive of sophisticated membrane remodelling capabilities. Our results provide strong support for hypotheses in which the eukaryotic host evolved from a bona fide archaeon, and demonstrate that many components that underpin eukaryote-specific features were already present in that ancestor. This provided the host with a rich genomic 'starter-kit' to support the increase in the cellular and genomic complexity that is characteristic of eukaryotes.},
}
@article {pmid25938369,
year = {2015},
author = {Allen, KD and Miller, DV and Rauch, BJ and Perona, JJ and White, RH},
title = {Homocysteine is biosynthesized from aspartate semialdehyde and hydrogen sulfide in methanogenic archaea.},
journal = {Biochemistry},
volume = {54},
number = {20},
pages = {3129-3132},
doi = {10.1021/acs.biochem.5b00118},
pmid = {25938369},
issn = {1520-4995},
mesh = {Aspartic Acid/*analogs &amp; derivatives/metabolism ; Biosynthetic Pathways ; Genes, Archaeal ; Homocysteine/*biosynthesis ; Hydrogen Sulfide/*metabolism ; Methanococcus/genetics/*metabolism ; },
abstract = {The biosynthetic route for homocysteine, intermediate in methionine biosynthesis, is unknown in some methanogenic archaea because homologues of the canonical required genes cannot be identified. Here we demonstrate that Methanocaldococcus jannaschii can biosynthesize homocysteine from aspartate semialdehyde and hydrogen sulfide. Additionally, we confirm the genes involved in this new pathway in Methanosarcina acetivorans. A possible series of reactions in which a thioaldehyde is formed and then reduced to a thiol are proposed. This represents a novel route for the biosynthesis of homocysteine and exemplifies unique aspects of sulfur chemistry occurring in prebiotic environments and in early life forms.},
}
@article {pmid25932531,
year = {2015},
author = {Atanasova, NS and Oksanen, HM and Bamford, DH},
title = {Haloviruses of archaea, bacteria, and eukaryotes.},
journal = {Current opinion in microbiology},
volume = {25},
number = {},
pages = {40-48},
doi = {10.1016/j.mib.2015.04.001},
pmid = {25932531},
issn = {1879-0364},
mesh = {Archaea/*virology ; Archaeal Viruses/*genetics/physiology ; Bacteria/*virology ; Capsid Proteins/genetics ; DNA, Viral/genetics ; Eukaryota/*virology ; Genome, Viral ; *Salinity ; Virion/physiology ; },
abstract = {Hypersaline environments up to near saturation are rich reservoirs of extremophilic viruses. One milliliter of salt water may contain up to 10(9) viruses which can also be trapped inside salt crystals. To date, most of the ∼100 known halovirus isolates infect extremely halophilic archaea, although a few bacterial and eukaryotic viruses have also been described. These isolates comprise tailed and tailless icosahedral, pleomorphic, and lemon-shaped viruses which have been classified according to features such as host range, genome type, and replication. Recent studies have revealed that viruses can be grouped into a few structure-based viral lineages derived from a common ancestor based on conserved virion architectural principles and the major capsid protein fold.},
}
@article {pmid25928466,
year = {2015},
author = {Takeuchi, N and Cordero, OX and Koonin, EV and Kaneko, K},
title = {Gene-specific selective sweeps in bacteria and archaea caused by negative frequency-dependent selection.},
journal = {BMC biology},
volume = {13},
number = {},
pages = {20},
pmid = {25928466},
issn = {1741-7007},
support = {//Intramural NIH HHS/United States ; },
mesh = {Archaea/*genetics ; Bacteria/*genetics ; Clone Cells ; Computer Simulation ; *Genes, Archaeal ; *Genes, Bacterial ; Host-Parasite Interactions/genetics ; Models, Genetic ; Recombination, Genetic ; *Selection, Genetic ; },
abstract = {BACKGROUND: Fixation of beneficial genes in bacteria and archaea (collectively, prokaryotes) is often believed to erase pre-existing genomic diversity through the hitchhiking effect, a phenomenon known as genome-wide selective sweep. Recent studies, however, indicate that beneficial genes spread through a prokaryotic population via recombination without causing genome-wide selective sweeps. These gene-specific selective sweeps seem to be at odds with the existing estimates of recombination rates in prokaryotes, which appear far too low to explain such phenomena.<br><br>RESULTS: We use mathematical modeling to investigate potential solutions to this apparent paradox. Most microbes in nature evolve in heterogeneous, dynamic communities, in which ecological interactions can substantially impact evolution. Here, we focus on the effect of negative frequency-dependent selection (NFDS) such as caused by viral predation (kill-the-winner dynamics). The NFDS maintains multiple genotypes within a population, so that a gene beneficial to every individual would have to spread via recombination, hence a gene-specific selective sweep. However, gene loci affected by NFDS often are located in variable regions of microbial genomes that contain genes involved in the mobility of selfish genetic elements, such as integrases or transposases. Thus, the NFDS-affected loci are likely to experience elevated rates of recombination compared with the other loci. Consequently, these loci might be effectively unlinked from the rest of the genome, so that NFDS would be unable to prevent genome-wide selective sweeps. To address this problem, we analyzed population genetic models of selective sweeps in prokaryotes under NFDS. The results indicate that NFDS can cause gene-specific selective sweeps despite the effect of locally elevated recombination rates, provided NFDS affects more than one locus and the basal rate of recombination is sufficiently low. Although these conditions might seem to contradict the intuition that gene-specific selective sweeps require high recombination rates, they actually decrease the effective rate of recombination at loci affected by NFDS relative to the per-locus basal level, so that NFDS can cause gene-specific selective sweeps.<br><br>CONCLUSION: Because many free-living prokaryotes are likely to evolve under NFDS caused by ubiquitous viruses, gene-specific selective sweeps driven by NFDS are expected to be a major, general phenomenon in prokaryotic populations.},
}
@article {pmid25924080,
year = {2015},
author = {Tucker, YT and Kotcon, J and Mroz, T},
title = {Methanogenic archaea in marcellus shale: a possible mechanism for enhanced gas recovery in unconventional shale resources.},
journal = {Environmental science &amp; technology},
volume = {49},
number = {11},
pages = {7048-7055},
doi = {10.1021/acs.est.5b00765},
pmid = {25924080},
issn = {1520-5851},
mesh = {Archaea/genetics/growth &amp; development/*metabolism ; Geologic Sediments/*microbiology ; Metagenomics ; Methane/*metabolism ; Natural Gas/*analysis ; *Oil and Gas Fields ; Quality Control ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; },
abstract = {Marcellus Shale occurs at depths of 1.5-2.5 km (5000 to 8000 feet) where most geologists generally assume that thermogenic processes are the only source of natural gas. However, methanogens in produced fluids and isotopic signatures of biogenic methane in this deep shale have recently been discovered. This study explores whether those methanogens are indigenous to the shale or are introduced during drilling and hydraulic fracturing. DNA was extracted from Marcellus Shale core samples, preinjected fluids, and produced fluids and was analyzed using Miseq sequencing of 16s rRNA genes. Methanogens present in shale cores were similar to methanogens in produced fluids. No methanogens were detected in injected fluids, suggesting that this is an unlikely source and that they may be native to the shale itself. Bench-top methane production tests of shale core and produced fluids suggest that these organisms are alive and active under simulated reservoir conditions. Growth conditions designed to simulate the hydrofracture processes indicated somewhat increased methane production; however, fluids alone produced relatively little methane. Together, these results suggest that some biogenic methane may be produced in these wells and that hydrofracture fluids currently used to stimulate gas recovery could stimulate methanogens and their rate of producing methane.},
}
@article {pmid25923659,
year = {2015},
author = {Dawson, KS and Osburn, MR and Sessions, AL and Orphan, VJ},
title = {Metabolic associations with archaea drive shifts in hydrogen isotope fractionation in sulfate-reducing bacterial lipids in cocultures and methane seeps.},
journal = {Geobiology},
volume = {13},
number = {5},
pages = {462-477},
doi = {10.1111/gbi.12140},
pmid = {25923659},
issn = {1472-4669},
mesh = {Deltaproteobacteria/growth &amp; development/*metabolism ; Deuterium/*analysis ; Hydrogen/*analysis ; *Lipid Metabolism ; Lipids/*chemistry ; Methanosarcina/growth &amp; development/*metabolism ; *Microbial Consortia ; Oregon ; Seawater/microbiology ; },
abstract = {Correlation between hydrogen isotope fractionation in fatty acids and carbon metabolism in pure cultures of bacteria indicates the potential of biomarker D/H analysis as a tool for diagnosing carbon substrate usage in environmental samples. However, most environments, in particular anaerobic habitats, are built from metabolic networks of micro-organisms rather than a single organism. The effect of these networks on D/H of lipids has not been explored and may complicate the interpretation of these analyses. Syntrophy represents an extreme example of metabolic interdependence. Here, we analyzed the effect of metabolic interactions on the D/H biosignatures of sulfate-reducing bacteria (SRB) using both laboratory maintained cocultures of the methanogen Methanosarcina acetivorans and the SRB Desulfococcus multivorans in addition to environmental samples harboring uncultured syntrophic consortia of anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing Deltaproteobacteria (SRB) recovered from deep-sea methane seeps. Consistent with previously reported trends, we observed a ~80‰ range in hydrogen isotope fractionation (ε(lipid-water)) for D. multivorans grown under different carbon assimilation conditions, with more D-enriched values associated with heterotrophic growth. In contrast, for cocultures of D. multivorans with M. acetivorans, we observed a reduced range of ε(lipid-water) values (~36‰) across substrates with shifts of up to 61‰ compared to monocultures. Sediment cores from methane seep settings in Hydrate Ridge (offshore Oregon, USA) showed similar D-enrichment in diagnostic SRB fatty acids coinciding with peaks in ANME/SRB consortia concentration suggesting that metabolic associations are connected to the observed shifts in ε(lipid-water) values.},
}
@article {pmid25918386,
year = {2015},
author = {Bhattacharya, A and Köhrer, C and Mandal, D and RajBhandary, UL},
title = {Nonsense suppression in archaea.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {112},
number = {19},
pages = {6015-6020},
pmid = {25918386},
issn = {1091-6490},
support = {R56 GM017151/GM/NIGMS NIH HHS/United States ; GM17151/GM/NIGMS NIH HHS/United States ; R01 GM017151/GM/NIGMS NIH HHS/United States ; F32 GM017151/GM/NIGMS NIH HHS/United States ; R37 GM017151/GM/NIGMS NIH HHS/United States ; },
mesh = {Archaea/*genetics/metabolism ; Base Sequence ; Codon, Nonsense ; *Codon, Terminator ; Escherichia coli/metabolism ; Genes, Suppressor ; Haloferax volcanii/*genetics/metabolism ; Molecular Sequence Data ; Novobiocin/chemistry ; Plasmids/metabolism ; Promoter Regions, Genetic ; RNA, Transfer/*metabolism ; Serine/chemistry ; *Suppression, Genetic ; Thymidine/chemistry ; Tryptophan/chemistry ; Uracil/chemistry ; beta-Galactosidase/metabolism ; },
abstract = {Bacterial strains carrying nonsense suppressor tRNA genes played a crucial role in early work on bacterial and bacterial viral genetics. In eukaryotes as well, suppressor tRNAs have played important roles in the genetic analysis of yeast and worms. Surprisingly, little is known about genetic suppression in archaea, and there has been no characterization of suppressor tRNAs or identification of nonsense mutations in any of the archaeal genes. Here, we show, using the β-gal gene as a reporter, that amber, ochre, and opal suppressors derived from the serine and tyrosine tRNAs of the archaeon Haloferax volcanii are active in suppression of their corresponding stop codons. Using a promoter for tRNA expression regulated by tryptophan, we also show inducible and regulatable suppression of all three stop codons in H. volcanii. Additionally, transformation of a ΔpyrE2 H. volcanii strain with plasmids carrying the genes for a pyrE2 amber mutant and the serine amber suppressor tRNA yielded transformants that grow on agar plates lacking uracil. Thus, an auxotrophic amber mutation in the pyrE2 gene can be complemented by expression of the amber suppressor tRNA. These results pave the way for generating archaeal strains carrying inducible suppressor tRNA genes on the chromosome and their use in archaeal and archaeviral genetics. We also provide possible explanations for why suppressor tRNAs have not been identified in archaea.},
}
@article {pmid25911472,
year = {2015},
author = {Najjari, A and Elshahed, MS and Cherif, A and Youssef, NH},
title = {Patterns and determinants of halophilic archaea (class halobacteria) diversity in tunisian endorheic salt lakes and sebkhet systems.},
journal = {Applied and environmental microbiology},
volume = {81},
number = {13},
pages = {4432-4441},
pmid = {25911472},
issn = {1098-5336},
mesh = {*Biodiversity ; DNA, Archaeal/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Halobacteriales/*classification/genetics/*isolation &amp; purification ; Lakes/*microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Tunisia ; },
abstract = {We examined the diversity and community structure of members of the halophilic Archaea (class Halobacteria) in samples from central and southern Tunisian endorheic salt lakes and sebkhet (also known as sebkha) systems using targeted 16S rRNA gene diversity survey and quantitative PCR (qPCR) approaches. Twenty-three different samples from four distinct locations exhibiting a wide range of salinities (2% to 37%) and physical characteristics (water, salt crust, sediment, and biofilm) were examined. A total of 4,759 operational taxonomic units at the 0.03 (species-level) cutoff (OTU0.03s) belonging to 45 currently recognized genera were identified, with 8 to 43 genera (average, 30) identified per sample. In spite of the large number of genera detected per sample, only a limited number (i.e., 2 to 16) usually constituted the majority (≥80%) of encountered sequences. Halobacteria diversity showed a strong negative correlation to salinity (Pearson correlation coefficient = -0.92), and community structure analysis identified salinity, rather than the location or physical characteristics of the sample, as the most important factor shaping the Halobacteria community structure. The relative abundance of genera capable of biosynthesis of the compatible solute(s) trehalose or 2-sulfotrehalose decreased with increasing salinities (Pearson correlation coefficient = -0.80). Indeed, qPCR analysis demonstrated that the Halobacteria otsB (trehalose-6-phosphatase)/16S rRNA gene ratio decreases with increasing salinities (Pearson correlation coefficient = -0.87). The results highlight patterns and determinants of Halobacteria diversity at a previously unexplored ecosystem and indicate that genera lacking trehalose biosynthetic capabilities are more adapted to growth in and colonization of hypersaline (>25% salt) ecosystems than trehalose producers.},
}
@article {pmid25907112,
year = {2015},
author = {Bang, C and Schmitz, RA},
title = {Archaea associated with human surfaces: not to be underestimated.},
journal = {FEMS microbiology reviews},
volume = {39},
number = {5},
pages = {631-648},
doi = {10.1093/femsre/fuv010},
pmid = {25907112},
issn = {1574-6976},
mesh = {Archaea/classification/immunology/*physiology ; Humans ; Immune System/immunology/*microbiology ; Intestines/microbiology ; *Microbiota ; },
abstract = {Over 40 years ago, Carl Woese and his colleagues discovered the existence of two distinctly different groups of prokaryotes-Bacteria and Archaea. In the meantime, extensive research revealed that several hundred of bacterial species are intensely associated with humans' health and disease. Archaea, originally identified and described to occur mainly in extreme environments, have been shown to be ubiquitous and to appear frequently and in high numbers as part of human microbiota in recent years. Despite the improvement in methodologies leading to increased detection, archaea are often still not considered in many studies focusing on the interdependency between members of the microbiota and components of the human immune system. As a consequence, the knowledge on functional role(s) of archaeal species within the human body is mainly limited to their contribution to nutrient degradation in the intestine, and evidence for immunogenic properties of archaea as part of the human microbiota is generally rare. In this review, the current knowledge of human mucosa-associated archaeal species, their interaction with the human immune system and their potential contribution to humans' health and disease will be discussed.},
}
@article {pmid25884952,
year = {2015},
author = {Xiao, D and Peng, SP and Wang, EY},
title = {Fermentation enhancement of methanogenic archaea consortia from an Illinois basin coalbed via DOL emulsion nutrition.},
journal = {PloS one},
volume = {10},
number = {4},
pages = {e0124386},
pmid = {25884952},
issn = {1932-6203},
mesh = {Archaea/*metabolism ; *Coal ; Culture Media ; Emulsions ; *Fermentation ; Hydrogen-Ion Concentration ; Illinois ; Methane/*metabolism ; },
abstract = {Microbially enhanced coalbed methane technology must be used to increase the methane content in mining and generate secondary biogenic gas. In this technology, the metabolic processes of methanogenic consortia are the basis for the production of biomethane from some of the organic compounds in coal. Thus, culture nutrition plays an important role in remediating the nutritional deficiency of a coal seam. To enhance the methane production rates for microorganism consortia, different types of nutrition solutions were examined in this study. Emulsion nutrition solutions containing a novel nutritional supplement, called dystrophy optional modification latex, increased the methane yield for methanogenic consortia. This new nutritional supplement can help methanogenic consortia form an enhanced anaerobic environment, optimize the microbial balance in the consortia, and improve the methane biosynthesis rate.},
}
@article {pmid25881705,
year = {2015},
author = {Wang, XL and Jiang, C and Liu, JH and Liu, XP},
title = {[An efficient genetic knockout system based on linear DNA fragment homologous recombination for halophilic archaea].},
journal = {Yi chuan = Hereditas},
volume = {37},
number = {4},
pages = {388-395},
doi = {10.16288/j.yczz.14-366},
pmid = {25881705},
issn = {0253-9772},
mesh = {DNA, Archaeal/*genetics ; Gene Deletion ; Gene Knockout Techniques/*methods ; Haloferax volcanii/*genetics ; *Homologous Recombination ; Plasmids/genetics ; },
abstract = {With the development of functional genomics, gene-knockout is becoming an important tool to elucidate gene functions in vivo. As a good model strain for archaeal genetics, Haloferax volcanii has received more attention. Although several genetic manipulation systems have been developed for some halophilic archaea, it is time-consuming because of the low percentage of positive clones during the second-recombination selection. These classical gene knockout methods are based on DNA recombination between the genomic homologous sequence and the circular suicide plasmid, which carries a pyrE selection marker and two DNA fragments homologous to the upstream and downstream fragments of the target gene. Many wild-type clones are obtained through a reverse recombination between the plasmid and genome in the classic gene knockout method. Therefore, it is necessary to develop an efficient gene knockout system to increase the positive clone percentage. Here we report an improved gene knockout method using a linear DNA cassette consisting of upstream and downstream homologous fragments, and the pyrE marker. Gene deletions were subsequently detected by colony PCR analysis. We determined the efficiency of our knockout method by deleting the xpb2 gene from the H. volcanii genome, with the percentage of positive clones higher than 50%. Our method provides an efficient gene knockout strategy for halophilic archaea.},
}
@article {pmid25862354,
year = {2015},
author = {Shi, Y and TaPa, M and Li, C and Yang, H and Zhang, T and Gao, Y and Sun, J and Zeng, J and Lin, Q and Cao, Z and OuTi, K and Li, Y and Lou, K},
title = {Diversity and space-time dynamics of endophytic archaea from sugar beet in the north slope of Tianshan Mountain revealed by 454 pyrosequencing and T-RFLP.},
journal = {World journal of microbiology &amp; biotechnology},
volume = {31},
number = {7},
pages = {1031-1039},
pmid = {25862354},
issn = {1573-0972},
mesh = {Archaea/*classification/genetics ; Beta vulgaris/*growth &amp; development/microbiology ; China ; Cluster Analysis ; DNA, Ribosomal/analysis ; Endophytes/*classification/genetics ; Genes, Archaeal ; High-Throughput Nucleotide Sequencing/methods ; *Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/analysis ; Sequence Analysis, DNA/methods ; },
abstract = {Plants harbor complex and variable microbial communities. Using molecular-based techniques targeting the 16S rRNA gene, we studied the developmental stages and geographical location diversity of endophytic archaea in two locations (Shihezi and Changji) and four periods (the seedling growth, rosette formation, tuber growth and sucrose accumulation sampling periods) in the north slope of Tianshan Mountain, China. Community structure of mixed sample from 60 sugar beet plants was examined using PCR-based 454 pyrosequencing and terminal restriction fragment length polymorphism (T-RFLP). In total, 5290 archaea 16S rRNA sequences were obtained from all sugar beet samples. The most abundant archaea groups in all sugar beet were Methanococci, the miscellaneous Crenarchaeotic Group and Thermoplasmata. There was a marked difference in diversity of endophytic archaea in sugar beet for different growth periods. The greatest number of Operational T-RFLP Units (OTUs) was detected during sucrose accumulation (298) and rosette formation (282). Endophytic archaea diversity was reduced during seedling growth (128 OTUs) and tuber growth (55 OTUs). Nine OTUs were common to all four periods of growth. There were more OTUs in Shihezi than in Changji. Clustering analysis and principal component analysis of T-RFLP data revealed distinct shifts in endophytic archaea community profiles that corresponded to plant growth stage rather than geographical location. The dynamics of endophytic archaea communities were influenced by plant growth stage. To our knowledge, this is the first report that archaea has been identified as endophytes associated with sugar beet by the culture-independent approach. The results suggest that the diversity of endophytic archaea is abundant in sugar beet.},
}
@article {pmid25856307,
year = {2015},
author = {Gutiérrez, MH and Galand, PE and Moffat, C and Pantoja, S},
title = {Melting glacier impacts community structure of Bacteria, Archaea and Fungi in a Chilean Patagonia fjord.},
journal = {Environmental microbiology},
volume = {17},
number = {10},
pages = {3882-3897},
doi = {10.1111/1462-2920.12872},
pmid = {25856307},
issn = {1462-2920},
mesh = {Archaea/*classification ; Bacteria/*classification ; Base Sequence ; Chile ; Climate Change ; Ecosystem ; Estuaries ; Fresh Water/*microbiology ; Fungi/*classification ; Ice Cover/*microbiology ; Microbiota/*genetics ; Molecular Sequence Data ; Proteobacteria ; RNA, Ribosomal, 16S/genetics ; Seasons ; Sequence Analysis, DNA ; },
abstract = {Jorge Montt glacier, located in the Patagonian Ice Fields, has undergone an unprecedented retreat during the past century. To study the impact of the meltwater discharge on the microbial community of the downstream fjord, we targeted Bacteria, Archaea and Fungi communities during austral autumn and winter. Our results showed a singular microbial community present in cold and low salinity surface waters during autumn, when a thicker meltwater layer was observed. Meltwater bacterial sequences were related to Cyanobacteria, Proteobacteria, Actinobacteria and Bacteriodetes previously identified in freshwater and cold ecosystems, suggesting the occurrence of microorganisms adapted to live in the extreme conditions of meltwater. For Fungi, representative sequences related to terrestrial and airborne fungal taxa indicated transport of allochthonous Fungi by the meltwater discharge. In contrast, bottom fjord waters from autumn and winter showed representative Operational Taxonomic Units (OTUs) related to sequences of marine microorganisms, which is consistent with current models of fjord circulation. We conclude that meltwater can significantly modify the structure of microbial communities and support the development of a major fraction of microorganisms in surface waters of Patagonian fjords.},
}
@article {pmid25852668,
year = {2015},
author = {Schirmack, J and Alawi, M and Wagner, D},
title = {Influence of Martian regolith analogs on the activity and growth of methanogenic archaea, with special regard to long-term desiccation.},
journal = {Frontiers in microbiology},
volume = {6},
number = {},
pages = {210},
pmid = {25852668},
issn = {1664-302X},
abstract = {Methanogenic archaea have been studied as model organisms for possible life on Mars for several reasons: they can grow lithoautotrophically by using hydrogen and carbon dioxide as energy and carbon sources, respectively; they are anaerobes; and they evolved at a time when conditions on early Earth are believed to have looked similar to those of early Mars. As Mars is currently dry and cold and as water might be available only at certain time intervals, any organism living on this planet would need to cope with desiccation. On Earth there are several regions with low water availability as well, e.g., permafrost environments, desert soils, and salt pans. Here, we present the results of a set of experiments investigating the influence of different Martian regolith analogs (MRAs) on the metabolic activity and growth of three methanogenic strains exposed to culture conditions as well as long-term desiccation. In most cases, concentrations below 1 wt% of regolith in the media resulted in an increase of methane production rates, whereas higher concentrations decreased the rates, thus prolonging the lag phase. Further experiments showed that methanogenic archaea are capable of producing methane when incubated on a water-saturated sedimentary matrix of regolith lacking nutrients. Survival of methanogens under these conditions was analyzed with a 400 day desiccation experiment in the presence of regolith analogs. All tested strains of methanogens survived the desiccation period as it was determined through reincubation on fresh medium and via qPCR following propidium monoazide treatment to identify viable cells. The survival of long-term desiccation and the ability of active metabolism on water-saturated MRAs strengthens the possibility of methanogenic archaea or physiologically similar organisms to exist in environmental niches on Mars. The best results were achieved in presence of a phyllosilicate, which provides insights of possible positive effects in habitats on Earth as well.},
}
@article {pmid25830311,
year = {2015},
author = {Huynh, HT and Pignoly, M and Nkamga, VD and Drancourt, M and Aboudharam, G},
title = {The repertoire of archaea cultivated from severe periodontitis.},
journal = {PloS one},
volume = {10},
number = {4},
pages = {e0121565},
pmid = {25830311},
issn = {1932-6203},
mesh = {Adult ; Aged ; Case-Control Studies ; DNA, Archaeal/genetics ; Dental Plaque/microbiology ; Female ; Humans ; Male ; Methanobrevibacter/*genetics/isolation &amp; purification ; Middle Aged ; Molecular Sequence Data ; Molecular Typing ; Periodontitis/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Young Adult ; },
abstract = {In previous studies, the abundance and diversity of methanogenic archaea in the dental microbiota have been analysed by the detection of specific DNA sequences by PCR-based investigations and metagenomic studies. Few data issued regarding methanogens actually living in dental plaque. We collected dental plaque specimens in 15 control individuals and 65 periodontitis patients. Dental plaque specimens were cultured in an anoxic liquid medium for methanogens in the presence of negative control tubes. Dental plaque methanogens were cultured from 1/15 (6.67%) control and 36/65 (55.38%) periodontitis patient samples (p<0.001). The cultures yielded Methanobrevibacter oralis in one control and thirty-one patients, Methanobrevibacter smithii in two patients and a potential new species named Methanobrevibacter sp. strain N13 in three patients with severe periodontitis. Our observations of living methanogens, strengthen previous observations made on DNA-based studies regarding the role of methanogens, in periodontitis.},
}
@article {pmid25829260,
year = {2015},
author = {Cerletti, M and Paggi, RA and Guevara, CR and Poetsch, A and De Castro, RE},
title = {Global role of the membrane protease LonB in Archaea: Potential protease targets revealed by quantitative proteome analysis of a lonB mutant in Haloferax volcanii.},
journal = {Journal of proteomics},
volume = {121},
number = {},
pages = {1-14},
doi = {10.1016/j.jprot.2015.03.016},
pmid = {25829260},
issn = {1876-7737},
mesh = {Amino Acids/chemistry ; Archaeal Proteins/*metabolism ; Carotenoids/chemistry ; Cell Membrane/metabolism ; Cytoplasm/metabolism ; Electrophoresis, Polyacrylamide Gel ; Haloferax volcanii/*enzymology ; Lipid Metabolism ; Membrane Proteins/*metabolism ; Mutation ; Peptide Hydrolases/*metabolism ; Proteome/*metabolism ; Proteomics ; Spectrometry, Mass, Electrospray Ionization ; },
abstract = {UNLABELLED: The membrane-associated LonB protease is essential for viability in Haloferax volcanii, however, the cellular processes affected by this protease in archaea are unknown. In this study, the impact of a lon conditional mutation (down-regulation) on H. volcanii physiology was examined by comparing proteomes of parental and mutant cells using shotgun proteomics. A total of 1778 proteins were identified (44% of H. volcanii predicted proteome) and 142 changed significantly in amount (≥2 fold). Of these, 66 were augmented in response to Lon deficiency suggesting they could be Lon substrates. The "Lon subproteome" included soluble and predicted membrane proteins expected to participate in diverse cellular processes. The dramatic stabilization of phytoene synthase (57 fold) in concert with overpigmentation of lon mutant cells suggests that Lon controls carotenogenesis in H. volcanii. Several hypothetical proteins, which may reveal novel functions and/or be involved in adaptation to extreme environments, were notably increased (300 fold). This study, which represents the first proteome examination of a Lon deficient archaeal cell, shows that Lon has a strong impact on H. volcanii physiology evidencing the cellular processes controlled by this protease in Archaea. Additionally, this work provides a platform for the discovery of novel targets of Lon proteases.<br><br>BIOLOGICAL SIGNIFICANCE: The proteome of a Lon-deficient archaeal cell was examined for the first time showing that Lon has a strong impact on H. volcanii physiology and evidencing the proteins and cellular processes controlled by this protease in Archaea. This work will facilitate future investigations aiming to address Lon function in archaea and provides a platform for the discovery of endogenous targets of the archaeal-type Lon as well as novel targets/processes regulated by Lon proteases. This knowledge will advance the understanding on archaeal physiology and the biological function of membrane proteases in microorganisms.},
}
@article {pmid25822915,
year = {2015},
author = {Aono, R and Sato, T and Imanaka, T and Atomi, H},
title = {A pentose bisphosphate pathway for nucleoside degradation in Archaea.},
journal = {Nature chemical biology},
volume = {11},
number = {5},
pages = {355-360},
pmid = {25822915},
issn = {1552-4469},
mesh = {Adenosine Diphosphate/metabolism ; Adenosine Triphosphate/metabolism ; Aldose-Ketose Isomerases/drug effects/metabolism ; Archaea/*metabolism ; Archaeal Proteins/drug effects/metabolism ; Escherichia coli/genetics ; Genetic Vectors ; Nucleosides/*metabolism ; Pentose Phosphate Pathway/genetics/*physiology ; Pentosephosphates/metabolism ; Plasmids/genetics ; *Ribulose-Bisphosphate Carboxylase ; Thermococcus/genetics/*metabolism ; Uridine Kinase/metabolism ; },
abstract = {Owing to the absence of the pentose phosphate pathway, the degradation pathway for the ribose moieties of nucleosides is unknown in Archaea. Here, in the archaeon Thermococcus kodakarensis, we identified a metabolic network that links the pentose moieties of nucleosides or nucleotides to central carbon metabolism. The network consists of three nucleoside phosphorylases, an ADP-dependent ribose-1-phosphate kinase and two enzymes of a previously identified NMP degradation pathway, ribose-1,5-bisphosphate isomerase and type III ribulose-1,5-bisphosphate carboxylase/oxygenase. Ribose 1,5-bisphosphate and ribulose 1,5-bisphosphate are intermediates of this pathway, which is thus designated the pentose bisphosphate pathway.},
}
@article {pmid25820379,
year = {2015},
author = {Boyd, ES},
title = {Archaea on the move.},
journal = {Environmental microbiology reports},
volume = {7},
number = {3},
pages = {385-387},
doi = {10.1111/1758-2229.12281},
pmid = {25820379},
issn = {1758-2229},
mesh = {Archaea/genetics/*physiology ; Gene Regulatory Networks ; *Locomotion ; },
}
@article {pmid25806405,
year = {2015},
author = {Gomes-Filho, JV and Zaramela, LS and Italiani, VC and Baliga, NS and Vêncio, RZ and Koide, T},
title = {Sense overlapping transcripts in IS1341-type transposase genes are functional non-coding RNAs in archaea.},
journal = {RNA biology},
volume = {12},
number = {5},
pages = {490-500},
pmid = {25806405},
issn = {1555-8584},
mesh = {Base Sequence ; Gene Expression Profiling ; *Genes, Archaeal ; Halobacterium salinarum/*genetics/growth &amp; development ; Molecular Sequence Data ; Nucleotide Motifs/genetics ; RNA, Messenger/genetics/metabolism ; RNA, Untranslated/*genetics ; Retroelements/genetics ; Transposases/*genetics ; },
abstract = {The existence of sense overlapping transcripts that share regulatory and coding information in the same genomic sequence shows an additional level of prokaryotic gene expression complexity. Here we report the discovery of ncRNAs associated with IS1341-type transposase (tnpB) genes, at the 3'-end of such elements, with examples in archaea and bacteria. Focusing on the model haloarchaeon Halobacterium salinarum NRC-1, we show the existence of sense overlapping transcripts (sotRNAs) for all its IS1341-type transposases. Publicly available transcriptome compendium show condition-dependent differential regulation between sotRNAs and their cognate genes. These sotRNAs allowed us to find a UUCA tetraloop motif that is present in other archaea (ncRNA family HgcC) and in a H. salinarum intergenic ncRNA derived from a palindrome associated transposable elements (PATE). Overexpression of one sotRNA and the PATE-derived RNA harboring the tetraloop motif improved H. salinarum growth, indicating that these ncRNAs are functional.},
}
@article {pmid25798780,
year = {2015},
author = {Paul, BG and Bagby, SC and Czornyj, E and Arambula, D and Handa, S and Sczyrba, A and Ghosh, P and Miller, JF and Valentine, DL},
title = {Targeted diversity generation by intraterrestrial archaea and archaeal viruses.},
journal = {Nature communications},
volume = {6},
number = {},
pages = {6585},
pmid = {25798780},
issn = {2041-1723},
support = {R01 AI096838/AI/NIAID NIH HHS/United States ; R01 AI069838/AI/NIAID NIH HHS/United States ; },
mesh = {Archaea/virology ; Archaeal Proteins/*genetics ; Archaeal Viruses/*genetics ; Base Sequence ; *Genetic Variation ; Metagenome/*genetics ; Molecular Sequence Data ; Mutation Rate ; Nanoarchaeota/*genetics/virology ; Retroelements ; },
abstract = {In the evolutionary arms race between microbes, their parasites, and their neighbours, the capacity for rapid protein diversification is a potent weapon. Diversity-generating retroelements (DGRs) use mutagenic reverse transcription and retrohoming to generate myriad variants of a target gene. Originally discovered in pathogens, these retroelements have been identified in bacteria and their viruses, but never in archaea. Here we report the discovery of intact DGRs in two distinct intraterrestrial archaeal systems: a novel virus that appears to infect archaea in the marine subsurface, and, separately, two uncultivated nanoarchaea from the terrestrial subsurface. The viral DGR system targets putative tail fibre ligand-binding domains, potentially generating >10(18) protein variants. The two single-cell nanoarchaeal genomes each possess ≥4 distinct DGRs. Against an expected background of low genome-wide mutation rates, these results demonstrate a previously unsuspected potential for rapid, targeted sequence diversification in intraterrestrial archaea and their viruses.},
}
@article {pmid25797330,
year = {2015},
author = {Zhang, Y and Chen, L and Dai, T and Sun, R and Wen, D},
title = {Ammonia manipulates the ammonia-oxidizing archaea and bacteria in the coastal sediment-water microcosms.},
journal = {Applied microbiology and biotechnology},
volume = {99},
number = {15},
pages = {6481-6491},
doi = {10.1007/s00253-015-6524-2},
pmid = {25797330},
issn = {1432-0614},
mesh = {Ammonia/*metabolism ; Archaea/*growth &amp; development/metabolism ; Bacteria/*growth &amp; development/metabolism ; *Biota ; DNA, Archaeal/chemistry/genetics ; DNA, Bacterial/chemistry/genetics ; Geologic Sediments/*microbiology ; Isotope Labeling ; Models, Theoretical ; Molecular Sequence Data ; Oxidation-Reduction ; Oxidoreductases/genetics ; Phylogeny ; Seawater/*chemistry ; Sequence Analysis, DNA ; },
abstract = {Ammonia was observed as a potential significant factor to manipulate the abundance and activity of ammonia-oxidizing microorganisms (AOMs) in water environments. For the first time, this study confirmed this phenomenon by laboratory cultivation. In a series of estuarine sediment-coastal water microcosms, we investigated the AOM's phylogenetic composition and activity change in response to ammonia concentration. Increase of ammonia concentration promoted bacterial amoA gene abundance in a linear pattern. The ratio of transcribed ammonia-oxidizing bacteria (AOB) amoA gene/ammonia-oxidizing archaea (AOA) amoA gene increased from 0.1 to 43 as NH4 (+)-N increased from less than 0.1 to 12 mg L(-1), and AOA amoA transcription was undetected under 20 mg NH4 (+)-N L(-1). The incubation of stable isotope probing (SIP) microcosms revealed a faster (13)C-NaHCO3 incorporation rate of AOA amoA gene under 0.1 mg NH4 (+)-N L(-1) and a sole (13)C-NaHCO3 utilization of the AOB amoA gene under 20 mg NH4 (+)-N L(-1). Our results indicate that ammonia concentration manipulates the structure of AOM. AOA prefers to live and perform higher amoA transcription activity than AOB in ammonia-limited water environments, and AOB tends to take the first contributor place in ammonia-rich ones.},
}
@article {pmid25797107,
year = {2015},
author = {Horz, HP and Robertz, N and Vianna, ME and Henne, K and Conrads, G},
title = {Relationship between methanogenic archaea and subgingival microbial complexes in human periodontitis.},
journal = {Anaerobe},
volume = {35},
number = {Pt A},
pages = {10-12},
doi = {10.1016/j.anaerobe.2015.02.008},
pmid = {25797107},
issn = {1095-8274},
mesh = {Adult ; Aged ; Aged, 80 and over ; Archaea/classification/genetics/isolation &amp; purification/*metabolism ; Bacterial Infections/*microbiology ; Biodiversity ; Female ; Humans ; Male ; Methane/*metabolism ; Middle Aged ; Periodontitis/*microbiology ; Prevotella intermedia/isolation &amp; purification/physiology ; },
abstract = {We compared the amounts of methanogenic archaea with ten of the most important periodontal pathogens in 125 clinical samples. Correlation analysis suggests that the support of the periodontitis-associated bacterial consortium by methanogenic archaea may be driven through direct or indirect interactions with Prevotella intermedia.},
}
@article {pmid25797103,
year = {2015},
author = {Wu, H and Meng, Q and Yu, Z},
title = {Effect of pH buffering capacity and sources of dietary sulfur on rumen fermentation, sulfide production, methane production, sulfate reducing bacteria, and total Archaea in in vitro rumen cultures.},
journal = {Bioresource technology},
volume = {186},
number = {},
pages = {25-33},
doi = {10.1016/j.biortech.2015.02.110},
pmid = {25797103},
issn = {1873-2976},
mesh = {Ammonia/metabolism ; Animals ; Archaea/*metabolism ; Buffers ; Diet/methods ; Fermentation/*physiology ; Hydrogen-Ion Concentration ; Methane/*metabolism ; Rumen/*metabolism/microbiology ; Sulfates/*metabolism ; Sulfides/*metabolism ; Sulfur/*metabolism ; },
abstract = {The effects of three types of dietary sulfur on in vitro fermentation characteristics, sulfide production, methane production, and microbial populations at two different buffer capacities were examined using in vitro rumen cultures. Addition of dry distilled grain with soluble (DDGS) generally decreased total gas production, degradation of dry matter and neutral detergent fiber, and concentration of total volatile fatty acids, while increasing ammonia concentration. High buffering capacity alleviated these adverse effects on fermentation. Increased sulfur content resulted in decreased methane emission, but total Archaea population was not changed significantly. The population of sulfate reducing bacteria was increased in a sulfur type-dependent manner. These results suggest that types of dietary sulfur and buffering capacity can affect rumen fermentation and sulfide production. Diet buffering capacity, and probably alkalinity, may be increased to alleviate some of the adverse effects associated with feeding DDGS at high levels.},
}
@article {pmid25794363,
year = {2015},
author = {, },
title = {Correction: a bioenergetic basis for membrane divergence in archaea and bacteria.},
journal = {PLoS biology},
volume = {13},
number = {3},
pages = {e1002102},
pmid = {25794363},
issn = {1545-7885},
}
@article {pmid25792437,
year = {2015},
author = {Aydin, S and Ince, B and Ince, O},
title = {Application of real-time PCR to determination of combined effect of antibiotics on Bacteria, Methanogenic Archaea, Archaea in anaerobic sequencing batch reactors.},
journal = {Water research},
volume = {76},
number = {},
pages = {88-98},
doi = {10.1016/j.watres.2015.02.043},
pmid = {25792437},
issn = {1879-2448},
mesh = {Anaerobiosis ; Anti-Bacterial Agents/*pharmacology ; Archaea/*drug effects/genetics ; Bacteria/*drug effects/genetics ; Bioreactors/*microbiology ; Erythromycin/pharmacology ; Euryarchaeota/drug effects/genetics ; Methane/metabolism ; Real-Time Polymerase Chain Reaction ; Sulfamethoxazole/pharmacology ; Tetracycline/pharmacology ; Waste Disposal, Fluid/*methods ; },
abstract = {This study evaluated the long-term effects of erythromycin-tetracycline-sulfamethoxazole (ETS) and sulfamethoxazole-tetracycline (ST) antibiotic combinations on the microbial community and examined the ways in which these antimicrobials impact the performance of anaerobic reactors. Quantitative real-time PCR was used to determine the effect that different antibiotic combinations had on the total and active Bacteria, Archae and Methanogenic Archae. Three primer sets that targeted metabolic genes encoding formylterahydrofolate synthetase, methyl-coenzyme M reductase and acetyl-coA synthetase were also used to determine the inhibition level on the mRNA expression of the homoacetogens, methanogens and specifically acetoclastic methanogens, respectively. These microorganisms play a vital role in the anaerobic degradation of organic waste and targeting these gene expressions offers operators or someone at a treatment plant the potential to control and the improve the anaerobic system. The results of the investigation revealed that acetogens have a competitive advantage over Archaea in the presence of ETS and ST combinations. Although the efficiency with which methane production takes place and the quantification of microbial populations in both the ETS and ST reactors decreased as antibiotic concentrations increased, the ETS batch reactor performed better than the ST batch reactor. According to the expression of genes results, the syntrophic interaction of acetogens and methanogens is critical to the performance of the ETS and ST reactors. Failure to maintain the stability of these microorganisms resulted in a decrease in the performance and stability of the anaerobic reactors.},
}
@article {pmid25789552,
year = {2015},
author = {Zuo, G and Xu, Z and Hao, B},
title = {Phylogeny and Taxonomy of Archaea: A Comparison of the Whole-Genome-Based CVTree Approach with 16S rRNA Sequence Analysis.},
journal = {Life (Basel, Switzerland)},
volume = {5},
number = {1},
pages = {949-968},
pmid = {25789552},
issn = {2075-1729},
abstract = {A tripartite comparison of Archaea phylogeny and taxonomy at and above the rank order is reported: (1) the whole-genome-based and alignment-free CVTree using 179 genomes; (2) the 16S rRNA analysis exemplified by the All-Species Living Tree with 366 archaeal sequences; and (3) the Second Edition of Bergey's Manual of Systematic Bacteriology complemented by some current literature. A high degree of agreement is reached at these ranks. From the newly proposed archaeal phyla, Korarchaeota, Thaumarchaeota, Nanoarchaeota and Aigarchaeota, to the recent suggestion to divide the class Halobacteria into three orders, all gain substantial support from CVTree. In addition, the CVTree helped to determine the taxonomic position of some newly sequenced genomes without proper lineage information. A few discrepancies between the CVTree and the 16S rRNA approaches call for further investigation.},
}
@article {pmid25786142,
year = {2015},
author = {Watanabe, S and Tanimoto, Y and Nishiwaki, H and Watanabe, Y},
title = {Identification and characterization of bifunctional proline racemase/hydroxyproline epimerase from archaea: discrimination of substrates and molecular evolution.},
journal = {PloS one},
volume = {10},
number = {3},
pages = {e0120349},
pmid = {25786142},
issn = {1932-6203},
mesh = {Amino Acid Isomerases/genetics/*metabolism ; Amino Acid Sequence ; Amino Acid Substitution ; Archaeal Proteins/genetics/*metabolism ; Biocatalysis ; Escherichia coli/genetics/metabolism ; Evolution, Molecular ; Gene Expression ; Hydroxyproline/*metabolism ; Kinetics ; Molecular Sequence Data ; Mutation ; Phylogeny ; Proline/*metabolism ; Recombinant Proteins/genetics/metabolism ; Sequence Alignment ; Sequence Homology, Amino Acid ; Stereoisomerism ; Substrate Specificity ; Thermococcus/classification/*enzymology/genetics ; },
abstract = {Proline racemase (ProR) is a member of the pyridoxal 5'-phosphate-independent racemase family, and is involved in the Stickland reaction (fermentation) in certain clostridia as well as the mechanisms underlying the escape of parasites from host immunity in eukaryotic Trypanosoma. Hydroxyproline epimerase (HypE), which is in the same protein family as ProR, catalyzes the first step of the trans-4-hydroxy-L-proline metabolism of bacteria. Their substrate specificities were previously considered to be very strict, in spite of similarities in their structures and catalytic mechanisms, and no racemase/epimerase from the ProR superfamily has been found in archaea. We here characterized the ProR-like protein (OCC_00372) from the hyperthermophilic archaeon, Thermococcus litoralis (TlProR). This protein could reversibly catalyze not only the racemization of proline, but also the epimerization of 4-hydroxyproline and 3-hydroxyproline with similar kinetic constants. Among the four (putative) ligand binding sites, one amino acid substitution was detected between TlProR (tryptophan at the position of 241) and natural ProR (phenylalanine). The W241F mutant showed a significant preference for proline over hydroxyproline, suggesting that this (hydrophobic and bulky) tryptophan residue played an importance role in the recognition of hydroxyproline (more hydrophilic and bulky than proline), and substrate specificity for hydroxyproline was evolutionarily acquired separately between natural HypE and ProR. A phylogenetic analysis indicated that such unique broad substrate specificity was derived from an ancestral enzyme of this superfamily.},
}
@article {pmid25772805,
year = {2015},
author = {Rodriguez-Corona, U and Sobol, M and Rodriguez-Zapata, LC and Hozak, P and Castano, E},
title = {Fibrillarin from Archaea to human.},
journal = {Biology of the cell},
volume = {107},
number = {6},
pages = {159-174},
doi = {10.1111/boc.201400077},
pmid = {25772805},
issn = {1768-322X},
mesh = {Animals ; Archaea/*genetics/*metabolism ; Chromosomal Proteins, Non-Histone/*genetics/*metabolism ; Humans ; Methylation ; Neoplasms/genetics/metabolism ; },
abstract = {Fibrillarin is an essential protein that is well known as a molecular marker of transcriptionally active RNA polymerase I. Fibrillarin methyltransferase activity is the primary known source of methylation for more than 100 methylated sites involved in the first steps of preribosomal processing and required for structural ribosome stability. High expression levels of fibrillarin have been observed in several types of cancer cells, particularly when p53 levels are reduced, because p53 is a direct negative regulator of fibrillarin transcription. Here, we show fibrillarin domain conservation, structure and interacting molecules in different cellular processes as well as with several viral proteins during virus infection.},
}
@article {pmid25764551,
year = {2015},
author = {Marusenko, Y and Garcia-Pichel, F and Hall, SJ},
title = {Ammonia-oxidizing archaea respond positively to inorganic nitrogen addition in desert soils.},
journal = {FEMS microbiology ecology},
volume = {91},
number = {2},
pages = {1-11},
doi = {10.1093/femsec/fiu023},
pmid = {25764551},
issn = {1574-6941},
mesh = {Ammonia/*metabolism ; Archaea/genetics/*metabolism ; Desert Climate ; Ecosystem ; Nitrogen/*metabolism ; Nitrosomonas/genetics/metabolism ; Oxidation-Reduction ; Soil ; *Soil Microbiology ; },
abstract = {In soils, nitrogen (N) addition typically enhances ammonia oxidation (AO) rates and increases the population density of ammonia-oxidizing bacteria (AOB), but not that of ammonia-oxidizing archaea (AOA). We asked if long-term inorganic N addition also has similar consequences in arid land soils, an understudied yet spatially ubiquitous ecosystem type. Using Sonoran Desert top soils from between and under shrubs within a long-term N-enrichment experiment, we determined community concentration-response kinetics of AO and measured the total and relative abundance of AOA and AOB based on amoA gene abundance. As expected, N addition increased maximum AO rates and the abundance of bacterial amoA genes compared to the controls. Surprisingly, N addition also increased the abundance of archaeal amoA genes. We did not detect any major effects of N addition on ammonia-oxidizing community composition. The ammonia-oxidizing communities in these desert soils were dominated by AOA as expected (78% of amoA gene copies were related to Nitrososphaera), but contained unusually high contributions of Nitrosomonas (18%) and unusually low numbers of Nitrosospira (2%). This study highlights unique traits of ammonia oxidizers in arid lands, which should be considered globally in predictions of AO responses to changes in N availability.},
}
@article {pmid25764468,
year = {2015},
author = {Fillol, M and Sànchez-Melsió, A and Gich, F and Borrego, CM},
title = {Diversity of Miscellaneous Crenarchaeotic Group archaea in freshwater karstic lakes and their segregation between planktonic and sediment habitats.},
journal = {FEMS microbiology ecology},
volume = {91},
number = {4},
pages = {},
doi = {10.1093/femsec/fiv020},
pmid = {25764468},
issn = {1574-6941},
mesh = {Base Sequence ; Crenarchaeota/*genetics/growth &amp; development/isolation &amp; purification ; DNA, Archaeal/genetics ; Euryarchaeota/*genetics/growth &amp; development/isolation &amp; purification ; Gene Library ; Geologic Sediments/*microbiology ; Lakes/*microbiology ; Molecular Sequence Data ; Phylogeny ; Plankton/microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; },
abstract = {The Miscellaneous Crenarchaeotic Group (MCG) is an archaeal lineage whose members are widespread and abundant in marine sediments. MCG archaea have also been consistently found in stratified euxinic lakes. In this work, we have studied archaeal communities in three karstic lakes to reveal potential habitat segregation of MCG subgroups between planktonic and sediment compartments. In the studied lakes, archaeal assemblages were strikingly similar to those of the marine subsurface with predominance of uncultured Halobacteria in the plankton and Thermoplasmata and MCG in anoxic, organic-rich sediments. Multivariate analyses identified sulphide and dissolved organic carbon as predictor variables of archaeal community composition. Quantification of MCG using a newly designed qPCR primer pair that improves coverage for MCG subgroups prevalent in the studied lakes revealed conspicuous populations in both the plankton and the sediment. Subgroups MCG-5a and -5b appear as planktonic specialists thriving in euxinic bottom waters, while subgroup MCG-6 emerges as a generalist group able to cope with varying reducing conditions. Besides, comparison of DNA- and cDNA-based pyrotag libraries revealed that rare subgroups in DNA libraries, i.e. MCG-15, were prevalent in cDNA-based datasets, suggesting that euxinic, organic-rich sediments of karstic lakes provide optimal niches for the activity of some specialized MCG subgroups.},
}
@article {pmid25749160,
year = {2014},
author = {Syutkin, AS and Pyatibratov, MG and Fedorov, OV},
title = {Flagella of halophilic archaea: differences in supramolecular organization.},
journal = {Biochemistry. Biokhimiia},
volume = {79},
number = {13},
pages = {1470-1482},
doi = {10.1134/S0006297914130033},
pmid = {25749160},
issn = {1608-3040},
mesh = {Archaea/physiology/*ultrastructure ; Archaeal Proteins/*chemistry/genetics/metabolism ; Flagella/physiology/*ultrastructure ; Flagellin/*chemistry/genetics/metabolism ; },
abstract = {Archaeal flagella are similar functionally to bacterial flagella, but structurally they are completely different. Helical archaeal flagellar filaments are formed of protein subunits called flagellins (archaellins). Notwithstanding progress in studies of archaeal flagella achieved in recent years, many problems in this area are still unsolved. In this review, we analyze the formation of these supramolecular structures by the example of flagellar filaments of halophilic archaea. Recent data on the structure of the flagellar filaments demonstrate that their supramolecular organization differs considerably in different haloarchaeal species.},
}
@article {pmid25747618,
year = {2015},
author = {Rosselló-Móra, R and Amann, R},
title = {Past and future species definitions for Bacteria and Archaea.},
journal = {Systematic and applied microbiology},
volume = {38},
number = {4},
pages = {209-216},
doi = {10.1016/j.syapm.2015.02.001},
pmid = {25747618},
issn = {1618-0984},
mesh = {Archaea/*classification/genetics ; Bacteria/*classification/genetics ; Genome, Archaeal/genetics ; Genome, Bacterial/genetics ; *Genomics ; *Sequence Analysis, DNA ; },
abstract = {Species is the basic unit of biological diversity. However, among the different microbiological disciplines there is an important degree of disagreement as to what this unit may be. In this minireview, we argue that the main point of disagreement is the definition (i.e. the way species are circumscribed by means of observable characters) rather than the concept (i.e. the idea of what a species may be as a unit of biodiversity, the meaning of the patterns of recurrence observed in nature, and the why of their existence). Taxonomists have defined species by means of genetic and expressed characters that ensure the members of the unit are monophyletic, and exhibit a large degree of genomic and phenotypic coherence. The new technologies allowing high-throughput data acquisition are expected to improve future classifications significantly and will lead to database-based taxonomy centered on portable and interactive data. Future species descriptions of Bacteria and Archaea should include a high quality genome sequence of at least the type strain as an obligatory requirement, just as today an almost full-length 16S rRNA gene sequence must be provided. Serious efforts are needed in order to re-evaluate the major guidelines for standard descriptions.},
}
@article {pmid25744648,
year = {2015},
author = {Li, H and Weng, BS and Huang, FY and Su, JQ and Yang, XR},
title = {pH regulates ammonia-oxidizing bacteria and archaea in paddy soils in Southern China.},
journal = {Applied microbiology and biotechnology},
volume = {99},
number = {14},
pages = {6113-6123},
doi = {10.1007/s00253-015-6488-2},
pmid = {25744648},
issn = {1432-0614},
mesh = {Ammonia/*metabolism ; Archaea/*classification/enzymology/genetics/metabolism ; Betaproteobacteria/*classification/enzymology/genetics/metabolism ; Biota/*drug effects ; China ; Cloning, Molecular ; Cluster Analysis ; Genetic Variation ; Hydrogen-Ion Concentration ; Molecular Sequence Data ; Nitrification ; Oxidation-Reduction ; Oxidoreductases/genetics ; Phylogeny ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Soil/*chemistry ; *Soil Microbiology ; },
abstract = {Ammonia-oxidizing archaea (AOA) and bacteria (AOB) play important roles in nitrogen cycling. However, the effects of environmental factors on the activity, abundance, and diversity of AOA and AOB and the relative contributions of these two groups to nitrification in paddy soils are not well explained. In this study, potential nitrification activity (PNA), abundance, and diversity of amoA genes from 12 paddy soils in Southern China were determined by potential nitrification assay, quantitative PCR, and cloning. The results showed that PNA was highly variable between paddy soils, ranging from 4.05 ± 0.21 to 9.81 ± 1.09 mg NOx-N kg(-1) dry soil day(-1), and no significant correlation with soil parameters was found. The abundance of AOA was predominant over AOB, indicating that AOA may be the major members in aerobic ammonia oxidation in these paddy soils. Community compositions of AOA and AOB were highly variable among samples, but the variations were best explained by pH. AOA sequences were affiliated to the Nitrosopumilus cluster and Nitrososphaera cluster, and AOB were classified into the lineages of Nitrosospira and Nitrosomonas, with Nitrosospira being predominant over Nitrosomonas, accounting for 83.6 % of the AOB community. Moreover, the majority of Nitrosomonas was determined in neutral soils. Canonical correspondence analysis (CCA) analysis further demonstrated that AOA and AOB community structures were significantly affected by pH, soil total organic carbon, total nitrogen, and C/N ratio, suggesting that these factors exert strong effects on the distribution of AOB and AOA in paddy soils in Southern China. In conclusion, our results imply that soil pH was a key explanatory variable for both AOA and AOB community structure and nitrification activity.},
}
@article {pmid25736866,
year = {2015},
author = {Tago, K and Okubo, T and Shimomura, Y and Kikuchi, Y and Hori, T and Nagayama, A and Hayatsu, M},
title = {Environmental factors shaping the community structure of ammonia-oxidizing bacteria and archaea in sugarcane field soil.},
journal = {Microbes and environments},
volume = {30},
number = {1},
pages = {21-28},
pmid = {25736866},
issn = {1347-4405},
mesh = {Ammonia/*metabolism ; Archaea/*classification/metabolism ; Bacteria/*classification/metabolism ; *Biota ; Cluster Analysis ; Hydrogen-Ion Concentration ; Oxidation-Reduction ; Oxidoreductases/genetics ; Phylogeny ; Polymerase Chain Reaction ; Saccharum/growth &amp; development ; Sequence Analysis, DNA ; Soil/chemistry ; *Soil Microbiology ; },
abstract = {The effects of environmental factors such as pH and nutrient content on the ecology of ammonia-oxidizing bacteria (AOB) and archaea (AOA) in soil has been extensively studied using experimental fields. However, how these environmental factors intricately influence the community structure of AOB and AOA in soil from farmers' fields is unclear. In the present study, the abundance and diversity of AOB and AOA in soils collected from farmers' sugarcane fields were investigated using quantitative PCR and barcoded pyrosequencing targeting the ammonia monooxygenase alpha subunit (amoA) gene. The abundances of AOB and AOA amoA genes were estimated to be in the range of 1.8 × 10(5)-9.2 × 10(6) and 1.7 × 10(6)-5.3 × 10(7) gene copies g dry soil(-1), respectively. The abundance of both AOB and AOA positively correlated with the potential nitrification rate. The dominant sequence reads of AOB and AOA were placed in Nitrosospira-related and Nitrososphaera-related clusters in all soils, respectively, which varied at the level of their sub-clusters in each soil. The relationship between these ammonia-oxidizing community structures and soil pH was shown to be significant by the Mantel test. The relative abundances of the OTU1 of Nitrosospira cluster 3 and Nitrososphaera subcluster 7.1 negatively correlated with soil pH. These results indicated that soil pH was the most important factor shaping the AOB and AOA community structures, and that certain subclusters of AOB and AOA adapted to and dominated the acidic soil of agricultural sugarcane fields.},
}
@article {pmid25727367,
year = {2016},
author = {Emerson, JB and Thomas, BC and Alvarez, W and Banfield, JF},
title = {Metagenomic analysis of a high carbon dioxide subsurface microbial community populated by chemolithoautotrophs and bacteria and archaea from candidate phyla.},
journal = {Environmental microbiology},
volume = {18},
number = {6},
pages = {1686-1703},
doi = {10.1111/1462-2920.12817},
pmid = {25727367},
issn = {1462-2920},
mesh = {Archaea/classification/*genetics/isolation &amp; purification/metabolism ; Bacteria/classification/*genetics/isolation &amp; purification/metabolism ; Biodiversity ; Carbon Cycle ; Carbon Dioxide/*metabolism ; Chemoautotrophic Growth ; Metagenome ; Metagenomics ; Phylogeny ; Sulfur/metabolism ; },
abstract = {Research on geologic carbon sequestration raises questions about potential impacts of subsurface microbiota on carbon cycling and biogeochemistry. Subsurface, high-CO2 systems are poorly biologically characterized, partly because of difficulty accessing high-volume, uncontaminated samples. CO2 -driven Crystal Geyser (CG, Utah, USA), an established geologic carbon sequestration analogue, provides high volumes of deep (∼ 200-500 m) subsurface fluids. We explored microbial diversity and metabolic potential in this high-CO2 environment by assembly and analysis of metagenomes recovered from geyser water filtrate. The system is dominated by neutrophilic, iron-oxidizing bacteria, including 'marine' Mariprofundus (Zetaproteobacteria) and 'freshwater' Gallionellales, sulfur-oxidizing Thiomicrospira crunogena and Thiobacillus-like Hydrogenophilales. Near-complete genomes were reconstructed for these bacteria. CG is notably populated by a wide diversity of bacteria and archaea from phyla lacking isolated representatives (candidate phyla) and from as-yet undefined lineages. Many bacteria affiliate with OD1, OP3, OP9, PER, ACD58, WWE3, BD1-5, OP11, TM7 and ZB2. The recovery of nearly 100 genes encoding ribulose-1,5 bisphosphate carboxylase-oxygenase subunit proteins of the Calvin cycle and AMP salvage pathways suggests a strong biological role in high-CO2 subsurface carbon cycling. Overall, we predict microbial impacts on subsurface biogeochemistry via iron, sulfur, and complex carbon oxidation, carbon and nitrogen fixation, fermentation, hydrogen metabolism, and aerobic and anaerobic respiration.},
}
@article {pmid25725631,
year = {2015},
author = {Chi, XQ and Liu, K and Zhou, NY},
title = {Effects of bioaugmentation in para-nitrophenol-contaminated soil on the abundance and community structure of ammonia-oxidizing bacteria and archaea.},
journal = {Applied microbiology and biotechnology},
volume = {99},
number = {14},
pages = {6069-6082},
doi = {10.1007/s00253-015-6462-z},
pmid = {25725631},
issn = {1432-0614},
mesh = {Ammonia/*metabolism ; Archaea/*classification/metabolism ; Bacteria/*classification/metabolism ; *Biota ; Denaturing Gradient Gel Electrophoresis ; Nitrophenols/*metabolism ; Oxidation-Reduction ; Real-Time Polymerase Chain Reaction ; *Soil Microbiology ; Soil Pollutants/*metabolism ; },
abstract = {Pseudomonas sp. strain WBC-3 mineralizes the priority pollutant para-nitrophenol (PNP) and releases nitrite (NO2 (-)), which is probably involved in the nitrification. In this study, the rate of PNP removal in soil bioaugmented with strain WBC-3 was more accelerated with more NO2 (-) accumulation than in uninoculated soils. Strain WBC-3 survived well and remained stable throughout the entire period. Real-time polymerase chain reaction (real-time PCR) indicated a higher abundance of ammonia-oxidizing bacteria (AOB) than ammonia-oxidizing archaea (AOA), suggesting that AOB played a greater role in nitrification in the original sampled soil. Real-time PCR and multivariate analysis based on the denaturing gradient gel electrophoresis showed that PNP contamination did not significantly alter the abundance and community structure of ammonia oxidizers except for inhibiting the AOB abundance. Bioaugmentation of PNP-contaminated soil showed a significant effect on AOB populations and community structure as well as AOA populations. In addition, ammonium (NH4 (+)) variation was found to be the primary factor affecting the AOB community structure, as determined by the correlation between the community structures of ammonia oxidizers and environmental factors. It is here proposed that the balance between archaeal and bacterial ammonia oxidation could be influenced significantly by the variation in NH4 (+) levels as caused by bioaugmentation of contaminated soil by a pollutant containing nitrogen.},
}
@article {pmid25709053,
year = {2015},
author = {Shi, Y and Huang, Z and Han, S and Fan, S and Yang, H},
title = {Phylogenetic diversity of Archaea in the intestinal tract of termites from different lineages.},
journal = {Journal of basic microbiology},
volume = {55},
number = {8},
pages = {1021-1028},
doi = {10.1002/jobm.201400678},
pmid = {25709053},
issn = {1521-4028},
mesh = {Animals ; Archaea/*classification/*genetics ; Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology ; Genes, rRNA ; Genetic Variation ; Isoptera/anatomy &amp; histology/classification/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Symbiosis ; },
abstract = {Termites are among the few arthropods that emit methane to the atmosphere, which is a significant source of global greenhouse gas due to their huge biomass on earth. In this study, phylogenetic diversity of Archaea of five termite species from different lineages were analyzed based on 16S rRNA genes. Archaea associated with wood-feeding lower termite, R. chinensis were exclusively Methanobrevibacter in the order Methanobacteriales. This type of methanogens was also found in Nasutitermes sp. and Microcerotermes sp. but not in the fungus-cultivating termites, Odontotermes formosanus and Macrotermes barneyi, which harbor Archaea of the order Methanoplasmatales and Methanosarcinales in their guts. Archaeal diversity of wood-feeding higher termites was higher than wood-feeding lower termites. The highest archaeal diversity was found in Nasutitermes sp. In addition to methanogens affiliated with the orders Methanobacteriales, Methanomicrobiales, and Methanoplasmatales, 37% of archaeal clones were affiliated with non-methanogenic Thaumarchaeota. The results of this study will be significant for further understanding of symbiotic relationship between intestinal microbiota and termites.},
}
@article {pmid25705674,
year = {2015},
author = {Cycoń, M and Piotrowska-Seget, Z},
title = {Community structure of ammonia-oxidizing archaea and ammonia-oxidizing bacteria in soil treated with the insecticide imidacloprid.},
journal = {BioMed research international},
volume = {2015},
number = {},
pages = {582938},
pmid = {25705674},
issn = {2314-6141},
mesh = {Ammonia/chemistry/*metabolism ; Archaea/*drug effects/metabolism ; Bacteria/*drug effects/metabolism ; Imidazoles/toxicity ; Insecticides/toxicity ; Neonicotinoids ; Nitrification/drug effects ; Nitro Compounds/toxicity ; Oxidation-Reduction ; *Soil Microbiology ; },
abstract = {The purpose of this experiment was to assess the effect of imidacloprid on the community structure of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in soil using the denaturing gradient gel electrophoresis (DGGE) approach. Analysis showed that AOA and AOB community members were affected by the insecticide treatment. However, the calculation of the richness (S) and the Shannon-Wiener index (H) values for soil treated with the field rate (FR) dosage of imidacloprid (1 mg/kg soil) showed no changes in measured indices for the AOA and AOB community members. In turn, the 10∗FR dosage of insecticide (10 mg/kg soil) negatively affected the AOA community, which was confirmed by the decrease of the S and H values in comparison with the values obtained for the control soil. In the case of AOB community, an initial decline followed by the increase of the S and H values was obtained. Imidacloprid decreased the nitrification rate while the ammonification process was stimulated by the addition of imidacloprid. Changes in the community structure of AOA and AOB could be due to an increase in the concentration of N-NH4 (+), known as the most important factor which determines the contribution of these microorganisms to soil nitrification.},
}
@article {pmid25702576,
year = {2015},
author = {Castelle, CJ and Wrighton, KC and Thomas, BC and Hug, LA and Brown, CT and Wilkins, MJ and Frischkorn, KR and Tringe, SG and Singh, A and Markillie, LM and Taylor, RC and Williams, KH and Banfield, JF},
title = {Genomic expansion of domain archaea highlights roles for organisms from new phyla in anaerobic carbon cycling.},
journal = {Current biology : CB},
volume = {25},
number = {6},
pages = {690-701},
doi = {10.1016/j.cub.2015.01.014},
pmid = {25702576},
issn = {1879-0445},
mesh = {Anaerobiosis/genetics ; Archaea/classification/*genetics/*metabolism ; Biodiversity ; Carbon Cycle/*genetics ; *Genome, Archaeal ; Metagenomics ; Models, Biological ; Models, Genetic ; Phylogeny ; },
abstract = {BACKGROUND: Archaea represent a significant fraction of Earth's biodiversity, yet they remain much less well understood than Bacteria. Gene surveys, a few metagenomic studies, and some single-cell sequencing projects have revealed numerous little-studied archaeal phyla. Certain lineages appear to branch deeply and may be part of a major phylum radiation. The structure of this radiation and the physiology of the organisms remain almost unknown.<br><br>RESULTS: We used genome-resolved metagenomic analyses to investigate the diversity, genomes sizes, metabolic capacities, and potential roles of Archaea in terrestrial subsurface biogeochemical cycles. We sequenced DNA from complex sediment and planktonic consortia from an aquifer adjacent to the Colorado River (USA) and reconstructed the first complete genomes for Archaea using cultivation-independent methods. To provide taxonomic context, we analyzed an additional 151 newly sampled archaeal sequences. We resolved two new phyla within a major, apparently deep-branching group of phyla (a superphylum). The organisms have small genomes, and metabolic predictions indicate that their primary contributions to Earth's biogeochemical cycles involve carbon and hydrogen metabolism, probably associated with symbiotic and/or fermentation-based lifestyles.<br><br>CONCLUSIONS: The results dramatically expand genomic sampling of the domain Archaea and clarify taxonomic designations within a major superphylum. This study, in combination with recently published work on bacterial phyla lacking cultivated representatives, reveals a fascinating phenomenon of major radiations of organisms with small genomes, novel proteome composition, and strong interdependence in both domains.},
}
@article {pmid25699024,
year = {2015},
author = {Albers, SV and Jarrell, KF},
title = {The archaellum: how Archaea swim.},
journal = {Frontiers in microbiology},
volume = {6},
number = {},
pages = {23},
pmid = {25699024},
issn = {1664-302X},
support = {311523/ERC_/European Research Council/International ; },
abstract = {Recent studies on archaeal motility have shown that the archaeal motility structure is unique in several aspects. Although it fulfills the same swimming function as the bacterial flagellum, it is evolutionarily and structurally related to the type IV pilus. This was the basis for the recent proposal to term the archaeal motility structure the "archaellum." This review illustrates the key findings that led to the realization that the archaellum was a novel motility structure and presents the current knowledge about the structural composition, mechanism of assembly and regulation, and the posttranslational modifications of archaella.},
}
@article {pmid25682761,
year = {2015},
author = {La Cono, V and Smedile, F and La Spada, G and Arcadi, E and Genovese, M and Ruggeri, G and Genovese, L and Giuliano, L and Yakimov, MM},
title = {Shifts in the meso- and bathypelagic archaea communities composition during recovery and short-term handling of decompressed deep-sea samples.},
journal = {Environmental microbiology reports},
volume = {7},
number = {3},
pages = {450-459},
doi = {10.1111/1758-2229.12272},
pmid = {25682761},
issn = {1758-2229},
mesh = {Adaptation, Biological ; Archaea/*classification/*isolation &amp; purification/physiology ; *Biota ; *Decompression ; Seawater/*microbiology ; },
abstract = {Dark ocean microbial communities are actively involved in chemoautotrophic and anaplerotic fixation of bicarbonate. Thus, aphotic pelagic realm of the ocean might represent a significant sink of CO2 and source of primary production. However, the estimated metabolic activities in the dark ocean are fraught with uncertainties. Typically, deep-sea samples are recovered to the sea surface for downstream processing on deck. Shifts in ambient settings, associated with such treatments, can likely change the metabolic activity and community structure of deep-sea adapted autochthonous microbial populations. To estimate influence of recovery and short-term handling of deep-sea samples, we monitored the succession of bathypelagic microbial community during its 3 days long on deck incubation. We demonstrated that at the end of exposition, the deep-sea archaeal population decreased threefold, whereas the bacterial fraction doubled in size. As revealed by phylogenetic analyses of amoA gene transcripts, dominance of the active ammonium-oxidizing bathypelagic Thaumarchaeota groups shifted over time very fast. These findings demonstrated the simultaneous existence of various 'deep-sea ecotypes', differentially reacting to the sampling and downstream handling. Our study supports the hypothesis that metabolically active members of meso- and bathypelagic Thaumarchaeota possess the habitat-specific distribution, metabolic complexity and genetic divergence at subpopulation level.},
}
@article {pmid25680859,
year = {2015},
author = {Baricz, A and Cristea, A and Muntean, V and Teodosiu, G and Andrei, A&#x15e; and Molnár, I and Alexe, M and Rakosy-Tican, E and Banciu, HL},
title = {Culturable diversity of aerobic halophilic archaea (Fam. Halobacteriaceae) from hypersaline, meromictic Transylvanian lakes.},
journal = {Extremophiles : life under extreme conditions},
volume = {19},
number = {2},
pages = {525-537},
pmid = {25680859},
issn = {1433-4909},
mesh = {Halobacteriaceae/classification/*genetics/isolation &amp; purification ; Lakes/chemistry/*microbiology ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Salinity ; *Salt Tolerance ; },
abstract = {Perennially stratified salt lakes situated in the Transylvanian Basin (Central Romania) were surveyed for the diversity of culturable halophilic archaea (Fam. Halobacteriaceae). The physical and chemical characteristics of the waters indicated that all the investigated lakes were meromictic and neutral hypersaline. Samples collected from upper, intermediate, and deeper water layers and sediments were used for the isolation of halophilic strains followed by 16S rRNA gene-based identification and phenotypic characterization. The phylogenetic analysis of the 16S rRNA gene sequences revealed that all 191 isolates reported in this study and 43 strains previously isolated were affiliated with the family Halobacteriaceae and classified to 18 genera. Haloferax was the most frequently isolated genus (~47 %), followed by Halobacterium spp. (~12 %), and Halorubrum spp. (~11 %). Highest culturable diversity was detected in Brâncoveanu Lake, the oldest and saltiest of all studied lakes, while the opposite was observed in the most stable and least human-impacted Fără Fund Lake. One strain from Ursu Lake might possibly constitute a novel Halorubrum species as shown by phylogenetic analysis. Several haloarchaeal taxa recently described in Asian (i.e., Iran, China) saline systems were also identified as inhabiting the Transylvanian salt lakes thus expanding our knowledege on the geographic distribution of Halobacteriaceae.},
}
@article {pmid25665572,
year = {2015},
author = {Smollett, K and Blombach, F and Werner, F},
title = {Transcription in Archaea: in vitro transcription assays for mjRNAP.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {1276},
number = {},
pages = {305-314},
doi = {10.1007/978-1-4939-2392-2_18},
pmid = {25665572},
issn = {1940-6029},
mesh = {DNA-Directed RNA Polymerases/*metabolism ; In Vitro Techniques/*methods ; Methanocaldococcus/*enzymology/*physiology ; Protein Subunits/metabolism ; Recombinant Proteins/*metabolism ; Temperature ; Transcription, Genetic/genetics/*physiology ; },
abstract = {The fully recombinant Methanocaldococcus jannaschii RNA polymerase allows for a detailed dissection of the different stages of the transcription. In the previous chapter, we discussed how to purify the different components of the M. jannaschii transcription system, the RNA polymerase subunits, and general transcription factors and how to assemble a functional M. jannaschii enzyme. Standard in vitro transcription assays can be used to examine the different stages of transcription. In this chapter, we describe how some of these assays have been optimized for M. jannaschii RNA polymerase, which transcribes at much higher temperatures than many other transcription complexes.},
}
@article {pmid25665571,
year = {2015},
author = {Smollett, K and Blombach, F and Werner, F},
title = {Transcription in Archaea: preparation of Methanocaldococcus jannaschii transcription machinery.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {1276},
number = {},
pages = {291-303},
doi = {10.1007/978-1-4939-2392-2_17},
pmid = {25665571},
issn = {1940-6029},
mesh = {*Biological Evolution ; DNA-Directed RNA Polymerases/genetics/*metabolism ; Methanocaldococcus/*enzymology/*physiology ; Molecular Biology/*methods ; Silver Staining ; Transcription, Genetic/*physiology ; },
abstract = {Archaeal RNA polymerase and general transcription factors are more closely related to those of eukaryotes than of bacteria. As such the study of transcription of archaea is important both in terms of examination of the evolution of the transcriptional machinery and as a simplified tool for eukaryotic transcription. In particular, the hyperthermophilic Methanocaldococcus jannaschii provides us with a fully recombinant RNA polymerase system allowing for much more detailed in vitro examination of the roles of different components during the transcription cycle than otherwise possible. The individual subunits of M. jannaschii enzyme are easily expressed and purified from heterologous expression systems. Forming functional RNA polymerase involves simply combining the different subunits under denaturing conditions and slowly removing the denaturant.},
}
@article {pmid25663452,
year = {2015},
author = {Danis, O and Ogan, A and Tatlican, P and Attar, A and Cakmakci, E and Mertoglu, B and Birbir, M},
title = {Preparation of poly(3-hydroxybutyrate-co-hydroxyvalerate) films from halophilic archaea and their potential use in drug delivery.},
journal = {Extremophiles : life under extreme conditions},
volume = {19},
number = {2},
pages = {515-524},
pmid = {25663452},
issn = {1433-4909},
mesh = {Archaea/genetics/*metabolism/ultrastructure ; Polyesters/*metabolism ; Starch/metabolism ; },
abstract = {Halophilic archaea offer a potential source for production of polyhydroxyalkanoates (PHAs). Hence, the experiments were carried out with five extremely halophilic archaeal isolates to determine the highest PHA-producing strain. PHA production of each isolates was separately examined in cheap carbon sources such as corn starch, sucrose, whey, apple, melon and tomato wastes. Corn starch was found to be a fairly effective substrate for PHA production. Among the strains studied here, the strain with the highest capability for PHA biosynthesis was found to be 1KYS1. Phylogenetic analysis based on 16S rRNA gene sequence comparison showed that 1KYS1 closely related to species of the genus Natrinema. The closest phylogenetic similarity was with the strain of Natrinema pallidum JCM 8980 (99 %). PHA content of 1KYS1 was about 53.14 % of the cell dry weight when starch was used as a carbon source. The formation of large and uniform PHA granules was confirmed by transmission electron microscopy and the biopolymer was identified as poly(3-hydroxybutyrate-co-hydroxyvalerate) (PHBV). PHBV produced by 1KYS1 was blended with low molar mass polyethylene glycol (PEG 300) to prepare biocompatible films for drug delivery. Rifampicin was used as a model drug and its release from PHBV films was investigated at pH 7.4, 37 °C. It was found that PHBV films obtained from 1KYS1 were very effective for drug delivery. In conclusion, PHBV of 1KYS1 may have a potential usage in drug delivery applications.},
}
@article {pmid25660375,
year = {2015},
author = {Petitjean, C and Deschamps, P and López-García, P and Moreira, D and Brochier-Armanet, C},
title = {Extending the conserved phylogenetic core of archaea disentangles the evolution of the third domain of life.},
journal = {Molecular biology and evolution},
volume = {32},
number = {5},
pages = {1242-1254},
doi = {10.1093/molbev/msv015},
pmid = {25660375},
issn = {1537-1719},
mesh = {Archaea/genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genome, Archaeal ; *Phylogeny ; RNA, Ribosomal/*genetics ; Ribosomal Proteins/genetics ; Ribosome Subunits, Small/*genetics ; Ribosomes/genetics ; },
abstract = {Initial studies of the archaeal phylogeny relied mainly on the analysis of the RNA component of the small subunit of the ribosome (SSU rRNA). The resulting phylogenies have provided interesting but partial information on the evolutionary history of the third domain of life because SSU rRNA sequences do not contain enough phylogenetic signal to resolve all nodes of the archaeal tree. Thus, many relationships, and especially the most ancient ones, remained elusive. Moreover, SSU rRNA phylogenies can be heavily biased by tree reconstruction artifacts. The sequencing of complete genomes allows using a variety of protein markers as an alternative to SSU rRNA. Taking advantage of the recent burst of archaeal complete genome sequences, we have carried out an in-depth phylogenomic analysis of this domain. We have identified 200 new protein families that, in addition to the ribosomal proteins and the subunits of the RNA polymerase, form a conserved phylogenetic core of archaeal genes. The accurate analysis of these markers combined with desaturation approaches shed new light on the evolutionary history of Archaea and reveals that several relationships recovered in recent analyses are likely the consequence of tree reconstruction artifacts. Among others, we resolve a number of important relationships, such as those among methanogens Class I, and we propose the definition of two new superclasses within the Euryarchaeota: Methanomada and Diaforarchaea.},
}
@article {pmid25629511,
year = {2014},
author = {Suzuki, T and Numata, T},
title = {Convergent evolution of AUA decoding in bacteria and archaea.},
journal = {RNA biology},
volume = {11},
number = {12},
pages = {1586-1596},
pmid = {25629511},
issn = {1555-8584},
mesh = {Anticodon/chemistry/*metabolism ; Archaea/classification/genetics/metabolism ; Bacteria/classification/genetics/metabolism ; Biological Evolution ; Codon/chemistry/*metabolism ; Cytidine/*analogs &amp; derivatives/chemistry/genetics/metabolism ; *Genetic Code ; Isoleucine/chemistry/genetics/metabolism ; Lysine/*analogs &amp; derivatives/chemistry/genetics/metabolism ; Methionine/chemistry/genetics/metabolism ; Models, Molecular ; Phylogeny ; Protein Biosynthesis ; Pyrimidine Nucleosides/chemistry/genetics/*metabolism ; RNA, Transfer/chemistry/genetics/*metabolism ; Ribosomes/metabolism ; },
abstract = {Deciphering AUA codons is a difficult task for organisms, because AUA and AUG specify isoleucine (Ile) and methionine (Met), separately. Each of the other purine-ending sense co-don sets (NNR) specifies a single amino acid in the universal genetic code. In bacteria and archaea, the cytidine derivatives, 2-lysylcytidine (L or lysidine) and 2-agmatinylcytidine (agm(2)C or agmatidine), respectively, are found at the first letter of the anticodon of tRNA(Ile) responsible for AUA codons. These modifications prevent base pairing with G of the third letter of AUG codon, and enable tRNA(Ile) to decipher AUA codon specifically. In addition, these modifications confer a charging ability of tRNA(Ile) with Ile. Despite their similar chemical structures, L and agm(2)C are synthesized by distinctive mechanisms and catalyzed by different classes of enzymes, implying that the analogous decoding systems for AUA codons were established by convergent evolution after the phylogenic split between bacteria and archaea-eukaryotes lineages following divergence from the last universal common ancestor (LUCA).},
}
@article {pmid25617114,
year = {2015},
author = {Bae, J and Kim, SM and Lee, SB},
title = {Identification and characterization of 2-keto-3-deoxy-L-rhamnonate dehydrogenase belonging to the MDR superfamily from the thermoacidophilic bacterium Sulfobacillus thermosulfidooxidans: implications to L-rhamnose metabolism in archaea.},
journal = {Extremophiles : life under extreme conditions},
volume = {19},
number = {2},
pages = {469-478},
pmid = {25617114},
issn = {1433-4909},
mesh = {Archaea/enzymology/*metabolism ; Archaeal Proteins/chemistry/genetics/metabolism ; Bacillales/*enzymology/metabolism ; Bacterial Proteins/chemistry/genetics/*metabolism ; Carbohydrate Dehydrogenases/chemistry/genetics/*metabolism ; Phylogeny ; Protein Binding ; Rhamnose/*metabolism ; },
abstract = {We identified the non-phosphorylated L-rhamnose metabolic pathway (Rha_NMP) genes that are homologous to those in the thermoacidophilic archaeon Thermoplasma acidophilum in the genome of the thermoacidophilic bacterium Sulfobacillus thermosulfidooxidans. However, unlike previously known 2-keto-3-deoxy-L-rhamnonate (L-KDR) dehydrogenase (KDRDH) which belongs to the short chain dehydrogenase/reductase superfamily, the putative KDRDHs in S. thermosulfidooxidans (Sulth_3557) and T. acidophilum (Ta0749) belong to the medium chain dehydrogenase/reductase (MDR) superfamily. We demonstrated that Sulth_3559 and Sulth_3557 proteins from S. thermosulfidooxidans function as L-rhamnose dehydrogenase and KDRDH, respectively. Sulth_3557 protein is an NAD(+)-specific KDRDH with optimal temperature and pH of 50 °C and 9.5, respectively. The K m and V max values for L-KDR were 2.0 mM and 12.8 U/mg, respectively. Sulth_3557 also showed weak 2,3-butanediol dehydrogenase activity. Phylogenetic analysis suggests that Sulth_3557 and its homologs form a new subfamily in the MDR superfamily. The results shown in this study imply that thermoacidophilic archaea metabolize L-rhamnose to pyruvate and L-lactate by using the MDR-family KDRDH similarly to that of the thermoacidophilic bacterium S. thermosulfidooxidans.},
}
@article {pmid25605423,
year = {2015},
author = {Lee, SH and Kim, SY and Ding, W and Kang, H},
title = {Impact of elevated CO2 and N addition on bacteria, fungi, and archaea in a marsh ecosystem with various types of plants.},
journal = {Applied microbiology and biotechnology},
volume = {99},
number = {12},
pages = {5295-5305},
doi = {10.1007/s00253-015-6385-8},
pmid = {25605423},
issn = {1432-0614},
mesh = {Archaea/classification/genetics/isolation &amp; purification/*metabolism ; Bacteria/classification/genetics/isolation &amp; purification/*metabolism ; Biodiversity ; Carbon Dioxide/*metabolism ; Ecosystem ; Fungi/classification/genetics/isolation &amp; purification/*metabolism ; Nitrogen/*metabolism ; Plants/classification/*metabolism ; Soil Microbiology ; Wetlands ; },
abstract = {The individual effects of either elevated CO2 or N deposition on soil microbial communities have been widely studied, but limited information is available regarding the responses of the bacteria, fungi, and archaea communities to both elevated CO2 and N in wetland ecosystems with different types of plants. Using a terminal restriction fragment length polymorphism (T-RFLP) analysis and real-time quantitative PCR (RT-Q-PCR), we compared communities of bacteria, fungi, and archaea in a marsh microcosm with one of seven macrophytes, Typha latifolia, Phragmites japonica, Miscanthus sacchariflorus, Scirpus lacustris, Juncus effusus, Phragmites australis, or Zizania latifolia, after exposing them to eCO2 and/or amended N for 110 days. Overall, our results showed that the elevated CO2 and N may affect the bacterial and archaeal communities, while they may not affect the fungal community in terms of both diversity and abundance. The effects of elevated CO2 and N on microbial community vary depending on the plant types, and each microbial community shows different responses to the elevated CO2 and N. In particular, elevated CO2 might force a shift in the archaeal community irrespective of the plant type, and the effect of elevated CO2 was enhanced when combined with the N effect. This study indicates that elevated CO2 and N addition could lead to changes in the community structures of bacteria and archaea. Our results also suggest that the fungal group is less sensitive to external changes, while the bacterial and archaeal groups are more sensitive to them. Finally, the characteristics of the plant type and relevant physicochemical factors induced by the elevated CO2 and N may be important key factors structuring the microbial community's response to environmental change, which implies the need for a more comprehensive approach to understanding the pattern of the wetland response to climate change.},
}
@article {pmid25604335,
year = {2015},
author = {Jabłoński, S and Rodowicz, P and Łukaszewicz, M},
title = {Methanogenic archaea database containing physiological and biochemical characteristics.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {65},
number = {Pt 4},
pages = {1360-1368},
doi = {10.1099/ijs.0.000065},
pmid = {25604335},
issn = {1466-5034},
mesh = {Anaerobiosis ; Archaea/*classification/growth &amp; development/metabolism ; Base Composition ; Carbon Cycle ; *Databases, Factual ; Ecosystem ; Methane/biosynthesis ; Methanosarcina/metabolism ; RNA, Ribosomal, 16S/genetics ; Temperature ; },
abstract = {The methanogenic archaea are a group of micro-organisms that have developed a unique metabolic pathway for obtaining energy. There are 150 characterized species in this group; however, novel species continue to be discovered. Since methanogens are considered a crucial part of the carbon cycle in the anaerobic ecosystem, characterization of these micro-organisms is important for understanding anaerobic ecology. A methanogens database (MDB; http://metanogen.biotech.uni.wroc.pl/), including physiological and biochemical characteristics of methanogens, was constructed based on the descriptions of isolated type strains. Analysis of the data revealed that methanogens are able to grow from 0 to 122 °C. Methanogens growing at the same temperature may have very different growth rates. There is no clear correlation between the optimal growth temperature and the DNA G+C content. The following substrate preferences are observed in the database: 74.5% of archaea species utilize H2+CO2, 33% utilize methyl compounds and 8.5% utilize acetate. Utilization of methyl compounds (mainly micro-organisms belonging to the genera Methanosarcina and Methanolobus) is seldom accompanied by an ability to utilize H2+CO2. Very often, data for described species are incomplete, especially substrate preferences. Additional research leading to completion of missing information and development of standards, especially for substrate utilization, would be very helpful.},
}
@article {pmid25586577,
year = {2015},
author = {Zhang, Y and Chen, L and Sun, R and Dai, T and Tian, J and Wen, D},
title = {Ammonia-oxidizing bacteria and archaea in wastewater treatment plant sludge and nearby coastal sediment in an industrial area in China.},
journal = {Applied microbiology and biotechnology},
volume = {99},
number = {10},
pages = {4495-4507},
doi = {10.1007/s00253-014-6352-9},
pmid = {25586577},
issn = {1432-0614},
mesh = {Ammonia/*metabolism ; Archaea/classification/genetics/isolation &amp; purification/*metabolism ; Bacteria/classification/genetics/isolation &amp; purification/*metabolism ; Biodiversity ; China ; Geologic Sediments/*microbiology ; Industrial Waste/analysis ; Molecular Sequence Data ; Phylogeny ; Sewage/*microbiology ; Wastewater/chemistry ; Water Purification/instrumentation ; },
abstract = {Under the increasing pressure of human activities, Hangzhou Bay has become one of the most seriously polluted waters along China's coast. Considering the excessive inorganic nitrogen detected in the bay, in this study, the impact of an effluent from a coastal industrial park on ammonia-oxidizing microorganisms (AOMs) of the receiving area was interpreted for the first time by molecular technologies. Revealed by real-time PCR, the ratio of archaeal amoA/bacterial amoA ranged from 5.68 × 10(-6) to 4.79 × 10(-5) in the activated sludge from two wastewater treatment plants (WWTPs) and 0.54-3.44 in the sediments from the effluent receiving coastal area. Analyzed by clone and pyrosequencing libraries, genus Nitrosomonas was the predominant ammonia-oxidizing bacteria (AOB), but no ammonia-oxidizing archaea (AOA) was abundant enough for sequencing in the activated sludge from the WWTPs; genus Nitrosomonas and Nitrosopumilus were the dominant AOB and AOA, respectively, in the coastal sediments. The different abundance of AOA but similar structure of AOB between the WWTPs and nearby coastal area probably indicated an anthropogenic impact on the microbial ecology in Hangzhou Bay.},
}
@article {pmid25585508,
year = {2015},
author = {Randau, L},
title = {Evolution of small guide RNA genes in hyperthermophilic archaea.},
journal = {Annals of the New York Academy of Sciences},
volume = {1341},
number = {},
pages = {188-193},
doi = {10.1111/nyas.12643},
pmid = {25585508},
issn = {1749-6632},
mesh = {Archaea/*genetics ; Base Sequence ; *Evolution, Molecular ; Gene Expression Regulation, Archaeal ; Genome, Archaeal/genetics ; Hot Temperature ; Models, Genetic ; RNA, Archaeal/*genetics/metabolism ; RNA, Guide, CRISPR-Cas Systems/*genetics/metabolism ; },
abstract = {Profiling the RNA production in hyperthermophilic archaea revealed an abundance of small RNA-guided processes near the upper temperature limit of life. Archaea utilize the base-pairing ability of RNA guide sequences to target ribosomal RNAs, transfer RNAs, messenger RNAs, and viral genomes. Cellular processes that are guided by small RNAs include the modification of RNA molecules, trans-splicing, gene regulation, and RNA and DNA degradation. Here, a brief overview of our knowledge on small guide RNA genes in archaeal genomes is provided and examples of their putative roles in genome evolution are described.},
}
@article {pmid25583072,
year = {2015},
author = {Makarova, KS and Galperin, MY and Koonin, EV},
title = {Comparative genomic analysis of evolutionarily conserved but functionally uncharacterized membrane proteins in archaea: Prediction of novel components of secretion, membrane remodeling and glycosylation systems.},
journal = {Biochimie},
volume = {118},
number = {},
pages = {302-312},
pmid = {25583072},
issn = {1638-6183},
support = {Z01 LM000061-15//Intramural NIH HHS/United States ; },
mesh = {Archaea/*physiology ; Archaeal Proteins/*metabolism ; *Biological Evolution ; Comparative Genomic Hybridization ; Computer Simulation ; Conserved Sequence ; Evolution, Molecular ; Genes, Archaeal/*genetics ; Glycosylation ; Membrane Proteins/*metabolism ; Phylogeny ; Protein Conformation ; },
abstract = {A systematic comparative genomic analysis of all archaeal membrane proteins that have been projected to the last archaeal common ancestor gene set led to the identification of several novel components of predicted secretion, membrane remodeling, and protein glycosylation systems. Among other findings, most crenarchaea have been shown to encode highly diverged orthologs of the membrane insertase YidC, which is nearly universal in bacteria, eukaryotes, and euryarchaea. We also identified a vast family of archaeal proteins, including the C-terminal domain of N-glycosylation protein AglD, as membrane flippases homologous to the flippase domain of bacterial multipeptide resistance factor MprF, a bifunctional lysylphosphatidylglycerol synthase and flippase. Additionally, several proteins were predicted to function as membrane transporters. The results of this work, combined with our previous analyses, reveal an unexpected diversity of putative archaeal membrane-associated functional systems that remain to be functionally characterized. A more general conclusion from this work is that the currently available collection of archaeal (and bacterial) genomes could be sufficient to identify (almost) all widespread functional modules and develop experimentally testable predictions of their functions.},
}
@article {pmid25581459,
year = {2015},
author = {Briegel, A and Ortega, DR and Huang, AN and Oikonomou, CM and Gunsalus, RP and Jensen, GJ},
title = {Structural conservation of chemotaxis machinery across Archaea and Bacteria.},
journal = {Environmental microbiology reports},
volume = {7},
number = {3},
pages = {414-419},
pmid = {25581459},
issn = {1758-2229},
support = {R01 GM101425/GM/NIGMS NIH HHS/United States ; GM101425/GM/NIGMS NIH HHS/United States ; },
mesh = {Archaea/*genetics/*physiology ; Bacteria/*genetics ; *Bacterial Physiological Phenomena ; *Chemotaxis ; Conserved Sequence ; Evolution, Molecular ; *Gene Regulatory Networks ; },
abstract = {Chemotaxis allows cells to sense and respond to their environment. In Bacteria, stimuli are detected by arrays of chemoreceptors that relay the signal to a two-component regulatory system. These arrays take the form of highly stereotyped super-lattices comprising hexagonally packed trimers-of-receptor-dimers networked by rings of histidine kinase and coupling proteins. This structure is conserved across chemotactic Bacteria, and between membrane-bound and cytoplasmic arrays, and gives rise to the highly cooperative, dynamic nature of the signalling system. The chemotaxis system, absent in eukaryotes, is also found in Archaea, where its structural details remain uncharacterized. Here we provide evidence that the chemotaxis machinery was not present in the last archaeal common ancestor, but rather was introduced in one of the waves of lateral gene transfer that occurred after the branching of Eukaryota but before the diversification of Euryarchaeota. Unlike in Bacteria, the chemotaxis system then evolved largely vertically in Archaea, with very few subsequent successful lateral gene transfer events. By electron cryotomography, we find that the structure of both membrane-bound and cytoplasmic chemoreceptor arrays is conserved between Bacteria and Archaea, suggesting the fundamental importance of this signalling architecture across diverse prokaryotic lifestyles.},
}
@article {pmid25581373,
year = {2015},
author = {Lagostina, L and Goldhammer, T and Røy, H and Evans, TW and Lever, MA and Jørgensen, BB and Petersen, DG and Schramm, A and Schreiber, L},
title = {Ammonia-oxidizing Bacteria of the Nitrosospira cluster 1 dominate over ammonia-oxidizing Archaea in oligotrophic surface sediments near the South Atlantic Gyre.},
journal = {Environmental microbiology reports},
volume = {7},
number = {3},
pages = {404-413},
pmid = {25581373},
issn = {1758-2229},
support = {294200/ERC_/European Research Council/International ; },
mesh = {Ammonia/*metabolism ; Archaea/*isolation &amp; purification/*metabolism ; Atlantic Ocean ; Bacteria/*isolation &amp; purification/*metabolism ; *Biodiversity ; Cluster Analysis ; Geologic Sediments/*microbiology ; Molecular Sequence Data ; Oxidation-Reduction ; Oxidoreductases/genetics ; Phylogeny ; Sequence Analysis, DNA ; Sequence Homology ; },
abstract = {Sediments across the Namibian continental margin feature a strong microbial activity gradient at their surface. This is reflected in ammonium concentrations of < 10 μM in oligotrophic abyssal plain sediments near the South Atlantic Gyre compared with ammonium concentrations of > 700 μM in upwelling areas near the coast. Here we address changes in apparent abundance and structure of ammonia-oxidizing archaeal and bacterial communities (AOA and AOB) along a transect of seven sediment stations across the Namibian shelf by analysing their respective ammonia monooxygenase genes (amoA). The relative abundance of archaeal and bacterial amoA (g(-1) DNA) decreased with increasing ammonium concentrations, and bacterial amoA frequently outnumbered archaeal amoA at the sediment-water interface [0-1 cm below seafloor (cmbsf)]. In contrast, AOA were apparently as abundant as AOB or dominated in several deeper (> 10 cmbsf), anoxic sediment layers. Phylogenetic analyses showed a change within the AOA community along the transect, from two clusters without cultured representatives at the gyre to Nitrososphaera and Nitrosopumilus clusters in the upwelling region. AOB almost exclusively belonged to the Nitrosospira cluster 1. Our results suggest that this predominantly marine AOB lineage without cultured representatives can thrive at low ammonium concentrations and is active in the marine nitrogen cycle.},
}
@article {pmid25569531,
year = {2015},
author = {Tonner, PD and Pittman, AM and Gulli, JG and Sharma, K and Schmid, AK},
title = {A regulatory hierarchy controls the dynamic transcriptional response to extreme oxidative stress in archaea.},
journal = {PLoS genetics},
volume = {11},
number = {1},
pages = {e1004912},
pmid = {25569531},
issn = {1553-7404},
mesh = {Archaea/genetics/physiology ; DNA-Binding Proteins/*genetics ; Gene Expression Regulation, Bacterial ; *Gene Regulatory Networks ; Nucleotide Motifs/genetics ; Oxidative Stress/*genetics ; Transcription Factor TFIIB/*genetics ; },
abstract = {Networks of interacting transcription factors are central to the regulation of cellular responses to abiotic stress. Although the architecture of many such networks has been mapped, their dynamic function remains unclear. Here we address this challenge in archaea, microorganisms possessing transcription factors that resemble those of both eukaryotes and bacteria. Using genome-wide DNA binding location analysis integrated with gene expression and cell physiological data, we demonstrate that a bacterial-type transcription factor (TF), called RosR, and five TFIIB proteins, homologs of eukaryotic TFs, combinatorially regulate over 100 target genes important for the response to extremely high levels of peroxide. These genes include 20 other transcription factors and oxidative damage repair genes. RosR promoter occupancy is surprisingly dynamic, with the pattern of target gene expression during the transition from rapid growth to stress correlating strongly with the pattern of dynamic binding. We conclude that a hierarchical regulatory network orchestrated by TFs of hybrid lineage enables dynamic response and survival under extreme stress in archaea. This raises questions regarding the evolutionary trajectory of gene networks in response to stress.},
}
@article {pmid25561057,
year = {2015},
author = {Dong, J and Ding, L and Wang, X and Chi, Z and Lei, J},
title = {Vertical profiles of community abundance and diversity of anaerobic methanotrophic archaea (ANME) and bacteria in a simple waste landfill in north China.},
journal = {Applied biochemistry and biotechnology},
volume = {175},
number = {5},
pages = {2729-2740},
doi = {10.1007/s12010-014-1456-3},
pmid = {25561057},
issn = {1559-0291},
mesh = {Archaea/classification/genetics/*isolation &amp; purification/*metabolism ; Autotrophic Processes ; Bacteria/classification/genetics/*isolation &amp; purification/*metabolism ; *Biodiversity ; China ; Geologic Sediments/*microbiology ; Methane/*metabolism ; Molecular Sequence Data ; Phylogeny ; Soil Microbiology ; Waste Disposal Facilities ; },
abstract = {Anaerobic methane oxidation (AMO) is considered to be an important sink of CH4 in habitats as marine sediments. But, few studies focused on AMO in landfills which may be an important sink of CH4 derived from waste fermentation. To show evidence of AMO and to uncover function anaerobic methanotroph (ANME) community in landfill, different age waste samples were collected in Jinqianpu landfill located in north China. Through high-throughput sequencing, Methanomicrobiales and Methanosarcinales archaea associated with ANME and reverse methanogenic archaea of Methanosarcina and Methanobacterium were detected. Sulfate-reducing bacteria (SRB) (Desulfobulbus and Desulfococcus) which could couple with ANME-conducting AMO were also found. But, the community structure of ANME had no significant difference with depths. From the results of investigation, we can come to a conclusion that sulfate-dependent anaerobic methane oxidation (SR-DAMO) would be the dominant AMO process in the landfill, while iron-dependent anaerobic methane oxidation (M/IR-DAMO) process was weak though concentration of ferric iron was large in the landfill. Denitrification-dependent anaerobic methane oxidation (NR-DAMO) was negative because of lack of nitrate and relevant function microorganisms in the landfill. Results also indicate that CH4 mitigation would have higher potential by increasing electron acceptor contents and promoting the growth of relevant function microorganisms.},
}
@article {pmid25560263,
year = {2015},
author = {Sinthusith, N and Terada, A and Hahn, M and Noophan, PL and Munakata-Marr, J and Figueroa, LA},
title = {Identification and quantification of bacteria and archaea responsible for ammonia oxidation in different activated sludge of full-scale wastewater treatment plants.},
journal = {Journal of environmental science and health. Part A, Toxic/hazardous substances &amp; environmental engineering},
volume = {50},
number = {2},
pages = {169-175},
doi = {10.1080/10934529.2014.975535},
pmid = {25560263},
issn = {1532-4117},
mesh = {Ammonia/*metabolism ; Archaea/classification/*isolation &amp; purification/*metabolism ; Bacteria/classification/isolation &amp; purification/*metabolism ; Bacterial Load ; Biota ; Japan ; Oxidation-Reduction ; Sewage/*microbiology ; Thailand ; United States ; Waste Disposal, Fluid/*methods ; },
abstract = {In this study, the abundance and sequences of the amoA gene in ammonia oxidizing bacteria (AOB) and ammonia oxidizing archaea (AOA) were defined in three wastewater treatment plants using activated sludge with biological nitrogen removal in different countries: Thailand, United States of America (USA), and Japan. Quantitative real-time polymerase chain reaction (PCR) and PCR coupled with denaturing gradient gel electrophoresis were used to find the comparative abundance and identity of AOB and AOA. The conditions at the Phuket WWTP in Thailand promoted the dominance of AOA amoA genes over AOB amoA genes, while conditions at the WWTPs in Japan and USA promoted growth of AOB. Three parameters that may have contributed to the AOA dominance in Phuket were longer SRT, higher temperature, and higher pH. The Phuket WWTP is a unique system that can be used to better understand the conditions that promote AOA growth and dominance over AOB. In addition, analysis of operational data in conjunction with AOA and AOB community structure from the Phuket WWTP may elucidate advantages of AOA in meeting stricter treatment standards.},
}
@article {pmid25534249,
year = {2015},
author = {Meinhardt, KA and Bertagnolli, A and Pannu, MW and Strand, SE and Brown, SL and Stahl, DA},
title = {Evaluation of revised polymerase chain reaction primers for more inclusive quantification of ammonia-oxidizing archaea and bacteria.},
journal = {Environmental microbiology reports},
volume = {7},
number = {2},
pages = {354-363},
doi = {10.1111/1758-2229.12259},
pmid = {25534249},
issn = {1758-2229},
mesh = {Ammonia/*metabolism ; Archaea/*classification/enzymology/*isolation &amp; purification/metabolism ; Bacteria/*classification/enzymology/*isolation &amp; purification/metabolism ; DNA Primers/genetics ; Microbiological Techniques/methods ; Oxidation-Reduction ; Oxidoreductases/*genetics ; Real-Time Polymerase Chain Reaction/*methods ; },
abstract = {Ammonia-oxidizing archaea (AOA) and bacteria (AOB) fill key roles in the nitrogen cycle. Thus, well-vetted methods for characterizing their distribution are essential for framing studies of their significance in natural and managed systems. Quantification of the gene coding for one subunit of the ammonia monooxygenase (amoA) by polymerase chain reaction is frequently employed to enumerate the two groups. However, variable amplification of sequence variants comprising this conserved genetic marker for ammonia oxidizers potentially compromises within- and between-system comparisons. We compared the performance of newly designed non-degenerate quantitative polymerase chain reaction primer sets to existing primer sets commonly used to quantify the amoA of AOA and AOB using a collection of plasmids and soil DNA samples. The new AOA primer set provided improved quantification of model mixtures of different amoA sequence variants and increased detection of amoA in DNA recovered from soils. Although both primer sets for the AOB provided similar results for many comparisons, the new primers demonstrated increased detection in environmental application. Thus, the new primer sets should provide a useful complement to primers now commonly used to characterize the environmental distribution of AOA and AOB.},
}
@article {pmid25527841,
year = {2014},
author = {Petitjean, C and Deschamps, P and López-García, P and Moreira, D},
title = {Rooting the domain archaea by phylogenomic analysis supports the foundation of the new kingdom Proteoarchaeota.},
journal = {Genome biology and evolution},
volume = {7},
number = {1},
pages = {191-204},
pmid = {25527841},
issn = {1759-6653},
mesh = {Archaea/*genetics ; Archaeal Proteins/genetics ; *Evolution, Molecular ; Genome, Archaeal ; *Genomics ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The first 16S rRNA-based phylogenies of the Archaea showed a deep division between two groups, the kingdoms Euryarchaeota and Crenarchaeota. This bipartite classification has been challenged by the recent discovery of new deeply branching lineages (e.g., Thaumarchaeota, Aigarchaeota, Nanoarchaeota, Korarchaeota, Parvarchaeota, Aenigmarchaeota, Diapherotrites, and Nanohaloarchaeota) which have also been given the same taxonomic status of kingdoms. However, the phylogenetic position of some of these lineages is controversial. In addition, phylogenetic analyses of the Archaea have often been carried out without outgroup sequences, making it difficult to determine if these taxa actually define lineages at the same level as the Euryarchaeota and Crenarchaeota. We have addressed the question of the position of the root of the Archaea by reconstructing rooted archaeal phylogenetic trees using bacterial sequences as outgroup. These trees were based on commonly used conserved protein markers (32 ribosomal proteins) as well as on 38 new markers identified through phylogenomic analysis. We thus gathered a total of 70 conserved markers that we analyzed as a concatenated data set. In contrast with previous analyses, our trees consistently placed the root of the archaeal tree between the Euryarchaeota (including the Nanoarchaeota and other fast-evolving lineages) and the rest of archaeal species, which we propose to class within the new kingdom Proteoarchaeota. This implies the relegation of several groups previously classified as kingdoms (e.g., Crenarchaeota, Thaumarchaeota, Aigarchaeota, and Korarchaeota) to a lower taxonomic rank. In addition to taxonomic implications, this profound reorganization of the archaeal phylogeny has also consequences on our appraisal of the nature of the last archaeal ancestor, which most likely was a complex organism with a gene-rich genome.},
}
@article {pmid25527539,
year = {2015},
author = {Lever, MA and Teske, AP},
title = {Diversity of methane-cycling archaea in hydrothermal sediment investigated by general and group-specific PCR primers.},
journal = {Applied and environmental microbiology},
volume = {81},
number = {4},
pages = {1426-1441},
pmid = {25527539},
issn = {1098-5336},
mesh = {Archaea/classification/genetics/*isolation &amp; purification/*metabolism ; Biodiversity ; DNA Primers/genetics ; Geologic Sediments/chemistry/*microbiology ; Methane/*metabolism ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; Species Specificity ; },
abstract = {The zonation of anaerobic methane-cycling Archaea in hydrothermal sediment of Guaymas Basin was studied by general primerpairs (mcrI, ME1/ME2, mcrIRD) targeting the alpha subunit of methyl coenzyme M reductase gene (mcrA) and by new group specific mcrA and 16S rRNA gene primer pairs. The mcrIRD primer pair outperformed the other general mcrA primer pairs indetection sensitivity and phylogenetic coverage. Methanotrophic ANME-1 Archaea were the only group detected with group specific primers only. The detection of 14 mcrA lineages surpasses the diversity previously found in this location. Most phylotypes have high sequence similarities to hydrogenotrophs, methylotrophs, and anaerobic methanotrophs previously detected at Guaymas Basin or at hydrothermal vents, cold seeps, and oil reservoirs worldwide. Additionally, five mcrA phylotypes belonging to newly defined lineages are detected. Two of these belong to deeply branching new orders, while the others are new species or genera of Methanopyraceae and Methermicoccaceae. Downcore diversity decreases from all groups detected in the upper 6 cm(2 to 40 °C, sulfate measurable to 4 cm) to only two groups below 6 cm (>40 °C). Despite the presence of hyperthermophilic genera (Methanopyrus, Methanocaldococcus) in cooler surface strata, no genes were detected below 10 cm (>60 °C). While mcrAbased and 16S rRNA gene-based community compositions are generally congruent, the deeply branching mcrA cannot be assigned to specific 16S rRNA gene lineages. Our study indicates that even among well-studied metabolic groups and in previously characterized model environments, major evolutionary branches are overlooked. Detecting these groups by improved molecular biological methods is a crucial first step toward understanding their roles in nature.},
}
@article {pmid25525409,
year = {2014},
author = {Wei, S and Cui, H and He, H and Hu, F and Su, X and Zhu, Y},
title = {Diversity and distribution of archaea community along a stratigraphic permafrost profile from Qinghai-Tibetan Plateau, China.},
journal = {Archaea (Vancouver, B.C.)},
volume = {2014},
number = {},
pages = {240817},
pmid = {25525409},
issn = {1472-3654},
mesh = {*Biota ; Cluster Analysis ; Crenarchaeota/*classification/genetics/*isolation &amp; purification ; DNA, Archaeal/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Denaturing Gradient Gel Electrophoresis ; Euryarchaeota/*classification/genetics/*isolation &amp; purification ; Molecular Sequence Data ; Permafrost/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Tibet ; },
abstract = {Accompanying the thawing permafrost expected to result from the climate change, microbial decomposition of the massive amounts of frozen organic carbon stored in permafrost is a potential emission source of greenhouse gases, possibly leading to positive feedbacks to the greenhouse effect. In this study, the community composition of archaea in stratigraphic soils from an alpine permafrost of Qinghai-Tibetan Plateau was investigated. Phylogenic analysis of 16S rRNA sequences revealed that the community was predominantly constituted by Crenarchaeota and Euryarchaeota. The active layer contained a proportion of Crenarchaeota at 51.2%, with the proportion of Euryarchaeota at 48.8%, whereas the permafrost contained 41.2% Crenarchaeota and 58.8% Euryarchaeota, based on 16S rRNA gene sequence analysis. OTU1 and OTU11, affiliated to Group 1.3b/MCG-A within Crenarchaeota and the unclassified group within Euryarchaeota, respectively, were widely distributed in all sediment layers. However, OTU5 affiliated to Group 1.3b/MCG-A was primarily distributed in the active layers. Sequence analysis of the DGGE bands from the 16S rRNAs of methanogenic archaea showed that the majority of methanogens belonged to Methanosarcinales and Methanomicrobiales affiliated to Euryarchaeota and the uncultured ZC-I cluster affiliated to Methanosarcinales distributed in all the depths along the permafrost profile, which indicated a dominant group of methanogens occurring in the cold ecosystems.},
}
@article {pmid25522598,
year = {2014},
author = {Zheng, Y and Wang, X and Gu, Y and Zhang, X},
title = {[Diversity of ammonia-oxidizing archaea in Tibetan Zoige plateau wetland ].},
journal = {Wei sheng wu xue bao = Acta microbiologica Sinica},
volume = {54},
number = {9},
pages = {1090-1096},
pmid = {25522598},
issn = {0001-6209},
mesh = {Ammonia/*metabolism ; Archaea/classification/genetics/*isolation &amp; purification/*metabolism ; *Biodiversity ; Ecosystem ; Molecular Sequence Data ; Oxidation-Reduction ; Phylogeny ; Soil/chemistry ; *Soil Microbiology ; Tibet ; },
abstract = {[ OBJECTIVE ] Investigation of ammonia-oxidizing archaea (AOA) in nature environments is important to understand the global nitrogen cycling. However, little is known about the AOA community in plateau wetland. Therefore, we studied the composition and diversity of AOA in Zoige plateau wetland swamp soil. [METHODS] Total DNA was extracted from the swamp soil of three typical wetlands including A'xi pastoral area, Maixi pastoral area and Fenqu pastoral area locate in Zoige plateau wetland, and amoA gene was amplified with universally AOA amoA gene primers and then cloned. Then 80 positive clones for each clone library were chosen for further restriction fragment length polymorphism (RFLP) analysis, and the typical RFLP types were selected for sequencing and clustered into operational taxonomic units (OTUs) at 98% cutoff using the Mothur software. The MEGA 5. 0 software was used for the amoA gene phylogeny analysis. [RESULTS] A total of 240 positive clones for all 3 libraries were used for RFLP analysis, and 15 specific amoA sequences were sequenced and clustered into 7 OTUs at 98% cutoff. Among them, OTU6 was detected in all of the 3 libraries and included 27% of the total specific clones. The phylogeny analysis showed that the 15 amoA sequences were grouped into 3 subgroups consisted of Zoige Wetland Clade 1 (4 OTUs), Zoige Wetland Clade 2 (2 OTUs) and Zoige Wetland Clade 3 (1 OTU). BLAST analysis showed that all OTUs were affiliated with the phylum Crenarchaeota. Correlation analysis showed that the Shannon diversity index (H') was significantly correlated with ammonia, nitrate/nitrite (P <0. 05). [ CONCLUSION] AOA in the Zoige plateau wetland swamp soil are all belonged to the Crenarchaeota, and their diversity is significantly correlated with soil ammonia, nitrate/nitrite content.},
}
@article {pmid25522589,
year = {2014},
author = {Wul, J and Cai, S and Liu, H and Hou, J and Han, J and Zhou, J and Hua, X},
title = {[Development of PhaP-tagged protein expression and purification systems for extremely halophilic archaea ].},
journal = {Wei sheng wu xue bao = Acta microbiologica Sinica},
volume = {54},
number = {9},
pages = {998-1009},
pmid = {25522589},
issn = {0001-6209},
mesh = {Amino Acid Sequence ; Archaeal Proteins/*genetics/isolation &amp; purification/metabolism ; Bacterial Proteins/*genetics/isolation &amp; purification/metabolism ; Chromatography, Affinity ; Cloning, Molecular ; DNA-Binding Proteins/*genetics/isolation &amp; purification/metabolism ; Genetic Vectors/genetics/metabolism ; Haloferax mediterranei/genetics/*metabolism ; Mutagenesis, Site-Directed ; Polyhydroxyalkanoates/biosynthesis ; Recombinant Fusion Proteins/chemistry/*genetics/*isolation &amp; purification ; Sodium Chloride/*metabolism ; },
abstract = {[ OBJECTIVE] To establish a convenient halophilic protein expression and purification system based on the haloarchaeal-type PhaP and polyhydroxyalkanoate (PHA) granule. [METHODS] We cloned a strong haloarchaeal promoter and the phaP-tag into the haloarchaea- Escherichia coli shuttle vector pWL502, and then used the constructed vector to express the PhaP-tagged haloarchaeal proteins in the phaP-deleted strain Haloferax mediterranei AphaP. We purified the PhaP-fusion proteins, which were associated with PHA granules, by sucrose density gradient centrifugation. We also inserted a haloarchaeal intein-containing fragment between phaP and multiple cloning sites, and modulated the intein splicing activity by site-directed mutagenesis. [RESULTS] We successfully constructed two expression vectors, pPM and pIP, in which PhaP was used as N-terminal and C-terminal fusion tag, respectively. The haloarchaeal proteins were effectively expressed by both vectors. The PhaP-tagged proteins were easily purified through the strategy of PHA granulemediated protein purification. In addition, we found that the intein-containing fragment Hbt21 from Halobacterium sp. NRC-1 had maintained splicing activity in H. mediterranei, and its C-terminal cleavage could be blocked or attenuated by mutating the conserved asparagine (N182) or serine (S183) , respectively. [ CONCLUSION] We have established a convenient and economical halophilic protein expression and purification system. We have also identified the splicing active sites of a haloarchaeal intein, which showed potential for removing the PhaP-tag from the purified proteins.},
}
@article {pmid25514401,
year = {2015},
author = {Zhang, J and Zhang, Y and Quan, X and Chen, S},
title = {Enhancement of anaerobic acidogenesis by integrating an electrochemical system into an acidogenic reactor: effect of hydraulic retention times (HRT) and role of bacteria and acidophilic methanogenic Archaea.},
journal = {Bioresource technology},
volume = {179},
number = {},
pages = {43-49},
doi = {10.1016/j.biortech.2014.11.102},
pmid = {25514401},
issn = {1873-2976},
mesh = {Acids/chemistry ; Anaerobiosis ; Archaea/*metabolism ; Bacteria/*metabolism ; Biological Oxygen Demand Analysis ; Bioreactors/*microbiology ; Cluster Analysis ; Electrochemistry/*methods ; Electrodes ; Fatty Acids, Volatile/analysis ; Hydrogen-Ion Concentration ; Iron/analysis ; Methane/*metabolism ; Polysaccharides/analysis ; Real-Time Polymerase Chain Reaction ; Sequence Analysis, DNA ; Sewage/microbiology ; Time Factors ; Waste Disposal, Fluid ; },
abstract = {In this study, an acidogenic reactor packed with a pair of Fe-carbon electrodes (R1) was developed to enhance anaerobic acidogenesis of organic wastewater at short hydraulic retention times. The results indicated that the acidogenic efficiency was improved by settling a bio-electrochemical system. When hydraulic retention times decreased from 12 to 3h, R1 showed 18.9% more chemical oxygen demand removal and 13.8% more acidification efficiency. After cutting off the voltage of R1, the COD removal decreased by about 5%. Coupling of Fe(2+) leaching and electric field accelerated the hydrolysis of polysaccharide, relieving its accumulation in the sludge phase. Several acidophilic methanogenic Archaea such as Methanosarcina sp. were enriched in R1, which was favorable for consuming organic acids and preventing excessive pH decline. Thus, the developed acidogenic reactor with Fe-carbon electrodes is expected to be potentially effective and useful for wastewater treatment.},
}
@article {pmid25501889,
year = {2015},
author = {Stempfhuber, B and Engel, M and Fischer, D and Neskovic-Prit, G and Wubet, T and Schöning, I and Gubry-Rangin, C and Kublik, S and Schloter-Hai, B and Rattei, T and Welzl, G and Nicol, GW and Schrumpf, M and Buscot, F and Prosser, JI and Schloter, M},
title = {pH as a Driver for Ammonia-Oxidizing Archaea in Forest Soils.},
journal = {Microbial ecology},
volume = {69},
number = {4},
pages = {879-883},
pmid = {25501889},
issn = {1432-184X},
mesh = {Ammonia/*metabolism ; Archaea/*physiology ; *Forests ; Germany ; Hydrogen-Ion Concentration ; *Microbiota ; Oxidation-Reduction ; Soil/chemistry ; *Soil Microbiology ; },
abstract = {In this study, we investigated the impact of soil pH on the diversity and abundance of archaeal ammonia oxidizers in 27 different forest soils across Germany. DNA was extracted from topsoil samples, the amoA gene, encoding ammonia monooxygenase, was amplified; and the amplicons were sequenced using a 454-based pyrosequencing approach. As expected, the ratio of archaeal (AOA) to bacterial (AOB) ammonia oxidizers' amoA genes increased sharply with decreasing soil pH. The diversity of AOA differed significantly between sites with ultra-acidic soil pH (<3.5) and sites with higher pH values. The major OTUs from soil samples with low pH could be detected at each site with a soil pH <3.5 but not at sites with pH >4.5, regardless of geographic position and vegetation. These OTUs could be related to the Nitrosotalea group 1.1 and the Nitrososphaera subcluster 7.2, respectively, and showed significant similarities to OTUs described from other acidic environments. Conversely, none of the major OTUs typical of sites with a soil pH >4.6 could be found in the ultra- and extreme acidic soils. Based on a comparison with the amoA gene sequence data from a previous study performed on agricultural soils, we could clearly show that the development of AOA communities in soils with ultra-acidic pH (<3.5) is mainly triggered by soil pH and is not influenced significantly by the type of land use, the soil type, or the geographic position of the site, which was observed for sites with acido-neutral soil pH.},
}
@article {pmid25501484,
year = {2015},
author = {Timmers, PH and Gieteling, J and Widjaja-Greefkes, HC and Plugge, CM and Stams, AJ and Lens, PN and Meulepas, RJ},
title = {Growth of anaerobic methane-oxidizing archaea and sulfate-reducing bacteria in a high-pressure membrane capsule bioreactor.},
journal = {Applied and environmental microbiology},
volume = {81},
number = {4},
pages = {1286-1296},
pmid = {25501484},
issn = {1098-5336},
support = {323009/ERC_/European Research Council/International ; },
mesh = {Archaea/classification/*growth &amp; development/isolation &amp; purification/metabolism ; Bioreactors/*microbiology ; Ecosystem ; Geologic Sediments/microbiology ; Methane/chemistry/*metabolism ; Molecular Sequence Data ; Oxidation-Reduction ; Phylogeny ; Pressure ; Sulfates/analysis/metabolism ; Sulfur-Reducing Bacteria/classification/*growth &amp; development/isolation &amp; purification/metabolism ; },
abstract = {Communities of anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria (SRB) grow slowly, which limits the ability to perform physiological studies. High methane partial pressure was previously successfully applied to stimulate growth, but it is not clear how different ANME subtypes and associated SRB are affected by it. Here, we report on the growth of ANME-SRB in a membrane capsule bioreactor inoculated with Eckernförde Bay sediment that combines high-pressure incubation (10.1 MPa methane) and thorough mixing (100 rpm) with complete cell retention by a 0.2-m-pore-size membrane. The results were compared to previously obtained data from an ambient-pressure (0.101 MPa methane) bioreactor inoculated with the same sediment. The rates of oxidation of labeled methane were not higher at 10.1 MPa, likely because measurements were done at ambient pressure. The subtype ANME-2a/b was abundant in both reactors, but subtype ANME-2c was enriched only at 10.1 MPa. SRB at 10.1 MPa mainly belonged to the SEEP-SRB2 and Eel-1 groups and the Desulfuromonadales and not to the typically found SEEP-SRB1 group. The increase of ANME-2a/b occurred in parallel with the increase of SEEP-SRB2, which was previously found to be associated only with ANME-2c. Our results imply that the syntrophic association is flexible and that methane pressure and sulfide concentration influence the growth of different ANME-SRB consortia. We also studied the effect of elevated methane pressure on methane production and oxidation by a mixture of methanogenic and sulfate-reducing sludge. Here, methane oxidation rates decreased and were not coupled to sulfide production, indicating trace methane oxidation during net methanogenesis and not anaerobic methane oxidation, even at a high methane partial pressure.},
}
@article {pmid25479061,
year = {2014},
author = {Bagchi, S and Vlaeminck, SE and Sauder, LA and Mosquera, M and Neufeld, JD and Boon, N},
title = {Temporal and spatial stability of ammonia-oxidizing archaea and bacteria in aquarium biofilters.},
journal = {PloS one},
volume = {9},
number = {12},
pages = {e113515},
pmid = {25479061},
issn = {1932-6203},
mesh = {Ammonia/metabolism ; Archaea/genetics/*metabolism ; Bacteria/metabolism ; Filtration ; Fresh Water/chemistry/*microbiology ; *Oxidation-Reduction ; Oxidoreductases ; RNA, Ribosomal, 16S/*genetics ; Soil Microbiology ; },
abstract = {Nitrifying biofilters are used in aquaria and aquaculture systems to prevent accumulation of ammonia by promoting rapid conversion to nitrate via nitrite. Ammonia-oxidizing archaea (AOA), as opposed to ammonia-oxidizing bacteria (AOB), were recently identified as the dominant ammonia oxidizers in most freshwater aquaria. This study investigated biofilms from fixed-bed aquarium biofilters to assess the temporal and spatial dynamics of AOA and AOB abundance and diversity. Over a period of four months, ammonia-oxidizing microorganisms from six freshwater and one marine aquarium were investigated at 4-5 time points. Nitrogen balances for three freshwater aquaria showed that active nitrification by aquarium biofilters accounted for ≥ 81-86% of total nitrogen conversion in the aquaria. Quantitative PCR (qPCR) for bacterial and thaumarchaeal ammonia monooxygenase (amoA) genes demonstrated that AOA were numerically dominant over AOB in all six freshwater aquaria tested, and contributed all detectable amoA genes in three aquarium biofilters. In the marine aquarium, however, AOB outnumbered AOA by three to five orders of magnitude based on amoA gene abundances. A comparison of AOA abundance in three carrier materials (fine sponge, rough sponge and sintered glass or ceramic rings) of two three-media freshwater biofilters revealed preferential growth of AOA on fine sponge. Denaturing gel gradient electrophoresis (DGGE) of thaumarchaeal 16S rRNA genes indicated that community composition within a given biofilter was stable across media types. In addition, DGGE of all aquarium biofilters revealed low AOA diversity, with few bands, which were stable over time. Nonmetric multidimensional scaling (NMDS) based on denaturing gradient gel electrophoresis (DGGE) fingerprints of thaumarchaeal 16S rRNA genes placed freshwater and marine aquaria communities in separate clusters. These results indicate that AOA are the dominant ammonia-oxidizing microorganisms in freshwater aquarium biofilters, and that AOA community composition within a given aquarium is stable over time and across biofilter support material types.},
}
@article {pmid25473158,
year = {2014},
author = {Gaci, N and Borrel, G and Tottey, W and O'Toole, PW and Brugère, JF},
title = {Archaea and the human gut: new beginning of an old story.},
journal = {World journal of gastroenterology},
volume = {20},
number = {43},
pages = {16062-16078},
pmid = {25473158},
issn = {2219-2840},
mesh = {Breath Tests ; Disease ; Euryarchaeota/classification/genetics/growth &amp; development/*metabolism ; Evolution, Molecular ; Gastrointestinal Tract/metabolism/*physiology ; Host-Pathogen Interactions ; Humans ; Methane/*metabolism ; *Microbiota ; Phylogeny ; },
abstract = {Methanogenic archaea are known as human gut inhabitants since more than 30 years ago through the detection of methane in the breath and isolation of two methanogenic species belonging to the order Methanobacteriales, Methanobrevibacter smithii and Methanosphaera stadtmanae. During the last decade, diversity of archaea encountered in the human gastrointestinal tract (GIT) has been extended by sequence identification and culturing of new strains. Here we provide an updated census of the archaeal diversity associated with the human GIT and their possible role in the gut physiology and health. We particularly focus on the still poorly characterized 7th order of methanogens, the Methanomassiliicoccales, associated to aged population. While also largely distributed in non-GIT environments, our actual knowledge on this novel order of methanogens has been mainly revealed through GIT inhabitants. They enlarge the number of final electron acceptors of the gut metabolites to mono- di- and trimethylamine. Trimethylamine is exclusively a microbiota-derived product of nutrients (lecithin, choline, TMAO, L-carnitine) from normal diet, from which seems originate two diseases, trimethylaminuria (or Fish-Odor Syndrome) and cardiovascular disease through the proatherogenic property of its oxidized liver-derived form. This therefore supports interest on these methanogenic species and its use as archaebiotics, a term coined from the notion of archaea-derived probiotics.},
}
@article {pmid25472601,
year = {2015},
author = {Hugoni, M and Domaizon, I and Taib, N and Biderre-Petit, C and Agogué, H and Galand, PE and Debroas, D and Mary, I},
title = {Temporal dynamics of active Archaea in oxygen-depleted zones of two deep lakes.},
journal = {Environmental microbiology reports},
volume = {7},
number = {2},
pages = {321-329},
doi = {10.1111/1758-2229.12251},
pmid = {25472601},
issn = {1758-2229},
mesh = {Ammonia/analysis ; Archaea/*classification/genetics/*growth &amp; development ; *Biota ; DNA, Archaeal/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Gene Expression Profiling ; Lakes/*microbiology ; Nitrification ; Oxidoreductases/genetics ; Oxygen/analysis ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Spatio-Temporal Analysis ; Water/chemistry ; },
abstract = {Deep lakes are of specific interest in the study of archaeal assemblages as chemical stratification in the water column allows niche differentiation and distinct community structure. Active archaeal community and potential nitrifiers were investigated monthly over 1 year by pyrosequencing 16S rRNA transcripts and genes, and by quantification of archaeal amoA genes in two deep lakes. Our results showed that the active archaeal community patterns of spatial and temporal distribution were different between these lakes. The meromictic lake characterized by a stable redox gradient but variability in nutrient concentrations exhibited large temporal rearrangements of the dominant euryarchaeal phylotypes, suggesting a variety of ecological niches and dynamic archaeal communities in the hypolimnion of this lake. Conversely, Thaumarchaeota Marine Group I (MGI) largely dominated in the second lake where deeper water layers exhibited only short periods of complete anoxia and constant low ammonia concentrations. Investigations conducted on archaeal amoA transcripts abundance suggested that not all lacustrine Thaumarchaeota conduct the process of nitrification. A high number of 16S rRNA transcripts associated to crenarchaeal group C3 or the Miscellaneous Euryarchaeotic Group indicates the potential for these uncharacterized groups to contribute to nutrient cycling in lakes.},
}
@article {pmid25462589,
year = {2014},
author = {Gschwendtner, S and Tejedor, J and Bimüller, C and Dannenmann, M and Kögel-Knabner, I and Schloter, M},
title = {Climate change induces shifts in abundance and activity pattern of bacteria and archaea catalyzing major transformation steps in nitrogen turnover in a soil from a mid-European beech forest.},
journal = {PloS one},
volume = {9},
number = {12},
pages = {e114278},
pmid = {25462589},
issn = {1932-6203},
mesh = {Archaea/*metabolism ; Bacteria/*metabolism ; Catalysis ; *Climate Change ; Europe ; Fagus/*metabolism ; Nitrogen/*metabolism ; *Soil ; },
abstract = {Ongoing climate change will lead to more extreme weather events, including severe drought periods and intense drying rewetting cycles. This will directly influence microbial nitrogen (N) turnover rates in soil by changing the water content and the oxygen partial pressure. Therefore, a space for time climate change experiment was conducted by transferring intact beech seedling-soil mesocosms from a northwest (NW) exposed site, representing today's climatic conditions, to a southwest (SW) exposed site, providing a model climate for future conditions with naturally occurring increased soil temperature (+0.8°C in average). In addition, severe drought and intense rainfall was simulated by a rainout shelter at SW and manual rewetting after 39 days drought, respectively. Soil samples were taken in June, at the end of the drought period (August), 24 and 72 hours after rewetting (August) and after a regeneration period of four weeks (September). To follow dynamics of bacterial and archaeal communities involved in N turnover, abundance and activity of nitrifiers, denitrifiers, N2-fixing microbes and N-mineralizers was analyzed based on marker genes and the related transcripts by qPCR from DNA and RNA directly extracted from soil. Abundance of the transcripts was reduced under climate change with most pronounced effects for denitrification. Our results revealed that already a transfer from NW to SW without further treatment resulted in decreased cnor and nosZ transcripts, encoding for nitric oxide reductase and nitrous oxide reductase, respectively, while nirK transcripts, encoding for nitrite reductase, remained unaffected. Severe drought additionally led to reduced nirK and cnor transcripts at SW. After rewetting, nirK transcripts increased rapidly at both sites, while cnor and nosZ transcripts increased only at NW. Our data indicate that the climate change influences activity pattern of microbial communities involved in denitrification processes to a different extend, which may impact emission rates of the greenhouse gas N2O.},
}
@article {pmid25460192,
year = {2015},
author = {Brablcová, L and Buriánková, I and Badurová, P and Chaudhary, PP and Rulík, M},
title = {Methanogenic archaea diversity in hyporheic sediments of a small lowland stream.},
journal = {Anaerobe},
volume = {32},
number = {},
pages = {24-31},
doi = {10.1016/j.anaerobe.2014.11.009},
pmid = {25460192},
issn = {1095-8274},
mesh = {Archaea/classification/*genetics/*metabolism ; *Biodiversity ; Czech Republic ; Denaturing Gradient Gel Electrophoresis ; Environment ; Geologic Sediments/*microbiology ; Methane/*metabolism ; Phylogeny ; *Rivers/microbiology ; Sequence Analysis, DNA ; },
abstract = {Abundance and diversity of methanogenic archaea were studied at five localities along a longitudinal profile of a Sitka stream (Czech Republic). Samples of hyporheic sediments were collected from two sediment depths (0-25 cm and 25-50 cm) by freeze-core method. Methanogen community was analyzed by fluorescence in situ hybridization (FISH), denaturing gradient gel electrophoresis (DGGE) and sequencing method. The proportion of methanogens to the DAPI-stained cells varied among all localities and depths with an average value 2.08 × 10(5) per g of dry sediment with the range from 0.37 to 4.96 × 10(5) cells per g of dry sediment. A total of 73 bands were detected at 19 different positions on the DGGE gel and the highest methanogen diversity was found at the downstream located sites. There was no relationship between methanogen diversity and sediment depth. Cluster analysis of DGGE image showed three main clusters consisting of localities that differed in the number and similarity of the DGGE bands. Sequencing analysis of representative DGGE bands revealed phylotypes affiliated with members belonging to the orders Methanosarcinales, Methanomicrobiales and Methanocellales. The knowledge about occurrence and diversity of methanogenic archaea in freshwater ecosystems are essential for methane dynamics in river sediments and can contribute to the understanding of global warming process.},
}
@article {pmid25427790,
year = {2015},
author = {Mueller, TJ and Grisewood, MJ and Nazem-Bokaee, H and Gopalakrishnan, S and Ferry, JG and Wood, TK and Maranas, CD},
title = {Methane oxidation by anaerobic archaea for conversion to liquid fuels.},
journal = {Journal of industrial microbiology &amp; biotechnology},
volume = {42},
number = {3},
pages = {391-401},
pmid = {25427790},
issn = {1476-5535},
mesh = {Anaerobiosis ; Archaea/*metabolism ; Biofuels/*supply &amp; distribution ; Carbon Cycle ; Carbon Dioxide/metabolism ; Methane/*metabolism ; Oxidation-Reduction ; Oxidoreductases/metabolism ; },
abstract = {Given the recent increases in natural gas reserves and associated drawbacks of current gas-to-liquids technologies, the development of a bioconversion process to directly convert methane to liquid fuels would generate considerable industrial interest. Several clades of anaerobic methanotrophic archaea (ANME) are capable of performing anaerobic oxidation of methane (AOM). AOM carried out by ANME offers carbon efficiency advantages over aerobic oxidation by conserving the entire carbon flux without losing one out of three carbon atoms to carbon dioxide. This review highlights the recent advances in understanding the key enzymes involved in AOM (i.e., methyl-coenzyme M reductase), the ecological niches of a number of ANME, the putative metabolic pathways for AOM, and the syntrophic consortia that they typically form.},
}
@article {pmid25420929,
year = {2015},
author = {Martens-Habbena, W and Qin, W and Horak, RE and Urakawa, H and Schauer, AJ and Moffett, JW and Armbrust, EV and Ingalls, AE and Devol, AH and Stahl, DA},
title = {The production of nitric oxide by marine ammonia-oxidizing archaea and inhibition of archaeal ammonia oxidation by a nitric oxide scavenger.},
journal = {Environmental microbiology},
volume = {17},
number = {7},
pages = {2261-2274},
doi = {10.1111/1462-2920.12677},
pmid = {25420929},
issn = {1462-2920},
mesh = {Ammonia/*metabolism ; Ammonium Compounds/metabolism ; Aquatic Organisms/metabolism ; Archaea/*metabolism ; Betaproteobacteria/metabolism ; Cyclic N-Oxides/*pharmacology ; Denitrification ; Imidazoles/*pharmacology ; Nitric Oxide/biosynthesis/*metabolism ; *Nitrification ; Nitrogen/metabolism ; Oxidation-Reduction ; Thiourea/*analogs &amp; derivatives/pharmacology ; },
abstract = {Nitrification is a critical process for the balance of reduced and oxidized nitrogen pools in nature, linking mineralization to the nitrogen loss processes of denitrification and anammox. Recent studies indicate a significant contribution of ammonia-oxidizing archaea (AOA) to nitrification. However, quantification of the relative contributions of AOA and ammonia-oxidizing bacteria (AOB) to in situ ammonia oxidation remains challenging. We show here the production of nitric oxide (NO) by Nitrosopumilus maritimus SCM1. Activity of SCM1 was always associated with the release of NO with quasi-steady state concentrations between 0.05 and 0.08 μM. NO production and metabolic activity were inhibited by the nitrogen free radical scavenger 2-phenyl-4,4,5,5,-tetramethylimidazoline-1-oxyl-3-oxide (PTIO). Comparison of marine and terrestrial AOB strains with SCM1 and the recently isolated marine AOA strain HCA1 demonstrated a differential sensitivity of AOB and AOA to PTIO and allylthiourea (ATU). Similar to the investigated AOA strains, bulk water column nitrification at coastal and open ocean sites with sub-micromolar ammonia/ammonium concentrations was inhibited by PTIO and insensitive to ATU. These experiments support predictions from kinetic, molecular and biogeochemical studies, indicating that marine nitrification at low ammonia/ammonium concentrations is largely driven by archaea and suggest an important role of NO in the archaeal metabolism.},
}
@article {pmid25420454,
year = {2014},
author = {Rzechorzek, NJ and Blackwood, JK and Bray, SM and Maman, JD and Pellegrini, L and Robinson, NP},
title = {Structure of the hexameric HerA ATPase reveals a mechanism of translocation-coupled DNA-end processing in archaea.},
journal = {Nature communications},
volume = {5},
number = {},
pages = {5506},
pmid = {25420454},
issn = {2041-1723},
support = {/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 104641//Wellcome Trust/United Kingdom ; G0701443/MRC_/Medical Research Council/United Kingdom ; 08279/Z/07/Z/WT_/Wellcome Trust/United Kingdom ; //Wellcome Trust/United Kingdom ; 084279//Wellcome Trust/United Kingdom ; },
mesh = {Adenosine Triphosphatases/*chemistry/genetics/*metabolism ; Amino Acid Sequence ; Archaea/chemistry/*enzymology/genetics ; Archaeal Proteins/chemistry/genetics/*metabolism ; DNA Breaks, Double-Stranded ; DNA, Archaeal/*genetics/metabolism ; Deoxyribonucleases/genetics/metabolism ; Models, Molecular ; Molecular Sequence Data ; Sequence Alignment ; *Translocation, Genetic ; },
abstract = {The HerA ATPase cooperates with the NurA nuclease and the Mre11-Rad50 complex for the repair of double-strand DNA breaks in thermophilic archaea. Here we extend our structural knowledge of this minimal end-resection apparatus by presenting the first crystal structure of hexameric HerA. The full-length structure visualizes at atomic resolution the N-terminal HerA-ATP synthase domain and a conserved C-terminal extension, which acts as a physical brace between adjacent protomers. The brace also interacts in trans with nucleotide-binding residues of the neighbouring subunit. Our observations support a model in which the coaxial interaction of the HerA ring with the toroidal NurA dimer generates a continuous channel traversing the complex. HerA-driven translocation would propel the DNA towards the narrow annulus of NurA, leading to duplex melting and nucleolytic digestion. This system differs substantially from the bacterial end-resection paradigms. Our findings suggest a novel mode of DNA-end processing by this integrated archaeal helicase-nuclease machine.},
}
@article {pmid25414355,
year = {2015},
author = {Stoddard, SF and Smith, BJ and Hein, R and Roller, BR and Schmidt, TM},
title = {rrnDB: improved tools for interpreting rRNA gene abundance in bacteria and archaea and a new foundation for future development.},
journal = {Nucleic acids research},
volume = {43},
number = {Database issue},
pages = {D593-8},
pmid = {25414355},
issn = {1362-4962},
support = {R01 GM099549/GM/NIGMS NIH HHS/United States ; M0099549//PHS HHS/United States ; },
mesh = {Archaea/classification ; Bacteria/classification ; *Databases, Nucleic Acid ; Gene Dosage ; *Genes, Archaeal ; *Genes, Bacterial ; *Genes, rRNA ; Genome, Archaeal ; Genome, Bacterial ; Internet ; Operon ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Software ; },
abstract = {Microbiologists utilize ribosomal RNA genes as molecular markers of taxonomy in surveys of microbial communities. rRNA genes are often co-located as part of an rrn operon, and multiple copies of this operon are present in genomes across the microbial tree of life. rrn copy number variability provides valuable insight into microbial life history, but introduces systematic bias when measuring community composition in molecular surveys. Here we present an update to the ribosomal RNA operon copy number database (rrnDB), a publicly available, curated resource for copy number information for bacteria and archaea. The redesigned rrnDB (http://rrndb.umms.med.umich.edu/) brings a substantial increase in the number of genomes described, improved curation, mapping of genomes to both NCBI and RDP taxonomies, and refined tools for querying and analyzing these data. With these changes, the rrnDB is better positioned to remain a comprehensive resource under the torrent of microbial genome sequencing. The enhanced rrnDB will contribute to the analysis of molecular surveys and to research linking genomic characteristics to life history.},
}
@article {pmid25409591,
year = {2015},
author = {Flood, M and Frabutt, D and Floyd, D and Powers, A and Ezegwe, U and Devol, A and Tiquia-Arashiro, SM},
title = {Ammonia-oxidizing bacteria and archaea in sediments of the Gulf of Mexico.},
journal = {Environmental technology},
volume = {36},
number = {1-4},
pages = {124-135},
doi = {10.1080/09593330.2014.942385},
pmid = {25409591},
issn = {0959-3330},
mesh = {Ammonia/*metabolism ; Archaea/classification/isolation &amp; purification/*physiology ; Bacteria/classification/*isolation &amp; purification ; *Bacterial Physiological Phenomena ; Geologic Sediments/*microbiology ; Gulf of Mexico ; Oxidation-Reduction ; Seawater/*microbiology ; Species Specificity ; },
abstract = {The diversity (richness and community composition) of ammonia-oxidizing archaea (AOA) and bacteria (AOB) within sediments of the Gulf of Mexico was examined. Using polymerase chain reaction primers designed to specifically target the archaeal ammonia monooxygenase-subunit (amoA) gene and bacterial amoA gene, we found AOA and AOB to be present in all three sampling sites. Archaeal amoA libraries were dominated by a few widely distributed Nitrosopumilus-like sequence types, whereas AOB diversity showed significant variation in both richness and community composition. Majority of the bacterial amoA sequences recovered belong to Betaproteobacteria and very few belong to Gammaproteobacteria. Results suggest that water depth and nutrient availability were identified as potential drivers that affected the selection of the AOA and AOB communities. Besides influencing the abundance of individual taxa, these environmental factors also had an impact on the overall richness of the overall AOA and AOB communities. The richness and diversity of AOA and AOB genes were higher at the shallowest sediments (100 m depth) and the deepest sediments (1300 m depth). The reduced diversity in the deepest sediments could be explained by much lower nutrient availability.},
}
@article {pmid25406237,
year = {2015},
author = {Liu, Q and Ren, M and Zhang, LL},
title = {Natribaculum breve gen. nov., sp. nov. and Natribaculum longum sp. nov., halophilic archaea isolated from saline soil.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {65},
number = {Pt 2},
pages = {604-608},
doi = {10.1099/ijs.0.060541-0},
pmid = {25406237},
issn = {1466-5034},
mesh = {Base Composition ; China ; DNA, Archaeal/genetics ; Genes, Archaeal ; Glycolipids/chemistry ; Halobacteriaceae/*classification/genetics/isolation &amp; purification ; Lipids/chemistry ; Molecular Sequence Data ; Nucleic Acid Hybridization ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Salinity ; Sequence Analysis, DNA ; *Soil Microbiology ; },
abstract = {Two halophilic archaeal strains, TRM20010(T) and TRM20345(T), were isolated from saline soil of the Lop Nur region in Xinjiang, north-west China. Cells from the two strains were pleomorphic rods, stained Gram-negative and produced red-pigmented colonies. Strains TRM20010(T) and TRM20345(T) were able to grow at 30-62 °C (optimum 37 °C), 0.9-5.1 M NaCl (optimum 2.6 and 3.4 M, respectively) and pH 6.0-10.0 (optimum pH 7.0-7.5) and neither strain required Mg(2+) for growth. The major polar lipids of the two strains were phosphatidylglycerol (PG), phosphatidylglycerol phosphate methyl ester (PGP-Me), two glycolipids chromatographically identical to galactosyl mannosyl glucosyl diether (TGD-1) and disulfated mannosyl glucosyl diether (S2-DGD). Phylogenetic analysis based on 16S rRNA and rpoB' genes revealed that strains TRM20010(T) and TRM20345(T) clustered together and formed a distinct clade separated from the related genera Halovivax, Haloterrigena, Halostagnicola, Natronolimnobius and Natrinema. The DNA G+C contents of strains TRM20010(T) and TRM20345(T) were 63.9 and 63.8 mol%, respectively. The DNA-DNA hybridization value between strain TRM20010(T) and strain TRM20345(T) was 42.8 %. The phenotypic, chemotaxonomic and phylogenetic properties suggested that strains TRM20010(T) and TRM20345(T) represent two novel species in a new genus within the family Halobacteriaceae, for which the names Natribaculum breve gen. nov., sp. nov. (type strain TRM20010(T) = CCTCC AB2013112(T) = NRRL B-59996(T)) and Natribaculum longum sp. nov. (type strain TRM20345(T) = CCTCC AB2013113(T) = NRRL B-59997(T)) are proposed.},
}
@article {pmid25404694,
year = {2015},
author = {Leyn, SA and Rodionov, DA},
title = {Comparative genomics of DtxR family regulons for metal homeostasis in Archaea.},
journal = {Journal of bacteriology},
volume = {197},
number = {3},
pages = {451-458},
pmid = {25404694},
issn = {1098-5530},
mesh = {Archaea/*genetics/*metabolism ; Binding Sites ; Computational Biology ; DNA, Archaeal/genetics ; Gene Order ; Genomics ; *Homeostasis ; Metals/*metabolism ; Phylogeny ; *Regulon ; Transcription Factors/*genetics/*metabolism ; },
abstract = {The DtxR family consists of metal-dependent transcription factors (DtxR-TFs) that regulate the expression of genes involved in metal homeostasis in the cell. The majority of characterized DtxR-TFs belong to Bacteria. In the current work, we applied a comparative genomics approach to predict DNA-binding sites and reconstruct regulons for DtxR-TFs in Archaea. As a result, we inferred 575 candidate binding sites for 139 DtxR-TFs in 77 genomes from 15 taxonomic orders. Novel DNA motifs of archaeal DtxR-TFs that have a common palindromic structure were classified into 10 distinct groups. By combining functional regulon reconstructions with phylogenetic analysis, we selected 28 DtxR-TF clades and assigned them metal specificities and regulator names. The reconstructed FetR (ferrous iron), MntR (manganese), and ZntR (zinc) regulons largely contain known or putative metal uptake transporters from the FeoAB, NRAMP, ZIP, and TroA families. A novel family of putative iron transporters (named Irt), including multiple FetR-regulated paralogs, was identified in iron-oxidizing Archaea from the Sulfolobales order. The reconstructed DtxR-TF regulons were reconciled with available transcriptomics data in Archaeoglobus, Halobacterium, and Thermococcus spp.},
}
@article {pmid25402442,
year = {2014},
author = {Hayden, CJ and Beman, JM},
title = {High abundances of potentially active ammonia-oxidizing bacteria and archaea in oligotrophic, high-altitude lakes of the Sierra Nevada, California, USA.},
journal = {PloS one},
volume = {9},
number = {11},
pages = {e111560},
pmid = {25402442},
issn = {1932-6203},
mesh = {*Altitude ; Ammonia/*metabolism ; Archaea/genetics/*metabolism ; Bacteria/genetics/*metabolism ; Biodiversity ; California ; Genes, Archaeal ; Genes, Bacterial ; Geography ; Lakes/*microbiology ; Nitrification ; Nitrogen Cycle ; Oxidation-Reduction ; },
abstract = {Nitrification plays a central role in the nitrogen cycle by determining the oxidation state of nitrogen and its subsequent bioavailability and cycling. However, relatively little is known about the underlying ecology of the microbial communities that carry out nitrification in freshwater ecosystems--and particularly within high-altitude oligotrophic lakes, where nitrogen is frequently a limiting nutrient. We quantified ammonia-oxidizing archaea (AOA) and bacteria (AOB) in 9 high-altitude lakes (2289-3160 m) in the Sierra Nevada, California, USA, in relation to spatial and biogeochemical data. Based on their ammonia monooxygenase (amoA) genes, AOB and AOA were frequently detected. AOB were present in 88% of samples and were more abundant than AOA in all samples. Both groups showed >100 fold variation in abundance between different lakes, and were also variable through time within individual lakes. Nutrient concentrations (ammonium, nitrite, nitrate, and phosphate) were generally low but also varied across and within lakes, suggestive of active internal nutrient cycling; AOB abundance was significantly correlated with phosphate (r(2) = 0.32, p<0.1), whereas AOA abundance was inversely correlated with lake elevation (r(2) = 0.43, p<0.05). We also measured low rates of ammonia oxidation--indicating that AOB, AOA, or both, may be biogeochemically active in these oligotrophic ecosystems. Our data indicate that dynamic populations of AOB and AOA are found in oligotrophic, high-altitude, freshwater lakes.},
}
@article {pmid25393412,
year = {2014},
author = {Becker, EA and Seitzer, PM and Tritt, A and Larsen, D and Krusor, M and Yao, AI and Wu, D and Madern, D and Eisen, JA and Darling, AE and Facciotti, MT},
title = {Phylogenetically driven sequencing of extremely halophilic archaea reveals strategies for static and dynamic osmo-response.},
journal = {PLoS genetics},
volume = {10},
number = {11},
pages = {e1004784},
pmid = {25393412},
issn = {1553-7404},
mesh = {Adaptation, Physiological/*genetics ; Archaea/*genetics ; Base Sequence ; Evolution, Molecular ; Genome, Archaeal ; Humans ; *Metagenomics ; Molecular Sequence Annotation ; Osmolar Concentration ; Phylogeny ; Salinity ; TATA-Box Binding Protein/*genetics ; },
abstract = {Organisms across the tree of life use a variety of mechanisms to respond to stress-inducing fluctuations in osmotic conditions. Cellular response mechanisms and phenotypes associated with osmoadaptation also play important roles in bacterial virulence, human health, agricultural production and many other biological systems. To improve understanding of osmoadaptive strategies, we have generated 59 high-quality draft genomes for the haloarchaea (a euryarchaeal clade whose members thrive in hypersaline environments and routinely experience drastic changes in environmental salinity) and analyzed these new genomes in combination with those from 21 previously sequenced haloarchaeal isolates. We propose a generalized model for haloarchaeal management of cytoplasmic osmolarity in response to osmotic shifts, where potassium accumulation and sodium expulsion during osmotic upshock are accomplished via secondary transport using the proton gradient as an energy source, and potassium loss during downshock is via a combination of secondary transport and non-specific ion loss through mechanosensitive channels. We also propose new mechanisms for magnesium and chloride accumulation. We describe the expansion and differentiation of haloarchaeal general transcription factor families, including two novel expansions of the TATA-binding protein family, and discuss their potential for enabling rapid adaptation to environmental fluxes. We challenge a recent high-profile proposal regarding the evolutionary origins of the haloarchaea by showing that inclusion of additional genomes significantly reduces support for a proposed large-scale horizontal gene transfer into the ancestral haloarchaeon from the bacterial domain. The combination of broad (17 genera) and deep (≥5 species in four genera) sampling of a phenotypically unified clade has enabled us to uncover both highly conserved and specialized features of osmoadaptation. Finally, we demonstrate the broad utility of such datasets, for metagenomics, improvements to automated gene annotation and investigations of evolutionary processes.},
}
@article {pmid25387612,
year = {2015},
author = {Kishishita, S and Fujii, T and Ishikawa, K},
title = {Heterologous expression of hyperthermophilic cellulases of archaea Pyrococcus sp. by fungus Talaromyces cellulolyticus.},
journal = {Journal of industrial microbiology &amp; biotechnology},
volume = {42},
number = {1},
pages = {137-141},
pmid = {25387612},
issn = {1476-5535},
mesh = {Cellulases/*biosynthesis ; *Gene Expression Regulation, Enzymologic ; Glucan 1,4-alpha-Glucosidase/genetics ; Promoter Regions, Genetic ; Pyrococcus/*enzymology/genetics ; Talaromyces/*metabolism ; },
abstract = {Talaromyces cellulolyticus (formerly known as Acremonium cellulolyticus) is one of the high cellulolytic enzyme-producing fungi. T. cellulolyticus exhibits the potential ability for high amount production of enzyme proteins. Using the homologous expression system under the control of a glucoamylase promoter, some kinds of cellulases of T. cellulolyticus can be expressed by T. cellulolyticus. On the other hand, hyperthermophilic cellulase has been expected to be useful in the industrial applications to biomass. The hyperthermophilic archaea Pyrococcus horikoshii and P. furiosus have GH family 5 and 12 hyperthermophilic endocellulase, respectively. The two kinds of hyperthermophilic endocellulases were successfully produced by T. cellulolyticus using the above expression system under the control of a glucoamylase promoter of T. cellulolyticus. These recombinant cellulases exhibited the same characteristics as those of the recombinant cellulases prepared in E. coli. The productions of the recombinant enzymes were estimated to be over 100 mg/L. In this study, we first report the overexpression of the hyperthermophilic enzymes of archaea using the fungal expression system.},
}
@article {pmid25381908,
year = {2015},
author = {Ding, K and Wen, X and Li, Y and Shen, B and Zhang, B},
title = {Ammonia-oxidizing archaea versus bacteria in two soil aquifer treatment systems.},
journal = {Applied microbiology and biotechnology},
volume = {99},
number = {3},
pages = {1337-1347},
doi = {10.1007/s00253-014-6188-3},
pmid = {25381908},
issn = {1432-0614},
mesh = {Ammonia/*metabolism ; Archaea/classification/genetics/isolation &amp; purification/*metabolism ; Bacteria/classification/genetics/isolation &amp; purification/*metabolism ; Groundwater/*microbiology ; Molecular Sequence Data ; Oxidation-Reduction ; Phylogeny ; Soil Microbiology ; Wastewater/*microbiology ; Water Purification/instrumentation/methods ; },
abstract = {So far, the contribution of ammonia-oxidizing archaea (AOA) to ammonia oxidation in wastewater treatment processes has not been well understood. In this study, two soil aquifer treatment (SATs) systems were built up to treat synthetic domestic wastewater (column 1) and secondary effluent (column 4), accomplishing an average of 95% ammonia removal during over 550 days of operation. Except at day 322, archaeal amoA genes always outnumbered bacterial amoA genes in both SATs as determined by using quantitative polymerase chain reaction (q-PCR). The ratios of archaeal amoA to 16S rRNA gene averaged at 0.70 ± 0.56 and 0.82 ± 0.62 in column 1 and column 4, respectively, indicating that all the archaea could be AOA carrying amoA gene in the SATs. The results of MiSeq-pyrosequencing targeting on archaeal and bacterial 16S rRNA genes with the primer pair of modified 515R/806R indicated that Nitrososphaera cluster affiliated with thaumarchaeal group I.1b was the dominant AOA species, while Nitrosospira cluster was the dominant ammonia-oxidizing bacteria (AOB). The statistical analysis showed significant relationship between AOA abundance (compared to AOB abundance) and inorganic and total nitrogen concentrations. Based on the mathematical model calculation for microbial growth, AOA had much greater capacity of ammonia oxidation as compared to the specific influent ammonia loading for AOA in the SATs, implying that a small fraction of the total AOA would actively work to oxidize ammonia chemoautotrophically whereas most of AOA would exhibit some level of functional redundancy. These results all pointed that AOA involved in microbial ammonia oxidation in the SATs.},
}
@article {pmid25370029,
year = {2014},
author = {Leuko, S and Rettberg, P and Pontifex, AL and Burns, BP},
title = {On the response of halophilic archaea to space conditions.},
journal = {Life (Basel, Switzerland)},
volume = {4},
number = {1},
pages = {66-76},
pmid = {25370029},
issn = {2075-1729},
abstract = {Microorganisms are ubiquitous and can be found in almost every habitat and ecological niche on Earth. They thrive and survive in a broad spectrum of environments and adapt to rapidly changing external conditions. It is of great interest to investigate how microbes adapt to different extreme environments and with modern human space travel, we added a new extreme environment: outer space. Within the last 50 years, technology has provided tools for transporting microbial life beyond Earth's protective shield in order to study in situ responses to selected conditions of space. This review will focus on halophilic archaea, as, due to their ability to survive in extremes, they are often considered a model group of organisms to study responses to the harsh conditions associated with space. We discuss ground-based simulations, as well as space experiments, utilizing archaea, examining responses and/or resistance to the effects of microgravity and UV in particular. Several halophilic archaea (e.g., Halorubrum chaoviator) have been exposed to simulated and actual space conditions and their survival has been determined as well as the protective effects of halite shown. Finally, the intriguing potential of archaea to survive on other planets or embedded in a meteorite is postulated.},
}
@article {pmid25368347,
year = {2014},
author = {Oren, A},
title = {Halophilic archaea on Earth and in space: growth and survival under extreme conditions.},
journal = {Philosophical transactions. Series A, Mathematical, physical, and engineering sciences},
volume = {372},
number = {2030},
pages = {},
doi = {10.1098/rsta.2014.0194},
pmid = {25368347},
issn = {1364-503X},
abstract = {Salts are abundant on Mars, and any liquid water that is present or may have been present on the planet is expected to be hypersaline. Halophilic archaea (family Halobacteriaceae) are the microorganisms best adapted to life at extremes of salinity on Earth. This paper reviews the properties of the Halobacteriaceae that may make the group good candidates for life also on Mars. Many species resist high UV and gamma radiation levels; one species has survived exposure to vacuum and radiation during a space flight; and there is at least one psychrotolerant species. Halophilic archaea may survive for millions of years within brine inclusions in salt crystals. Many species have different modes of anaerobic metabolism, and some can use light as an energy source using the light-driven proton pump bacteriorhodopsin. They are also highly tolerant to perchlorate, recently shown to be present in Martian soils, and some species can even use perchlorate as an electron acceptor to support anaerobic growth. The presence of characteristic carotenoid pigments (α-bacterioruberin and derivatives) makes the Halobacteriaceae easy to identify by Raman spectroscopy. Thus, if present on Mars, such organisms may be detected by Raman instrumentation planned to explore Mars during the upcoming ExoMars mission.},
}
@article {pmid25367104,
year = {2015},
author = {Pump, J and Pratscher, J and Conrad, R},
title = {Colonization of rice roots with methanogenic archaea controls photosynthesis-derived methane emission.},
journal = {Environmental microbiology},
volume = {17},
number = {7},
pages = {2254-2260},
doi = {10.1111/1462-2920.12675},
pmid = {25367104},
issn = {1462-2920},
mesh = {Euryarchaeota/classification/genetics/*metabolism ; Methane/*biosynthesis ; Oryza/*metabolism/*microbiology ; Oxidoreductases/genetics ; Photosynthesis/physiology ; Plant Roots/*microbiology ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Soil ; Soil Microbiology ; },
abstract = {The methane emitted from rice fields originates to a large part (up to 60%) from plant photosynthesis and is formed on the rice roots by methanogenic archaea. To investigate to which extent root colonization controls methane (CH4) emission, we pulse-labeled rice microcosms with (13) CO2 to determine the rates of (13) CH4 emission exclusively derived from photosynthates. We also measured emission of total CH4 ((12+13) CH4), which was largely produced in the soil. The total abundances of archaea and methanogens on the roots and in the soil were analysed by quantitative polymerase chain reaction of the archaeal 16S rRNA gene and the mcrA gene coding for a subunit of the methyl coenzyme M reductase respectively. The composition of archaeal and methanogenic communities was determined with terminal restriction fragment length polymorphism (T-RFLP). During the vegetative growth stages, emission rates of (13) CH4 linearly increased with the abundance of methanogenic archaea on the roots and then decreased during the last plant growth stage. Rates of (13) CH4 emission and the abundance of methanogenic archaea were lower when the rice was grown in quartz-vermiculite with only 10% rice soil. Rates of total CH4 emission were not systematically related to the abundance of methanogenic archaea in soil plus roots. The composition of the archaeal communities was similar under all conditions; however, the analysis of mcrA genes indicated that the methanogens differed between the soil and root. Our results support the hypothesis that rates of photosynthesis-driven CH4 emission are limited by the abundance of methanogens on the roots.},
}
@article {pmid25352841,
year = {2014},
author = {Oren, A},
title = {DNA as genetic material and as a nutrient in halophilic Archaea.},
journal = {Frontiers in microbiology},
volume = {5},
number = {},
pages = {539},
pmid = {25352841},
issn = {1664-302X},
}
@article {pmid25351144,
year = {2015},
author = {Cersosimo, LM and Lachance, H and St-Pierre, B and van Hoven, W and Wright, AD},
title = {Examination of the rumen bacteria and methanogenic archaea of wild impalas (Aepyceros melampus melampus) from Pongola, South Africa.},
journal = {Microbial ecology},
volume = {69},
number = {3},
pages = {577-585},
pmid = {25351144},
issn = {1432-184X},
mesh = {Animals ; Antelopes/*microbiology ; Archaea/classification/genetics/*isolation &amp; purification ; Bacteria/classification/genetics/*isolation &amp; purification ; *Gastrointestinal Microbiome ; Male ; Molecular Sequence Data ; RNA, Archaeal/genetics ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Rumen/microbiology ; South Africa ; },
abstract = {Although the rumen microbiome of domesticated ruminants has been evaluated, few studies have explored the rumen microbiome of wild ruminants, and no studies have identified the rumen microbiome in the impala (Aepyceros melampus melampus). In the present study, next-generation sequencing and real-time polymerase chain reaction were used to investigate the diversity and density of the bacteria and methanogenic archaea residing in the rumen of five adult male impalas, culled during the winter dry season in Pongola, South Africa. A total of 15,323 bacterial 16S rRNA gene sequences (from five impala), representing 3,892 different phylotypes, were assigned to 1,902 operational taxonomic units (OTUs). A total of 20,124 methanogen 16S rRNA gene sequence reads (from four impala), of which 5,028 were unique, were assigned to 344 OTUs. From the total sequence reads, Bacteroidetes, Proteobacteria, and Firmicutes were the most abundant bacterial phyla. While the majority of the bacterial genera found were unclassified, Prevotella and Cupriavidus were the most abundant classified genera. For methanogens, the genera Methanobrevibacter and Methanosphaera represented 94.3% and 4.0% of the classified sequences, respectively. Most notable was the identification of Methanobrevibacter thaueri-like 16S rRNA gene sequence reads in all four impala samples, representing greater than 30% of each individual's total sequences. Both data sets are accessible through NCBI's Sequence Read Archive (SRA), under study accession number SRP [048619]. The densities of bacteria (1.26 × 10(10)-3.82 × 10(10) cells/ml whole rumen contents) and methanogens (4.48 × 10(8)-7.2 × 10(9) cells/ml of whole rumen contents) from five individual impala were similar to those typically observed in domesticated ruminants.},
}
@article {pmid25344977,
year = {2014},
author = {Efenberger, M and Wódz, K and Brzezińska-Błaszczyk, E},
title = {[Archaea--the significant inhabitants of human microbiome].},
journal = {Przeglad lekarski},
volume = {71},
number = {6},
pages = {346-351},
pmid = {25344977},
issn = {0033-2240},
mesh = {Archaea/*cytology/drug effects/*physiology ; Drug Resistance, Microbial ; Gastrointestinal Diseases/microbiology ; Humans ; Microbiota/*physiology ; },
abstract = {Archaea, along with bacteria and eucarya are the three domains of life. These microorganisms inhabit variable natural environments but they are also important part of human physiological flora. In this paper we describe archaeal morphology and physiology. We also review the state of knowledge about archaea associated with human microbiome. The potential role of these microorganisms in etiopathogenesis of some human diseases is discussed, as well. Finally, we consider archaeal susceptibility/resistance to antimicrobial agents, including antibiotics.},
}
@article {pmid25344857,
year = {2015},
author = {Puthiya Veettil, V and Abdulaziz, A and Chekidhenkuzhiyil, J and Kalanthingal Ramkollath, L and Karayadi Hamza, F and Kizhakkepat Kalam, B and Kallungal Ravunnikutty, M and Nair, S},
title = {Bacterial domination over archaea in ammonia oxidation in a monsoon-driven tropical estuary.},
journal = {Microbial ecology},
volume = {69},
number = {3},
pages = {544-553},
pmid = {25344857},
issn = {1432-184X},
mesh = {Ammonia/*metabolism ; Archaea/genetics/*physiology ; *Bacterial Physiological Phenomena/genetics ; DNA, Bacterial/genetics/metabolism ; Estuaries ; India ; Molecular Sequence Data ; Oxidation-Reduction ; RNA, Ribosomal, 16S/genetics/metabolism ; Seawater/*microbiology ; Sequence Analysis, DNA ; Tropical Climate ; },
abstract = {Autotrophic ammonia oxidizing microorganisms, which are responsible for the rate-limiting step of nitrification in most aquatic systems, have not been studied in tropical estuaries. Cochin estuary (CE) is one of the largest, productive, and monsoon-driven estuary in India opening into the southeast Arabian Sea. CE receives surplus quantities of ammonia through industrial and domestic discharges. The distribution of ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA), and anaerobic ammonia-oxidizing bacteria (anammox) were studied using fluorescence in situ hybridization (FISH) and their relative contribution to the process as well as the governing factors were examined and reported for the first time from CE. The order of occurrence of these assemblages was β-proteobacteria (0.79 to 2 × 10(5) cells ml(-1)) > γ-proteobacteria (0.9 to 4.6 × 10(4) cells ml(-1)) > anammox (0.49 to 1.9 × 10(4) cells ml(-1)) > AOA (0.56 to 6.3 × 10(3) cells ml(-1)). Phylogenetic analysis of DGGE bands showed major affiliation of AOB to β-proteobacteria, while AOA was affiliated to Crenarchaeota. The abundance of AOB was mostly influenced by ammonia concentrations. The recovered ammonia oxidation rate of AOB was in the range of 45-65%, whereas for AOA, it was 15-45%, indicating that AOB were mostly responsible for the ammonia oxidation in CE during the study period. Overall, the present study provides an insight into the relevance and contribution of different groups of ammonia oxidizing bacteria in CE and emphasizes the need for further in depth studies across space and on season scale.},
}
@article {pmid25338080,
year = {2014},
author = {Jaakkola, ST and Zerulla, K and Guo, Q and Liu, Y and Ma, H and Yang, C and Bamford, DH and Chen, X and Soppa, J and Oksanen, HM},
title = {Halophilic archaea cultivated from surface sterilized middle-late eocene rock salt are polyploid.},
journal = {PloS one},
volume = {9},
number = {10},
pages = {e110533},
pmid = {25338080},
issn = {1932-6203},
mesh = {Base Sequence ; Biological Evolution ; China ; DNA, Archaeal/*genetics ; *Genome, Archaeal ; Geologic Sediments/microbiology ; Halobacteriaceae/classification/*genetics/isolation &amp; purification ; Molecular Sequence Data ; Phylogeny ; *Polyploidy ; RNA, Ribosomal, 16S/*genetics ; Salts ; },
abstract = {Live bacteria and archaea have been isolated from several rock salt deposits of up to hundreds of millions of years of age from all around the world. A key factor affecting their longevity is the ability to keep their genomic DNA intact, for which efficient repair mechanisms are needed. Polyploid microbes are known to have an increased resistance towards mutations and DNA damage, and it has been suggested that microbes from deeply buried rock salt would carry several copies of their genomes. Here, cultivable halophilic microbes were isolated from a surface sterilized middle-late Eocene (38-41 million years ago) rock salt sample, drilled from the depth of 800 m at Yunying salt mine, China. Eight unique isolates were obtained, which represented two haloarchaeal genera, Halobacterium and Halolamina. We used real-time PCR to show that our isolates are polyploid, with genome copy numbers of 11-14 genomes per cell in exponential growth phase. The ploidy level was slightly downregulated in stationary growth phase, but the cells still had an average genome copy number of 6-8. The polyploidy of halophilic archaea living in ancient rock salt might be a factor explaining how these organisms are able to overcome the challenge of prolonged survival during their entombment.},
}
@article {pmid25331558,
year = {2015},
author = {Lazar, CS and Biddle, JF and Meador, TB and Blair, N and Hinrichs, KU and Teske, AP},
title = {Environmental controls on intragroup diversity of the uncultured benthic archaea of the miscellaneous Crenarchaeotal group lineage naturally enriched in anoxic sediments of the White Oak River estuary (North Carolina, USA).},
journal = {Environmental microbiology},
volume = {17},
number = {7},
pages = {2228-2238},
doi = {10.1111/1462-2920.12659},
pmid = {25331558},
issn = {1462-2920},
mesh = {Adaptation, Physiological/*genetics ; Biodiversity ; Crenarchaeota/*classification/genetics ; DNA, Archaeal/genetics ; *Estuaries ; Geologic Sediments/*microbiology ; North Carolina ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Rivers ; },
abstract = {Sediments of the White Oak River (WOR) estuary are situated on the coast of North Carolina harbour, one of the most diverse known populations of uncultured Archaea, specifically the miscellaneous Crenarchaeotal group (MCG). In order to constrain the environmental factors influencing the uncultured archaeal groups in the WOR estuary, biogeochemical profiles as well as archaeal 16S rRNA genes from sediment pushcores were analysed. The relative fraction of MCG Archaea in clone libraries decreased at shallow sediment depths (27% of the total MCG). A LINKTREE analysis of the MCG intragroup diversity reinforced the observation that the MCG subgroup 6 was found predominantly within sulfide-depleted shallow sediment layers; other subgroups (especially MCG-1 and MCG-5/8) occurred preferentially in deeper, more strongly reducing sediment layers. The available evidence from this study and published MCG distribution patterns indicates that the MCG-6 subgroup is a specialized MCG lineage that, in contrast to other MCG subgroups, prefers suboxic sediment horizons with minimal or no free sulfide. Collectively, our results reveal the habitat preferences of different MCG subgroups in the WOR sediments and suggest that physiological adaptations to distinct sedimentary geochemical niches evolved in different MCG subgroups.},
}
@article {pmid25330320,
year = {2014},
author = {Barreto, DP and Conrad, R and Klose, M and Claus, P and Enrich-Prast, A},
title = {Distance-decay and taxa-area relationships for bacteria, archaea and methanogenic archaea in a tropical lake sediment.},
journal = {PloS one},
volume = {9},
number = {10},
pages = {e110128},
pmid = {25330320},
issn = {1932-6203},
mesh = {Archaea/*classification/genetics/*metabolism ; Bacteria/*classification/genetics ; Geologic Sediments/*microbiology ; Lakes/*microbiology ; Methane/*biosynthesis ; *Phylogeny ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The study of of the distribution of microorganisms through space (and time) allows evaluation of biogeographic patterns, like the species-area index (z). Due to their high dispersal ability, high reproduction rates and low rates of extinction microorganisms tend to be widely distributed, and they are thought to be virtually cosmopolitan and selected primarily by environmental factors. Recent studies have shown that, despite these characteristics, microorganisms may behave like larger organisms and exhibit geographical distribution. In this study, we searched patterns of spatial diversity distribution of bacteria and archaea in a contiguous environment. We collected 26 samples of a lake sediment, distributed in a nested grid, with distances between samples ranging from 0.01 m to 1000 m. The samples were analyzed using T-RFLP (Terminal restriction fragment length polymorphism) targeting mcrA (coding for a subunit of methyl-coenzyme M reductase) and the genes of Archaeal and Bacterial 16S rRNA. From the qualitative and quantitative results (relative abundance of operational taxonomic units) we calculated the similarity index for each pair to evaluate the taxa-area and distance decay relationship slopes by linear regression. All results were significant, with mcrA genes showing the highest slope, followed by Archaeal and Bacterial 16S rRNA genes. We showed that the microorganisms of a methanogenic community, that is active in a contiguous environment, display spatial distribution and a taxa-area relationship.},
}
@article {pmid25326317,
year = {2014},
author = {Li, GP and Jiang, L and Ni, JZ and Liu, Q and Zhang, Y},
title = {Computational identification of a new SelD-like family that may participate in sulfur metabolism in hyperthermophilic sulfur-reducing archaea.},
journal = {BMC genomics},
volume = {15},
number = {1},
pages = {908},
pmid = {25326317},
issn = {1471-2164},
mesh = {Amino Acid Sequence ; Archaeal Proteins/chemistry/*genetics ; Computational Biology/*methods ; Conserved Sequence ; Crenarchaeota/chemistry/*enzymology/genetics ; Gene Expression Regulation, Archaeal ; Phosphotransferases/chemistry/*genetics ; Phylogeny ; Selenium/metabolism ; Sulfur/*metabolism ; },
abstract = {BACKGROUND: Selenium (Se) and sulfur (S) are closely related elements that exhibit similar chemical properties. Some genes related to S metabolism are also involved in Se utilization in many organisms. However, the evolutionary relationship between the two utilization traits is unclear.<br><br>RESULTS: In this study, we conducted a comparative analysis of the selenophosphate synthetase (SelD) family, a key protein for all known Se utilization traits, in all sequenced archaea. Our search showed a very limited distribution of SelD and Se utilization in this kingdom. Interestingly, a SelD-like protein was detected in two orders of Crenarchaeota: Sulfolobales and Thermoproteales. Sequence and phylogenetic analyses revealed that SelD-like protein contains the same domain and conserved functional residues as those of SelD, and might be involved in S metabolism in these S-reducing organisms. Further genome-wide analysis of patterns of gene occurrence in different thermoproteales suggested that several genes, including SirA-like, Prx-like and adenylylsulfate reductase, were strongly related to SelD-like gene. Based on these findings, we proposed a simple model wherein SelD-like may play an important role in the biosynthesis of certain thiophosphate compound.<br><br>CONCLUSIONS: Our data suggest novel genes involved in S metabolism in hyperthermophilic S-reducing archaea, and may provide a new window for understanding the complex relationship between Se and S metabolism in archaea.},
}
@article {pmid25326303,
year = {2015},
author = {Li, J and Nedwell, DB and Beddow, J and Dumbrell, AJ and McKew, BA and Thorpe, EL and Whitby, C},
title = {amoA Gene abundances and nitrification potential rates suggest that benthic ammonia-oxidizing bacteria and not Archaea dominate N cycling in the Colne Estuary, United Kingdom.},
journal = {Applied and environmental microbiology},
volume = {81},
number = {1},
pages = {159-165},
pmid = {25326303},
issn = {1098-5336},
mesh = {Ammonia/*metabolism ; Archaea/*classification/genetics/isolation &amp; purification/*metabolism ; Bacteria/*classification/genetics/isolation &amp; purification/*metabolism ; Denaturing Gradient Gel Electrophoresis ; *Estuaries ; Geologic Sediments/*microbiology ; Molecular Sequence Data ; Nitrification ; Oxidation-Reduction ; Oxidoreductases/genetics ; Seasons ; Sequence Analysis, DNA ; United Kingdom ; },
abstract = {Nitrification, mediated by ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA), is important in global nitrogen cycling. In estuaries where gradients of salinity and ammonia concentrations occur, there may be differential selections for ammonia-oxidizer populations. The aim of this study was to examine the activity, abundance, and diversity of AOA and AOB in surface oxic sediments of a highly nutrified estuary that exhibits gradients of salinity and ammonium. AOB and AOA communities were investigated by measuring ammonia monooxygenase (amoA) gene abundance and nitrification potentials both spatially and temporally. Nitrification potentials differed along the estuary and over time, with the greatest nitrification potentials occurring mid-estuary (8.2 μmol N grams dry weight [gdw](-1) day(-1) in June, increasing to 37.4 μmol N gdw(-1) day(-1) in January). At the estuary head, the nitrification potential was 4.3 μmol N gdw(-1) day(-1) in June, increasing to 11.7 μmol N gdw(-1) day(-1) in January. At the estuary head and mouth, nitrification potentials fluctuated throughout the year. AOB amoA gene abundances were significantly greater (by 100-fold) than those of AOA both spatially and temporally. Nitrosomonas spp. were detected along the estuary by denaturing gradient gel electrophoresis (DGGE) band sequence analysis. In conclusion, AOB dominated over AOA in the estuarine sediments, with the ratio of AOB/AOA amoA gene abundance increasing from the upper (freshwater) to lower (marine) regions of the Colne estuary. These findings suggest that in this nutrified estuary, AOB (possibly Nitrosomonas spp.) were of major significance in nitrification.},
}
@article {pmid25324835,
year = {2014},
author = {Magalhães, CM and Machado, A and Frank-Fahle, B and Lee, CK and Cary, SC},
title = {The ecological dichotomy of ammonia-oxidizing archaea and bacteria in the hyper-arid soils of the Antarctic Dry Valleys.},
journal = {Frontiers in microbiology},
volume = {5},
number = {},
pages = {515},
pmid = {25324835},
issn = {1664-302X},
abstract = {The McMurdo Dry Valleys of Antarctica are considered to be one of the most physically and chemically extreme terrestrial environments on the Earth. However, little is known about the organisms involved in nitrogen transformations in these environments. In this study, we investigated the diversity and abundance of ammonia-oxidizing archaea (AOA) and bacteria (AOB) in four McMurdo Dry Valleys with highly variable soil geochemical properties and climatic conditions: Miers Valley, Upper Wright Valley, Beacon Valley and Battleship Promontory. The bacterial communities of these four Dry Valleys have been examined previously, and the results suggested that the extremely localized bacterial diversities are likely driven by the disparate physicochemical conditions associated with these locations. Here we showed that AOB and AOA amoA gene diversity was generally low; only four AOA and three AOB operational taxonomic units (OTUs) were identified from a total of 420 AOA and AOB amoA clones. Quantitative PCR analysis of amoA genes revealed clear differences in the relative abundances of AOA and AOB amoA genes among samples from the four dry valleys. Although AOB amoA gene dominated the ammonia-oxidizing community in soils from Miers Valley and Battleship Promontory, AOA amoA gene were more abundant in samples from Upper Wright and Beacon Valleys, where the environmental conditions are considerably harsher (e.g., extremely low soil C/N ratios and much higher soil electrical conductivity). Correlations between environmental variables and amoA genes copy numbers, as examined by redundancy analysis (RDA), revealed that higher AOA/AOB ratios were closely related to soils with high salts and Cu contents and low pH. Our findings hint at a dichotomized distribution of AOA and AOB within the Dry Valleys, potentially driven by environmental constraints.},
}
@article {pmid25320442,
year = {2014},
author = {Devivaraprasad Reddy, A and Subrahmanyam, G and Shivani Kallappa, G and Karunasagar, I and Karunasagar, I},
title = {Detection of ammonia-oxidizing archaea in fish processing effluent treatment plants.},
journal = {Indian journal of microbiology},
volume = {54},
number = {4},
pages = {434-438},
pmid = {25320442},
issn = {0046-8991},
abstract = {Ammonia oxidation is the rate limiting step in nitrification and thus have an important role in removal of ammonia in natural and engineered systems with participation of both ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). However, their relative distribution and activity in fish processing effluent treatment plants (FPETPs) though significant, is hitherto unreported. Presence of AOA in sludge samples obtained from FPETPs was studied by amplification and sequencing of thaumarchaeal ammonia monooxygenase subunit A (AOA-amoA) gene. Different primer sets targeting 16S rRNA and AOA-amoA gene were used for the detection of AOA in FPETPs. Phylogenetic analysis of the gene revealed that the AOA was affiliated with thaumarchaeal group 1.1a lineage (marine cluster). Quantitative real time PCR of amoA gene was used to study the copy number of AOA and AOB in FPETPs. The AOA-amoA and AOB-amoA gene copy numbers of sludge samples ranged from 2.2 × 10(6) to 4.2 × 10(8) and 1.1 × 10(7) to 8.5 × 10(8) mg(-1) sludge respectively. Primer sets Arch-amoAF/Arch-amoAR and 340F/1000R were found to be useful for the sensitive detection of AOA-amoA and Archaeal 16S rRNA genes respectively in FPETPs. Their presence suggests the widespread occurrence and possible usefulness in removing ammonia from FPETPs which is in line with reports from other waste water treatment plants.},
}
@article {pmid25293379,
year = {2014},
author = {Chai, J and Kora, G and Ahn, TH and Hyatt, D and Pan, C},
title = {Functional phylogenomics analysis of bacteria and archaea using consistent genome annotation with UniFam.},
journal = {BMC evolutionary biology},
volume = {14},
number = {},
pages = {207},
pmid = {25293379},
issn = {1471-2148},
mesh = {Archaea/*genetics ; Bacteria/*genetics ; Databases, Protein ; Genome, Archaeal ; Genome, Bacterial ; Molecular Sequence Annotation/*methods ; Phylogeny ; },
abstract = {BACKGROUND: Phylogenetic studies have provided detailed knowledge on the evolutionary mechanisms of genes and species in Bacteria and Archaea. However, the evolution of cellular functions, represented by metabolic pathways and biological processes, has not been systematically characterized. Many clades in the prokaryotic tree of life have now been covered by sequenced genomes in GenBank. This enables a large-scale functional phylogenomics study of many computationally inferred cellular functions across all sequenced prokaryotes.<br><br>RESULTS: A total of 14,727 GenBank prokaryotic genomes were re-annotated using a new protein family database, UniFam, to obtain consistent functional annotations for accurate comparison. The functional profile of a genome was represented by the biological process Gene Ontology (GO) terms in its annotation. The GO term enrichment analysis differentiated the functional profiles between selected archaeal taxa. 706 prokaryotic metabolic pathways were inferred from these genomes using Pathway Tools and MetaCyc. The consistency between the distribution of metabolic pathways in the genomes and the phylogenetic tree of the genomes was measured using parsimony scores and retention indices. The ancestral functional profiles at the internal nodes of the phylogenetic tree were reconstructed to track the gains and losses of metabolic pathways in evolutionary history.<br><br>CONCLUSIONS: Our functional phylogenomics analysis shows divergent functional profiles of taxa and clades. Such function-phylogeny correlation stems from a set of clade-specific cellular functions with low parsimony scores. On the other hand, many cellular functions are sparsely dispersed across many clades with high parsimony scores. These different types of cellular functions have distinct evolutionary patterns reconstructed from the prokaryotic tree.},
}
@article {pmid25279954,
year = {2014},
author = {Anderson, RE and Sogin, ML and Baross, JA},
title = {Evolutionary strategies of viruses, bacteria and archaea in hydrothermal vent ecosystems revealed through metagenomics.},
journal = {PloS one},
volume = {9},
number = {10},
pages = {e109696},
pmid = {25279954},
issn = {1932-6203},
mesh = {Archaea/*genetics ; Bacteria/*genetics ; *Biological Evolution ; Ecosystem ; Host-Pathogen Interactions ; Hydrothermal Vents/*microbiology/*virology ; Lysogeny ; Metagenomics/*methods ; Phylogeny ; Seawater/microbiology/virology ; Viruses/*genetics ; },
abstract = {The deep-sea hydrothermal vent habitat hosts a diverse community of archaea and bacteria that withstand extreme fluctuations in environmental conditions. Abundant viruses in these systems, a high proportion of which are lysogenic, must also withstand these environmental extremes. Here, we explore the evolutionary strategies of both microorganisms and viruses in hydrothermal systems through comparative analysis of a cellular and viral metagenome, collected by size fractionation of high temperature fluids from a diffuse flow hydrothermal vent. We detected a high enrichment of mobile elements and proviruses in the cellular fraction relative to microorganisms in other environments. We observed a relatively high abundance of genes related to energy metabolism as well as cofactors and vitamins in the viral fraction compared to the cellular fraction, which suggest encoding of auxiliary metabolic genes on viral genomes. Moreover, the observation of stronger purifying selection in the viral versus cellular gene pool suggests viral strategies that promote prolonged host integration. Our results demonstrate that there is great potential for hydrothermal vent viruses to integrate into hosts, facilitate horizontal gene transfer, and express or transfer genes that manipulate the hosts' functional capabilities.},
}
@article {pmid25257534,
year = {2014},
author = {Visone, V and Vettone, A and Serpe, M and Valenti, A and Perugino, G and Rossi, M and Ciaramella, M},
title = {Chromatin structure and dynamics in hot environments: architectural proteins and DNA topoisomerases of thermophilic archaea.},
journal = {International journal of molecular sciences},
volume = {15},
number = {9},
pages = {17162-17187},
pmid = {25257534},
issn = {1422-0067},
mesh = {Archaea/genetics/*physiology ; Archaeal Proteins/chemistry/genetics/*physiology ; Chromatin/metabolism/*ultrastructure ; Climate ; DNA Topoisomerases/genetics/*physiology ; DNA Topoisomerases, Type I/chemistry/physiology ; DNA, Archaeal/chemistry/genetics/metabolism ; DNA-Binding Proteins/chemistry/genetics/physiology ; Gene Expression Regulation, Archaeal ; Genes, Archaeal ; Histones/chemistry/genetics/physiology ; *Hot Temperature ; Nucleic Acid Conformation ; Nucleosomes/metabolism/ultrastructure ; Protein Binding ; Protein Conformation ; Structure-Activity Relationship ; },
abstract = {In all organisms of the three living domains (Bacteria, Archaea, Eucarya) chromosome-associated proteins play a key role in genome functional organization. They not only compact and shape the genome structure, but also regulate its dynamics, which is essential to allow complex genome functions. Elucidation of chromatin composition and regulation is a critical issue in biology, because of the intimate connection of chromatin with all the essential information processes (transcription, replication, recombination, and repair). Chromatin proteins include architectural proteins and DNA topoisomerases, which regulate genome structure and remodelling at two hierarchical levels. This review is focussed on architectural proteins and topoisomerases from hyperthermophilic Archaea. In these organisms, which live at high environmental temperature (>80 °C <113 °C), chromatin proteins and modulation of the DNA secondary structure are concerned with the problem of DNA stabilization against heat denaturation while maintaining its metabolic activity.},
}
@article {pmid25250654,
year = {2014},
author = {Snelling, TJ and Genç, B and McKain, N and Watson, M and Waters, SM and Creevey, CJ and Wallace, RJ},
title = {Diversity and community composition of methanogenic archaea in the rumen of Scottish upland sheep assessed by different methods.},
journal = {PloS one},
volume = {9},
number = {9},
pages = {e106491},
pmid = {25250654},
issn = {1932-6203},
support = {BBS/E/D/20211551/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/J004413/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/J004243/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/J004235/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/D/20211553/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Animals ; Biodiversity ; DNA, Archaeal/chemistry/genetics ; Euryarchaeota/genetics/growth &amp; development ; *Genetic Variation ; Geography ; Metagenome/genetics ; Methanobacteriaceae/growth &amp; development ; Methanobacteriales/classification/*genetics/growth &amp; development ; Methanobrevibacter/genetics/growth &amp; development ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Rumen/*microbiology ; Scotland ; Sequence Analysis, DNA ; Sheep ; },
abstract = {Ruminal archaeomes of two mature sheep grazing in the Scottish uplands were analysed by different sequencing and analysis methods in order to compare the apparent archaeal communities. All methods revealed that the majority of methanogens belonged to the Methanobacteriales order containing the Methanobrevibacter, Methanosphaera and Methanobacteria genera. Sanger sequenced 1.3 kb 16S rRNA gene amplicons identified the main species of Methanobrevibacter present to be a SGMT Clade member Mbb. millerae (≥ 91% of OTUs); Methanosphaera comprised the remainder of the OTUs. The primers did not amplify ruminal Thermoplasmatales-related 16S rRNA genes. Illumina sequenced V6-V8 16S rRNA gene amplicons identified similar Methanobrevibacter spp. and Methanosphaera clades and also identified the Thermoplasmatales-related order as 13% of total archaea. Unusually, both methods concluded that Mbb. ruminantium and relatives from the same clade (RO) were almost absent. Sequences mapping to rumen 16S rRNA and mcrA gene references were extracted from Illumina metagenome data. Mapping of the metagenome data to 16S rRNA gene references produced taxonomic identification to Order level including 2-3% Thermoplasmatales, but was unable to discriminate to species level. Mapping of the metagenome data to mcrA gene references resolved 69% to unclassified Methanobacteriales. Only 30% of sequences were assigned to species level clades: of the sequences assigned to Methanobrevibacter, most mapped to SGMT (16%) and RO (10%) clades. The Sanger 16S amplicon and Illumina metagenome mcrA analyses showed similar species richness (Chao1 Index 19-35), while Illumina metagenome and amplicon 16S rRNA analysis gave lower richness estimates (10-18). The values of the Shannon Index were low in all methods, indicating low richness and uneven species distribution. Thus, although much information may be extracted from the other methods, Illumina amplicon sequencing of the V6-V8 16S rRNA gene would be the method of choice for studying rumen archaeal communities.},
}
@article {pmid25249790,
year = {2014},
author = {Nasir, A and Kim, KM and Caetano-Anollés, G},
title = {A phylogenomic census of molecular functions identifies modern thermophilic archaea as the most ancient form of cellular life.},
journal = {Archaea (Vancouver, B.C.)},
volume = {2014},
number = {},
pages = {706468},
pmid = {25249790},
issn = {1472-3654},
mesh = {Archaea/*genetics ; *Evolution, Molecular ; *Phylogeny ; },
abstract = {The origins of diversified life remain mysterious despite considerable efforts devoted to untangling the roots of the universal tree of life. Here we reconstructed phylogenies that described the evolution of molecular functions and the evolution of species directly from a genomic census of gene ontology (GO) definitions. We sampled 249 free-living genomes spanning organisms in the three superkingdoms of life, Archaea, Bacteria, and Eukarya, and used the abundance of GO terms as molecular characters to produce rooted phylogenetic trees. Results revealed an early thermophilic origin of Archaea that was followed by genome reduction events in microbial superkingdoms. Eukaryal genomes displayed extraordinary functional diversity and were enriched with hundreds of novel molecular activities not detected in the akaryotic microbial cells. Remarkably, the majority of these novel functions appeared quite late in evolution, synchronized with the diversification of the eukaryal superkingdom. The distribution of GO terms in superkingdoms confirms that Archaea appears to be the simplest and most ancient form of cellular life, while Eukarya is the most diverse and recent.},
}
@article {pmid25239794,
year = {2014},
author = {Iriarte, A and Jara, E and Leytón, L and Diana, L and Musto, H},
title = {General trends in selectively driven codon usage biases in the domain archaea.},
journal = {Journal of molecular evolution},
volume = {79},
number = {3-4},
pages = {105-110},
pmid = {25239794},
issn = {1432-1432},
mesh = {Archaea/*genetics ; *Codon ; *Evolution, Molecular ; *Phylogeny ; },
abstract = {Since the advent of rapid techniques for sequencing DNA in the mid 70's, it became clear that all codons coding for the same amino acid are not used according to neutral expectations. In the last 30 years, several theories were proposed for explaining this fact. However, the most important concepts were the result of analyses carried out in Bacteria, and unicellular and multicellular eukaryotes like mammals (in other words, in two of the three Domains of life). In this communication, we study the main forces that shape codon usage in Archaeae under an evolutionary perspective. This is important because, as known, the orthologous genes related with the informational system in this Domain (replication, transcription and translation) are more similar to eukaryotes than to Bacteria. Our results show that the effect of selection acting at the level of translation is present in the Domain but mainly restricted to only a phylum (Euryarchaeota) and therefore is not as extended as in Bacteria. Besides, we describe the phylogenetic distribution of translational optimal codons and estimate the effect of selection acting at the level of accuracy. Finally, we discuss these results under some peculiarities that characterize this Domain.},
}
@article {pmid25228232,
year = {2015},
author = {Du, J and Hu, Y and Qi, W and Zhang, Y and Jing, Z and Norton, M and Li, YY},
title = {Influence of four antimicrobials on methane-producing archaea and sulfate-reducing bacteria in anaerobic granular sludge.},
journal = {Chemosphere},
volume = {140},
number = {},
pages = {184-190},
doi = {10.1016/j.chemosphere.2014.08.028},
pmid = {25228232},
issn = {1879-1298},
mesh = {Acetates ; Anaerobiosis ; Anti-Infective Agents/*toxicity ; Archaea/*drug effects/metabolism ; Bacteria/*drug effects/metabolism ; Biodegradation, Environmental ; Bioreactors/microbiology ; Desulfovibrio ; Ethanol ; Methane/metabolism ; Sewage/microbiology ; Sulfates/metabolism ; Waste Disposal, Fluid/methods ; },
abstract = {The influence of Cephalexin (CLX), Tetracycline (TC), Erythromycin (ERY) and Sulfathiazole (ST) on methane-producing archaea (MPA) and sulfate-reducing bacteria (SRB) in anaerobic sludge was investigated using acetate or ethanol as substrate. With antimicrobial concentrations below 400mgL(-1), the relative specific methanogenic activity (SMA) was above 50%, so that the antimicrobials exerted slight effects on archaea. However ERY and ST at 400mgL(-1) caused a 74.5% and 57.6% inhibition to specific sulfidogenic activity (SSA) when the sludge granules were disrupted and ethanol used as substrate. After disruption, microbial tolerance to antimicrobials decreased, but the rate at which MPA utilized acetate and ethanol increased from 0.95gCOD·(gVSS⋅d)(-1) to 1.45gCOD·(gVSS⋅d)(-1) and 0.90gCOD·(gVSS⋅d)(-1) to 1.15gCOD·(gVSS⋅d)(-1) respectively. The ethanol utilization rate for SRB also increased after disruption from 0.35gCOD·(gVSS⋅d)(-1) to 0.46gCOD·(gVSS⋅d)(-1). Removal rates for CLX approaching 20.0% and 25.0% were obtained used acetate and ethanol respectively. The disintegration of granules improved the CLX removal rate to 65% and 78%, but ST was not removed during this process.},
}
@article {pmid25227989,
year = {2014},
author = {Zhang, F and Pita, L and Erwin, PM and Abaid, S and López-Legentil, S and Hill, RT},
title = {Symbiotic archaea in marine sponges show stability and host specificity in community structure and ammonia oxidation functionality.},
journal = {FEMS microbiology ecology},
volume = {90},
number = {3},
pages = {699-707},
doi = {10.1111/1574-6941.12427},
pmid = {25227989},
issn = {1574-6941},
mesh = {Ammonia/*metabolism ; Animals ; Archaea/*classification/genetics ; Archaeal Proteins/genetics/metabolism ; Caribbean Region ; Ecology ; Ecosystem ; Host Specificity ; Mediterranean Sea ; Oxidation-Reduction ; Oxidoreductases/genetics ; Phylogeny ; Porifera/classification/*microbiology ; RNA, Ribosomal, 16S/genetics ; Seawater ; },
abstract = {Archaea associated with marine sponges are active and influence the nitrogen metabolism of sponges. However, we know little about their occurrence, specificity, and persistence. We aimed to elucidate the relative importance of host specificity and biogeographic background in shaping the symbiotic archaeal communities. We investigated these communities in sympatric sponges from the Mediterranean (Ircinia fasciculata and Ircinia oros, sampled in summer and winter) and from the Caribbean (Ircinia strobilina and Mycale laxissima). PCR cloning and sequencing of archaeal 16S rRNA and amoA genes showed that the archaeal community composition and structure were different from that in seawater and varied among sponge species. We found that the communities were dominated by ammonia-oxidizing archaea closely related to Nitrosopumilus. The community in M. laxissima differed from that in Ircinia spp., including the sympatric sponge I. strobilina; yet, geographical clusters within Ircinia spp. were observed. Whereas archaeal phylotypes in Ircinia spp. were persistent and belong to 'sponge-enriched' clusters, archaea in M. laxissima were closely related with those from diverse habitats (i.e. seawater and sediments). For all four sponge species, the expression of the archaeal amoA gene was confirmed. Our results indicate that host-specific processes, such as host ecological strategy and evolutionary history, control the sponge-archaeal communities.},
}
@article {pmid25219966,
year = {2014},
author = {Jain, S and Caforio, A and Fodran, P and Lolkema, JS and Minnaard, AJ and Driessen, AJM},
title = {Identification of CDP-archaeol synthase, a missing link of ether lipid biosynthesis in Archaea.},
journal = {Chemistry &amp; biology},
volume = {21},
number = {10},
pages = {1392-1401},
doi = {10.1016/j.chembiol.2014.07.022},
pmid = {25219966},
issn = {1879-1301},
mesh = {Archaea/*enzymology ; Archaeal Proteins/chemistry/genetics/*metabolism ; Computational Biology ; Escherichia coli/metabolism ; Ethers/chemistry ; Glyceryl Ethers/chemistry/metabolism ; Lipids/*biosynthesis/chemistry ; },
abstract = {Archaeal membrane lipid composition is distinct from Bacteria and Eukarya, consisting of isoprenoid chains etherified to the glycerol carbons. Biosynthesis of these lipids is poorly understood. Here we identify and characterize the archaeal membrane protein CDP-archaeol synthase (CarS) that catalyzes the transfer of the nucleotide to its specific archaeal lipid substrate, leading to the formation of a CDP-activated precursor (CDP-archaeol) to which polar head groups are attached. The discovery of CarS enabled reconstitution of the entire archaeal lipid biosynthesis pathway in vitro, starting from simple isoprenoid building blocks and using a set of five purified enzymes. The cell free synthetic strategy for archaeal lipids we describe opens opportunity for studies of archaeal lipid biochemistry. Additionally, insights into archaeal lipid biosynthesis reported here allow addressing the evolutionary hypothesis of the lipid divide between Archaea and Bacteria.},
}
@article {pmid25217724,
year = {2014},
author = {Henriet, O and Fourmentin, J and Delincé, B and Mahillon, J},
title = {Exploring the diversity of extremely halophilic archaea in food-grade salts.},
journal = {International journal of food microbiology},
volume = {191},
number = {},
pages = {36-44},
doi = {10.1016/j.ijfoodmicro.2014.08.019},
pmid = {25217724},
issn = {1879-3460},
mesh = {*Biodiversity ; *Food Microbiology ; Halobacteriaceae/*classification/genetics/*isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; *Salts ; },
abstract = {Salting is one of the oldest means of food preservation: adding salt decreases water activity and inhibits microbial development. However, salt is also a source of living bacteria and archaea. The occurrence and diversity of viable archaea in this extreme environment were assessed in 26 food-grade salts from worldwide origin by cultivation on four culture media. Additionally, metagenomic analysis of 16S rRNA gene was performed on nine salts. Viable archaea were observed in 14 salts and colony counts reached more than 10(5)CFU per gram in three salts. All archaeal isolates identified by 16S rRNA gene sequencing belonged to the Halobacteriaceae family and were related to 17 distinct genera among which Haloarcula, Halobacterium and Halorubrum were the most represented. High-throughput sequencing generated extremely different profiles for each salt. Four of them contained a single major genus (Halorubrum, Halonotius or Haloarcula) while the others had three or more genera of similar occurrence. The number of distinct genera per salt ranged from 21 to 27. Halorubrum had a significant contribution to the archaeal diversity in seven salts; this correlates with its frequent occurrence in crystallization ponds. On the contrary, Haloquadratum walsbyi, the halophilic archaea most commonly found in solar salterns, was a minor actor of the food-grade salt diversity. Our results indicate that the occurrence and diversity of viable halophilic archaea in salt can be important, while their fate in the gastrointestinal tract after ingestion remains largely unknown.},
}
@article {pmid25172135,
year = {2015},
author = {Chen, Q and Qi, L and Bi, Q and Dai, P and Sun, D and Sun, C and Liu, W and Lu, L and Ni, W and Lin, X},
title = {Comparative effects of 3,4-dimethylpyrazole phosphate (DMPP) and dicyandiamide (DCD) on ammonia-oxidizing bacteria and archaea in a vegetable soil.},
journal = {Applied microbiology and biotechnology},
volume = {99},
number = {1},
pages = {477-487},
doi = {10.1007/s00253-014-6026-7},
pmid = {25172135},
issn = {1432-0614},
mesh = {Archaea/*drug effects/growth &amp; development ; Bacteria/*drug effects/growth &amp; development ; Biota/*drug effects ; Cluster Analysis ; DNA, Archaeal/chemistry/genetics ; DNA, Bacterial/chemistry/genetics ; Guanidines/*metabolism ; Molecular Sequence Data ; Nitrification/drug effects ; Phylogeny ; Polymorphism, Restriction Fragment Length ; Pyrazoles/*metabolism ; Real-Time Polymerase Chain Reaction ; Sequence Analysis, DNA ; *Soil Microbiology ; Vegetables/growth &amp; development ; },
abstract = {Nitrification inhibitors (NIs) 3,4-dimethylpyrazole phosphate (DMPP) and dicyandiamide (DCD) have been used extensively to improve nitrogen fertilizer utilization in farmland. However, their comparative effects on ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) in agricultural soils are still unclear. Here, we compared the impacts of these two inhibitors on soil nitrification, AOA and AOB abundance as well as their community structure in a vegetable soil by using real-time PCR and terminal restriction fragment length polymorphism (T-RFLP). Our results showed that urea application significantly increased the net nitrification rates, but were significantly inhibited by both NIs, and the inhibitory effect of DMPP was significantly greater than that of DCD. AOB growth was more greatly inhibited by DMPP than by DCD, and the net nitrification rate was significantly related to AOB abundance, but not to AOA abundance. Application of urea and NIs to soil did not change the diversity of the AOA community, with the T-RFs remaining in proportions that were similar to control soils, while the community structure of AOB exhibited obvious shifts within all different treatments compared to the control. Phylogenetic analysis showed that all AOA sequences fell within group 1.1a and group 1.1b, and the AOB community consisted of Nitrosospira cluster 3, cluster 0, and unidentified species. These results suggest that DMPP exhibited a stronger inhibitory effect on nitrification than DCD by inhibiting AOB rather than AOA.},
}
@article {pmid25169021,
year = {2014},
author = {Offre, P and Kerou, M and Spang, A and Schleper, C},
title = {Variability of the transporter gene complement in ammonia-oxidizing archaea.},
journal = {Trends in microbiology},
volume = {22},
number = {12},
pages = {665-675},
doi = {10.1016/j.tim.2014.07.007},
pmid = {25169021},
issn = {1878-4380},
mesh = {Amino Acid Sequence ; Ammonia/*metabolism ; Archaea/*genetics/metabolism ; Archaeal Proteins/*genetics/metabolism ; Carrier Proteins/*genetics/metabolism ; Genome, Archaeal ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Ammonia-oxidizing archaea (AOA) are a widespread and abundant component of microbial communities in many different ecosystems. The extent of physiological differences between individual AOA is, however, unknown. Here, we compare the transporter gene complements of six AOA, from four different environments and two major clades, to assess their potential for substrate uptake and efflux. Each of the corresponding AOA genomes encode a unique set of transporters and although the composition of AOA transporter complements follows a phylogenetic pattern, few transporter families are conserved in all investigated genomes. A comparison of ammonia transporters encoded by archaeal and bacterial ammonia oxidizers highlights the variance among AOA lineages as well as their distinction from the ammonia-oxidizing bacteria, and suggests differential ecological adaptations.},
}
@article {pmid25165621,
year = {2014},
author = {Seedorf, H and Kittelmann, S and Henderson, G and Janssen, PH},
title = {RIM-DB: a taxonomic framework for community structure analysis of methanogenic archaea from the rumen and other intestinal environments.},
journal = {PeerJ},
volume = {2},
number = {},
pages = {e494},
pmid = {25165621},
issn = {2167-8359},
abstract = {Methane is formed by methanogenic archaea in the rumen as one of the end products of feed fermentation in the ruminant digestive tract. To develop strategies to mitigate anthropogenic methane emissions due to ruminant farming, and to understand rumen microbial differences in animal feed conversion efficiency, it is essential that methanogens can be identified and taxonomically classified with high accuracy. Currently available taxonomic frameworks offer only limited resolution beyond the genus level for taxonomic assignments of sequence data stemming from high throughput sequencing technologies. Therefore, we have developed a QIIME-compatible database (DB) designed for species-level taxonomic assignment of 16S rRNA gene amplicon data targeting methanogenic archaea from the rumen, and from animal and human intestinal tracts. Called RIM-DB (Rumen and Intestinal Methanogen-DB), it contains a set of 2,379 almost full-length chimera-checked 16S rRNA gene sequences, including 20 previously unpublished sequences from isolates from three different orders. The taxonomy encompasses the recently-proposed seventh order of methanogens, the Methanomassiliicoccales, and allows differentiation between defined groups within this order. Sequence reads from rumen contents from a range of ruminant-diet combinations were taxonomically assigned using RIM-DB, Greengenes and SILVA. This comparison clearly showed that taxonomic assignments with RIM-DB resulted in the most detailed assignment, and only RIM-DB taxonomic assignments allowed methanogens to be distinguished taxonomically at the species level. RIM-DB complements the use of comprehensive databases such as Greengenes and SILVA for community structure analysis of methanogens from the rumen and other intestinal environments, and allows identification of target species for methane mitigation strategies.},
}
@article {pmid25158512,
year = {2014},
author = {Wang, X and Zhao, DY and Zeng, J and Yu, DW and Wu, QL},
title = {[Effects of Corbicula fluminea bioturbation on the community composition and abundance of ammonia-oxidizing archaea and bacteria in surface sediments].},
journal = {Huan jing ke xue= Huanjing kexue},
volume = {35},
number = {6},
pages = {2314-2321},
pmid = {25158512},
issn = {0250-3301},
mesh = {Ammonia/*metabolism ; Animals ; Archaea/*classification ; Bacteria/*classification ; Biodiversity ; *Corbicula ; Genes, Archaeal ; Genes, Bacterial ; Geologic Sediments/*microbiology ; Oxidation-Reduction ; },
abstract = {To better understand the effects of Corbicula fluminea bioturbation on the ammonia-oxidizing microorganisms in the surface sediment, sediment-water microcosms with different densities of Corbicula fluminea were constructed. Clone libraries and real-time qPCR were applied to analyze the community composition and abundance of ammonia-oxidizing archaea (AOA) and bacteria (AOB) in the surface sediments. The results obtained indicated that the bioturbation of Corbicula fluminea accelerated the release of nitrogen from the surface sediment. In the amoA gene clone libraries, the identified AOA amoA gene sequences affiliated with the two known clusters (marine and soil clusters). The identified AOB amoA gene sequences mostly belonged to the Nitrosomonas of beta-Proteobacteria. The abundance of the bacterial amoA gene was higher than that of the archaeal amoA gene in all treatments. With increasing density of Corbicula fluminea, decreased abundances of the bacterial amoA gene were observed. At the same time, the diversity of AOA and AOB reduced in the Corbicula fluminea containing microcosms. In conclusion, the bioturbation of Corbicula fluminea could affected the community composition and abundance of ammonia-oxidizing microorganisms in surface sediments.},
}
@article {pmid25157079,
year = {2015},
author = {Saier, MH and Reddy, BL},
title = {Holins in bacteria, eukaryotes, and archaea: multifunctional xenologues with potential biotechnological and biomedical applications.},
journal = {Journal of bacteriology},
volume = {197},
number = {1},
pages = {7-17},
pmid = {25157079},
issn = {1098-5530},
support = {R01 GM077402/GM/NIGMS NIH HHS/United States ; GM077402/GM/NIGMS NIH HHS/United States ; },
mesh = {Archaea/*metabolism ; Bacteria/*metabolism ; Bacteriophages/genetics/*metabolism ; Eukaryota/*metabolism ; Gene Expression Regulation, Viral/physiology ; Viral Proteins/genetics/*metabolism ; },
abstract = {Holins form pores in the cytoplasmic membranes of bacteria for the primary purpose of releasing endolysins that hydrolyze the cell wall and induce cell death. Holins are encoded within bacteriophage genomes, where they promote cell lysis for virion release, and within bacterial genomes, where they serve a diversity of potential or established functions. These include (i) release of gene transfer agents, (ii) facilitation of programs of differentiation such as those that allow sporulation and spore germination, (iii) contribution to biofilm formation, (iv) promotion of responses to stress conditions, and (v) release of toxins and other proteins. There are currently 58 recognized families of holins and putative holins with members exhibiting between 1 and 4 transmembrane α-helical spanners, but many more families have yet to be discovered. Programmed cell death in animals involves holin-like proteins such as Bax and Bak that may have evolved from bacterial holins. Holin homologues have also been identified in archaea, suggesting that these proteins are ubiquitous throughout the three domains of life. Phage-mediated cell lysis of dual-membrane Gram-negative bacteria also depends on outer membrane-disrupting "spanins" that function independently of, but in conjunction with, holins and endolysins. In this minireview, we provide an overview of their modes of action and the first comprehensive summary of the many currently recognized and postulated functions and uses of these cell lysis systems. It is anticipated that future studies will result in the elucidation of many more such functions and the development of additional applications.},
}
@article {pmid25148780,
year = {2014},
author = {Sun, W and Xia, C and Xu, M and Guo, J and Sun, G and Wang, A},
title = {Community structure and distribution of planktonic ammonia-oxidizing archaea and bacteria in the Dongjiang River, China.},
journal = {Research in microbiology},
volume = {165},
number = {8},
pages = {657-670},
doi = {10.1016/j.resmic.2014.08.003},
pmid = {25148780},
issn = {1769-7123},
mesh = {Ammonia/*metabolism ; Ammonium Compounds/analysis ; Archaea/*classification/genetics/*isolation &amp; purification/metabolism ; Bacteria/*classification/genetics/*isolation &amp; purification/metabolism ; *Biota ; China ; Cluster Analysis ; Molecular Sequence Data ; Nitrification ; Oxidation-Reduction ; Oxidoreductases/genetics ; Phylogeny ; Real-Time Polymerase Chain Reaction ; Rivers/chemistry/*microbiology ; Sequence Analysis, DNA ; Sequence Homology ; },
abstract = {Ammonia-oxidizing archaea (AOA) and bacteria (AOB) are widely distributed in the natural environment and play crucial roles in the nitrification process and the removal of nitrogen (N). Although planktonic microbial community plays an important role in river biogeochemical cycles, few studies have attempted to address the characteristics of AOA and AOB in the water column of river ecosystems. This study examined the community structures, distributions and abundance of planktonic AOA and AOB in the Dongjiang River and their responses to the changes in environmental parameters through quantitative polymerase chain reaction, cloning, and sequencing of ammonia mono-oxygenase (amoA). The abundance ratio of AOB to AOA varied from 0.07 to 9.4 along the river and was positively correlated with the concentration of ammonium. Significantly positive correlations were observed between the abundance of AOB and potential nitrification rates, which suggested that the contribution of AOB to nitrification was greater than that of AOA in the river. Phylogenetic analyses showed that AOA communities could be divided into three branches of Thaumarchaeota: Group 1.1a, Group 1.1a associated and Group 1.1b, with most sequences belonging to Group 1.1a. All AOB sequences fell within Nitrosomonas and Nitrosospira species, and the majority of sequences were affiliated with the latter. Multivariate statistical analyses indicated that the community distributions of AOA and AOB were significantly correlated with the concentrations of nitrate and total suspended solids, respectively. These findings fundamentally improved our understanding of the role of planktonic AOA and AOB in nitrogen cycling and their responses to changes in environmental factors in the river ecosystem.},
}
@article {pmid25144201,
year = {2014},
author = {Takahashi, S and Tomita, J and Nishioka, K and Hisada, T and Nishijima, M},
title = {Development of a prokaryotic universal primer for simultaneous analysis of Bacteria and Archaea using next-generation sequencing.},
journal = {PloS one},
volume = {9},
number = {8},
pages = {e105592},
pmid = {25144201},
issn = {1932-6203},
mesh = {Animals ; Archaea/*genetics ; Bacteria/*genetics ; DNA Primers ; Feces/microbiology ; *High-Throughput Nucleotide Sequencing ; RNA, Ribosomal, 16S/genetics ; Reproducibility of Results ; Sensitivity and Specificity ; Swine ; },
abstract = {For the analysis of microbial community structure based on 16S rDNA sequence diversity, sensitive and robust PCR amplification of 16S rDNA is a critical step. To obtain accurate microbial composition data, PCR amplification must be free of bias; however, amplifying all 16S rDNA species with equal efficiency from a sample containing a large variety of microorganisms remains challenging. Here, we designed a universal primer based on the V3-V4 hypervariable region of prokaryotic 16S rDNA for the simultaneous detection of Bacteria and Archaea in fecal samples from crossbred pigs (Landrace × Large white × Duroc) using an Illumina MiSeq next-generation sequencer. In-silico analysis showed that the newly designed universal prokaryotic primers matched approximately 98.0% of Bacteria and 94.6% of Archaea rRNA gene sequences in the Ribosomal Database Project database. For each sequencing reaction performed with the prokaryotic universal primer, an average of 69,330 (± 20,482) reads were obtained, of which archaeal rRNA genes comprised approximately 1.2% to 3.2% of all prokaryotic reads. In addition, the detection frequency of Bacteria belonging to the phylum Verrucomicrobia, including members of the classes Verrucomicrobiae and Opitutae, was higher in the NGS analysis using the prokaryotic universal primer than that performed with the bacterial universal primer. Importantly, this new prokaryotic universal primer set had markedly lower bias than that of most previously designed universal primers. Our findings demonstrate that the prokaryotic universal primer set designed in the present study will permit the simultaneous detection of Bacteria and Archaea, and will therefore allow for a more comprehensive understanding of microbial community structures in environmental samples.},
}
@article {pmid25140167,
year = {2014},
author = {Perras, AK and Wanner, G and Klingl, A and Mora, M and Auerbach, AK and Heinz, V and Probst, AJ and Huber, H and Rachel, R and Meck, S and Moissl-Eichinger, C},
title = {Grappling archaea: ultrastructural analyses of an uncultivated, cold-loving archaeon, and its biofilm.},
journal = {Frontiers in microbiology},
volume = {5},
number = {},
pages = {397},
pmid = {25140167},
issn = {1664-302X},
abstract = {Similarly to Bacteria, Archaea are microorganisms that interact with their surrounding environment in a versatile manner. To date, interactions based on cellular structure and surface appendages have mainly been documented using model systems of cultivable archaea under laboratory conditions. Here, we report on the microbial interactions and ultrastructural features of the uncultivated SM1 Euryarchaeon, which is highly dominant in its biotope. Therefore, biofilm samples taken from the Sippenauer Moor, Germany, were investigated via transmission electron microscopy (TEM; negative staining, thin-sectioning) and scanning electron microscopy (SEM) in order to elucidate the fine structures of the microbial cells and the biofilm itself. The biofilm consisted of small archaeal cocci (0.6 μm diameter), arranged in a regular pattern (1.0-2.0 μm distance from cell to cell), whereas each archaeon was connected to 6 other archaea on average. Extracellular polymeric substances (EPS) were limited to the close vicinity of the archaeal cells, and specific cell surface appendages (hami, Moissl et al., 2005) protruded beyond the EPS matrix enabling microbial interaction by cell-cell contacts among the archaea and between archaea and bacteria. All analyzed hami revealed their previously described architecture of nano-grappling hooks and barb-wire basal structures. Considering the archaeal cell walls, the SM1 Euryarchaea exhibited a double-membrane, which has rarely been reported for members of this phylogenetic domain. Based on these findings, the current generalized picture on archaeal cell walls needs to be revisited, as archaeal cell structures are more complex and sophisticated than previously assumed, particularly when looking into the uncultivated majority.},
}
@article {pmid25124552,
year = {2014},
author = {Borrel, G and Parisot, N and Harris, HM and Peyretaillade, E and Gaci, N and Tottey, W and Bardot, O and Raymann, K and Gribaldo, S and Peyret, P and O'Toole, PW and Brugère, JF},
title = {Comparative genomics highlights the unique biology of Methanomassiliicoccales, a Thermoplasmatales-related seventh order of methanogenic archaea that encodes pyrrolysine.},
journal = {BMC genomics},
volume = {15},
number = {},
pages = {679},
pmid = {25124552},
issn = {1471-2164},
mesh = {Archaeal Proteins/genetics ; Biosynthetic Pathways ; Clustered Regularly Interspaced Short Palindromic Repeats ; Codon, Terminator ; Energy Metabolism ; Genome, Archaeal ; Lysine/*analogs &amp; derivatives/genetics ; Molecular Sequence Data ; Phylogeny ; RNA, Archaeal/genetics ; RNA, Ribosomal/genetics ; Replication Origin ; Thermoplasmales/*genetics ; },
abstract = {BACKGROUND: A seventh order of methanogens, the Methanomassiliicoccales, has been identified in diverse anaerobic environments including the gastrointestinal tracts (GIT) of humans and other animals and may contribute significantly to methane emission and global warming. Methanomassiliicoccales are phylogenetically distant from all other orders of methanogens and belong to a large evolutionary branch composed by lineages of non-methanogenic archaea such as Thermoplasmatales, the Deep Hydrothermal Vent Euryarchaeota-2 (DHVE-2, Aciduliprofundum boonei) and the Marine Group-II (MG-II). To better understand this new order and its relationship to other archaea, we manually curated and extensively compared the genome sequences of three Methanomassiliicoccales representatives derived from human GIT microbiota, "Candidatus Methanomethylophilus alvus", "Candidatus Methanomassiliicoccus intestinalis" and Methanomassiliicoccus luminyensis.<br><br>RESULTS: Comparative analyses revealed atypical features, such as the scattering of the ribosomal RNA genes in the genome and the absence of eukaryotic-like histone gene otherwise present in most of Euryarchaeota genomes. Previously identified in Thermoplasmatales genomes, these features are presently extended to several completely sequenced genomes of this large evolutionary branch, including MG-II and DHVE2. The three Methanomassiliicoccales genomes share a unique composition of genes involved in energy conservation suggesting an original combination of two main energy conservation processes previously described in other methanogens. They also display substantial differences with each other, such as their codon usage, the nature and origin of their CRISPRs systems and the genes possibly involved in particular environmental adaptations. The genome of M. luminyensis encodes several features to thrive in soil and sediment conditions suggesting its larger environmental distribution than GIT. Conversely, "Ca. M. alvus" and "Ca. M. intestinalis" do not present these features and could be more restricted and specialized on GIT. Prediction of the amber codon usage, either as a termination signal of translation or coding for pyrrolysine revealed contrasted patterns among the three genomes and suggests a different handling of the Pyl-encoding capacity.<br><br>CONCLUSIONS: This study represents the first insights into the genomic organization and metabolic traits of the seventh order of methanogens. It suggests contrasted evolutionary history among the three analyzed Methanomassiliicoccales representatives and provides information on conserved characteristics among the overall methanogens and among Thermoplasmata.},
}
@article {pmid25118885,
year = {2014},
author = {Yarza, P and Yilmaz, P and Pruesse, E and Glöckner, FO and Ludwig, W and Schleifer, KH and Whitman, WB and Euzéby, J and Amann, R and Rosselló-Móra, R},
title = {Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences.},
journal = {Nature reviews. Microbiology},
volume = {12},
number = {9},
pages = {635-645},
pmid = {25118885},
issn = {1740-1534},
mesh = {Archaea/*classification/genetics ; Bacteria/*classification/genetics ; Computational Biology ; DNA, Archaeal/chemistry/genetics ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Databases, Nucleic Acid ; Phylogeny ; RNA, Ribosomal, 16S/chemistry/*genetics ; Ribotyping ; Sequence Analysis, DNA ; },
abstract = {Publicly available sequence databases of the small subunit ribosomal RNA gene, also known as 16S rRNA in bacteria and archaea, are growing rapidly, and the number of entries currently exceeds 4 million. However, a unified classification and nomenclature framework for all bacteria and archaea does not yet exist. In this Analysis article, we propose rational taxonomic boundaries for high taxa of bacteria and archaea on the basis of 16S rRNA gene sequence identities and suggest a rationale for the circumscription of uncultured taxa that is compatible with the taxonomy of cultured bacteria and archaea. Our analyses show that only nearly complete 16S rRNA sequences give accurate measures of taxonomic diversity. In addition, our analyses suggest that most of the 16S rRNA sequences of the high taxa will be discovered in environmental surveys by the end of the current decade.},
}
@article {pmid25116890,
year = {2014},
author = {Sojo, V and Pomiankowski, A and Lane, N},
title = {A bioenergetic basis for membrane divergence in archaea and bacteria.},
journal = {PLoS biology},
volume = {12},
number = {8},
pages = {e1001926},
pmid = {25116890},
issn = {1545-7885},
mesh = {Archaea/*metabolism ; Bacteria/*metabolism ; Cell Membrane/*metabolism ; Cell Membrane Permeability ; *Energy Metabolism ; Ion Transport ; Membrane Lipids/chemistry ; Models, Biological ; Proton Pumps/metabolism ; Protons ; Sodium/metabolism ; Sodium-Hydrogen Exchangers/metabolism ; Thermodynamics ; },
abstract = {Membrane bioenergetics are universal, yet the phospholipid membranes of archaea and bacteria-the deepest branches in the tree of life-are fundamentally different. This deep divergence in membrane chemistry is reflected in other stark differences between the two domains, including ion pumping and DNA replication. We resolve this paradox by considering the energy requirements of the last universal common ancestor (LUCA). We develop a mathematical model based on the premise that LUCA depended on natural proton gradients. Our analysis shows that such gradients can power carbon and energy metabolism, but only in leaky cells with a proton permeability equivalent to fatty acid vesicles. Membranes with lower permeability (equivalent to modern phospholipids) collapse free-energy availability, precluding exploitation of natural gradients. Pumping protons across leaky membranes offers no advantage, even when permeability is decreased 1,000-fold. We hypothesize that a sodium-proton antiporter (SPAP) provided the first step towards modern membranes. SPAP increases the free energy available from natural proton gradients by ∼60%, enabling survival in 50-fold lower gradients, thereby facilitating ecological spread and divergence. Critically, SPAP also provides a steadily amplifying advantage to proton pumping as membrane permeability falls, for the first time favoring the evolution of ion-tight phospholipid membranes. The phospholipids of archaea and bacteria incorporate different stereoisomers of glycerol phosphate. We conclude that the enzymes involved took these alternatives by chance in independent populations that had already evolved distinct ion pumps. Our model offers a quantitatively robust explanation for why membrane bioenergetics are universal, yet ion pumps and phospholipid membranes arose later and independently in separate populations. Our findings elucidate the paradox that archaea and bacteria share DNA transcription, ribosomal translation, and ATP synthase, yet differ in equally fundamental traits that depend on the membrane, including DNA replication.},
}
@article {pmid25116054,
year = {2014},
author = {Gindner, A and Hausner, W and Thomm, M},
title = {The TrmB family: a versatile group of transcriptional regulators in Archaea.},
journal = {Extremophiles : life under extreme conditions},
volume = {18},
number = {5},
pages = {925-936},
pmid = {25116054},
issn = {1433-4909},
mesh = {Amino Acid Sequence ; Archaea/genetics/*metabolism ; Archaeal Proteins/chemistry/genetics/*metabolism ; Base Sequence ; Carbohydrate Metabolism ; Molecular Sequence Data ; Transcription Factors/chemistry/genetics/*metabolism ; },
abstract = {Microbes are organisms which are well adapted to their habitat. Their survival depends on the regulation of gene expression levels in response to environmental signals. The most important step in regulation of gene expression takes place at the transcriptional level. This regulation is intriguing in Archaea because the eu-karyotic-like transcription apparatus is modulated by bacterial-like transcription regulators. The transcriptional regulator of mal operon (TrmB) family is well known as a very large group of regulators in Archaea with more than 250 members to date. One special feature of these regulators is that some of them can act as repressor, some as activator and others as both repressor and activator. This review gives a short updated overview of the TrmB family and their regulatory patterns in different Archaea as a lot of new data have been published on this topic since the last review from 2008.},
}
@article {pmid25108574,
year = {2015},
author = {García-Maldonado, JQ and Bebout, BM and Everroad, RC and López-Cortés, A},
title = {Evidence of novel phylogenetic lineages of methanogenic archaea from hypersaline microbial mats.},
journal = {Microbial ecology},
volume = {69},
number = {1},
pages = {106-117},
pmid = {25108574},
issn = {1432-184X},
mesh = {Archaea/classification/*genetics ; DNA, Archaeal/genetics ; Ecosystem ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Salinity ; },
abstract = {Methanogenesis in hypersaline and high-sulfate environments is typically dominated by methylotrophic methanogens because sulfate reduction is thermodynamically favored over hydrogenotrophic methanogenesis in these environments. We characterized the community composition of methanogenic archaea in both unmanipulated and incubated microbial mats from different hypersaline environments in Baja California Sur, Mexico. Clone libraries of methyl coenzyme-M reductase (mcrA) sequences and DGGE band patterns of 16S rRNA and mcrA sequences showed that the methanogen community in these microbial mats is dominated by methylotrophic methanogens of the genus Methanohalophilus. However, phylogenetic analyses of mcrA sequences from these mats also revealed two new lineages corresponding to putative hydrogenotrophic methanogens related with the strictly hydrogenotrophic order Methanomicrobiales. Stimulated methane production under decreased salinity and sulfate concentrations also suggested the presence of hydrogenotrophic methanogens in these samples. The relative abundance of mcrA gene and transcripts, estimated by SYBR green I qPCR assays, suggested the activity of different phylogenetic groups of methanogens, including the two novel clusters, in unmanipulated samples of hypersaline microbial mats. Using geochemical and molecular approaches, we show that substrate limitation and values of salinity and sulfate higher than 3 % and 25 mM (respectively) are potential environmental constraints for methanogenesis in these environments. Microcosm experiments with modifications of salinity and sulfate concentrations and TMA addition showed that upper salt and sulfate concentrations for occurrence of methylotrophic methanogenesis were 28 % and 263 mM, respectively. This study provides phylogenetic information about uncultivated and undescribed methanogenic archaea from hypersaline environments.},
}
@article {pmid25107970,
year = {2014},
author = {Cotta, SR and Dias, AC and Marriel, IE and Andreote, FD and Seldin, L and van Elsas, JD},
title = {Different effects of transgenic maize and nontransgenic maize on nitrogen-transforming archaea and bacteria in tropical soils.},
journal = {Applied and environmental microbiology},
volume = {80},
number = {20},
pages = {6437-6445},
pmid = {25107970},
issn = {1098-5336},
mesh = {Ammonia/metabolism ; Brazil ; Denaturing Gradient Gel Electrophoresis ; *Microbial Consortia ; Molecular Sequence Data ; Nitrogen Fixation ; Oxidation-Reduction ; Oxidoreductases/genetics ; *Plants, Genetically Modified/growth &amp; development ; Polymerase Chain Reaction ; Rhizosphere ; *Soil Microbiology ; *Zea mays/genetics/growth &amp; development ; },
abstract = {The composition of the rhizosphere microbiome is a result of interactions between plant roots, soil, and environmental conditions. The impact of genetic variation in plant species on the composition of the root-associated microbiota remains poorly understood. This study assessed the abundances and structures of nitrogen-transforming (ammonia-oxidizing) archaea and bacteria as well as nitrogen-fixing bacteria driven by genetic modification of their maize host plants. The data show that significant changes in the abundances (revealed by quantitative PCR) of ammonia-oxidizing bacterial and archaeal communities occurred as a result of the maize host being genetically modified. In contrast, the structures of the total communities (determined by PCR-denaturing gradient gel electrophoresis) were mainly driven by factors such as soil type and season and not by plant genotype. Thus, the abundances of ammonia-oxidizing bacterial and archaeal communities but not structures of those communities were revealed to be responsive to changes in maize genotype, allowing the suggestion that community abundances should be explored as candidate bioindicators for monitoring the possible impacts of cultivation of genetically modified plants.},
}
@article {pmid25107965,
year = {2014},
author = {Allen, KD and Wegener, G and White, RH},
title = {Discovery of multiple modified F(430) coenzymes in methanogens and anaerobic methanotrophic archaea suggests possible new roles for F(430) in nature.},
journal = {Applied and environmental microbiology},
volume = {80},
number = {20},
pages = {6403-6412},
pmid = {25107965},
issn = {1098-5336},
mesh = {Anaerobiosis ; Euryarchaeota/isolation &amp; purification/metabolism ; Mass Spectrometry/methods ; Metalloporphyrins/*chemistry/isolation &amp; purification/*metabolism ; Methanocaldococcus/chemistry/*metabolism ; Methanococcus/*metabolism ; Molecular Structure ; Spectrophotometry, Ultraviolet ; },
abstract = {Methane is a potent greenhouse gas that is generated and consumed in anaerobic environments through the energy metabolism of methanogens and anaerobic methanotrophic archaea (ANME), respectively. Coenzyme F430 is essential for methanogenesis, and a structural variant of F430, 17(2)-methylthio-F430 (F430-2), is found in ANME and is presumably essential for the anaerobic oxidation of methane. Here we use liquid chromatography-high-resolution mass spectrometry to identify several new structural variants of F430 in the cell extracts of selected methanogens and ANME. Methanocaldococcus jannaschii and Methanococcus maripaludis contain an F430 variant (denoted F430-3) that has an M(+) of 1,009.2781. This mass increase of 103.9913 over that of F430 corresponds to C3H4O2S and is consistent with the addition of a 3-mercaptopropionate moiety bound as a thioether followed by a cyclization. The UV absorbance spectrum of F430-3 was different from that of F430 and instead matched that of an F430 derivative where the 17(3) keto moiety had been reduced. This is the first report of a modified F430 in methanogens. In a search for F430-2 and F430-3 in other methanogens and ANME, we have identified a total of nine modified F430 structures. One of these compounds may be an abiotic oxidative product of F430, but the others represent naturally modified versions of F430. This work indicates that F430-related molecules have additional functions in nature and will inspire further research to determine the biochemical role(s) of these variants and the pathways involved in their biosynthesis.},
}
@article {pmid25102811,
year = {2014},
author = {Oren, A},
title = {Taxonomy of halophilic Archaea: current status and future challenges.},
journal = {Extremophiles : life under extreme conditions},
volume = {18},
number = {5},
pages = {825-834},
pmid = {25102811},
issn = {1433-4909},
mesh = {*Genome, Archaeal ; Halobacteriaceae/*classification/genetics/physiology ; *Phylogeny ; Salt Tolerance ; },
abstract = {Several groups of Archaea, all Euryarchaeota, develop in hypersaline environments (from >10% salt up to saturation). The cultured diversity of halophilic Archaea includes the family Halobacteriaceae of aerobic or facultative anaerobic, generally red-pigmented species (47 genera and 165 species as of February 2014) and seven representatives of four genera of methanogens, most of which obtain energy from methylated amines under anaerobic conditions. Metagenomic studies have identified an additional deep lineage of Archaea in salt lakes and ponds with brines approaching NaCl saturation. Genomic information is now available for representatives of these 'Nanohaloarchaea', but no members of this lineage have yet been cultured. Multilocus sequence analysis is becoming increasingly popular in taxonomic studies of the Halobacteriaceae, and such studies have demonstrated that recombination of genetic traits occurs at an extremely high frequency at least in some genera. Metagenomic studies in an Antarctic lake showed that large identical regions of up to 35 kb in length can be shared by members of different genera living together in the same environment. Such observations have important implications not only for the taxonomy of the Halobacteriaceae, but also for species concepts and questions on taxonomy and classification for prokaryotic microorganisms in general.},
}
@article {pmid25101062,
year = {2014},
author = {Makarova, KS and Krupovic, M and Koonin, EV},
title = {Evolution of replicative DNA polymerases in archaea and their contributions to the eukaryotic replication machinery.},
journal = {Frontiers in microbiology},
volume = {5},
number = {},
pages = {354},
pmid = {25101062},
issn = {1664-302X},
abstract = {The elaborate eukaryotic DNA replication machinery evolved from the archaeal ancestors that themselves show considerable complexity. Here we discuss the comparative genomic and phylogenetic analysis of the core replication enzymes, the DNA polymerases, in archaea and their relationships with the eukaryotic polymerases. In archaea, there are three groups of family B DNA polymerases, historically known as PolB1, PolB2 and PolB3. All three groups appear to descend from the last common ancestors of the extant archaea but their subsequent evolutionary trajectories seem to have been widely different. Although PolB3 is present in all archaea, with the exception of Thaumarchaeota, and appears to be directly involved in lagging strand replication, the evolution of this gene does not follow the archaeal phylogeny, conceivably due to multiple horizontal transfers and/or dramatic differences in evolutionary rates. In contrast, PolB1 is missing in Euryarchaeota but otherwise seems to have evolved vertically. The third archaeal group of family B polymerases, PolB2, includes primarily proteins in which the catalytic centers of the polymerase and exonuclease domains are disrupted and accordingly the enzymes appear to be inactivated. The members of the PolB2 group are scattered across archaea and might be involved in repair or regulation of replication along with inactivated members of the RadA family ATPases and an additional, uncharacterized protein that are encoded within the same predicted operon. In addition to the family B polymerases, all archaea, with the exception of the Crenarchaeota, encode enzymes of a distinct family D the origin of which is unclear. We examine multiple considerations that appear compatible with the possibility that family D polymerases are highly derived homologs of family B. The eukaryotic DNA polymerases show a highly complex relationship with their archaeal ancestors including contributions of proteins and domains from both the family B and the family D archaeal polymerases.},
}
@article {pmid25093819,
year = {2014},
author = {Kyrpides, NC and Hugenholtz, P and Eisen, JA and Woyke, T and Göker, M and Parker, CT and Amann, R and Beck, BJ and Chain, PS and Chun, J and Colwell, RR and Danchin, A and Dawyndt, P and Dedeurwaerdere, T and DeLong, EF and Detter, JC and De Vos, P and Donohue, TJ and Dong, XZ and Ehrlich, DS and Fraser, C and Gibbs, R and Gilbert, J and Gilna, P and Glöckner, FO and Jansson, JK and Keasling, JD and Knight, R and Labeda, D and Lapidus, A and Lee, JS and Li, WJ and Ma, J and Markowitz, V and Moore, ER and Morrison, M and Meyer, F and Nelson, KE and Ohkuma, M and Ouzounis, CA and Pace, N and Parkhill, J and Qin, N and Rossello-Mora, R and Sikorski, J and Smith, D and Sogin, M and Stevens, R and Stingl, U and Suzuki, K and Taylor, D and Tiedje, JM and Tindall, B and Wagner, M and Weinstock, G and Weissenbach, J and White, O and Wang, J and Zhang, L and Zhou, YG and Field, D and Whitman, WB and Garrity, GM and Klenk, HP},
title = {Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains.},
journal = {PLoS biology},
volume = {12},
number = {8},
pages = {e1001920},
pmid = {25093819},
issn = {1545-7885},
mesh = {Archaea/classification/genetics ; Bacteria/classification/genetics ; Databases, Genetic ; Genome, Archaeal/*genetics ; Genome, Bacterial/*genetics ; *Genomics ; Phylogeny ; *Sequence Analysis, DNA ; },
abstract = {Microbes hold the key to life. They hold the secrets to our past (as the descendants of the earliest forms of life) and the prospects for our future (as we mine their genes for solutions to some of the planet's most pressing problems, from global warming to antibiotic resistance). However, the piecemeal approach that has defined efforts to study microbial genetic diversity for over 20 years and in over 30,000 genome projects risks squandering that promise. These efforts have covered less than 20% of the diversity of the cultured archaeal and bacterial species, which represent just 15% of the overall known prokaryotic diversity. Here we call for the funding of a systematic effort to produce a comprehensive genomic catalog of all cultured Bacteria and Archaea by sequencing, where available, the type strain of each species with a validly published name (currently∼11,000). This effort will provide an unprecedented level of coverage of our planet's genetic diversity, allow for the large-scale discovery of novel genes and functions, and lead to an improved understanding of microbial evolution and function in the environment.},
}
@article {pmid25070168,
year = {2014},
author = {Thion, C and Prosser, JI},
title = {Differential response of nonadapted ammonia-oxidising archaea and bacteria to drying-rewetting stress.},
journal = {FEMS microbiology ecology},
volume = {90},
number = {2},
pages = {380-389},
doi = {10.1111/1574-6941.12395},
pmid = {25070168},
issn = {1574-6941},
mesh = {Ammonia/analysis/*metabolism ; Archaea/classification/*metabolism ; Bacteria/classification/*metabolism ; *Climate Change ; Droughts ; Nitrification ; Oxidation-Reduction ; RNA, Ribosomal, 16S ; *Soil Microbiology ; Water/metabolism ; },
abstract = {Climate change is expected to increase the frequency of severe drought events followed by heavy rainfall, which will influence growth and activity of soil microorganisms, through osmotic stress and changes in nutrient concentration. There is evidence of rapid recovery of processes and adaptation of communities in soils regularly experiencing drying/rewetting and lower resistance and resilience in nonadapted soils. A microcosm-based study of ammonia-oxidising archaea (AOA) and bacteria (AOB), employing a grassland soil that rarely experiences drought, was used to test this hypothesis and also whether AOB were more resistant and resilient, through greater tolerance of high ammonia concentrations produced during drought and rewetting. Treated soils were dried, incubated for 3 weeks, rewetted, incubated for a further 3 weeks and compared to untreated soils, maintained at a constant moisture content. Nitrate accumulation and AOA and AOB abundance (abundance of respective amoA genes) and community composition (DGGE analysis of AOA amoA and AOB 16S rRNA genes) were poorly adapted to drying-rewetting. AOA abundance and community composition were less resistant than AOB during drought and less resilient after rewetting, at times when ammonium concentration was higher. Data provide evidence for poor adaptation of microbial communities and processes to drying-rewetting in soils with no history of drought and indicate niche differentiation of AOA and AOB associated with high ammonia concentration.},
}
@article {pmid25064091,
year = {2014},
author = {Boujelben, I and Martínez-García, M and van Pelt, J and Maalej, S},
title = {Diversity of cultivable halophilic archaea and bacteria from superficial hypersaline sediments of Tunisian solar salterns.},
journal = {Antonie van Leeuwenhoek},
volume = {106},
number = {4},
pages = {675-692},
doi = {10.1007/s10482-014-0238-9},
pmid = {25064091},
issn = {1572-9699},
mesh = {Archaea/*classification/genetics/*isolation &amp; purification/metabolism ; Bacteria/*classification/genetics/*isolation &amp; purification/metabolism ; Cluster Analysis ; DNA, Archaeal/chemistry/genetics ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Geologic Sediments/*microbiology ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seasons ; Sequence Analysis, DNA ; Tunisia ; },
abstract = {Prokaryotes in the superficial sediments are ecologically important microorganisms that are responsible for the decomposition, mineralization and subsequent recycling of organic matter. The aim of this study was to explore the phylogenetic and functional diversity of halophilic archaea and bacteria isolated from the superficial sediments of solar salterns at Sfax, Tunisia. Sixty four strains were isolated from crystallizer (TS18) and non-crystallizer (M1) ponds and submitted to genotypic characterization and evaluation by amplified ribosomal RNA restriction analysis (ARDRA) techniques. Our findings revealed that the archaeal diversity observed for 29 isolates generated five distinct patterns from the non-crystallizer M1 pond, with Halorubrum chaoviator as the most prevalent cultivable species. However, in the TS18 crystallizer pond, ten restriction patterns were observed, with the prevalence of haloarchaea EB27K, a not yet identified genotype. The construction of a neighbour-joining tree of 16S rRNA gene sequences resulted in the division of the potential new species into two major groups, with four strains closely related to the sequence of the unculturable haloarchaeon EB27K and one strain to the recently described Halovenus aranensis strain. The 35 bacterial strains observed in this work were present only in the non-crystallizer pond (M1) and presented two distinct ARDRA patterns. These strains belonged to the γ-proteobacteria subdivision, with members of Salicola marasensis (83%) being the most predominant species among the isolates. 16S rRNA gene sequencing revealed that Salicola strains displayed different degrees of homogeneity. The results from pulsed field gel electrophoresis assays showed that the Salicola isolates could be clustered in two distinct groups with different genome sizes.},
}
@article {pmid25063662,
year = {2014},
author = {Connelly, TL and Baer, SE and Cooper, JT and Bronk, DA and Wawrik, B},
title = {Urea uptake and carbon fixation by marine pelagic bacteria and archaea during the Arctic summer and winter seasons.},
journal = {Applied and environmental microbiology},
volume = {80},
number = {19},
pages = {6013-6022},
pmid = {25063662},
issn = {1098-5336},
mesh = {Archaea/genetics/isolation &amp; purification/*metabolism ; Arctic Regions ; Bacteria/genetics/isolation &amp; purification/*metabolism ; Base Sequence ; Betaproteobacteria/genetics/isolation &amp; purification/metabolism ; Carbon/*metabolism ; Carbon Cycle ; Carbon Isotopes/analysis ; Climate Change ; Crenarchaeota/genetics/isolation &amp; purification/metabolism ; Molecular Sequence Data ; Nitrates/metabolism ; Nitrification ; Nitrogen/metabolism ; Nitrogen Isotopes/analysis ; Plankton/genetics/isolation &amp; purification/metabolism ; Proteobacteria/genetics/isolation &amp; purification/metabolism ; RNA, Ribosomal, 16S/genetics ; Seasons ; Seawater/microbiology ; Sequence Analysis, DNA ; Urea/*metabolism ; },
abstract = {How Arctic climate change might translate into alterations of biogeochemical cycles of carbon (C) and nitrogen (N) with respect to inorganic and organic N utilization is not well understood. This study combined 15N uptake rate measurements for ammonium, nitrate, and urea with 15N- and 13C-based DNA stable-isotope probing (SIP). The objective was to identify active bacterial and archeal plankton and their role in N and C uptake during the Arctic summer and winter seasons. We hypothesized that bacteria and archaea would successfully compete for nitrate and urea during the Arctic winter but not during the summer, when phytoplankton dominate the uptake of these nitrogen sources. Samples were collected at a coastal station near Barrow, AK, during August and January. During both seasons, ammonium uptake rates were greater than those for nitrate or urea, and nitrate uptake rates remained lower than those for ammonium or urea. SIP experiments indicated a strong seasonal shift of bacterial and archaeal N utilization from ammonium during the summer to urea during the winter but did not support a similar seasonal pattern of nitrate utilization. Analysis of 16S rRNA gene sequences obtained from each SIP fraction implicated marine group I Crenarchaeota (MGIC) as well as Betaproteobacteria, Firmicutes, SAR11, and SAR324 in N uptake from urea during the winter. Similarly, 13C SIP data suggested dark carbon fixation for MGIC, as well as for several proteobacterial lineages and the Firmicutes. These data are consistent with urea-fueled nitrification by polar archaea and bacteria, which may be advantageous under dark conditions.},
}
@article {pmid25028969,
year = {2014},
author = {Šustr, V and Chroňáková, A and Semanová, S and Tajovský, K and Šimek, M},
title = {Methane production and methanogenic Archaea in the digestive tracts of millipedes (Diplopoda).},
journal = {PloS one},
volume = {9},
number = {7},
pages = {e102659},
pmid = {25028969},
issn = {1932-6203},
mesh = {Animals ; Arthropods/*microbiology ; Base Sequence ; *Biodiversity ; Czech Republic ; Denaturing Gradient Gel Electrophoresis ; Euryarchaeota/*genetics/metabolism/*physiology ; Feces/chemistry ; Gastrointestinal Tract/*microbiology ; Methane/*biosynthesis/metabolism ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Romania ; Sequence Analysis, DNA ; Slovakia ; },
abstract = {Methane production by intestinal methanogenic Archaea and their community structure were compared among phylogenetic lineages of millipedes. Tropical and temperate millipedes of 35 species and 17 families were investigated. Species that emitted methane were mostly in the juliform orders Julida, Spirobolida, and Spirostreptida. The irregular phylogenetic distribution of methane production correlated with the presence of the methanogen-specific mcrA gene. The study brings the first detailed survey of methanogens' diversity in the digestive tract of millipedes. Sequences related to Methanosarcinales, Methanobacteriales, Methanomicrobiales and some unclassified Archaea were detected using molecular profiling (DGGE). The differences in substrate preferences of the main lineages of methanogenic Archaea found in different millipede orders indicate that the composition of methanogen communities may reflect the differences in available substrates for methanogenesis or the presence of symbiotic protozoa in the digestive tract. We conclude that differences in methane production in the millipede gut reflect differences in the activity and proliferation of intestinal methanogens rather than an absolute inability of some millipede taxa to host methanogens. This inference was supported by the general presence of methanogenic activity in millipede faecal pellets and the presence of the 16S rRNA gene of methanogens in all tested taxa in the two main groups of millipedes, the Helminthophora and the Pentazonia.},
}
@article {pmid25012975,
year = {2014},
author = {Grasso, S and Tell, G},
title = {Base excision repair in Archaea: back to the future in DNA repair.},
journal = {DNA repair},
volume = {21},
number = {},
pages = {148-157},
doi = {10.1016/j.dnarep.2014.05.006},
pmid = {25012975},
issn = {1568-7856},
mesh = {Archaea/*genetics ; Archaeal Proteins/*genetics/metabolism ; *DNA Repair ; DNA Repair Enzymes/*genetics/metabolism ; Evolution, Molecular ; },
abstract = {Together with Bacteria and Eukarya, Archaea represents one of the three domain of life. In contrast with the morphological difference existing between Archaea and Eukarya, these two domains are closely related. Phylogenetic analyses confirm this evolutionary relationship showing that most of the proteins involved in DNA transcription and replication are highly conserved. On the contrary, information is scanty about DNA repair pathways and their mechanisms. In the present review the most important proteins involved in base excision repair, namely glycosylases, AP lyases, AP endonucleases, polymerases, sliding clamps, flap endonucleases, and ligases, will be discussed and compared with bacterial and eukaryotic ones. Finally, possible applications and future perspectives derived from studies on Archaea and their repair pathways, will be taken into account.},
}
@article {pmid25002468,
year = {2014},
author = {Liu, Y and Nakamura, A and Nakazawa, Y and Asano, N and Ford, KA and Hohn, MJ and Tanaka, I and Yao, M and Söll, D},
title = {Ancient translation factor is essential for tRNA-dependent cysteine biosynthesis in methanogenic archaea.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {111},
number = {29},
pages = {10520-10525},
pmid = {25002468},
issn = {1091-6490},
support = {R01 GM022854/GM/NIGMS NIH HHS/United States ; R37 GM022854/GM/NIGMS NIH HHS/United States ; GM22854/GM/NIGMS NIH HHS/United States ; },
mesh = {Acetylation ; Archaea/*metabolism ; Archaeal Proteins/chemistry/*metabolism ; Conserved Sequence ; Crystallography, X-Ray ; Cysteine/*biosynthesis ; Kinetics ; Methanococcus/*metabolism ; Models, Molecular ; Peptide Initiation Factors/chemistry/*metabolism ; Protein Binding ; Protein Structure, Tertiary ; RNA, Transfer, Cys/chemistry/*metabolism ; },
abstract = {Methanogenic archaea lack cysteinyl-tRNA synthetase; they synthesize Cys-tRNA and cysteine in a tRNA-dependent manner. Two enzymes are required: Phosphoseryl-tRNA synthetase (SepRS) forms phosphoseryl-tRNA(Cys) (Sep-tRNA(Cys)), which is converted to Cys-tRNA(Cys) by Sep-tRNA:Cys-tRNA synthase (SepCysS). This represents the ancestral pathway of Cys biosynthesis and coding in archaea. Here we report a translation factor, SepCysE, essential for methanococcal Cys biosynthesis; its deletion in Methanococcus maripaludis causes Cys auxotrophy. SepCysE acts as a scaffold for SepRS and SepCysS to form a stable high-affinity complex for tRNA(Cys) causing a 14-fold increase in the initial rate of Cys-tRNA(Cys) formation. Based on our crystal structure (2.8-Å resolution) of a SepCysS⋅SepCysE complex, a SepRS⋅SepCysE⋅SepCysS structure model suggests that this ternary complex enables substrate channeling of Sep-tRNA(Cys). A phylogenetic analysis suggests coevolution of SepCysE with SepRS and SepCysS in the last universal common ancestral state. Our findings suggest that the tRNA-dependent Cys biosynthesis proceeds in a multienzyme complex without release of the intermediate and this mechanism may have facilitated the addition of Cys to the genetic code.},
}
@article {pmid25002421,
year = {2014},
author = {Jiang, H and Huang, L and Deng, Y and Wang, S and Zhou, Y and Liu, L and Dong, H},
title = {Latitudinal distribution of ammonia-oxidizing bacteria and archaea in the agricultural soils of eastern China.},
journal = {Applied and environmental microbiology},
volume = {80},
number = {18},
pages = {5593-5602},
pmid = {25002421},
issn = {1098-5336},
mesh = {Ammonia/*metabolism ; Archaea/*classification/isolation &amp; purification/*metabolism ; Bacteria/*classification/isolation &amp; purification/*metabolism ; Biota ; Carbon/analysis ; China ; Climate ; Cluster Analysis ; DNA Barcoding, Taxonomic ; Hydrogen-Ion Concentration ; Oxidation-Reduction ; Oxidoreductases/genetics ; RNA, Ribosomal, 16S/genetics ; Real-Time Polymerase Chain Reaction ; Soil/chemistry ; *Soil Microbiology ; },
abstract = {The response of soil ammonia-oxidizing bacterial (AOB) and archaeal (AOA) communities to individual environmental variables (e.g., pH, temperature, and carbon- and nitrogen-related soil nutrients) has been extensively studied, but how these environmental conditions collectively shape AOB and AOA distributions in unmanaged agricultural soils across a large latitudinal gradient remains poorly known. In this study, the AOB and AOA community structure and diversity in 26 agricultural soils collected from eastern China were investigated by using quantitative PCR and bar-coded 454 pyrosequencing of the amoA gene that encodes the alpha subunit of ammonia monooxygenase. The sampling locations span over a 17° latitude gradient and cover a range of climatic conditions. The Nitrosospira and Nitrososphaera were the dominant clusters of AOB and AOA, respectively; but the subcluster-level composition of Nitrosospira-related AOB and Nitrososphaera-related AOA varied across the latitudinal gradient. Variance partitioning analysis showed that geography and climatic conditions (e.g., mean annual temperature and precipitation), as well as carbon-/nitrogen-related soil nutrients, contributed more to the AOB and AOA community variations (∼50% in total) than soil pH (∼10% in total). These results are important in furthering our understanding of environmental conditions influencing AOB and AOA community structure across a range of environmental gradients.},
}
@article {pmid24999826,
year = {2014},
author = {Zhalnina, KV and Dias, R and Leonard, MT and Dorr de Quadros, P and Camargo, FA and Drew, JC and Farmerie, WG and Daroub, SH and Triplett, EW},
title = {Genome sequence of Candidatus Nitrososphaera evergladensis from group I.1b enriched from Everglades soil reveals novel genomic features of the ammonia-oxidizing archaea.},
journal = {PloS one},
volume = {9},
number = {7},
pages = {e101648},
pmid = {24999826},
issn = {1932-6203},
mesh = {Adaptation, Physiological/genetics ; Ammonia/*metabolism ; Archaea/cytology/*genetics/*metabolism/physiology ; Biological Transport/genetics ; Carbon/metabolism ; Carbon Cycle/genetics ; Cell Division/genetics ; Chemotaxis/genetics ; DNA Repair/genetics ; DNA Replication/genetics ; Energy Metabolism/genetics ; *Genomics ; Metals, Heavy/toxicity ; Molecular Sequence Annotation ; Nitrogen/metabolism ; Oceans and Seas ; Osmotic Pressure ; Oxidation-Reduction ; Phylogeny ; *Soil Microbiology ; Terpenes/metabolism ; },
abstract = {The activity of ammonia-oxidizing archaea (AOA) leads to the loss of nitrogen from soil, pollution of water sources and elevated emissions of greenhouse gas. To date, eight AOA genomes are available in the public databases, seven are from the group I.1a of the Thaumarchaeota and only one is from the group I.1b, isolated from hot springs. Many soils are dominated by AOA from the group I.1b, but the genomes of soil representatives of this group have not been sequenced and functionally characterized. The lack of knowledge of metabolic pathways of soil AOA presents a critical gap in understanding their role in biogeochemical cycles. Here, we describe the first complete genome of soil archaeon Candidatus Nitrososphaera evergladensis, which has been reconstructed from metagenomic sequencing of a highly enriched culture obtained from an agricultural soil. The AOA enrichment was sequenced with the high throughput next generation sequencing platforms from Pacific Biosciences and Ion Torrent. The de novo assembly of sequences resulted in one 2.95 Mb contig. Annotation of the reconstructed genome revealed many similarities of the basic metabolism with the rest of sequenced AOA. Ca. N. evergladensis belongs to the group I.1b and shares only 40% of whole-genome homology with the closest sequenced relative Ca. N. gargensis. Detailed analysis of the genome revealed coding sequences that were completely absent from the group I.1a. These unique sequences code for proteins involved in control of DNA integrity, transporters, two-component systems and versatile CRISPR defense system. Notably, genomes from the group I.1b have more gene duplications compared to the genomes from the group I.1a. We suggest that the presence of these unique genes and gene duplications may be associated with the environmental versatility of this group.},
}
@article {pmid24990376,
year = {2014},
author = {Gadelle, D and Krupovic, M and Raymann, K and Mayer, C and Forterre, P},
title = {DNA topoisomerase VIII: a novel subfamily of type IIB topoisomerases encoded by free or integrated plasmids in Archaea and Bacteria.},
journal = {Nucleic acids research},
volume = {42},
number = {13},
pages = {8578-8591},
pmid = {24990376},
issn = {1362-4962},
support = {340440/ERC_/European Research Council/International ; },
mesh = {Amino Acid Sequence ; Archaea/*enzymology/genetics ; Archaeal Proteins/chemistry/classification/genetics/metabolism ; Bacteria/*enzymology ; Bacterial Proteins/chemistry/classification/genetics/metabolism ; Conserved Sequence ; DNA Topoisomerases/chemistry/*classification/genetics/metabolism ; Genome, Bacterial ; Phylogeny ; Plasmids/genetics ; },
abstract = {Type II DNA topoisomerases are divided into two families, IIA and IIB. Types IIA and IIB enzymes share homologous B subunits encompassing the ATP-binding site, but have non-homologous A subunits catalyzing DNA cleavage. Type IIA topoisomerases are ubiquitous in Bacteria and Eukarya, whereas members of the IIB family are mostly present in Archaea and plants. Here, we report the detection of genes encoding type IIB enzymes in which the A and B subunits are fused into a single polypeptide. These proteins are encoded in several bacterial genomes, two bacterial plasmids and one archaeal plasmid. They form a monophyletic group that is very divergent from archaeal and eukaryotic type IIB enzymes (DNA topoisomerase VI). We propose to classify them into a new subfamily, denoted DNA topoisomerase VIII. Bacterial genes encoding a topoisomerase VIII are present within integrated mobile elements, most likely derived from conjugative plasmids. Purified topoisomerase VIII encoded by the plasmid pPPM1a from Paenibacillus polymyxa M1 had ATP-dependent relaxation and decatenation activities. In contrast, the enzyme encoded by mobile elements integrated into the genome of Ammonifex degensii exhibited DNA cleavage activity producing a full-length linear plasmid and that from Microscilla marina exhibited ATP-independent relaxation activity. Topoisomerases VIII, the smallest known type IIB enzymes, could be new promising models for structural and mechanistic studies.},
}
@article {pmid24987307,
year = {2014},
author = {Caetano-Anollés, G and Nasir, A and Zhou, K and Caetano-Anollés, D and Mittenthal, JE and Sun, FJ and Kim, KM},
title = {Archaea: the first domain of diversified life.},
journal = {Archaea (Vancouver, B.C.)},
volume = {2014},
number = {},
pages = {590214},
pmid = {24987307},
issn = {1472-3654},
mesh = {Archaea/genetics/*physiology ; *Biological Evolution ; *Phylogeny ; United States ; },
abstract = {The study of the origin of diversified life has been plagued by technical and conceptual difficulties, controversy, and apriorism. It is now popularly accepted that the universal tree of life is rooted in the akaryotes and that Archaea and Eukarya are sister groups to each other. However, evolutionary studies have overwhelmingly focused on nucleic acid and protein sequences, which partially fulfill only two of the three main steps of phylogenetic analysis, formulation of realistic evolutionary models, and optimization of tree reconstruction. In the absence of character polarization, that is, the ability to identify ancestral and derived character states, any statement about the rooting of the tree of life should be considered suspect. Here we show that macromolecular structure and a new phylogenetic framework of analysis that focuses on the parts of biological systems instead of the whole provide both deep and reliable phylogenetic signal and enable us to put forth hypotheses of origin. We review over a decade of phylogenomic studies, which mine information in a genomic census of millions of encoded proteins and RNAs. We show how the use of process models of molecular accumulation that comply with Weston's generality criterion supports a consistent phylogenomic scenario in which the origin of diversified life can be traced back to the early history of Archaea.},
}
@article {pmid24948879,
year = {2014},
author = {Wang, S and Xu, Y and Lu, Z},
title = {Genome-wide miRNA seeds prediction in Archaea.},
journal = {Archaea (Vancouver, B.C.)},
volume = {2014},
number = {},
pages = {671059},
pmid = {24948879},
issn = {1472-3654},
mesh = {Archaea/*genetics ; Computational Biology/methods ; *Genes, Archaeal ; *Genome, Archaeal ; MicroRNAs/*genetics ; },
abstract = {Growing evidence indicates that miRNA genes exist in the archaeal genome, though the functional role of such noncoding RNA remains unclear. Here, we integrated the phylogenetic information of available archaeal genomes to predict miRNA seeds (typically defined as the 2-8 nucleotides of mature miRNAs) on the genomic scale. Finally, we found 2649 candidate seeds with significant conservation signal. Eleven of 29 unique seeds from previous study support our result (P value <0.01), which demonstrates that the pipeline is suitable to predict experimentally detectable miRNA seeds. The statistical significance of the overlap between the detected archaeal seeds and known eukaryotic seeds shows that the miRNA may evolve before the divergence of these two domains of cellular life. In addition, miRNA targets are enriched for genes involved in transcriptional regulation, which is consistent with the situation in eukaryote. Our research will enhance the regulatory network analysis in Archaea.},
}
@article {pmid24915454,
year = {2014},
author = {Bang, C and Weidenbach, K and Gutsmann, T and Heine, H and Schmitz, RA},
title = {The intestinal archaea Methanosphaera stadtmanae and Methanobrevibacter smithii activate human dendritic cells.},
journal = {PloS one},
volume = {9},
number = {6},
pages = {e99411},
pmid = {24915454},
issn = {1932-6203},
mesh = {Antimicrobial Cationic Peptides/genetics/metabolism ; Cytokines/metabolism ; Dendritic Cells/*immunology/*microbiology/ultrastructure ; Epithelial Cells/immunology/microbiology ; Gene Expression Regulation ; HEK293 Cells ; Humans ; Intestines/*microbiology ; Methanobacteriaceae/*physiology ; Methanobrevibacter/*physiology ; Monocytes/cytology ; Phagocytosis ; Receptors, Cell Surface/metabolism ; },
abstract = {The methanoarchaea Methanosphaera stadtmanae and Methanobrevibacter smithii are known to be part of the indigenous human gut microbiota. Although the immunomodulatory effects of bacterial gut commensals have been studied extensively in the last decade, the impact of methanoarchaea in human's health and disease was rarely examined. Consequently, we studied and report here on the effects of M. stadtmanae and M. smithii on human immune cells. Whereas exposure to M. stadtmanae leads to substantial release of proinflammatory cytokines in monocyte-derived dendritic cells (moDCs), only weak activation was detected after incubation with M. smithii. Phagocytosis of M. stadtmanae by moDCs was demonstrated by confocal microscopy as well as transmission electronic microscopy (TEM) and shown to be crucial for cellular activation by using specific inhibitors. Both strains, albeit to different extents, initiate a maturation program in moDCs as revealed by up-regulation of the cell-surface receptors CD86 and CD197 suggesting additional activation of adaptive immune responses. Furthermore, M. stadtmanae and M. smithii were capable to alter the gene expression of antimicrobial peptides in moDCs to different extents. Taken together, our findings strongly argue that the archaeal gut inhabitants M. stadtmanae and M. smithii are specifically recognized by the human innate immune system. Moreover, both strains are capable of inducing an inflammatory cytokine response to different extents arguing that they might have diverse immunomodulatory functions. In conclusion, we propose that the impact of intestinal methanoarchaea on pathological conditions involving the gut microbiota has been underestimated until now.},
}
@article {pmid24914732,
year = {2014},
author = {Vinokur, JM and Korman, TP and Cao, Z and Bowie, JU},
title = {Evidence of a novel mevalonate pathway in archaea.},
journal = {Biochemistry},
volume = {53},
number = {25},
pages = {4161-4168},
pmid = {24914732},
issn = {1520-4995},
support = {5T32GM008496/GM/NIGMS NIH HHS/United States ; },
mesh = {Mevalonic Acid/*analogs &amp; derivatives/metabolism ; Organophosphates/*metabolism ; Phosphorylation ; Phosphotransferases/genetics/*metabolism ; Thermoplasma/*metabolism ; },
abstract = {Isoprenoids make up a remarkably diverse class of more than 25000 biomolecules that include familiar compounds such as cholesterol, chlorophyll, vitamin A, ubiquinone, and natural rubber. The two essential building blocks of all isoprenoids, isopentenyl pyrophosphate (IPP) and dimethylallyl pyrophosphate (DMAPP), are ubiquitous in the three domains of life. In most eukaryotes and archaea, IPP and DMAPP are generated through the mevalonate pathway. We have identified two novel enzymes, mevalonate-3-kinase and mevalonate-3-phosphate-5-kinase from Thermoplasma acidophilum, which act sequentially in a putative alternate mevalonate pathway. We propose that a yet unidentified ATP-independent decarboxylase acts upon mevalonate 3,5-bisphosphate, yielding isopentenyl phosphate, which is subsequently phosphorylated by the known isopentenyl phosphate kinase from T. acidophilum to generate the universal isoprenoid precursor, IPP.},
}
@article {pmid24894983,
year = {2014},
author = {Kothe, E},
title = {Special focus: Archaea.},
journal = {Journal of basic microbiology},
volume = {54},
number = {6},
pages = {471},
doi = {10.1002/jobm.201470063},
pmid = {24894983},
issn = {1521-4028},
mesh = {Archaea/classification/genetics/*isolation &amp; purification/*physiology ; Biotechnology/*methods ; *Metabolic Networks and Pathways ; },
}
@article {pmid24880629,
year = {2014},
author = {Xie, W and Zhang, C and Zhou, X and Wang, P},
title = {Salinity-dominated change in community structure and ecological function of Archaea from the lower Pearl River to coastal South China Sea.},
journal = {Applied microbiology and biotechnology},
volume = {98},
number = {18},
pages = {7971-7982},
doi = {10.1007/s00253-014-5838-9},
pmid = {24880629},
issn = {1432-0614},
mesh = {Archaea/*genetics/isolation &amp; purification ; China ; DNA, Archaeal/genetics ; DNA, Ribosomal/genetics ; Estuaries ; Rivers/microbiology ; *Salinity ; Seawater/*microbiology ; },
abstract = {Archaea have multiple roles in global biogeochemical cycles. However, we still have limited knowledge about how environmental factors affect the diversity and function of different archaeal lineages. The goal of this study was to examine the change in the abundance and community structure of Archaea in the sediments collected from the lower Pearl River (mainly North River tributary), its estuary, and coastal South China Sea (SCS) in order to evaluate how archaeal ecological function might change along the salinity gradient. Pyrosequencing of the 16S rDNA gene of Archaea was performed on sediment samples from Feilaixia Dam on the North River tributary to Wanshan islands, which have a salinity range of 0.1 to 31.2‰. Consistent with the salt tolerance of cultivated representatives, methanogens in the genera Methanoregula, Methanosaeta, and Methanosarcina and Nitrososphaera within Thaumarchaeota of the ammonia-oxidizing Archaea (AOA) were abundant in freshwater sediments of the North River tributary, whereas the marine-associated genera Methanococcoides and Nitrosopumilus were the most abundant methanogens and AOA, respectively, in the estuary and coastal SCS. However, the percentages of total methanogens decreased and Thaumarchaeota increased with salinity, respectively. The phylum Crenarchaeota was largely represented by class-level lineages with no cultivated representatives, which collectively were more abundant in the estuary and coastal SCS in comparison to freshwater sites. This study indicates that salinity is the dominating factor affecting archaeal community structure and ecological function from the North River tributary of the Pearl River, its estuary, and coastal SCS, which is consistent with salinity control on microbial diversity in other regions of the world.},
}
@article {pmid24875627,
year = {2014},
author = {Ramey, CJ and Sclafani, RA},
title = {Functional conservation of the pre-sensor one beta-finger hairpin (PS1-hp) structures in mini-chromosome maintenance proteins of Saccharomyces cerevisiae and archaea.},
journal = {G3 (Bethesda, Md.)},
volume = {4},
number = {7},
pages = {1319-1326},
pmid = {24875627},
issn = {2160-1836},
support = {R01 GM035078/GM/NIGMS NIH HHS/United States ; P30CA046934/CA/NCI NIH HHS/United States ; P30 CA046934/CA/NCI NIH HHS/United States ; T32 GM008730/GM/NIGMS NIH HHS/United States ; GM35078/GM/NIGMS NIH HHS/United States ; },
mesh = {Amino Acid Sequence ; Archaea/genetics/*metabolism ; Archaeal Proteins/chemistry/genetics/*metabolism ; Chromatin Immunoprecipitation ; DNA Replication ; Minichromosome Maintenance Proteins/chemistry/genetics/*metabolism ; Molecular Sequence Data ; Plasmids/metabolism ; Protein Structure, Tertiary ; S Phase ; Saccharomyces cerevisiae/genetics/*metabolism ; Saccharomyces cerevisiae Proteins/chemistry/genetics/*metabolism ; Sequence Alignment ; },
abstract = {Mini-chromosome maintenance (MCM) proteins form complexes that are required for DNA replication and are highly conserved throughout evolution. The replicative helicase of eukaryotic organisms is composed of the six paralogs MCM2-7, which form a heterohexameric ring structure. In contrast, the structure of the archaean replicative MCM helicase is a single Mcm protein that forms a homohexameric complex. Atomic structures of archaeal MCMs have identified multiple beta-finger structures in Mcm proteins whose in vivo function is unknown. In the present study, we have investigated the physiological role of the pre-sensor 1 beta-hairpin (PS1-hp) beta-fingers of Saccharomyces cerevisiae Mcm4p and Mcm5p in DNA replication initiation and elongation in vivo. The PS1-hp beta-finger mutant of Mcm5p (mcm5-HAT K506A::URA3) has a growth defect at both 18° and 37°. Mutation of the Mcm4p PS1-hp beta-finger (mcm4-HA K658A::TRP1) does not have a growth defect, indicating different functional contributions of the PS1-hp beta-finger structures of different MCM helicase subunits. Both Mcm4p and Mcm5p PS1-hp beta-finger mutants can coimmunoprecipitate Mcm2p, indicating the formation of the hexameric MCM helicase complex. Both PS1-hp beta-finger mutants have a plasmid loss phenotype that is suppressible by origin dosage, indicating a defective replication initiation. Surprisingly, a defect in the binding of PS1-hp MCM mutants to origins of DNA replication was not found by chromatin immunoprecipitation, suggesting a novel interpretation in which the defect is in a subsequent step of DNA strand separation by the MCM helicase. The double mutant mcm4-HA K658A::TRP1 mcm5-HAT K506A::URA3 is lethal, displaying a terminal MCM mutant phenotype of large budded cells.},
}
@article {pmid24875358,
year = {2014},
author = {Feng, Y and Song, X and Lin, J and Xuan, J and Cui, Q and Wang, J},
title = {Structure determination of archaea-specific ribosomal protein L46a reveals a novel protein fold.},
journal = {Biochemical and biophysical research communications},
volume = {450},
number = {1},
pages = {67-72},
doi = {10.1016/j.bbrc.2014.05.077},
pmid = {24875358},
issn = {1090-2104},
mesh = {Amino Acid Sequence ; Archaeal Proteins/*chemistry/*ultrastructure ; Binding Sites ; *Models, Chemical ; *Models, Molecular ; Molecular Sequence Data ; Protein Folding ; Ribosomal Proteins/*chemistry/*ultrastructure ; Sequence Homology, Amino Acid ; },
abstract = {Three archaea-specific ribosomal proteins recently identified show no sequence homology with other known proteins. Here we determined the structure of L46a, the most conserved one among the three proteins, from Sulfolobus solfataricus P2 using NMR spectroscopy. The structure presents a twisted β-sheet formed by the N-terminal part and two helices at the C-terminus. The L46a structure has a positively charged surface which is conserved in the L46a protein family and is the potential rRNA-binding site. Searching homologous structures in Protein Data Bank revealed that the structure of L46a represents a novel protein fold. The backbone dynamics identified by NMR relaxation experiments reveal significant flexibility at the rRNA binding surface. The potential position of L46a on the ribosome was proposed by fitting the structure into a previous electron microscopy map of the ribosomal 50S subunit, which indicated that L46a contacts to domain I of 23S rRNA near a multifunctional ribosomal protein L7ae.},
}
@article {pmid24865847,
year = {2014},
author = {Zorgani, MA and Patron, K and Desvaux, M},
title = {New insight in the structural features of haloadaptation in α-amylases from halophilic Archaea following homology modeling strategy: folded and stable conformation maintained through low hydrophobicity and highly negative charged surface.},
journal = {Journal of computer-aided molecular design},
volume = {28},
number = {7},
pages = {721-734},
pmid = {24865847},
issn = {1573-4951},
mesh = {Amino Acid Sequence ; Archaea ; Haloarcula/chemistry/enzymology ; Halobacteriales/chemistry ; Hydrophobic and Hydrophilic Interactions ; Models, Molecular ; *Protein Conformation ; *Protein Folding ; Protein Structure, Secondary ; *Structural Homology, Protein ; alpha-Amylases/*chemistry ; },
abstract = {Proteins from halophilic archaea, which live in extreme saline conditions, have evolved to remain folded, active and stable at very high ionic strengths. Understanding the mechanism of haloadaptation is the first step toward engineering of halostable biomolecules. Amylases are one of the main enzymes used in industry. Yet, no three-dimensional structure has been experimentally resolved for α-amylases from halophilic archaea. In this study, homology structure modeling of α-amylases from the halophilic archaea Haloarcula marismortui, Haloarcula hispanica, and Halalkalicoccus jeotgali were performed. The resulting models were subjected to energy minimization, evaluation, and structural analysis. Calculations of the amino acid composition, salt bridges and hydrophobic interactions were also performed and compared to a set of non-halophilic counterparts. It clearly appeared that haloarchaeal α-amylases exhibited lower propensities for helix formation and higher propensities for coil-forming regions. Furthermore, they could maintain a folded and stable conformation in high salt concentration through highly negative charged surface with over representation of acidic residues, especially Asp, and low hydrophobicity with increase of salt bridges and decrease in hydrophobic interactions on the protein surface. This study sheds some light on the stability of α-amylases from halophilic archaea and provides strong basis not only to understand haloadaptation mechanisms of proteins in microorganisms from hypersalines environments but also for biotechnological applications.},
}
@article {pmid24859768,
year = {2014},
author = {Li, CL and Jiang, YT and Liu, DL and Qian, J and Liang, JP and Shu, R},
title = {Prevalence and quantification of the uncommon Archaea phylotype Thermoplasmata in chronic periodontitis.},
journal = {Archives of oral biology},
volume = {59},
number = {8},
pages = {822-828},
doi = {10.1016/j.archoralbio.2014.05.011},
pmid = {24859768},
issn = {1879-1506},
mesh = {Adult ; Case-Control Studies ; Chronic Periodontitis/*microbiology ; DNA, Bacterial/analysis ; Dental Plaque/microbiology ; Euryarchaeota/*isolation &amp; purification ; Female ; Humans ; Male ; Middle Aged ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/analysis ; Real-Time Polymerase Chain Reaction ; },
abstract = {OBJECTIVE: Chronic periodontitis is a chronic inflammatory disease of the periodontal tissues and is caused by invasion of certain types of bacteria and Archaea, with Methanobrevibacter oralis as the predominant archaeon. In this study, we investigated the prevalence and quantity of the newly discovered Archaea phylotype Thermoplasmata in patients with chronic periodontitis.<br><br>METHODS: Subgingival plaque samples were obtained from 49 patients with chronic periodontitis and 45 periodontally healthy subjects. Qualitative analyses of Archaea and class Thermoplasmata were carried out by amplification of 16S rRNA genes in DNA extracts from plaque samples, and all the samples were quantitatively analyzed by real-time polymerase chain reaction (PCR).<br><br>RESULTS: The prevalence of Archaea in patients with chronic periodontitis was 69.4% according to the conventional PCR results, but was 87.8% according to real-time PCR. In the control group, three samples were detected as positive, but none of these were confirmed in qualitative analyses. The prevalence of class Thermoplasmata was 18.4% by nested PCR and 24.5% by quantitative PCR in the chronic periodontitis group. The prevalence of Thermoplasmata was significantly lower than that of total Archaea. The relative abundances of Archaea and Thermoplasmata varied among samples. Thermoplasmata were not the predominant archaeons in the subgingival dental plaque. Among the clinical parameters of patients with periodontitis, probing depth was positively associated with Archaea detection.<br><br>CONCLUSIONS: The existence of Archaea was correlated closely with the presence of chronic periodontitis. Thermoplasmata represented a minor archaeon in periodontal infection.},
}
@article {pmid24847024,
year = {2014},
author = {Jarrell, KF and Ding, Y and Meyer, BH and Albers, SV and Kaminski, L and Eichler, J},
title = {N-linked glycosylation in Archaea: a structural, functional, and genetic analysis.},
journal = {Microbiology and molecular biology reviews : MMBR},
volume = {78},
number = {2},
pages = {304-341},
pmid = {24847024},
issn = {1098-5557},
mesh = {Archaea/genetics/*metabolism ; Glycosylation ; Hexosyltransferases/metabolism ; Membrane Proteins/metabolism ; Metabolic Networks and Pathways ; Polysaccharides/genetics/metabolism ; Prokaryotic Cells/metabolism ; *Protein Processing, Post-Translational ; },
abstract = {N-glycosylation of proteins is one of the most prevalent posttranslational modifications in nature. Accordingly, a pathway with shared commonalities is found in all three domains of life. While excellent model systems have been developed for studying N-glycosylation in both Eukarya and Bacteria, an understanding of this process in Archaea was hampered until recently by a lack of effective molecular tools. However, within the last decade, impressive advances in the study of the archaeal version of this important pathway have been made for halophiles, methanogens, and thermoacidophiles, combining glycan structural information obtained by mass spectrometry with bioinformatic, genetic, biochemical, and enzymatic data. These studies reveal both features shared with the eukaryal and bacterial domains and novel archaeon-specific aspects. Unique features of N-glycosylation in Archaea include the presence of unusual dolichol lipid carriers, the use of a variety of linking sugars that connect the glycan to proteins, the presence of novel sugars as glycan constituents, the presence of two very different N-linked glycans attached to the same protein, and the ability to vary the N-glycan composition under different growth conditions. These advances are the focus of this review, with an emphasis on N-glycosylation pathways in Haloferax, Methanococcus, and Sulfolobus.},
}
@article {pmid24843170,
year = {2014},
author = {Könneke, M and Schubert, DM and Brown, PC and Hügler, M and Standfest, S and Schwander, T and Schada von Borzyskowski, L and Erb, TJ and Stahl, DA and Berg, IA},
title = {Ammonia-oxidizing archaea use the most energy-efficient aerobic pathway for CO2 fixation.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {111},
number = {22},
pages = {8239-8244},
pmid = {24843170},
issn = {1091-6490},
mesh = {Acetyl Coenzyme A/metabolism ; Aerobiosis/*physiology ; Ammonia/*metabolism ; Archaea/*enzymology/genetics/metabolism ; Autotrophic Processes/*physiology ; Carbon Cycle/*physiology ; Carbon Dioxide/*metabolism ; Energy Metabolism/genetics/physiology ; Evolution, Molecular ; Hydro-Lyases/genetics/metabolism ; Oxidation-Reduction ; Photosynthesis/genetics/physiology ; Phylogeny ; },
abstract = {Archaea of the phylum Thaumarchaeota are among the most abundant prokaryotes on Earth and are widely distributed in marine, terrestrial, and geothermal environments. All studied Thaumarchaeota couple the oxidation of ammonia at extremely low concentrations with carbon fixation. As the predominant nitrifiers in the ocean and in various soils, ammonia-oxidizing archaea contribute significantly to the global nitrogen and carbon cycles. Here we provide biochemical evidence that thaumarchaeal ammonia oxidizers assimilate inorganic carbon via a modified version of the autotrophic hydroxypropionate/hydroxybutyrate cycle of Crenarchaeota that is far more energy efficient than any other aerobic autotrophic pathway. The identified genes of this cycle were found in the genomes of all sequenced representatives of the phylum Thaumarchaeota, indicating the environmental significance of this efficient CO2-fixation pathway. Comparative phylogenetic analysis of proteins of this pathway suggests that the hydroxypropionate/hydroxybutyrate cycle emerged independently in Crenarchaeota and Thaumarchaeota, thus supporting the hypothesis of an early evolutionary separation of both archaeal phyla. We conclude that high efficiency of anabolism exemplified by this autotrophic cycle perfectly suits the lifestyle of ammonia-oxidizing archaea, which thrive at a constantly low energy supply, thus offering a biochemical explanation for their ecological success in nutrient-limited environments.},
}
@article {pmid24837075,
year = {2014},
author = {Urbonavičius, J and Meškys, R and Grosjean, H},
title = {Biosynthesis of wyosine derivatives in tRNA(Phe) of Archaea: role of a remarkable bifunctional tRNA(Phe):m1G/imG2 methyltransferase.},
journal = {RNA (New York, N.Y.)},
volume = {20},
number = {6},
pages = {747-753},
pmid = {24837075},
issn = {1469-9001},
mesh = {Anticodon/genetics ; Archaea/*genetics/metabolism ; Biosynthetic Pathways/*genetics ; Guanosine/*analogs &amp; derivatives/biosynthesis/genetics/metabolism ; Nucleosides/genetics/metabolism ; RNA, Transfer, Phe/*biosynthesis/genetics/metabolism ; tRNA Methyltransferases/*biosynthesis/genetics/metabolism ; },
abstract = {The presence of tricyclic wyosine derivatives 3'-adjacent to anticodon is a hallmark of tRNA(Phe) in eukaryotes and archaea. In yeast, formation of wybutosine (yW) results from five enzymes acting in a strict sequential order. In archaea, the intermediate compound imG-14 (4-demethylwyosine) is a target of three different enzymes, leading to the formation of distinct wyosine derivatives (yW-86, imG, and imG2). We focus here on a peculiar methyltransferase (aTrm5a) that catalyzes two distinct reactions: N(1)-methylation of guanosine and C(7)-methylation of imG-14, whose function is to allow the production of isowyosine (imG2), an intermediate of the 7-methylwyosine (mimG) biosynthetic pathway. Based on the formation of mesomeric forms of imG-14, a rationale for such dual enzymatic activities is proposed. This bifunctional tRNA:m(1)G/imG2 methyltransferase, acting on two chemically distinct guanosine derivatives located at the same position of tRNA(Phe), is unique to certain archaea and has no homologs in eukaryotes. This enzyme here referred to as Taw22, probably played an important role in the emergence of the multistep biosynthetic pathway of wyosine derivatives in archaea and eukaryotes.},
}
@article {pmid24836521,
year = {2015},
author = {Jaehme, M and Slotboom, DJ},
title = {Diversity of membrane transport proteins for vitamins in bacteria and archaea.},
journal = {Biochimica et biophysica acta},
volume = {1850},
number = {3},
pages = {565-576},
doi = {10.1016/j.bbagen.2014.05.006},
pmid = {24836521},
issn = {0006-3002},
mesh = {Archaeal Proteins/chemistry/genetics/*metabolism ; Bacterial Proteins/chemistry/genetics/*metabolism ; Biological Transport ; Genetic Variation ; Membrane Transport Proteins/chemistry/genetics/*metabolism ; Models, Molecular ; Molecular Structure ; Protein Binding ; Protein Structure, Tertiary ; Vitamins/chemistry/*metabolism/pharmacokinetics ; },
abstract = {BACKGROUND: All organisms use cofactors to extend the catalytic capacities of proteins. Many bacteria and archaea can synthesize cofactors from primary metabolites, but there are also prokaryotes that do not have the complete biosynthetic pathways for all essential cofactors. These organisms are dependent on the uptake of cofactors, or at least their precursors that cannot be synthesized, from the environment. Even in those organisms that contain complete biosynthetic pathways membrane transporters are usually present, because the synthesis of cofactors is more costly than uptake.<br><br>SCOPE OF REVIEW: Here we give an overview of bacterial and archaeal transport systems for B-type vitamins, which are either cofactors or precursors thereof.<br><br>MAJOR CONCLUSIONS: Prokaryotic vitamin transporters are extremely diverse, and found in many families of transporters. A few of these transport systems have been characterized in detail, but for most of them mechanistic insight is lacking.<br><br>GENERAL SIGNIFICANCE: The lack of structural and functional understanding of bacterial vitamin transporters is unfortunate because they may be targets for new antibiotics. This article is part of a Special Issue entitled Structural biochemistry and biophysics of membrane proteins. Guest Editor: Bjorn Pedersen.},
}
@article {pmid24819357,
year = {2014},
author = {Bollmann, A and Bullerjahn, GS and McKay, RM},
title = {Abundance and diversity of ammonia-oxidizing archaea and bacteria in sediments of trophic end members of the Laurentian Great Lakes, Erie and Superior.},
journal = {PloS one},
volume = {9},
number = {5},
pages = {e97068},
pmid = {24819357},
issn = {1932-6203},
mesh = {Ammonia/*metabolism ; Archaea/classification/genetics/*isolation &amp; purification/metabolism ; Bacteria/classification/genetics/*isolation &amp; purification/metabolism ; *Biodiversity ; *Food Chain ; Geologic Sediments/*microbiology ; High-Throughput Nucleotide Sequencing ; Lakes/*microbiology ; Oxidation-Reduction ; Phylogeny ; },
abstract = {Ammonia oxidation is the first step of nitrification carried out by ammonia-oxidizing Archaea (AOA) and Bacteria (AOB). Lake Superior and Erie are part of the Great Lakes system differing in trophic status with Lake Superior being oligotrophic and Lake Erie meso- to eutrophic. Sediment samples were collected from both lakes and used to characterize abundance and diversity of AOA and AOB based on the ammonia monooxygenase (amoA) gene. Diversity was accessed by a pyro-sequencing approach and the obtained sequences were used to determine the phylogeny and alpha and beta diversity of the AOA and AOB populations. In Lake Erie copy numbers of bacterial amoA genes were in the same order of magnitude or even higher than the copy numbers of the archaeal amoA genes, while in Lake Superior up to 4 orders of magnitude more archaeal than bacterial amoA copies were detected. The AOB detected in the samples from Lake Erie belonged to AOB that are frequently detected in freshwater. Differences were detected between the phylogenetic affiliations of the AOA from the two lakes. Most sequences detected in Lake Erie clustered in the Nitrososphaera cluster (Thaumarchaeal soil group I.1b) where as most of the sequences in Lake Superior were found in the Nitrosopumilus cluster (Thaumarchaeal marine group I.1a) and the Nitrosotalea cluster. Pearson correlations and canonical correspondence analysis (CCA) showed that the differences in abundance and diversity of AOA are very likely related to the sampling location and thereby to the different trophic states of the lakes.},
}
@article {pmid24808892,
year = {2014},
author = {Wu, Z and Liu, J and Yang, H and Xiang, H},
title = {DNA replication origins in archaea.},
journal = {Frontiers in microbiology},
volume = {5},
number = {},
pages = {179},
pmid = {24808892},
issn = {1664-302X},
abstract = {DNA replication initiation, which starts at specific chromosomal site (known as replication origins), is the key regulatory stage of chromosome replication. Archaea, the third domain of life, use a single or multiple origin(s) to initiate replication of their circular chromosomes. The basic structure of replication origins is conserved among archaea, typically including an AT-rich unwinding region flanked by several conserved repeats (origin recognition box, ORB) that are located adjacent to a replication initiator gene. Both the ORB sequence and the adjacent initiator gene are considerably diverse among different replication origins, while in silico and genetic analyses have indicated the specificity between the initiator genes and their cognate origins. These replicator-initiator pairings are reminiscent of the oriC-dnaA system in bacteria, and a model for the negative regulation of origin activity by a downstream cluster of ORB elements has been recently proposed in haloarchaea. Moreover, comparative genomic analyses have revealed that the mosaics of replicator-initiator pairings in archaeal chromosomes originated from the integration of extrachromosomal elements. This review summarizes the research progress in understanding of archaeal replication origins with particular focus on the utilization, control and evolution of multiple replication origins in haloarchaea.},
}
@article {pmid24803846,
year = {2014},
author = {Abecia, L and Waddams, KE and Martínez-Fernandez, G and Martín-García, AI and Ramos-Morales, E and Newbold, CJ and Yáñez-Ruiz, DR},
title = {An antimethanogenic nutritional intervention in early life of ruminants modifies ruminal colonization by Archaea.},
journal = {Archaea (Vancouver, B.C.)},
volume = {2014},
number = {},
pages = {841463},
pmid = {24803846},
issn = {1472-3654},
mesh = {Animals ; Archaea/*classification/drug effects/genetics/*isolation &amp; purification ; *Biodiversity ; Diet/*methods ; *Goats ; Hydrocarbons, Halogenated/*administration &amp; dosage ; Longitudinal Studies ; Rumen/*microbiology ; Sequence Analysis, DNA ; },
abstract = {The aim of this work was to study whether feeding a methanogen inhibitor from birth of goat kids and their does has an impact on the archaeal population colonizing the rumen and to what extent the impact persists later in life. Sixteen goats giving birth to two kids were used. Eight does were treated (D+) with bromochloromethane after giving birth and over 2 months. The other 8 goats were not treated (D-). One kid per doe in both groups was treated with bromochloromethane (k+) for 3 months while the other was untreated (k-), resulting in four experimental groups: D+/k+, D+/k-, D-/k+, and D-/k-. Rumen samples were collected from kids at weaning and 1 and 4 months after (3 and 6 months after birth) and from does at the end of the treating period (2 months). Pyrosequencing analyses showed a modified archaeal community composition colonizing the rumen of kids, although such effect did not persist entirely 4 months after; however, some less abundant groups remained different in treated and control animals. The different response on the archaeal community composition observed between offspring and adult goats suggests that the competition occurring in the developing rumen to occupy different niches offer potential for intervention.},
}
@article {pmid24798206,
year = {2014},
author = {Park, SJ and Ghai, R and Martín-Cuadrado, AB and Rodríguez-Valera, F and Chung, WH and Kwon, K and Lee, JH and Madsen, EL and Rhee, SK},
title = {Genomes of two new ammonia-oxidizing archaea enriched from deep marine sediments.},
journal = {PloS one},
volume = {9},
number = {5},
pages = {e96449},
pmid = {24798206},
issn = {1932-6203},
mesh = {Ammonia/metabolism ; Archaea/classification/*genetics/metabolism ; *Genome, Archaeal ; Geologic Sediments/*microbiology ; Oxidation-Reduction ; Phylogeny ; },
abstract = {Ammonia-oxidizing archaea (AOA) are ubiquitous and abundant and contribute significantly to the carbon and nitrogen cycles in the ocean. In this study, we assembled AOA draft genomes from two deep marine sediments from Donghae, South Korea, and Svalbard, Arctic region, by sequencing the enriched metagenomes. Three major microorganism clusters belonging to Thaumarchaeota, Epsilonproteobacteria, and Gammaproteobacteria were deduced from their 16S rRNA genes, GC contents, and oligonucleotide frequencies. Three archaeal genomes were identified, two of which were distinct and were designated Ca. "Nitrosopumilus koreensis" AR1 and "Nitrosopumilus sediminis" AR2. AR1 and AR2 exhibited average nucleotide identities of 85.2% and 79.5% to N. maritimus, respectively. The AR1 and AR2 genomes contained genes pertaining to energy metabolism and carbon fixation as conserved in other AOA, but, conversely, had fewer heme-containing proteins and more copper-containing proteins than other AOA. Most of the distinctive AR1 and AR2 genes were located in genomic islands (GIs) that were not present in other AOA genomes or in a reference water-column metagenome from the Sargasso Sea. A putative gene cluster involved in urea utilization was found in the AR2 genome, but not the AR1 genome, suggesting niche specialization in marine AOA. Co-cultured bacterial genome analysis suggested that bacterial sulfur and nitrogen metabolism could be involved in interactions with AOA. Our results provide fundamental information concerning the metabolic potential of deep marine sedimentary AOA.},
}
@article {pmid24790526,
year = {2014},
author = {Sarmiento, F and Long, F and Cann, I and Whitman, WB},
title = {Diversity of the DNA replication system in the Archaea domain.},
journal = {Archaea (Vancouver, B.C.)},
volume = {2014},
number = {},
pages = {675946},
pmid = {24790526},
issn = {1472-3654},
mesh = {Archaea/*enzymology/*genetics ; *DNA Replication ; *Genetic Variation ; },
abstract = {The precise and timely duplication of the genome is essential for cellular life. It is achieved by DNA replication, a complex process that is conserved among the three domains of life. Even though the cellular structure of archaea closely resembles that of bacteria, the information processing machinery of archaea is evolutionarily more closely related to the eukaryotic system, especially for the proteins involved in the DNA replication process. While the general DNA replication mechanism is conserved among the different domains of life, modifications in functionality and in some of the specialized replication proteins are observed. Indeed, Archaea possess specific features unique to this domain. Moreover, even though the general pattern of the replicative system is the same in all archaea, a great deal of variation exists between specific groups.},
}
@article {pmid24756125,
year = {2014},
author = {Abubakr, A and Alimon, AR and Yaakub, H and Abdullah, N and Ivan, M},
title = {Effect of feeding palm oil by-products based diets on total bacteria, cellulolytic bacteria and methanogenic archaea in the rumen of goats.},
journal = {PloS one},
volume = {9},
number = {4},
pages = {e95713},
pmid = {24756125},
issn = {1932-6203},
mesh = {*Animal Feed/analysis ; Animal Nutritional Physiological Phenomena ; Animals ; *Archaea/genetics ; *Bacteria/genetics ; *Goats ; Microbiota ; Palm Oil ; *Plant Oils/administration &amp; dosage ; Rumen/*microbiology/*physiology ; },
abstract = {Rumen microorganisms are responsible for digestion and utilization of dietary feeds by host ruminants. Unconventional feed resources could be used as alternatives in tropical areas where feed resources are insufficient in terms of quality and quantity. The objective of the present experiment was to evaluate the effect of diets based on palm oil (PO), decanter cake (DC) or palm kernel cake (PKC) on rumen total bacteria, selected cellulolytic bacteria, and methanogenic archaea. Four diets: control diet (CD), decanter cake diet (DCD), palm kernel cake diet (PKCD) and CD plus 5% PO diet (CPOD) were fed to rumen cannulated goats and rumen samples were collected at the start of the experimental diets (day 0) and on days 4, 6, 8, 12, 18, 24 and 30 post dietary treatments. Feeding DCD and PKCD resulted in significantly higher (P<0.05) DNA copy number of total bacteria, Fibrobacter succinogenes, Ruminococcus flavefeciens, and Ruminococcus albus. Rumen methanogenic archaea was significantly lower (P<0.05) in goats fed PKCD and CPOD and the trend showed a severe reduction on days 4 and 6 post experimental diets. In conclusion, results indicated that feeding DCD and PKC increased the populations of cellulolytic bacteria and decreased the density of methanogenic archaea in the rumen of goats.},
}
@article {pmid24755959,
year = {2014},
author = {Babski, J and Maier, LK and Heyer, R and Jaschinski, K and Prasse, D and Jäger, D and Randau, L and Schmitz, RA and Marchfelder, A and Soppa, J},
title = {Small regulatory RNAs in Archaea.},
journal = {RNA biology},
volume = {11},
number = {5},
pages = {484-493},
pmid = {24755959},
issn = {1555-8584},
mesh = {Archaea/*genetics/metabolism ; Base Pairing ; Clustered Regularly Interspaced Short Palindromic Repeats/genetics ; Gene Expression Profiling ; Gene Expression Regulation, Archaeal ; Genomics ; RNA, Antisense/*genetics/metabolism ; RNA, Archaeal/*genetics/metabolism ; RNA, Small Untranslated/*genetics/metabolism ; RNA, Transfer/chemistry/genetics ; },
abstract = {Small regulatory RNAs (sRNAs) are universally distributed in all three domains of life, Archaea, Bacteria, and Eukaryotes. In bacteria, sRNAs typically function by binding near the translation start site of their target mRNAs and thereby inhibit or activate translation. In eukaryotes, miRNAs and siRNAs typically bind to the 3'-untranslated region (3'-UTR) of their target mRNAs and influence translation efficiency and/or mRNA stability. In archaea, sRNAs have been identified in all species investigated using bioinformatic approaches, RNomics, and RNA-Seq. Their size can vary significantly between less than 50 to more than 500 nucleotides. Differential expression of sRNA genes has been studied using northern blot analysis, microarrays, and RNA-Seq. In addition, biological functions have been unraveled by genetic approaches, i.e., by characterization of designed mutants. As in bacteria, it was revealed that archaeal sRNAs are involved in many biological processes, including metabolic regulation, adaptation to extreme conditions, stress responses, and even in regulation of morphology and cellular behavior. Recently, the first target mRNAs were identified in archaea, including one sRNA that binds to the 5'-region of two mRNAs in Methanosarcina mazei Gö1 and a few sRNAs that bind to 3'-UTRs in Sulfolobus solfataricus, three Pyrobaculum species, and Haloferax volcanii, indicating that archaeal sRNAs appear to be able to target both the 5'-UTR or the 3'-UTRs of their respective target mRNAs. In addition, archaea contain tRNA-derived fragments (tRFs), and one tRF has been identified as a major ribosome-binding sRNA in H. volcanii, which downregulates translation in response to stress. Besides regulatory sRNAs, archaea contain further classes of sRNAs, e.g., CRISPR RNAs (crRNAs) and snoRNAs.},
}
@article {pmid24755063,
year = {2014},
author = {Lu, D and Xie, G and Gao, R},
title = {Cloning, purification, and characterization of inorganic pyrophosphatase from the hyperthermophilic archaea Pyrococcus horikoshii.},
journal = {Protein expression and purification},
volume = {99},
number = {},
pages = {94-98},
doi = {10.1016/j.pep.2014.04.006},
pmid = {24755063},
issn = {1096-0279},
mesh = {Cloning, Molecular ; Enzyme Stability ; Escherichia coli/genetics ; Hot Temperature ; Hydrogen-Ion Concentration ; Inorganic Pyrophosphatase/*biosynthesis/genetics/isolation &amp; purification ; Pyrococcus horikoshii/*enzymology/genetics ; Substrate Specificity ; },
abstract = {The gene encoding inorganic pyrophosphatase (PPiase) from the hyperthermophilic archaea Pyrococcus horikoshii (Pho PPiase) was cloned in the Escherichia coli strain BL21/pET15b, and the recombinant PPiase was purified by Ni-chelating chromatography in only an one-step procedure. The PPiase showed optimal activity at 88°C and pH of 10.3. Kinetic analysis revealed Km, kcat, Vm of 14.27μM, 3436s(-1), and 34.35μmol/min/mg protein, respectively. Pho PPiase was stable against denaturant chemicals as well as heat. It retained 19.61% of the original activity after incubation at 100°C for 12h and 25.96% of the original activity in the presence of 8M urea after incubation at 50°C for 120h. Pho PPiase showed high specificity for inorganic pyrophosphate but low reactivity to sodium tripolyphosphate and sodium tetrapolyphosphate. ADP and ATP could not serve as substrates.},
}
@article {pmid24747819,
year = {2014},
author = {Munk, B and Lebuhn, M},
title = {Process diagnosis using methanogenic Archaea in maize-fed, trace element depleted fermenters.},
journal = {Anaerobe},
volume = {29},
number = {},
pages = {22-28},
doi = {10.1016/j.anaerobe.2014.04.002},
pmid = {24747819},
issn = {1095-8274},
mesh = {Biofuels ; Bioreactors ; Cobalt/metabolism/pharmacology ; DNA, Archaeal/*genetics ; Fermentation/drug effects ; Genetic Variation ; Hydrogen-Ion Concentration ; Metagenome ; Methane/*biosynthesis ; Methanobacteriaceae/drug effects/*genetics/metabolism ; Microbial Consortia/drug effects/*genetics ; Pressure ; RNA, Ribosomal, 16S/*genetics ; Real-Time Polymerase Chain Reaction ; Selenium/metabolism/pharmacology ; Temperature ; Trace Elements/metabolism/pharmacology ; Zea mays/*metabolism ; },
abstract = {A mesophilic maize-fed pilot-scale fermenter was severely acidified due to trace element (TE) deficiency. Mainly cobalt (0.07 mg * kg(-1) fresh mass (FM)), selenium (0.007 mg * kg(-1) FM) and sodium (13 mg * kg(-1) FM) were depleted. From this inoculum, three lab-scale flow-through fermenters were operated to analyse micronutrient deficiencies and population dynamics in more detail. One fermenter was supplemented with selenium, one with cobalt, and one served as control. After starvation and recovery of the fermenters, the organic loading rate (OLR) was increased. In parallel, the concentration (Real-Time PCR) of methanogens and their population composition (amplicon sequencing) was determined at the DNA and mRNA level. The parameters Metabolic Quotient (MQ) and cDNA/DNA were calculated to assess the activity of the methanogens. The control without TE supplementation acidified first at an OLR of 4.0 kg volatile solids (VS) * m(-3) * d(-1) while the singular addition of selenium and of cobalt positively influenced the fermenter stability up to an OLR of 4.5 or 5.0 kg VS * m(-3) * d(-1), respectively. In the stable process, the methanogenic populations were dominated by probably residual hydrogenotrophic Methanoculleus sp. (DNA-level), but representatives of versatile Methanosarcina sp. were most active (cDNA-level). When the TE supplemented fermenters began to acidify, Methanosarcina spp. were dominant in the whole (DNA-level) and the active (cDNA-level) community. The acidified control fermenter was dominated by Methanobacteriaceae genus IV. Until acidification, the concentration of methanogens increased with higher OLRs. The MQ indicated stress metabolism approximately one month before the TVA/TIC ratio reached a critical level of 0.7, demonstrating its suitability as early warning parameter of process acidification. The development of the cDNA/DNA ratio also reflected the increasing methanogenic activity with higher OLRs. Highest cDNA/DNA values (ca. 2) were obtained at metabolic strain of the methanogens, at the onset of acidification.},
}
@article {pmid24712910,
year = {2014},
author = {Chen, YL and Hu, HW and Han, HY and Du, Y and Wan, SQ and Xu, ZW and Chen, BD},
title = {Abundance and community structure of ammonia-oxidizing Archaea and Bacteria in response to fertilization and mowing in a temperate steppe in Inner Mongolia.},
journal = {FEMS microbiology ecology},
volume = {89},
number = {1},
pages = {67-79},
doi = {10.1111/1574-6941.12336},
pmid = {24712910},
issn = {1574-6941},
mesh = {Ammonia/*metabolism ; Archaea/genetics/*metabolism ; Bacteria/genetics/*metabolism ; China ; Fertilizers/microbiology ; Hydrogen-Ion Concentration ; *Nitrification ; Oxidation-Reduction ; Phylogeny ; Polymorphism, Restriction Fragment Length ; *Soil Microbiology ; },
abstract = {Based on a 6-year field trial in a temperate steppe in Inner Mongolia, we investigated the effects of nitrogen (N) and phosphorus (P) fertilization and mowing on the abundance and community compositions of ammonia-oxidizing Bacteria (AOB) and Archaea (AOA) upon early (May) and peak (August) plant growth using quantitative PCR (qPCR), terminal-restriction fragment length polymorphism (T-RFLP), cloning and sequencing. The results showed that N fertilization changed AOB community composition and increased AOB abundance in both May and August, but significantly decreased AOA abundance in May. By contrast, P fertilization significantly influenced AOB abundance only in August. Mowing significantly decreased AOA abundance and had little effect on AOA community compositions in May, while significantly influencing AOB abundance in both May and August, Moreover, AOA and AOB community structures showed obvious seasonal variations between May and August. Phylogenetic analysis showed that all AOA sequences fell into the Nitrososphaera cluster, and the AOB community was dominated by Nitrosospira Cluster 3. The results suggest that fertilization and mowing play important roles in affecting the abundance and community compositions of AOA and AOB.},
}
@article {pmid24711725,
year = {2014},
author = {Radeva, G and Kenarova, A and Bachvarova, V and Flemming, K and Popov, I and Vassilev, D and Selenska-Pobell, S},
title = {Phylogenetic diversity of archaea and the archaeal ammonia monooxygenase gene in uranium mining-impacted locations in Bulgaria.},
journal = {Archaea (Vancouver, B.C.)},
volume = {2014},
number = {},
pages = {196140},
pmid = {24711725},
issn = {1472-3654},
mesh = {Bulgaria ; Cluster Analysis ; Crenarchaeota/*classification/*genetics ; DNA, Archaeal/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; *Genetic Variation ; Molecular Sequence Data ; Oxidoreductases/*genetics ; *Phylogeny ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; },
abstract = {Uranium mining and milling activities adversely affect the microbial populations of impacted sites. The negative effects of uranium on soil bacteria and fungi are well studied, but little is known about the effects of radionuclides and heavy metals on archaea. The composition and diversity of archaeal communities inhabiting the waste pile of the Sliven uranium mine and the soil of the Buhovo uranium mine were investigated using 16S rRNA gene retrieval. A total of 355 archaeal clones were selected, and their 16S rDNA inserts were analysed by restriction fragment length polymorphism (RFLP) discriminating 14 different RFLP types. All evaluated archaeal 16S rRNA gene sequences belong to the 1.1b/Nitrososphaera cluster of Crenarchaeota. The composition of the archaeal community is distinct for each site of interest and dependent on environmental characteristics, including pollution levels. Since the members of 1.1b/Nitrososphaera cluster have been implicated in the nitrogen cycle, the archaeal communities from these sites were probed for the presence of the ammonia monooxygenase gene (amoA). Our data indicate that amoA gene sequences are distributed in a similar manner as in Crenarchaeota, suggesting that archaeal nitrification processes in uranium mining-impacted locations are under the control of the same key factors controlling archaeal diversity.},
}
@article {pmid24669219,
year = {2014},
author = {Min, BR and Solaiman, S and Shange, R and Eun, JS},
title = {Gastrointestinal Bacterial and Methanogenic Archaea Diversity Dynamics Associated with Condensed Tannin-Containing Pine Bark Diet in Goats Using 16S rDNA Amplicon Pyrosequencing.},
journal = {International journal of microbiology},
volume = {2014},
number = {},
pages = {141909},
pmid = {24669219},
issn = {1687-918X},
abstract = {Eighteen Kiko-cross meat goats (n = 6) were used to collect gastrointestinal (GI) bacteria and methanogenic archaea for diversity measures when fed condensed tannin-containing pine bark (PB). Three dietary treatments were tested: control diet (0% PB and 30% wheat straw (WS); 0.17% condensed tannins (CT) dry matter (DM)); 15% PB and 15% WS (1.6% CT DM), and 30% PB and 0% WS (3.2% CT DM). A 16S rDNA bacterial tag-encoded FLX amplicon pyrosequencing technique was used to characterize and elucidate changes in GI bacteria and methanogenic archaea diversity among the diets. Proteobacteria was the most dominant phylum in goats with mean relative abundance values ranging from 39.7 (30% PB) to 46.5% (control) and 47.1% (15% PB). Other phyla individually accounted for fewer than 25% of the relative abundance observed. Predominant methanogens were Methanobrevibacter (75, 72, and 49%), Methanosphaera (3.3, 2.3, and 3.4%), and Methanobacteriaceae (1.2, 0.6, and 0.7%) population in control, 15, and 30% PB, respectively. Among methanogens, Methanobrevibacter was linearly decreased (P = 0.05) with increasing PB supplementation. These results indicate that feeding PB selectively altered bacteria and methanogenic archaeal populations in the GI tract of goats.},
}
@article {pmid24667707,
year = {2014},
author = {Ran, W and Kristensen, DM and Koonin, EV},
title = {Coupling between protein level selection and codon usage optimization in the evolution of bacteria and archaea.},
journal = {mBio},
volume = {5},
number = {2},
pages = {e00956-14},
pmid = {24667707},
issn = {2150-7511},
mesh = {Archaea/*genetics/*metabolism ; Bacteria/*genetics/*metabolism ; *Biological Evolution ; *Codon ; *Protein Biosynthesis ; Selection, Genetic ; },
abstract = {The relationship between the selection affecting codon usage and selection on protein sequences of orthologous genes in diverse groups of bacteria and archaea was examined by using the Alignable Tight Genome Clusters database of prokaryote genomes. The codon usage bias is generally low, with 57.5% of the gene-specific optimal codon frequencies (Fopt) being below 0.55. This apparent weak selection on codon usage contrasts with the strong purifying selection on amino acid sequences, with 65.8% of the gene-specific dN/dS ratios being below 0.1. For most of the genomes compared, a limited but statistically significant negative correlation between Fopt and dN/dS was observed, which is indicative of a link between selection on protein sequence and selection on codon usage. The strength of the coupling between the protein level selection and codon usage bias showed a strong positive correlation with the genomic GC content. Combined with previous observations on the selection for GC-rich codons in bacteria and archaea with GC-rich genomes, these findings suggest that selection for translational fine-tuning could be an important factor in microbial evolution that drives the evolution of genome GC content away from mutational equilibrium. This type of selection is particularly pronounced in slowly evolving, "high-status" genes. A significantly stronger link between the two aspects of selection is observed in free-living bacteria than in parasitic bacteria and in genes encoding metabolic enzymes and transporters than in informational genes. These differences might reflect the special importance of translational fine-tuning for the adaptability of gene expression to environmental changes. The results of this work establish the coupling between protein level selection and selection for translational optimization as a distinct and potentially important factor in microbial evolution. IMPORTANCE Selection affects the evolution of microbial genomes at many levels, including both the structure of proteins and the regulation of their production. Here we demonstrate the coupling between the selection on protein sequences and the optimization of codon usage in a broad range of bacteria and archaea. The strength of this coupling varies over a wide range and strongly and positively correlates with the genomic GC content. The cause(s) of the evolution of high GC content is a long-standing open question, given the universal mutational bias toward AT. We propose that optimization of codon usage could be one of the key factors that determine the evolution of GC-rich genomes. This work establishes the coupling between selection at the level of protein sequence and at the level of codon choice optimization as a distinct aspect of genome evolution.},
}
@article {pmid24650628,
year = {2014},
author = {Grüber, G and Manimekalai, MS and Mayer, F and Müller, V},
title = {ATP synthases from archaea: the beauty of a molecular motor.},
journal = {Biochimica et biophysica acta},
volume = {1837},
number = {6},
pages = {940-952},
doi = {10.1016/j.bbabio.2014.03.004},
pmid = {24650628},
issn = {0006-3002},
mesh = {Archaea/*enzymology ; Archaeal Proteins/chemistry/*physiology ; Binding Sites ; Biocatalysis ; Catalytic Domain ; Mitochondrial Proton-Translocating ATPases/chemistry/*physiology ; Models, Molecular ; Molecular Motor Proteins/chemistry/*physiology ; },
abstract = {Archaea live under different environmental conditions, such as high salinity, extreme pHs and cold or hot temperatures. How energy is conserved under such harsh environmental conditions is a major question in cellular bioenergetics of archaea. The key enzymes in energy conservation are the archaeal A1AO ATP synthases, a class of ATP synthases distinct from the F1FO ATP synthase ATP synthase found in bacteria, mitochondria and chloroplasts and the V1VO ATPases of eukaryotes. A1AO ATP synthases have distinct structural features such as a collar-like structure, an extended central stalk, and two peripheral stalks possibly stabilizing the A1AO ATP synthase during rotation in ATP synthesis/hydrolysis at high temperatures as well as to provide the storage of transient elastic energy during ion-pumping and ATP synthesis/-hydrolysis. High resolution structures of individual subunits and subcomplexes have been obtained in recent years that shed new light on the function and mechanism of this unique class of ATP synthases. An outstanding feature of archaeal A1AO ATP synthases is their diversity in size of rotor subunits and the coupling ion used for ATP synthesis with H(+), Na(+) or even H(+) and Na(+) using enzymes. The evolution of the H(+) binding site to a Na(+) binding site and its implications for the energy metabolism and physiology of the cell are discussed.},
}
@article {pmid24639674,
year = {2014},
author = {Liang, R and Grizzle, RS and Duncan, KE and McInerney, MJ and Suflita, JM},
title = {Roles of thermophilic thiosulfate-reducing bacteria and methanogenic archaea in the biocorrosion of oil pipelines.},
journal = {Frontiers in microbiology},
volume = {5},
number = {},
pages = {89},
pmid = {24639674},
issn = {1664-302X},
abstract = {Thermophilic sulfide-producing microorganisms from an oil pipeline network were enumerated with different sulfur oxyanions as electron acceptors at 55°C. Most-probable number (MPN) analysis showed that thiosulfate-reducing bacteria were the most numerous sulfidogenic microorganisms in pipeline inspection gauge (PIG) scrapings. Thiosulfate-reducing and methanogenic enrichments were obtained from the MPN cultures that were able to use yeast extract as the electron donor. Molecular analysis revealed that both enrichments harbored the same dominant bacterium, which belonged to the genus Anaerobaculum. The dominant archaeon in the methanogenic enrichment was affiliated with the genus Methanothermobacter. With yeast extract as the electron donor, the general corrosion rate by the thiosulfate-reducing enrichment (8.43 ± 1.40 milli-inch per year, abbreviated as mpy) was about 5.5 times greater than the abiotic control (1.49 ± 0.15 mpy), while the comparable measures for the methanogenic culture were 2.03 ± 0.49 mpy and 0.62 ± 0.07 mpy, respectively. Total iron analysis in the cultures largely accounted for the mass loss of iron measured in the weight loss determinations. Profilometry analysis of polished steel coupons incubated in the presence of the thiosulfate-reducing enrichment revealed 59 pits over an area of 71.16 mm(2), while only 6 pits were evident in the corresponding methanogenic incubations. The results show the importance of thiosulfate-utilizing, sulfide-producing fermentative bacteria such as Anaerobaculum sp. in the corrosion of carbon steel, but also suggest that Anaerobaculum sp. are of far less concern when growing syntrophically with methanogens.},
}
@article {pmid24639207,
year = {2014},
author = {Stantscheff, R and Kuever, J and Rabenstein, A and Seyfarth, K and Dröge, S and König, H},
title = {Isolation and differentiation of methanogenic Archaea from mesophilic corn-fed on-farm biogas plants with special emphasis on the genus Methanobacterium.},
journal = {Applied microbiology and biotechnology},
volume = {98},
number = {12},
pages = {5719-5735},
doi = {10.1007/s00253-014-5652-4},
pmid = {24639207},
issn = {1432-0614},
mesh = {Animals ; Animals, Domestic ; Archaea/*classification/*metabolism ; *Biodiversity ; *Biofuels ; Cluster Analysis ; DNA, Archaeal/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Denaturing Gradient Gel Electrophoresis ; Germany ; Methane/*metabolism ; Molecular Sequence Data ; Molecular Typing ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 23S/genetics ; Sequence Analysis, DNA ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; },
abstract = {In this study, methanogenic Archaea were isolated from five full-scale agricultural biogas plants (BGPs) located in Rhineland-Palatinate and Saarland, Germany, digesting maize silage and cattle manure. According to partial 16S rRNA gene sequences, the strains isolated from enrichment cultures were related to Methanoculleus bourgensis, Methanosarcina mazei, Methanosaeta concilii, and Methanobacterium formicicum. The 16S rRNA gene libraries of two representative BGPs screened with the direct amplified rDNA restriction analysis approach also revealed these Archaea to be present. Comparative phylogenetic analyses of reference strains and the isolates of genus Methanobacterium based on 16S and 23S rRNA gene sequences suggest two major groups of isolates, with both of them closely associated with Methanobacterium formicicum strain MF(T). The affiliation of Methanobacterium isolates is further supported by denaturating gradient gel electrophoresis of 16S rRNA gene amplificates, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, and specifically amplified polymorphic DNA-PCR (SAPD-PCR), a novel fingerprint approach applied to methanogenic Archaea for the first time. Signature sequence 03Mbf derived from the application of SAPD-PCR was subsequently used to develop a PCR-based primer system for the detection of Methanobacterium formicicum-related isolates and the reference strain in BGP samples. Amplification of 03Mbf fragments down to a minimal titer of 10(3) cells of Methanobacterium formicicum-related isolate Mb9 was possible under BGP fermenter-comparable conditions.},
}
@article {pmid24639204,
year = {2014},
author = {Zhou, Z and Han, P and Gu, JD},
title = {New PCR primers based on mcrA gene for retrieving more anaerobic methanotrophic archaea from coastal reedbed sediments.},
journal = {Applied microbiology and biotechnology},
volume = {98},
number = {10},
pages = {4663-4670},
doi = {10.1007/s00253-014-5599-5},
pmid = {24639204},
issn = {1432-0614},
mesh = {DNA Primers/*genetics ; DNA, Archaeal/chemistry/genetics ; Geologic Sediments/*microbiology ; Methanomicrobiales/enzymology/*genetics/*isolation &amp; purification ; Molecular Sequence Data ; Oxidoreductases/*genetics ; Polymerase Chain Reaction/*methods ; Sequence Analysis, DNA ; },
abstract = {Two pairs of PCR primes ANMEallF/R and ANME23F/R were designed by Codehop method based on sequences available to retrieve more anaerobic methanotrophic (ANME) archaea mcrA gene sequences and ANME 2 and 3 subtypes from reedbed in two seasons. Overall, the PCR primers showed slightly favor for ANME group mcrA gene sequences. Due to the predominance of methanogens mainly affiliated to Methanomicrobiales in the samples, a large portion of mcrA gene sequences amplified in the clone libraries belonged to methanogens. Differences in PCR primers and performance affected the mcrA gene-PCR-amplified community composition to a minor extent. PCR primers targeting ANME mcrA group g-h were designed to apply real-time PCR for quantifying more groups of mcrA gene-affiliated ANME archaea and tested with these same samples, and the most abundant group in the whole ANME mcrA community was ANME group g-h. In addition, a stable mcrA gene-harboring archaeal community pattern was detected in the reedbed sediment samples collected from two distinctively different seasons. The PCR and qPCR primers designed in this study can expand our knowledge on the distribution of ANME mcrA genes and community composition in the ecosystem to better understand the carbon cycle.},
}
@article {pmid24612643,
year = {2014},
author = {Habouzit, F and Hamelin, J and Santa-Catalina, G and Steyer, JP and Bernet, N},
title = {Biofilm development during the start-up period of anaerobic biofilm reactors: the biofilm Archaea community is highly dependent on the support material.},
journal = {Microbial biotechnology},
volume = {7},
number = {3},
pages = {257-264},
pmid = {24612643},
issn = {1751-7915},
mesh = {Anaerobiosis ; Archaea/*classification/genetics/physiology ; Bacteria/*classification/genetics ; Bacterial Physiological Phenomena ; Biofilms/*growth &amp; development ; Bioreactors/*microbiology ; *Biota ; Electrophoresis, Capillary ; *Environmental Microbiology ; Methane/metabolism ; Polymorphism, Single-Stranded Conformational ; },
abstract = {To evaluate the impact of the nature of the support material on its colonization by a methanogenic consortium, four substrata made of different materials: polyvinyl chloride, 2 polyethylene and polypropylene were tested during the start-up of lab-scale fixed-film reactors. The reactor performances were evaluated and compared together with the analysis of the biofilms. Biofilm growth was quantified and the structure of bacterial and archaeal communities were characterized by molecular fingerprinting profiles (capillary electrophoresis-single strand conformation polymorphism). The composition of the inoculum was shown to have a major impact on the bacterial composition of the biofilm, whatever the nature of the support material or the organic loading rate applied to the reactors during the start-up period. In contrast, the biofilm archaeal populations were independent of the inoculum used but highly dependent on the support material. Supports favouring Archaea colonization, the limiting factor in the overall process, should be preferred.},
}
@article {pmid24612368,
year = {2014},
author = {Lin, TJ and Breves, EA and Dyar, MD and Ver Eecke, HC and Jamieson, JW and Holden, JF},
title = {Magnetite formation from ferrihydrite by hyperthermophilic archaea from Endeavour Segment, Juan de Fuca Ridge hydrothermal vent chimneys.},
journal = {Geobiology},
volume = {12},
number = {3},
pages = {200-211},
doi = {10.1111/gbi.12083},
pmid = {24612368},
issn = {1472-4669},
mesh = {Ferric Compounds/*metabolism ; Ferrosoferric Oxide/*metabolism ; Hydrothermal Vents/chemistry/*microbiology ; Iron/chemistry ; Oxidation-Reduction ; Pacific Ocean ; Photomicrography ; Pyrodictiaceae/growth &amp; development/*metabolism ; Spectroscopy, Mossbauer ; Sulfides/metabolism ; },
abstract = {Hyperthermophilic iron reducers are common in hydrothermal chimneys found along the Endeavour Segment in the northeastern Pacific Ocean based on culture-dependent estimates. However, information on the availability of Fe(III) (oxyhydr) oxides within these chimneys, the types of Fe(III) (oxyhydr) oxides utilized by the organisms, rates and environmental constraints of hyperthermophilic iron reduction, and mineral end products is needed to determine their biogeochemical significance and are addressed in this study. Thin-section petrography on the interior of a hydrothermal chimney from the Dante edifice at Endeavour showed a thin coat of Fe(III) (oxyhydr) oxide associated with amorphous silica on the exposed outer surfaces of pyrrhotite, sphalerite, and chalcopyrite in pore spaces, along with anhydrite precipitation in the pores that is indicative of seawater ingress. The iron sulfide minerals were likely oxidized to Fe(III) (oxyhydr) oxide with increasing pH and Eh due to cooling and seawater exposure, providing reactants for bioreduction. Culture-dependent estimates of hyperthermophilic iron reducer abundances in this sample were 1740 and 10 cells per gram (dry weight) of material from the outer surface and the marcasite-sphalerite-rich interior, respectively. Two hyperthermophilic iron reducers, Hyperthermus sp. Ro04 and Pyrodictium sp. Su06, were isolated from other active hydrothermal chimneys on the Endeavour Segment. Strain Ro04 is a neutrophilic (pH opt 7-8) heterotroph, while strain Su06 is a mildly acidophilic (pH opt 5), hydrogenotrophic autotroph, both with optimal growth temperatures of 90-92 °C. Mössbauer spectroscopy of the iron oxides before and after growth demonstrated that both organisms form nanophase (<12 nm) magnetite [Fe3 O4 ] from laboratory-synthesized ferrihydrite [Fe10 O14 (OH)2 ] with no detectable mineral intermediates. They produced up to 40 mm Fe(2+) in a growth-dependent manner, while all abiotic and biotic controls produced <3 mm Fe(2+) . Hyperthermophilic iron reducers may have a growth advantage over other hyperthermophiles in hydrothermal systems that are mildly acidic where mineral weathering at increased temperatures occurs.},
}
@article {pmid24607972,
year = {2014},
author = {Garrett, RA},
title = {A backward view from 16S rRNA to archaea to the universal tree of life to progenotes: reminiscences of Carl Woese.},
journal = {RNA biology},
volume = {11},
number = {3},
pages = {232-235},
doi = {10.4161/rna.28228},
pmid = {24607972},
issn = {1555-8584},
mesh = {Archaea/*classification/genetics ; Biological Evolution ; Phylogeny ; RNA, Ribosomal/chemistry/genetics ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, RNA ; },
abstract = {I first became aware of Carl Woese in the mid-1970s when he and George Fox criticized a few of the 16S rRNA oligonucleotide sequences emerging from Strasbourg in the 10-12 y RNA sequencing project of the first 16S rRNA from Escherichia coli, some of which we were using for assembling RNA binding sites of ribosomal proteins. When I realized that they were attempting to sequence 16S rRNAs from a range of bacteria to classify them phylogenetically, I seriously questioned their sanity. Not because of the goal, which was admirable, but because of the sheer technical difficulty, and slowness, of sequencing large RNA molecules using the original Sanger RNA sequencing method, not to mention the health hazards of regularly preparing rRNA using 20-30 mCi [ (32)P]. My view changed radically, however, with their subsequent prediction of 5S rRNA secondary structures using a phylogenetic approach. Previously, the molecular biology community had been competing to generate the maximum numbers of base pairs in the model RNA molecule E. coli 5S RNA when Fox and Woese introduced the concept of compensatory base changes based on phylogeny for defining secondary structure and applied it to 5S RNA, they found evidence for only about 50% base pairing. This approach had previously been used for tRNA secondary structure predictions but its more general significance had never been acknowledged. Carl subsequently persuaded Harry Noller to apply the same method to predicting secondary structures of the large rRNAs.},
}
@article {pmid24600042,
year = {2014},
author = {Bräsen, C and Esser, D and Rauch, B and Siebers, B},
title = {Carbohydrate metabolism in Archaea: current insights into unusual enzymes and pathways and their regulation.},
journal = {Microbiology and molecular biology reviews : MMBR},
volume = {78},
number = {1},
pages = {89-175},
pmid = {24600042},
issn = {1098-5557},
mesh = {Archaea/*metabolism ; Bacteria/metabolism ; *Carbohydrate Metabolism ; Enzymes/*metabolism ; Gene Expression Regulation, Archaeal ; Gluconeogenesis ; Glycolysis ; Hexoses/metabolism ; Metabolic Networks and Pathways ; Methanosarcina/metabolism ; Pentoses/metabolism ; Pyrococcus furiosus/metabolism ; Sulfolobus/metabolism ; Thermococcus/metabolism ; },
abstract = {The metabolism of Archaea, the third domain of life, resembles in its complexity those of Bacteria and lower Eukarya. However, this metabolic complexity in Archaea is accompanied by the absence of many "classical" pathways, particularly in central carbohydrate metabolism. Instead, Archaea are characterized by the presence of unique, modified variants of classical pathways such as the Embden-Meyerhof-Parnas (EMP) pathway and the Entner-Doudoroff (ED) pathway. The pentose phosphate pathway is only partly present (if at all), and pentose degradation also significantly differs from that known for bacterial model organisms. These modifications are accompanied by the invention of "new," unusual enzymes which cause fundamental consequences for the underlying regulatory principles, and classical allosteric regulation sites well established in Bacteria and Eukarya are lost. The aim of this review is to present the current understanding of central carbohydrate metabolic pathways and their regulation in Archaea. In order to give an overview of their complexity, pathway modifications are discussed with respect to unusual archaeal biocatalysts, their structural and mechanistic characteristics, and their regulatory properties in comparison to their classic counterparts from Bacteria and Eukarya. Furthermore, an overview focusing on hexose metabolic, i.e., glycolytic as well as gluconeogenic, pathways identified in archaeal model organisms is given. Their energy gain is discussed, and new insights into different levels of regulation that have been observed so far, including the transcript and protein levels (e.g., gene regulation, known transcription regulators, and posttranslational modification via reversible protein phosphorylation), are presented.},
}
@article {pmid24589203,
year = {2014},
author = {Gorman-Lewis, D and Martens-Habbena, W and Stahl, DA},
title = {Thermodynamic characterization of proton-ionizable functional groups on the cell surfaces of ammonia-oxidizing bacteria and archaea.},
journal = {Geobiology},
volume = {12},
number = {2},
pages = {157-171},
doi = {10.1111/gbi.12075},
pmid = {24589203},
issn = {1472-4669},
mesh = {Ammonia/metabolism ; Archaea/*chemistry/metabolism ; Bacteria/*chemistry/metabolism ; Calorimetry ; Models, Theoretical ; Oxidation-Reduction ; Potentiometry ; Protons ; Species Specificity ; Thermodynamics ; },
abstract = {The ammonia-oxidizing archaeon Nitrosopumilus maritimus strain SCM1 (strain SCM1), a representative of the Thaumarchaeota archaeal phylum, can sustain high specific rates of ammonia oxidation at ammonia concentrations too low to sustain metabolism by ammonia-oxidizing bacteria (AOB). One structural and biochemical difference between N. maritimus and AOB that might be related to the oligotrophic adaptation of strain SCM1 is the cell surface. A proteinaceous surface layer (S-layer) comprises the outermost boundary of the strain SCM1 cell envelope, as opposed to the lipopolysaccharide coat of Gram-negative AOB. In this work, we compared the surface reactivities of two archaea having an S-layer (strain SCM1 and Sulfolobus acidocaldarius) with those of four representative AOB (Nitrosospira briensis, Nitrosomonas europaea, Nitrosolobus multiformis, and Nitrosococcus oceani) using potentiometric and calorimetric titrations to evaluate differences in proton-ionizable surface sites. Strain SCM1 and S. acidocaldarius have a wider range of proton buffering (approximately pH 10-3.5) than the AOB (approximately pH 10-4), under the conditions investigated. Thermodynamic parameters describing proton-ionizable sites (acidity constants, enthalpies, and entropies of protonation) are consistent with these archaea having proton-ionizable amino acid side chains containing carboxyl, imidazole, thiol, hydroxyl, and amine functional groups. Phosphorous-bearing acidic functional groups, which might also be present, could be masked by imidazole and thiol functional groups. Parameters for the AOB are consistent with surface structures containing anionic oxygen ligands (carboxyl- and phosphorous-bearing acidic functional groups), thiols, and amines. In addition, our results showed that strain SCM1 has more reactive surface sites than the AOB and a high concentration of sites consistent with aspartic and/or glutamic acid. Because these alternative boundary layers mediate interaction with the local external environment, these data provide the basis for further comparisons of the thermodynamic behavior of surface reactivity toward essential nutrients.},
}
@article {pmid24586878,
year = {2014},
author = {de Gannes, V and Eudoxie, G and Hickey, WJ},
title = {Impacts of edaphic factors on communities of ammonia-oxidizing archaea, ammonia-oxidizing bacteria and nitrification in tropical soils.},
journal = {PloS one},
volume = {9},
number = {2},
pages = {e89568},
pmid = {24586878},
issn = {1932-6203},
mesh = {Ammonia/*metabolism ; Archaea/*metabolism ; Bacteria/*metabolism ; Nitrification ; Soil Microbiology ; },
abstract = {Nitrification is a key process in soil nitrogen (N) dynamics, but relatively little is known about it in tropical soils. In this study, we examined soils from Trinidad to determine the edaphic drivers affecting nitrification levels and community structure of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) in non-managed soils. The soils were naturally vegetated, ranged in texture from sands to clays and spanned pH 4 to 8. The AOA were detected by qPCR in all soils (ca. 10(5) to 10(6) copies archaeal amoA g(-1) soil), but AOB levels were low and bacterial amoA was infrequently detected. AOA abundance showed a significant negative correlation (p<0.001) with levels of soil organic carbon, clay and ammonium, but was not correlated to pH. Structures of AOA and AOB communities, as determined by amoA terminal restriction fragment (TRF) analysis, differed significantly between soils (p<0.001). Variation in AOA TRF profiles was best explained by ammonium-N and either Kjeldahl N or total N (p<0.001) while variation in AOB TRF profiles was best explained by phosphorus, bulk density and iron (p<0.01). In clone libraries, phylotypes of archaeal amoA (predominantly Nitrososphaera) and bacterial amoA (predominanatly Nitrosospira) differed between soils, but variation was not correlated with pH. Nitrification potential was positively correlated with clay content and pH (p<0.001), but not to AOA or AOB abundance or community structure. Collectively, the study showed that AOA and AOB communities were affected by differing sets of edaphic factors, notably that soil N characteristics were significant for AOA, but not AOB, and that pH was not a major driver for either community. Thus, the effect of pH on nitrification appeared to mainly reflect impacts on AOA or AOB activity, rather than selection for AOA or AOB phylotypes differing in nitrifying capacity.},
}
@article {pmid24573438,
year = {2014},
author = {Koga, Y},
title = {From promiscuity to the lipid divide: on the evolution of distinct membranes in Archaea and Bacteria.},
journal = {Journal of molecular evolution},
volume = {78},
number = {3-4},
pages = {234-242},
pmid = {24573438},
issn = {1432-1432},
mesh = {Archaea/*metabolism ; Bacteria/*metabolism ; *Biological Evolution ; Glycerolphosphate Dehydrogenase/metabolism ; Glycolysis ; Membrane Lipids/chemistry/*metabolism ; Models, Biological ; Molecular Structure ; Phospholipids/chemistry/metabolism ; Phosphorylation ; Species Specificity ; },
abstract = {The structural and biosynthetic features of archaeal phospholipids provide clues to the membrane lipid composition in the last universal common ancestor (LUCA) membranes. The evident similarity of the phospholipid biosynthetic pathways in Archaea and Bacteria suggests that one set of these biosynthetic enzymes would have worked on a wide range of lipids composed of enantiomeric glycerophosphate backbones linked with a variety of hydrocarbon chains. This notion was supported by the discovery of a wide range reactivity of enzymes belonging to the CDP-alcohol phosphatidyltransferase family. It is hypothesized that lipid promiscuity is generated from the prebiotic surface metabolism on pyrite proposed by Wächtershäuser. The significance of the phosphate groups on the intermediates of phospholipid biosynthesis and the extra anionic groups of a polar head group suggested the likely involvement of surface metabolism. Anionic groups are essential for surface metabolism. Since the early chemical evolution reactions are presumed to be non-specific, every combination of the available lipid component parts would be expected to be formed. The mixed lipid membranes present in LUCA were segregated and this led to the differentiation of Archaea and Bacteria, as described previously. The proper arrangement of membrane lipids was generated by the physicochemical drive arising from the promiscuity of the primordial membrane lipids.},
}
@article {pmid24568033,
year = {2013},
author = {Plasencia, A and Gich, F and Fillol, M and Borrego, CM},
title = {Phylogenetic characterization and quantification of ammonia-oxidizing archaea and bacteria from Lake Kivu in a long-term microcosm incubation.},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {16},
number = {3},
pages = {177-189},
doi = {10.2436/20.1501.01.192},
pmid = {24568033},
issn = {1139-6709},
mesh = {Ammonia/*metabolism ; Archaea/*classification/genetics/isolation &amp; purification/*metabolism ; Bacteria/*classification/genetics/isolation &amp; purification/*metabolism ; Bacterial Proteins/genetics ; Lakes/chemistry/*microbiology ; Molecular Sequence Data ; Oxidation-Reduction ; Oxidoreductases/genetics ; *Phylogeny ; Spain ; },
abstract = {A microcosm cultivation-based method was set up to investigate the growth of ammonia-oxidizing archaea (AOA), isolated from a water sample acquired at a depth of 50 m from the northern basin of Lake Kivu. For this purpose, both CARD-FISH and qPCR targeting of archaeal 16S rRNA and amoA genes were used. Archaeal cell growth at the end of the 246-day microcosm experiment accounted for 35% of the SybrGold-stained cells, which corresponded to 6.61 x 10(6) cells/ml and 1.76 +/- 0.09 x 10(6) archaeal 16S rRNA gene copies/ml. Clone libraries and DGGE fingerprinting confirmed the dominance of AOA phylotypes in the archaeal community microcosm. The majority of the identified archaeal 16S rRNA gene sequences in the clone libraries were affiliated with Thaumarchaeota Marine Group 1 .1a. Subsequent cultivation of the AOA community on deep-well microtiter plates in medium containing different carbon sources to stimulate archaeal growth failed to show significant differences in archaeal abundance (ANOVA t14 = -1.058, P = 0.308 and ANOVA t14= 1.584, P = 0.135 for yeast extract and simple organic acids, respectively). The lack of growth stimulation by organic compounds is in concordance with the oligotrophic status of Lake Kivu. Finally, the addition of antibiotics to the growth medium resulted in archaeal cell counts that were significantly lower than those obtained from cultures in antibiotic-free medium (ANOVA t14 = 12.12, P < 0.001).},
}
@article {pmid24563191,
year = {2014},
author = {Abell, GC and Ross, DJ and Keane, J and Holmes, BH and Robert, SS and Keough, MJ and Eyre, BD and Volkman, JK},
title = {Niche differentiation of ammonia-oxidising archaea (AOA) and bacteria (AOB) in response to paper and pulp mill effluent.},
journal = {Microbial ecology},
volume = {67},
number = {4},
pages = {758-768},
pmid = {24563191},
issn = {1432-184X},
mesh = {Archaea/classification/*drug effects/genetics/metabolism ; Archaeal Proteins/genetics/metabolism ; Bacteria/classification/*drug effects/genetics/metabolism ; Bacterial Proteins/genetics/metabolism ; Biota/*drug effects ; *Industrial Waste ; Molecular Sequence Data ; Oxidoreductases/genetics/metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Real-Time Polymerase Chain Reaction ; Rivers/*microbiology ; Sequence Analysis, DNA ; Tasmania ; Water Pollutants, Chemical/*pharmacology ; },
abstract = {Sediment organic loading has been shown to affect estuarine nitrification and denitrification, resulting in changes to sediment biogeochemistry and nutrient fluxes detrimental to estuarine health. This study examined the effects of organic loading on nutrient fluxes and microbial communities in sediments receiving effluent from a paper and pulp mill (PPM) by applying microcosm studies and molecular microbial ecology techniques. Three sites near the PPM outfall were compared to three control sites, one upstream and two downstream of the outfall. The control sites showed coupled nitrification-denitrification with minimal ammonia release from the sediment. In contrast, the impacted sites were characterised by nitrate uptake and substantial ammonia efflux from the sediments, consistent with a decoupling of nitrification and denitrification. Analysis of gene diversity demonstrated that the composition of nitrifier communities was not significantly different at the impacted sites compared to the control sites; however, analysis of gene abundance indicated that whilst there was no difference in total bacteria, total archaea or ammonia-oxidising archaea (AOA) abundance between the control and impacted sites, there was a significant reduction in ammonia-oxidising bacteria (AOB) at the impacted sites. The results of this study demonstrate an effect of organic loading on estuarine sediment biogeochemistry and highlight an apparent niche differentiation between AOA and AOB.},
}
@article {pmid24558638,
year = {2014},
author = {Florek, MC and Gilbert, DP and Plague, GR},
title = {Insertion sequence distribution bias in Archaea.},
journal = {Mobile genetic elements},
volume = {4},
number = {1},
pages = {e27829},
pmid = {24558638},
issn = {2159-2543},
support = {R15 GM081862/GM/NIGMS NIH HHS/United States ; },
abstract = {Insertion sequences (IS) are common transposable elements in Archaea. Intergenic IS elements are usually less harmful than intragenic ISs, simply because they are less likely to disrupt host gene function. However, because regulatory sequences are intergenic and upstream of genes, we hypothesized that not all intergenic regions are selectively equivalent for IS insertion. We tested this hypothesis by analyzing the distributions of intergenic IS elements within 155 fully sequenced archaeal genomes. Of the 22 genomes with enough IS elements for statistical analysis, five have significantly fewer ISs between divergently oriented neighboring genes than expected by chance, and seven have significantly more ISs between convergently oriented genes. Furthermore, of the 85 genomes with at least one expected IS within each of the three possible neighboring gene orientations (i.e., divergent, convergent, and tandem), 73 genomes have fewer ISs between divergently oriented genes than expected, and 60 have more ISs between convergently oriented genes than expected (both values deviate significantly from binomial probabilities of random distribution). We suspect that these non-random IS distributions are molded by natural selection resulting from differential disruption of neighboring gene regulation, and that this selective pressure has affected transposable element distributions in prokaryotes for billions of years.},
}
@article {pmid24554702,
year = {2014},
author = {Kennelly, PJ},
title = {Protein Ser/Thr/Tyr phosphorylation in the Archaea.},
journal = {The Journal of biological chemistry},
volume = {289},
number = {14},
pages = {9480-9487},
pmid = {24554702},
issn = {1083-351X},
mesh = {Archaea/*enzymology/genetics ; Archaeal Proteins/genetics/*metabolism ; Protein Serine-Threonine Kinases/genetics/*metabolism ; },
abstract = {The third domain of life, the Archaea (formerly Archaebacteria), is populated by a physiologically diverse set of microorganisms, many of which reside at the ecological extremes of our global environment. Although ostensibly prokaryotic in morphology, the Archaea share much closer evolutionary ties with the Eukarya than with the superficially more similar Bacteria. Initial genomic, proteomic, and biochemical analyses have revealed the presence of "eukaryotic" protein kinases and phosphatases and an intriguing set of serine-, threonine-, and tyrosine-phosphorylated proteins in the Archaea that may offer new insights into this important regulatory mechanism.},
}
@article {pmid24554021,
year = {2014},
author = {Subrahmanyam, G and Shen, JP and Liu, YR and Archana, G and He, JZ},
title = {Response of ammonia-oxidizing archaea and bacteria to long-term industrial effluent-polluted soils, Gujarat, Western India.},
journal = {Environmental monitoring and assessment},
volume = {186},
number = {7},
pages = {4037-4050},
pmid = {24554021},
issn = {1573-2959},
mesh = {Ammonia/analysis/metabolism ; Archaea/classification/drug effects/*physiology ; Bacteria/drug effects/growth &amp; development/*metabolism ; *Environmental Monitoring ; India ; Nitrification/drug effects ; Oxidoreductases/analysis ; Soil/chemistry ; *Soil Microbiology ; },
abstract = {Soil nitrifiers have been showing an important role in assessing environmental pollution as sensitive biomarkers. In this study, the abundance and diversity of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) were investigated in long-term industrial waste effluent (IWE) polluted soils. Three different IWE polluted soils characterized as uncontaminated (R1), moderately contaminated (R2), and highly contaminated (R3) were collected in triplicate along Mahi River basin, Gujarat, Western India. Quantitative numbers of ammonia monooxygenase α-subunit (amoA) genes as well as 16S rRNA genes indicated apparent deleterious effect of IWE on abundance of soil AOA, AOB, bacteria, and archaeal populations. Relatively, AOB was more abundant than AOA in the highly contaminated soil R3, while predominance of AOA was noticed in uncontaminated (R1) and moderately contaminated (R2) soils. Soil potential nitrification rate (PNR) significantly (P < 0.05) decreased in polluted soils R2 and R3. Reduced diversity accompanied by apparent community shifts of both AOB and AOA populations was detected in R2 and R3 soils. AOB were dominated with Nitrosospira-like sequences, whereas AOA were dominated by Thaumarchaeal "group 1.1b (Nitrososphaera clusters)." We suggest that the significant reduction in abundance and diversity AOA and AOB could serve as relevant bioindicators for soil quality monitoring of polluted sites. These results could be further useful for better understanding of AOB and AOA communities in polluted soils.},
}
@article {pmid24535255,
year = {2014},
author = {Liu, D and Ding, W and Yuan, J and Xiang, J and Lin, Y},
title = {Substrate and/or substrate-driven changes in the abundance of methanogenic archaea cause seasonal variation of methane production potential in species-specific freshwater wetlands.},
journal = {Applied microbiology and biotechnology},
volume = {98},
number = {10},
pages = {4711-4721},
doi = {10.1007/s00253-014-5571-4},
pmid = {24535255},
issn = {1432-0614},
mesh = {Archaea/*classification/genetics/growth &amp; development/*metabolism ; Cluster Analysis ; DNA, Archaeal/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Fresh Water/chemistry/*microbiology ; Methane/*metabolism ; Molecular Sequence Data ; Organic Chemicals/analysis ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seasons ; Sequence Analysis, DNA ; *Wetlands ; },
abstract = {There are large temporal and spatial variations of methane (CH4) emissions from natural wetlands. To understand temporal changes of CH4 production potential (MPP), soil samples were collected from a permanently inundated Carex lasiocarpa marsh and a summer inundated Calamagrostis angustifolia marsh over the period from June to October of 2011. MPP, dissolved organic carbon (DOC) concentration, abundance and community structure of methanogenic archaea were assessed. In the C. lasiocarpa marsh, DOC concentration, MPP and the methanogen population showed similar seasonal variations and maximal values in September. MPP and DOC in the C. angustifolia marsh exhibited seasonal variations and values peaked during August, while the methanogen population decreased with plant growth. Methanogen abundance correlated significantly (P = 0.02) with DOC only for the C. lasiocarpa marsh. During the sampling period, the dominant methanogens were the Methanosaetaceae and Zoige cluster I (ZC-Ι) in the C. angustifolia marsh, and Methanomicrobiales and ZC-Ι in the C. lasiocarpa marsh. MPP correlated significantly (P = 0.04) with DOC and methanogen population in the C. lasiocarpa marsh but only with DOC in the C. angustifolia marsh. Addition of C. lasiocarpa litter enhanced MPP more effectively than addition of C. angustifolia litter, indicating that temporal variation of substrates is controlled by litter deposition in the C. lasiocarpa marsh while living plant matter is more important in the C. angustifolia marsh. This study indicated that there was no apparent shift in the dominant types of methanogen during the growth season in the species-specific freshwater wetlands. Temporal variation of MPP is controlled by substrates and substrate-driven changes in the abundance of methanogenic archaea in the C. lasiocarpa marsh, while MPP depends only on substrate availability derived from root exudates or soil organic matter in the C. angustifolia marsh.},
}
@article {pmid24531374,
year = {2014},
author = {Vestergaard, G and Garrett, RA and Shah, SA},
title = {CRISPR adaptive immune systems of Archaea.},
journal = {RNA biology},
volume = {11},
number = {2},
pages = {156-167},
pmid = {24531374},
issn = {1555-8584},
mesh = {Adaptation, Physiological ; Archaea/classification/*immunology ; CRISPR-Associated Proteins/classification/genetics ; CRISPR-Cas Systems ; *Clustered Regularly Interspaced Short Palindromic Repeats ; DNA, Archaeal ; Evolution, Molecular ; Genes, Archaeal ; Genome, Archaeal ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {CRISPR adaptive immune systems were analyzed for all available completed genomes of archaea, which included representatives of each of the main archaeal phyla. Initially, all proteins encoded within, and proximal to, CRISPR-cas loci were clustered and analyzed using a profile-profile approach. Then cas genes were assigned to gene cassettes and to functional modules for adaptation and interference. CRISPR systems were then classified primarily on the basis of their concatenated Cas protein sequences and gene synteny of the interference modules. With few exceptions, they could be assigned to the universal Type I or Type III systems. For Type I, subtypes I-A, I-B, and I-D dominate but the data support the division of subtype I-B into two subtypes, designated I-B and I-G. About 70% of the Type III systems fall into the universal subtypes III-A and III-B but the remainder, some of which are phyla-specific, diverge significantly in Cas protein sequences, and/or gene synteny, and they are classified separately. Furthermore, a few CRISPR systems that could not be assigned to Type I or Type III are categorized as variant systems. Criteria are presented for assigning newly sequenced archaeal CRISPR systems to the different subtypes. Several accessory proteins were identified that show a specific gene linkage, especially to Type III interference modules, and these may be cofunctional with the CRISPR systems. Evidence is presented for extensive exchange having occurred between adaptation and interference modules of different archaeal CRISPR systems, indicating the wide compatibility of the functionally diverse interference complexes with the relatively conserved adaptation modules.},
}
@article {pmid24510212,
year = {2014},
author = {Lorantfy, B and Renkecz, T and Koch, C and Horvai, G and Lendl, B and Herwig, C},
title = {Identification of lipophilic bioproduct portfolio from bioreactor samples of extreme halophilic archaea with HPLC-MS/MS.},
journal = {Analytical and bioanalytical chemistry},
volume = {406},
number = {9-10},
pages = {2421-2432},
doi = {10.1007/s00216-014-7626-x},
pmid = {24510212},
issn = {1618-2650},
mesh = {Archaea/*chemistry/*metabolism ; Bioreactors/*microbiology ; Carotenoids/chemistry/metabolism ; Chromatography, High Pressure Liquid/*methods ; Lipid Metabolism ; Lipids/chemistry ; Sodium Chloride/metabolism ; Tandem Mass Spectrometry/*methods ; },
abstract = {Extreme halophilic archaea are a yet unexploited source of natural carotenoids. At elevated salinities, however, material corrosivity issues occur and the performance of analytical methods is strongly affected. The goal of this study was to develop a method for identification and downstream processing of potentially valuable bioproducts produced by archaea. To circumvent extreme salinities during analysis, a direct sample preparation method was established to selectively extract both the polar and the nonpolar lipid contents of extreme halophiles with hexane, acetone and the mixture of MeOH/MTBE/water, respectively. Halogenated solvents, as used in conventional extraction methods, were omitted because of environmental considerations and potential process scale-up. The HPLC-MS/MS method using atmospheric pressure chemical ionization was developed and tuned with three commercially available C40 carotenoid standards, covering the wide polarity range of natural carotenoids, containing different number of OH-groups. The chromatographic separation was achieved on a C30 RP-HPLC column with a MeOH/MTBE/water gradient. Polar lipids, the geometric isomers of the C50 carotenoid bacterioruberin, and vitamin MK-8 were the most valuable products found in bioreactor samples. In contrast to literature on shake flask cultivations, no anhydrous analogues of bacterioruberin, as by-products of the carotenoid biosynthesis, were detected in bioreactor samples. This study demonstrates the importance of sample preparation and the applicability of HPLC-MS/MS methods on real samples from extreme halophilic strains. Furthermore, from a biotechnological point-of-view, this study would like to reveal the relevance of using controlled and defined bioreactor cultivations instead of shake flask cultures in the early stage of potential bioproduct profiling.},
}
@article {pmid24508643,
year = {2014},
author = {Daquiado, AR and Cho, KM and Kim, TY and Kim, SC and Chang, HH and Lee, YB},
title = {Methanogenic archaea diversity in Hanwoo (Bos taurus coreanae) rumen fluid, rectal dung, and barn floor manure using a culture-independent method based on mcrA gene sequences.},
journal = {Anaerobe},
volume = {27},
number = {},
pages = {77-81},
doi = {10.1016/j.anaerobe.2014.01.008},
pmid = {24508643},
issn = {1095-8274},
mesh = {Animals ; Archaea/*classification/genetics/*isolation &amp; purification/metabolism ; *Biodiversity ; Cattle ; DNA, Archaeal/chemistry/genetics ; Feces/*microbiology ; Manure/*microbiology ; Methane/*metabolism ; Molecular Sequence Data ; Oxidoreductases/genetics ; Rumen/*microbiology ; Sequence Analysis, DNA ; },
abstract = {The diversity of methanogenic archaea associated with Korean Hanwoo cattle was analyzed using mcrA gene sequences from samples of rumen fluid (RF), rectal dung (RD), and barn floor manure (BFM). The predominant species were Methanobrevibacter ruminantium in RF and BFM(63.6% and 62.4%, respectively) and Methanocorpusculum labreanum in RD (53.2%).},
}
@article {pmid24505069,
year = {2014},
author = {Chun, J and Rainey, FA},
title = {Integrating genomics into the taxonomy and systematics of the Bacteria and Archaea.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {64},
number = {Pt 2},
pages = {316-324},
doi = {10.1099/ijs.0.054171-0},
pmid = {24505069},
issn = {1466-5034},
mesh = {Archaea/*classification ; Bacteria/*classification ; Classification/*methods ; Genomics/*methods ; Nucleic Acid Hybridization/methods ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/methods ; },
abstract = {The polyphasic approach used today in the taxonomy and systematics of the Bacteria and Archaea includes the use of phenotypic, chemotaxonomic and genotypic data. The use of 16S rRNA gene sequence data has revolutionized our understanding of the microbial world and led to a rapid increase in the number of descriptions of novel taxa, especially at the species level. It has allowed in many cases for the demarcation of taxa into distinct species, but its limitations in a number of groups have resulted in the continued use of DNA-DNA hybridization. As technology has improved, next-generation sequencing (NGS) has provided a rapid and cost-effective approach to obtaining whole-genome sequences of microbial strains. Although some 12,000 bacterial or archaeal genome sequences are available for comparison, only 1725 of these are of actual type strains, limiting the use of genomic data in comparative taxonomic studies when there are nearly 11,000 type strains. Efforts to obtain complete genome sequences of all type strains are critical to the future of microbial systematics. The incorporation of genomics into the taxonomy and systematics of the Bacteria and Archaea coupled with computational advances will boost the credibility of taxonomy in the genomic era. This special issue of International Journal of Systematic and Evolutionary Microbiology contains both original research and review articles covering the use of genomic sequence data in microbial taxonomy and systematics. It includes contributions on specific taxa as well as outlines of approaches for incorporating genomics into new strain isolation to new taxon description workflows.},
}
@article {pmid24489835,
year = {2014},
author = {Borziak, K and Posner, MG and Upadhyay, A and Danson, MJ and Bagby, S and Dorus, S},
title = {Comparative genomic analysis reveals 2-oxoacid dehydrogenase complex lipoylation correlation with aerobiosis in archaea.},
journal = {PloS one},
volume = {9},
number = {1},
pages = {e87063},
pmid = {24489835},
issn = {1932-6203},
mesh = {Aerobiosis ; Alcohol Oxidoreductases/*genetics/metabolism ; Anaerobiosis ; Archaea/*enzymology/*genetics ; Biotin/metabolism ; Genes, Archaeal ; Genomics/*methods ; Ligases/genetics ; *Lipoylation ; *Multigene Family ; Phylogeny ; Substrate Specificity ; Thioctic Acid/metabolism ; },
abstract = {Metagenomic analyses have advanced our understanding of ecological microbial diversity, but to what extent can metagenomic data be used to predict the metabolic capacity of difficult-to-study organisms and their abiotic environmental interactions? We tackle this question, using a comparative genomic approach, by considering the molecular basis of aerobiosis within archaea. Lipoylation, the covalent attachment of lipoic acid to 2-oxoacid dehydrogenase multienzyme complexes (OADHCs), is essential for metabolism in aerobic bacteria and eukarya. Lipoylation is catalysed either by lipoate protein ligase (LplA), which in archaea is typically encoded by two genes (LplA-N and LplA-C), or by a lipoyl(octanoyl) transferase (LipB or LipM) plus a lipoic acid synthetase (LipA). Does the genomic presence of lipoylation and OADHC genes across archaea from diverse habitats correlate with aerobiosis? First, analyses of 11,826 biotin protein ligase (BPL)-LplA-LipB transferase family members and 147 archaeal genomes identified 85 species with lipoylation capabilities and provided support for multiple ancestral acquisitions of lipoylation pathways during archaeal evolution. Second, with the exception of the Sulfolobales order, the majority of species possessing lipoylation systems exclusively retain LplA, or either LipB or LipM, consistent with archaeal genome streamlining. Third, obligate anaerobic archaea display widespread loss of lipoylation and OADHC genes. Conversely, a high level of correspondence is observed between aerobiosis and the presence of LplA/LipB/LipM, LipA and OADHC E2, consistent with the role of lipoylation in aerobic metabolism. This correspondence between OADHC lipoylation capacity and aerobiosis indicates that genomic pathway profiling in archaea is informative and that well characterized pathways may be predictive in relation to abiotic conditions in difficult-to-study extremophiles. Given the highly variable retention of gene repertoires across the archaea, the extension of comparative genomic pathway profiling to broader metabolic and homeostasis networks should be useful in revealing characteristics from metagenomic datasets related to adaptations to diverse environments.},
}
@article {pmid24477923,
year = {2014},
author = {Polónia, AR and Cleary, DF and Duarte, LN and de Voogd, NJ and Gomes, NC},
title = {Composition of Archaea in seawater, sediment, and sponges in the Kepulauan Seribu reef system, Indonesia.},
journal = {Microbial ecology},
volume = {67},
number = {3},
pages = {553-567},
pmid = {24477923},
issn = {1432-184X},
mesh = {Animals ; Archaea/classification/genetics/isolation &amp; purification/metabolism/*physiology ; *Biodiversity ; *Coral Reefs ; Geologic Sediments/*microbiology ; Indonesia ; Molecular Sequence Data ; Phylogeny ; Porifera/*microbiology ; Seawater/*microbiology ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {Coral reefs are among the most diverse and productive ecosystems in the world. Most research has, however, focused on eukaryotes such as corals and fishes. Recently, there has been increasing interest in the composition of prokaryotes, particularly those inhabiting corals and sponges, but these have mainly focused on bacteria. There have been very few studies of coral reef Archaea, despite the fact that Archaea have been shown to play crucial roles in nutrient dynamics, including nitrification and methanogenesis, of oligotrophic environments such as coral reefs. Here, we present the first study to assess Archaea in four different coral reef biotopes (seawater, sediment, and two sponge species, Stylissa massa and Xestospongia testudinaria). The archaeal community of both sponge species and sediment was dominated by Crenarchaeota, while the seawater community was dominated by Euryarchaeota. The biotope explained more than 72% of the variation in archaeal composition. The number of operational taxonomic units (OTUs) was highest in sediment and seawater biotopes and substantially lower in both sponge hosts. No "sponge-specific" archaeal OTUs were found, i.e., OTUs found in both sponge species but absent from nonhost biotopes. Despite both sponge species hosting phylogenetically distinct microbial assemblages, there were only minor differences in Kyoto Encyclopedia of Genes and Genomes (KEGG) functional pathways. In contrast, most functional pathways differed significantly between microbiomes from sponges and nonhost biotopes including all energy metabolic pathways. With the exception of the methane and nitrogen metabolic pathway, all energy metabolic pathways were enriched in sponges when compared to nonhost biotopes.},
}
@article {pmid24455858,
year = {2013},
author = {Vorob'eva, LI and Khodzhaev, EIu and Novikova, TM and Chudinova, EM},
title = {[Antistress cross-effects of extracellular metabolites of bacteria, archaea, and yeasts: a review].},
journal = {Prikladnaia biokhimiia i mikrobiologiia},
volume = {49},
number = {4},
pages = {333-344},
doi = {10.7868/s0555109913040144},
pmid = {24455858},
issn = {0555-1099},
mesh = {Archaea/growth &amp; development/*metabolism ; Archaeal Proteins/metabolism ; Bacteria/growth &amp; development/*metabolism ; Bacterial Proteins/metabolism ; Fungal Proteins/metabolism ; Heat-Shock Proteins/metabolism ; Quorum Sensing ; Signal Transduction ; *Stress, Physiological ; Yeasts/growth &amp; development/*metabolism ; },
abstract = {This paper reviews examples of specific and global responses of microorganisms and the characteristics of stress responses involving extracellular signaling metabolites. Information regarding the protective and reactivating effects produced by active exometabolites of representatives of domains of bacteria, archaea, and eukaryotes is summarized, and interdomain cross-responses to stressors are demonstrated.},
}
@article {pmid24411446,
year = {2014},
author = {Oztetik, E and Cakir, A},
title = {New food for an old mouth: new enzyme for an ancient archaea.},
journal = {Enzyme and microbial technology},
volume = {55},
number = {},
pages = {58-64},
doi = {10.1016/j.enzmictec.2013.12.004},
pmid = {24411446},
issn = {1879-0909},
mesh = {Archaeal Proteins/*metabolism ; Cytosol/enzymology ; Diazonium Compounds/metabolism ; Glutathione/metabolism ; Glutathione Peroxidase/*metabolism ; Haloarcula/*enzymology/ultrastructure ; Hydrogen-Ion Concentration ; Kinetics ; Osmolar Concentration ; Oxidation-Reduction ; Salinity ; Temperature ; },
abstract = {As a multifunctional group of enzymes, glutathione S-transferases (GSTs) are capable of inactivation, degradation or excretion of wide range of compounds catalytically or non-catalytically. However, to date, no study has been addresses the presence of GSTs in archaea based on their enzymatic functions. In this study, beside glutathione (GSH) amount measurement, the determination of GST activity in halophilic archaeon called Haloarcula hispanica ATCC 33960 were aimed. According to the results, specific activity was determined as 19.68 nmol min[-1] mg[-1] protein and GSH content were found to be as 194 μg g[-1] K(m) and V(max) values for CDNB and GSH calculated from Lineweaver-Burk plot were 0.46 mM and 27.93 nmol min[-1] mg[-1], 0.13 mM and 22.03 nmol min[-1] mg[-1], respectively. Hanes-Woolf and Eadie-Hofstee plots for CDNB and GSH were also found to be in co-relation with the results obtained from Lineweaver-Burk plot. To the best of our knowledge, GST enzymes have not been identified in archaea yet, at least based on their catalytic activities. Therefore, it is the first report on this area.},
}
@article {pmid24401864,
year = {2014},
author = {Stieglmeier, M and Mooshammer, M and Kitzler, B and Wanek, W and Zechmeister-Boltenstern, S and Richter, A and Schleper, C},
title = {Aerobic nitrous oxide production through N-nitrosating hybrid formation in ammonia-oxidizing archaea.},
journal = {The ISME journal},
volume = {8},
number = {5},
pages = {1135-1146},
pmid = {24401864},
issn = {1751-7370},
support = {P 23000/FWF_/Austrian Science Fund FWF/Austria ; },
mesh = {Ammonia/metabolism ; Archaea/*metabolism ; Bacteria/metabolism ; Denitrification ; Ecosystem ; Nitrification ; Nitrous Oxide/*metabolism ; Oxidation-Reduction ; *Soil Microbiology ; },
abstract = {Soil emissions are largely responsible for the increase of the potent greenhouse gas nitrous oxide (N2O) in the atmosphere and are generally attributed to the activity of nitrifying and denitrifying bacteria. However, the contribution of the recently discovered ammonia-oxidizing archaea (AOA) to N2O production from soil is unclear as is the mechanism by which they produce it. Here we investigate the potential of Nitrososphaera viennensis, the first pure culture of AOA from soil, to produce N2O and compare its activity with that of a marine AOA and an ammonia-oxidizing bacterium (AOB) from soil. N. viennensis produced N2O at a maximum yield of 0.09% N2O per molecule of nitrite under oxic growth conditions. N2O production rates of 4.6±0.6 amol N2O cell(-1) h(-1) and nitrification rates of 2.6±0.5 fmol NO2(-) cell(-1) h(-1) were in the same range as those of the AOB Nitrosospira multiformis and the marine AOA Nitrosopumilus maritimus grown under comparable conditions. In contrast to AOB, however, N2O production of the two archaeal strains did not increase when the oxygen concentration was reduced, suggesting that they are not capable of denitrification. In (15)N-labeling experiments we provide evidence that both ammonium and nitrite contribute equally via hybrid N2O formation to the N2O produced by N. viennensis under all conditions tested. Our results suggest that archaea may contribute to N2O production in terrestrial ecosystems, however, they are not capable of nitrifier-denitrification and thus do not produce increasing amounts of the greenhouse gas when oxygen becomes limiting.},
}
@article {pmid24398374,
year = {2014},
author = {Raymann, K and Forterre, P and Brochier-Armanet, C and Gribaldo, S},
title = {Global phylogenomic analysis disentangles the complex evolutionary history of DNA replication in archaea.},
journal = {Genome biology and evolution},
volume = {6},
number = {1},
pages = {192-212},
pmid = {24398374},
issn = {1759-6653},
mesh = {Archaea/*genetics/metabolism ; Archaeal Proteins/genetics/metabolism ; *DNA Replication ; DNA, Archaeal/*genetics/metabolism ; *Evolution, Molecular ; Gene Transfer, Horizontal ; *Genome, Archaeal ; *Phylogeny ; },
abstract = {The archaeal machinery responsible for DNA replication is largely homologous to that of eukaryotes and is clearly distinct from its bacterial counterpart. Moreover, it shows high diversity in the various archaeal lineages, including different sets of components, heterogeneous taxonomic distribution, and a large number of additional copies that are sometimes highly divergent. This has made the evolutionary history of this cellular system particularly challenging to dissect. Here, we have carried out an exhaustive identification of homologs of all major replication components in over 140 complete archaeal genomes. Phylogenomic analysis allowed assigning them to either a conserved and probably essential core of replication components that were mainly vertically inherited, or to a variable and highly divergent shell of extra copies that have likely arisen from integrative elements. This suggests that replication proteins are frequently exchanged between extrachromosomal elements and cellular genomes. Our study allowed clarifying the history that shaped this key cellular process (ancestral components, horizontal gene transfers, and gene losses), providing important evolutionary and functional information. Finally, our precise identification of core components permitted to show that the phylogenetic signal carried by DNA replication is highly consistent with that harbored by two other key informational machineries (translation and transcription), strengthening the existence of a robust organismal tree for the Archaea.},
}
@article {pmid24395078,
year = {2014},
author = {Pawlowski, A and Rissanen, I and Bamford, JK and Krupovic, M and Jalasvuori, M},
title = {Gammasphaerolipovirus, a newly proposed bacteriophage genus, unifies viruses of halophilic archaea and thermophilic bacteria within the novel family Sphaerolipoviridae.},
journal = {Archives of virology},
volume = {159},
number = {6},
pages = {1541-1554},
doi = {10.1007/s00705-013-1970-6},
pmid = {24395078},
issn = {1432-8798},
mesh = {Archaea/*virology ; Bacteriophages/*classification/genetics/*isolation &amp; purification/ultrastructure ; Cluster Analysis ; DNA Viruses/*classification/genetics/*isolation &amp; purification/ultrastructure ; DNA, Viral/genetics ; Genes, Viral ; Molecular Sequence Data ; Prophages/classification/genetics/isolation &amp; purification/ultrastructure ; Sequence Analysis, DNA ; Sequence Homology ; Thermus thermophilus/*virology ; Virion/ultrastructure ; },
abstract = {A new family of viruses named Sphaerolipoviridae has been proposed recently. It comprises icosahedral, tailless haloarchaeal viruses with an internal lipid membrane located between the protein capsid and the dsDNA genome. The proposed family Sphaerolipoviridae was divided into two genera: Alphasphaerolipovirus, including Haloarcula hispanica viruses SH1, PH1 and HHIV-2, and Betasphaerolipovirus, including Natrinema virus SNJ1. Here, we propose to expand the family Sphaerolipoviridae to include a group of bacteriophages infecting extreme thermophilic Thermus thermophilus and sharing a number of structural and genomic properties with archaeal sphaerolipoviruses. This new group comprises two members, lytic phage P23-77 and temperate phage IN93, as well as putative members P23-72 and P23-65H. In addition, several related proviruses have been discovered as integrated elements in bacterial genomes of the families Thermus and Meiothermus. Morphology of the virus particles and the overall capsid architecture of these bacteriophages resembles that of archaeal members of the Sphaerolipoviridae, including an unusual capsid arrangement in a T = 28 dextro lattice. Alpha- and betasphaerolipoviruses share with P23-77-like bacteriophages a conserved block of core genes that encode a putative genome-packaging ATPase and the two major capsid proteins (MCPs). The recently determined X-ray structure of the small and large MCPs of P23-77 revealed a single beta-barrel (jelly-roll) fold that is superimposable with the cryo-EM density maps of the SH1 capsomers. Given the common features of these viruses, we propose to include the so far unclassified P23-77-like bacteriophages into a new genus, "Gammasphaerolipovirus", within the family Sphaerolipoviridae.},
}
@article {pmid24386380,
year = {2013},
author = {Jackson, SA and Flemer, B and McCann, A and Kennedy, J and Morrissey, JP and O'Gara, F and Dobson, AD},
title = {Archaea appear to dominate the microbiome of Inflatella pellicula deep sea sponges.},
journal = {PloS one},
volume = {8},
number = {12},
pages = {e84438},
pmid = {24386380},
issn = {1932-6203},
mesh = {Animals ; Aquatic Organisms/*genetics ; Archaea/*genetics ; Microbiota/*genetics ; Porifera/*microbiology ; RNA, Archaeal/*genetics ; RNA, Ribosomal, 16S/*genetics ; },
abstract = {Microbes associated with marine sponges play significant roles in host physiology. Remarkable levels of microbial diversity have been observed in sponges worldwide through both culture-dependent and culture-independent studies. Most studies have focused on the structure of the bacterial communities in sponges and have involved sponges sampled from shallow waters. Here, we used pyrosequencing of 16S rRNA genes to compare the bacterial and archaeal communities associated with two individuals of the marine sponge Inflatella pellicula from the deep-sea, sampled from a depth of 2,900 m, a depth which far exceeds any previous sequence-based report of sponge-associated microbial communities. Sponge-microbial communities were also compared to the microbial community in the surrounding seawater. Sponge-associated microbial communities were dominated by archaeal sequencing reads with a single archaeal OTU, comprising ~60% and ~72% of sequences, being observed from Inflatella pellicula. Archaeal sequencing reads were less abundant in seawater (~11% of sequences). Sponge-associated microbial communities were less diverse and less even than any other sponge-microbial community investigated to date with just 210 and 273 OTUs (97% sequence identity) identified in sponges, with 4 and 6 dominant OTUs comprising ~88% and ~89% of sequences, respectively. Members of the candidate phyla, SAR406, NC10 and ZB3 are reported here from sponges for the first time, increasing the number of bacterial phyla or candidate divisions associated with sponges to 43. A minor cohort from both sponge samples (~0.2% and ~0.3% of sequences) were not classified to phylum level. A single OTU, common to both sponge individuals, dominates these unclassified reads and shares sequence homology with a sponge associated clone which itself has no known close relative and may represent a novel taxon.},
}
@article {pmid25732342,
year = {2014},
author = {Soppa, J},
title = {Polyploidy in archaea and bacteria: about desiccation resistance, giant cell size, long-term survival, enforcement by a eukaryotic host and additional aspects.},
journal = {Journal of molecular microbiology and biotechnology},
volume = {24},
number = {5-6},
pages = {409-419},
doi = {10.1159/000368855},
pmid = {25732342},
issn = {1660-2412},
mesh = {Archaea/*genetics/physiology ; Bacteria/*genetics ; Bacterial Physiological Phenomena ; *Polyploidy ; *Stress, Physiological ; },
abstract = {During recent years, it has become clear that many species of archaea and bacteria are polyploid and contain more than 10 copies of their chromosome. In this contribution, eight examples are discussed to highlight different aspects of polyploidy in prokaryotes. The species discussed are the bacteria Azotobacter vinelandii, Deinococcus radiodurans, Sinorhizobium meliloti, and Epulopiscium as well as the archaea Methanocaldococcus jannaschii, Methanococcus maripaludis, Haloferax volcanii, and haloarchaeal isolates from salt deposits. The topics include possible laboratory artifacts, resistance against double-strand breaks, long-term survival, relaxation of DNA segregation and septum formation, enforced polyploidy by a eukaryotic host, genome equalization by gene conversion, and the nongenetic usage of genomic DNA as a phosphate storage polymer. Together, the selected topics give an overview of the biodiversity of polyploidy in archaea and bacteria.},
}
@article {pmid24348094,
year = {2013},
author = {Forterre, P},
title = {The common ancestor of archaea and eukarya was not an archaeon.},
journal = {Archaea (Vancouver, B.C.)},
volume = {2013},
number = {},
pages = {372396},
pmid = {24348094},
issn = {1472-3654},
mesh = {Archaea/*classification/genetics ; Bacteria/classification/genetics ; Biological Evolution ; Cell Lineage/*genetics ; DNA, Archaeal/*genetics ; DNA, Bacterial/genetics ; Eukaryota/*classification/genetics ; Evolution, Molecular ; Phylogeny ; },
abstract = {It is often assumed that eukarya originated from archaea. This view has been recently supported by phylogenetic analyses in which eukarya are nested within archaea. Here, I argue that these analyses are not reliable, and I critically discuss archaeal ancestor scenarios, as well as fusion scenarios for the origin of eukaryotes. Based on recognized evolutionary trends toward reduction in archaea and toward complexity in eukarya, I suggest that their last common ancestor was more complex than modern archaea but simpler than modern eukaryotes (the bug in-between scenario). I propose that the ancestors of archaea (and bacteria) escaped protoeukaryotic predators by invading high temperature biotopes, triggering their reductive evolution toward the "prokaryotic" phenotype (the thermoreduction hypothesis). Intriguingly, whereas archaea and eukarya share many basic features at the molecular level, the archaeal mobilome resembles more the bacterial than the eukaryotic one. I suggest that selection of different parts of the ancestral virosphere at the onset of the three domains played a critical role in shaping their respective biology. Eukarya probably evolved toward complexity with the help of retroviruses and large DNA viruses, whereas similar selection pressure (thermoreduction) could explain why the archaeal and bacterial mobilomes somehow resemble each other.},
}
@article {pmid24335827,
year = {2014},
author = {Wang, FP and Zhang, Y and Chen, Y and He, Y and Qi, J and Hinrichs, KU and Zhang, XX and Xiao, X and Boon, N},
title = {Methanotrophic archaea possessing diverging methane-oxidizing and electron-transporting pathways.},
journal = {The ISME journal},
volume = {8},
number = {5},
pages = {1069-1078},
pmid = {24335827},
issn = {1751-7370},
mesh = {Acetates/metabolism ; Archaea/enzymology/genetics/*metabolism ; Electrons ; Gene Expression Regulation, Archaeal ; Genome, Archaeal ; Geologic Sediments/*microbiology ; Hydrogen/metabolism ; Methane/*metabolism ; Oxidation-Reduction ; Oxidoreductases ; },
abstract = {Anaerobic oxidation of methane (AOM) is a crucial process limiting the flux of methane from marine environments to the atmosphere. The process is thought to be mediated by three groups of uncultivated methane-oxidizing archaea (ANME-1, 2 and 3). Although the responsible microbes have been intensively studied for more than a decade, central mechanistic details remain unresolved. On the basis of an integrated analysis of both environmental metatranscriptome and single-aggregate genome of a highly active AOM enrichment dominated by ANME-2a, we provide evidence for a complete and functioning AOM pathway in ANME-2a. All genes required for performing the seven steps of methanogenesis from CO2 were found present and actively expressed. Meanwhile, genes for energy conservation and electron transportation including those encoding F420H2 dehydrogenase (Fpo), the cytoplasmic and membrane-associated Coenzyme B-Coenzyme M heterodisulfide (CoB-S-SCoM) reductase (HdrABC, HdrDE), cytochrome C and the Rhodobacter nitrogen fixation (Rnf) complex were identified and expressed, whereas genes encoding for hydrogenases were absent. Thus, ANME-2a is likely performing AOM through a complete reversal of methanogenesis from CO2 reduction without involvement of canonical hydrogenase. ANME-2a is demonstrated to possess versatile electron transfer pathways that would provide the organism with more flexibility in substrate utilization and capacity for rapid adjustment to fluctuating environments. This work lays the foundation for understanding the environmental niche differentiation, physiology and evolution of different ANME subgroups.},
}
@article {pmid24335300,
year = {2014},
author = {Krupovic, M and Quemin, ER and Bamford, DH and Forterre, P and Prangishvili, D},
title = {Unification of the globally distributed spindle-shaped viruses of the Archaea.},
journal = {Journal of virology},
volume = {88},
number = {4},
pages = {2354-2358},
pmid = {24335300},
issn = {1098-5514},
mesh = {Archaea/*virology ; Archaeal Viruses/classification/*genetics/*ultrastructure ; Base Sequence ; Chromosome Mapping ; DNA Viruses/classification/*genetics/*ultrastructure ; Evolution, Molecular ; Fuselloviridae/classification/genetics ; Genetic Markers/genetics ; Microscopy, Electron ; *Models, Molecular ; Molecular Sequence Data ; *Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; Viral Structural Proteins/genetics ; },
abstract = {Viruses with spindle-shaped virions are abundant in diverse environments. Over the years, such viruses have been isolated from a wide range of archaeal hosts. Evolutionary relationships between them remained enigmatic, however. Here, using structural proteins as markers, we define familial ties among these "dark horses" of the virosphere and segregate all spindle-shaped viruses into two distinct evolutionary lineages, corresponding to Bicaudaviridae and Fuselloviridae. Our results illuminate the utility of structure-based virus classification and bring additional order to the virosphere.},
}
@article {pmid24320900,
year = {2013},
author = {Lira, EA and Ramiro, FS and Chiarelli, FM and Dias, RR and Feres, M and Figueiredo, LC and Faveri, M},
title = {Reduction in prevalence of Archaea after periodontal therapy in subjects with generalized aggressive periodontitis.},
journal = {Australian dental journal},
volume = {58},
number = {4},
pages = {442-447},
doi = {10.1111/adj.12123},
pmid = {24320900},
issn = {1834-7819},
mesh = {Adult ; Aggressive Periodontitis/*microbiology/*therapy ; Amoxicillin/therapeutic use ; Anti-Bacterial Agents/*therapeutic use ; Archaea/genetics/*isolation &amp; purification ; Combined Modality Therapy/methods ; Dental Plaque/microbiology/therapy ; *Dental Scaling ; Double-Blind Method ; Drug Therapy, Combination/methods ; Female ; Gene Amplification ; Humans ; Male ; Metronidazole/administration &amp; dosage/therapeutic use ; Middle Aged ; RNA, Archaeal/genetics ; RNA, Ribosomal, 16S/genetics ; *Root Planing ; Treatment Outcome ; },
abstract = {BACKGROUND: There is evidence of a possible relationship between Archaea and periodontal disease; however, to date few studies have assessed the changes in prevalence of this domain after periodontal therapy. The aim of this randomized double-blind and placebo-controlled study was to assess if periodontal treatment with or without systemic antibiotic would change the prevalence of Archaea after periodontal therapy.<br><br>METHODS: Thirty subjects were randomly assigned to receive scaling and root planing (SRP) alone or combined with metronidazole (MTZ) + amoxicillin (AMX) for 14&#xa0;days. Clinical and microbiological examinations were performed at baseline and at six months post-SRP. Nine subgingival plaque samples per subject were analysed for the presence of Archaea.<br><br>RESULTS: SRP alone or combined with MTZ + AMX significantly reduced the prevalence of subjects colonized by Archaea at six months post-therapy. However, no significant differences between treatment groups were observed (p&#xa0;>&#xa0;0.05). Both therapies led to a statistically significant decrease in the mean percentage of sites colonized by Archaea (p&#xa0;<&#xa0;0.05). A negative Spearman correlation was observed between the presence of Archaea and the mean clinical attachment gain at six months post-therapy (r(2) = -0.61; 95% CI -0.80- -0.31; p&#xa0;=&#xa0;0.003).<br><br>CONCLUSIONS: SRP alone or combined with MTZ + AMX provides a similar reduction in the prevalence of Archaea in the subgingival biofilm of subjects with generalized aggressive periodontitis.},
}
@article {pmid24318009,
year = {2014},
author = {Gao, J and Luo, X and Wu, G and Li, T and Peng, Y},
title = {Abundance and diversity based on amoA genes of ammonia-oxidizing archaea and bacteria in ten wastewater treatment systems.},
journal = {Applied microbiology and biotechnology},
volume = {98},
number = {7},
pages = {3339-3354},
doi = {10.1007/s00253-013-5428-2},
pmid = {24318009},
issn = {1432-0614},
mesh = {Ammonia/*metabolism ; Archaea/*classification/enzymology/genetics/metabolism ; Bacteria/*classification/enzymology/genetics/metabolism ; *Biota ; DNA, Archaeal/chemistry/genetics ; DNA, Bacterial/chemistry/genetics ; Molecular Sequence Data ; Oxidation-Reduction ; Oxidoreductases/*genetics ; Real-Time Polymerase Chain Reaction ; Sequence Analysis, DNA ; Wastewater/*microbiology ; },
abstract = {The abundance and diversity of amoA genes of ammonia-oxidizing archaea (AOA) and bacteria (AOB) were investigated in ten wastewater treatment systems (WTSs) by polymerase chain reaction (PCR), cloning, sequencing, and quantitative real-time PCR (qPCR). The ten WTSs included four full-scale municipal WTSs, three full-scale industrial WTSs, and three lab-scale WTSs. AOB were present in all the WTSs, whereas AOA were detected in nine WTSs. QPCR data showed that AOB amoA genes (4.625 × 10(4)-9.99 × 10(9) copies g(-1) sludge) outnumbered AOA amoA genes (<limit of detection-1.90 × 10(7) copies g(-1) sludge) in each WTS, indicating that AOB may play an important role than AOA in ammonia oxidization in WTSs. Interestingly, it was found that AOA and AOB coexisted with anaerobic ammonia oxidation (anammox) bacteria in three anammox WTSs with relatively higher abundance. In a full-scale industrial WTS where effluent ammonia was higher than influent ammonia, both AOA and AOB showed higher abundance. The phylogenetic analysis of AOB amoA genes showed that genera Nitrosomonas was the most dominant species in the ten WTSs; Nitrosomonas europaea cluster was the dominant major cluster, followed by Nitrosomonas-like cluster and Nitrosomonas oligotropha cluster; and AOB species showed higher diversity than AOA species. AOA were found to be affiliated with two major clusters: Nitrososphaera cluster and Nitrosopumilus cluster. Nitrososphaera cluster was the most dominant species in different samples and distributed worldwide.},
}
@article {pmid24307170,
year = {2014},
author = {Guo, L and Ding, J and Guo, R and Hou, Y and Wang, DC and Huang, L},
title = {Biochemical and structural insights into RNA binding by Ssh10b, a member of the highly conserved Sac10b protein family in Archaea.},
journal = {The Journal of biological chemistry},
volume = {289},
number = {3},
pages = {1478-1490},
pmid = {24307170},
issn = {1083-351X},
mesh = {Archaeal Proteins/*chemistry/genetics/metabolism ; Nucleic Acid Conformation ; Protein Binding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; RNA, Archaeal/*chemistry/genetics/metabolism ; RNA, Double-Stranded/*chemistry/genetics/metabolism ; RNA-Binding Proteins/*chemistry/genetics/metabolism ; Sulfolobus/*chemistry/genetics/metabolism ; },
abstract = {Proteins of the Sac10b family are highly conserved in Archaea. Ssh10b, a member of the Sac10b family from the hyperthermophilic crenarchaeon Sulfolobus shibatae, binds to RNA in vivo. Here we show that binding by Ssh10b destabilizes RNA secondary structure. Structural analysis of Ssh10b in complex with a 25-bp RNA duplex containing local distortions reveals that Ssh10b binds the two RNA strands symmetrically as a tetramer with each dimer bound asymmetrically to a single RNA strand. Amino acid residues involved in double-stranded RNA binding are similar, but non-identical, to those in dsDNA binding. The dimer-dimer interaction mediated by the intermolecular β-sheet appears to facilitate the destabilization of base pairing in the secondary structure of RNA. Our results suggest that proteins of the Sac10b family may play important roles in RNA transactions requiring destabilization of RNA secondary structure in Sulfolobus.},
}
@article {pmid24278322,
year = {2013},
author = {Buriánková, I and Brablcová, L and Mach, V and Dvořák, P and Chaudhary, PP and Rulík, M},
title = {Identification of methanogenic archaea in the hyporheic sediment of Sitka stream.},
journal = {PloS one},
volume = {8},
number = {11},
pages = {e80804},
pmid = {24278322},
issn = {1932-6203},
mesh = {Archaea/*genetics ; Czech Republic ; Environmental Microbiology ; Gene Library ; Genes, Archaeal ; Geologic Sediments/*microbiology ; Methane/*metabolism ; Molecular Sequence Data ; Phylogeny ; Rivers/*microbiology ; },
abstract = {Methanogenic archaea produce methane as a metabolic product under anoxic conditions and they play a crucial role in the global methane cycle. In this study molecular diversity of methanogenic archaea in the hyporheic sediment of the lowland stream Sitka (Olomouc, Czech Republic) was analyzed by PCR amplification, cloning and sequencing analysis of the methyl coenzyme M reductase alpha subunit (mcrA) gene. Sequencing analysis of 60 clones revealed 24 different mcrA phylotypes from hyporheic sedimentary layers to a depth of 50 cm. Phylotypes were affiliated with Methanomicrobiales, Methanosarcinales and Methanobacteriales orders. Only one phylotype remains unclassified. The majority of the phylotypes showed higher affiliation with uncultured methanogens than with known methanogenic species. The presence of relatively rich assemblage of methanogenic archaea confirmed that methanogens may be an important component of hyporheic microbial communities and may affect CH4 cycling in rivers.},
}
@article {pmid24278010,
year = {2013},
author = {Warnecke, T and Becker, EA and Facciotti, MT and Nislow, C and Lehner, B},
title = {Conserved substitution patterns around nucleosome footprints in eukaryotes and Archaea derive from frequent nucleosome repositioning through evolution.},
journal = {PLoS computational biology},
volume = {9},
number = {11},
pages = {e1003373},
pmid = {24278010},
issn = {1553-7358},
support = {MOPS86705//Canadian Institutes of Health Research/Canada ; },
mesh = {Archaea/*genetics ; Eukaryota/*genetics ; *Evolution, Molecular ; Genomics ; Haloferax volcanii ; Humans ; *Models, Genetic ; Mutation ; Nucleosomes/*genetics ; Phylogeny ; },
abstract = {Nucleosomes, the basic repeat units of eukaryotic chromatin, have been suggested to influence the evolution of eukaryotic genomes, both by altering the propensity of DNA to mutate and by selection acting to maintain or exclude nucleosomes in particular locations. Contrary to the popular idea that nucleosomes are unique to eukaryotes, histone proteins have also been discovered in some archaeal genomes. Archaeal nucleosomes, however, are quite unlike their eukaryotic counterparts in many respects, including their assembly into tetramers (rather than octamers) from histone proteins that lack N- and C-terminal tails. Here, we show that despite these fundamental differences the association between nucleosome footprints and sequence evolution is strikingly conserved between humans and the model archaeon Haloferax volcanii. In light of this finding we examine whether selection or mutation can explain concordant substitution patterns in the two kingdoms. Unexpectedly, we find that neither the mutation nor the selection model are sufficient to explain the observed association between nucleosomes and sequence divergence. Instead, we demonstrate that nucleosome-associated substitution patterns are more consistent with a third model where sequence divergence results in frequent repositioning of nucleosomes during evolution. Indeed, we show that nucleosome repositioning is both necessary and largely sufficient to explain the association between current nucleosome positions and biased substitution patterns. This finding highlights the importance of considering the direction of causality between genetic and epigenetic change.},
}
@article {pmid24277848,
year = {2013},
author = {Smyshlyaev, G and Voigt, F and Blinov, A and Barabas, O and Novikova, O},
title = {Acquisition of an Archaea-like ribonuclease H domain by plant L1 retrotransposons supports modular evolution.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {110},
number = {50},
pages = {20140-20145},
pmid = {24277848},
issn = {1091-6490},
mesh = {Amino Acid Sequence ; Archaea/*enzymology/genetics ; Base Sequence ; *Evolution, Molecular ; Genome, Plant/*genetics ; Molecular Sequence Data ; Plants/*genetics ; Protein Structure, Tertiary/genetics ; Retroelements/*genetics ; Ribonuclease H/*genetics ; Sequence Alignment ; Sequence Analysis, DNA ; },
abstract = {Although a variety of non-LTR retrotransposons of the L1 superfamily have been found in plant genomes over recent decades, their diversity, distribution, and evolution have yet to be analyzed in depth. Here, we perform comprehensive comparative and evolutionary analyses of L1 retrotransposons from 29 genomes of land plants covering a wide range of taxa. We identify numerous L1 elements in these genomes and detect a striking diversity of their domain composition. We show that all known land plant L1 retrotransposons can be grouped into five major families based on their phylogenetic relationships and domain composition. Moreover, we trace the putative evolution timeline that created the current variants and reveal that evolutionary events included losses and acquisitions of diverse putative RNA-binding domains and the acquisition of an Archaea-like ribonuclease H (RNH) domain. We also show that the latter RNH domain is autonomously active in vitro and speculate that retrotransposons may play a role in the horizontal transfer of RNH between plants, Archaea, and bacteria. The acquisition of an Archaea-like RNH domain by plant L1 retrotransposons negates the hypothesis that RNH domains in non-LTR retrotransposons have a single origin and provides evidence that acquisition happened at least twice. Together, our data indicate that the evolution of the investigated retrotransposons can be mainly characterized by repeated events of domain rearrangements and identify modular evolution as a major trend in the evolution of plant L1 retrotransposons.},
}
@article {pmid24273535,
year = {2013},
author = {Yang, J and Jiang, H and Dong, H and Wang, H and Wu, G and Hou, W and Liu, W and Zhang, C and Sun, Y and Lai, Z},
title = {amoA-encoding archaea and thaumarchaeol in the lakes on the northeastern Qinghai-Tibetan Plateau, China.},
journal = {Frontiers in microbiology},
volume = {4},
number = {},
pages = {329},
pmid = {24273535},
issn = {1664-302X},
abstract = {All known ammonia-oxidizing archaea (AOA) belong to the phylum Thaumarchaeota within the domain Archaea. AOA possess the diagnostic amoA gene (encoding the alpha subunit of ammonia monooxygenase) and produce lipid biomarker thaumarchaeol. Although the abundance and diversity of amoA gene-encoding archaea (AEA) in freshwater lakes have been well-studied, little is known about AEA ecology in saline/hypersaline lakes. In this study, the distribution of the archaeal amoA gene and thaumarchaeol were investigated in nine Qinghai-Tibetan lakes with a salinity range from freshwater to salt-saturation (salinity: 325 g L(-) (1)). The results showed that the archaeal amoA gene was present in hypersaline lakes with salinity up to 160 g L(-) (1). The archaeal amoA gene diversity in Tibetan lakes was different from those in other lakes worldwide, suggesting Tibetan lakes (high elevation, strong ultraviolet, and dry climate) may host a unique AEA population of different evolutionary origin from those in other lakes. Thaumarchaeol was present in all of the studied hypersaline lakes, even in those where no AEA amoA gene was observed. Future research is needed to determine the ecological function of AEA and possible sources of thaumarchaeol in the Qinghai-Tibetan hypersaline lakes.},
}
@article {pmid24269814,
year = {2014},
author = {Morii, H and Ogawa, M and Fukuda, K and Taniguchi, H},
title = {Ubiquitous distribution of phosphatidylinositol phosphate synthase and archaetidylinositol phosphate synthase in Bacteria and Archaea, which contain inositol phospholipid.},
journal = {Biochemical and biophysical research communications},
volume = {443},
number = {1},
pages = {86-90},
doi = {10.1016/j.bbrc.2013.11.054},
pmid = {24269814},
issn = {1090-2104},
mesh = {Archaea/*enzymology ; Archaeal Proteins/chemistry/*classification ; Bacteria/*enzymology ; Bacterial Proteins/chemistry/*classification ; CDP-Diacylglycerol-Inositol 3-Phosphatidyltransferase/chemistry/*classification ; Humans ; Inositol Phosphates/chemistry/metabolism ; Myo-Inositol-1-Phosphate Synthase/chemistry/*classification ; Phosphatidylinositols/analysis/*metabolism ; Phylogeny ; Substrate Specificity ; },
abstract = {In Eukarya, phosphatidylinositol (PI) is biosynthesized from CDP-diacylglycerol (CDP-DAG) and inositol. In Archaea and Bacteria, on the other hand, we found a novel inositol phospholipid biosynthetic pathway. The precursors, inositol 1-phosphate, CDP-archaeol (CDP-ArOH), and CDP-DAG, form archaetidylinositol phosphate (AIP) and phosphatidylinositol phosphate (PIP) as intermediates. These intermediates are dephosphorylated to synthesize archaetidylinositol (AI) and PI. To date, the activities of the key enzymes (AIP synthase, PIP synthase) have been confirmed in only three genera (two archaeal genera, Methanothermobacter and Pyrococcus, and one bacterial genus, Mycobacterium). In the present study, we demonstrated that this novel biosynthetic pathway is universal in both Archaea and Bacteria, which contain inositol phospholipid, and elucidate the specificity of PIP synthase and AIP synthase for lipid substrates. PIP and AIP synthase activity were confirmed in all recombinant cells transformed with the respective gene constructs for four bacterial species (Streptomyces avermitilis, Propionibacterium acnes, Corynebacterium glutamicum, and Rhodococcus equi) and two archaeal species (Aeropyrum pernix and Sulfolobus solfataricus). Inositol was not incorporated. CDP-ArOH was used as the substrate for PIP synthase in Bacteria, and CDP-DAG was used as the substrate for AIP synthase in Archaea, despite their fundamentally different structures. PI synthase activity was observed in two eukaryotic species, Saccharomyces cerevisiae and Homo sapiens; however, inositol 1-phosphate was not incorporated. In Eukarya, the only pathway converts free inositol and CDP-DAG directly into PI. Phylogenic analysis of PIP synthase, AIP synthase, and PI synthase revealed that they are closely related enzymes.},
}
@article {pmid24247281,
year = {2014},
author = {Brugère, JF and Borrel, G and Gaci, N and Tottey, W and O'Toole, PW and Malpuech-Brugère, C},
title = {Archaebiotics: proposed therapeutic use of archaea to prevent trimethylaminuria and cardiovascular disease.},
journal = {Gut microbes},
volume = {5},
number = {1},
pages = {5-10},
pmid = {24247281},
issn = {1949-0984},
mesh = {Archaea/isolation &amp; purification/*metabolism ; Cardiovascular Diseases/metabolism/microbiology/*prevention &amp; control ; Humans ; Metabolism, Inborn Errors/metabolism/microbiology/*prevention &amp; control ; Methylamines/metabolism/*urine ; Microbiota ; Probiotics/*administration &amp; dosage ; },
abstract = {Trimethylamine (TMA) is produced by gut bacteria from dietary ingredients. In individuals with a hereditary defect in flavin-containing monooxygenase 3, bacterial TMA production is believed to contribute to the symptoms of trimethylaminuria (TMAU; fish-odor syndrome). Intestinal microbiota TMA metabolism may also modulate atherosclerosis risk by affecting trimethylamine oxide (TMAO) production levels. We propose that reducing TMA formation in the gut by converting it to an inert molecule could be used to prevent or limit these human diseases, while avoiding the major drawbacks of other clinical interventions. Reducing TMA levels by microbiological interventions could also be helpful in some vaginoses. Particular members of a recently discovered group of methanogens, that are variably present in the human gut, are unusual in being apparently restricted to utilizing only methyl compounds including TMA as substrates. We confirmed experimentally that one of these strains tested, Methanomassiliicoccus luminyensis B10, is able to deplete TMA, by reducing it with H 2 for methanogenesis. We therefore suggest that members of this archaeal lineage could be used as treatments for metabolic disorders.},
}
@article {pmid24242890,
year = {2014},
author = {Wang, Z and Wang, Z and Huang, C and Pei, Y},
title = {Vertical distribution of ammonia-oxidizing archaea (AOA) in the hyporheic zone of a eutrophic river in North China.},
journal = {World journal of microbiology &amp; biotechnology},
volume = {30},
number = {4},
pages = {1335-1346},
pmid = {24242890},
issn = {1573-0972},
mesh = {Ammonia/*metabolism ; Archaea/*classification/*metabolism ; *Biodiversity ; China ; DNA, Archaeal/chemistry/genetics ; Molecular Sequence Data ; Oxidation-Reduction ; Oxidoreductases/genetics ; Rivers/*microbiology ; Sequence Analysis, DNA ; },
abstract = {Nitrification plays a significant role in the global nitrogen cycle, and this concept has been challenged with the discovery of ammonia-oxidizing archaea (AOA) in the environment. In this paper, the vertical variations of the diversity and abundance of AOA in the hyporheic zone of the Fuyang River in North China were investigated by molecular techniques, including clone libraries, phylogenetic analysis and real-time polymerase chain reaction. The archaeal amoA gene was detected in all sediments along the profile, and all AOA fell within marine group 1.1a and soil group1.1b of the Thaumarchaeota phylum, with the latter being the dominant type. The diversity of AOA decreased with the sediment depth, and there was a shift in AOA community between top-sediments (0-5 cm) and sub-sediments (5-70 cm). The abundance of the archaeal amoA gene (1.48 × 10[7] to 5.50 × 10[7] copies g[-1] dry sediment) was higher than that of the bacterial amoA gene (4.01 × 10[4] to 1.75 × 10[5] copies g[-1] dry sediment) in sub-sediments, resulting in a log10 ratio of AOA to ammonia-oxidizing bacteria (AOB) from 2.27 to 2.69, whereas AOB outnumbered AOA in top-sediments with a low log10 ratio of (-0.24). The variations in the AOA community were primarily attributed to the combined effect of the nutrients (ammonium-N, nitrate-N and total organic carbon) and oxygen in sediments. Ammonium-N was the major factor influencing the relative abundance of AOA and AOB, although other factors, such as total organic carbon, were involved. This study helps elucidate the roles of AOA and AOB in the nitrogen cycling of hyporheic zone.},
}
@article {pmid24225887,
year = {2014},
author = {Jung, MY and Well, R and Min, D and Giesemann, A and Park, SJ and Kim, JG and Kim, SJ and Rhee, SK},
title = {Isotopic signatures of N2O produced by ammonia-oxidizing archaea from soils.},
journal = {The ISME journal},
volume = {8},
number = {5},
pages = {1115-1125},
pmid = {24225887},
issn = {1751-7370},
mesh = {Ammonia/*metabolism ; Archaea/*classification/*metabolism ; Nitrification ; *Nitrogen Cycle ; Nitrous Oxide/*metabolism ; Oxidation-Reduction ; Phylogeny ; *Soil Microbiology ; },
abstract = {N2O gas is involved in global warming and ozone depletion. The major sources of N2O are soil microbial processes. Anthropogenic inputs into the nitrogen cycle have exacerbated these microbial processes, including nitrification. Ammonia-oxidizing archaea (AOA) are major members of the pool of soil ammonia-oxidizing microorganisms. This study investigated the isotopic signatures of N2O produced by soil AOA and associated N2O production processes. All five AOA strains (I.1a, I.1a-associated and I.1b clades of Thaumarchaeota) from soil produced N2O and their yields were comparable to those of ammonia-oxidizing bacteria (AOB). The levels of site preference (SP), δ(15)N(bulk) and δ(18)O -N2O of soil AOA strains were 13-30%, -13 to -35% and 22-36%, respectively, and strains MY1-3 and other soil AOA strains had distinct isotopic signatures. A (15)N-NH4(+)-labeling experiment indicated that N2O originated from two different production pathways (that is, ammonia oxidation and nitrifier denitrification), which suggests that the isotopic signatures of N2O from AOA may be attributable to the relative contributions of these two processes. The highest N2O production yield and lowest site preference of acidophilic strain CS may be related to enhanced nitrifier denitrification for detoxifying nitrite. Previously, it was not possible to detect N2O from soil AOA because of similarities between its isotopic signatures and those from AOB. Given the predominance of AOA over AOB in most soils, a significant proportion of the total N2O emissions from soil nitrification may be attributable to AOA.},
}
@article {pmid24204702,
year = {2013},
author = {Tanabe, AS and Toju, H},
title = {Two new computational methods for universal DNA barcoding: a benchmark using barcode sequences of bacteria, archaea, animals, fungi, and land plants.},
journal = {PloS one},
volume = {8},
number = {10},
pages = {e76910},
pmid = {24204702},
issn = {1932-6203},
mesh = {Animals ; Archaea/classification/genetics ; Bacteria/classification/genetics ; Benchmarking/*methods ; Computational Biology/*methods ; DNA/analysis/*genetics ; DNA Barcoding, Taxonomic/*methods ; DNA, Ribosomal Spacer/genetics ; Electron Transport Complex IV/genetics ; Embryophyta/classification/genetics ; Fungi/classification/genetics ; Genes, Chloroplast/genetics ; RNA, Ribosomal, 16S/genetics ; Reproducibility of Results ; },
abstract = {Taxonomic identification of biological specimens based on DNA sequence information (a.k.a. DNA barcoding) is becoming increasingly common in biodiversity science. Although several methods have been proposed, many of them are not universally applicable due to the need for prerequisite phylogenetic/machine-learning analyses, the need for huge computational resources, or the lack of a firm theoretical background. Here, we propose two new computational methods of DNA barcoding and show a benchmark for bacterial/archeal 16S, animal COX1, fungal internal transcribed spacer, and three plant chloroplast (rbcL, matK, and trnH-psbA) barcode loci that can be used to compare the performance of existing and new methods. The benchmark was performed under two alternative situations: query sequences were available in the corresponding reference sequence databases in one, but were not available in the other. In the former situation, the commonly used "1-nearest-neighbor" (1-NN) method, which assigns the taxonomic information of the most similar sequences in a reference database (i.e., BLAST-top-hit reference sequence) to a query, displays the highest rate and highest precision of successful taxonomic identification. However, in the latter situation, the 1-NN method produced extremely high rates of misidentification for all the barcode loci examined. In contrast, one of our new methods, the query-centric auto-k-nearest-neighbor (QCauto) method, consistently produced low rates of misidentification for all the loci examined in both situations. These results indicate that the 1-NN method is most suitable if the reference sequences of all potentially observable species are available in databases; otherwise, the QCauto method returns the most reliable identification results. The benchmark results also indicated that the taxon coverage of reference sequences is far from complete for genus or species level identification in all the barcode loci examined. Therefore, we need to accelerate the registration of reference barcode sequences to apply high-throughput DNA barcoding to genus or species level identification in biodiversity research.},
}
@article {pmid24191610,
year = {2013},
author = {Li, Z and Jin, W and Liang, Z and Yue, Y and Lv, J},
title = {Abundance and diversity of ammonia-oxidizing archaea in response to various habitats in Pearl River Delta of China, a subtropical maritime zone.},
journal = {Journal of environmental sciences (China)},
volume = {25},
number = {6},
pages = {1195-1205},
doi = {10.1016/s1001-0742(12)60178-8},
pmid = {24191610},
issn = {1001-0742},
mesh = {Ammonia/*metabolism ; Archaea/*metabolism ; China ; *Ecosystem ; Oxidation-Reduction ; Rivers ; },
abstract = {Ammonia-oxidizing archaea (AOA) are widely considered key to ammonia oxidation in various environments. However, little work has been conducted to simultaneously investigate the abundance and diversity of AOA as well as correlations between archaeal amoA genotypes and environmental parameters of different ecosystems at one district. To understand the abundance, diversity, and distribution of AOA in Pearl River Delta of China in response to various habitats, the archaeal amoA genes in soil, marine, river, lake, hot spring and wastewater treatment plant (WWTP) samples were investigated using real-time fluorescent quantitative PCR and clone libraries. Our analyses indicated that the diversity of AOA in various habitats was different and could be clustered into five major clades, i.e., estuary sediment, marine water/sediment, soil, hot spring and Cluster 1. Phylogenetic analyses revealed that the structure of AOA communities in similar ecological habitats exhibited strong relation. The canonical correspondence method indicated that the AOA community structure was strongly correlated to temperature, pH, total organic carbon, total nitrogen and dissolved oxygen variables. Assessing AOA amoA gene copy numbers, ranging from 6.84 x 10(6) to 9.45 x 10(7) copies/g in dry soil/sediment, and 6.06 x 10(6) to 2.41 x 10(7) copies/L in water samples, were higher than ammonia-oxidizing bacteria (AOB) by 1-2 orders of magnitude. However, AOA amoA copy numbers were much lower than AOB in WWTP activated sludge samples. Overall, these studies suggested that AOA may be a major contributor to ammonia oxidation in natural habitats but play a minor role in highly aerated activated sludge. The result also showed the ratio of AOA to AOB amoA gene abundance was positively correlated with temperature and less correlated with other environmental parameters. New data from our study provide increasing evidence for the relative abundance and diversity of ammonia-oxidizing archaea in the global nitrogen cycle.},
}
@article {pmid24152714,
year = {2014},
author = {Erwin, PM and Pineda, MC and Webster, N and Turon, X and López-Legentil, S},
title = {Down under the tunic: bacterial biodiversity hotspots and widespread ammonia-oxidizing archaea in coral reef ascidians.},
journal = {The ISME journal},
volume = {8},
number = {3},
pages = {575-588},
pmid = {24152714},
issn = {1751-7370},
mesh = {Ammonia/metabolism ; Animals ; Archaea/*classification/genetics ; Bacteria/*classification/genetics ; Biodiversity ; *Coral Reefs ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/chemistry/*microbiology ; Urochordata/*microbiology ; },
abstract = {Ascidians are ecologically important components of marine ecosystems yet the ascidian microbiota remains largely unexplored beyond a few model species. We used 16S rRNA gene tag pyrosequencing to provide a comprehensive characterization of microbial symbionts in the tunic of 42 Great Barrier Reef ascidian samples representing 25 species. Results revealed high bacterial biodiversity (3 217 unique operational taxonomic units (OTU0.03) from 19 described and 14 candidate phyla) and the widespread occurrence of ammonia-oxidizing Thaumarchaeota in coral reef ascidians (24 of 25 host species). The ascidian microbiota was clearly differentiated from seawater microbial communities and included symbiont lineages shared with other invertebrate hosts as well as unique, ascidian-specific phylotypes. Several rare seawater microbes were markedly enriched (200-700 fold) in the ascidian tunic, suggesting that the rare biosphere of seawater may act as a conduit for horizontal symbiont transfer. However, most OTUs (71%) were rare and specific to single hosts and a significant correlation between host relatedness and symbiont community similarity was detected, indicating a high degree of host-specificity and potential role of vertical transmission in structuring these communities. We hypothesize that the complex ascidian microbiota revealed herein is maintained by the dynamic microenvironments within the ascidian tunic, offering optimal conditions for different metabolic pathways such as ample chemical substrate (ammonia-rich host waste) and physical habitat (high oxygen, low irradiance) for nitrification. Thus, ascidian hosts provide unique and fertile niches for diverse microorganisms and may represent an important and previously unrecognized habitat for nitrite/nitrate regeneration in coral reef ecosystems.},
}
@article {pmid24146954,
year = {2013},
author = {Wu, D and Jospin, G and Eisen, JA},
title = {Systematic identification of gene families for use as "markers" for phylogenetic and phylogeny-driven ecological studies of bacteria and archaea and their major subgroups.},
journal = {PloS one},
volume = {8},
number = {10},
pages = {e77033},
pmid = {24146954},
issn = {1932-6203},
mesh = {Archaea/*classification/*genetics ; Bacteria/*classification/*genetics ; Bacterial Proteins/genetics ; Cluster Analysis ; Genetic Markers ; Genomics/methods ; *Multigene Family ; *Phylogeny ; },
abstract = {With the astonishing rate that genomic and metagenomic sequence data sets are accumulating, there are many reasons to constrain the data analyses. One approach to such constrained analyses is to focus on select subsets of gene families that are particularly well suited for the tasks at hand. Such gene families have generally been referred to as "marker" genes. We are particularly interested in identifying and using such marker genes for phylogenetic and phylogeny-driven ecological studies of microbes and their communities (e.g., construction of species trees, phylogenetic based assignment of metagenomic sequence reads to taxonomic groups, phylogeny-based assessment of alpha- and beta-diversity of microbial communities from metagenomic data). We therefore refer to these as PhyEco (for phylogenetic and phylogenetic ecology) markers. The dual use of these PhyEco markers means that we needed to develop and apply a set of somewhat novel criteria for identification of the best candidates for such markers. The criteria we focused on included universality across the taxa of interest, ability to be used to produce robust phylogenetic trees that reflect as much as possible the evolution of the species from which the genes come, and low variation in copy number across taxa. We describe here an automated protocol for identifying potential PhyEco markers from a set of complete genome sequences. The protocol combines rapid searching, clustering and phylogenetic tree building algorithms to generate protein families that meet the criteria listed above. We report here the identification of PhyEco markers for different taxonomic levels including 40 for "all bacteria and archaea", 114 for "all bacteria (greatly expanding on the ∼30 commonly used), and 100 s to 1000 s for some of the individual phyla of bacteria. This new list of PhyEco markers should allow much more detailed automated phylogenetic and phylogenetic ecology analyses of these groups than possible previously.},
}
@article {pmid24141944,
year = {2014},
author = {Meyer, A and Focks, A and Radl, V and Welzl, G and Schöning, I and Schloter, M},
title = {Influence of land use intensity on the diversity of ammonia oxidizing bacteria and archaea in soils from grassland ecosystems.},
journal = {Microbial ecology},
volume = {67},
number = {1},
pages = {161-166},
pmid = {24141944},
issn = {1432-184X},
mesh = {Agriculture/methods ; Ammonia/*metabolism ; Archaea/*classification/metabolism ; Bacteria/*classification/metabolism ; Ecosystem ; Fertilizers ; Germany ; Nitrification ; Oxidoreductases/genetics ; *Phylogeny ; Poaceae ; Polymorphism, Restriction Fragment Length ; Seasons ; *Soil Microbiology ; },
abstract = {In the present study, the influence of the land use intensity on the diversity of ammonia oxidizing bacteria (AOB) and archaea (AOA) in soils from different grassland ecosystems has been investigated in spring and summer of the season (April and July). Diversity of AOA and AOB was studied by TRFLP fingerprinting of amoA amplicons. The diversity from AOB was low and dominated by a peak that could be assigned to Nitrosospira. The obtained profiles for AOB were very stable and neither influenced by the land use intensity nor by the time point of sampling. In contrast, the obtained patterns for AOA were more complex although one peak that could be assigned to Nitrosopumilus was dominating all profiles independent from the land use intensity and the sampling time point. Overall, the AOA profiles were much more dynamic than those of AOB and responded clearly to the land use intensity. An influence of the sampling time point was again not visible. Whereas AOB profiles were clearly linked to potential nitrification rates in soil, major TRFs from AOA were negatively correlated to DOC and ammonium availability and not related to potential nitrification rates.},
}
@article {pmid24126762,
year = {2013},
author = {Hunter, P},
title = {Molecular fossils probe life's origins. Research into molecular fossils and modern viruses is shedding light on the evolution of archaea, prokaryotes and eukaryotes.},
journal = {EMBO reports},
volume = {14},
number = {11},
pages = {964-967},
pmid = {24126762},
issn = {1469-3178},
mesh = {Animals ; Archaea/*genetics ; *Biological Evolution ; Eukaryota/*genetics ; *Fossils ; Genome ; Humans ; *Origin of Life ; Oxidation-Reduction ; Prokaryotic Cells/*metabolism ; Viruses/*genetics ; },
}
@article {pmid24118021,
year = {2014},
author = {Mayer, F and Müller, V},
title = {Adaptations of anaerobic archaea to life under extreme energy limitation.},
journal = {FEMS microbiology reviews},
volume = {38},
number = {3},
pages = {449-472},
doi = {10.1111/1574-6976.12043},
pmid = {24118021},
issn = {1574-6976},
mesh = {ATP Synthetase Complexes/chemistry/metabolism ; *Adaptation, Physiological ; Anaerobiosis ; Archaea/enzymology/metabolism/*physiology ; *Energy Metabolism ; },
abstract = {Some anaerobic archaea live on substrates that do not allow the synthesis of 1 mol of ATP per mol of substrate. Energy conservation in these cases is only possible by a chemiosmotic mechanism that involves the generation of an electrochemical ion gradient across the cytoplasmatic membrane that then drives ATP synthesis via an A1AO ATP synthase. The minimal amount of energy required is thus depending on the magnitude of the electrochemical ion gradient, the phosphorylation potential, and the ion/ATP ratio of the ATP synthase. Methanogens, Thermococcus, Pyrococcus, and Ignicoccus have evolved different ways to energize their membranes, such as methyltransferases, H+, or NAD+ reducing electron transport systems fueled by reduced ferredoxin or H2 -dependent sulfur reduction that all operate at the thermodynamic limit of life. The structure and function of the enzymes involved are discussed. Despite the differences in membrane energization, they have in common an A1AO ATP synthase that shows an extraordinary divergence in rotor composition and structural adaptations to life under these conditions. In sum, adaptation of anaerobic archaea to energy-limited substrates involves chemiosmotic energy coupling, often with Na+ as coupling ion and a structurally and functionally highly adapted ATP synthase.},
}
@article {pmid24112809,
year = {2014},
author = {Kim, JG and Park, SJ and Quan, ZX and Jung, MY and Cha, IT and Kim, SJ and Kim, KH and Yang, EJ and Kim, YN and Lee, SH and Rhee, SK},
title = {Unveiling abundance and distribution of planktonic Bacteria and Archaea in a polynya in Amundsen Sea, Antarctica.},
journal = {Environmental microbiology},
volume = {16},
number = {6},
pages = {1566-1578},
doi = {10.1111/1462-2920.12287},
pmid = {24112809},
issn = {1462-2920},
mesh = {Antarctic Regions ; Archaea/*genetics ; Cluster Analysis ; Flavobacteriaceae/*genetics ; Gammaproteobacteria/*genetics ; Genes, Archaeal ; Genes, Bacterial ; Ice Cover ; Microbiota/genetics ; Molecular Typing ; Oceans and Seas ; Phylogeny ; Plankton/genetics ; RNA, Ribosomal, 16S/genetics ; Seawater/microbiology ; *Water Microbiology ; },
abstract = {Polynyas, areas of open water surrounded by sea ice, are sites of intense primary production and ecological hotspots in the Antarctic Ocean. This study determined the spatial variation in communities of prokaryotes in a polynya in the Amundsen Sea using 454 pyrosequencing technology, and the results were compared with biotic and abiotic environmental factors. The bacterial abundance was correlated with that of phytoplankton, Phaeocystis spp. and diatoms. A cluster analysis indicated that the bacterial communities in the surface waters of the polynya were distinct from those under the sea ice. Overall, two bacterial clades, Polaribacter (20-64%) and uncultivated Oceanospirillaceae (7-34%), dominated the surface water in the polynya while the Pelagibacter clade was abundant at all depths (7-42%). The archaeal communities were not as diverse as the bacterial communities in the polynya, and marine group I was dominant (> 80%). Canonical correspondence analysis indicated that the oceanographic properties facilitated the development of distinct prokaryotic assemblages in the polynya. This analysis of the diversity and composition of the psychrophilic prokaryotes associated with high phytoplankton production provides new insights into the roles of prokaryotes in biogeochemical cycles in high-latitude polynyas.},
}
@article {pmid24108328,
year = {2014},
author = {Meng, J and Xu, J and Qin, D and He, Y and Xiao, X and Wang, F},
title = {Genetic and functional properties of uncultivated MCG archaea assessed by metagenome and gene expression analyses.},
journal = {The ISME journal},
volume = {8},
number = {3},
pages = {650-659},
pmid = {24108328},
issn = {1751-7370},
mesh = {Archaea/*classification/*genetics/metabolism ; Carboxy-Lyases/metabolism ; DNA Topoisomerases, Type I/genetics ; Estuaries ; Geologic Sediments/*microbiology ; Metagenome ; Molecular Sequence Data ; Phylogeny ; RNA, Archaeal/genetics ; RNA, Ribosomal, 16S/genetics/metabolism ; Ribosomal Proteins/genetics ; },
abstract = {The Miscellaneous Crenarchaeota group (MCG) Archaea is one of the predominant archaeal groups in anoxic environments and may have significant roles in the global biogeochemical cycles. However, no isolate of MCG has been cultivated or characterized to date. In this study, we investigated the genetic organization, ecophysiological properties and evolutionary relationships of MCG archaea with other archaeal members using metagenome information and the result of gene expression experiments. A comparison of the gene organizations and similarities around the 16S rRNA genes from all available MCG fosmid and cosmid clones revealed no significant synteny among genomic fragments, demonstrating that there are large genetic variations within members of the MCG. Phylogenetic analyses of large-subunit+small-subunit rRNA, concatenated ribosomal protein genes and topoisomerases IB gene (TopoIB) all demonstrate that MCG constituted a sister lineage to the newly proposed archaeal phylum Aigarchaeota and Thaumarchaeota. Genes involved in protocatechuate degradation and chemotaxis were found in a MCG fosmid 75G8 genome fragment, suggesting that this MCG member may have a role in the degradation of aromatic compounds. Moreover, the expression of a putative 4-carboxymuconolactone decarboxylase was observed when the sediment was supplemented with protocatechuate, further supporting the hypothesis that this MCG member degrades aromatic compounds.},
}
@article {pmid24107237,
year = {2014},
author = {Dekas, AE and Chadwick, GL and Bowles, MW and Joye, SB and Orphan, VJ},
title = {Spatial distribution of nitrogen fixation in methane seep sediment and the role of the ANME archaea.},
journal = {Environmental microbiology},
volume = {16},
number = {10},
pages = {3012-3029},
doi = {10.1111/1462-2920.12247},
pmid = {24107237},
issn = {1462-2920},
mesh = {Ammonium Compounds/analysis ; Archaea/classification/*metabolism ; Deltaproteobacteria/metabolism ; Ecosystem ; Geologic Sediments/*microbiology ; Methane/*metabolism ; Nitrates/analysis ; Nitrites/analysis ; *Nitrogen Fixation ; Phylogeny ; Seawater/chemistry ; },
abstract = {Nitrogen (N2) fixation was investigated at Mound 12, Costa Rica, to determine its spatial distribution and biogeochemical controls in deep-sea methane seep sediment. Using (15)N2 tracer experiments and isotope ratio mass spectrometry analysis, we observed that seep N2 fixation is methane-dependent, and that N2 fixation rates peak in a narrow sediment depth horizon corresponding to increased abundance of aggregates of anaerobic methanotrophic archaea (ANME-2) and sulfate-reducing bacteria (SRB). Using fluorescence in situ hybridization coupled to nanoscale secondary ion mass spectrometry (FISH-NanoSIMS), we directly measured (15)N2 uptake by ANME-2/SRB aggregates (n = 26) and observed maximum (15)N incorporation within ANME-2-dominated areas of the aggregates, consistent with previous analyses. NanoSIMS analysis of single cells (n = 34) from the same microcosm experiment revealed no (15)N2 uptake. Together, these observations suggest that ANME-2, and possibly physically associated SRB, mediate the majority of new nitrogen production within the seep ecosystem. ANME-2 diazotrophy was observed while in association with members of two distinct orders of SRB: Desulfobacteraceae and Desulfobulbaceae. The rate of N2 fixation per unit volume biomass was independent of the identity of the associated SRB, aggregate size and morphology. Our results show that the distribution of seep N2 fixation is heterogeneous, laterally and with depth in the sediment, and is likely influenced by chemical gradients affecting the abundance and activity of ANME-2/SRB aggregates.},
}
@article {pmid24106795,
year = {2013},
author = {Lv, J and Wang, S and Zeng, C and Huang, Y and Chen, X},
title = {Construction of a shuttle expression vector with a promoter functioning in both halophilic Archaea and Bacteria.},
journal = {FEMS microbiology letters},
volume = {349},
number = {1},
pages = {9-15},
doi = {10.1111/1574-6968.12278},
pmid = {24106795},
issn = {1574-6968},
mesh = {Archaea/*genetics ; Archaeal Proteins/genetics ; Bacteria/*genetics ; Escherichia coli/genetics ; Genetic Vectors/*genetics ; Haloferax volcanii/genetics ; Promoter Regions, Genetic/*genetics ; },
abstract = {A shuttle expression vector, designated as pAJ, was constructed based on the Haloferax volcanii-Escherichia coli shuttle vector pSY1. This new construct contains the amyH promoter from Haloarcula hispanica and was able to confer the promoter activity in both Hfx. volcanii and E. coli. pAJ successfully expressed proteins in Hfx. volcanii or E. coli, rendering it feasible to express target proteins in corresponding domains. In addition, pAJ contains a multiple cloning site with 11 restriction sites and a 6×His tag sequence, and the vector size was decreased to 8903 bp. To the best of our knowledge, pAJ is the first reported shuttle expression vector that can express proteins in both Bacteria and Archaea. Importantly, pAJ can even express the haloarchaeal heat shock protein DnaK in both domains. In conclusion, this novel vector only provides researchers with a new means to manipulate genes or express proteins in Haloarchaea but also serves as a convenient tool for the comparative study of the function of some highly conserved genes in Haloarchaea and in Bacteria.},
}
@article {pmid24096423,
year = {2013},
author = {Lloyd, KG and May, MK and Kevorkian, RT and Steen, AD},
title = {Meta-analysis of quantification methods shows that archaea and bacteria have similar abundances in the subseafloor.},
journal = {Applied and environmental microbiology},
volume = {79},
number = {24},
pages = {7790-7799},
pmid = {24096423},
issn = {1098-5336},
mesh = {Archaea/*isolation &amp; purification ; Bacteria/*isolation &amp; purification ; Geologic Sediments/*microbiology ; Microbiological Techniques/*methods ; },
abstract = {There is no universally accepted method to quantify bacteria and archaea in seawater and marine sediments, and different methods have produced conflicting results with the same samples. To identify best practices, we compiled data from 65 studies, plus our own measurements, in which bacteria and archaea were quantified with fluorescent in situ hybridization (FISH), catalyzed reporter deposition FISH (CARD-FISH), polyribonucleotide FISH, or quantitative PCR (qPCR). To estimate efficiency, we defined "yield" to be the sum of bacteria and archaea counted by these techniques divided by the total number of cells. In seawater, the yield was high (median, 71%) and was similar for FISH, CARD-FISH, and polyribonucleotide FISH. In sediments, only measurements by CARD-FISH in which archaeal cells were permeabilized with proteinase K showed high yields (median, 84%). Therefore, the majority of cells in both environments appear to be alive, since they contain intact ribosomes. In sediments, the sum of bacterial and archaeal 16S rRNA gene qPCR counts was not closely related to cell counts, even after accounting for variations in copy numbers per genome. However, qPCR measurements were precise relative to other qPCR measurements made on the same samples. qPCR is therefore a reliable relative quantification method. Inconsistent results for the relative abundance of bacteria versus archaea in deep subsurface sediments were resolved by the removal of CARD-FISH measurements in which lysozyme was used to permeabilize archaeal cells and qPCR measurements which used ARCH516 as an archaeal primer or TaqMan probe. Data from best-practice methods showed that archaea and bacteria decreased as the depth in seawater and marine sediments increased, although archaea decreased more slowly.},
}
@article {pmid24092004,
year = {2014},
author = {Wang, J and Wang, W and Gu, JD},
title = {Community structure and abundance of ammonia-oxidizing archaea and bacteria after conversion from soybean to rice paddy in albic soils of Northeast China.},
journal = {Applied microbiology and biotechnology},
volume = {98},
number = {6},
pages = {2765-2778},
doi = {10.1007/s00253-013-5213-2},
pmid = {24092004},
issn = {1432-0614},
mesh = {Ammonia/*metabolism ; Archaea/*classification/metabolism ; Bacteria/*classification/metabolism ; *Biota ; China ; Denaturing Gradient Gel Electrophoresis ; Gene Library ; Molecular Sequence Data ; Oryza/*growth &amp; development ; Oxidation-Reduction ; Oxidoreductases/genetics ; Real-Time Polymerase Chain Reaction ; Sequence Analysis, DNA ; *Soil Microbiology ; Glycine max/*growth &amp; development ; },
abstract = {Community composition of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in the albic soil grown with soybean and rice for different years was investigated by construction of clone libraries, denaturing gradient gel electrophoresis (DGGE), and quantitative polymerase chain reaction (q-PCR) by PCR amplification of the ammonia monooxygenase subunit A (amoA) gene. Soil samples were collected at two layers (0-5 and 20-25 cm) from a soybean field and four rice paddy fields with 1, 5, 9, and 17 years of continuous rice cultivation. Both the community structures and abundances of AOA and AOB showed detectable changes after conversion from soybean to rice paddy judged by clone library, DGGE, and q-PCR analyses. In general, the archaeal amoA gene abundance increased after conversion to rice cultivation, while bacterial amoA gene abundance decreased. The abundances of both AOA and AOB were higher in the surface layer than the bottom one in the soybean field, but a reverse trend was observed for AOB in all paddy samples regardless of the duration of paddy cultivation. Phylogenetic analysis identified nine subclusters of AOA and seven subclusters of AOB. Community composition of both AOA and AOB was correlated with available ammonium and increased pH value caused by flooding in multiple variance analysis. Community shift of AOB was also observed in different paddy fields, but the two layers did not show any detectable changes in DGGE analysis. Conversion from soybean to rice cultivation changed the community structure and abundance of AOA and AOB in albic agricultural soil, which requires that necessary cultivation practice be followed to manage the N utilization more effectively.},
}
@article {pmid24086729,
year = {2013},
author = {Silveira, CB and Cardoso, AM and Coutinho, FH and Lima, JL and Pinto, LH and Albano, RM and Clementino, MM and Martins, OB and Vieira, RP},
title = {Tropical aquatic Archaea show environment-specific community composition.},
journal = {PloS one},
volume = {8},
number = {9},
pages = {e76321},
pmid = {24086729},
issn = {1932-6203},
mesh = {Adaptation, Biological/*physiology ; Archaea/*physiology ; Base Sequence ; Biota/*physiology ; Brazil ; DNA Primers/genetics ; *Environment ; Gene Library ; Geologic Sediments/*microbiology ; Likelihood Functions ; Models, Genetic ; Molecular Sequence Data ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Species Specificity ; Tropical Climate ; *Water Microbiology ; },
abstract = {The Archaea domain is ubiquitously distributed and extremely diverse, however, environmental factors that shape archaeal community structure are not well known. Aquatic environments, including the water column and sediments harbor many new uncultured archaeal species from which metabolic and ecological roles remain elusive. Some environments are especially neglected in terms of archaeal diversity, as is the case of pristine tropical areas. Here we investigate the archaeal composition in marine and freshwater systems from Ilha Grande, a South Atlantic tropical environment. All sampled habitats showed high archaeal diversity. No OTUs were shared between freshwater, marine and mangrove sediment samples, yet these environments are interconnected and geographically close, indicating environment-specific community structuring. Group II Euryarchaeota was the main clade in marine samples, while the new putative phylum Thaumarchaeota and LDS/RCV Euryarchaeota dominated freshwaters. Group III Euryarchaeota, a rare clade, was also retrieved in reasonable abundance in marine samples. The archaeal community from mangrove sediments was composed mainly by members of mesophilic Crenarchaeota and by a distinct clade forming a sister-group to Crenarchaeota and Thaumarchaeota. Our results show strong environment-specific community structuring in tropical aquatic Archaea, as previously seen for Bacteria.},
}
@article {pmid24077726,
year = {2014},
author = {Wang, J and Dong, H and Wang, W and Gu, JD},
title = {Reverse-transcriptional gene expression of anammox and ammonia-oxidizing archaea and bacteria in soybean and rice paddy soils of Northeast China.},
journal = {Applied microbiology and biotechnology},
volume = {98},
number = {6},
pages = {2675-2686},
doi = {10.1007/s00253-013-5242-x},
pmid = {24077726},
issn = {1432-0614},
mesh = {Ammonia/*metabolism ; Archaea/*enzymology/genetics/growth &amp; development/metabolism ; Bacteria/*enzymology/growth &amp; development/metabolism ; China ; DNA, Archaeal/chemistry/genetics ; DNA, Bacterial/chemistry/genetics ; *Gene Expression Profiling ; Molecular Sequence Data ; Oryza/growth &amp; development ; Oxidation-Reduction ; Oxidoreductases/*biosynthesis/genetics ; Real-Time Polymerase Chain Reaction ; Sequence Analysis, DNA ; *Soil Microbiology ; Glycine max/growth &amp; development ; },
abstract = {The relative gene expression of hydrazine oxidoreductase encoding gene (hzo) for anaerobic ammonium oxidizing bacteria (anammox) and ammonia monooxygenase encoding gene (amoA) for both ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in Sanjiang Plain soybean and rice paddy soils of Northeast China was investigated by using real-time reverse-transcriptional quantitative PCR. Metabolically active populations of anammox, AOA, and AOB in rice paddy soils were evident by the presence and successful quantification of hzo mRNA and amoA mRNA genes. The expression ratio of amoA gene for both AOA and AOB varied between soybean soils and different rice paddy soils while the expression of hzo gene for anammox was detectable only in rice paddy soils by showing a diverse relative expression ratio in each soil sample. Gene expression of both archaeal and bacterial amoA genes in rice paddy soils differed among the three sampling depths, but that of hzo was not. Both archaeal and bacterial amoA genes showed an increase trend of expression level with continuation of rice paddy cultivation, but the low expression ratio of hzo gene indicated a relatively small contribution of anammox in overall removal of inorganic nitrogen through N2 even under anoxic and high nitrogen input in agriculture. Bacterial amoA gene from two soybean fields and three rice paddy fields were also analyzed for community composition by denaturing gradient gel electrophoresis fingerprint. Community shift was observed between soybean and paddy fields and within each of them. The consistent occurrence of three bands 5, 6, and 7 in all samples showed their high adaptability for both arid cultivation and continuous rice paddy cultivation. Our data suggest that AOA and AOB are playing a more important role in nitrogen transformation in agricultural soils in oxic or anoxic environment and anammox bacteria may also contribute but in a less extent to N transformation in these agricultural soils under anoxic condition.},
}
@article {pmid24050175,
year = {2013},
author = {Farkas, JA and Picking, JW and Santangelo, TJ},
title = {Genetic techniques for the archaea.},
journal = {Annual review of genetics},
volume = {47},
number = {},
pages = {539-561},
doi = {10.1146/annurev-genet-111212-133225},
pmid = {24050175},
issn = {1545-2948},
support = {R01 GM100329/GM/NIGMS NIH HHS/United States ; GM100329/GM/NIGMS NIH HHS/United States ; GM098716/GM/NIGMS NIH HHS/United States ; },
mesh = {Archaea/classification/*genetics/physiology ; Archaeal Proteins/genetics/physiology ; Biodiversity ; DNA, Archaeal/genetics ; *Gene Expression Regulation, Archaeal ; Gene Transfer Techniques ; Genes, Archaeal ; Genes, Reporter ; *Genetic Techniques ; Genetic Vectors/genetics ; Genotype ; *Microbiological Techniques ; Phenotype ; Phylogeny ; Plasmids/genetics ; Promoter Regions, Genetic ; Selection, Genetic ; },
abstract = {Genetic techniques for the Archaea have undergone a rapid expansion in complexity, resulting in increased exploration of the role of Archaea in the environment and detailed analyses of the molecular physiology and information-processing systems in the third domain of life. Complementary gains in describing the ever-increasing diversity of archaeal organisms have allowed these techniques to be leveraged in new and imaginative ways to elucidate shared and unique aspects of archaeal diversity and metabolism. In this review, we introduce the four archaeal clades for which advanced genetic techniques are available--the methanogens, halophiles, Sulfolobales, and Thermococcales--with the aim of providing an overall profile of the advantages and disadvantages of working within each clade, as essentially all of the genetically accessible archaeal organisms require unique culturing techniques that present real challenges. We discuss the full repertoire of techniques possible within these clades while highlighting the recent advances that have been made by taking advantage of the most prominent techniques and approaches.},
}
@article {pmid24039236,
year = {2013},
author = {Pedro-Roig, L and Lange, C and Bonete, MJ and Soppa, J and Maupin-Furlow, J},
title = {Nitrogen regulation of protein-protein interactions and transcript levels of GlnK PII regulator and AmtB ammonium transporter homologs in Archaea.},
journal = {MicrobiologyOpen},
volume = {2},
number = {5},
pages = {826-840},
pmid = {24039236},
issn = {2045-8827},
support = {R01 GM057498/GM/NIGMS NIH HHS/United States ; },
mesh = {Ammonia/*metabolism/pharmacology ; Archaeal Proteins/*genetics/metabolism ; Cation Transport Proteins/*genetics/metabolism ; *Gene Expression Regulation, Archaeal ; Haloferax mediterranei/drug effects/*genetics/metabolism ; Nitrogen/*metabolism/pharmacology ; Protein Interaction Mapping ; RNA, Archaeal/genetics/metabolism ; RNA, Messenger/genetics/metabolism ; Signal Transduction ; Transcription, Genetic ; },
abstract = {Gene homologs of GlnK PII regulators and AmtB-type ammonium transporters are often paired on prokaryotic genomes, suggesting these proteins share an ancient functional relationship. Here, we demonstrate for the first time in Archaea that GlnK associates with AmtB in membrane fractions after ammonium shock, thus, providing a further insight into GlnK-AmtB as an ancient nitrogen sensor pair. For this work, Haloferax mediterranei was advanced for study through the generation of a pyrE2-based counterselection system that was used for targeted gene deletion and expression of Flag-tagged proteins from their native promoters. AmtB1-Flag was detected in membrane fractions of cells grown on nitrate and was found to coimmunoprecipitate with GlnK after ammonium shock. Thus, in analogy to bacteria, the archaeal GlnK PII may block the AmtB1 ammonium transporter under nitrogen-rich conditions. In addition to this regulated protein-protein interaction, the archaeal amtB-glnK gene pairs were found to be highly regulated by nitrogen availability with transcript levels high under conditions of nitrogen limitation and low during nitrogen excess. While transcript levels of glnK-amtB are similarly regulated by nitrogen availability in bacteria, transcriptional regulators of the bacterial glnK promoter including activation by the two-component signal transduction proteins NtrC (GlnG, NRI) and NtrB (GlnL, NRII) and sigma factor σ(N) (σ(54)) are not conserved in archaea suggesting a novel mechanism of transcriptional control.},
}
@article {pmid24037372,
year = {2013},
author = {Naor, A and Yair, Y and Gophna, U},
title = {A halocin-H4 mutant Haloferax mediterranei strain retains the ability to inhibit growth of other halophilic archaea.},
journal = {Extremophiles : life under extreme conditions},
volume = {17},
number = {6},
pages = {973-979},
pmid = {24037372},
issn = {1433-4909},
mesh = {Archaeal Proteins/genetics/*toxicity ; Cell Proliferation/drug effects ; Genes, Archaeal ; Halobacterium salinarum/*drug effects/physiology ; Haloferax mediterranei/*chemistry/genetics ; Haloferax volcanii/*drug effects/physiology ; *Mutation ; Peptides/genetics/*toxicity ; },
abstract = {Many members of the Halobacteriaceae were found to produce halocins, molecules that inhibit the growth of other halophilic archaea. Halocin H4 that is produced by Haloferax mediterranei and inhibits the growth of Halobacterium salinarum is one of the best studied halocins to date. The gene encoding this halocin had been previously identified as halH4, located on one of Hfx. mediterranei megaplasmids. We generated a mutant of the halH4 gene and examined the killing ability of the Haloferax mediterranei halH4 mutant with respect to both Halobacterium salinarum and Haloferax volcanii. We showed that both wild-type Hfx. mediterranei and the halH4 mutant strain efficiently inhibited the growth of both species, indicating halocin redundancy. Surprisingly, the halH4 deletion mutant exhibited faster growth in standard medium than the wild type, and is likely to have a better response to several nucleotides, which could explain this phenotype.},
}
@article {pmid24025872,
year = {2013},
author = {Ashok, N and Warad, S and Singh, VP and Chaudhari, H and Narayanan, A and Rodrigues, J},
title = {Prevalence of archaea in chronic periodontitis patients in an Indian population.},
journal = {Indian journal of dental research : official publication of Indian Society for Dental Research},
volume = {24},
number = {3},
pages = {289-293},
doi = {10.4103/0970-9290.117988},
pmid = {24025872},
issn = {1998-3603},
mesh = {Adult ; Archaea/*isolation &amp; purification ; Case-Control Studies ; Chronic Periodontitis/epidemiology/*microbiology ; Dental Plaque/microbiology ; Female ; Humans ; India/epidemiology ; Male ; Middle Aged ; Polymerase Chain Reaction ; Prevalence ; },
abstract = {AIM: The aim of this study was to investigate the prevalence of archaea in the subgingival crevices of patients with chronic periodontitis in an Indian population.<br><br>MATERIALS AND METHODS: Thirty four chronic periodontitis patients and 16 healthy subjects were included in the study. Thirty four subgingival plaque samples were collected from chronic periodontitis patients, of which 17 samples were from deep pockets and 17 were from shallow pockets. Sixteen subgingival plaque samples were collected from healthy subjects. The presence of archaea in plaque samples was detected by polymerase chain reaction.<br><br>RESULTS: Prevalence of archaea in chronic periodontitis patients was 29.4% and in healthy subjects was 11.8%, which was not a statistically significant difference. However, prevalence of archaea, in deep periodontal pockets was 47.1%, in shallow periodontal pockets was 11.8% and in healthy sulcus was 12.5%, respectively. Thus, showing a statistically significant difference between prevalence of archaea in deep periodontal pockets (47.1%) and healthy sulcus (12.5%) and also between deep periodontal pockets (47.1%) and shallow pockets (11.8%), respectively.<br><br>CONCLUSION: Archaea were detected commonly in severe periodontitis suggesting that these microorganisms might be involved in the pathogenesis of periodontal diseases.},
}
@article {pmid24024741,
year = {2013},
author = {Werner, F},
title = {Molecular mechanisms of transcription elongation in archaea.},
journal = {Chemical reviews},
volume = {113},
number = {11},
pages = {8331-8349},
doi = {10.1021/cr4002325},
pmid = {24024741},
issn = {1520-6890},
support = {096553//Wellcome Trust/United Kingdom ; WT096553MA/WT_/Wellcome Trust/United Kingdom ; BB/H019332/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Archaea/*enzymology/genetics/metabolism ; Archaeal Proteins/chemistry/genetics/metabolism ; DNA-Directed RNA Polymerases/chemistry/genetics/metabolism ; Promoter Regions, Genetic ; Protein Structure, Tertiary ; Protein Subunits/chemistry/genetics/metabolism ; *Transcription Elongation, Genetic ; Transcriptional Elongation Factors/genetics/metabolism ; },
}
@article {pmid24021277,
year = {2013},
author = {Kim, MK and An, YJ and Cha, SS},
title = {The crystal structure of a novel phosphopantothenate synthetase from the hyperthermophilic archaea, Thermococcus onnurineus NA1.},
journal = {Biochemical and biophysical research communications},
volume = {439},
number = {4},
pages = {533-538},
doi = {10.1016/j.bbrc.2013.09.008},
pmid = {24021277},
issn = {1090-2104},
mesh = {Adenosine Triphosphate/chemistry/metabolism ; Archaeal Proteins/*chemistry/genetics/metabolism ; Crystallography, X-Ray ; Kinetics ; Peptide Synthases/*chemistry/genetics/metabolism ; Phosphotransferases (Alcohol Group Acceptor)/chemistry/metabolism ; Thermococcus/*enzymology/metabolism ; },
abstract = {Pantothenate is the essential precursor of coenzyme A (CoA), a fundamental cofactor in all aspects of metabolism. In bacteria and eukaryotes, pantothenate synthetase (PS) catalyzes the last step in the pantothenate biosynthetic pathway, and pantothenate kinase (PanK) phosphorylates pantothenate for its entry into the CoA biosynthetic pathway. However, genes encoding PS and PanK have not been identified in archaeal genomes. Recently, a comparative genomic analysis and the identification and characterization of two novel archaea-specific enzymes show that archaeal pantoate kinase (PoK) and phosphopantothenate synthetase (PPS) represent counterparts to the PS/PanK pathway in bacteria and eukaryotes. The TON1374 protein from Thermococcus onnurineus NA1 is a PPS, that shares 54% sequence identity with the first reported archaeal PPS candidate, MM2281, from Methanosarcina mazei and 91% sequence identity with TK1686, the PPS from Thermococcus kodakarensis. Here, we report the apo and ATP-complex structures of TON1374 and discuss the substrate-binding mode and reaction mechanism.},
}
@article {pmid24018967,
year = {2013},
author = {Lee, HS},
title = {Diversity of halophilic archaea in fermented foods and human intestines and their application.},
journal = {Journal of microbiology and biotechnology},
volume = {23},
number = {12},
pages = {1645-1653},
doi = {10.4014/jmb.1308.08015},
pmid = {24018967},
issn = {1738-8872},
mesh = {Archaea/*classification/*isolation &amp; purification ; *Biodiversity ; *Food Microbiology ; Humans ; Intestines/*microbiology ; },
abstract = {Archaea are prokaryotic organisms distinct from bacteria in the structural and molecular biological sense, and these microorganisms are known to thrive mostly at extreme environments. In particular, most studies on halophilic archaea have been focused on environmental and ecological researches. However, new species of halophilic archaea are being isolated and identified from high salt-fermented foods consumed by humans, and it has been found that various types of halophilic archaea exist in food products by culture-independent molecular biological methods. In addition, even if the numbers are not quite high, DNAs of various halophilic archaea are being detected in human intestines and much interest is given to their possible roles. This review aims to summarize the types and characteristics of halophilic archaea reported to be present in foods and human intestines and to discuss their application as well.},
}
@article {pmid24005842,
year = {2013},
author = {Hong, Y and Youshao, W and Chen, F},
title = {Archaea dominate ammonia oxidizers in the permian water ecosystem of midland basin.},
journal = {Microbes and environments},
volume = {28},
number = {3},
pages = {396-399},
pmid = {24005842},
issn = {1347-4405},
mesh = {Ammonia/*metabolism ; Archaea/classification/genetics/*isolation &amp; purification/metabolism ; Biodiversity ; *Ecosystem ; Geologic Sediments/microbiology ; Molecular Sequence Data ; Oxidation-Reduction ; Phylogeny ; Seawater/*microbiology ; },
abstract = {We investigated the existence and characteristics of ammonia oxidizers in Permian water from Midland Basin. Molecular surveys targeting the amoA gene showed that only ammonia-oxidizing archaea (AOA) exist and have potential activity in this special environment. In contrast, no ammonia-oxidizing bacteria (AOB) were detected in the water. Phylogenetic analysis indicated that 72-89% of the total screened AOA clones were affiliated with those found in underground water, and 10-24% of the AOA clones were related to those found in marine water or sediments. Our results indicate AOA might be the most abundant ammonia-oxidizing microbes in this ecological niche.},
}
@article {pmid24004388,
year = {2013},
author = {Scheller, S and Goenrich, M and Thauer, RK and Jaun, B},
title = {Methyl-coenzyme M reductase from methanogenic archaea: isotope effects on the formation and anaerobic oxidation of methane.},
journal = {Journal of the American Chemical Society},
volume = {135},
number = {40},
pages = {14975-14984},
doi = {10.1021/ja406485z},
pmid = {24004388},
issn = {1520-5126},
mesh = {Anaerobiosis ; Catalytic Domain ; Isotopes ; Kinetics ; Methane/*biosynthesis/*metabolism ; Methanobacteriaceae/*enzymology ; Models, Molecular ; Oxidation-Reduction ; Oxidoreductases/chemistry/*metabolism ; },
abstract = {The nickel enzyme methyl-coenzyme M reductase (MCR) catalyzes two important transformations in the global carbon cycle: methane formation and its reverse, the anaerobic oxidation of methane. MCR uses the methyl thioether methyl-coenzyme M (CH3-S-CH2CH2-SO3(-), Me-S-CoM) and the thiol coenzyme B (CoB-SH) as substrates and converts them reversibly to methane and the corresponding heterodisulfide (CoB-S-S-CoM). The catalytic mechanism is still unknown. Here, we present isotope effects for this reaction in both directions, catalyzed by the enzyme isolated from Methanothermobacter marburgensis . For methane formation, a carbon isotope effect ((12)CH3-S-CoM/(13)CH3-S-CoM) of 1.04 ± 0.01 was measured, showing that breaking of the C-S bond in the substrate Me-S-CoM is the rate-limiting step. A secondary isotope effect of 1.19 ± 0.01 per D in the methyl group of CD3-S-CoM indicates a geometric change of the methyl group from tetrahedral to trigonal planar upon going to the transition state of the rate-limiting step. This finding is consistent with an almost free methyl radical in the highest transition state. Methane activation proceeds with a primary isotope effect of 2.44 ± 0.22 for the C-H vs C-D bond breakage and a secondary isotope effect corresponding to 1.17 ± 0.05 per D. These values are consistent with isotope effects reported for oxidative cleavage/reductive coupling occurring at transition metal centers during C-H activation but are also in the range expected for the radical substitution mechanism proposed by Siegbahn et al. The isotope effects presented here constitute boundary conditions for any suggested or calculated mechanism.},
}
@article {pmid24003767,
year = {2013},
author = {Scheller, S and Goenrich, M and Thauer, RK and Jaun, B},
title = {Methyl-coenzyme M reductase from methanogenic archaea: isotope effects on label exchange and ethane formation with the homologous substrate ethyl-coenzyme M.},
journal = {Journal of the American Chemical Society},
volume = {135},
number = {40},
pages = {14985-14995},
doi = {10.1021/ja4064876},
pmid = {24003767},
issn = {1520-5126},
mesh = {Ethane/*metabolism ; Isotopes ; Kinetics ; Mesna/*chemistry/*metabolism ; Methanosarcina barkeri/*enzymology ; Models, Molecular ; Oxidoreductases/chemistry/*metabolism ; Protein Conformation ; Sequence Homology ; },
abstract = {Ethyl-coenzyme M (CH3CH2-S-CH2CH2-SO3(-), Et-S-CoM) serves as a homologous substrate for the enzyme methyl-coenzyme M reductase (MCR) resulting in the product ethane instead of methane. The catalytic reaction proceeds via an intermediate that already contains all six C-H bonds of the product. Because product release occurs after a second, rate-limiting step, many cycles of intermediate formation and reconversion to substrate occur before a substantial amount of ethane is released. In deuterated buffer, the intermediate becomes labeled, and C-H activation in the back reaction rapidly leads to labeled Et-S-CoM, which enables intermediate formation to be detected. Here, we present a comprehensive analysis of this pre-equilibrium. (2)H- and (13)C-labeled isotopologues of Et-S-CoM were used as the substrates, and the time course of each isotopologue was followed by NMR spectroscopy. A kinetic simulation including kinetic isotope effects allowed determination of the primary and α- and β-secondary isotope effects for intermediate formation and for the C-H/C-D bond activation in the ethane-containing intermediate. The values obtained are in accordance with those found for the native substrate Me-S-CoM (see preceding publication, Scheller, S.; Goenrich, M.; Thauer, R. K.; Jaun, B. J. Am. Chem. Soc. 2013, 135, DOI: 10.1021/ja406485z) and thus imply the same catalytic mechanism for both substrates. The experiment by Floss and co-workers, demonstrating a net inversion of configuration to chiral ethane with CH3CDT-S-CoM as the substrate, is compatible with the observed rapid isotope exchange if the isotope effects measured here are taken into account.},
}
@article {pmid23994053,
year = {2014},
author = {Lorantfy, B and Seyer, B and Herwig, C},
title = {Stoichiometric and kinetic analysis of extreme halophilic Archaea on various substrates in a corrosion resistant bioreactor.},
journal = {New biotechnology},
volume = {31},
number = {1},
pages = {80-89},
doi = {10.1016/j.nbt.2013.08.003},
pmid = {23994053},
issn = {1876-4347},
mesh = {*Bioreactors ; Biotechnology/*instrumentation/*methods ; Corrosion ; Haloferax mediterranei/*drug effects ; Kinetics ; },
abstract = {Extreme halophilic Archaea are extremophile species which can thrive in hypersaline environments of up to 3-5 M sodium chloride concentration. Although their ecology and physiology are widely identified on the microbiological level, little emphasis has been laid on quantitative bioprocess development with extreme halophiles. The goal of this study was to establish, on the one hand, a methodological basis for quantitative bioprocess analysis of extreme halophilic Archaea with an extreme halophilic strain as an example. Firstly, as a novel usage, a corrosion resistant bioreactor setup for extreme halophiles has been implemented. Then, paying special attention to total bioprocess quantification approaches, an indirect method for biomass quantification using on-line process signals was introduced. Subsequently, robust quantitative data evaluation methods for halophiles could be developed, providing defined and controlled cultivation conditions in the bioreactor and therefore obtaining suitable quality of on-line as well as off-line datasets. On the other hand, new physiological results of extreme halophiles in bioreactor have also been obtained based on the quantitative methodological tools. For the first time, quantitative data on stoichiometry and kinetics were collected and evaluated on different carbon sources. The results on various substrates were interpreted, with proposed metabolic mechanisms, by linking to the reported primary carbon metabolism of extreme halophilic Archaea. Moreover, results of chemostat cultures demonstrated that extreme halophilic organisms show Monod-kinetics on different sole carbon sources. A diauxic growth pattern was described on a mixture of substrates in batch cultivations. In addition, the methodologies presented here enable one to characterize the utilized strain Haloferax mediterranei (HFX) as a potential new host organism. Thus, this study offers a strong methodological basis as well as a fundamental physiological assessment for bioreactor quantification of extreme halophiles that can serve as primary knowledge for applications of extreme halophiles in biotechnology.},
}
@article {pmid25509397,
year = {2013},
author = {Vorob'eva, LI and Khodzhaev, EIu and Novikova, TM and Muliukin, AL and Chudinova, EM and Kozlova, AN and Él'-rgistan, GI},
title = {[Stress-protective and cross action of the extracellular reactivating factor of the microorganisms of the domains Bacteria, Archaea, and Eukaryota].},
journal = {Mikrobiologiia},
volume = {82},
number = {5},
pages = {588-594},
pmid = {25509397},
issn = {0026-3656},
mesh = {*Adaptation, Physiological ; Haloarcula marismortui/*physiology ; Propionibacteriaceae/*physiology ; Saccharomyces cerevisiae/*physiology ; Stress, Physiological/*physiology ; },
abstract = {Cross protection of members of the domains Bacteria, Archaea, and lower Eukaryota from stress factors due to the action of extracellular low-molecular metabolites with adaptogenic functions was shown. The adaptogen produced by Luteococcus japonicus subsp. casei and described previously as a reactivating factor (RF) was shown to protect the yeasts Saccharomyces cerevisiae, archaea Haloarcula marismorti, and the cells of higher eukaryotes (HeLa) against weak stressor impacts. Production of an archaeal extracellular metabolite with a weak adaptogenic effect of the producer cells and capable of a threefold increase in survival of heat-inactivated yeast cells was discovered. Our results confirm the similarity of the compensatory adaptive reactions in prokaryotes (bacteria and archaea) and eukaryotes.},
}
@article {pmid23964350,
year = {2013},
author = {Aminov, RI},
title = {Role of archaea in human disease.},
journal = {Frontiers in cellular and infection microbiology},
volume = {3},
number = {},
pages = {42},
pmid = {23964350},
issn = {2235-2988},
mesh = {Archaea/*pathogenicity/*physiology ; Communicable Diseases/*etiology ; Humans ; },
}
@article {pmid23934495,
year = {2013},
author = {Gagen, EJ and Huber, H and Meador, T and Hinrichs, KU and Thomm, M},
title = {Novel cultivation-based approach to understanding the miscellaneous crenarchaeotic group (MCG) archaea from sedimentary ecosystems.},
journal = {Applied and environmental microbiology},
volume = {79},
number = {20},
pages = {6400-6406},
pmid = {23934495},
issn = {1098-5336},
support = {247153/ERC_/European Research Council/International ; },
mesh = {Cluster Analysis ; Crenarchaeota/*classification/growth &amp; development/*isolation &amp; purification ; Culture Media/*chemistry ; DNA, Archaeal/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; *Ecosystem ; Geologic Sediments/*microbiology ; Microbiological Techniques/*methods ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; },
abstract = {The uncultured miscellaneous crenarchaeotic group (MCG) archaea comprise one of the most abundant microbial groups in the Earth's subsurface environment. However, very little information is available regarding the lifestyle, physiology, and factors controlling the distribution of members of this group. We established a novel method using both cultivation and molecular techniques, including a pre-PCR propidium monoazide treatment, to investigate viable members of the MCG in vitro. Enrichment cultures prepared from estuarine sediment were provided with one of a variety of carbon substrates or cultivation conditions and incubated for 3 weeks. Compared with the samples from time zero, there was an order-of-magnitude increase in the number of MCG 16S rRNA genes in almost all cultures, indicating that MCG archaea are amenable to in vitro cultivation. None of the tested substrates or conditions significantly stimulated growth of MCG archaea more than the basal medium alone; however, glycerol (0.02%) had a significantly inhibitory effect (P < 0.05). Diversity analysis of populations resulting from four culture treatments (basal medium, addition of amino acids, H2-CO2 as the gas phase, or initial aerobic conditions) revealed that the majority of viable MCG archaea were affiliated with the MCG-8 and MCG-4 clusters. There were no significant differences in MCG diversity between these treatments, also indicating that some members of MCG-4 and MCG-8 are tolerant of initially oxic conditions. The methods outlined here will be useful for further investigation of MCG archaea and comparison of substrates and cultivation conditions that influence their growth in vitro.},
}
@article {pmid23929527,
year = {2013},
author = {Atanasova, NS and Pietilä, MK and Oksanen, HM},
title = {Diverse antimicrobial interactions of halophilic archaea and bacteria extend over geographical distances and cross the domain barrier.},
journal = {MicrobiologyOpen},
volume = {2},
number = {5},
pages = {811-825},
pmid = {23929527},
issn = {2045-8827},
mesh = {*Antibiosis ; Antimicrobial Cationic Peptides/isolation &amp; purification/metabolism/pharmacology ; Archaea/*classification/drug effects/genetics/metabolism ; Bacteria/*classification/drug effects/genetics/metabolism ; Culture Media ; DNA, Bacterial/*classification/genetics ; Ecosystem ; Europe ; Israel ; Peptides/isolation &amp; purification/metabolism/pharmacology ; *Phylogeny ; Phylogeography ; RNA, Ribosomal, 16S/*classification/genetics ; Salinity ; Sodium Chloride ; },
abstract = {The significance of antimicrobial substances, halocins, produced by halophilic archaea and bacteria thriving in hypersaline environments is relatively unknown. It is suggested that their production might increase species diversity and give transient competitive advances to the producer strain. Halocin production is considered to be common among halophilic archaea, but there is a lack of information about halocins produced by bacteria in highly saline environments. We studied the antimicrobial activity of 68 halophilic archaea and 22 bacteria isolated from numerous geographically distant hypersaline environments. Altogether 144 antimicrobial interactions were found between the strains and aside haloarchaea, halophilic bacteria from various genera were identified as halocin producers. Close to 80% of the interactions were detected between microorganisms from different genera and in few cases, even across the domain boundary. Several of the strains produced halocins with a wide inhibitory spectrum as has been observed before. Most of the antimicrobial interactions were found between strains from distant sampling sites indicating that hypersaline environments around the world have similar microorganisms with the potential to produce wide activity range antimicrobials.},
}
@article {pmid23915818,
year = {2013},
author = {Oger, PM and Cario, A},
title = {Adaptation of the membrane in Archaea.},
journal = {Biophysical chemistry},
volume = {183},
number = {},
pages = {42-56},
doi = {10.1016/j.bpc.2013.06.020},
pmid = {23915818},
issn = {1873-4200},
mesh = {*Adaptation, Physiological ; Archaea/*physiology ; Cell Membrane/chemistry ; Glyceryl Ethers/chemistry ; Membrane Lipids/*chemistry/physiology ; },
abstract = {Microbes often face contrasted and fluctuating environmental conditions, to which they need to adapt or die. Because membranes play a central role in regulating fluxes inward and outward from the cells, maintaining the appropriate structure of the membrane is crucial to maintain cellular integrity and functions. This is achieved in bacteria and eucarya by a modification of the membrane lipid compositions, a strategy termed homeoviscous adaptation. We review here evidence for homeoviscous adaptation in Archaea, and discuss the limits of this strategy and our knowledge in this very peculiar domain of life.},
}
@article {pmid23909555,
year = {2014},
author = {Ke, X and Lu, Y and Conrad, R},
title = {Different behaviour of methanogenic archaea and Thaumarchaeota in rice field microcosms.},
journal = {FEMS microbiology ecology},
volume = {87},
number = {1},
pages = {18-29},
doi = {10.1111/1574-6941.12188},
pmid = {23909555},
issn = {1574-6941},
mesh = {Archaea/classification/genetics/*isolation &amp; purification/*metabolism ; DNA, Archaeal/genetics ; Methane/*metabolism ; Nitrogen/metabolism ; Oryza/*microbiology ; Phylogeny ; Plant Roots/microbiology ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; },
abstract = {Archaea in rice fields play an important role in carbon and nitrogen cycling. They comprise methane-producing Euryarchaeota as well as ammonia-oxidizing Thaumarchaeota, but their community structures and population dynamics have not yet been studied in the same system. Different soil compartments (surface, bulk, rhizospheric soil) and ages of roots (young and old roots) at two N fertilization levels and at three time points (the panicle initiation, heading and maturity periods) of the season were assayed by determining the abundance (using qPCR) and composition (using T-RFLP and cloning/sequencing) of archaeal genes (mcrA, amoA, 16S rRNA gene). The community of total Archaea in soil and root samples mainly consisted of the methanogens and the Thaumarchaeota and their abundance increased over the season. Methanogens proliferated everywhere, but Thaumarchaeota proliferated only on the roots and in response to nitrogen fertilization. The community structures of Archaea, methanogens and Thaumarchaeota were different in soil and root samples indicating niche differentiation. While Methanobacteriales were generally present, Methanosarcinaceae and Methanocellales were the dominant methanogens in soil and root samples, respectively. The results emphasize the specific colonization of roots by two ecophysiologically different groups of archaea which may belong to the core root biome.},
}
@article {pmid23907256,
year = {2014},
author = {Yuan, J and Ding, W and Liu, D and Xiang, J and Lin, Y},
title = {Methane production potential and methanogenic archaea community dynamics along the Spartina alterniflora invasion chronosequence in a coastal salt marsh.},
journal = {Applied microbiology and biotechnology},
volume = {98},
number = {4},
pages = {1817-1829},
doi = {10.1007/s00253-013-5104-6},
pmid = {23907256},
issn = {1432-0614},
mesh = {Archaea/*metabolism ; Ecosystem ; Methane/*metabolism ; Methylamines/metabolism ; Poaceae ; Soil ; },
abstract = {Invasion by the exotic species Spartina alterniflora, which has high net primary productivity and superior reproductive capacity compared with native plants, has led to rapid organic carbon accumulation and increased methane (CH4) emission in the coastal salt marsh of China. To elucidate the mechanisms underlying this effect, the methanogen community structure and CH4 production potential as well as soil organic carbon (SOC), dissolved organic carbon, dissolved organic acids, methylated amines, aboveground biomass, and litter mass were measured during the invasion chronosequence (0-16 years). The CH4 production potential in the S. alterniflora marsh (range, 2.94-3.95 μg kg(-1) day(-1)) was significantly higher than that in the bare tidal mudflat. CH4 production potential correlated significantly with SOC, acetate, and trimethylamine concentrations in the 0-20 cm soil layer. The abundance of methanogenic archaea also correlated significantly with SOC, and the dominant species clearly varied with S. alterniflora-driven SOC accumulation. The acetotrophic Methanosaetaceae family members comprised a substantial proportion of the methanogenic archaea in the bare tidal mudflat while Methanosarcinaceae family members utilized methylated amines as substrates in the S. alterniflora marsh. Ordination analysis indicated that trimethylamine concentration was the primary factor inducing the shift in the methanogenic archaea composition, and regressive analysis indicated that the facultative family Methanosarcinaceae increased linearly with trimethylamine concentration in the increasingly sulfate-rich salt marsh. Our results indicate that increased CH4 production during the S. alterniflora invasion chronosequence was due to increased levels of the non-competitive substrate trimethylamine and a shift in the methanogenic archaea community.},
}
@article {pmid23897211,
year = {2013},
author = {Ma, B and Lv, X and Warren, A and Gong, J},
title = {Shifts in diversity and community structure of endophytic bacteria and archaea across root, stem and leaf tissues in the common reed, Phragmites australis, along a salinity gradient in a marine tidal wetland of northern China.},
journal = {Antonie van Leeuwenhoek},
volume = {104},
number = {5},
pages = {759-768},
doi = {10.1007/s10482-013-9984-3},
pmid = {23897211},
issn = {1572-9699},
mesh = {Archaea/classification/*isolation &amp; purification ; Bacteria/classification/*isolation &amp; purification ; *Biota ; China ; Endophytes/classification/*isolation &amp; purification ; Plant Leaves/microbiology ; Plant Roots/microbiology ; Plant Stems/microbiology ; Poaceae/metabolism/*microbiology ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Salts/*metabolism ; Wetlands ; },
abstract = {The effects of salt stress on endophytic prokaryotic communities in plants are largely unknown, and the distribution patterns of bacterial and archaeal endophytes in different tissues of a plant species are rarely compared. We investigated the endophytic bacterial and archaeal communities in roots, stems and leaves of the common reed, Phragmites australis, collected from three tidal zones along a salinity gradient, using terminal restriction fragment (T-RF) length polymorphism analysis of the 16S rRNA genes. The results showed that the bacterial diversity in the roots was significantly higher than that in the leaves, whereas similar archaeal diversity was revealed for either plant tissues or tidal zones. Network analysis revealed that T-RFs were grouped largely by tissue, and the major groups were generally linked by a few common T-RFs. Unique T-RFs in roots were mainly present in plants growing in the supratidal zone, but unique T-RFs in stems and leaves were mainly present in those from the middle and high tidal zones. Non-metric multidimensional scaling ordination and analysis of similarity revealed that bacterial communities were significantly different among tissues (P < 0.05), but similar among tidal zones (P = 0.49). However, the archaeal communities differed among tidal zones (P < 0.05), but were similar among tissues (P = 0.89). This study indicates that: (1) the endophytic archaeal communities are influenced more significantly than the endophytic bacterial communities by soil salinity, and (2) the differential distribution patterns of bacterial and archaeal endophytes in plant tissues along a salinity gradient imply that these two groups play different roles in coastal hydrophytes.},
}
@article {pmid23894103,
year = {2013},
author = {Kort, JC and Esser, D and Pham, TK and Noirel, J and Wright, PC and Siebers, B},
title = {A cool tool for hot and sour Archaea: proteomics of Sulfolobus solfataricus.},
journal = {Proteomics},
volume = {13},
number = {18-19},
pages = {2831-2850},
doi = {10.1002/pmic.201300088},
pmid = {23894103},
issn = {1615-9861},
support = {BB/F003420/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Archaeal Proteins/*metabolism ; Carbohydrate Metabolism ; Proteome/metabolism ; Proteomics/*methods ; Stress, Physiological ; Sulfolobus solfataricus/*metabolism ; },
abstract = {In recent years, much progress has been made in proteomic studies to unravel metabolic pathways and basic cellular processes. This is especially interesting for members of the Archaea, the third domain of life. Archaea exhibit extraordinary features and many of their cultivable representatives are adaptable to extreme environments. Archaea harbor many unique traits besides bacterial attributes, such as size, shape, and DNA structure and eukaryal characteristics like information processing. Sulfolobus solfataricus P2, a thermoacidophilic archaeal representative, is a well-established model organism adapted to low-pH environments (pH 2-3) and high temperatures (80°C). The genome has a size of 3 Mbp and its sequence has been deciphered. Approximately 3033 predicted open reading frames have been identified and the genome is characterized by a great number of diverse insertion sequence elements. In unraveling the organisms' metabolism and lifestyle, proteomic analyses have played a major role. Much effort has been directed at this organism and is reviewed here. With the help of proteomics, unique metabolic pathways were resolved in S. solfataricus, targets for regulatory protein phosphorylation identified, and cellular responses upon virus infection as well as oxidative stress analyzed.},
}
@article {pmid23893102,
year = {2013},
author = {Lindås, AC and Bernander, R},
title = {The cell cycle of archaea.},
journal = {Nature reviews. Microbiology},
volume = {11},
number = {9},
pages = {627-638},
pmid = {23893102},
issn = {1740-1534},
mesh = {Archaea/*cytology/genetics ; Cell Cycle/physiology ; Cell Division/physiology ; Chromosomes, Archaeal ; },
abstract = {Growth and proliferation of all cell types require intricate regulation and coordination of chromosome replication, genome segregation, cell division and the systems that determine cell shape. Recent findings have provided insight into the cell cycle of archaea, including the multiple-origin mode of DNA replication, the initial characterization of a genome segregation machinery and the discovery of a novel cell division system. The first archaeal cytoskeletal protein, crenactin, was also recently described and shown to function in cell shape determination. Here, we outline the current understanding of the archaeal cell cycle and cytoskeleton, with an emphasis on species in the genus Sulfolobus, and consider the major outstanding questions in the field.},
}
@article {pmid23892291,
year = {2013},
author = {Todor, H and Sharma, K and Pittman, AM and Schmid, AK},
title = {Protein-DNA binding dynamics predict transcriptional response to nutrients in archaea.},
journal = {Nucleic acids research},
volume = {41},
number = {18},
pages = {8546-8558},
pmid = {23892291},
issn = {1362-4962},
mesh = {Archaeal Proteins/*metabolism ; *Gene Expression Regulation, Archaeal ; *Gene Regulatory Networks ; Glucose/metabolism ; Halobacterium salinarum/*genetics/metabolism ; Phosphotransferases (Paired Acceptors)/genetics ; Promoter Regions, Genetic ; Transcription Factors/*metabolism ; Transcription, Genetic ; },
abstract = {Organisms across all three domains of life use gene regulatory networks (GRNs) to integrate varied stimuli into coherent transcriptional responses to environmental pressures. However, inferring GRN topology and regulatory causality remains a central challenge in systems biology. Previous work characterized TrmB as a global metabolic transcription factor in archaeal extremophiles. However, it remains unclear how TrmB dynamically regulates its ∼100 metabolic enzyme-coding gene targets. Using a dynamic perturbation approach, we elucidate the topology of the TrmB metabolic GRN in the model archaeon Halobacterium salinarum. Clustering of dynamic gene expression patterns reveals that TrmB functions alone to regulate central metabolic enzyme-coding genes but cooperates with various regulators to control peripheral metabolic pathways. Using a dynamical model, we predict gene expression patterns for some TrmB-dependent promoters and infer secondary regulators for others. Our data suggest feed-forward gene regulatory topology for cobalamin biosynthesis. In contrast, purine biosynthesis appears to require TrmB-independent regulators. We conclude that TrmB is an important component for mediating metabolic modularity, integrating nutrient status and regulating gene expression dynamics alone and in concert with secondary regulators.},
}
@article {pmid23887358,
year = {2013},
author = {Salgaonkar, BB and Mani, K and Bragança, JM},
title = {Accumulation of polyhydroxyalkanoates by halophilic archaea isolated from traditional solar salterns of India.},
journal = {Extremophiles : life under extreme conditions},
volume = {17},
number = {5},
pages = {787-795},
pmid = {23887358},
issn = {1433-4909},
mesh = {*Ecosystem ; Haloferax/classification/genetics/isolation &amp; purification/*metabolism ; India ; Phylogeny ; Polyhydroxyalkanoates/*metabolism ; *Salinity ; Salt Tolerance ; },
abstract = {Extremely halophilic archaeal isolates obtained from brine and sediment samples of solar salterns of Goa and Tamil Nadu, India were screened for accumulation of polyhydroxyalkanoates (PHA). Seven polymer accumulating haloarchaeal strains (TN4, TN5, TN6, TN7, TN9, TN10 and BBK2) were selected based on their growth and intensity of fluorescence when grown on 20 % NaCl synthetic medium supplemented with 2 % glucose and incorporated with Nile red dye. The polymer was quantified by conversion of PHA to crotonic acid which gave a characteristic absorption maxima at 235 nm. On the basis of phenotypic and genotypic characterization the cultures TN4, TN5, TN6, TN7, TN10 and BBK2 were grouped under genus Haloferax whereas isolate TN9 was grouped under the genus Halogeometricum. Growth kinetics and polymer accumulation studies revealed that the culture Halogeometricum borinquense strain TN9 accumulates PHA maximally at the mid-log phase, i.e. 5th day of growth (approx. 14 wt% PHA of CDW). Analysis of the polymer by IR, (1)H NMR and (13)C NMR confirmed it to be a homopolymer of 3-hydroxybutyrate.},
}
@article {pmid23880418,
year = {2013},
author = {Swanson, CA and Sliwinski, MK},
title = {One-dimensional TRFLP-SSCP is an effective DNA fingerprinting strategy for soil Archaea that is able to simultaneously differentiate broad taxonomic clades based on terminal fragment length polymorphisms and closely related sequences based on single stranded conformation polymorphisms.},
journal = {Journal of microbiological methods},
volume = {94},
number = {3},
pages = {317-324},
doi = {10.1016/j.mimet.2013.07.003},
pmid = {23880418},
issn = {1872-8359},
mesh = {*Archaea/classification/genetics/isolation &amp; purification ; DNA Fingerprinting/*methods ; Gene Library ; Genes, Archaeal/genetics ; Iowa ; Phylogeny ; Polymorphism, Restriction Fragment Length/*genetics ; Polymorphism, Single-Stranded Conformational/*genetics ; *Soil Microbiology ; },
abstract = {DNA fingerprinting methods provide a means to rapidly compare microbial assemblages from environmental samples without the need to first cultivate species in the laboratory. The profiles generated by these techniques are able to identify statistically significant temporal and spatial patterns, correlations to environmental gradients, and biological variability to estimate the number of replicates for clone libraries or next generation sequencing (NGS) surveys. Here we describe an improved DNA fingerprinting technique that combines terminal restriction fragment length polymorphisms (TRFLP) and single stranded conformation polymorphisms (SSCP) so that both can be used to profile a sample simultaneously rather than requiring two sequential steps as in traditional two-dimensional (2-D) gel electrophoresis. For the purpose of profiling Archaeal 16S rRNA genes from soil, the dynamic range of this combined 1-D TRFLP-SSCP approach was superior to TRFLP and SSCP. 1-D TRFLP-SSCP was able to distinguish broad taxonomic clades with genetic distances greater than 10%, such as Euryarchaeota and the Thaumarchaeal clades g_Ca. Nitrososphaera (formerly 1.1b) and o_NRP-J (formerly 1.1c) better than SSCP. In addition, 1-D TRFLP-SSCP was able to simultaneously distinguish closely related clades within a genus such as s_SCA1145 and s_SCA1170 better than TRFLP. We also tested the utility of 1-D TRFLP-SSCP fingerprinting of environmental assemblages by comparing this method to the generation of a 16S rRNA clone library of soil Archaea from a restored Tallgrass prairie. This study shows 1-D TRFLP-SSCP fingerprinting provides a rapid and phylogenetically informative screen of Archaeal 16S rRNA genes in soil samples.},
}
@article {pmid23865623,
year = {2013},
author = {Yelton, AP and Comolli, LR and Justice, NB and Castelle, C and Denef, VJ and Thomas, BC and Banfield, JF},
title = {Comparative genomics in acid mine drainage biofilm communities reveals metabolic and structural differentiation of co-occurring archaea.},
journal = {BMC genomics},
volume = {14},
number = {},
pages = {485},
pmid = {23865623},
issn = {1471-2164},
mesh = {Aerobiosis/genetics ; Aldehyde Oxidoreductases/genetics ; Amino Acids/biosynthesis ; *Biofilms ; Cell Wall/metabolism ; Drug Resistance/genetics ; Electron Transport ; Energy Metabolism/genetics ; Fermentation ; Genes, Archaeal/genetics ; Genomic Islands/genetics ; *Genomics ; Glyoxylates/metabolism ; Hydrogen-Ion Concentration ; Iron/metabolism ; Metals/toxicity ; *Mining ; Molecular Imaging ; Molecular Sequence Annotation ; Multienzyme Complexes/genetics ; Phylogeny ; Thermoplasmales/cytology/*genetics/metabolism/*physiology ; Trehalose/biosynthesis ; },
abstract = {BACKGROUND: Metal sulfide mineral dissolution during bioleaching and acid mine drainage (AMD) formation creates an environment that is inhospitable to most life. Despite dominance by a small number of bacteria, AMD microbial biofilm communities contain a notable variety of coexisting and closely related Euryarchaea, most of which have defied cultivation efforts. For this reason, we used metagenomics to analyze variation in gene content that may contribute to niche differentiation among co-occurring AMD archaea. Our analyses targeted members of the Thermoplasmatales and related archaea. These results greatly expand genomic information available for this archaeal order.<br><br>RESULTS: We reconstructed near-complete genomes for uncultivated, relatively low abundance organisms A-, E-, and Gplasma, members of Thermoplasmatales order, and for a novel organism, Iplasma. Genomic analyses of these organisms, as well as Ferroplasma type I and II, reveal that all are facultative aerobic heterotrophs with the ability to use many of the same carbon substrates, including methanol. Most of the genomes share genes for toxic metal resistance and surface-layer production. Only Aplasma and Eplasma have a full suite of flagellar genes whereas all but the Ferroplasma spp. have genes for pili production. Cryogenic-electron microscopy (cryo-EM) and tomography (cryo-ET) strengthen these metagenomics-based ultrastructural predictions. Notably, only Aplasma, Gplasma and the Ferroplasma spp. have predicted iron oxidation genes and Eplasma and Iplasma lack most genes for cobalamin, valine, (iso)leucine and histidine synthesis.<br><br>CONCLUSION: The Thermoplasmatales AMD archaea share a large number of metabolic capabilities. All of the uncultivated organisms studied here (A-, E-, G-, and Iplasma) are metabolically very similar to characterized Ferroplasma spp., differentiating themselves mainly in their genetic capabilities for biosynthesis, motility, and possibly iron oxidation. These results indicate that subtle, but important genomic differences, coupled with unknown differences in gene expression, distinguish these organisms enough to allow for co-existence. Overall this study reveals shared features of organisms from the Thermoplasmatales lineage and provides new insights into the functioning of AMD communities.},
}
@article {pmid23853523,
year = {2013},
author = {Emerson, JB and Andrade, K and Thomas, BC and Norman, A and Allen, EE and Heidelberg, KB and Banfield, JF},
title = {Virus-host and CRISPR dynamics in Archaea-dominated hypersaline Lake Tyrrell, Victoria, Australia.},
journal = {Archaea (Vancouver, B.C.)},
volume = {2013},
number = {},
pages = {370871},
pmid = {23853523},
issn = {1472-3654},
mesh = {Archaea/*genetics/metabolism ; Bacteria/*genetics/metabolism ; DNA, Archaeal/analysis/genetics ; DNA, Bacterial/analysis/genetics ; DNA, Intergenic/analysis/genetics ; DNA, Viral/analysis/genetics ; *Inverted Repeat Sequences ; Lakes/*microbiology ; Metagenomics ; Microbial Consortia/*genetics ; Plankton ; RNA, Ribosomal, 16S/genetics ; *Salinity ; Victoria ; Viruses/*genetics/metabolism ; },
abstract = {The study of natural archaeal assemblages requires community context, namely, a concurrent assessment of the dynamics of archaeal, bacterial, and viral populations. Here, we use filter size-resolved metagenomic analyses to report the dynamics of 101 archaeal and bacterial OTUs and 140 viral populations across 17 samples collected over different timescales from 2007-2010 from Australian hypersaline Lake Tyrrell (LT). All samples were dominated by Archaea (75-95%). Archaeal, bacterial, and viral populations were found to be dynamic on timescales of months to years, and different viral assemblages were present in planktonic, relative to host-associated (active and provirus) size fractions. Analyses of clustered regularly interspaced short palindromic repeat (CRISPR) regions indicate that both rare and abundant viruses were targeted, primarily by lower abundance hosts. Although very few spacers had hits to the NCBI nr database or to the 140 LT viral populations, 21% had hits to unassembled LT viral concentrate reads. This suggests local adaptation to LT-specific viruses and/or undersampling of haloviral assemblages in public databases, along with successful CRISPR-mediated maintenance of viral populations at abundances low enough to preclude genomic assembly. This is the first metagenomic report evaluating widespread archaeal dynamics at the population level on short timescales in a hypersaline system.},
}
@article {pmid23849004,
year = {2013},
author = {Rusch, A and Gaidos, E},
title = {Nitrogen-cycling bacteria and archaea in the carbonate sediment of a coral reef.},
journal = {Geobiology},
volume = {11},
number = {5},
pages = {472-484},
doi = {10.1111/gbi.12048},
pmid = {23849004},
issn = {1472-4669},
mesh = {Archaea/classification/*genetics/*metabolism ; Archaeal Proteins/genetics/metabolism ; Bacteria/classification/*genetics/*metabolism ; Bacterial Proteins/genetics/metabolism ; Carbonates/metabolism ; Coral Reefs ; Geologic Sediments/chemistry/*microbiology ; Hawaii ; Molecular Sequence Data ; Nitrates/metabolism ; Nitrites/metabolism ; *Nitrogen Cycle ; Oxidation-Reduction ; Phylogeny ; Real-Time Polymerase Chain Reaction ; Seawater/chemistry/microbiology ; Sequence Analysis, DNA ; },
abstract = {In the coarse-grained carbonate sediments of coral reefs, advective porewater flow and the respiration of organic matter establish redox zones that are the scene of microbially mediated transformations of N compounds. To investigate the geobiology of N cycling in reef sediments, the benthic microbiota of Checker Reef in Kaneohe Bay, Hawaii, were surveyed for candidate nitrate reducers, ammonifying nitrite reducers, aerobic and anaerobic ammonia oxidizers (anammox) by identifying phylotypes of their key metabolic genes (napA, narG, nrfA, amoA) and ribotypes (unique RNA sequences) of anammox-like 16S rRNA. Putative proteobacteria with the catalytic potential for nitrate reduction were identified in oxic, interfacial and anoxic habitats. The estimated richness of napA (≥202 in anoxic sediment) and narG (≥373 and ≥441 in oxic and interfacial sediment, respectively) indicates a diverse guild of nitrate reducers. The guild of nrfA hosts in interfacial reef sediment was dominated by Vibrio species. The identified members of the aerobic ammonium oxidizing guild (amoA hosts) were Crenarchaeota or close relatives of Nitrosomonadales. Putative anammox bacteria were detected in the RNA pool of Checker Reef sediment. More than half of these ribotypes show ≥90% identity with homologous sequences of Scalindua spp., while no evidence was found for members of the genera Brocadia or Kuenenia. In addition to exploring the diversity of these four nitrogen-cycling microbial guilds in coral reef sediments, the abundances of aerobic ammonium oxidizers (amoA), nitrite oxidizers (nxrAB), ammonifying nitrite reducers (nrfA) and denitrifiers (nosZ) were estimated using real-time PCR. Representatives of all targeted guilds were detected, suggesting that most processes of the biogeochemical N cycle can be catalyzed by the benthic microbiota of tropical coral reefs.},
}
@article {pmid23847601,
year = {2013},
author = {Peng, X and Jayakumar, A and Ward, BB},
title = {Community composition of ammonia-oxidizing archaea from surface and anoxic depths of oceanic oxygen minimum zones.},
journal = {Frontiers in microbiology},
volume = {4},
number = {},
pages = {177},
pmid = {23847601},
issn = {1664-302X},
abstract = {Ammonia-oxidizing archaea (AOA) have been reported at high abundance in much of the global ocean, even in environments, such as pelagic oxygen minimum zones (OMZs), where conditions seem unlikely to support aerobic ammonium oxidation. Due to the lack of information on any potential alternative metabolism of AOA, the AOA community composition might be expected to differ between oxic and anoxic environments. This hypothesis was tested by evaluating AOA community composition using a functional gene microarray that targets the ammonia monooxygenase gene subunit A (amoA). The relationship between environmental parameters and the biogeography of the Arabian Sea and the Eastern Tropical South Pacific (ETSP) AOA assemblages was investigated using principal component analysis (PCA) and redundancy analysis (RDA). In both the Arabian Sea and the ETSP, AOA communities within the core of the OMZ were not significantly different from those inhabiting the oxygenated surface waters above the OMZ. The AOA communities in the Arabian Sea were significantly different from those in the ETSP. In both oceans, the abundance of archaeal amoA gene in the core of the OMZ was higher than that in the surface waters. Our results indicate that AOA communities are distinguished by their geographic origin. RDA suggested that temperature (higher in the Arabian Sea than in the ETSP) was the main factor that correlated with the differences between the AOA communities. Physicochemical properties that characterized the different environments of the OMZ and surface waters played a less important role, than did geography, in shaping the AOA community composition.},
}
@article {pmid23843726,
year = {2013},
author = {Hoppert, M and Krüger, M and Reitner, J and Cockell, C},
title = {Archaea in past and present geobiochemical processes and elemental cycles.},
journal = {Archaea (Vancouver, B.C.)},
volume = {2013},
number = {},
pages = {930493},
doi = {10.1155/2013/930493},
pmid = {23843726},
issn = {1472-3654},
mesh = {Archaea/classification/genetics/*physiology ; Biodiversity ; Methane/chemistry ; Soil Microbiology ; },
}
@article {pmid23841049,
year = {2013},
author = {Sosa, D and Miramontes, P and Li, W and Mireles, V and Bobadilla, JR and José, MV},
title = {Periodic distribution of a putative nucleosome positioning motif in human, nonhuman primates, and archaea: mutual information analysis.},
journal = {International journal of genomics},
volume = {2013},
number = {},
pages = {963956},
pmid = {23841049},
issn = {2314-436X},
abstract = {Recently, Trifonov's group proposed a 10-mer DNA motif YYYYYRRRRR as a solution of the long-standing problem of sequence-based nucleosome positioning. To test whether this generic decamer represents a biological meaningful signal, we compare the distribution of this motif in primates and Archaea, which are known to contain nucleosomes, and in Eubacteria, which do not possess nucleosomes. The distribution of the motif is analyzed by the mutual information function (MIF) with a shifted version of itself (MIF profile). We found common features in the patterns of this generic decamer on MIF profiles among primate species, and interestingly we found conspicuous but dissimilar MIF profiles for each Archaea tested. The overall MIF profiles for each chromosome in each primate species also follow a similar pattern. Trifonov's generic decamer may be a highly conserved motif for the nucleosome positioning, but we argue that this is not the only motif. The distribution of this generic decamer exhibits previously unidentified periodicities, which are associated to highly repetitive sequences in the genome. Alu repetitive elements contribute to the most fundamental structure of nucleosome positioning in higher Eukaryotes. In some regions of primate chromosomes, the distribution of the decamer shows symmetrical patterns including inverted repeats.},
}
@article {pmid23832972,
year = {2013},
author = {Zhang, WY and Huo, YY and Zhang, XQ and Zhu, XF and Wu, M},
title = {Halolamina salifodinae sp. nov. and Halolamina salina sp. nov., two extremely halophilic archaea isolated from a salt mine.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {63},
number = {Pt 12},
pages = {4380-4385},
doi = {10.1099/ijs.0.050864-0},
pmid = {23832972},
issn = {1466-5034},
mesh = {Base Composition ; China ; DNA, Archaeal/genetics ; Glycolipids/chemistry ; Halobacteriaceae/*classification/genetics/isolation &amp; purification ; *Mining ; Molecular Sequence Data ; Nucleic Acid Hybridization ; Phosphatidylglycerols/chemistry ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Sodium Chloride ; },
abstract = {Two strictly aerobic, extremely halophilic archaea, strains WSY15-H1(T) and WSY15-H3(T), were isolated from a salt mine in Wensu county, Xinjiang province, China. Cells of the two strains were Gram-stain-negative, non-motile and pleomorphic. Colonies were pink- and red-pigmented, respectively. Strain WSY15-H1(T) grew at 20-45 °C (optimum 37-42 °C), 1.6-5.4 M NaCl (optimum 3.4-3.9 M), 0-2.0 M MgCl2 (optimum 0.1-0.5 M) and pH 6.0-9.0 (optimum 7.0), whereas strain WSY15-H3(T) grew at 20-50 °C (optimum 37 °C), 1.9-5.4 M NaCl (optimum 3.4 M), 0.02-2.5 M MgCl2 (optimum 0.5-1.0 M) and pH 6.0-7.5 (optimum 6.5). The minimal NaCl concentrations to prevent cell lysis were 9 % (w/v) for strain WSY15-H1(T) and 8 % (w/v) for strain WSY15-H3(T). The major polar lipids of the two isolates were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester and phosphatidylglycerol sulfate, as well as nine glycolipids for strain WSY15-H1(T) and seven glycolipids for strain WSY15-H3(T); two of these glycolipids (GL1 and GL3) were chromatographically identical to bis-sulfated diglycosyl diether (S2-DGD-1) and sulfated diglycosyl diether (S-DGD-1), respectively. The genomic DNA G+C contents of strains WSY15-H1(T) and WSY15-H3(T) were 65.4 and 66.2 mol%. On the basis of 16S rRNA gene sequence analysis, strains WSY15-H1(T) and WSY15-H3(T) shared 97.0% similarity with each other and showed respectively 98.4 and 97.6% sequence similarity to Halolamina pelagica TBN21(T), which was the only type strain that had higher than 91% sequence similarity with the two isolates. Analysis of phylogenetic relationships and DNA-DNA relatedness indicated that strains WSY15-H1(T) and WSY15-H3(T) represent two novel lineages with closest affinity to H. pelagica TBN21(T). Based on phenotypic, chemotaxonomic and genotypic characteristics, two novel species of the genus Halolamina are proposed, Halolamina salifodinae sp. nov. (type strain WSY15-H1(T) = JCM 18548(T) = GCMCC 1.12371(T)) and Halolamina salina sp. nov. (type strain WSY15-H3(T) = JCM 18549(T) = GCMCC 1.12285(T)).},
}
@article {pmid23826954,
year = {2013},
author = {Hou, J and Cao, X and Song, C and Zhou, Y},
title = {Predominance of ammonia-oxidizing archaea and nirK-gene-bearing denitrifiers among ammonia-oxidizing and denitrifying populations in sediments of a large urban eutrophic lake (Lake Donghu).},
journal = {Canadian journal of microbiology},
volume = {59},
number = {7},
pages = {456-464},
doi = {10.1139/cjm-2013-0083},
pmid = {23826954},
issn = {1480-3275},
mesh = {Ammonia/*metabolism ; Archaea/*classification/genetics/isolation &amp; purification/metabolism ; Bacteria/*classification/genetics/isolation &amp; purification/metabolism ; Biodiversity ; Cities ; Crenarchaeota/genetics/isolation &amp; purification/metabolism ; Denitrification ; *Eutrophication ; Genes, Archaeal ; Genes, Bacterial ; Geologic Sediments/microbiology ; Lakes/*microbiology ; Nitrite Reductases/genetics ; Oxidation-Reduction ; Oxidoreductases/genetics ; },
abstract = {The coupled nitrification-denitrification process plays a pivotal role in cycling and removal of nitrogen in aquatic ecosystems. In the present study, the communities of ammonia oxidizers and denitrifiers in the sediments of 2 basins (Guozhenghu Basin and Tuanhu Basin) of a large urban eutrophic lake (Lake Donghu) were determined using the ammonia monooxygenase subunit A (amoA) gene and the nitrite reductase gene. At all sites of this study, the archaeal amoA gene predominated over the bacterial amoA gene, whereas the functional gene for denitrification nirK gene far outnumbered the nirS gene. Spatially, compared with the Tuanhu Basin, the Guozhenghu Basin showed a significantly greater abundance of the archaeal amoA gene but less abundance of the nirK and nirS genes, while there was no significant difference of bacterial amoA gene copy numbers between the 2 basins. Unlike the archaeal amoA gene, the nirK gene showed a significant difference in community structure between the 2 basins. Archaeal amoA diversity was limited to the water-sediment cluster of Crenarchaeota, in sharp contrast with nirK for which 22 distinct operational taxonomic units were found. Accumulation of organic substances were found to be positively related to nirK and nirS gene copy numbers but negatively related to archaeal amoA gene copy numbers, whereas the abundance of the bacterial amoA gene was related to ammonia concentration.},
}
@article {pmid23825970,
year = {2013},
author = {Edelheit, S and Schwartz, S and Mumbach, MR and Wurtzel, O and Sorek, R},
title = {Transcriptome-wide mapping of 5-methylcytidine RNA modifications in bacteria, archaea, and yeast reveals m5C within archaeal mRNAs.},
journal = {PLoS genetics},
volume = {9},
number = {6},
pages = {e1003602},
pmid = {23825970},
issn = {1553-7404},
mesh = {Archaea/genetics ; Bacillus subtilis/genetics ; Cytidine/*analogs &amp; derivatives/genetics ; Escherichia coli/genetics ; Gene Expression Profiling ; Genome ; High-Throughput Nucleotide Sequencing ; *Methylation ; RNA, Messenger/*genetics ; RNA, Ribosomal/*genetics ; RNA, Transfer/*genetics ; Saccharomyces cerevisiae/genetics ; },
abstract = {The presence of 5-methylcytidine (m(5)C) in tRNA and rRNA molecules of a wide variety of organisms was first observed more than 40 years ago. However, detection of this modification was limited to specific, abundant, RNA species, due to the usage of low-throughput methods. To obtain a high resolution, systematic, and comprehensive transcriptome-wide overview of m(5)C across the three domains of life, we used bisulfite treatment on total RNA from both gram positive (B. subtilis) and gram negative (E. coli) bacteria, an archaeon (S. solfataricus) and a eukaryote (S. cerevisiae), followed by massively parallel sequencing. We were able to recover most previously documented m(5)C sites on rRNA in the four organisms, and identified several novel sites in yeast and archaeal rRNAs. Our analyses also allowed quantification of methylated m(5)C positions in 64 tRNAs in yeast and archaea, revealing stoichiometric differences between the methylation patterns of these organisms. Molecules of tRNAs in which m(5)C was absent were also discovered. Intriguingly, we detected m(5)C sites within archaeal mRNAs, and identified a consensus motif of AUCGANGU that directs methylation in S. solfataricus. Our results, which were validated using m(5)C-specific RNA immunoprecipitation, provide the first evidence for mRNA modifications in archaea, suggesting that this mode of post-transcriptional regulation extends beyond the eukaryotic domain.},
}
@article {pmid23822830,
year = {2013},
author = {Takano, K and Aoi, A and Koga, Y and Kanaya, S},
title = {Evolvability of thermophilic proteins from archaea and bacteria.},
journal = {Biochemistry},
volume = {52},
number = {28},
pages = {4774-4780},
doi = {10.1021/bi400652c},
pmid = {23822830},
issn = {1520-4995},
mesh = {Archaeal Proteins/*chemistry/genetics ; Bacterial Proteins/*chemistry/genetics ; *Directed Molecular Evolution ; Models, Molecular ; Polymerase Chain Reaction ; Temperature ; },
abstract = {Proteins from thermophiles possess high thermostability. The stabilization mechanisms differ between archaeal and bacterial proteins, whereby archaeal proteins are mainly stabilized via hydrophobic interactions and bacterial proteins by ion pairs. High stability is an important factor in promoting protein evolution, but the precise means by which different stabilization mechanisms affect the evolution process remain unclear. In this study, we investigated a random mutational drift of esterases from thermophilic archaea and bacteria at high temperatures. Our results indicate that mutations in archaeal proteins lead to improved function with no loss of stability, while mutant bacterial proteins are largely destabilized with decreased activity at high temperatures. On the basis of these findings, we suggest that archaeal proteins possess higher "evolvability" than bacterial proteins under temperature selection and are additionally able to evolve into eukaryotic proteins.},
}
@article {pmid23818497,
year = {2013},
author = {O'Donnell, M and Langston, L and Stillman, B},
title = {Principles and concepts of DNA replication in bacteria, archaea, and eukarya.},
journal = {Cold Spring Harbor perspectives in biology},
volume = {5},
number = {7},
pages = {},
pmid = {23818497},
issn = {1943-0264},
support = {R37 GM038839/GM/NIGMS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; P30 CA045508/CA/NCI NIH HHS/United States ; P01 CA013106/CA/NCI NIH HHS/United States ; R01 GM038839/GM/NIGMS NIH HHS/United States ; CA13016/CA/NCI NIH HHS/United States ; GM38839/GM/NIGMS NIH HHS/United States ; GM45436/GM/NIGMS NIH HHS/United States ; R01 GM045436/GM/NIGMS NIH HHS/United States ; },
mesh = {Archaea/*genetics ; Bacteria/*genetics ; DNA Damage ; DNA Replication/*physiology ; Eukaryota/*genetics ; *Models, Genetic ; },
abstract = {The accurate copying of genetic information in the double helix of DNA is essential for inheritance of traits that define the phenotype of cells and the organism. The core machineries that copy DNA are conserved in all three domains of life: bacteria, archaea, and eukaryotes. This article outlines the general nature of the DNA replication machinery, but also points out important and key differences. The most complex organisms, eukaryotes, have to coordinate the initiation of DNA replication from many origins in each genome and impose regulation that maintains genomic integrity, not only for the sake of each cell, but for the organism as a whole. In addition, DNA replication in eukaryotes needs to be coordinated with inheritance of chromatin, developmental patterning of tissues, and cell division to ensure that the genome replicates once per cell division cycle.},
}
@article {pmid23808334,
year = {2013},
author = {Offre, P and Spang, A and Schleper, C},
title = {Archaea in biogeochemical cycles.},
journal = {Annual review of microbiology},
volume = {67},
number = {},
pages = {437-457},
doi = {10.1146/annurev-micro-092412-155614},
pmid = {23808334},
issn = {1545-3251},
support = {I 487/FWF_/Austrian Science Fund FWF/Austria ; },
mesh = {Anaerobiosis ; Archaea/classification/genetics/*metabolism ; Carbon/metabolism ; *Ecological and Environmental Phenomena ; Methane/metabolism ; Nitrogen/metabolism ; Oxidation-Reduction ; Phylogeny ; Sulfates/metabolism ; },
abstract = {Archaea constitute a considerable fraction of the microbial biomass on Earth. Like Bacteria they have evolved a variety of energy metabolisms using organic and/or inorganic electron donors and acceptors, and many of them are able to fix carbon from inorganic sources. Archaea thus play crucial roles in the Earth's global geochemical cycles and influence greenhouse gas emissions. Methanogenesis and anaerobic methane oxidation are important steps in the carbon cycle; both are performed exclusively by anaerobic archaea. Oxidation of ammonia to nitrite is performed by Thaumarchaeota. They represent the only archaeal group that resides in large numbers in the global aerobic terrestrial and marine environments on Earth. Sulfur-dependent archaea are confined mostly to hot environments, but metal leaching by acidophiles and reduction of sulfate by anaerobic, nonthermophilic methane oxidizers have a potential impact on the environment. The metabolisms of a large number of archaea, in particular those dominating the subsurface, remain to be explored.},
}
@article {pmid25509388,
year = {2013},
author = {Korneeva, VA and Briukhanov, AL and Pimenov, NV},
title = {[Molecular biology detection of methanogenic archaea in oxidised water of Black sea].},
journal = {Mikrobiologiia},
volume = {82},
number = {4},
pages = {510-512},
pmid = {25509388},
issn = {0026-3656},
mesh = {Black Sea ; *Euryarchaeota/classification/genetics/isolation &amp; purification ; Oxidation-Reduction ; *Water Microbiology ; },
}
@article {pmid23806640,
year = {2013},
author = {Toffano-Nioche, C and Luo, Y and Kuchly, C and Wallon, C and Steinbach, D and Zytnicki, M and Jacq, A and Gautheret, D},
title = {Detection of non-coding RNA in bacteria and archaea using the DETR'PROK Galaxy pipeline.},
journal = {Methods (San Diego, Calif.)},
volume = {63},
number = {1},
pages = {60-65},
doi = {10.1016/j.ymeth.2013.06.003},
pmid = {23806640},
issn = {1095-9130},
mesh = {Archaea/genetics ; Bacteria/genetics ; Base Sequence ; Computational Biology/*methods ; High-Throughput Nucleotide Sequencing/*methods ; RNA, Messenger/genetics/*isolation &amp; purification ; RNA, Untranslated/genetics/*isolation &amp; purification ; },
abstract = {RNA-seq experiments are now routinely used for the large scale sequencing of transcripts. In bacteria or archaea, such deep sequencing experiments typically produce 10-50 million fragments that cover most of the genome, including intergenic regions. In this context, the precise delineation of the non-coding elements is challenging. Non-coding elements include untranslated regions (UTRs) of mRNAs, independent small RNA genes (sRNAs) and transcripts produced from the antisense strand of genes (asRNA). Here we present a computational pipeline (DETR'PROK: detection of ncRNAs in prokaryotes) based on the Galaxy framework that takes as input a mapping of deep sequencing reads and performs successive steps of clustering, comparison with existing annotation and identification of transcribed non-coding fragments classified into putative 5' UTRs, sRNAs and asRNAs. We provide a step-by-step description of the protocol using real-life example data sets from Vibrio splendidus and Escherichia coli.},
}
@article {pmid23799070,
year = {2013},
author = {Hoffmann, C and Dollive, S and Grunberg, S and Chen, J and Li, H and Wu, GD and Lewis, JD and Bushman, FD},
title = {Archaea and fungi of the human gut microbiome: correlations with diet and bacterial residents.},
journal = {PloS one},
volume = {8},
number = {6},
pages = {e66019},
pmid = {23799070},
issn = {1932-6203},
support = {R01 DK089472/DK/NIDDK NIH HHS/United States ; UH2 DK083981/DK/NIDDK NIH HHS/United States ; UH3 DK083981/DK/NIDDK NIH HHS/United States ; UH2/3 DK083981/DK/NIDDK NIH HHS/United States ; K24 DK078228/DK/NIDDK NIH HHS/United States ; P30 DK050306/DK/NIDDK NIH HHS/United States ; S10 RR024525/RR/NCRR NIH HHS/United States ; UL1RR024134/RR/NCRR NIH HHS/United States ; DK 089472/DK/NIDDK NIH HHS/United States ; K24-DK078228/DK/NIDDK NIH HHS/United States ; S10RR024525/RR/NCRR NIH HHS/United States ; UL1 RR024134/RR/NCRR NIH HHS/United States ; },
mesh = {Archaea/classification/*isolation &amp; purification ; Bacteria/classification/*isolation &amp; purification ; *Diet ; Fungi/classification/*isolation &amp; purification ; Humans ; Intestines/*microbiology ; *Microbiota ; },
abstract = {Diet influences health as a source of nutrients and toxins, and by shaping the composition of resident microbial populations. Previous studies have begun to map out associations between diet and the bacteria and viruses of the human gut microbiome. Here we investigate associations of diet with fungal and archaeal populations, taking advantage of samples from 98 well-characterized individuals. Diet was quantified using inventories scoring both long-term and recent diet, and archaea and fungi were characterized by deep sequencing of marker genes in DNA purified from stool. For fungi, we found 66 genera, with generally mutually exclusive presence of either the phyla Ascomycota or Basiodiomycota. For archaea, Methanobrevibacter was the most prevalent genus, present in 30% of samples. Several other archaeal genera were detected in lower abundance and frequency. Myriad associations were detected for fungi and archaea with diet, with each other, and with bacterial lineages. Methanobrevibacter and Candida were positively associated with diets high in carbohydrates, but negatively with diets high in amino acids, protein, and fatty acids. A previous study emphasized that bacterial population structure was associated primarily with long-term diet, but high Candida abundance was most strongly associated with the recent consumption of carbohydrates. Methobrevibacter abundance was associated with both long term and recent consumption of carbohydrates. These results confirm earlier targeted studies and provide a host of new associations to consider in modeling the effects of diet on the gut microbiome and human health.},
}
@article {pmid23794621,
year = {2013},
author = {VanNice, JC and Skaff, DA and Wyckoff, GJ and Miziorko, HM},
title = {Expression in Haloferax volcanii of 3-hydroxy-3-methylglutaryl coenzyme A synthase facilitates isolation and characterization of the active form of a key enzyme required for polyisoprenoid cell membrane biosynthesis in halophilic archaea.},
journal = {Journal of bacteriology},
volume = {195},
number = {17},
pages = {3854-3862},
pmid = {23794621},
issn = {1098-5530},
mesh = {Acyl Coenzyme A/metabolism ; Amino Acid Sequence ; Cell Membrane/*enzymology/*metabolism ; Enzyme Inhibitors/metabolism ; Gene Expression ; Gene Expression Regulation, Archaeal ; Gene Expression Regulation, Enzymologic ; Haloferax volcanii/*enzymology/genetics/*metabolism ; Hydroxymethylglutaryl-CoA Synthase/*genetics ; Kinetics ; Molecular Sequence Data ; Plasmids ; Sequence Alignment ; Terpenes/*metabolism ; },
abstract = {Enzymes of the isoprenoid biosynthetic pathway in halophilic archaea remain poorly characterized, and parts of the pathway remain cryptic. This situation may be explained, in part, by the difficulty of expressing active, functional recombinant forms of these enzymes. The use of newly available expression plasmids and hosts has allowed the expression and isolation of catalytically active Haloferax volcanii 3-hydroxy-3-methylglutaryl coenzyme A (CoA) synthase (EC 2.3.310). This accomplishment has permitted studies that represent, to the best of our knowledge, the first characterization of an archaeal hydroxymethylglutaryl CoA synthase. Kinetic characterization indicates that, under optimal assay conditions, which include 4 M KCl, the enzyme exhibits catalytic efficiency and substrate saturation at metabolite levels comparable to those reported for the enzyme from nonhalophilic organisms. This enzyme is unique in that it is the first hydroxymethylglutaryl CoA synthase that is insensitive to feedback substrate inhibition by acetoacetyl-CoA. The enzyme supports reaction catalysis in the presence of various organic solvents. Haloferax 3-hydroxy-3-methylglutaryl CoA synthase is sensitive to inactivation by hymeglusin, a specific inhibitor known to affect prokaryotic and eukaryotic forms of the enzyme, with experimentally determined Ki and kinact values of 570 ± 120 nM and 17 ± 3 min(-1), respectively. In in vivo experiments, hymeglusin blocks the propagation of H. volcanii cells, indicating the critical role that the mevalonate pathway plays in isoprenoid biosynthesis by these archaea.},
}
@article {pmid23792929,
year = {2013},
author = {Tan, H and Xu, M and Li, X and Zhang, H and Zhang, C},
title = {Effects of chlorimuron-ethyl application with or without urea fertilization on soil ammonia-oxidizing bacteria and archaea.},
journal = {Journal of hazardous materials},
volume = {260},
number = {},
pages = {368-374},
doi = {10.1016/j.jhazmat.2013.05.043},
pmid = {23792929},
issn = {1873-3336},
mesh = {Ammonia/chemistry ; Archaea/*drug effects ; Bacteria/*drug effects ; Fertilizers ; Herbicides ; Hydrogen-Ion Concentration ; Nitrification ; Nitrogen/chemistry ; Oxidoreductases/genetics ; Pyrimidines/*chemistry ; Real-Time Polymerase Chain Reaction ; Soil/chemistry ; Soil Microbiology ; Soil Pollutants/*analysis ; Sulfonylurea Compounds/*chemistry ; Temperature ; Urea/*chemistry ; },
abstract = {Chlorimuron-ethyl (CE) has been widely used in modern agriculture, but little is known regarding the influence of CE on ammonia-oxidizing bacteria (AOB) and archaea (AOA) populations in soils. In this study, microcosm incubation of aquic brown soil was conducted for 60 d. Associated changes in the population sizes of AOB and AOA in response to CE application with or without urea fertilization were examined via quantitative real-time PCR (qPCR) assays of the ammonia monooxygenase gene (amoA). The half-life of CE ranged from 11.80 d to 14.54 d in the tested soil. Compared to the untreated control, the application of CE alone had no strong effects on soil pH, and urea fertilization temporarily increased soil pH in the first 7 days. The abundance of the AOA amoA gene was greater than the abundance of the AOB amoA gene in all treatments, but both were significantly suppressed by CE application in a dose-dependent manner. Urea fertilization generally increased AOB and AOA amoA gene abundances, except that the AOA amoA gene level was slightly reduced at the early stage of the incubation period. AOB and AOA preferred different N levels for growth, with AOB only growing significantly at high NH4(+) levels and AOA growing substantially at low NH4(+) levels. The stimulation effects of urea fertilization on AOA and AOB amoA gene abundances were strongly suppressed by the CE application. This study indicated that the CE application substantially suppressed soil nitrification via inhibiting the AOB and AOA population regardless of urea fertilization, which resulted in significant changes in the soil NH4(+)-N and NO3(-)-N levels. Furthermore, AOB and AOA inhabiting separate ecological niches with different NH4(+) levels played various roles in N cycling.},
}
@article {pmid23776475,
year = {2013},
author = {Probst, AJ and Auerbach, AK and Moissl-Eichinger, C},
title = {Archaea on human skin.},
journal = {PloS one},
volume = {8},
number = {6},
pages = {e65388},
pmid = {23776475},
issn = {1932-6203},
mesh = {Ammonia/metabolism ; Archaea/*genetics/metabolism ; Azides ; Base Sequence ; Bayes Theorem ; Cloning, Molecular ; DNA Primers/genetics ; Germany ; Humans ; In Situ Hybridization, Fluorescence ; Microbiota/*genetics ; Models, Genetic ; Molecular Sequence Data ; Oxidation-Reduction ; *Phylogeny ; Propidium/analogs &amp; derivatives ; RNA, Ribosomal, 16S/genetics ; Real-Time Polymerase Chain Reaction ; Sequence Analysis, DNA ; Skin/*microbiology ; },
abstract = {The recent era of exploring the human microbiome has provided valuable information on microbial inhabitants, beneficials and pathogens. Screening efforts based on DNA sequencing identified thousands of bacterial lineages associated with human skin but provided only incomplete and crude information on Archaea. Here, we report for the first time the quantification and visualization of Archaea from human skin. Based on 16 S rRNA gene copies Archaea comprised up to 4.2% of the prokaryotic skin microbiome. Most of the gene signatures analyzed belonged to the Thaumarchaeota, a group of Archaea we also found in hospitals and clean room facilities. The metabolic potential for ammonia oxidation of the skin-associated Archaea was supported by the successful detection of thaumarchaeal amoA genes in human skin samples. However, the activity and possible interaction with human epithelial cells of these associated Archaea remains an open question. Nevertheless, in this study we provide evidence that Archaea are part of the human skin microbiome and discuss their potential for ammonia turnover on human skin.},
}
@article {pmid23739466,
year = {2013},
author = {Leahy, SC and Kelly, WJ and Ronimus, RS and Wedlock, N and Altermann, E and Attwood, GT},
title = {Genome sequencing of rumen bacteria and archaea and its application to methane mitigation strategies.},
journal = {Animal : an international journal of animal bioscience},
volume = {7 Suppl 2},
number = {},
pages = {235-243},
doi = {10.1017/S1751731113000700},
pmid = {23739466},
issn = {1751-732X},
mesh = {Air Pollutants/*metabolism ; Animals ; Archaea/classification/*genetics ; Bacteria/classification/*genetics ; Breeding ; *Environmental Restoration and Remediation ; Fermentation ; *Genome, Archaeal ; *Genome, Bacterial ; Livestock/genetics/*microbiology ; Methane/*metabolism ; Rumen/metabolism/microbiology ; Sequence Analysis, DNA/veterinary ; },
abstract = {Ruminant-derived methane (CH4), a potent greenhouse gas, is a consequence of microbial fermentation in the digestive tract of livestock. Development of mitigation strategies to reduce CH4 emissions from farmed animals is currently the subject of both scientific and environmental interest. Methanogens are the sole producers of ruminant CH4, and therefore CH4 abatement strategies can either target the methanogens themselves or target the other members of the rumen microbial community that produce substrates necessary for methanogenesis. Understanding the relationship that methanogens have with other rumen microbes is crucial when considering CH4 mitigation strategies for ruminant livestock. Genome sequencing of rumen microbes is an important tool to improve our knowledge of the processes that underpin those relationships. Currently, several rumen bacterial and archaeal genome projects are either complete or underway. Genome sequencing is providing information directly applicable to CH4 mitigation strategies based on vaccine and small molecule inhibitor approaches. In addition, genome sequencing is contributing information relevant to other CH4 mitigation strategies. These include the selection and breeding of low CH4-emitting animals through the interpretation of large-scale DNA and RNA sequencing studies and the modification of other microbial groups within the rumen, thereby changing the dynamics of microbial fermentation.},
}
@article {pmid23757139,
year = {2013},
author = {Gaudin, M and Gauliard, E and Schouten, S and Houel-Renault, L and Lenormand, P and Marguet, E and Forterre, P},
title = {Hyperthermophilic archaea produce membrane vesicles that can transfer DNA.},
journal = {Environmental microbiology reports},
volume = {5},
number = {1},
pages = {109-116},
doi = {10.1111/j.1758-2229.2012.00348.x},
pmid = {23757139},
issn = {1758-2229},
mesh = {Archaeal Proteins/*metabolism ; Cell Membrane/chemistry ; DNA, Archaeal/*chemistry ; Hydrothermal Vents/microbiology ; Oceans and Seas ; Organelles/*metabolism ; Plasmids/genetics ; Thermococcus/*isolation &amp; purification ; },
abstract = {Thermococcales are hyperthermophilic archaea found in deep-sea hydrothermal vents. They have been recently reported to produce membrane vesicles (MVs) into their culture medium. Here, we have characterized the mode of production and determined the biochemical composition of MVs from two species of Thermococcales, Thermococcus gammatolerans and Thermococcus kodakaraensis. We observed that MVs are produced by a budding process from the cell membrane reminiscent of ectosome (microparticle) formation in eukaryotes. MVs and cell membranes from the same species have a similar protein and lipid composition, confirming that MVs are produced from cell membranes. The major protein present in cell membranes and MVs of both species is the oligopeptide binding protein OppA. This protein is also abundant in MVs from cells grown in minimal medium, suggesting that OppA could be involved in processes other than peptides scavenging. We have previously shown that MVs from Thermococcales harbour DNA and protect DNA against thermodegradation. Here, we show that T. kodakaraensis cells transformed with the shuttle plasmid pLC70 release MVs harbouring this plasmid. Notably, these MVs can be used to transfer pLC70 into plasmid-free cells, suggesting that MVs could be involved in DNA transfer between cells at high temperature.},
}
@article {pmid23754419,
year = {2013},
author = {Snyder, JC and Samson, RY and Brumfield, SK and Bell, SD and Young, MJ},
title = {Functional interplay between a virus and the ESCRT machinery in archaea.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {110},
number = {26},
pages = {10783-10787},
pmid = {23754419},
issn = {1091-6490},
mesh = {Archaeal Proteins/genetics/*metabolism ; Archaeal Viruses/*pathogenicity/*physiology/ultrastructure ; Endosomal Sorting Complexes Required for Transport/genetics/*metabolism ; Genes, Archaeal ; Host-Pathogen Interactions/genetics/physiology ; Microscopy, Immunoelectron ; Models, Biological ; Mutation ; Sulfolobus/genetics/*metabolism/*virology ; Virus Assembly/physiology ; Virus Release/physiology ; },
abstract = {Recently it has been discovered that a number of eukaryotic viruses, including HIV, coopt the cellular Endosomal Sorting Complex Required for Transport (ESCRT) machinery to affect egress from infected cells. Strikingly, the ESCRT apparatus is conserved in a subset of Archaea, including members of the genus Sulfolobus where it plays a role in cytokinesis. In the current work, we reveal that the archaeal virus Sulfolobus turreted icosahedral virus isolated from Yellowstone National Park's acidic hot springs also exploits the host ESCRT machinery in its replication cycle. Moreover, perturbation of normal ESCRT function abrogates viral replication and, thus, prevents establishment of a productive Sulfolobus turreted icosahedral virus infection. We propose that the Sulfolobus ESCRT machinery is involved in viral assembly within the cytoplasm and in escape from the infected cell by using a unique lysis mechanism. Our results support an ancient origin for viruses "hijacking" ESCRT proteins to complete their replication cycle and thus identify a critical host-virus interaction conserved between two domains of life.},
}
@article {pmid23746269,
year = {2013},
author = {Kandiba, L and Eichler, J},
title = {Analysis of putative nonulosonic acid biosynthesis pathways in Archaea reveals a complex evolutionary history.},
journal = {FEMS microbiology letters},
volume = {345},
number = {2},
pages = {110-120},
doi = {10.1111/1574-6968.12193},
pmid = {23746269},
issn = {1574-6968},
mesh = {Archaea/classification/enzymology/genetics/*metabolism ; Archaeal Proteins/genetics/*metabolism ; *Biological Evolution ; *Biosynthetic Pathways ; Glycosylation ; Phylogeny ; Sugar Acids/*metabolism ; },
abstract = {Sialic acids and the other nonulosonic acid sugars, legionaminic acid and pseudaminic acid, are nine carbon-containing sugars that can be detected as components of the glycans decorating proteins and other molecules in Eukarya and Bacteria. Yet, despite the prevalence of N-glycosylation in Archaea and the variety of sugars recruited for the archaeal version of this post-translational modification, only a single report of a nonulosonic acid sugar in an archaeal N-linked glycan has appeared. Hence, to obtain a clearer picture of nonulosonic acid sugar biosynthesis capability in Archaea, 122 sequenced genomes were scanned for the presence of genes involved in the biogenesis of these sugars. The results reveal that while Archaea and Bacteria share a common route of sialic acid biosynthesis, numerous archaeal nonulosonic acid sugar biosynthesis pathway components were acquired from elsewhere via various routes. Still, the limited number of Archaea encoding components involved in the synthesis of nonulosonic acid sugars implies that such saccharides are not major components of glycans in this domain.},
}
@article {pmid23739307,
year = {2013},
author = {Fernandes, J and Wang, A and Su, W and Rozenbloom, SR and Taibi, A and Comelli, EM and Wolever, TM},
title = {Age, dietary fiber, breath methane, and fecal short chain fatty acids are interrelated in Archaea-positive humans.},
journal = {The Journal of nutrition},
volume = {143},
number = {8},
pages = {1269-1275},
doi = {10.3945/jn.112.170894},
pmid = {23739307},
issn = {1541-6100},
support = {486906//Canadian Institutes of Health Research/Canada ; },
mesh = {Adolescent ; Adult ; Age Factors ; Archaea/*isolation &amp; purification ; Body Mass Index ; Breath Tests ; Colon/chemistry/microbiology ; Cross-Sectional Studies ; Dietary Fiber/*administration &amp; dosage ; Energy Intake ; Fatty Acids, Volatile/*analysis ; Feces/*chemistry/*microbiology ; Female ; Fermentation ; Humans ; Male ; Methane/analysis ; Middle Aged ; RNA, Ribosomal, 16S/isolation &amp; purification ; Young Adult ; },
abstract = {Recent attention has focused on the significance of colonic Archaea in human health and energy metabolism. The main objectives of this study were to determine the associations among the number of fecal Archaea, body mass index (BMI), fecal short chain fatty acid (SCFA) concentrations, and dietary intakes of healthy humans. We collected demographic information, 3-d diet records, and breath and fecal samples from 95 healthy participants who were divided into 2 groups: detectable Archaea (>10(6) copies/g; Arch+ve) and undetectable Archaea. Dietary intakes, BMI, and fecal SCFAs were similar in both groups. The mean number of Archaea 16S rRNA gene copies detected in Arch+ve participants' feces was 8.9 ± 0.2 log/g wet weight. In Arch+ve participants, there were positive correlations between breath methane and age (r = 0.52; P = 0.001), total dietary fiber (TDF) intake (r = 0.57; P = 0.0003), and log number of fecal Archaea 16S rRNA gene copies (r = 0.35; P = 0.03). In the Arch+ve group, negative correlations were observed between TDF/1000 kcal and fecal total SCFA (r = -0.46; P ≤ 0.01) and between breath methane and fecal total SCFA (r = -0.42; P = 0.01). Principal component analysis identified a distinct Archaea factor with positive loadings of age, breath methane, TDF, TDF/1000 kcal, and number of log Archaea 16S rRNA gene copies. The results suggest that colonic Archaea is not associated with obesity in healthy humans. The presence of Archaea in humans may influence colonic fermentation by altering SCFA metabolism and fecal SCFA profile.},
}
@article {pmid23715690,
year = {2013},
author = {Pollack, JD and Gerard, D and Pearl, DK},
title = {Uniquely localized intra-molecular amino acid concentrations at the glycolytic enzyme catalytic/active centers of Archaea, Bacteria and Eukaryota are associated with their proposed temporal appearances on earth.},
journal = {Origins of life and evolution of the biosphere : the journal of the International Society for the Study of the Origin of Life},
volume = {43},
number = {2},
pages = {161-187},
pmid = {23715690},
issn = {1573-0875},
mesh = {Amino Acid Sequence ; Amino Acids/analysis/*chemistry ; Archaea/*enzymology ; Bacteria/*enzymology ; *Catalytic Domain ; Conserved Sequence ; Earth, Planet ; Enzymes/*chemistry/metabolism ; Eukaryota/*enzymology ; *Evolution, Molecular ; Isoleucine/analysis ; Leucine/analysis ; Logistic Models ; Molecular Sequence Data ; Valine/analysis ; },
abstract = {The distributions of amino acids at most-conserved sites nearest catalytic/active centers (C/AC) in 4,645 sequences of ten enzymes of the glycolytic Embden-Meyerhof-Parnas pathway in Archaea, Bacteria and Eukaryota are similar to the proposed temporal order of their appearance on Earth. Glycine, isoleucine, leucine, valine, glutamic acid and possibly lysine often described as prebiotic, i.e., existing or occurring before the emergence of life, were localized in positional and conservational defined aggregations in all enzymes of all Domains. The distributions of all 20 biologic amino acids in most-conserved sites nearest their C/ACs were quite different either from distributions in sites less-conserved and further from their C/ACs or from all amino acids regardless of their position or conservation. The major concentrations of glycine, e.g., perhaps the earliest prebiotic amino acid, occupies ≈ 16 % of all the most-conserved sites within a volume of ≈ 7-8 Å radius from their C/ACs and decreases linearly towards the molecule's peripheries. Spatially localized major concentrations of isoleucine, leucine and valine are in the mid-conserved and mid-distant sites from their C/ACs in protein interiors. Lysine and glutamic acid comprise ≈ 25-30 % of all amino acids within an irregular volume bounded by ≈ 24-28 Å radii from their C/ACs at the most-distant least-conserved sites. The unreported characteristics of these amino acids: their spatially and conservationally identified concentrations in Archaea, Bacteria and Eukaryota, suggest some common structural organization of glycolytic enzymes that may be relevant to their evolution and that of other proteins. We discuss our data in relation to enzyme evolution, their reported prebiotic putative temporal appearances on Earth, abundances, biological "cost", neighbor-sequence preferences or "ordering" and some thermodynamic parameters.},
}
@article {pmid23696792,
year = {2013},
author = {Majhi, MC and Behera, AK and Kulshreshtha, NM and Mahmooduzafar, and Kumar, R and Kumar, A},
title = {ExtremeDB: a unified web repository of extremophilic archaea and bacteria.},
journal = {PloS one},
volume = {8},
number = {5},
pages = {e63083},
pmid = {23696792},
issn = {1932-6203},
mesh = {Archaea/genetics/*metabolism ; Bacteria/genetics/*metabolism ; *Databases, Factual ; Genome, Archaeal/genetics ; Genome, Bacterial/genetics ; *Internet ; Proteome/metabolism ; },
abstract = {Extremophiles are the microorganisms which can survive under extreme conditions of temperature, pressure, pH, salinity etc. They have gained much attention for their potential role in biotechnological and industrial applications. The large amount of experimental data in the literature is so diverse, that it becomes difficult and time consuming for the researcher to implement it in various areas of research. Therefore, a systematic arrangement of data and redirection in a similar fashion through web interface can assist researchers in analyzing the data as per their requirement. ExtremeDB is a freely available web based relational database which integrates general characteristics, genome-proteome information, industrial applications and recent scientific investigations of the seven major groups of 865 extremophillic microorganisms. The search options are user friendly and analyses tools such as Compare and Extreme BLAST have been incorporated for comparative analysis of two or more extremophiles and determining the sequence similarity of a given protein/nucleotide in relation to other extremophiles respectively. The effort put forth herein in the form of database, would open up new avenues on the potential utility of extremophiles in applied research. ExtremeDB is freely accessible via http://extrem.igib.res.in.},
}
@article {pmid23686819,
year = {2014},
author = {Wang, Y and Zhu, G and Song, L and Wang, S and Yin, C},
title = {Manure fertilization alters the population of ammonia-oxidizing bacteria rather than ammonia-oxidizing archaea in a paddy soil.},
journal = {Journal of basic microbiology},
volume = {54},
number = {3},
pages = {190-197},
doi = {10.1002/jobm.201200671},
pmid = {23686819},
issn = {1521-4028},
mesh = {Ammonia/chemistry/*metabolism ; Archaea/*metabolism ; Bacteria/*metabolism ; *Fertilizers ; *Manure ; Nitrification/genetics ; Oxidation-Reduction ; Soil/*chemistry ; *Soil Microbiology ; },
abstract = {Manure fertilizers are widely used in agriculture and highly impacted the soil microbial communities such as ammonia oxidizers. However, the knowledge on the communities of archaeal versus bacterial ammonia oxidizers in paddy soil affected by manure fertilization remains largely unknown, especially for a long-term influence. In present work, the impact of manure fertilization on the population of ammonia oxidizers, related potential nitrification rates (PNRs) and the key factors manipulating the impact were investigated through studying two composite soil cores (long-term fed with manure fertilization versus undisturbed). Moreover, soil incubated with NH(4)(+) for 5 weeks was designed to verify the field research. The results showed that the copy numbers of bacterial amoA gene in the manure fed soil were significant higher than those in the unfed soil (p < 0.05), suggesting a clear stimulating effect of long-term manure fertilization on the population of ammonia-oxidizing bacteria (AOB). The detected PNRs in the manure fed soil core (14-218 nmol L(-1) N g(-1) h(-1)) were significant higher than those in the unfed soil core (5-72 nmol L(-1) N g(-1) h(-1) ; p < 0.05). Highly correlations between the PNRs and the bacterial amoA gene copies rather than archaeal amoA gene were observed, indicating strong nitrification capacity related to bacterial ammonia oxidizers. The NH(4)(+) -N significantly correlated to the abundance of AOB (p < 0.01) and explained 96.1% of the environmental variation, showing the NH(4)(+) -N was the main factor impacting the population of AOB. The incubation experiment demonstrated a clear increase of the bacterial amoA gene abundance (2.0 × 10(6) to 8.4 × 10(6) g(-1) d.w.s. and 1.6 × 10(4) to 4.8 × 10(5) g(-1) d.w.s.) in both soil but not for the archaeal amoA gene, in agreement with the field observation. Overall, our results suggested that manure fertilization promoted the population size of bacterial ammonia oxidizers rather than their archaeal counterparts whether in long-term or short-term usage and the NH(4)(+) -N was the key impact factor.},
}
@article {pmid23658767,
year = {2013},
author = {Khelaifia, S and Brunel, JM and Drancourt, M},
title = {In-vitro archaeacidal activity of biocides against human-associated archaea.},
journal = {PloS one},
volume = {8},
number = {5},
pages = {e62738},
pmid = {23658767},
issn = {1932-6203},
mesh = {Chlorhexidine/chemistry/pharmacology ; Cholestanols/chemical synthesis/chemistry/*pharmacology ; Culture Media ; Disinfectants/chemistry/*pharmacology ; Humans ; Methanobacteriaceae/*drug effects/growth &amp; development/ultrastructure ; Microbial Sensitivity Tests ; Microscopy, Electron ; Molecular Structure ; Peracetic Acid/chemistry/pharmacology ; Structure-Activity Relationship ; },
abstract = {BACKGROUND: Several methanogenic archaea have been detected in the human intestinal microbiota. These intestinal archaea may contaminate medical devices such as colonoscopes. However, no biocide activity has been reported among these human-associated archaea.<br><br>METHODOLOGY: The minimal archaeacidal concentration (MAC) of peracetic acid, chlorhexidine, squalamine and twelve parent synthetic derivatives reported in this study was determined against five human-associated methanogenic archaea including Methanobrevibacter smithii, Methanobrevibacter oralis, Methanobrevibacter arboriphilicus, Methanosphaera stadtmanae, Methanomassiliicoccus luminyensis and two environmental methanogens Methanobacterium beijingense and Methanosaeta concilii by using a serial dilution technique in Hungates tubes.<br><br>PRINCIPAL FINDINGS: MAC of squalamine derivative S1 was 0.05 mg/L against M. smithii strains, M. oralis, M. arboriphilicus, M. concilii and M. beijingense whereas MAC of squalamine and derivatives S2-S12 varied from 0.5 to 5 mg/L. For M. stadtmanae and M. luminyensis, MAC of derivative S1 was 0.1 mg/L and varied from 1 to &#x2265; 10 mg/L for squalamine and its parent derivatives S2-S12. Under the same experimental conditions, chlorhexidine and peracetic acid lead to a MAC of 0.2 and 1.5 mg/L, respectively against all tested archaea.<br><br>CONCLUSIONS/SIGNIFICANCE: Squalamine derivative S1 exhibited a 10-200 higher archaeacidal activity than other tested squalamine derivatives, on the majority of human-associated archaea. As previously reported and due to their week corrosivity and their wide spectrum of antibacterial and antifungal properties, squalamine and more precisely derivative S1 appear as promising compounds to be further tested for the decontamination of medical devices contaminated by human-associated archaea.},
}
@article {pmid23657360,
year = {2013},
author = {Horak, RE and Qin, W and Schauer, AJ and Armbrust, EV and Ingalls, AE and Moffett, JW and Stahl, DA and Devol, AH},
title = {Ammonia oxidation kinetics and temperature sensitivity of a natural marine community dominated by Archaea.},
journal = {The ISME journal},
volume = {7},
number = {10},
pages = {2023-2033},
pmid = {23657360},
issn = {1751-7370},
mesh = {Ammonia/*metabolism ; Archaea/genetics/metabolism/*physiology ; Kinetics ; Oxidation-Reduction ; Oxidoreductases/genetics/metabolism ; Seawater/chemistry/*microbiology ; *Temperature ; },
abstract = {Archaeal ammonia oxidizers (AOAs) are increasingly recognized as prominent members of natural microbial assemblages. Evidence that links the presence of AOA with in situ ammonia oxidation activity is limited, and the abiotic factors that regulate the distribution of AOA natural assemblages are not well defined. We used quantitative PCR to enumerate amoA (encodes α-subunit of ammonia monooxygenase) abundances; AOA amoA gene copies greatly outnumbered ammonia-oxidizing bacteria and amoA transcripts were derived primarily from AOA throughout the water column of Hood Canal, Puget Sound, WA, USA. We generated a Michaelis-Menten kinetics curve for ammonia oxidation by the natural community and found that the measured Km of 98±14 nmol l(-1) was close to that for cultivated AOA representative Nitrosopumilus maritimus SCM1. Temperature did not have a significant effect on ammonia oxidation rates for incubation temperatures ranging from 8 to 20 °C, which is within the temperature range for depths of measurable ammonia oxidation at the site. This study provides substantial evidence, through both amoA gene copies and transcript abundances and the kinetics response, that AOA are the dominant active ammonia oxidizers in this marine environment. We propose that future ammonia oxidation experiments use a Km for the natural community to better constrain ammonia oxidation rates determined with the commonly used (15)NH4(+) dilution technique.},
}
@article {pmid23651536,
year = {2013},
author = {Khelaifia, S and Ramonet, PY and Bedotto Buffet, M and Drancourt, M},
title = {A semi-automated protocol for Archaea DNA extraction from stools.},
journal = {BMC research notes},
volume = {6},
number = {},
pages = {186},
pmid = {23651536},
issn = {1756-0500},
mesh = {Archaea/genetics/*isolation &amp; purification ; *Automation ; Base Sequence ; DNA Primers ; DNA, Archaeal/*isolation &amp; purification ; Feces/*microbiology ; Humans ; Real-Time Polymerase Chain Reaction ; },
abstract = {BACKGROUND: The PCR-based detection of archaea DNA in human specimens relies on efficient DNA extraction. We previously designed one such protocol involving only manual steps. In an effort to reduce the workload involved, we compared this manual protocol to semi-automated and automated protocols for archaea DNA extraction from human specimens.<br><br>FINDINGS: We tested 110 human stool specimens using each protocol. An automated protocol using the EZ1 Advanced XL extractor with the V 1.066069118 Qiagen DNA bacteria card and the EZ1&#xae; DNA Tissue Kit (Qiagen, Courtaboeuf, France) yielded 35/110 (32%) positives for the real-time PCR detection of the Methanobrevibacter smithii 16S rRNA gene, with average Ct values of 36.1. A semi-automated protocol combining glass-powder crushing, overnight proteinase K digestion and lysis in the buffer from the EZ1 kit yielded 90/110 (82%) positive specimens (P&#x2009;=&#x2009;0.001) with an average Ct value of 27.4 (P&#x2009;=&#x2009;0.001). The manual protocol yielded 100/110 (91%) positive specimens (P&#x2009;=&#x2009;0.001) with an average Ct value of 30.33 (P&#x2009;=&#x2009;0.001). However, neither the number of positive specimens nor the Ct values were significantly different between the manual protocol and the semi-automated protocol (P&#x2009;>&#x2009;0.1 and P&#x2009;>&#x2009;0.1).<br><br>CONCLUSION: Proteinase K digestion and glass powder crushing dramatically increase the extraction yield of archaea DNA from human stools. The semi-automated protocol described here was more rapid than the manual protocol and yielded significantly more archaeal DNA. It could be applied for extracting total stool DNA for further PCR amplification.},
}
@article {pmid23636492,
year = {2013},
author = {Zhao, D and Zeng, J and Wan, W and Liang, H and Huang, R and Wu, QL},
title = {Vertical distribution of ammonia-oxidizing archaea and bacteria in sediments of a eutrophic lake.},
journal = {Current microbiology},
volume = {67},
number = {3},
pages = {327-332},
pmid = {23636492},
issn = {1432-0991},
mesh = {Ammonia/*metabolism ; Archaea/*classification/*isolation &amp; purification ; Bacteria/*classification/*isolation &amp; purification ; *Biota ; DNA, Archaeal/chemistry/genetics ; DNA, Bacterial/chemistry/genetics ; Lakes/*microbiology ; Molecular Sequence Data ; Oxidation-Reduction ; Oxidoreductases/genetics ; Real-Time Polymerase Chain Reaction ; Sequence Analysis, DNA ; },
abstract = {In order to characterize the vertical variation of abundance and community composition of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in sediments of a eutrophic lake, Lake Taihu, molecular techniques including real-time PCR, clone library, and sequencing were carried out in this study. Abundances of archaeal amoA gene (ranged from 2.34 × 10(6) to 4.43 × 10(7) copies [g dry sediment](-1)) were higher than those of bacterial amoA gene (ranged from 5.02 × 10(4) to 6.91 × 10(6) copies [g dry sediment](-1)) for all samples and both of them exhibited negative correlations with the increased depths. Diversities of archaeal and bacterial amoA gene increased with the elevated depths. There were no significant variations of AOB community structures derived from different sediment depths, whereas obvious differences were observed for the AOA community compositions. The information acquired in this study would be useful to elucidate the roles of AOA and AOB in the nitrogen cycling of freshwater ecosystems.},
}
@article {pmid23634960,
year = {2013},
author = {Szwergold, BS},
title = {Maillard reactions in hyperthermophilic archaea: implications for better understanding of non-enzymatic glycation in biology.},
journal = {Rejuvenation research},
volume = {16},
number = {4},
pages = {259-272},
doi = {10.1089/rej.2012.1401},
pmid = {23634960},
issn = {1557-8577},
mesh = {Archaea/*metabolism ; Glycation End Products, Advanced/chemistry/metabolism ; Glycosylation ; Humans ; *Maillard Reaction ; Schiff Bases/chemistry/metabolism ; *Temperature ; },
abstract = {Maillard reactions are an unavoidable feature of life that appear to be damaging to cell and organisms. Consequently, all living systems must have ways to protect themselves against this process. As of 2012, several such defense mechanisms have been identified. They are all enzymatic and were found in mesophilic organisms. To date, no systematic study of Maillard reactions and the relevant defense mechanisms has been conducted in thermophiles (50°C-80°C) or hyperthermophiles (80°C-120°C). This is surprisingly because Maillard reactions become significantly faster and potent with increasing temperatures. This review examines this neglected issue in two well-defined sets of hyperthermophiles. My analysis suggests that hyperthermophiles cope with glycation stress by several mechanisms: • Absence of glycation-prone head groups (such as ethanoalamine) from hyperthermophilic phospholipids • Protection of reactive carbohydrates and labile metabolic intermediates by substrate channeling. • Conversion of excess reactive sugars such as glucose to non-reactive compounds including trehalose, di-myo-inositol-phosphate and mannosylglycerate. • Detoxification of methylglyoxal and other ketoaldehydes by conversion to inert products through a variety of reductases and dehydrogenases. • Scavenging of the remaining carbonyls by nucleophilic amines, including a variety of novel polyamines. Disruption of the Maillard process at its early stages, rather than repair of damage caused by it at later stages, appears to be the preferred strategy in the organisms examined. The most unique among these mechanisms appears to be a polyamine-based scavenging system. Undertaking research of the Maillard process in hyperthermophiles is important in its own right and is also likely to provide new insights for the control of these reactions in humans, especially in diseases such as diabetes mellitus.},
}
@article {pmid23624046,
year = {2013},
author = {Gao, JF and Luo, X and Wu, GX and Li, T and Peng, YZ},
title = {Quantitative analyses of the composition and abundance of ammonia-oxidizing archaea and ammonia-oxidizing bacteria in eight full-scale biological wastewater treatment plants.},
journal = {Bioresource technology},
volume = {138},
number = {},
pages = {285-296},
doi = {10.1016/j.biortech.2013.03.176},
pmid = {23624046},
issn = {1873-2976},
mesh = {Ammonia/*metabolism ; Archaea/genetics/*metabolism ; Bacteria/genetics/*metabolism ; Base Sequence ; Biodegradation, Environmental ; Genes, Archaeal/genetics ; Genes, Bacterial/genetics ; Genetic Variation ; Molecular Sequence Data ; Oxidation-Reduction ; Phylogeny ; Principal Component Analysis ; Waste Disposal, Fluid ; Wastewater/*microbiology ; Water Purification/*methods ; },
abstract = {This study investigated the diversity and abundance of AOA and AOB amoA genes in eight full-scale wastewater treatment plants (WWTPs). Although the process principles and system operations of the eight WWTPs were different, quantitative real-time PCR measurements showed that AOB amoA genes outnumbered AOA amoA genes with the ratio varying from 2.56 to 2.41×10(3), and ammonia may be partially oxidized by AOA. Phylogenetic analyses based on cloning and sequencing showed that Nitrososphaera cluster was the most dominant AOA species and might be distributed worldwide, and Nitrosopumilis cluster was few. Statistical analysis indicated that there might be versatile AOA ecotypes and some AOA might be not obligate autotrophic. The Nitrosomonas europaea cluster and Nitrosomonas oligotropha cluster were the two most dominant AOB species, and AOB species showed higher diversity than AOA species.},
}
@article {pmid23619304,
year = {2013},
author = {Ziegler, S and Dolch, K and Geiger, K and Krause, S and Asskamp, M and Eusterhues, K and Kriews, M and Wilhelms-Dick, D and Goettlicher, J and Majzlan, J and Gescher, J},
title = {Oxygen-dependent niche formation of a pyrite-dependent acidophilic consortium built by archaea and bacteria.},
journal = {The ISME journal},
volume = {7},
number = {9},
pages = {1725-1737},
pmid = {23619304},
issn = {1751-7370},
mesh = {Aerobiosis ; Anaerobiosis ; Archaea/genetics/*physiology ; Bacteria/genetics ; *Bacterial Physiological Phenomena ; *Biodiversity ; *Biofilms ; Carbon Cycle ; Hydrogen-Ion Concentration ; Iron/*metabolism ; Microbial Consortia/*physiology ; Mining ; Oxygen/*metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sulfides/*metabolism ; },
abstract = {Biofilms can provide a number of different ecological niches for microorganisms. Here, a multispecies biofilm was studied in which pyrite-oxidizing microbes are the primary producers. Its stability allowed not only detailed fluorescence in situ hybridization (FISH)-based characterization of the microbial population in different areas of the biofilm but also to integrate these results with oxygen and pH microsensor measurements conducted before. The O2 concentration declined rapidly from the outside to the inside of the biofilm. Hence, part of the population lives under microoxic or anoxic conditions. Leptospirillum ferrooxidans strains dominate the microbial population but are only located in the oxic periphery of the snottite structure. Interestingly, archaea were identified only in the anoxic parts of the biofilm. The archaeal community consists mainly of so far uncultured Thermoplasmatales as well as novel ARMAN (Archaeal Richmond Mine Acidophilic Nanoorganism) species. Inductively coupled plasma analysis and X-ray absorption near edge structure spectra provide further insight in the biofilm characteristics but revealed no other major factors than oxygen affecting the distribution of bacteria and archaea. In addition to catalyzed reporter deposition FISH and oxygen microsensor measurements, microautoradiographic FISH was used to identify areas in which active CO2 fixation takes place. Leptospirilla as well as acidithiobacilli were identified as primary producers. Fixation of gaseous CO2 seems to proceed only in the outer rim of the snottite. Archaea inhabiting the snottite core do not seem to contribute to the primary production. This work gives insight in the ecological niches of acidophilic microorganisms and their role in a consortium. The data provided the basis for the enrichment of uncultured archaea.},
}
@article {pmid23613876,
year = {2013},
author = {Khelaifia, S and Raoult, D and Drancourt, M},
title = {A versatile medium for cultivating methanogenic archaea.},
journal = {PloS one},
volume = {8},
number = {4},
pages = {e61563},
pmid = {23613876},
issn = {1932-6203},
mesh = {Archaea/*drug effects/*growth &amp; development ; Cell Culture Techniques/*methods ; Culture Media/*pharmacology ; Humans ; Methane/*metabolism ; Time Factors ; },
abstract = {BACKGROUND: Methanobrevibacter smithii, Methanobrevibacter oralis, Methanosphaera stadtmanae, Methanomassilicoccus luminyensis and Methanobrevibacter arboriphilicus have been cultured from human digestive microbiota. Each one of these fastidious methanogenic archaea requires a specific medium for its growth, hampering their routine isolation and the culture.<br><br>A new culture medium here referred as SAB medium was optimized and tested to cultivate methanogens associated with human microbiota, as well as two mesophile methanogens Methanobacterium beijingense and Methanosaeta concilii. It was further tested for the isolation of archaea from 20 human stool specimens including 10 specimens testing positive for PCR detection of M. smithii. After inoculating 10(5) colony-forming-unit archaea/mL or 1 g stool specimen in parallel in SAB medium and reference DSMZ medium in the presence of negative controls, growth of archaea was determined by optical microscopy and the measurement of methane production by gas chromatography. While the negative controls remained sterile, all tested archaea grew significantly more rapidly in SAB medium than in reference medium in 1-3 days (P<0.05, Student test). Among PCR-positive stool specimens, 10/10 grew in the SAB medium, 6/10 in DSMZ 119 medium, 5/10 in DSMZ 322 medium and 3/10 in DSMZ 334 c medium. Four out of ten PCR-negative stool specimens grew after a 3-week incubation in the SAB-medium whereas no growth was detected in any of the reference media. 16S rRNA gene sequencing yielded 99-100% sequence similarity with reference M. smithii except for one specimen that yielded 99-100% sequence similarity with reference Methanobrevibacter millerae.<br><br>CONCLUSIONS/SIGNIFICANCE: SAB medium allows for the versatile isolation and growth of methanogenic archaea associated with human gut microbiota including the archaea missed by inoculation of reference media. Implementation of the SAB medium in veterinary and medical microbiology laboratories will ease the routine culture-based detection of methanogenic archaea in clinical and environmental specimens.},
}
@article {pmid23603537,
year = {2013},
author = {Zhang, YM and Shao, ZQ and Yang, LT and Sun, XQ and Mao, YF and Chen, JQ and Wang, B},
title = {Non-random arrangement of synonymous codons in archaea coding sequences.},
journal = {Genomics},
volume = {101},
number = {6},
pages = {362-367},
doi = {10.1016/j.ygeno.2013.04.008},
pmid = {23603537},
issn = {1089-8646},
mesh = {Codon/*genetics ; Evolution, Molecular ; Genome, Archaeal ; Methanosarcina/*genetics ; *Open Reading Frames ; Phylogeny ; },
abstract = {Non-random arrangement of synonymous codons in coding sequences has been recently reported in eukaryotic and bacterial genomes, but the case in archaeal genomes is largely undetermined. Here, we systematically investigated 122 archaeal genomes for their synonymous codon co-occurrence patterns. We found that in most archaeal coding sequences, the order of synonymous codons is not arranged randomly, but rather some successive codon pairs appear significantly more often than expected. Importantly, such codon pairing bias (CPB) pattern in archaea does not seem to completely follow the co-tRNA codon pairing (CCP) rule previously reported for eukaryotes, but largely obeys an identical codon pairing (ICP) rule. Further, synonymous codon permutation test demonstrated that in many archaeal genomes, random mutation alone is unable to cause the observed high level of ICP bias, which strongly indicates that selection force has been involved to shape synonymous codon orders, potentially meeting a global requirement to optimize translation rate.},
}
@article {pmid23597763,
year = {2013},
author = {Jing, Z and Hu, Y and Niu, Q and Liu, Y and Li, YY and Wang, XC},
title = {UASB performance and electron competition between methane-producing archaea and sulfate-reducing bacteria in treating sulfate-rich wastewater containing ethanol and acetate.},
journal = {Bioresource technology},
volume = {137},
number = {},
pages = {349-357},
doi = {10.1016/j.biortech.2013.03.137},
pmid = {23597763},
issn = {1873-2976},
mesh = {Acetates/*chemistry ; Archaea/*metabolism ; *Bioreactors ; Cloning, Molecular ; Electrons ; Ethanol/*chemistry ; Methane/biosynthesis ; RNA, Ribosomal, 16S/chemistry ; Sulfates/*metabolism ; Wastewater/*chemistry ; },
abstract = {To find an appropriate method for sulfate-rich wastewater containing ethanol and acetate with COD/sulfate ratio of 1, a UASB reactor was operated for more than 180 days. The influences of HRT (hydraulic retention time) and OLR (organic loading rate) on organics and sulfate removal, gas production, and electrons utilization were investigated. The sludge activity and microorganism composition were also determined. The results indicated that this system removed more than 80% of COD and 30% of sulfate with HRT above 6h and OLR below 12.3 gCOD/L d. Further HRT decrease caused volatile fatty acids accumulation and performance deterioration. Except at HRT of 2h, COD and electron flow were mostly utilized by methane-producing archaea (MPA), and methane yield remained in the range of 0.18-0.24 LCH4/gCOD. Methane was mainly generated by Methanosaeta concilii GP6 with acetate as substrate, whereas sulfate was mainly reduced by incomplete-oxidizing Desulfovibrio species with ethanol as substrate.},
}
@article {pmid23567024,
year = {2013},
author = {Kaminski, L and Lurie-Weinberger, MN and Allers, T and Gophna, U and Eichler, J},
title = {Phylogenetic- and genome-derived insight into the evolution of N-glycosylation in Archaea.},
journal = {Molecular phylogenetics and evolution},
volume = {68},
number = {2},
pages = {327-339},
doi = {10.1016/j.ympev.2013.03.024},
pmid = {23567024},
issn = {1095-9513},
mesh = {Archaea/enzymology/genetics ; Archaeal Proteins/*genetics/metabolism ; Codon ; Evolution, Molecular ; Gene Duplication ; Gene Transfer, Horizontal ; *Genome, Archaeal ; Glycoproteins/*genetics/metabolism ; Glycosylation ; Haloferax/enzymology/*genetics ; Hexosyltransferases/genetics ; Membrane Proteins/genetics ; Multigene Family ; Phylogeny ; Protein Processing, Post-Translational/*genetics ; },
abstract = {N-glycosylation, the covalent attachment of oligosaccharides to target protein Asn residues, is a post-translational modification that occurs in all three domains of life. In Archaea, the N-linked glycans that decorate experimentally characterized glycoproteins reveal a diversity in composition and content unequaled by their bacterial or eukaryal counterparts. At the same time, relatively little is known of archaeal N-glycosylation pathways outside of a handful of model strains. To gain insight into the distribution and evolutionary history of the archaeal version of this universal protein-processing event, 168 archaeal genome sequences were scanned for the presence of aglB, encoding the known archaeal oligosaccharyltransferase, an enzyme key to N-glycosylation. Such analysis predicts the presence of AglB in 166 species, with some species seemingly containing multiple versions of the protein. Phylogenetic analysis reveals that the events leading to aglB duplication occurred at various points during archaeal evolution. In many cases, aglB is found as part of a cluster of putative N-glycosylation genes. The presence, arrangement and nucleotide composition of genes in aglB-based clusters in five species of the halophilic archaeon Haloferax points to lateral gene transfer as contributing to the evolution of archaeal N-glycosylation.},
}
@article {pmid23565112,
year = {2013},
author = {Boyd, ES and Hamilton, TL and Wang, J and He, L and Zhang, CL},
title = {The role of tetraether lipid composition in the adaptation of thermophilic archaea to acidity.},
journal = {Frontiers in microbiology},
volume = {4},
number = {},
pages = {62},
pmid = {23565112},
issn = {1664-302X},
abstract = {Diether and tetraether lipids are fundamental components of the archaeal cell membrane. Archaea adjust the degree of tetraether lipid cyclization in order to maintain functional membranes and cellular homeostasis when confronted with pH and/or thermal stress. Thus, the ability to adjust tetraether lipid composition likely represents a critical phenotypic trait that enabled archaeal diversification into environments characterized by extremes in pH and/or temperature. Here we assess the relationship between geochemical variation, core- and polar-isoprenoid glycerol dibiphytanyl glycerol tetraether (C-iGDGT and P-iGDGT, respectively) lipid composition, and archaeal 16S rRNA gene diversity and abundance in 27 geothermal springs in Yellowstone National Park, Wyoming. The composition and abundance of C-iGDGT and P-iGDGT lipids recovered from geothermal ecosystems were distinct from surrounding soils, indicating that they are synthesized endogenously. With the exception of GDGT-0 (no cyclopentyl rings), the abundances of individual C-iGDGT and P-iGDGT lipids were significantly correlated. The abundance of a number of individual tetraether lipids varied positively with the relative abundance of individual 16S rRNA gene sequences, most notably crenarchaeol in both the core and polar GDGT fraction and sequences closely affiliated with Candidatus Nitrosocaldus yellowstonii. This finding supports the proposal that crenarchaeol is a biomarker for nitrifying archaea. Variation in the degree of cyclization of C- and P-iGDGT lipids recovered from geothermal mats and sediments could best be explained by variation in spring pH, with lipids from acidic environments tending to have, on average, more internal cyclic rings than those from higher pH ecosystems. Likewise, variation in the phylogenetic composition of archaeal 16S rRNA genes could best be explained by spring pH. In turn, the phylogenetic similarity of archaeal 16S rRNA genes was significantly correlated with the similarity in the composition of C- and P-iGDGT lipids. Taken together, these data suggest that the ability to adjust the composition of GDGT lipid membranes played a central role in the diversification of archaea into or out of environments characterized by extremes of low pH and high temperature.},
}
@article {pmid23561316,
year = {2013},
author = {Khelaifia, S and Brunel, JM and Raoult, D and Drancourt, M},
title = {Hydrophobicity of imidazole derivatives correlates with improved activity against human methanogenic archaea.},
journal = {International journal of antimicrobial agents},
volume = {41},
number = {6},
pages = {544-547},
doi = {10.1016/j.ijantimicag.2013.02.013},
pmid = {23561316},
issn = {1872-7913},
mesh = {Anti-Infective Agents/chemical synthesis/chemistry/*pharmacology ; Archaea/*drug effects/metabolism ; Humans ; Hydrophobic and Hydrophilic Interactions ; Imidazoles/chemical synthesis/chemistry/*pharmacology ; Methane/metabolism ; Microbial Sensitivity Tests ; },
abstract = {Methanogenic archaea are involved in periodontitis in humans. They have also been implicated in digestive tract pathologies and obesity. These microorganisms are broadly resistant to antibiotics, except for metronidazole and ornidazole. In this study, eight imidazole derivatives were synthesised and their in vitro cytotoxicity and activity against six species of methanogenic archaea, including Methanobrevibacter smithii, Methanobrevibacter oralis, Methanosphaera stadtmanae, Methanobacterium beijingense, Methanosaeta concilii and Methanomassiliicoccus luminyensis, were tested. Whilst the effective half-maximum cytotoxic concentrations (EC50 values) of all compounds were ≤50 mg/L, minimum inhibitory concentrations (MICs) were 0.05-0.8 mg/L for most methanogenic archaea and 0.1-1mg/L for M. stadtmanae. These results indicated a >20-400 therapeutic index (EC50/MIC) for these compounds, which compared with metronidazole exhibited 1-log increased activity against methanogenic archaea cultured from the human microbiota. These compounds are therefore promising molecules for the treatment of methanogenic archaea-related infections.},
}
@article {pmid23552622,
year = {2013},
author = {Winter, C and Matthews, B and Suttle, CA},
title = {Effects of environmental variation and spatial distance on bacteria, archaea and viruses in sub-polar and arctic waters.},
journal = {The ISME journal},
volume = {7},
number = {8},
pages = {1507-1518},
pmid = {23552622},
issn = {1751-7370},
support = {P 24413/FWF_/Austrian Science Fund FWF/Austria ; },
mesh = {Archaea/genetics/*physiology ; Arctic Regions ; Bacteria/genetics ; *Bacterial Physiological Phenomena ; *Biodiversity ; Canada ; *Environment ; Oceans and Seas ; RNA, Ribosomal, 16S/genetics ; Salinity ; Seawater/*microbiology/*virology ; Temperature ; *Virus Physiological Phenomena ; Viruses/genetics ; Water Microbiology ; },
abstract = {We investigated the influence of environmental parameters and spatial distance on bacterial, archaeal and viral community composition from 13 sites along a 3200-km long voyage from Halifax to Kugluktuk (Canada) through the Labrador Sea, Baffin Bay and the Arctic Archipelago. Variation partitioning was used to disentangle the effects of environmental parameters, spatial distance and spatially correlated environmental parameters on prokaryotic and viral communities. Viral and prokaryotic community composition were related in the Labrador Sea, but were independent of each other in Baffin Bay and the Arctic Archipelago. In oceans, the dominant dispersal mechanism for prokaryotes and viruses is the movement of water masses, thus, dispersal for both groups is passive and similar. Nevertheless, spatial distance explained 7-19% of the variation in viral community composition in the Arctic Archipelago, but was not a significant predictor of bacterial or archaeal community composition in either sampling area, suggesting a decoupling of the processes regulating community composition within these taxonomic groups. According to the metacommunity theory, patterns in bacterial and archaeal community composition suggest a role for species sorting, while patterns of virus community composition are consistent with species sorting in the Labrador Sea and suggest a potential role of mass effects in the Arctic Archipelago. Given that, a specific prokaryotic taxon may be infected by multiple viruses with high reproductive potential, our results suggest that viral community composition was subject to a high turnover relative to prokaryotic community composition in the Arctic Archipelago.},
}
@article {pmid23550964,
year = {2013},
author = {Delgado-Baquerizo, M and Gallardo, A and Wallenstein, MD and Maestre, FT},
title = {Vascular plants mediate the effects of aridity and soil properties on ammonia-oxidizing bacteria and archaea.},
journal = {FEMS microbiology ecology},
volume = {85},
number = {2},
pages = {273-282},
doi = {10.1111/1574-6941.12119},
pmid = {23550964},
issn = {1574-6941},
support = {242658/ERC_/European Research Council/International ; },
mesh = {Ammonia/*metabolism ; Archaea/genetics/isolation &amp; purification/*metabolism ; Bacteria/genetics/isolation &amp; purification/*metabolism ; *Ecosystem ; Environment ; Nitrification ; Oxidation-Reduction ; Plant Physiological Phenomena ; Soil/chemistry ; *Soil Microbiology ; },
abstract = {An integrated perspective of the most important factors driving the abundance of ammonia-oxidizing bacteria (AOB) and archaea (AOA) in natural ecosystems is lacking, especially in drylands. We evaluated how different climatic, abiotic, and nutrient-related factors determine AOA and AOB abundance in bare and vegetated microsites from grasslands throughout the Mediterranean Basin. We found a strong negative relationship between the abundance of AOA genes and soil fertility (availability of C, N, and P). Aridity and other abiotic factors (pH, sand content, and electrical conductivity) were more important than soil fertility in modulating the AOA/AOB ratio. AOB were more abundant under vegetated microsites, while AOA, highly resistant to stressful conditions, were more abundant in bare ground areas. These results suggest that AOA may carry out nitrification in less fertile microsites, while AOB predominate under more fertile conditions. Our results indicate that the influence of aridity and pH on the relative dominance of AOA and AOB genes is ultimately determined by local-scale environmental changes promoted by perennial vegetation. Thus, in spatially heterogeneous ecosystems such as drylands, there is a mutual exclusion and niche division between these microorganisms, suggesting that they may be functionally complementary.},
}
@article {pmid23535597,
year = {2013},
author = {Lloyd, KG and Schreiber, L and Petersen, DG and Kjeldsen, KU and Lever, MA and Steen, AD and Stepanauskas, R and Richter, M and Kleindienst, S and Lenk, S and Schramm, A and Jørgensen, BB},
title = {Predominant archaea in marine sediments degrade detrital proteins.},
journal = {Nature},
volume = {496},
number = {7444},
pages = {215-218},
pmid = {23535597},
issn = {1476-4687},
mesh = {Adhesins, Bacterial/metabolism ; Archaea/classification/enzymology/genetics/*metabolism ; Cysteine Endopeptidases/metabolism ; Geologic Sediments/chemistry/*microbiology ; Gingipain Cysteine Endopeptidases ; Marine Biology ; Molecular Sequence Data ; Peptide Hydrolases/*metabolism ; Phylogeny ; Proteolysis ; RNA, Ribosomal, 16S/genetics ; Single-Cell Analysis ; },
abstract = {Half of the microbial cells in the Earth's oceans are found in sediments. Many of these cells are members of the Archaea, single-celled prokaryotes in a domain of life separate from Bacteria and Eukaryota. However, most of these archaea lack cultured representatives, leaving their physiologies and placement on the tree of life uncertain. Here we show that the uncultured miscellaneous crenarchaeotal group (MCG) and marine benthic group-D (MBG-D) are among the most numerous archaea in the marine sub-sea floor. Single-cell genomic sequencing of one cell of MCG and three cells of MBG-D indicated that they form new branches basal to the archaeal phyla Thaumarchaeota and Aigarchaeota, for MCG, and the order Thermoplasmatales, for MBG-D. All four cells encoded extracellular protein-degrading enzymes such as gingipain and clostripain that are known to be effective in environments chemically similar to marine sediments. Furthermore, we found these two types of peptidase to be abundant and active in marine sediments, indicating that uncultured archaea may have a previously undiscovered role in protein remineralization in anoxic marine sediments.},
}
@article {pmid23533332,
year = {2013},
author = {Wrede, C and Walbaum, U and Ducki, A and Heieren, I and Hoppert, M},
title = {Localization of Methyl-Coenzyme M reductase as metabolic marker for diverse methanogenic Archaea.},
journal = {Archaea (Vancouver, B.C.)},
volume = {2013},
number = {},
pages = {920241},
pmid = {23533332},
issn = {1472-3654},
mesh = {Anaerobiosis ; Antibodies/metabolism ; Archaea/*chemistry/*enzymology ; Cell Membrane/chemistry/enzymology ; Cytoplasm/chemistry/enzymology ; Methane/metabolism ; Oxidation-Reduction ; Oxidoreductases/*analysis ; Staining and Labeling/methods ; },
abstract = {Methyl-Coenzyme M reductase (MCR) as key enzyme for methanogenesis as well as for anaerobic oxidation of methane represents an important metabolic marker for both processes in microbial biofilms. Here, the potential of MCR-specific polyclonal antibodies as metabolic marker in various methanogenic Archaea is shown. For standard growth conditions in laboratory culture, the cytoplasmic localization of the enzyme in Methanothermobacter marburgensis, Methanothermobacter wolfei, Methanococcus maripaludis, Methanosarcina mazei, and in anaerobically methane-oxidizing biofilms is demonstrated. Under growth limiting conditions on nickel-depleted media, at low linear growth of cultures, a fraction of 50-70% of the enzyme was localized close to the cytoplasmic membrane, which implies "facultative" membrane association of the enzyme. This feature may be also useful for assessment of growth-limiting conditions in microbial biofilms.},
}
@article {pmid23533330,
year = {2013},
author = {Browne, PD and Cadillo-Quiroz, H},
title = {Contribution of transcriptomics to systems-level understanding of methanogenic Archaea.},
journal = {Archaea (Vancouver, B.C.)},
volume = {2013},
number = {},
pages = {586369},
pmid = {23533330},
issn = {1472-3654},
mesh = {Archaea/*genetics/*metabolism ; Gene Expression Regulation, Archaeal ; High-Throughput Nucleotide Sequencing/methods ; Methane/*metabolism ; *Systems Biology ; *Transcriptome ; },
abstract = {Methane-producing Archaea are of interest due to their contribution to atmospheric change and for their roles in technological applications including waste treatment and biofuel production. Although restricted to anaerobic environments, methanogens are found in a wide variety of habitats, where they commonly live in syntrophic relationships with bacterial partners. Owing to tight thermodynamic constraints of methanogenesis alone or in syntrophic metabolism, methanogens must carefully regulate their catabolic pathways including the regulation of RNA transcripts. The transcriptome is a dynamic and important control point in microbial systems. This paper assesses the impact of mRNA (transcriptome) studies on the understanding of methanogenesis with special consideration given to how methanogenesis is regulated to cope with nutrient limitation, environmental variability, and interactions with syntrophic partners. In comparison with traditional microarray-based transcriptome analyses, next-generation high-throughput RNA sequencing is greatly advantageous in assessing transcription start sites, the extent of 5' untranslated regions, operonic structure, and the presence of small RNAs. We are still in the early stages of understanding RNA regulation but it is already clear that determinants beyond transcript abundance are highly relevant to the lifestyles of methanogens, requiring further study.},
}
@article {pmid23530864,
year = {2013},
author = {Bertram, S and Blumenberg, M and Michaelis, W and Siegert, M and Krüger, M and Seifert, R},
title = {Methanogenic capabilities of ANME-archaea deduced from (13) C-labelling approaches.},
journal = {Environmental microbiology},
volume = {15},
number = {8},
pages = {2384-2393},
doi = {10.1111/1462-2920.12112},
pmid = {23530864},
issn = {1462-2920},
mesh = {Anaerobiosis/physiology ; Archaea/chemistry/isolation &amp; purification/*metabolism ; Black Sea ; Carbon Isotopes/analysis ; Isotope Labeling ; Lipids/biosynthesis/chemistry ; Methane/biosynthesis/chemistry ; Methanol/chemistry ; Oxidation-Reduction ; Seawater/*microbiology ; Sulfates ; },
abstract = {Anaerobic methanotrophic archaea (ANME) are ubiquitous in marine sediments where sulfate dependent anaerobic oxidation of methane (AOM) occurs. Despite considerable progress in the understanding of AOM, physiological details are still widely unresolved. We investigated two distinct microbial mat samples from the Black Sea that were dominated by either ANME-1 or ANME-2. The (13) C lipid stable isotope probing (SIP) method using labelled substances, namely methane, bicarbonate, acetate, and methanol, was applied, and the substrate-dependent methanogenic capabilities were tested. Our data provide strong evidence for a versatile physiology of both, ANME-1 and ANME-2. Considerable methane production rates (MPRs) from CO2 -reduction were observed, particularly from ANME-2 dominated samples and in the presence of methane, which supports the hypothesis of a co-occurrence of methanotrophy and methanogenesis in the AOM systems (AOM/MPR up to 2:1). The experiments also revealed strong methylotrophic capabilities through (13) C-assimilation from labelled methanol, which was independent of the presence of methane. Additionally, high MPRs from methanol were detected in both of the mat samples. As demonstrated by the (13) C-uptake into lipids, ANME-1 was found to thrive also under methane free conditions. Finally, C35 -isoprenoid hydrocarbons were identified as new lipid biomarkers for ANME-1, most likely functioning as a hydrogen sink during methanogenesis.},
}
@article {pmid23530048,
year = {2013},
author = {Niu, Y and Xia, Y and Wang, S and Li, J and Niu, C and Li, X and Zhao, Y and Xiong, H and Li, Z and Lou, H and Cao, Q},
title = {A prototypic lysine methyltransferase 4 from archaea with degenerate sequence specificity methylates chromatin proteins Sul7d and Cren7 in different patterns.},
journal = {The Journal of biological chemistry},
volume = {288},
number = {19},
pages = {13728-13740},
pmid = {23530048},
issn = {1083-351X},
mesh = {Amino Acid Motifs ; Amino Acid Sequence ; Amino Acid Substitution ; Archaeal Proteins/*chemistry/genetics ; Chromatin/chemistry ; Conserved Sequence ; DNA, Archaeal/chemistry ; DNA-Binding Proteins/*chemistry ; Methylation ; Molecular Sequence Data ; Protein Methyltransferases/*chemistry/genetics ; *Protein Processing, Post-Translational ; Substrate Specificity ; Sulfolobus/*enzymology ; },
abstract = {BACKGROUND: The origin of eukaryotic histone modification enzymes still remains obscure.<br><br>RESULTS: Prototypic KMT4/Dot1 from Archaea targets chromatin proteins (Sul7d and Cren7) and shows increased activity on Sul7d, but not Cren7, in the presence of DNA.<br><br>CONCLUSION: Promiscuous aKMT4 could be regulated by chromatin environment.<br><br>SIGNIFICANCE: This study supports the prokaryotic origin model of eukaryotic histone methyltransferases and sheds light on chromatin dynamics in Archaea. Histone methylation is one of the major epigenetic modifications even in early diverging unicellular eukaryotes. We show that a widespread lysine methyltransferase from Archaea (aKMT4), bears striking structural and functional resemblance to the core of distantly related eukaryotic KMT4/Dot1. aKMT4 methylates a set of various proteins, including the chromatin proteins Sul7d and Cren7, and RNA exosome components. Csl4- and Rrp4-exosome complexes are methylated in different patterns. aKMT4 can self-methylate intramolecularly and compete with other proteins for the methyl group. Automethylation is inhibited by suitable substrates or DNA in a concentration-dependent manner. The automethylated enzyme shows relatively compromised activity. aKMT4-8A mutant with abrogated automethylation shows a more than 150% increase in methylation of substrates, suggesting a possible mechanism to regulate methyltransferase activity. More interestingly, methylation of Sul7d, but not Cren7, by aKMT4 is significantly enhanced by DNA. MS/MS and kinetic analysis further suggest that aKMT4 methylates Sul7d in the chromatin context. These data provide a clue to the possible regulation of aKMT4 activity by the local chromatin environment, albeit as a promiscuous enzyme required for extensive and variegated lysine methylation in Sulfolobus. This study supports the prokaryotic origin model of eukaryotic histone modification enzymes and sheds light on regulation of archaeal chromatin.},
}
@article {pmid23525724,
year = {2013},
author = {Ciesielski, S and Bułkowska, K and Dabrowska, D and Kaczmarczyk, D and Kowal, P and Możejko, J},
title = {Ribosomal intergenic spacer analysis as a tool for monitoring methanogenic Archaea changes in an anaerobic digester.},
journal = {Current microbiology},
volume = {67},
number = {2},
pages = {240-248},
pmid = {23525724},
issn = {1432-0991},
mesh = {Anaerobiosis ; Archaea/classification/genetics/*isolation &amp; purification/metabolism ; Bioreactors ; DNA Primers/genetics ; DNA, Archaeal/*genetics ; DNA, Ribosomal Spacer/*genetics ; Medicago sativa/metabolism/microbiology ; Methane/*metabolism ; Polymerase Chain Reaction/*methods ; RNA, Ribosomal, 16S ; Zea mays/metabolism/microbiology ; },
abstract = {The applicability of a newly-designed PCR primer pair in examination of methanogenic Archaea in a digester treating plant biomass was evaluated by Ribosmal Intergenic Spacer Analysis (RISA). To find a suitable approach, three variants of RISA were tested: (1) standard, polyacrylamide gel-based, (2) automated, utilized capillary electrophoresis (GA-ARISA), and (3) automated microfluidics-based (MF-ARISA). All three techniques yielded a consistent picture of archaeal community structure changes during anaerobic digestion monitored for more than 6 weeks. While automated variants were more practical for handling and rapid analysis of methanogenic Archaea, the gel-based technique was advantageous when micro-organism identification was required. A DNA-sequence analysis of dominant bands extracted from the gel revealed that the main role in methane synthesis was played by micro-organisms affiliated with Methanosarcina barkeri. The obtained results revealed that RISA is a robust method allowing for detailed analysis of archaeal community structure during organic biomass conversion into biogas. In addition, our results showed that GA-ARISA has a higher resolution and reproducibility than other variants of RISA and could be used as a technique for tracking changes in methanogenic Archaea in an anaerobic digester.},
}
@article {pmid23515915,
year = {2013},
author = {Catão, E and Castro, AP and Barreto, CC and Krüger, RH and Kyaw, CM},
title = {Diversity of Archaea in Brazilian savanna soils.},
journal = {Archives of microbiology},
volume = {195},
number = {7},
pages = {507-512},
doi = {10.1007/s00203-013-0882-x},
pmid = {23515915},
issn = {1432-072X},
mesh = {Archaea/*classification/*genetics/isolation &amp; purification ; Brazil ; Genes, Archaeal ; Genes, rRNA ; Metagenome ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Soil/chemistry ; *Soil Microbiology ; Trees ; },
abstract = {Although the richness of Bacteria and Fungi in Cerrado' soils has been reported, here we report, for the first time, the archaeal community in Cerrado's soils. DNA extracted from soil of two distinct vegetation types, a dense subtype of sensu strict (cerrado denso) and riverbank forest (mata de galeria), was used to amplify Archaea-specific 16S rRNA gene. All of the fragments sequenced were classified as Archaea into the phylum Thaumarchaeota, predominantly affiliated to groups I.1b and I.1c. Sequences affiliated to the group I.1a were found only in the soil from riverbank forest. Soils from 'cerrado denso' had greater Archaea richness than those from 'mata de galeria' based on the richness indexes and on the rarefaction curve. β-Diversity analysis showed significant differences between the sequences from the two soil areas studied because of their different thaumarchaeal group composition. These results provide information about the third domain of life from Cerrado soils.},
}
@article {pmid23495939,
year = {2013},
author = {Sorek, R and Lawrence, CM and Wiedenheft, B},
title = {CRISPR-mediated adaptive immune systems in bacteria and archaea.},
journal = {Annual review of biochemistry},
volume = {82},
number = {},
pages = {237-266},
doi = {10.1146/annurev-biochem-072911-172315},
pmid = {23495939},
issn = {1545-4509},
support = {R01 GM108888/GM/NIGMS NIH HHS/United States ; GM 103500/GM/NIGMS NIH HHS/United States ; },
mesh = {Adaptive Immunity/*genetics ; Archaea/genetics/*immunology ; Bacteria/genetics/*immunology ; Inverted Repeat Sequences/*genetics/immunology ; RNA, Archaeal/*genetics/immunology ; RNA, Bacterial/*genetics/immunology ; Signal Transduction/*genetics/immunology ; },
abstract = {Effective clearance of an infection requires that the immune system rapidly detects and neutralizes invading parasites while strictly avoiding self-antigens that would result in autoimmunity. The cellular machinery and complex signaling pathways that coordinate an effective immune response have generally been considered properties of the eukaryotic immune system. However, a surprisingly sophisticated adaptive immune system that relies on small RNAs for sequence-specific targeting of foreign nucleic acids was recently discovered in bacteria and archaea. Molecular vaccination in prokaryotes is achieved by integrating short fragments of foreign nucleic acids into a repetitive locus in the host chromosome known as a CRISPR (clustered regularly interspaced short palindromic repeat). Here we review the mechanisms of CRISPR-mediated immunity and discuss the ecological and evolutionary implications of these adaptive defense systems.},
}
@article {pmid23473400,
year = {2013},
author = {Hou, J and Song, C and Cao, X and Zhou, Y},
title = {Shifts between ammonia-oxidizing bacteria and archaea in relation to nitrification potential across trophic gradients in two large Chinese lakes (Lake Taihu and Lake Chaohu).},
journal = {Water research},
volume = {47},
number = {7},
pages = {2285-2296},
doi = {10.1016/j.watres.2013.01.042},
pmid = {23473400},
issn = {1879-2448},
mesh = {Ammonia/*metabolism ; Archaea/*metabolism ; Bacteria/genetics/*metabolism ; Base Sequence ; China ; Environmental Microbiology ; *Eutrophication ; Genes, Bacterial/genetics ; Geography ; Geologic Sediments/microbiology ; Lakes/*microbiology ; Molecular Sequence Data ; *Nitrification ; Oxidation-Reduction ; Phylogeny ; Polymorphism, Restriction Fragment Length ; },
abstract = {Ammonia oxidation plays a pivotal role in the cycling and removal of nitrogen in aquatic ecosystems. Recent findings have expanded the known ammonia-oxidizing prokaryotes from Bacteria to Archaea. However, the relative importance of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) in nitrification is still debated. Here we showed that, in two large eutrophic lakes in China (Lake Taihu and Lake Chaohu), the abundance of AOA and AOB varied in opposite patterns according to the trophic state, although both AOA and AOB were abundant. In detail, from mesotrophic to eutrophic sites, the AOA abundance decreased, while the AOB increased in abundance and outnumbered the AOA at hypertrophic sites. In parallel, the nitrification rate increased along these trophic gradients and was significantly correlated with both the AOB abundance and the numerical ratio of AOB to AOA. Phylogenetic analysis of bacterial amoA sequences showed that Nitrosomonas oligotropha- and Nitrosospira-affiliated AOB dominated in both lakes, while Nitrosomonas communis-related AOB were only detected at the eutrophic sites. The diversity of AOB increased from mesotrophic to eutrophic sites and was positively correlated with the nitrification rate. Overall, this study enhances our understanding of the ecology of ammonia-oxidizing prokaryotes by elucidating conditions that AOB may numerically predominated over AOA, and indicated that AOA may play a less important role than AOB in the nitrification process of eutrophic lakes.},
}
@article {pmid23471408,
year = {2013},
author = {Schönknecht, G and Chen, WH and Ternes, CM and Barbier, GG and Shrestha, RP and Stanke, M and Bräutigam, A and Baker, BJ and Banfield, JF and Garavito, RM and Carr, K and Wilkerson, C and Rensing, SA and Gagneul, D and Dickenson, NE and Oesterhelt, C and Lercher, MJ and Weber, AP},
title = {Gene transfer from bacteria and archaea facilitated evolution of an extremophilic eukaryote.},
journal = {Science (New York, N.Y.)},
volume = {339},
number = {6124},
pages = {1207-1210},
doi = {10.1126/science.1231707},
pmid = {23471408},
issn = {1095-9203},
mesh = {Adaptation, Physiological/*genetics ; Adenosine Triphosphatases/genetics ; Archaea/classification/genetics ; Bacteria/classification/genetics ; DNA, Algal ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genes, Archaeal ; *Genes, Bacterial ; Genome, Plant/*genetics ; Phylogeny ; Rhodophyta/*genetics/*microbiology/physiology ; },
abstract = {Some microbial eukaryotes, such as the extremophilic red alga Galdieria sulphuraria, live in hot, toxic metal-rich, acidic environments. To elucidate the underlying molecular mechanisms of adaptation, we sequenced the 13.7-megabase genome of G. sulphuraria. This alga shows an enormous metabolic flexibility, growing either photoautotrophically or heterotrophically on more than 50 carbon sources. Environmental adaptation seems to have been facilitated by horizontal gene transfer from various bacteria and archaea, often followed by gene family expansion. At least 5% of protein-coding genes of G. sulphuraria were probably acquired horizontally. These proteins are involved in ecologically important processes ranging from heavy-metal detoxification to glycerol uptake and metabolism. Thus, our findings show that a pan-domain gene pool has facilitated environmental adaptation in this unicellular eukaryote.},
}
@article {pmid23470997,
year = {2013},
author = {Makarova, KS and Wolf, YI and Koonin, EV},
title = {Comparative genomics of defense systems in archaea and bacteria.},
journal = {Nucleic acids research},
volume = {41},
number = {8},
pages = {4360-4377},
pmid = {23470997},
issn = {1362-4962},
support = {//Intramural NIH HHS/United States ; },
mesh = {Adaptive Immunity ; Archaea/genetics/*immunology ; Bacteria/genetics/*immunology ; DNA Restriction-Modification Enzymes/metabolism ; *Genome, Archaeal ; *Genome, Bacterial ; Genomics ; Immunity, Innate ; },
abstract = {Our knowledge of prokaryotic defense systems has vastly expanded as the result of comparative genomic analysis, followed by experimental validation. This expansion is both quantitative, including the discovery of diverse new examples of known types of defense systems, such as restriction-modification or toxin-antitoxin systems, and qualitative, including the discovery of fundamentally new defense mechanisms, such as the CRISPR-Cas immunity system. Large-scale statistical analysis reveals that the distribution of different defense systems in bacterial and archaeal taxa is non-uniform, with four groups of organisms distinguishable with respect to the overall abundance and the balance between specific types of defense systems. The genes encoding defense system components in bacterial and archaea typically cluster in defense islands. In addition to genes encoding known defense systems, these islands contain numerous uncharacterized genes, which are candidates for new types of defense systems. The tight association of the genes encoding immunity systems and dormancy- or cell death-inducing defense systems in prokaryotic genomes suggests that these two major types of defense are functionally coupled, providing for effective protection at the population level.},
}
@article {pmid23468838,
year = {2013},
author = {Cao, H and Auguet, JC and Gu, JD},
title = {Global ecological pattern of ammonia-oxidizing archaea.},
journal = {PloS one},
volume = {8},
number = {2},
pages = {e52853},
pmid = {23468838},
issn = {1932-6203},
mesh = {Ammonia/*metabolism ; Archaea/classification/genetics/*metabolism ; Biodiversity ; *Ecosystem ; Genes, Archaeal ; Oxidation-Reduction ; Phylogeny ; },
abstract = {BACKGROUND: The global distribution of ammonia-oxidizing archaea (AOA), which play a pivotal role in the nitrification process, has been confirmed through numerous ecological studies. Though newly available amoA (ammonia monooxygenase subunit A) gene sequences from new environments are accumulating rapidly in public repositories, a lack of information on the ecological and evolutionary factors shaping community assembly of AOA on the global scale is apparent.<br><br>METHODOLOGY AND RESULTS: We conducted a meta-analysis on uncultured AOA using over ca. 6,200 archaeal amoA gene sequences, so as to reveal their community distribution patterns along a wide spectrum of physicochemical conditions and habitat types. The sequences were dereplicated at 95% identity level resulting in a dataset containing 1,476 archaeal amoA gene sequences from eight habitat types: namely soil, freshwater, freshwater sediment, estuarine sediment, marine water, marine sediment, geothermal system, and symbiosis. The updated comprehensive amoA phylogeny was composed of three major monophyletic clusters (i.e. Nitrosopumilus, Nitrosotalea, Nitrosocaldus) and a non-monophyletic cluster constituted mostly by soil and sediment sequences that we named Nitrososphaera. Diversity measurements indicated that marine and estuarine sediments as well as symbionts might be the largest reservoirs of AOA diversity. Phylogenetic analyses were further carried out using macroevolutionary analyses to explore the diversification pattern and rates of nitrifying archaea. In contrast to other habitats that displayed constant diversification rates, marine planktonic AOA interestingly exhibit a very recent and accelerating diversification rate congruent with the lowest phylogenetic diversity observed in their habitats. This result suggested the existence of AOA communities with different evolutionary history in the different habitats.<br><br>CONCLUSION AND SIGNIFICANCE: Based on an up-to-date amoA phylogeny, this analysis provided insights into the possible evolutionary mechanisms and environmental parameters that shape AOA community assembly at global scale.},
}
@article {pmid23466705,
year = {2013},
author = {Alves, RJ and Wanek, W and Zappe, A and Richter, A and Svenning, MM and Schleper, C and Urich, T},
title = {Nitrification rates in Arctic soils are associated with functionally distinct populations of ammonia-oxidizing archaea.},
journal = {The ISME journal},
volume = {7},
number = {8},
pages = {1620-1631},
pmid = {23466705},
issn = {1751-7370},
support = {P 23000/FWF_/Austrian Science Fund FWF/Austria ; },
mesh = {Ammonia/*metabolism ; Archaea/*classification/genetics/growth &amp; development/metabolism/*physiology ; Arctic Regions ; Bacteria/classification/genetics/metabolism ; *Biodiversity ; Molecular Sequence Data ; *Nitrification ; Oxidation-Reduction ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Soil/*chemistry ; *Soil Microbiology ; },
abstract = {The functioning of Arctic soil ecosystems is crucially important for global climate, and basic knowledge regarding their biogeochemical processes is lacking. Nitrogen (N) is the major limiting nutrient in these environments, and its availability is strongly dependent on nitrification. However, microbial communities driving this process remain largely uncharacterized in Arctic soils, namely those catalyzing the rate-limiting step of ammonia (NH3) oxidation. Eleven Arctic soils were analyzed through a polyphasic approach, integrating determination of gross nitrification rates, qualitative and quantitative marker gene analyses of ammonia-oxidizing archaea (AOA) and bacteria (AOB) and enrichment of AOA in laboratory cultures. AOA were the only NH3 oxidizers detected in five out of 11 soils and outnumbered AOB in four of the remaining six soils. The AOA identified showed great phylogenetic diversity and a multifactorial association with the soil properties, reflecting an overall distribution associated with tundra type and with several physico-chemical parameters combined. Remarkably, the different gross nitrification rates between soils were associated with five distinct AOA clades, representing the great majority of known AOA diversity in soils, which suggests differences in their nitrifying potential. This was supported by selective enrichment of two of these clades in cultures with different NH3 oxidation rates. In addition, the enrichments provided the first direct evidence for NH3 oxidation by an AOA from an uncharacterized Thaumarchaeota-AOA lineage. Our results indicate that AOA are functionally heterogeneous and that the selection of distinct AOA populations by the environment can be a determinant for nitrification activity and N availability in soils.},
}
@article {pmid23446883,
year = {2012},
author = {Maier, LK and Fischer, S and Stoll, B and Brendel, J and Pfeiffer, F and Dyall-Smith, M and Marchfelder, A},
title = {The immune system of halophilic archaea.},
journal = {Mobile genetic elements},
volume = {2},
number = {5},
pages = {228-232},
pmid = {23446883},
issn = {2159-2543},
abstract = {Prokaryotes have developed several strategies to defend themselves against foreign genetic elements. One of those defense mechanisms is the recently identified CRISPR/Cas system, which is used by approximately half of all bacterial and almost all archaeal organisms. The CRISPR/Cas system differs from the other defense strategies because it is adaptive, hereditary and it recognizes the invader by a sequence specific mechanism. To identify the invading foreign nucleic acid, a crRNA that matches the invader DNA is required, as well as a short sequence motif called protospacer adjacent motif (PAM). We recently identified the PAM sequences for the halophilic archaeon Haloferax volcanii, and found that several motifs were active in triggering the defense reaction. In contrast, selection of protospacers from the invader seems to be based on fewer PAM sequences, as evidenced by comparative sequence data. This suggests that the selection of protospacers has stricter requirements than the defense reaction. Comparison of CRISPR-repeat sequences carried by sequenced haloarchaea revealed that in more than half of the species, the repeat sequence is conserved and that they have the same CRISPR/Cas type.},
}
@article {pmid23425063,
year = {2014},
author = {Saengkerdsub, S and Ricke, SC},
title = {Ecology and characteristics of methanogenic archaea in animals and humans.},
journal = {Critical reviews in microbiology},
volume = {40},
number = {2},
pages = {97-116},
doi = {10.3109/1040841X.2013.763220},
pmid = {23425063},
issn = {1549-7828},
mesh = {Animals ; Archaea/*classification/immunology/*metabolism ; *Biota ; Diet ; Humans ; Methane/*metabolism ; Microbial Interactions ; Microbiological Techniques/methods ; Molecular Biology/methods ; Oxidoreductases/genetics ; RNA, Ribosomal, 16S/genetics ; },
abstract = {In this review, the molecular techniques used in animal-based-methanogen studies will be discussed along with how methanogens interact not only with other microorganisms but with their animal hosts as well. These methods not only indicate the diversity and levels of methanogens, but also provide insight on their ecological functions. Most molecular techniques have been based on either 16S rRNA genes or methyl-coenzyme M reductase, a ubiquitous enzyme in methanogens. The most predominant methanogens in animals belong to the genus Methanobrevibacter. Besides methanogens contributing to overall H2 balance, methanogens also have mutual interactions with other bacteria. In addition to shared metabolic synergism, the host animal retrieves additional energy from the diet when methanogens are co-colonized with other normal flora. By comparing genes in methanogens with other bacteria, possible gene transfer between methanogens and other bacteria in the same environments appears to occur. Finally, diets in conjunction with the genetics of methanogens and hosts may represent the biological framework that dictate the extent of methanogen prevalence in these ecosystems. In addition, host evolution including the immune system could serve as an additional selective pressure for methanogen colonization.},
}
@article {pmid23416999,
year = {2013},
author = {Mayrhofer-Iro, M and Ladurner, A and Meissner, C and Derntl, C and Reiter, M and Haider, F and Dimmel, K and Rössler, N and Klein, R and Baranyi, U and Scholz, H and Witte, A},
title = {Utilization of virus φCh1 elements to establish a shuttle vector system for Halo(alkali)philic Archaea via transformation of Natrialba magadii.},
journal = {Applied and environmental microbiology},
volume = {79},
number = {8},
pages = {2741-2748},
pmid = {23416999},
issn = {1098-5336},
mesh = {DNA, Viral/chemistry/genetics ; Escherichia coli/genetics ; Genes, Reporter ; *Genetic Vectors ; Halobacteriaceae/*genetics ; Haloferax/genetics ; Myoviridae/*genetics ; Transfection ; *Transformation, Genetic ; },
abstract = {In the study described here, we successfully developed a transformation system for halo(alkali)philic members of the Archaea. This transformation system comprises a series of Natrialba magadii/Escherichia coli shuttle vectors based on a modified method to transform halophilic members of the Archaea and genomic elements of the N. magadii virus Ch1. The shuttle vector pRo-5, based on the repH-containing region of Ch1, stably replicated in E. coli and N. magadii and in several halophilic and haloalkaliphilic members of the Archaea not transformable so far. The Ch1 operon ORF53/ORF54 (repH) was essential for pRo-5 replication and was thus identified as the minimal replication origin. The plasmid allowed homologous and heterologous gene expression, as exemplified by the expression of Ch1 ORF3452, which encodes a structural protein, and the reporter gene bgaH of Haloferax lucentense in N. magadii. The new transformation/vector system will facilitate genetic studies within N. magadii and other haloalkaliphilic archaea and will allow the detailed characterization of the gene functions of N. magadii virus Ch1 in their extreme environments.},
}
@article {pmid23412053,
year = {2013},
author = {Li, J and Zhang, L and Ban, Q and Jha, AK and Xu, Y},
title = {Diversity and distribution of methanogenic archaea in an anaerobic baffled reactor (ABR) treating sugar refinery wastewater.},
journal = {Journal of microbiology and biotechnology},
volume = {23},
number = {2},
pages = {137-143},
doi = {10.4014/jmb.1204.04043},
pmid = {23412053},
issn = {1738-8872},
mesh = {Anaerobiosis ; Archaea/*classification/genetics/*physiology ; *Biodiversity ; Bioreactors/*microbiology ; DNA, Archaeal/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Denaturing Gradient Gel Electrophoresis ; Methane/*metabolism ; Molecular Sequence Data ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Wastewater/*microbiology ; },
abstract = {The diversity and distribution of methanogenic archaea in a four-compartment anaerobic baffled reactor (ABR) treating sugar refinery wastewater were investigated by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE). At an organic loading rate of 5.33 kg COD/m3·day, the ABR could perform steadily with the mean chemical oxygen demand (COD) removal of 94.8% and the specific CH4 yield of 0.21 l/g COD(removed). The CH4 content in the biogas was increased along the compartments, whereas the percentage of H2 was decreased, indicating the distribution characteristics of the methanogens occurred longitudinally down the ABR. A high phylogenetic and ecological diversity of methanogens was found in the ABR, and all the detected methanogens were classified into six groups, including Methanomicrobiales, Methanosarcinales, Methanobacteriales, Crenarchaeota, Arc I, and Unidentified. Among the methanogenic population, the acid-tolerant hydrogenotrophic methanogens including Methanoregula and Methanosphaerula dominated the first two compartments. In the last two compartments, the dominant methanogenic population was Methanosaeta, which was the major acetate oxidizer under methanogenic conditions and could promote the formation of granular sludge. The distribution of the hydrogenotrophic (acid-tolerant) and acetotrophic methanogens in sequence along the compartments allowed the ABR to perform more efficiently and steadily.},
}
@article {pmid23404650,
year = {2013},
author = {Chen, J and Wang, F and Jiang, L and Yin, X and Xiao, X},
title = {Stratified communities of active archaea in shallow sediments of the Pearl River Estuary, Southern China.},
journal = {Current microbiology},
volume = {67},
number = {1},
pages = {41-50},
pmid = {23404650},
issn = {1432-0991},
mesh = {Anaerobiosis ; Archaea/*classification/*genetics/physiology ; *Biodiversity ; China ; Cluster Analysis ; DNA, Archaeal/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; *Estuaries ; Geologic Sediments/*microbiology ; Methane/metabolism ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Rivers/*microbiology ; Sequence Analysis, DNA ; },
abstract = {Marine subsurface sediments represent a novel archaeal biosphere with unknown physiology. To get to know the composition and ecological roles of the archaeal communities within the sediments of the Pearl River Estuary, Southern China, the diversity and vertical distribution of active archaea in a sediment core were characterized by 16S rRNA phylogenetic analysis of clone libraries derived from RNA. In this study, the archaeal diversity above, within, and beneath the sulfate-methane transition zone (SMTZ) in the Pearl River Estuary sediment core was described. The majority of the clones obtained from the metabolically active fraction of the archaeal community were most closely related to miscellaneous crenarchaeotal group and terrestrial miscellaneous euryarchaeotal group. Notably, although the Pearl River Estuary sediment belong to high methane and high organic carbon environment, sequences affiliated with methanotrophic and methanogenic archaea were detected as minor group in 16S rRNA clone libraries. No obvious evidence suggested that these unknown archaeal phylotypes related directly to anaerobic oxidation of methane in SMTZ. This is the first phylogenetic analysis of the metabolically active fraction of the archaeal community in the coastal sediment environments.},
}
@article {pmid23401664,
year = {2013},
author = {Torres-Alvarado, Mdel R and Fernández, FJ and Ramírez Vives, F and Varona-Cordero, F},
title = {Dynamics of the methanogenic archaea in tropical estuarine sediments.},
journal = {Archaea (Vancouver, B.C.)},
volume = {2013},
number = {},
pages = {582646},
pmid = {23401664},
issn = {1472-3654},
mesh = {Acetates/metabolism ; Archaea/*growth &amp; development/*metabolism ; Cell Count ; Geologic Sediments/*microbiology ; Methane/*metabolism ; Models, Biological ; Sulfates/metabolism ; Temperature ; Tropical Climate ; Water/chemistry ; },
abstract = {Methanogenesis may represent a key process in the terminal phases of anaerobic organic matter mineralization in sediments of coastal lagoons. The aim of the present work was to study the temporal and spatial dynamics of methanogenic archaea in sediments of tropical coastal lagoons and their relationship with environmental changes in order to determine how these influence methanogenic community. Sediment samples were collected during the dry (February, May, and early June) and rainy seasons (July, October, and November). Microbiological analysis included the quantification of viable methanogenic archaea (MA) with three substrates and the evaluation of kinetic activity from acetate in the presence and absence of sulfate. The environmental variables assessed were temperature, pH, Eh, salinity, sulfate, solids content, organic carbon, and carbohydrates. MA abundance was significantly higher in the rainy season (10(6)-10(7) cells/g) compared with the dry season (10(4)-10(6) cells/g), with methanol as an important substrate. At spatial level, MA were detected in the two layers analyzed, and no important variations were observed either in MA abundance or activity. Salinity, sulfate, solids, organic carbon, and Eh were the environmental variables related to methanogenic community. A conceptual model is proposed to explain the dynamics of the MA.},
}
@article {pmid23395876,
year = {2013},
author = {Hugoni, M and Etien, S and Bourges, A and Lepère, C and Domaizon, I and Mallet, C and Bronner, G and Debroas, D and Mary, I},
title = {Dynamics of ammonia-oxidizing Archaea and Bacteria in contrasted freshwater ecosystems.},
journal = {Research in microbiology},
volume = {164},
number = {4},
pages = {360-370},
doi = {10.1016/j.resmic.2013.01.004},
pmid = {23395876},
issn = {1769-7123},
mesh = {Ammonia/*metabolism ; Archaea/classification/genetics/*growth &amp; development/*metabolism ; Bacteria/classification/genetics/*growth &amp; development/*metabolism ; *Biota ; France ; Fresh Water/*microbiology ; Molecular Sequence Data ; Oxidation-Reduction ; Seasons ; Sequence Analysis, DNA ; },
abstract = {Thaumarchaeota have been recognized as the main drivers of aerobic ammonia oxidation in many ecosystems. However, little is known about the role of ammonia-oxidizing Archaea (AOA) and Bacteria (AOB) in lacustrine ecosystems. In this study, the photic zone of three contrasted freshwater ecosystems located in France was sampled during two periods: winter homothermy (H) and summer thermal stratification (TS), to investigate the distribution of planktonic AOA and AOB. We showed that AOB were predominant in nutrient-rich ecosystems, whereas AOA dominated when ammonia concentrations were the lowest and during winter, which could provide a favorable environment for their growth. Moreover, analyses of archaeal libraries revealed the ubiquity of the thaumarchaeal I.1a clade associated with higher diversity of AOA in the most nutrient-poor lake. More generally, this work assesses the presence of AOA in lakes, but also highlights the existence of clades typically associated with lacustrine and hot spring ecosystems and specific ecological niches occupied by these microorganisms.},
}
@article {pmid23376264,
year = {2013},
author = {Jehlička, J and Edwards, HG and Oren, A},
title = {Bacterioruberin and salinixanthin carotenoids of extremely halophilic Archaea and Bacteria: a Raman spectroscopic study.},
journal = {Spectrochimica acta. Part A, Molecular and biomolecular spectroscopy},
volume = {106},
number = {},
pages = {99-103},
doi = {10.1016/j.saa.2012.12.081},
pmid = {23376264},
issn = {1873-3557},
mesh = {Bacteroidetes/*chemistry ; Carotenoids/*chemistry/isolation &amp; purification ; Glycosides/*chemistry/isolation &amp; purification ; Haloarcula/chemistry ; Halobacteriaceae/*chemistry ; Halobacterium salinarum/chemistry ; Halorubrum/chemistry ; Spectrum Analysis, Raman ; },
abstract = {Laboratory cultures of a number of red extremely halophilic Archaea (Halobacterium salinarum strains NRC-1 and R1, Halorubrum sodomense, Haloarcula valismortis) and of Salinibacter ruber, a red extremely halophilic member of the Bacteria, have been investigated by Raman spectroscopy using 514.5nm excitation to characterize their carotenoids. The 50-carbon carotenoid α-bacterioruberin was detected as the major carotenoid in all archaeal strains. Raman spectroscopy also detected bacterioruberin as the main pigment in a red pellet of cells collected from a saltern crystallizer pond. Salinibacter contains the C40-carotenoid acyl glycoside salinixanthin (all-E, 2'S)-2'-hydroxy-1'-[6-O-(methyltetradecanoyl)-β-d-glycopyranosyloxy]-3',4'-didehydro-1',2'-dihydro-β,ψ-carotene-4-one), for which the Raman bands assignments of are given here for the first time.},
}
@article {pmid23365509,
year = {2013},
author = {Rusch, A},
title = {Molecular tools for the detection of nitrogen cycling Archaea.},
journal = {Archaea (Vancouver, B.C.)},
volume = {2013},
number = {},
pages = {676450},
pmid = {23365509},
issn = {1472-3654},
mesh = {Archaea/*genetics/isolation &amp; purification/*metabolism ; DNA Primers/*genetics ; DNA, Archaeal/chemistry/*genetics ; *Environmental Microbiology ; Metabolic Networks and Pathways/*genetics ; Molecular Sequence Data ; Nitrogen/*metabolism ; Sensitivity and Specificity ; Sequence Analysis, DNA ; },
abstract = {Archaea are widespread in extreme and temperate environments, and cultured representatives cover a broad spectrum of metabolic capacities, which sets them up for potentially major roles in the biogeochemistry of their ecosystems. The detection, characterization, and quantification of archaeal functions in mixed communities require Archaea-specific primers or probes for the corresponding metabolic genes. Five pairs of degenerate primers were designed to target archaeal genes encoding key enzymes of nitrogen cycling: nitrite reductases NirA and NirB, nitrous oxide reductase (NosZ), nitrogenase reductase (NifH), and nitrate reductases NapA/NarG. Sensitivity towards their archaeal target gene, phylogenetic specificity, and gene specificity were evaluated in silico and in vitro. Owing to their moderate sensitivity/coverage, the novel nirB-targeted primers are suitable for pure culture studies only. The nirA-targeted primers showed sufficient sensitivity and phylogenetic specificity, but poor gene specificity. The primers designed for amplification of archaeal nosZ performed well in all 3 criteria; their discrimination against bacterial homologs appears to be weakened when Archaea are strongly outnumbered by bacteria in a mixed community. The novel nifH-targeted primers showed high sensitivity and gene specificity, but failed to discriminate against bacterial homologs. Despite limitations, 4 of the new primer pairs are suitable tools in several molecular methods applied in archaeal ecology.},
}
@article {pmid23357171,
year = {2013},
author = {Bauer, RJ and Graham, BW and Trakselis, MA},
title = {Novel interaction of the bacterial-Like DnaG primase with the MCM helicase in archaea.},
journal = {Journal of molecular biology},
volume = {425},
number = {8},
pages = {1259-1273},
doi = {10.1016/j.jmb.2013.01.025},
pmid = {23357171},
issn = {1089-8638},
mesh = {DNA Helicases/*metabolism ; DNA Mutational Analysis ; DNA Primase/*metabolism ; DNA, Archaeal/metabolism ; Electrophoretic Mobility Shift Assay ; Models, Biological ; Models, Chemical ; Protein Binding ; Protein Interaction Mapping ; Sulfolobus solfataricus/*enzymology ; },
abstract = {DNA priming and unwinding activities are coupled within bacterial primosome complexes to initiate synthesis on the lagging strand during DNA replication. Archaeal organisms contain conserved primase genes homologous to both the bacterial DnaG and archaeo-eukaryotic primase families. The inclusion of multiple DNA primases within a whole domain of organisms complicates the assignment of the metabolic roles of each. In support of a functional bacterial-like DnaG primase participating in archaeal DNA replication, we have detected an interaction of Sulfolobus solfataricus DnaG (SsoDnaG) with the replicative S. solfataricus minichromosome maintenance (SsoMCM) helicase on DNA. The interaction site has been mapped to the N-terminal tier of SsoMCM analogous to bacterial primosome complexes. Mutagenesis within the metal binding site of SsoDnaG verifies a functional homology with bacterial DnaG that perturbs priming activity and DNA binding. The complex of SsoDnaG with SsoMCM stimulates the ATPase activity of SsoMCM but leaves the priming activity of SsoDnaG unchanged. Competition for binding DNA between SsoDnaG and SsoMCM can reduce the unwinding ability. Fluorescent gel shift experiments were used to quantify the binding of the ternary SsoMCM-DNA-SsoDnaG complex. This direct interaction of a bacterial-like primase with a eukaryotic-like helicase suggests that formation of a unique but homologous archaeal primosome complex is possible but may require other components to stimulate activities. Identification of this archaeal primosome complex broadly impacts evolutionary relationships of DNA replication.},
}
@article {pmid23356326,
year = {2013},
author = {Prangishvili, D and Koonin, EV and Krupovic, M},
title = {Genomics and biology of Rudiviruses, a model for the study of virus-host interactions in Archaea.},
journal = {Biochemical Society transactions},
volume = {41},
number = {1},
pages = {443-450},
pmid = {23356326},
issn = {1470-8752},
support = {Z01 LM000061-15//Intramural NIH HHS/United States ; Z01 LM000073-12//Intramural NIH HHS/United States ; },
mesh = {DNA-Binding Proteins/metabolism ; *Genome, Viral ; *Host-Pathogen Interactions ; Microscopy, Electron ; Rudiviridae/*genetics ; Transcription, Genetic ; Virion/ultrastructure ; Virus Replication ; },
abstract = {Archaeal viruses, especially viruses that infect hyperthermophilic archaea of the phylum Crenarchaeota, constitute one of the least understood parts of the virosphere. However, owing to recent substantial research efforts by several groups, archaeal viruses are starting to gradually reveal their secrets. In the present review, we summarize the current knowledge on one of the emerging model systems for studies on crenarchaeal viruses, the Rudiviridae. We discuss the recent advances towards understanding the function and structure of the proteins encoded by the rudivirus genomes, their role in the virus life cycle, and outline the directions for further research on this model system. In addition, a revised genome annotation of SIRV2 (Sulfolobus islandicus rod-shaped virus 2) is presented. Future studies on archaeal viruses, combined with the knowledge on viruses of bacteria and eukaryotes, should lead to a better global understanding of the diversity and evolution of virus-host interactions in the viral world.},
}
@article {pmid23356325,
year = {2013},
author = {Marguet, E and Gaudin, M and Gauliard, E and Fourquaux, I and le Blond du Plouy, S and Matsui, I and Forterre, P},
title = {Membrane vesicles, nanopods and/or nanotubes produced by hyperthermophilic archaea of the genus Thermococcus.},
journal = {Biochemical Society transactions},
volume = {41},
number = {1},
pages = {436-442},
doi = {10.1042/BST20120293},
pmid = {23356325},
issn = {1470-8752},
mesh = {Archaeal Proteins/metabolism ; Cell Membrane/metabolism ; Culture Media ; DNA, Archaeal/genetics ; Microscopy, Electron, Transmission ; *Nanotubes ; Thermococcus/genetics/*metabolism/ultrastructure ; },
abstract = {Thermococcus species produce MVs (membrane vesicles) into their culture medium. These MVs are formed by a budding process from the cell envelope, similar to ectosome formation in eukaryotic cells. The major protein present in MVs of Thermococci is a peptide-binding receptor of the OppA (oligopeptide-binding protein A) family. In addition, some of them contain a homologue of stomatin, a universal membrane protein involved in vesiculation. MVs produced by Thermococcus species can recruit endogenous or exogenous plasmids and plasmid transfer through MVs has been demonstrated in Thermococcus kodakaraensis. MVs are frequently secreted in clusters surrounded by S-layer, producing either big protuberances (nanosphere) or tubular structures (nanotubes). Thermococcus gammatolerans and T. kodakaraensis produce nanotubes containing strings of MVs, resembling the recently described nanopods in bacteria, whereas Thermococcus sp. 5-4 produces filaments whose internal membrane is continuous. These nanotubes can bridge neighbouring cells, forming cellular networks somehow resembling nanotubes recently observed in Firmicutes. As suggested for bacteria, archaeal nanopods and/or nanotubes could be used to expand the metabolic sphere around cells and/or to promote intercellular communication.},
}
@article {pmid23356323,
year = {2013},
author = {Atomi, H and Tomita, H and Ishibashi, T and Yokooji, Y and Imanaka, T},
title = {CoA biosynthesis in archaea.},
journal = {Biochemical Society transactions},
volume = {41},
number = {1},
pages = {427-431},
doi = {10.1042/BST20120311},
pmid = {23356323},
issn = {1470-8752},
mesh = {Biological Evolution ; Coenzyme A/*biosynthesis ; Pantothenic Acid/metabolism ; Phosphotransferases/metabolism ; Thermococcus/enzymology/genetics/*metabolism ; },
abstract = {CoA is a ubiquitous molecule in all three domains of life and is involved in various metabolic pathways. The enzymes and reactions involved in CoA biosynthesis in eukaryotes and bacteria have been identified. By contrast, the proteins/genes involved in CoA biosynthesis in archaea have not been fully clarified, and much has to be learned before we obtain a general understanding of how this molecule is synthesized. In the present paper, we review the current status of the research on CoA biosynthesis in the archaea, and discuss important questions that should be addressed in the near future.},
}
@article {pmid23356322,
year = {2013},
author = {Schlegel, K and Müller, V},
title = {Evolution of Na(+) and H(+) bioenergetics in methanogenic archaea.},
journal = {Biochemical Society transactions},
volume = {41},
number = {1},
pages = {421-426},
doi = {10.1042/BST20120294},
pmid = {23356322},
issn = {1470-8752},
mesh = {Archaea/genetics/*metabolism ; *Energy Metabolism ; Hydrogen/*metabolism ; Methane/*metabolism ; Sodium/*metabolism ; },
abstract = {Methanogenic archaea live at the thermodynamic limit of life and use sophisticated mechanisms for ATP synthesis and energy coupling. The group of methanogens without cytochromes use an Na(+) current across the membrane for ATP synthesis, whereas the cytochrome-containing methanogens have additional coupling sites that also translocate protons. The ATP synthase in this group is promiscuous and uses Na(+) and H(+) simultaneously.},
}
@article {pmid23356318,
year = {2013},
author = {Esser, D and Siebers, B},
title = {Atypical protein kinases of the RIO family in archaea.},
journal = {Biochemical Society transactions},
volume = {41},
number = {1},
pages = {399-404},
doi = {10.1042/BST20120317},
pmid = {23356318},
issn = {1470-8752},
mesh = {Genes, Archaeal ; Multigene Family ; Protein Kinases/*metabolism ; Sulfolobus solfataricus/*enzymology/genetics ; },
abstract = {Atypical protein kinases of the RIO (right open reading frame) kinase family are found in all three domains of life, emphasizing their essential function. In all archaeal genomes sequenced to date, typically two, but at least one, members of the RIO kinase family have been identified. Although the function of RIO kinases in Archaea remains to be resolved, bioinformatics analysis (e.g. comparison of the phylogenetic distribution and gene neighbourhood analysis, as well as interaction analysis) in combination with the available phosphoproteome study of Sulfolobus solfataricus provided some first hints to the possible function as well as revealed some putative target proteins for RIO kinases in Archaea. This study suggests a possible function of archaeal RIO kinases in RNA and/or DNA binding/processing translation initiation or ribosomal biogenesis resembling the assumed physiological role in yeast.},
}
@article {pmid23356309,
year = {2013},
author = {Prasse, D and Ehlers, C and Backofen, R and Schmitz, RA},
title = {Regulatory RNAs in archaea: first target identification in Methanoarchaea.},
journal = {Biochemical Society transactions},
volume = {41},
number = {1},
pages = {344-349},
doi = {10.1042/BST20120280},
pmid = {23356309},
issn = {1470-8752},
mesh = {Archaea/*genetics ; RNA Processing, Post-Transcriptional ; RNA, Archaeal/*genetics ; },
abstract = {sRNAs (small non-coding RNAs) representing important players in many cellular and regulatory processes have been identified in all three domains of life. In Eukarya and Bacteria, functions have been assigned for many sRNAs, whereas the sRNA populations in Archaea are considerably less well characterized. Recent analyses on a genome-wide scale particularly using high-throughput sequencing techniques demonstrated the presence of high numbers of sRNA candidates in several archaea. However, elucidation of the molecular mechanism of sRNA action, as well as understanding their physiological roles, is in general still challenging, particularly in Archaea, since efficient genetic tools are missing. The identification of cellular targets of identified archaeal sRNAs by experimental approaches or computational prediction programs has begun only recently. At present, targets have been identified for one archaeal sRNA, sRNA162 in Methanosarcina mazei, which interacts with the 5' region of its targets, a cis-encoded and a trans-encoded target, blurring the paradigm of a border between cis- and trans-encoded sRNAs. Besides, the first experimental implications have been obtained in Haloarchaea and Pyrobaculum that archaeal sRNAs also target 3' regions of mRNAs. The present review summarizes our current knowledge on archaeal sRNAs and their biological functions and targets.},
}
@article {pmid23356308,
year = {2013},
author = {Soppa, J},
title = {Evolutionary advantages of polyploidy in halophilic archaea.},
journal = {Biochemical Society transactions},
volume = {41},
number = {1},
pages = {339-343},
doi = {10.1042/BST20120315},
pmid = {23356308},
issn = {1470-8752},
mesh = {Archaea/*genetics/radiation effects ; *Evolution, Molecular ; Gene Conversion ; Gene Dosage ; Genes, Archaeal ; *Polyploidy ; },
abstract = {Several species of haloarchaea have been shown to be polyploid and thus this trait might be typical for and widespread in haloarchaea. In the present paper, nine different possible evolutionary advantages of polyploidy for haloarchaea are discussed, including low mutation rate, radiation/desiccation resistance, gene redundancy and survival over geological times and at extraterrestrial sites. Experimental indications exist for all but one of these evolutionary advantages. Several of the advantages require gene conversion, which has been shown to be present and active in haloarchaea.},
}
@article {pmid23353769,
year = {2013},
author = {Eichler, J},
title = {Extreme sweetness: protein glycosylation in archaea.},
journal = {Nature reviews. Microbiology},
volume = {11},
number = {3},
pages = {151-156},
pmid = {23353769},
issn = {1740-1534},
mesh = {Archaea/metabolism/*physiology ; Computational Biology ; Genome, Archaeal ; *Glycosylation ; Metabolic Networks and Pathways/*genetics ; Sequence Analysis, DNA ; },
abstract = {Although N-glycosylation was first reported in archaea almost 40 years ago, detailed insights into this process have become possible only recently, with the availability of complete genome sequences for almost 200 archaeal species and the development of appropriate molecular tools. As a result of these advances, recent efforts have not only succeeded in delineating the pathways involved in archaeal N-glycosylation, but also begun to reveal how such post-translational protein modification helps archaea to survive in some of the harshest environments on the planet.},
}
@article {pmid23346081,
year = {2012},
author = {Peng, X and Yando, E and Hildebrand, E and Dwyer, C and Kearney, A and Waciega, A and Valiela, I and Bernhard, AE},
title = {Differential responses of ammonia-oxidizing archaea and bacteria to long-term fertilization in a New England salt marsh.},
journal = {Frontiers in microbiology},
volume = {3},
number = {},
pages = {445},
pmid = {23346081},
issn = {1664-302X},
abstract = {Since the discovery of ammonia-oxidizing archaea (AOA), new questions have arisen about population and community dynamics and potential interactions between AOA and ammonia-oxidizing bacteria (AOB). We investigated the effects of long-term fertilization on AOA and AOB in the Great Sippewissett Marsh, Falmouth, MA, USA to address some of these questions. Sediment samples were collected from low and high marsh habitats in July 2009 from replicate plots that received low (LF), high (HF), and extra high (XF) levels of a mixed NPK fertilizer biweekly during the growing season since 1974. Additional untreated plots were included as controls (C). Terminal restriction fragment length polymorphism analysis of the amoA genes revealed distinct shifts in AOB communities related to fertilization treatment, but the response patterns of AOA were less consistent. Four AOB operational taxonomic units (OTUs) predictably and significantly responded to fertilization, but only one AOA OTU showed a significant pattern. Betaproteobacterial amoA gene sequences within the Nitrosospira-like cluster dominated at C and LF sites, while sequences related to Nitrosomonas spp. dominated at HF and XF sites. We identified some clusters of AOA sequences recovered primarily from high fertilization regimes, but other clusters consisted of sequences recovered from all fertilization treatments, suggesting greater physiological diversity. Surprisingly, fertilization appeared to have little impact on abundance of AOA or AOB. In summary, our data reveal striking patterns for AOA and AOB in response to long-term fertilization, and also suggest a missing link between community composition and abundance and nitrogen processing in the marsh.},
}
@article {pmid23341965,
year = {2013},
author = {Daebeler, A and Gansen, M and Frenzel, P},
title = {Methyl fluoride affects methanogenesis rather than community composition of methanogenic archaea in a rice field soil.},
journal = {PloS one},
volume = {8},
number = {1},
pages = {e53656},
pmid = {23341965},
issn = {1932-6203},
mesh = {Acetates/metabolism ; Agriculture ; Archaea/*drug effects/*metabolism ; Base Sequence ; *Biota ; Carbon Isotopes ; Hydrocarbons, Fluorinated/*pharmacology ; Isotope Labeling ; Metabolome/drug effects ; Methane/*metabolism ; Molecular Sequence Data ; Multivariate Analysis ; Oryza/*growth &amp; development ; Oxidation-Reduction/drug effects ; Phylogeny ; Polymorphism, Restriction Fragment Length ; Reference Standards ; *Soil Microbiology ; },
abstract = {The metabolic pathways of methane formation vary with environmental conditions, but whether this can also be linked to changes in the active archaeal community structure remains uncertain. Here, we show that the suppression of aceticlastic methanogenesis by methyl fluoride (CH(3)F) caused surprisingly little differences in community composition of active methanogenic archaea from a rice field soil. By measuring the natural abundances of carbon isotopes we found that the effective dose for a 90% inhibition of aceticlastic methanogenesis in anoxic paddy soil incubations was <0.75% CH(3)F (v/v). The construction of clone libraries as well as t-RFLP analysis revealed that the active community, as indicated by mcrA transcripts (encoding the α subunit of methyl-coenzyme M reductase, a key enzyme for methanogenesis), remained stable over a wide range of CH(3)F concentrations and represented only a subset of the methanogenic community. More precisely, Methanocellaceae were of minor importance, but Methanosarcinaceae dominated the active population, even when CH(3)F inhibition only allowed for aceticlastic methanogenesis. In addition, we detected mcrA gene fragments of a so far unrecognised phylogenetic cluster. Transcription of this phylotype at methyl fluoride concentrations suppressing aceticlastic methanogenesis suggests that the respective organisms perform hydrogenotrophic methanogenesis. Hence, the application of CH(3)F combined with transcript analysis is not only a useful tool to measure and assign in situ acetate usage, but also to explore substrate usage by as yet uncultivated methanogens.},
}
@article {pmid23340109,
year = {2013},
author = {Ács, N and Kovács, E and Wirth, R and Bagi, Z and Strang, O and Herbel, Z and Rákhely, G and Kovács, KL},
title = {Changes in the Archaea microbial community when the biogas fermenters are fed with protein-rich substrates.},
journal = {Bioresource technology},
volume = {131},
number = {},
pages = {121-127},
doi = {10.1016/j.biortech.2012.12.134},
pmid = {23340109},
issn = {1873-2976},
mesh = {Archaea/genetics/*isolation &amp; purification/*metabolism ; Batch Cell Culture Techniques/*methods ; Biofuels/*microbiology ; Bioreactors/*microbiology ; Methane/isolation &amp; purification/*metabolism ; Microbial Consortia/*physiology ; Proteins/*metabolism ; Species Specificity ; },
abstract = {Terminal restriction fragment length polymorphism (T-RFLP) was applied to study the changes in the composition of the methanogens of biogas-producing microbial communities on adaptation to protein-rich monosubstrates such as casein and blood. Specially developed laboratory scale (5-L) continuously stirred tank reactors have been developed and used in these experiments. Sequencing of the appropriate T-RF fragments selected from a methanogen-specific (mcrA gene-based) library revealed that the methanogens responded to the unconventional substrates by changing the community structure. T-RFLP of the 16S rDNA gene confirmed the findings.},
}
@article {pmid23330917,
year = {2013},
author = {Bergauer, K and Sintes, E and van Bleijswijk, J and Witte, H and Herndl, GJ},
title = {Abundance and distribution of archaeal acetyl-CoA/propionyl-CoA carboxylase genes indicative for putatively chemoautotrophic Archaea in the tropical Atlantic's interior.},
journal = {FEMS microbiology ecology},
volume = {84},
number = {3},
pages = {461-473},
pmid = {23330917},
issn = {1574-6941},
support = {I 486/FWF_/Austrian Science Fund FWF/Austria ; P 23234/FWF_/Austrian Science Fund FWF/Austria ; Z 194/FWF_/Austrian Science Fund FWF/Austria ; },
mesh = {Acetyl-CoA Carboxylase/genetics ; Archaea/enzymology/*genetics/*metabolism ; Atlantic Ocean ; *Carbon Cycle ; Carbon Dioxide/metabolism ; Carbon-Nitrogen Ligases/*genetics ; *Chemoautotrophic Growth ; Darkness ; *Genes, Archaeal ; Genes, rRNA ; Methylmalonyl-CoA Decarboxylase/genetics/metabolism ; Oxidoreductases/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics/metabolism ; Seawater/*microbiology ; },
abstract = {Recently, evidence suggests that dark CO2 fixation in the pelagic realm of the ocean does not only occur in the suboxic and anoxic water bodies but also in the oxygenated meso- and bathypelagic waters of the North Atlantic. To elucidate the significance and phylogeny of the key organisms mediating dark CO2 fixation in the tropical Atlantic, we quantified functional genes indicative for CO2 fixation. We used a Q-PCR-based assay targeting the bifunctional acetyl-CoA/propionyl-CoA carboxylase (accA subunit), a key enzyme powering inter alia the 3-hydroxypropionate/4-hydroxybutyrate cycle (HP/HB) and the archaeal ammonia monooxygenase (amoA). Quantification of accA-like genes revealed a consistent depth profile in the upper mesopelagial with increasing gene abundances from subsurface layers towards the oxygen minimum zone (OMZ), coinciding with an increase in archaeal amoA gene abundance. Gene abundance profiles of metabolic marker genes (accA, amoA) were correlated with thaumarchaeal 16S rRNA gene abundances as well as CO2 fixation rates to link the genetic potential to actual rate measurements. AccA gene abundances correlated with archaeal amoA gene abundance throughout the water column (r(2) = 0.309, P < 0.0001). Overall, a substantial genetic predisposition of CO2 fixation was present in the dark realm of the tropical Atlantic in both Archaea and Bacteria. Hence, dark ocean CO2 fixation might be more widespread among prokaryotes inhabiting the oxygenated water column of the ocean's interior than hitherto assumed.},
}
@article {pmid23326206,
year = {2012},
author = {Wrede, C and Dreier, A and Kokoschka, S and Hoppert, M},
title = {Archaea in symbioses.},
journal = {Archaea (Vancouver, B.C.)},
volume = {2012},
number = {},
pages = {596846},
pmid = {23326206},
issn = {1472-3654},
mesh = {Animals ; Archaea/*physiology ; Bacterial Physiological Phenomena ; Ecosystem ; Eukaryota/physiology ; Humans ; Metagenome ; Methane/biosynthesis ; Symbiosis/*physiology ; },
abstract = {During the last few years, the analysis of microbial diversity in various habitats greatly increased our knowledge on the kingdom Archaea. At the same time, we became aware of the multiple ways in which Archaea may interact with each other and with organisms of other kingdoms. The large group of euryarchaeal methanogens and their methane oxidizing relatives, in particular, take part in essential steps of the global methane cycle. Both of these processes, which are in reverse to each other, are partially conducted in a symbiotic interaction with different partners, either ciliates and xylophagous animals or sulfate reducing bacteria. Other symbiotic interactions are mostly of unknown ecological significance but depend on highly specific mechanisms. This paper will give an overview on interactions between Archaea and other organisms and will point out the ecological relevance of these symbiotic processes, as long as these have been already recognized.},
}
@article {pmid23306641,
year = {2013},
author = {Limpiyakorn, T and Fürhacker, M and Haberl, R and Chodanon, T and Srithep, P and Sonthiphand, P},
title = {amoA-encoding archaea in wastewater treatment plants: a review.},
journal = {Applied microbiology and biotechnology},
volume = {97},
number = {4},
pages = {1425-1439},
doi = {10.1007/s00253-012-4650-7},
pmid = {23306641},
issn = {1432-0614},
mesh = {Ammonia/metabolism ; Archaea/classification/*enzymology/genetics/isolation &amp; purification ; Archaeal Proteins/genetics/*metabolism ; Oxidation-Reduction ; Oxidoreductases/genetics/*metabolism ; Phylogeny ; Wastewater/chemistry/*microbiology ; Water Purification/instrumentation ; },
abstract = {Recent evidence from natural environments suggests that in addition to ammonia-oxidizing bacteria, ammonia-oxidizing archaea (AOA) affiliated with Thaumarcheota, a new phylum of the domain Archaea, also oxidize ammonia to nitrite and thus participate in the global nitrogen cycle. Besides natural environments, modern data indicate the presence of amoA-encoding archaea (AEA) in wastewater treatment plants (WWTPs). To further elucidate whether AEA in WWTPs are AOA and to clarify the role of AEA in WWTPs, this paper reviews the current knowledge on this matter for wastewater engineers and people in related fields. The initial section coveys a microbiological point of view and is particularly based upon data from AOA cultures. The later section summarizes what is currently known about AEA in relation to WWTPs. Based on the reviewed data, future research pathways are proposed in an effort to further what is known about AEA in wastewater treatment systems.},
}
@article {pmid23304073,
year = {2012},
author = {Corcelli, A and Chong, PL and Koga, Y},
title = {Lipid biology of archaea.},
journal = {Archaea (Vancouver, B.C.)},
volume = {2012},
number = {},
pages = {710836},
doi = {10.1155/2012/710836},
pmid = {23304073},
issn = {1472-3654},
mesh = {Archaea/*metabolism ; *Lipid Metabolism ; },
}
@article {pmid23304072,
year = {2012},
author = {Lombard, J and López-García, P and Moreira, D},
title = {Phylogenomic investigation of phospholipid synthesis in archaea.},
journal = {Archaea (Vancouver, B.C.)},
volume = {2012},
number = {},
pages = {630910},
pmid = {23304072},
issn = {1472-3654},
mesh = {Acyl Carrier Protein/genetics/metabolism ; Archaea/enzymology/*genetics/*metabolism ; Archaeal Proteins/genetics/metabolism ; Evolution, Molecular ; Fatty Acids/biosynthesis ; Genome, Archaeal ; Glycerophosphates/metabolism ; Metabolic Networks and Pathways ; Nucleotidyltransferases/genetics/metabolism ; Phospholipids/*biosynthesis ; Phylogeny ; Terpenes/metabolism ; },
abstract = {Archaea have idiosyncratic cell membranes usually based on phospholipids containing glycerol-1-phosphate linked by ether bonds to isoprenoid lateral chains. Since these phospholipids strongly differ from those of bacteria and eukaryotes, the origin of the archaeal membranes (and by extension, of all cellular membranes) was enigmatic and called for accurate evolutionary studies. In this paper we review some recent phylogenomic studies that have revealed a modified mevalonate pathway for the synthesis of isoprenoid precursors in archaea and suggested that this domain uses an atypical pathway of synthesis of fatty acids devoid of any acyl carrier protein, which is essential for this activity in bacteria and eukaryotes. In addition, we show new or updated phylogenetic analyses of enzymes likely responsible for the isoprenoid chain synthesis from their precursors and the phospholipid synthesis from glycerol phosphate, isoprenoids, and polar head groups. These results support that most of these enzymes can be traced back to the last archaeal common ancestor and, in many cases, even to the last common ancestor of all living organisms.},
}
@article {pmid23282134,
year = {2012},
author = {Somboonna, N and Assawamakin, A and Wilantho, A and Tangphatsornruang, S and Tongsima, S},
title = {Metagenomic profiles of free-living archaea, bacteria and small eukaryotes in coastal areas of Sichang island, Thailand.},
journal = {BMC genomics},
volume = {13 Suppl 7},
number = {Suppl 7},
pages = {S29},
pmid = {23282134},
issn = {1471-2164},
mesh = {Archaea/classification/*genetics ; Bacteria/classification/*genetics ; Fungi/classification/*genetics ; *Metagenomics ; Phylogeny ; Principal Component Analysis ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 18S/genetics ; Seawater/microbiology ; Thailand ; },
abstract = {BACKGROUND: Tha Wang and Tham Phang coasts, though situated at similar oceanographic positions on Sichang island, Chonburi province, Thailand, are different in bay geography and amount of municipal disturbances. These affect the marine ecosystems. The study used metagenomics combined with 16S and 18S rDNA pyrosequencing to identify types and distributions of archaea, bacteria, fungi and small eukaryotes of sizes ranges 0.45 and ~30 μm.<br><br>RESULTS: Following the open bay geography and minimal municipal sewages, Tham Phang coast showed the cleaner water properties, described by color, salinity, pH, conductivity and percent dissolved oxygen. The 16S and 18S rDNA metagenomic profiles for Tha Wang and Tham Phang coasts revealed many differences, highlighting by low Lennon and Yue &amp; Clayton theta similarity indices (66.03-73.03% for 16S rDNA profiles, 2.85-25.38% for 18S rDNA profiles). For 16S rDNA, the percent compositions of species belonging to Proteobacteria, Bacteroidetes, Cyanobacteria, Firmicutes, Verrucomicrobia, Gammatimonadetes, Tenericutes, Acidobacteria, Spirochaetes, Chlamydiae, Euryarchaeota, Nitrospirae, Planctomycetes, Thermotogae and Aquificae were higher or distinctly present in Tha Wang. In Tham Phang, except Actinobacteria, the fewer number of prokaryotic species existed. For 18S rDNA, fungi represented 74.745% of the species in Tha Wang, whereas only 6.728% in Tham Phang. Basidiomycota (71.157%) and Ascomycota (3.060%) were the major phyla in Tha Wang. Indeed, Tha Wang-to-Tham Phang percent composition ratios for fungi Basidiomycota and Chytridiomycota were 1264.701 and 25.422, respectively. In Tham Phang, Brachiopoda (lamp shells) and Mollusca (snails) accounted for 80.380% of the 18S rDNA species detected, and their proportions were approximately tenfold greater than those in Tha Wang. Overall, coastal Tham Phang comprised abundant animal species.<br><br>CONCLUSIONS: Tha Wang contained numerous archaea, bacteria and fungi, many of which could synthesize useful biotechnology gas and enzymes that could also function in high-saline and high-temperature conditions. Tham Phang contained less abundant archaea, bacteria and fungi, and the majority of the extracted metagenomes belonged to animal kingdom. Many microorganisms in Tham Phang were essential for nutrient-recycling and pharmaceuticals, for instances, Streptomyces, Pennicilium and Saccharomyces. Together, the study provided metagenomic profiles of free-living prokaryotes and eukaryotes in coastal areas of Sichang island.},
}
@article {pmid23298390,
year = {2013},
author = {Blainey, PC},
title = {The future is now: single-cell genomics of bacteria and archaea.},
journal = {FEMS microbiology reviews},
volume = {37},
number = {3},
pages = {407-427},
pmid = {23298390},
issn = {1574-6976},
support = {R01 HG004863/HG/NHGRI NIH HHS/United States ; },
mesh = {Archaea/*genetics ; Bacteria/*genetics ; Computational Biology ; Genetics, Microbial/methods ; *Genome, Archaeal ; *Genome, Bacterial ; Genomics/*methods ; High-Throughput Nucleotide Sequencing ; },
abstract = {Interest in the expanding catalog of uncultivated microorganisms, increasing recognition of heterogeneity among seemingly similar cells, and technological advances in whole-genome amplification and single-cell manipulation are driving considerable progress in single-cell genomics. Here, the spectrum of applications for single-cell genomics, key advances in the development of the field, and emerging methodology for single-cell genome sequencing are reviewed by example with attention to the diversity of approaches and their unique characteristics. Experimental strategies transcending specific methodologies are identified and organized as a road map for future studies in single-cell genomics of environmental microorganisms. Over the next decade, increasingly powerful tools for single-cell genome sequencing and analysis will play key roles in accessing the genomes of uncultivated organisms, determining the basis of microbial community functions, and fundamental aspects of microbial population biology.},
}
@article {pmid23298189,
year = {2013},
author = {Lu, L and Jia, Z},
title = {Urease gene-containing Archaea dominate autotrophic ammonia oxidation in two acid soils.},
journal = {Environmental microbiology},
volume = {15},
number = {6},
pages = {1795-1809},
doi = {10.1111/1462-2920.12071},
pmid = {23298189},
issn = {1462-2920},
mesh = {Acids/chemistry ; Ammonia/*metabolism ; Archaea/*enzymology/*genetics/growth &amp; development ; Autotrophic Processes/genetics ; Biodiversity ; Carbon Isotopes/analysis ; Molecular Sequence Data ; Nitrification ; Nitrogen/metabolism ; Nitrogen Cycle ; Oxidation-Reduction ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Soil/chemistry ; *Soil Microbiology ; Urease/*genetics/metabolism ; },
abstract = {The metabolic traits of ammonia-oxidizing archaea (AOA) and bacteria (AOB) interacting with their environment determine the nitrogen cycle at the global scale. Ureolytic metabolism has long been proposed as a mechanism for AOB to cope with substrate paucity in acid soil, but it remains unclear whether urea hydrolysis could afford AOA greater ecological advantages. By combining DNA-based stable isotope probing (SIP) and high-throughput pyrosequencing, here we show that autotrophic ammonia oxidation in two acid soils was predominately driven by AOA that contain ureC genes encoding the alpha subunit of a putative archaeal urease. In urea-amended SIP microcosms of forest soil (pH 5.40) and tea orchard soil (pH 3.75), nitrification activity was stimulated significantly by urea fertilization when compared with water-amended soils in which nitrification resulted solely from the oxidation of ammonia generated through mineralization of soil organic nitrogen. The stimulated activity was paralleled by changes in abundance and composition of archaeal amoA genes. Time-course incubations indicated that archaeal amoA genes were increasingly labelled by (13) CO2 in both microcosms amended with water and urea. Pyrosequencing revealed that archaeal populations were labelled to a much greater extent in soils amended with urea than water. Furthermore, archaeal ureC genes were successfully amplified in the (13) C-DNA, and acetylene inhibition suggests that autotrophic growth of urease-containing AOA depended on energy generation through ammonia oxidation. The sequences of AOB were not detected, and active AOA were affiliated with the marine Group 1.1a-associated lineage. The results suggest that ureolytic N metabolism could afford AOA greater advantages for autotrophic ammonia oxidation in acid soil, but the mechanism of how urea activates AOA cells remains unclear.},
}
@article {pmid23283946,
year = {2013},
author = {Pietilä, MK and Laurinmäki, P and Russell, DA and Ko, CC and Jacobs-Sera, D and Butcher, SJ and Bamford, DH and Hendrix, RW},
title = {Insights into head-tailed viruses infecting extremely halophilic archaea.},
journal = {Journal of virology},
volume = {87},
number = {6},
pages = {3248-3260},
pmid = {23283946},
issn = {1098-5514},
mesh = {Archaea/*virology ; Archaeal Viruses/*genetics/isolation &amp; purification/physiology/*ultrastructure ; Capsid/ultrastructure ; Cryoelectron Microscopy ; DNA, Viral/*chemistry/*genetics ; *Genome, Viral ; Imaging, Three-Dimensional ; Microbial Viability/drug effects ; Molecular Sequence Data ; Sequence Analysis, DNA ; Sodium Chloride/metabolism ; Virion/*ultrastructure ; },
abstract = {Extremophilic archaea, both hyperthermophiles and halophiles, dominate in habitats where rather harsh conditions are encountered. Like all other organisms, archaeal cells are susceptible to viral infections, and to date, about 100 archaeal viruses have been described. Among them, there are extraordinary virion morphologies as well as the common head-tailed viruses. Although approximately half of the isolated archaeal viruses belong to the latter group, no three-dimensional virion structures of these head-tailed viruses are available. Thus, rigorous comparisons with bacteriophages are not yet warranted. In the present study, we determined the genome sequences of two of such viruses of halophiles and solved their capsid structures by cryo-electron microscopy and three-dimensional image reconstruction. We show that these viruses are inactivated, yet remain intact, at low salinity and that their infectivity is regained when high salinity is restored. This enabled us to determine their three-dimensional capsid structures at low salinity to a ∼10-Å resolution. The genetic and structural data showed that both viruses belong to the same T-number class, but one of them has enlarged its capsid to accommodate a larger genome than typically associated with a T=7 capsid by inserting an additional protein into the capsid lattice.},
}
@article {pmid23283522,
year = {2013},
author = {Jia, B and Cheong, GW and Zhang, S},
title = {Multifunctional enzymes in archaea: promiscuity and moonlight.},
journal = {Extremophiles : life under extreme conditions},
volume = {17},
number = {2},
pages = {193-203},
pmid = {23283522},
issn = {1433-4909},
mesh = {Archaea/*enzymology/genetics ; Evolution, Molecular ; Glycolysis ; Hydrolases/chemistry/genetics/metabolism ; Pentose Phosphate Pathway ; Protein Structure, Tertiary ; Transferases/chemistry/genetics/metabolism ; },
abstract = {Enzymes from many archaea colonizing extreme environments are of great interest because of their potential for various biotechnological processes and scientific value of evolution. Many enzymes from archaea have been reported to catalyze promiscuous reactions or moonlight in different functions. Here, we summarize known archaeal enzymes of both groups that include different kinds of proteins. Knowledge of their biochemical properties and three-dimensional structures has proved invaluable in understanding mechanism, application, and evolutionary implications of this manifestation. In addition, the review also summarizes the methods to unravel the extra function which almost was discovered serendipitously. The study of these amazing enzymes will provide clues to optimize protein engineering applications and how enzymes might have evolved on Earth.},
}
@article {pmid23277575,
year = {2013},
author = {Vajrala, N and Martens-Habbena, W and Sayavedra-Soto, LA and Schauer, A and Bottomley, PJ and Stahl, DA and Arp, DJ},
title = {Hydroxylamine as an intermediate in ammonia oxidation by globally abundant marine archaea.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {110},
number = {3},
pages = {1006-1011},
pmid = {23277575},
issn = {1091-6490},
mesh = {Adenosine Triphosphate/biosynthesis ; Ammonia/*metabolism ; Aquatic Organisms/metabolism ; Archaea/*metabolism ; Hydroxylamine/*metabolism ; Kinetics ; Oxidation-Reduction ; Oxidoreductases/metabolism ; Oxygen Consumption ; },
abstract = {The ammonia-oxidizing archaea have recently been recognized as a significant component of many microbial communities in the biosphere. Although the overall stoichiometry of archaeal chemoautotrophic growth via ammonia (NH(3)) oxidation to nitrite (NO(2)(-)) is superficially similar to the ammonia-oxidizing bacteria, genome sequence analyses point to a completely unique biochemistry. The only genomic signature linking the bacterial and archaeal biochemistries of NH(3) oxidation is a highly divergent homolog of the ammonia monooxygenase (AMO). Although the presumptive product of the putative AMO is hydroxylamine (NH(2)OH), the absence of genes encoding a recognizable ammonia-oxidizing bacteria-like hydroxylamine oxidoreductase complex necessitates either a novel enzyme for the oxidation of NH(2)OH or an initial oxidation product other than NH(2)OH. We now show through combined physiological and stable isotope tracer analyses that NH(2)OH is both produced and consumed during the oxidation of NH(3) to NO(2)(-) by Nitrosopumilus maritimus, that consumption is coupled to energy conversion, and that NH(2)OH is the most probable product of the archaeal AMO homolog. Thus, despite their deep phylogenetic divergence, initial oxidation of NH(3) by bacteria and archaea appears mechanistically similar. They however diverge biochemically at the point of oxidation of NH(2)OH, the archaea possibly catalyzing NH(2)OH oxidation using a novel enzyme complex.},
}
@article {pmid23276916,
year = {2013},
author = {Bartolucci, S and Contursi, P and Fiorentino, G and Limauro, D and Pedone, E},
title = {Responding to toxic compounds: a genomic and functional overview of Archaea.},
journal = {Frontiers in bioscience (Landmark edition)},
volume = {18},
number = {1},
pages = {165-189},
doi = {10.2741/4094},
pmid = {23276916},
issn = {2768-6698},
mesh = {Adaptation, Physiological ; Adenosine Triphosphatases/metabolism ; Archaea/drug effects/genetics/*physiology ; Biodegradation, Environmental ; Environmental Pollution ; *Genomics ; Hydrocarbons, Aromatic/metabolism ; *Inactivation, Metabolic ; Membrane Transport Proteins/genetics ; Metals/metabolism/*toxicity ; Multidrug Resistance-Associated Proteins/genetics ; Xenobiotics/*toxicity ; },
abstract = {Archaea occupy a considerable diversity of niches ranging from extreme of pH, salinity to temperature that cannot be tolerated by other forms of life. There is an increasing consciousness that they have a key role both on the biogeochemical cycling of elements and in the bioremediation of polluted habitat. A greater understanding of metal homeostasis and resistance to toxic compounds in this life domain is required to design new strategies for the bioremediation of contaminated sites. This review describes the strategies developed by Archaea to transform xenobiotic compounds and metal ions present in the environment. The adaptation and/or response to such chemicals and the molecular mechanisms of resistance evolved in Archaea are discussed.},
}
@article {pmid25371333,
year = {2013},
author = {Jarrell, KF and Ding, Y and Nair, DB and Siu, S},
title = {Surface appendages of archaea: structure, function, genetics and assembly.},
journal = {Life (Basel, Switzerland)},
volume = {3},
number = {1},
pages = {86-117},
pmid = {25371333},
issn = {2075-1729},
abstract = {Organisms representing diverse subgroupings of the Domain Archaea are known to possess unusual surface structures. These can include ones unique to Archaea such as cannulae and hami as well as archaella (archaeal flagella) and various types of pili that superficially resemble their namesakes in Bacteria, although with significant differences. Major advances have occurred particularly in the study of archaella and pili using model organisms with recently developed advanced genetic tools. There is common use of a type IV pili-model of assembly for several archaeal surface structures including archaella, certain pili and sugar binding structures termed bindosomes. In addition, there are widespread posttranslational modifications of archaellins and pilins with N-linked glycans, with some containing novel sugars. Archaeal surface structures are involved in such diverse functions as swimming, attachment to surfaces, cell to cell contact resulting in genetic transfer, biofilm formation, and possible intercellular communication. Sometimes functions are co-dependent on other surface structures. These structures and the regulation of their assembly are important features that allow various Archaea, including thermoacidophilic, hyperthermophilic, halophilic, and anaerobic ones, to survive and thrive in the extreme environments that are commonly inhabited by members of this domain.},
}
@article {pmid23274043,
year = {2013},
author = {Krishnamurthi, S and Chakrabarti, T},
title = {Diversity of bacteria and archaea from a landfill in Chandigarh, India as revealed by culture-dependent and culture-independent molecular approaches.},
journal = {Systematic and applied microbiology},
volume = {36},
number = {1},
pages = {56-68},
doi = {10.1016/j.syapm.2012.08.009},
pmid = {23274043},
issn = {1618-0984},
mesh = {Archaea/*classification/genetics/growth &amp; development/*isolation &amp; purification ; Bacteria/*classification/genetics/growth &amp; development/*isolation &amp; purification ; Bacterial Typing Techniques ; *Biodiversity ; Cluster Analysis ; Colony Count, Microbial ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; India ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; },
abstract = {The bacterial community structure of a municipal landfill in Chandigarh, India was analysed by culture-dependent as well as culture-independent molecular approaches, and archaeal structure by the latter method. Samples were collected in two phases from the surface and a depth of 0.91 m in June, 2004 and from 0.91 m, 1.52 m and 1.68 m in May, 2005. After serial dilutions, samples were plated onto tryptic soy agar (TSA), plate count agar (PCA), tryptic soy broth agar (TSBA) and TSBA100 (TSBA diluted 100 times and solidified with agarose), and incubated aerobically at 30°C. The number of bacteria (CFU) on different media ranged between 9.4×10[5]g[-1] (on PCA) and 1.9×10[7]g[-1] (on TSA) (wet weight). The numbers of bacteria enumerated from plates incubated anaerobically (anaerobic agar and reinforced clostridial agar) were 2.1×10[7]and 1.7×10[6]g[-1], respectively. Of the 468 isolated and purified bacteria (183 in the first phase and 285 in the second phase), 135 were characterised using phenotypic characteristics as well as 16S rRNA gene sequence analysis. It was found that members of the phylum Firmicutes were overwhelmingly predominant (86.6%) in the landfill, followed by Actinobacteria (9.6%) and Proteobacteria (3.7%). Among the Firmicutes, at least 17 species from the single genus Bacillus were the most abundant inhabitants of the landfill. Detailed polyphasic characterisation of many of these isolates led to the discovery of a novel genus Paenisporosarcina (and the species P. quisquiliarum), a novel species of Microbacterium, M. immunditiarum, and reclassification of Sporosarcina macmurdoensis, Pelagibacillus goriensis, Bacillus silvestris, Bacillus insolitus, Bacillus psychrotolerans and Bacillus psychrodurans. Culture-independent analysis of two 16S rRNA gene libraries also revealed that the phylum Firmicutes was the predominant group in this community. The diversity of Archaea was found to be limited mainly to members of two orders: Methanosarcinales and Methanomicrobiales of the phylum Euryarchaeota. When these results were compared to those reported earlier on similar studies, it was found that irrespective of differences in composition of municipal solid waste (especially compostable organic matter and paper) and climate, the members of bacterial and archaeal communities in landfills of many countries remained broadly similar.},
}
@article {pmid23266104,
year = {2013},
author = {Nürenberg, E and Tampé, R},
title = {Tying up loose ends: ribosome recycling in eukaryotes and archaea.},
journal = {Trends in biochemical sciences},
volume = {38},
number = {2},
pages = {64-74},
doi = {10.1016/j.tibs.2012.11.003},
pmid = {23266104},
issn = {0968-0004},
mesh = {ATP-Binding Cassette Transporters/chemistry/metabolism ; Adenosine Triphosphate/metabolism ; Animals ; Archaea/genetics/*metabolism ; Eukaryota/genetics/*metabolism ; Humans ; Models, Molecular ; *Protein Biosynthesis ; Protein Structure, Tertiary ; Ribosomes/chemistry/genetics/*metabolism ; },
abstract = {Ribosome recycling is the final - or first - step of the cyclic process of mRNA translation. In eukaryotes and archaea, dissociation of the two ribosomal subunits proceeds in a fundamentally different way than in bacteria. It requires the ABC-type ATPase ABCE1 [previously named RNase L inhibitor (Rli)1 or host protein (HP)68], but the reaction and its regulation remain enigmatic. Here, we focus on ribosome recycling in its physiological context, including translation termination and reinitiation. The regulation of this crucial event can only be described by a systems biology approach, involving a network of proteins modulating mRNA translation. The key role of ABCE1, and what is known about the structure and function of this versatile protein, is discussed.},
}
@article {pmid23258706,
year = {2013},
author = {Perrochia, L and Crozat, E and Hecker, A and Zhang, W and Bareille, J and Collinet, B and van Tilbeurgh, H and Forterre, P and Basta, T},
title = {In vitro biosynthesis of a universal t6A tRNA modification in Archaea and Eukarya.},
journal = {Nucleic acids research},
volume = {41},
number = {3},
pages = {1953-1964},
pmid = {23258706},
issn = {1362-4962},
mesh = {Adenosine/*analogs &amp; derivatives/chemistry/metabolism ; Adenosine Triphosphate/metabolism ; Archaeal Proteins/*metabolism ; Bacterial Proteins/metabolism ; Biocatalysis ; DNA-Binding Proteins/metabolism ; Endopeptidases/metabolism ; Protein Kinases/metabolism ; Pyrococcus abyssi/*enzymology ; RNA, Transfer/chemistry/*metabolism ; RNA-Binding Proteins/*metabolism ; Saccharomyces cerevisiae Proteins/metabolism ; },
abstract = {N(6)-threonylcarbamoyladenosine (t(6)A) is a modified nucleotide found in all transfer RNAs (tRNAs) decoding codons starting with adenosine. Its role is to facilitate codon-anticodon pairing and to prevent frameshifting during protein synthesis. Genetic studies demonstrated that two universal proteins, Kae1/YgjD and Sua5/YrdC, are necessary for t(6)A synthesis in Saccharomyces cerevisiae and Escherichia coli. In Archaea and Eukarya, Kae1 is part of a conserved protein complex named kinase, endopeptidase and other proteins of small size (KEOPS), together with three proteins that have no bacterial homologues. Here, we reconstituted for the first time an in vitro system for t(6)A modification in Archaea and Eukarya, using purified KEOPS and Sua5. We demonstrated binding of tRNAs to archaeal KEOPS and detected two distinct adenosine triphosphate (ATP)-dependent steps occurring in the course of the synthesis. Our data, together with recent reconstitution of an in vitro bacterial system, indicated that t(6)A cannot be catalysed by Sua5/YrdC and Kae1/YgjD alone but requires accessory proteins that are not universal. Remarkably, we observed interdomain complementation when bacterial, archaeal and eukaryotic proteins were combined in vitro, suggesting a conserved catalytic mechanism for the biosynthesis of t(6)A in nature. These findings shed light on the reaction mechanism of t(6)A synthesis and evolution of molecular systems that promote translation fidelity in present-day cells.},
}
@article {pmid23258541,
year = {2013},
author = {Hawkins, AS and Han, Y and Bennett, RK and Adams, MW and Kelly, RM},
title = {Role of 4-hydroxybutyrate-CoA synthetase in the CO2 fixation cycle in thermoacidophilic archaea.},
journal = {The Journal of biological chemistry},
volume = {288},
number = {6},
pages = {4012-4022},
pmid = {23258541},
issn = {1083-351X},
support = {R01 GM090209/GM/NIGMS NIH HHS/United States ; R01GM90209/GM/NIGMS NIH HHS/United States ; },
mesh = {Archaeal Proteins/chemistry/genetics/*metabolism ; Carbon Dioxide/*metabolism ; Catalysis ; Catalytic Domain ; Coenzyme A-Transferases/chemistry/genetics/*metabolism ; Genome, Archaeal/physiology ; Hydroxybutyrates/chemistry/*metabolism ; Sulfolobaceae/*enzymology/genetics ; },
abstract = {Metallosphaera sedula is an extremely thermoacidophilic archaeon that grows heterotrophically on peptides and chemolithoautotrophically on hydrogen, sulfur, or reduced metals as energy sources. During autotrophic growth, carbon dioxide is incorporated into cellular carbon via the 3-hydroxypropionate/4-hydroxybutyrate cycle (3HP/4HB). To date, all of the steps in the pathway have been connected to enzymes encoded in specific genes, except for the one responsible for ligation of coenzyme A (CoA) to 4HB. Although several candidates for this step have been identified through bioinformatic analysis of the M. sedula genome, none have been shown to catalyze this biotransformation. In this report, transcriptomic analysis of cells grown under strict H(2)-CO(2) autotrophy was consistent with the involvement of Msed_0406 and Msed_0394. Recombinant versions of these enzymes catalyzed the ligation of CoA to 4HB, with similar affinities for 4HB (K(m) values of 1.9 and 1.5 mm for Msed_0406 and Msed_0394, respectively) but with different rates (1.69 and 0.22 μmol × min(-1) × mg(-1) for Msed_0406 and Msed_0394, respectively). Neither Msed_0406 nor Msed_0394 have close homologs in other Sulfolobales, although low sequence similarity is not unusual for acyl-adenylate-forming enzymes. The capacity of these two enzymes to use 4HB as a substrate may have arisen from simple modifications to acyl-adenylate-forming enzymes. For example, a single amino acid substitution (W424G) in the active site of the acetate/propionate synthetase (Msed_1353), an enzyme that is highly conserved among the Sulfolobales, changed its substrate specificity to include 4HB. The identification of the 4-HB CoA synthetase now completes the set of enzymes comprising the 3HP/4HB cycle.},
}
@article {pmid23254852,
year = {2012},
author = {Orange, F and Disnar, JR and Gautret, P and Westall, F and Bienvenu, N and Lottier, N and Prieur, D},
title = {Preservation and evolution of organic matter during experimental fossilisation of the hyperthermophilic archaea Methanocaldococcus jannaschii.},
journal = {Origins of life and evolution of the biosphere : the journal of the International Society for the Study of the Origin of Life},
volume = {42},
number = {6},
pages = {587-609},
pmid = {23254852},
issn = {1573-0875},
mesh = {Biological Evolution ; Chromatography, Gas ; Chromatography, High Pressure Liquid ; *Fossils ; Gas Chromatography-Mass Spectrometry ; Geologic Sediments/*chemistry ; Methanococcales/*chemistry ; Organic Chemicals/*chemistry ; *Origin of Life ; },
abstract = {Identification of the earliest traces of life is made difficult by the scarcity of the preserved microbial remains and by the alteration and potential contamination of the organic matter (OM) content of rocks. These factors can confuse interpretations of the biogenicity and syngenicity of fossilised structures and organic molecules found in ancient rocks. In order to improve our knowledge of the fossilisation processes and their effects at the molecular level, we made a preliminary study of the fate of OM during experimental fossilisation. Changes in the composition and quantity of amino acids, monosaccharides and fatty acids were followed with HPLC, GC and GC-MS analyses during 1 year of silicification of the hyperthermophilic Archaea Methanocaldococcus jannaschii. Although the cells themselves did not fossilise and the accompanying extracellular polymeric substances (EPS) did, our analyses showed that the OM initially present in both cells and EPS was uniformly preserved in the precipitated silica, with amino acids and fatty acids being the best preserved compounds. This study thus completes previous data obtained by electron microscopy investigations of simulated microbial fossilisation and can help better identification and interpretation of microbial biosignatures in both ancient rocks and in recent hydrothermal formations and sediments.},
}
@article {pmid23253149,
year = {2013},
author = {La Cono, V and La Spada, G and Arcadi, E and Placenti, F and Smedile, F and Ruggeri, G and Michaud, L and Raffa, C and De Domenico, E and Sprovieri, M and Mazzola, S and Genovese, L and Giuliano, L and Slepak, VZ and Yakimov, MM},
title = {Partaking of Archaea to biogeochemical cycling in oxygen-deficient zones of meromictic saline Lake Faro (Messina, Italy).},
journal = {Environmental microbiology},
volume = {15},
number = {6},
pages = {1717-1733},
doi = {10.1111/1462-2920.12060},
pmid = {23253149},
issn = {1462-2920},
mesh = {Anaerobiosis ; Archaea/classification/genetics/*metabolism ; Biodiversity ; Carbon Dioxide/metabolism ; *Ecosystem ; Environmental Microbiology ; Genes, Archaeal/genetics ; Italy ; Lakes/*microbiology ; Mediterranean Sea ; Molecular Sequence Data ; Oxygen/chemistry ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Salinity ; },
abstract = {We used a combination of molecular and microbiological approaches to determine the activity, abundance and diversity of archaeal populations inhabiting meromictic saline Lake Faro (Messina, Italy). Analysis of archaeal 16S rRNA, amoA, accA and hbd genes and transcripts revealed that sub- and anoxic layers of Lake Faro are primarily inhabited by the organisms related to the clusters of Marine Group I.1a of Thaumarchaeota frequently recovered from oxygen-depleted marine ecosystems. These organisms dominated the metabolically active archaea down to the bottom of the lake, indicating their adaptation to recurrent changes in the levels of water column hypoxia. The upper microaerobic layer of Lake Faro redoxcline has the maximal rates of dark primary production much lower than those of other previously studied pelagic redoxclines, but comparable to the values of meso- and bathypelagic areas of Mediterranean Sea. Application of bacterial inhibitors, especially azide, significantly declined the CO2 fixation rates in the low interface and monimolimnion, whereas archaea-specific inhibitor had effect only in upper part of the redoxcline. Based on these findings, we hypothesize that dark bicarbonate fixation in suboxic zone of Lake Faro results mainly from archaeal activity which is affected by the predicted lack in oxygen in lower layers.},
}
@article {pmid23243390,
year = {2012},
author = {Cameron, V and House, CH and Brantley, SL},
title = {A first analysis of metallome biosignatures of hyperthermophilic Archaea.},
journal = {Archaea (Vancouver, B.C.)},
volume = {2012},
number = {},
pages = {789278},
pmid = {23243390},
issn = {1472-3654},
mesh = {Aerobiosis ; Anaerobiosis ; Escherichia coli/chemistry/growth &amp; development ; Metals/*analysis ; Methanococcus/*chemistry/growth &amp; development ; Pyrococcus furiosus/*chemistry/growth &amp; development ; Trace Elements/*analysis ; },
abstract = {To date, no experimental data has been reported for the metallome of hyperthermophilic microorganisms although their metal requirements for growth are known to be unique. Here, experiments were conducted to determine (i) cellular trace metal concentrations of the hyperthermophilic Archaea Methanococcus jannaschii and Pyrococcus furiosus, and (ii) a first estimate of the metallome for these hyperthermophilic species via ICP-MS. The metal contents of these cells were compared to parallel experiments using the mesophilic bacterium Escherichia coli grown under aerobic and anaerobic conditions. Fe and Zn were typically the most abundant metals in cells. Metal concentrations for E. coli grown aerobically decreased in the order Fe > Zn > Cu > Mo > Ni > W > Co. In contrast, M. jannaschii and P. furiosus show almost the reverse pattern with elevated Ni, Co, and W concentrations. Of the three organisms, a biosignature is potentially demonstrated for the methanogen M. jannaschii that may, in part, be related to the metallome requirements of methanogenesis. The bioavailability of trace metals more than likely has varied through time. If hyperthermophiles are very ancient, then the trace metal patterns observed here may begin to provide some insights regarding Earth's earliest cells and in turn, early Earth chemistry.},
}
@article {pmid23241446,
year = {2012},
author = {Wolf, YI and Makarova, KS and Yutin, N and Koonin, EV},
title = {Updated clusters of orthologous genes for Archaea: a complex ancestor of the Archaea and the byways of horizontal gene transfer.},
journal = {Biology direct},
volume = {7},
number = {},
pages = {46},
pmid = {23241446},
issn = {1745-6150},
support = {//Intramural NIH HHS/United States ; },
mesh = {Archaea/*genetics ; Archaeal Proteins/genetics ; Cluster Analysis ; Databases, Protein ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Genes, Archaeal ; *Genome, Archaeal ; Genomics ; Multigene Family ; Phylogeny ; Sequence Alignment ; },
abstract = {BACKGROUND: Collections of Clusters of Orthologous Genes (COGs) provide indispensable tools for comparative genomic analysis, evolutionary reconstruction and functional annotation of new genomes. Initially, COGs were made for all complete genomes of cellular life forms that were available at the time. However, with the accumulation of thousands of complete genomes, construction of a comprehensive COG set has become extremely computationally demanding and prone to error propagation, necessitating the switch to taxon-specific COG collections. Previously, we reported the collection of COGs for 41 genomes of Archaea (arCOGs). Here we present a major update of the arCOGs and describe evolutionary reconstructions to reveal general trends in the evolution of Archaea.<br><br>RESULTS: The updated version of the arCOG database incorporates 91% of the pangenome of 120 archaea (251,032 protein-coding genes altogether) into 10,335 arCOGs. Using this new set of arCOGs, we performed maximum likelihood reconstruction of the genome content of archaeal ancestral forms and gene gain and loss events in archaeal evolution. This reconstruction shows that the last Common Ancestor of the extant Archaea was an organism of greater complexity than most of the extant archaea, probably with over 2,500 protein-coding genes. The subsequent evolution of almost all archaeal lineages was apparently dominated by gene loss resulting in genome streamlining. Overall, in the evolution of Archaea as well as a representative set of bacteria that was similarly analyzed for comparison, gene losses are estimated to outnumber gene gains at least 4 to 1. Analysis of specific patterns of gene gain in Archaea shows that, although some groups, in particular Halobacteria, acquire substantially more genes than others, on the whole, gene exchange between major groups of Archaea appears to be largely random, with no major 'highways' of horizontal gene transfer.<br><br>CONCLUSIONS: The updated collection of arCOGs is expected to become a key resource for comparative genomics, evolutionary reconstruction and functional annotation of new archaeal genomes. Given that, in spite of the major increase in the number of genomes, the conserved core of archaeal genes appears to be stabilizing, the major evolutionary trends revealed here have a chance to stand the test of time.<br><br>REVIEWERS: This article was reviewed by (for complete reviews see the Reviewers' Reports section): Dr. PLG, Prof. PF, Dr. PL (nominated by Prof. JPG).},
}
@article {pmid23240084,
year = {2012},
author = {Ammar, R and Torti, D and Tsui, K and Gebbia, M and Durbic, T and Bader, GD and Giaever, G and Nislow, C},
title = {Chromatin is an ancient innovation conserved between Archaea and Eukarya.},
journal = {eLife},
volume = {1},
number = {},
pages = {e00078},
pmid = {23240084},
issn = {2050-084X},
support = {//Canadian Institutes of Health Research/Canada ; },
mesh = {Biological Evolution ; Chromatin Assembly and Disassembly ; DNA Replication ; Eukaryotic Cells/cytology/metabolism ; Gene Expression Profiling ; *Gene Expression Regulation, Archaeal ; *Genome, Archaeal ; Haloferax volcanii/chemistry/*genetics/metabolism ; Histones/*genetics/metabolism ; Molecular Sequence Annotation ; Nucleosomes/*chemistry/metabolism ; Promoter Regions, Genetic ; Transcription Factors/*genetics/metabolism ; Transcription Initiation Site ; Transcription, Genetic ; },
abstract = {The eukaryotic nucleosome is the fundamental unit of chromatin, comprising a protein octamer that wraps ∼147 bp of DNA and has essential roles in DNA compaction, replication and gene expression. Nucleosomes and chromatin have historically been considered to be unique to eukaryotes, yet studies of select archaea have identified homologs of histone proteins that assemble into tetrameric nucleosomes. Here we report the first archaeal genome-wide nucleosome occupancy map, as observed in the halophile Haloferax volcanii. Nucleosome occupancy was compared with gene expression by compiling a comprehensive transcriptome of Hfx. volcanii. We found that archaeal transcripts possess hallmarks of eukaryotic chromatin structure: nucleosome-depleted regions at transcriptional start sites and conserved -1 and +1 promoter nucleosomes. Our observations demonstrate that histones and chromatin architecture evolved before the divergence of Archaea and Eukarya, suggesting that the fundamental role of chromatin in the regulation of gene expression is ancient.DOI:http://dx.doi.org/10.7554/eLife.00078.001.},
}
@article {pmid23226971,
year = {2012},
author = {Blank, CE},
title = {Low rates of lateral gene transfer among metabolic genes define the evolving biogeochemical niches of archaea through deep time.},
journal = {Archaea (Vancouver, B.C.)},
volume = {2012},
number = {},
pages = {843539},
pmid = {23226971},
issn = {1472-3654},
mesh = {Archaea/*genetics ; Archaeal Proteins/genetics ; Cluster Analysis ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Metabolic Networks and Pathways/*genetics ; Phylogeny ; Sequence Homology ; },
abstract = {Phylogenomic analyses of archaeal genome sequences are providing windows into the group's evolutionary past, even though most archaeal taxa lack a conventional fossil record. Here, phylogenetic analyses were performed using key metabolic genes that define the metabolic niche of microorganisms. Such genes are generally considered to have undergone high rates of lateral gene transfer. Many gene sequences formed clades that were identical, or similar, to the tree constructed using large numbers of genes from the stable core of the genome. Surprisingly, such lateral transfer events were readily identified and quantifiable, occurring only a relatively small number of times in the archaeal domain of life. By placing gene acquisition events into a temporal framework, the rates by which new metabolic genes were acquired can be quantified. The highest lateral transfer rates were among cytochrome oxidase genes that use oxygen as a terminal electron acceptor (with a total of 12-14 lateral transfer events, or 3.4-4.0 events per billion years, across the entire archaeal domain). Genes involved in sulfur or nitrogen metabolism had much lower rates, on the order of one lateral transfer event per billion years. This suggests that lateral transfer rates of key metabolic proteins are rare and not rampant.},
}
@article {pmid23220959,
year = {2013},
author = {Smith, DJ and Timonen, HJ and Jaffe, DA and Griffin, DW and Birmele, MN and Perry, KD and Ward, PD and Roberts, MS},
title = {Intercontinental dispersal of bacteria and archaea by transpacific winds.},
journal = {Applied and environmental microbiology},
volume = {79},
number = {4},
pages = {1134-1139},
pmid = {23220959},
issn = {1098-5336},
mesh = {*Air Microbiology ; Archaea/classification/genetics/*isolation &amp; purification ; Bacteria/classification/genetics/*isolation &amp; purification ; *Biodiversity ; Metagenome ; Microarray Analysis ; North America ; *Phylogeography ; RNA, Ribosomal, 16S/genetics ; Wind ; },
abstract = {Microorganisms are abundant in the upper atmosphere, particularly downwind of arid regions, where winds can mobilize large amounts of topsoil and dust. However, the challenge of collecting samples from the upper atmosphere and reliance upon culture-based characterization methods have prevented a comprehensive understanding of globally dispersed airborne microbes. In spring 2011 at the Mt. Bachelor Observatory in North America (2.8 km above sea level), we captured enough microbial biomass in two transpacific air plumes to permit a microarray analysis using 16S rRNA genes. Thousands of distinct bacterial taxa spanning a wide range of phyla and surface environments were detected before, during, and after each Asian long-range transport event. Interestingly, the transpacific plumes delivered higher concentrations of taxa already in the background air (particularly Proteobacteria, Actinobacteria, and Firmicutes). While some bacterial families and a few marine archaea appeared for the first and only time during the plumes, the microbial community compositions were similar, despite the unique transport histories of the air masses. It seems plausible, when coupled with atmospheric modeling and chemical analysis, that microbial biogeography can be used to pinpoint the source of intercontinental dust plumes. Given the degree of richness measured in our study, the overall contribution of Asian aerosols to microbial species in North American air warrants additional investigation.},
}
@article {pmid23209375,
year = {2012},
author = {Winter, JA and Bunting, KA},
title = {Rings in the extreme: PCNA interactions and adaptations in the archaea.},
journal = {Archaea (Vancouver, B.C.)},
volume = {2012},
number = {},
pages = {951010},
pmid = {23209375},
issn = {1472-3654},
mesh = {*Adaptation, Biological ; Archaea/*genetics/physiology ; Archaeal Proteins/*genetics/metabolism ; DNA Repair ; DNA Replication ; *Evolution, Molecular ; Models, Molecular ; Proliferating Cell Nuclear Antigen/*genetics/metabolism ; },
abstract = {Biochemical and structural analysis of archaeal proteins has enabled us to gain great insight into many eukaryotic processes, simultaneously offering fascinating glimpses into the adaptation and evolution of proteins at the extremes of life. The archaeal PCNAs, central to DNA replication and repair, are no exception. Characterisation of the proteins alone, and in complex with both peptides and protein binding partners, has demonstrated the diversity and subtlety in the regulatory role of these sliding clamps. Equally, studies have provided valuable detailed insight into the adaptation of protein interactions and mechanisms that are necessary for life in extreme environments.},
}
@article {pmid23209374,
year = {2012},
author = {Webb, KM and DiRuggiero, J},
title = {Role of Mn2+ and compatible solutes in the radiation resistance of thermophilic bacteria and archaea.},
journal = {Archaea (Vancouver, B.C.)},
volume = {2012},
number = {},
pages = {845756},
pmid = {23209374},
issn = {1472-3654},
support = {P30 ES00319/ES/NIEHS NIH HHS/United States ; },
mesh = {Antioxidants/metabolism ; Archaea/*metabolism/*radiation effects ; Bacteria/*metabolism/*radiation effects ; Cations, Divalent/metabolism ; Cell Survival/radiation effects ; Glyceric Acids/metabolism ; Inositol Phosphates/metabolism ; Manganese/*metabolism ; Mannose/analogs &amp; derivatives/metabolism ; Microbial Viability/radiation effects ; *Radiation ; Reactive Oxygen Species/metabolism ; Trehalose/metabolism ; },
abstract = {Radiation-resistant bacteria have garnered a great deal of attention from scientists seeking to expose the mechanisms underlying their incredible survival abilities. Recent analyses showed that the resistance to ionizing radiation (IR) in the archaeon Halobacterium salinarum is dependent upon Mn-antioxidant complexes responsible for the scavenging of reactive oxygen species (ROS) generated by radiation. Here we examined the role of the compatible solutes trehalose, mannosylglycerate, and di-myo-inositol phosphate in the radiation resistance of aerobic and anaerobic thermophiles. We found that the IR resistance of the thermophilic bacteria Rubrobacter xylanophilus and Rubrobacter radiotolerans was highly correlated to the accumulation of high intracellular concentration of trehalose in association with Mn, supporting the model of Mn(2+)-dependent ROS scavenging in the aerobes. In contrast, the hyperthermophilic archaea Thermococcus gammatolerans and Pyrococcus furiosus did not contain significant amounts of intracellular Mn, and we found no significant antioxidant activity from mannosylglycerate and di-myo-inositol phosphate in vitro. We therefore propose that the low levels of IR-generated ROS under anaerobic conditions combined with highly constitutively expressed detoxification systems in these anaerobes are key to their radiation resistance and circumvent the need for the accumulation of Mn-antioxidant complexes in the cell.},
}
@article {pmid23198809,
year = {2013},
author = {Yasuda, T and Waki, M and Kuroda, K and Hanajima, D and Fukumoto, Y and Yamagishi, T and Suwa, Y and Suzuki, K},
title = {Responses of community structure of amoA-encoding archaea and ammonia-oxidizing bacteria in ammonia biofilter with rockwool mixtures to the gradual increases in ammonium and nitrate.},
journal = {Journal of applied microbiology},
volume = {114},
number = {3},
pages = {746-761},
doi = {10.1111/jam.12091},
pmid = {23198809},
issn = {1365-2672},
mesh = {Air Pollutants/*metabolism ; Ammonia/*metabolism ; Archaea/genetics/*metabolism ; Bacteria/genetics/*metabolism ; Bioreactors ; Denaturing Gradient Gel Electrophoresis ; Denitrification ; Filtration ; Microbial Consortia ; Nitrates/*metabolism ; Nitrogen/chemistry ; Nitrogen Isotopes/chemistry ; Oxidoreductases/genetics ; Phylogeny ; Quaternary Ammonium Compounds ; Real-Time Polymerase Chain Reaction ; Water/chemistry ; },
abstract = {AIMS: To investigate community shifts of amoA-encoding archaea (AEA) and ammonia-oxidizing bacteria (AOB) in biofilter under nitrogen accumulation process.<br><br>METHODS AND RESULTS: A laboratory-scale rockwool biofilter with an irrigated water circulation system was operated for 436 days with ammonia loading rates of 49-63 NH(3) g m(-3) day(-1). The AEA and AOB communities were investigated by denaturing gradient gel electrophoresis, sequencing and real-time PCR analysis based on amoA genes. The results indicated that changes in abundance and community compositions occurred in a different manner between archaeal and bacterial amoA during the operation. However, both microbial community structures mainly varied when free ammonia (FA) concentrations in circulation water were increasing, which caused a temporal decline in reactor performance. Dominant amoA sequences after this transition were related to Thaumarchaeotal Group I.1b, Nitrosomonas europaea lineages and one subcluster within Nitrosospira sp. cluster 3, for archaea and bacteria, respectively.<br><br>CONCLUSIONS: The specific FA in circulation water seems to be the important factor, which relates to the AOB and AEA community shifts in the biofilter besides ammonium and pH.<br><br>One of the key factors for regulating AEA and AOB communities was proposed that is useful for optimizing biofiltration technology.},
}
@article {pmid23189241,
year = {2012},
author = {Wang, X and Lv, B and Cai, G and Fu, L and Wu, Y and Wang, X and Ren, B and Ma, H},
title = {A proton shelter inspired by the sugar coating of acidophilic archaea.},
journal = {Scientific reports},
volume = {2},
number = {},
pages = {892},
pmid = {23189241},
issn = {2045-2322},
mesh = {Archaea/*metabolism ; Biomimetic Materials/chemistry ; Carbohydrates/*chemistry ; Cell Membrane/chemistry/metabolism ; Hot Springs ; Hydrogen-Ion Concentration ; Methacrylates/chemistry ; Polyethylene Glycols/chemistry ; Polymethacrylic Acids ; Protons ; },
abstract = {The acidophilic archaeons are a group of single-celled microorganisms that flourish in hot acid springs (usually pH < 3) but maintain their internal pH near neutral. Although there is a lack of direct evidence, the abundance of sugar modifications on the cell surface has been suggested to provide the acidophiles with protection against proton invasion. In this study, a hydroxyl (OH)-rich polymer brush layer was prepared to mimic the OH-rich sugar coating. Using a novel pH-sensitive dithioacetal molecule as a probe, we studied the proton-resisting property and found that a 10-nm-thick polymer layer was able to raise the pH from 1.0 to > 5.0, indicating that the densely packed OH-rich layer is a proton shelter. As strong evidence for the role of sugar coatings as proton barriers, this biomimetic study provides insight into evolutionary biology, and the results also could be expanded for the development of biocompatible anti-acid materials.},
}
@article {pmid23188094,
year = {2012},
author = {Gupta, GD and Kale, A and Kumar, V},
title = {Molecular evolution of translin superfamily proteins within the genomes of eubacteria, archaea and eukaryotes.},
journal = {Journal of molecular evolution},
volume = {75},
number = {5-6},
pages = {155-167},
pmid = {23188094},
issn = {1432-1432},
mesh = {Amino Acid Motifs ; Amino Acid Sequence ; Animals ; Archaea/genetics ; Carrier Proteins/chemistry/genetics/metabolism ; DNA-Binding Proteins/chemistry/*genetics/metabolism ; Eubacterium/genetics ; Eukaryota/genetics ; *Evolution, Molecular ; *Genome ; Humans ; Models, Molecular ; Molecular Sequence Data ; *Multigene Family ; Phylogeny ; Protein Conformation ; RNA-Binding Proteins/chemistry/*genetics/metabolism ; Sequence Alignment ; },
abstract = {Translin and its interacting partner protein, TRAX, are members of the translin superfamily. These proteins are involved in mRNA regulation and in promoting RISC activity by removing siRNA passenger strand cleavage products, and have been proposed to play roles in DNA repair and recombination. Both homomeric translin and heteromeric translin-TRAX complex bind to ssDNA and RNA; however, the heteromeric complex is a key activator in siRNA-mediated silencing in human and drosophila. The residues critical for RNase activity of the complex reside in TRAX sequence. Both translin and TRAX are well conserved in eukaryotes. In present work, a single translin superfamily protein is detected in Chloroflexi eubacteria, in the known phyla of archaea and in some unicellular eukaryotes. The prokaryotic proteins essentially share unique sequence motifs with eukaryotic TRAX, while the proteins possessing both the unique sequences and conserved indels of TRAX or translin can be identified from protists. Intriguingly, TRAX protein in all the known genomes of extant Chloroflexi share high sequence similarity and conserved indels with the archaeal protein, suggesting occurrence of TRAX at least at the time of Chloroflexi divergence as well as evolutionary relationship between Chloroflexi and archaea. The mirror phylogeny in phylogenetic tree, constructed using diverse translin and TRAX sequences, indicates gene duplication event leading to evolution of translin in unicellular eukaryotes, prior to divergence of multicellular eukayrotes. Since Chloroflexi has been debated to be near the last universal common ancestor, the present analysis indicates that TRAX may be useful to understand the tree of life.},
}
@article {pmid23181628,
year = {2012},
author = {Petitjean, C and Moreira, D and López-García, P and Brochier-Armanet, C},
title = {Horizontal gene transfer of a chloroplast DnaJ-Fer protein to Thaumarchaeota and the evolutionary history of the DnaK chaperone system in Archaea.},
journal = {BMC evolutionary biology},
volume = {12},
number = {},
pages = {226},
pmid = {23181628},
issn = {1471-2148},
mesh = {Archaea/*genetics ; Binding Sites/genetics ; Chlorophyta/genetics ; Chloroplast Proteins/*genetics ; Cyanobacteria/genetics ; Databases, Nucleic Acid ; Evolution, Molecular ; Ferredoxins/classification/*genetics ; *Gene Transfer, Horizontal ; Genome, Archaeal/genetics ; Genomics/methods ; HSP40 Heat-Shock Proteins/classification/*genetics ; HSP70 Heat-Shock Proteins/*genetics ; Molecular Chaperones/genetics ; Phylogeny ; Plants/genetics ; Recombinant Fusion Proteins/genetics ; },
abstract = {BACKGROUND: In 2004, we discovered an atypical protein in metagenomic data from marine thaumarchaeotal species. This protein, referred as DnaJ-Fer, is composed of a J domain fused to a Ferredoxin (Fer) domain. Surprisingly, the same protein was also found in Viridiplantae (green algae and land plants). Because J domain-containing proteins are known to interact with the major chaperone DnaK/Hsp70, this suggested that a DnaK protein was present in Thaumarchaeota. DnaK/Hsp70, its co-chaperone DnaJ and the nucleotide exchange factor GrpE are involved, among others, in heat shocks and heavy metal cellular stress responses.<br><br>RESULTS: Using phylogenomic approaches we have investigated the evolutionary history of the DnaJ-Fer protein and of interacting proteins DnaK, DnaJ and GrpE in Thaumarchaeota. These proteins have very complex histories, involving several inter-domain horizontal gene transfers (HGTs) to explain the contemporary distribution of these proteins in archaea. These transfers include one from Cyanobacteria to Viridiplantae and one from Viridiplantae to Thaumarchaeota for the DnaJ-Fer protein, as well as independent HGTs from Bacteria to mesophilic archaea for the DnaK/DnaJ/GrpE system, followed by HGTs among mesophilic and thermophilic archaea.<br><br>CONCLUSIONS: We highlight the chimerical origin of the set of proteins DnaK, DnaJ, GrpE and DnaJ-Fer in Thaumarchaeota and suggest that the HGT of these proteins has played an important role in the adaptation of several archaeal groups to mesophilic and thermophilic environments from hyperthermophilic ancestors. Finally, the evolutionary history of DnaJ-Fer provides information useful for the relative dating of the diversification of Archaeplastida and Thaumarchaeota.},
}
@article {pmid23178669,
year = {2013},
author = {Probst, AJ and Holman, HY and DeSantis, TZ and Andersen, GL and Birarda, G and Bechtel, HA and Piceno, YM and Sonnleitner, M and Venkateswaran, K and Moissl-Eichinger, C},
title = {Tackling the minority: sulfate-reducing bacteria in an archaea-dominated subsurface biofilm.},
journal = {The ISME journal},
volume = {7},
number = {3},
pages = {635-651},
pmid = {23178669},
issn = {1751-7370},
mesh = {Archaea/classification/genetics/metabolism/*physiology ; Bacteria/classification/genetics/metabolism ; *Bacterial Physiological Phenomena ; *Biodiversity ; *Biofilms ; DNA, Bacterial/genetics ; Hydrogensulfite Reductase/genetics ; In Situ Hybridization, Fluorescence ; Natural Springs/chemistry/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Spectroscopy, Fourier Transform Infrared ; },
abstract = {Archaea are usually minor components of a microbial community and dominated by a large and diverse bacterial population. In contrast, the SM1 Euryarchaeon dominates a sulfidic aquifer by forming subsurface biofilms that contain a very minor bacterial fraction (5%). These unique biofilms are delivered in high biomass to the spring outflow that provides an outstanding window to the subsurface. Despite previous attempts to understand its natural role, the metabolic capacities of the SM1 Euryarchaeon remain mysterious to date. In this study, we focused on the minor bacterial fraction in order to obtain insights into the ecological function of the biofilm. We link phylogenetic diversity information with the spatial distribution of chemical and metabolic compounds by combining three different state-of-the-art methods: PhyloChip G3 DNA microarray technology, fluorescence in situ hybridization (FISH) and synchrotron radiation-based Fourier transform infrared (SR-FTIR) spectromicroscopy. The results of PhyloChip and FISH technologies provide evidence for selective enrichment of sulfate-reducing bacteria, which was confirmed by the detection of bacterial dissimilatory sulfite reductase subunit B (dsrB) genes via quantitative PCR and sequence-based analyses. We further established a differentiation of archaeal and bacterial cells by SR-FTIR based on typical lipid and carbohydrate signatures, which demonstrated a co-localization of organic sulfate, carbonated mineral and bacterial signatures in the biofilm. All these results strongly indicate an involvement of the SM1 euryarchaeal biofilm in the global cycles of sulfur and carbon and support the hypothesis that sulfidic springs are important habitats for Earth's energy cycles. Moreover, these investigations of a bacterial minority in an Archaea-dominated environment are a remarkable example of the great power of combining highly sensitive microarrays with label-free infrared imaging.},
}
@article {pmid23167813,
year = {2013},
author = {Eichler, J and Maupin-Furlow, J},
title = {Post-translation modification in Archaea: lessons from Haloferax volcanii and other haloarchaea.},
journal = {FEMS microbiology reviews},
volume = {37},
number = {4},
pages = {583-606},
pmid = {23167813},
issn = {1574-6976},
support = {R01 GM057498/GM/NIGMS NIH HHS/United States ; },
mesh = {Archaea/*metabolism ; Archaeal Proteins/*metabolism ; Haloferax volcanii/*metabolism ; *Protein Processing, Post-Translational ; Proteome/*metabolism ; },
abstract = {As an ever-growing number of genome sequences appear, it is becoming increasingly clear that factors other than genome sequence impart complexity to the proteome. Of the various sources of proteomic variability, post-translational modifications (PTMs) most greatly serve to expand the variety of proteins found in the cell. Likewise, modulating the rates at which different proteins are degraded also results in a constantly changing cellular protein profile. While both strategies for generating proteomic diversity are adopted by organisms across evolution, the responsible pathways and enzymes in Archaea are often less well described than are their eukaryotic and bacterial counterparts. Studies on halophilic archaea, in particular Haloferax volcanii, originally isolated from the Dead Sea, are helping to fill the void. In this review, recent developments concerning PTMs and protein degradation in the haloarchaea are discussed.},
}
@article {pmid23163210,
year = {2012},
author = {Yildiz, E and Ozcan, B and Caliskan, M},
title = {Isolation, characterization and phylogenetic analysis of halophilic archaea from a salt mine in central Anatolia (Turkey).},
journal = {Polish journal of microbiology},
volume = {61},
number = {2},
pages = {111-117},
pmid = {23163210},
issn = {1733-1331},
mesh = {DNA, Ribosomal/genetics ; Halobacteriales/*classification/genetics/*isolation &amp; purification/metabolism ; Molecular Sequence Data ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sodium Chloride/*metabolism ; Turkey ; Water Microbiology ; },
abstract = {The haloarchaeal diversity of a salt mine, a natural cave in central Anatolia, was investigated using convential microbiological and molecular biology methods. Eight halophilic archaeal isolates selected based on their colony morphology and whole cell protein profiles were taxonomically classified on the basis of their morphological, physiological, biochemical properties, polar lipid and protein profiles and 16S rDNA sequences. From the 16S rDNA sequences comparisons it was established that the isolates CH2, CH3 and CHC resembled Halorubrum saccharovorum by 98.8%, 98.9% and 99.5%, respectively. There was a 99.7% similarity between the isolate CH11 and Halobacterium noricense and 99.2% between the isolate CHA1 and Haloarcula argentinensis. The isolate CH8K and CH8B revealed a similarity rate of 99.8% and 99.3% to Halococcus dombrowskii, respectively. It was concluded that the isolates named CH2, CH3 and CHC were clustered in the genus Halorubrum and that CHA1 and CH7 in the genus Haloarcula, CH8K and CH8B in the genus Halococcus and CH11 in the genus Halobacterium.},
}
@article {pmid23155770,
year = {2012},
author = {Sambasiva Rao, KR and Srinivasa Rao, D},
title = {A comparative-based phylogenetic study in the evolution of 16S rRNA and rad a genes in Archaea.},
journal = {International journal of data mining and bioinformatics},
volume = {6},
number = {4},
pages = {396-405},
doi = {10.1504/ijdmb.2012.049277},
pmid = {23155770},
issn = {1748-5673},
mesh = {Archaea/*genetics ; *Evolution, Molecular ; Genome ; Genomics/*methods ; *Phylogeny ; RNA, Archaeal/*genetics ; RNA, Ribosomal, 16S/*genetics ; },
abstract = {Archaea are ubiquitous in their presence and abundant not only in extreme environments, but also in soil, oceans and freshwater, where they may fulfil a key role in the biogeochemical cycles of the earth. The identification of archaeal genomic signatures elucidates us a measure of distinctiveness of Archaea as a coherent group, although these signatures can differ according to the degree of stringency. The 16S rRNA and the Rad A genes are highly conserved in living organisms and are very useful for the phylogenetic analysis. Phylogenetic trees are constructed using the molecular evolutionary genetics analysis (MEGA) tool by neighbour joining (NJ) method and repeated bootstrapping for 5000 times was performed. The two trees were then compared using the Compare2trees and statistically analysed using the MEGA tool. The two phylogenetic trees show a similarity of 54.9%. In both the trees, the taxon Thaumarchaeota shows a high level of variance. The species Cenarchaeum symbiosum A shows a high level of similarity with the sequences of higher organisms (Euryarcheota-eukaryota), which shows that it has branched away to higher organisms from a closely related Protozoa, Eubacteria ancestor.},
}
@article {pmid23151644,
year = {2013},
author = {Kozubal, MA and Romine, M and Jennings, Rd and Jay, ZJ and Tringe, SG and Rusch, DB and Beam, JP and McCue, LA and Inskeep, WP},
title = {Geoarchaeota: a new candidate phylum in the Archaea from high-temperature acidic iron mats in Yellowstone National Park.},
journal = {The ISME journal},
volume = {7},
number = {3},
pages = {622-634},
pmid = {23151644},
issn = {1751-7370},
mesh = {Archaea/*classification/enzymology/*genetics/isolation &amp; purification ; Carbon/metabolism ; Energy Metabolism ; Genome, Archaeal/genetics ; Hot Springs/chemistry/*microbiology ; *Hot Temperature ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 23S/genetics ; Species Specificity ; },
abstract = {Geothermal systems in Yellowstone National Park (YNP) provide an outstanding opportunity to understand the origin and evolution of metabolic processes necessary for life in extreme environments including low pH, high temperature, low oxygen and elevated concentrations of reduced iron. Previous phylogenetic studies of acidic ferric iron mats from YNP have revealed considerable diversity of uncultivated and undescribed archaea. The goal of this study was to obtain replicate de novo genome assemblies for a dominant archaeal population inhabiting acidic iron-oxide mats in YNP. Detailed analysis of conserved ribosomal and informational processing genes indicates that the replicate assemblies represent a new candidate phylum within the domain Archaea referred to here as 'Geoarchaeota' or 'novel archaeal group 1 (NAG1)'. The NAG1 organisms contain pathways necessary for the catabolism of peptides and complex carbohydrates as well as a bacterial-like Form I carbon monoxide dehydrogenase complex likely used for energy conservation. Moreover, this novel population contains genes involved in the metabolism of oxygen including a Type A heme copper oxidase, a bd-type terminal oxidase and a putative oxygen-sensing protoglobin. NAG1 has a variety of unique bacterial-like cofactor biosynthesis and transport genes and a Type3-like CRISPR system. Discovery of NAG1 is critical to our understanding of microbial community structure and function in extant thermophilic iron-oxide mats of YNP, and will provide insight regarding the evolution of Archaea in early Earth environments that may have important analogs active in YNP today.},
}
@article {pmid23140889,
year = {2013},
author = {Maupin-Furlow, JA},
title = {Ubiquitin-like proteins and their roles in archaea.},
journal = {Trends in microbiology},
volume = {21},
number = {1},
pages = {31-38},
pmid = {23140889},
issn = {1878-4380},
support = {R01 GM057498/GM/NIGMS NIH HHS/United States ; GM57498/GM/NIGMS NIH HHS/United States ; },
mesh = {Archaea/*physiology ; Archaeal Proteins/*physiology ; *Protein Processing, Post-Translational ; Sulfur/metabolism ; Ubiquitins/*physiology ; },
abstract = {This review highlights the finding that ubiquitin-like (Ubl) proteins of archaea (termed SAMPs) function not only as sulfur carriers but also as protein modifiers. UbaA (an E1 ubiquitin-activating enzyme homolog of archaea) is required for the SAMPs to be covalently attached to proteins. The SAMPs and UbaA are also needed to form sulfur-containing biomolecules (e.g., thiolated tRNA and molybdenum cofactor). These findings provide a new perspective on how Ubl proteins can serve as both sulfur carriers and protein modifiers in the absence of canonical E2 ubiquitin conjugating or E3 ubiquitin ligase enzyme homologs.},
}
@article {pmid23133575,
year = {2012},
author = {Nikolic, N and Smole, Z and Krisko, A},
title = {Proteomic properties reveal phyloecological clusters of Archaea.},
journal = {PloS one},
volume = {7},
number = {10},
pages = {e48231},
pmid = {23133575},
issn = {1932-6203},
mesh = {Archaea/metabolism/*physiology ; Archaeal Proteins/*metabolism ; Cluster Analysis ; Ecology ; Genes, Archaeal ; Hydrogen Bonding ; Multigene Family ; Phylogeny ; Protein Array Analysis ; Protein Binding ; Proteome ; Proteomics/*methods ; RNA, Ribosomal, 16S/metabolism ; Temperature ; },
abstract = {In this study, we propose a novel way to describe the variety of environmental adaptations of Archaea. We have clustered 57 Archaea by using a non-redundant set of proteomic features, and verified that the clusters correspond to environmental adaptations to the archaeal habitats. The first cluster consists dominantly of hyperthermophiles and hyperthermoacidophilic aerobes. The second cluster joins together halophilic and extremely halophilic Archaea, while the third cluster contains mesophilic (mostly methanogenic) Archaea together with thermoacidophiles. The non-redundant subset of proteomic features was found to consist of five features: the ratio of charged residues to uncharged, average protein size, normalized frequency of beta-sheet, normalized frequency of extended structure and number of hydrogen bond donors. We propose this clustering to be termed phyloecological clustering. This approach could give additional insights into relationships among archaeal species that may be hidden by sole phylogenetic analysis.},
}
@article {pmid23116157,
year = {2013},
author = {Posner, MG and Upadhyay, A and Crennell, SJ and Watson, AJ and Dorus, S and Danson, MJ and Bagby, S},
title = {Post-translational modification in the archaea: structural characterization of multi-enzyme complex lipoylation.},
journal = {The Biochemical journal},
volume = {449},
number = {2},
pages = {415-425},
doi = {10.1042/BJ20121150},
pmid = {23116157},
issn = {1470-8728},
support = {MC_U117533887/MRC_/Medical Research Council/United Kingdom ; },
mesh = {Adenosine Monophosphate/chemistry/metabolism ; Archaeal Proteins/chemistry/genetics/*metabolism ; Binding Sites ; Crystallography, X-Ray ; Dihydrolipoyllysine-Residue Acetyltransferase/chemistry/genetics/metabolism ; Isoenzymes/chemistry/genetics/metabolism ; Lipoylation ; Magnetic Resonance Spectroscopy ; Models, Molecular ; Multiprotein Complexes/chemistry/metabolism ; Peptide Synthases/chemistry/genetics/*metabolism ; Protein Binding ; Protein Conformation ; *Protein Processing, Post-Translational ; Protein Structure, Tertiary ; Recombinant Proteins/chemistry/metabolism ; Substrate Specificity ; Thermoplasma/*enzymology ; Thioctic Acid/chemistry/metabolism ; },
abstract = {Lipoylation, the covalent attachment of lipoic acid to 2-oxoacid dehydrogenase multi-enzyme complexes, is essential for metabolism in aerobic bacteria and eukarya. In Escherichia coli, lipoylation is catalysed by LplA (lipoate protein ligase) or by LipA (lipoic acid synthetase) and LipB [lipoyl(octanoyl) transferase] combined. Whereas bacterial and eukaryotic LplAs comprise a single two-domain protein, archaeal LplA function typically involves two proteins, LplA-N and LplA-C. In the thermophilic archaeon Thermoplasma acidophilum, LplA-N and LplA-C are encoded by overlapping genes in inverted orientation (lpla-c is upstream of lpla-n). The T. acidophilum LplA-N structure is known, but the LplA-C structure is unknown and LplA-C's role in lipoylation is unclear. In the present study, we have determined the structures of the substrate-free LplA-N-LplA-C complex and E2lipD (dihydrolipoyl acyltransferase lipoyl domain) that is lipoylated by LplA-N-LplA-C, and carried out biochemical analyses of this archaeal lipoylation system. Our data reveal the following: (i) LplA-C is disordered but folds upon association with LplA-N; (ii) LplA-C induces a conformational change in LplA-N involving substantial shortening of a loop that could repress catalytic activity of isolated LplA-N; (iii) the adenylate-binding region of LplA-N-LplA-C includes two helices rather than the purely loop structure of varying order observed in other LplA structures; (iv) LplAN-LplA-C and E2lipD do not interact in the absence of substrate; (v) LplA-N-LplA-C undergoes a conformational change (the details of which are currently undetermined) during lipoylation; and (vi) LplA-N-LplA-C can utilize octanoic acid as well as lipoic acid as substrate. The elucidated functional inter-dependence of LplA-N and LplA-C is consistent with their evolutionary co-retention in archaeal genomes.},
}
@article {pmid23111319,
year = {2013},
author = {Naor, A and Gophna, U},
title = {Cell fusion and hybrids in Archaea: prospects for genome shuffling and accelerated strain development for biotechnology.},
journal = {Bioengineered},
volume = {4},
number = {3},
pages = {126-129},
pmid = {23111319},
issn = {2165-5987},
mesh = {Archaea/cytology/*genetics ; Biotechnology ; Cell Fusion ; DNA Shuffling ; *Gene Transfer, Horizontal ; *Genome, Archaeal ; },
abstract = {The ability to exchange DNA between cells is a molecular process that exists in different species in the domain Archaea. Such horizontal gene transfer events were shown to take place between distant species of archaea and to result in the transfer of large genomic regions. Here we describe recent progress in this field, discuss the potential use of natural gene exchange processes to perform genome shuffling and argue its possible biotechnological applications.},
}
@article {pmid23108528,
year = {2013},
author = {Zheng, Y and Hou, L and Liu, M and Lu, M and Zhao, H and Yin, G and Zhou, J},
title = {Diversity, abundance, and activity of ammonia-oxidizing bacteria and archaea in Chongming eastern intertidal sediments.},
journal = {Applied microbiology and biotechnology},
volume = {97},
number = {18},
pages = {8351-8363},
doi = {10.1007/s00253-012-4512-3},
pmid = {23108528},
issn = {1432-0614},
mesh = {Ammonia/*metabolism ; Archaea/classification/genetics/*isolation &amp; purification/*metabolism ; Archaeal Proteins/genetics ; Bacteria/classification/genetics/*isolation &amp; purification/*metabolism ; Bacterial Proteins/genetics ; *Biodiversity ; China ; Geologic Sediments/*microbiology ; Molecular Sequence Data ; Oxidation-Reduction ; Oxidoreductases/genetics ; Phylogeny ; Wetlands ; },
abstract = {Ammonia oxidation plays a pivotal role in the cycling and removal of nitrogen in aquatic sediments. Certain bacterial groups and a novel group of archaea, which is affiliated with the novel phylum Thaumarchaeota, can perform this initial nitrification step. We examined the diversity and abundance of ammonia-oxidizing β-Proteobacteria (β-AOB) and ammonia-oxidizing archaea (AOA) in the sediments of Chongming eastern tidal flat using the ammonia monooxygenase-α subunit (amoA) gene as functional markers. Clone library analysis showed that AOA had a higher diversity of amoA gene than β-AOB. The β-Proteobacterial amoA community composition correlated significantly with water soluble salts in the sediments, whereas the archaeal amoA community composition was correlated more with nitrate concentrations. Quantitative PCR (qPCR) results indicated that the abundance of β-AOB amoA gene (9.11 × 10(4)-6.47 × 10(5) copies g(-1) sediment) was always greater than that of AOA amoA gene (7.98 × 10(3)-3.51 × 10(5) copies g(-1) sediment) in all the samples analyzed in this study. The β-Proteobacterial amoA gene abundance was closely related to organic carbon, while no significant correlations were observed between archaeal amoA gene abundance and the environmental factors. Potential nitrification rates were significantly greater in summer than in winter and correlated strongly with the abundance of amoA genes. Additionally, a greater contribution of single amoA gene to potential nitrification occurred in summer (1.03-5.39 pmol N copy(-1) day(-1)) compared with winter (0.16-0.38 pmol N copy(-1) day(-1)), suggesting a higher activity of ammonia-oxidizing prokaryotes in warm seasons.},
}
@article {pmid23097517,
year = {2012},
author = {Williams, TA and Foster, PG and Nye, TM and Cox, CJ and Embley, TM},
title = {A congruent phylogenomic signal places eukaryotes within the Archaea.},
journal = {Proceedings. Biological sciences},
volume = {279},
number = {1749},
pages = {4870-4879},
pmid = {23097517},
issn = {1471-2954},
support = {BB/C006143/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/C508777/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Archaea/*classification/*genetics ; Eukaryota/*classification/*genetics ; *Evolution, Molecular ; Genes, rRNA ; Phylogeny ; Proteins/genetics ; Sequence Analysis, RNA ; Sequence Homology ; },
abstract = {Determining the relationships among the major groups of cellular life is important for understanding the evolution of biological diversity, but is difficult given the enormous time spans involved. In the textbook 'three domains' tree based on informational genes, eukaryotes and Archaea share a common ancestor to the exclusion of Bacteria. However, some phylogenetic analyses of the same data have placed eukaryotes within the Archaea, as the nearest relatives of different archaeal lineages. We compared the support for these competing hypotheses using sophisticated phylogenetic methods and an improved sampling of archaeal biodiversity. We also employed both new and existing tests of phylogenetic congruence to explore the level of uncertainty and conflict in the data. Our analyses suggested that much of the observed incongruence is weakly supported or associated with poorly fitting evolutionary models. All of our phylogenetic analyses, whether on small subunit and large subunit ribosomal RNA or concatenated protein-coding genes, recovered a monophyletic group containing eukaryotes and the TACK archaeal superphylum comprising the Thaumarchaeota, Aigarchaeota, Crenarchaeota and Korarchaeota. Hence, while our results provide no support for the iconic three-domain tree of life, they are consistent with an extended eocyte hypothesis whereby vital components of the eukaryotic nuclear lineage originated from within the archaeal radiation.},
}
@article {pmid23078250,
year = {2013},
author = {Nguyen-Hieu, T and Khelaifia, S and Aboudharam, G and Drancourt, M},
title = {Methanogenic archaea in subgingival sites: a review.},
journal = {APMIS : acta pathologica, microbiologica, et immunologica Scandinavica},
volume = {121},
number = {6},
pages = {467-477},
doi = {10.1111/apm.12015},
pmid = {23078250},
issn = {1600-0463},
mesh = {Anti-Infective Agents/pharmacology ; DNA, Archaeal/*analysis ; Databases, Factual ; Dental Plaque/microbiology ; Genes, Archaeal ; Genetic Variation ; Humans ; Methanobacteriales/genetics/*pathogenicity ; Periodontitis/diagnosis/drug therapy/epidemiology/*microbiology ; Prevalence ; RNA, Ribosomal, 16S/*analysis ; Severity of Illness Index ; },
abstract = {Archaea are non-bacterial prokaryotes associated with oral microbiota in humans, but their roles in oral pathologies remain controversial. Several studies reported the molecular detection of methanogenic archaea from periodontitis, but the significance of this association has not been confirmed yet. An electronic search was therefore conducted in MEDLINE-Pubmed to identify all papers published in English connecting archaea and periodontal infections. Data analysis of the selected studies showed that five genera of methanogenic archaea have been detected in the subgingival microbiota, Methanobrevibacter oralis being the most frequently detected species in 41% of periodontitis patients and 55% of periodontal pockets compared to 6% of healthy subjects and 5% of periodontally-healthy sites (p < 10(-5) , Chi-squared test). Based on the five determination-criteria proposed by Socransky (association with disease, elimination of the organism, host response, animal pathogenicity and mechanisms of pathogenicity), M. oralis is a periodontal pathogen. The methanogenic archaea load correlating with periodontitis severity further supports the pathogenic role of methanogenic archaea in periodontitis. Therefore, detection and quantification of M. oralis in periodontal pockets could help the laboratory diagnosis and follow-up of periodontitis. Determining the origin, diversity and pathogenesis of archaea in periodontal infections warrants further investigations.},
}
@article {pmid23074249,
year = {2012},
author = {Kirchman, DL},
title = {Marine archaea take a short cut in the nitrogen cycle.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {109},
number = {44},
pages = {17732-17733},
pmid = {23074249},
issn = {1091-6490},
mesh = {Archaea/*metabolism ; *Marine Biology ; *Nitrification ; Urea/*metabolism ; },
}
@article {pmid23060865,
year = {2012},
author = {Atomi, H and Imanaka, T and Fukui, T},
title = {Overview of the genetic tools in the Archaea.},
journal = {Frontiers in microbiology},
volume = {3},
number = {},
pages = {337},
pmid = {23060865},
issn = {1664-302X},
abstract = {This section provides an overview of the genetic systems developed in the Archaea. Genetic manipulation is possible in many members of the halophiles, methanogens, Sulfolobus, and Thermococcales. We describe the selection/counterselection principles utilized in each of these groups, which consist of antibiotics and their resistance markers, and auxotrophic host strains and complementary markers. The latter strategy utilizes techniques similar to those developed in yeast. However, Archaea are resistant to many of the antibiotics routinely used for selection in the Bacteria, and a number of strategies specific to the Archaea have been developed. In addition, examples utilizing the genetic systems developed for each group will be briefly described.},
}
@article {pmid23053110,
year = {2013},
author = {Sasaki, K and Morita, M and Sasaki, D and Ohmura, N and Igarashi, Y},
title = {The membraneless bioelectrochemical reactor stimulates hydrogen fermentation by inhibiting methanogenic archaea.},
journal = {Applied microbiology and biotechnology},
volume = {97},
number = {15},
pages = {7005-7013},
doi = {10.1007/s00253-012-4465-6},
pmid = {23053110},
issn = {1432-0614},
mesh = {Archaea/genetics/*metabolism ; Biomass ; *Bioreactors ; *Electrochemical Techniques ; *Fermentation ; Hydrogen/*metabolism ; *Membranes, Artificial ; Methane/*metabolism ; Phylogeny ; Polymorphism, Restriction Fragment Length ; Real-Time Polymerase Chain Reaction ; },
abstract = {The membraneless bioelectrochemical reactor (Ml-BER) is useful for dark hydrogen fermentation. The effect of the electrochemical reaction on microorganisms in the Ml-BER was investigated using glucose as the substrate and compared with organisms in a membraneless non-bioelectrochemical reactor (Ml-NBER) and bioelectrochemical reactor (BER) with a proton exchange membrane. The potentials on the working electrode of the Ml-BER and BER with membrane were regulated to -0.9 V (versus Ag/AgCl) to avoid water electrolysis with a carbon electrode. The Ml-BER showed suppressed methane production (19.8 ± 9.1 mg-C·L(-1)·day(-1)) and increased hydrogen production (12.6 ± 3.1 mg-H·L(-1)·day(-1)) at pHout 6.2 ± 0.1, and the major intermediate was butyrate (24.9 ± 2.4 mM), suggesting efficient hydrogen fermentation. In contrast, the Ml-NBER showed high methane production (239.3 ± 17.9 mg-C·L(-1)·day(-1)) and low hydrogen production (0.2 ± 0.0 mg-H·L(-1)·day(-1)) at pHout 6.3 ± 0.1. In the cathodic chamber of the BER with membrane, methane production was high (276.3 ± 20.4 mg-C·L(-1)·day(-1)) (pHout, 7.2 ± 0.1). In the anodic chamber of the BER with membrane (anode-BER), gas production was low because of high lactate production (43.6 ± 1.7 mM) at pHout 5.0 ± 0.1. Methanogenic archaea were not detected in the Ml-BER and anode-BER. However, Methanosarcina sp. and Methanobacterium sp. were found in Ml-NBER. Prokaryotic copy numbers in the Ml-BER and Ml-NBER were similar, as were the bacterial community structures. Thus, the electrochemical reaction in the Ml-BER affected hydrogenotrophic and acetoclastic methanogens, but not the bacterial community.},
}
@article {pmid23053098,
year = {2013},
author = {Chen, CH and Gao, DW and Tao, Y},
title = {Diversity and distribution of ammonia-oxidizing Archaea in the seasonally frozen soils in Northeastern China.},
journal = {Applied microbiology and biotechnology},
volume = {97},
number = {14},
pages = {6571-6579},
doi = {10.1007/s00253-012-4448-7},
pmid = {23053098},
issn = {1432-0614},
mesh = {Ammonia/*metabolism ; Archaea/classification/genetics/*isolation &amp; purification/*metabolism ; Bacterial Proteins/genetics ; *Biodiversity ; China ; Molecular Sequence Data ; Oxidation-Reduction ; Oxidoreductases/genetics ; Phylogeny ; Seasons ; Soil/chemistry ; *Soil Microbiology ; },
abstract = {The genetic diversity and distribution of ammonia-oxidizing Archaea (AOA) in nine seasonally frozen soils sampled around the city of Harbin, China, is analyzed based on archaeal amoA gene. Soil samples are divided into four groups by its properties: fertilized/unfertilized mesic (well-balanced supply of moisture) soils and fertilized/unfertilized hydric (abundant of moisture) soils. Clone libraries based on AOA amoA gene polymerase chain reaction products are constructed, and the phylogenetic analysis at 5 % cutoff level shows that AOA members mainly belong to the soil/sediment lineage which includes four clusters, and very few archaeal amoA gene sequences fall into the marine lineage. The four groups of soils have different archaeal amoA gene assemblage, and the available nitrogen and organic carbon are significantly correlated with diversity indexes. The result shows that long-term artificial amendment such as fertilization and agriculture cultivation has an important impact on AOA community shift in terrestrial environment. Moisture may drive the shape of different AOA communities by changing the aerobic environment into anaerobic. Soil composition is another noticeable factor effect AOA community, which can help the shape of a special AOA community with only two species.},
}
@article {pmid23039205,
year = {2012},
author = {Hayden, HL and Mele, PM and Bougoure, DS and Allan, CY and Norng, S and Piceno, YM and Brodie, EL and Desantis, TZ and Andersen, GL and Williams, AL and Hovenden, MJ},
title = {Changes in the microbial community structure of bacteria, archaea and fungi in response to elevated CO(2) and warming in an Australian native grassland soil.},
journal = {Environmental microbiology},
volume = {14},
number = {12},
pages = {3081-3096},
doi = {10.1111/j.1462-2920.2012.02855.x},
pmid = {23039205},
issn = {1462-2920},
mesh = {Archaea/genetics/*metabolism ; Australia ; Bacteria/*metabolism ; *Biota ; Carbon Dioxide/analysis/*metabolism ; Climate Change ; Ecosystem ; Fungi/genetics/*metabolism ; Hot Temperature ; Poaceae/chemistry/microbiology/parasitology ; Soil/analysis/*parasitology ; *Soil Microbiology ; },
abstract = {The microbial community structure of bacteria, archaea and fungi is described in an Australian native grassland soil after more than 5 years exposure to different atmospheric CO2 concentrations ([CO2]) (ambient, +550 ppm) and temperatures (ambient, + 2°C) under different plant functional types (C3 and C4 grasses) and at two soil depths (0-5 cm and 5-10 cm). Archaeal community diversity was influenced by elevated [CO2], while under warming archaeal 16S rRNA gene copy numbers increased for C4 plant Themeda triandra and decreased for the C3 plant community (P < 0.05). Fungal community diversity resulted in three groups based upon elevated [CO2], elevated [CO2] plus warming and ambient [CO2]. Overall bacterial community diversity was influenced primarily by depth. Specific bacterial taxa changed in richness and relative abundance in response to climate change factors when assessed by a high-resolution 16S rRNA microarray (PhyloChip). Operational taxonomic unit signal intensities increased under elevated [CO2] for both Firmicutes and Bacteroidetes, and increased under warming for Actinobacteria and Alphaproteobacteria. For the interaction of elevated [CO2] and warming there were 103 significant operational taxonomic units (P < 0.01) representing 15 phyla and 30 classes. The majority of these operational taxonomic units increased in abundance for elevated [CO2] plus warming plots, while abundance declined in warmed or elevated [CO2] plots. Bacterial abundance (16S rRNA gene copy number) was significantly different for the interaction of elevated [CO2] and depth (P < 0.05) with decreased abundance under elevated [CO2] at 5-10 cm, and for Firmicutes under elevated [CO2] (P < 0.05). Bacteria, archaea and fungi in soil responded differently to elevated [CO2], warming and their interaction. Taxa identified as significantly climate-responsive could show differing trends in the direction of response ('+' or '-') under elevated CO2 or warming, which could then not be used to predict their interactive effects supporting the need to investigate interactive effects for climate change. The approach of focusing on specific taxonomic groups provides greater potential for understanding complex microbial community changes in ecosystems under climate change.},
}
@article {pmid23032759,
year = {2012},
author = {Munk, B and Bauer, C and Gronauer, A and Lebuhn, M},
title = {A metabolic quotient for methanogenic Archaea.},
journal = {Water science and technology : a journal of the International Association on Water Pollution Research},
volume = {66},
number = {11},
pages = {2311-2317},
doi = {10.2166/wst.2012.436},
pmid = {23032759},
issn = {0273-1223},
mesh = {Archaea/*metabolism ; *Biofuels ; Bioreactors ; DNA, Archaeal/analysis ; Methane/*metabolism ; Real-Time Polymerase Chain Reaction ; },
abstract = {Biogas production from renewable resources is an alternative to generate energy and concomitantly save fossil fuels and mitigate greenhouse gas emissions. As methanogenesis is a major bottleneck in the biogas process, the determination of the specific activity of methanogenic Archaea can be a good indicator of the process state. A new parameter, the metabolic quotient (MQ), was developed to evaluate the specific activity of methanogens. A standard was created from mesophilic maize-fed fermenters to calculate the expected concentration of methanogens for a given methane productivity at stable process stages. The MQ, the ratio of the predicted to the actual concentration of methanogens, defines their metabolic activity. The MQ was able to indicate methanogenic cell stress metabolism and imminent process failure before conventional chemical parameters. As a further approach, the methanogenic activity was determined by quantification of mRNA transcripts in relation to the mcrA/mrtA-gene, coding for a key enzyme subunit of methanogenesis. The cDNA/DNA ratio reflected the specific actual process activity of the methanogens. As both methods are potent parameters for the early detection of process failure, biogas plant operators may avoid economical losses by their preventive application.},
}
@article {pmid23028926,
year = {2012},
author = {Susanti, D and Mukhopadhyay, B},
title = {An intertwined evolutionary history of methanogenic archaea and sulfate reduction.},
journal = {PloS one},
volume = {7},
number = {9},
pages = {e45313},
pmid = {23028926},
issn = {1932-6203},
mesh = {Archaea/*metabolism ; Biological Evolution ; Methane/metabolism ; Oxidation-Reduction ; Sulfates/*metabolism ; },
abstract = {Hydrogenotrophic methanogenesis and dissimilatory sulfate reduction, two of the oldest energy conserving respiratory systems on Earth, apparently could not have evolved in the same host, as sulfite, an intermediate of sulfate reduction, inhibits methanogenesis. However, certain methanogenic archaea metabolize sulfite employing a deazaflavin cofactor (F(420))-dependent sulfite reductase (Fsr) where N- and C-terminal halves (Fsr-N and Fsr-C) are homologs of F(420)H(2) dehydrogenase and dissimilatory sulfite reductase (Dsr), respectively. From genome analysis we found that Fsr was likely assembled from freestanding Fsr-N homologs and Dsr-like proteins (Dsr-LP), both being abundant in methanogens. Dsr-LPs fell into two groups defined by following sequence features: Group I (simplest), carrying a coupled siroheme-[Fe(4)-S(4)] cluster and sulfite-binding Arg/Lys residues; Group III (most complex), with group I features, a Dsr-type peripheral [Fe(4)-S(4)] cluster and an additional [Fe(4)-S(4)] cluster. Group II Dsr-LPs with group I features and a Dsr-type peripheral [Fe(4)-S(4)] cluster were proposed as evolutionary intermediates. Group III is the precursor of Fsr-C. The freestanding Fsr-N homologs serve as F(420)H(2) dehydrogenase unit of a putative novel glutamate synthase, previously described membrane-bound electron transport system in methanogens and of assimilatory type sulfite reductases in certain haloarchaea. Among archaea, only methanogens carried Dsr-LPs. They also possessed homologs of sulfate activation and reduction enzymes. This suggested a shared evolutionary history for methanogenesis and sulfate reduction, and Dsr-LPs could have been the source of the oldest (3.47-Gyr ago) biologically produced sulfide deposit.},
}
@article {pmid23027926,
year = {2012},
author = {Alonso-Sáez, L and Waller, AS and Mende, DR and Bakker, K and Farnelid, H and Yager, PL and Lovejoy, C and Tremblay, J&#xc9; and Potvin, M and Heinrich, F and Estrada, M and Riemann, L and Bork, P and Pedrós-Alió, C and Bertilsson, S},
title = {Role for urea in nitrification by polar marine Archaea.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {109},
number = {44},
pages = {17989-17994},
pmid = {23027926},
issn = {1091-6490},
mesh = {Archaea/*metabolism ; In Situ Hybridization, Fluorescence ; *Marine Biology ; Metagenomics ; Molecular Sequence Data ; *Nitrification ; Polymerase Chain Reaction ; Urea/*metabolism ; },
abstract = {Despite the high abundance of Archaea in the global ocean, their metabolism and biogeochemical roles remain largely unresolved. We investigated the population dynamics and metabolic activity of Thaumarchaeota in polar environments, where these microorganisms are particularly abundant and exhibit seasonal growth. Thaumarchaeota were more abundant in deep Arctic and Antarctic waters and grew throughout the winter at surface and deeper Arctic halocline waters. However, in situ single-cell activity measurements revealed a low activity of this group in the uptake of both leucine and bicarbonate (<5% Thaumarchaeota cells active), which is inconsistent with known heterotrophic and autotrophic thaumarchaeal lifestyles. These results suggested the existence of alternative sources of carbon and energy. Our analysis of an environmental metagenome from the Arctic winter revealed that Thaumarchaeota had pathways for ammonia oxidation and, unexpectedly, an abundance of genes involved in urea transport and degradation. Quantitative PCR analysis confirmed that most polar Thaumarchaeota had the potential to oxidize ammonia, and a large fraction of them had urease genes, enabling the use of urea to fuel nitrification. Thaumarchaeota from Arctic deep waters had a higher abundance of urease genes than those near the surface suggesting genetic differences between closely related archaeal populations. In situ measurements of urea uptake and concentration in Arctic waters showed that small-sized prokaryotes incorporated the carbon from urea, and the availability of urea was often higher than that of ammonium. Therefore, the degradation of urea may be a relevant pathway for Thaumarchaeota and other microorganisms exposed to the low-energy conditions of dark polar waters.},
}
@article {pmid23024044,
year = {2012},
author = {Li, XR and Xiao, YP and Ren, WW and Liu, ZF and Shi, JH and Quan, ZX},
title = {Abundance and composition of ammonia-oxidizing bacteria and archaea in different types of soil in the Yangtze River estuary.},
journal = {Journal of Zhejiang University. Science. B},
volume = {13},
number = {10},
pages = {769-782},
pmid = {23024044},
issn = {1862-1783},
mesh = {Ammonia/*metabolism ; Archaea/classification/genetics/*isolation &amp; purification/*metabolism ; Archaeal Proteins/genetics ; Bacteria/classification/genetics/*isolation &amp; purification/*metabolism ; Bacterial Proteins/genetics ; Biodiversity ; China ; Conservation of Natural Resources ; DNA, Archaeal/genetics/isolation &amp; purification ; DNA, Bacterial/genetics/isolation &amp; purification ; Estuaries ; Genes, Archaeal ; Genes, Bacterial ; Molecular Sequence Data ; Nitrification ; Nitrogen Cycle ; Oxidation-Reduction ; Oxidoreductases/genetics ; Phylogeny ; Rivers/microbiology ; *Soil Microbiology ; },
abstract = {Tidal flats are soil resources of great significance. Nitrification plays a central role in the nitrogen cycle and is often a critical first step in nitrogen removal from estuarine and coastal environments. We determined the abundance as well as composition of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) in different soils during land reclamation process. The abundance of AOA was higher than that of AOB in farm land and wild land while AOA was not detected in tidal flats using real-time polymerase chain reaction (PCR). The different abundances of AOB and AOA were negatively correlated with the salinity. The diversities of AOB and AOA were also investigated using clone libraries by amplification of amoA gene. Among AOB, nearly all sequences belonged to the Nitrosomonas lineage in the initial land reclamation process, i.e., tidal flats, while both Nitrosomonas and Nitrosospira lineages were detected in later and transition phases of land reclamation process, farm land and wild land. The ratio of the numbers of sequences of Nitrosomonas and Nitrosospira lineages was positively correlated with the salinity and the net nitrification rate. As for AOA, there was no obvious correlation with the changes in the physicochemical properties of the soil. This study suggests that AOB may be more import than AOA with respect to influencing the different land reclamation process stages.},
}
@article {pmid23015064,
year = {2012},
author = {Cobucci-Ponzano, B and Rossi, M and Moracci, M},
title = {Translational recoding in archaea.},
journal = {Extremophiles : life under extreme conditions},
volume = {16},
number = {6},
pages = {793-803},
pmid = {23015064},
issn = {1433-4909},
mesh = {Archaea/*genetics/metabolism ; Archaeal Proteins/*biosynthesis/genetics ; *Frameshifting, Ribosomal ; Lysine/analogs &amp; derivatives/metabolism ; Selenocysteine/metabolism ; },
abstract = {Translational recoding includes a group of events occurring during gene translation, namely stop codon readthrough, programmed ±1 frameshifting, and ribosome bypassing, which have been found in organisms from all domains of life. They serve to regulate protein expression at translational level and represent a relatively less known exception to the traditional central 'dogma' of biology that information flows as DNA→RNA→protein and that it is stored in a co-linear way between the 5'→3' of nucleic acids and N→C-terminal of polypeptides. In archaea, in which translational recoding regulates the decoding of the 21st and the 22nd amino acids selenocysteine and pyrrolysine, respectively, only one case of programmed -1 frameshifting has been reported so far and further examples, although promising, have not been confirmed yet. We here summarize the current state-of-the-art of this field that, especially in archaea, has relevant implications for the physiology of life in extreme environments and for the origin of life.},
}
@article {pmid23001661,
year = {2012},
author = {Paul, K and Nonoh, JO and Mikulski, L and Brune, A},
title = {"Methanoplasmatales," Thermoplasmatales-related archaea in termite guts and other environments, are the seventh order of methanogens.},
journal = {Applied and environmental microbiology},
volume = {78},
number = {23},
pages = {8245-8253},
pmid = {23001661},
issn = {1098-5336},
mesh = {Animals ; Arthropods/*microbiology ; Cluster Analysis ; DNA, Archaeal/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; *Environmental Microbiology ; Euryarchaeota/*classification/*genetics/metabolism ; Gastrointestinal Tract/microbiology ; Humans ; *Metagenome ; Methane/*metabolism ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; },
abstract = {The Euryarchaeota comprise both methanogenic and nonmethanogenic orders and many lineages of uncultivated archaea with unknown properties. One of these deep-branching lineages, distantly related to the Thermoplasmatales, has been discovered in various environments, including marine habitats, soil, and also the intestinal tracts of termites and mammals. By comparative phylogenetic analysis, we connected this lineage of 16S rRNA genes to a large clade of unknown mcrA gene sequences, a functional marker for methanogenesis, obtained from the same habitats. The identical topologies of 16S rRNA and mcrA gene trees and the perfect congruence of all branches, including several novel groups that we obtained from the guts of termites and cockroaches, strongly suggested that they stem from the same microorganisms. This was further corroborated by two highly enriched cultures of closely related methanogens from the guts of a higher termite (Cubitermes ugandensis) and a millipede (Anadenobolus sp.), which represented one of the arthropod-specific clusters in the respective trees. Numerous other pairs of habitat-specific sequence clusters were obtained from the guts of other termites and cockroaches but were also found in previously published data sets from the intestinal tracts of mammals (e.g., rumen cluster C) and other environments. Together with the recently described Methanomassiliicoccus luminyensis isolated from human feces, which falls into rice cluster III, the results of our study strongly support the idea that the entire clade of "uncultured Thermoplasmatales" in fact represents the seventh order of methanogenic archaea, for which the provisional name "Methanoplasmatales" is proposed.},
}
@article {pmid23001646,
year = {2012},
author = {Justice, NB and Pan, C and Mueller, R and Spaulding, SE and Shah, V and Sun, CL and Yelton, AP and Miller, CS and Thomas, BC and Shah, M and VerBerkmoes, N and Hettich, R and Banfield, JF},
title = {Heterotrophic archaea contribute to carbon cycling in low-pH, suboxic biofilm communities.},
journal = {Applied and environmental microbiology},
volume = {78},
number = {23},
pages = {8321-8330},
pmid = {23001646},
issn = {1098-5336},
mesh = {Aerobiosis ; Anaerobiosis ; Archaea/classification/genetics/*metabolism/*physiology ; Bacteria/classification/genetics/*metabolism ; *Bacterial Physiological Phenomena ; Biofilms/*growth &amp; development ; *Biota ; Carbon/*metabolism ; Environmental Microbiology ; Genes, rRNA ; Heterotrophic Processes ; Hydrogen-Ion Concentration ; Metagenome ; RNA, Archaeal/genetics ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; },
abstract = {Archaea are widely distributed and yet are most often not the most abundant members of microbial communities. Here, we document a transition from Bacteria- to Archaea-dominated communities in microbial biofilms sampled from the Richmond Mine acid mine drainage (AMD) system (∼pH 1.0, ∼38°C) and in laboratory-cultivated biofilms. This transition occurs when chemoautotrophic microbial communities that develop at the air-solution interface sink to the sediment-solution interface and degrade under microaerobic and anaerobic conditions. The archaea identified in these sunken biofilms are from the class Thermoplasmata, and in some cases, the highly divergent ARMAN nanoarchaeal lineage. In several of the sunken biofilms, nanoarchaea comprise 10 to 25% of the community, based on fluorescent in situ hybridization and metagenomic analyses. Comparative community proteomic analyses show a persistence of bacterial proteins in sunken biofilms, but there is clear evidence for amino acid modifications due to acid hydrolysis. Given the low representation of bacterial cells in sunken biofilms based on microscopy, we infer that hydrolysis reflects proteins derived from lysed cells. For archaea, we detected ∼2,400 distinct proteins, including a subset involved in proteolysis and peptide uptake. Laboratory cultivation experiments using complex carbon substrates demonstrated anaerobic enrichment of Ferroplasma and Aplasma coupled to the reduction of ferric iron. These findings indicate dominance of acidophilic archaea in degrading biofilms and suggest that they play roles in anaerobic nutrient cycling at low pH.},
}
@article {pmid22994489,
year = {2012},
author = {Stahl, DA and de la Torre, JR},
title = {Physiology and diversity of ammonia-oxidizing archaea.},
journal = {Annual review of microbiology},
volume = {66},
number = {},
pages = {83-101},
doi = {10.1146/annurev-micro-092611-150128},
pmid = {22994489},
issn = {1545-3251},
mesh = {Ammonia/*metabolism ; Archaea/*genetics/*physiology ; *Genetic Variation ; Metabolic Networks and Pathways ; Nitrogen/metabolism ; Oxidation-Reduction ; },
abstract = {The discovery of ammonia-oxidizing archaea (AOA), now generally recognized to exert primary control over ammonia oxidation in terrestrial, marine, and geothermal habitats, necessitates a reassessment of the nitrogen cycle. In particular, the unusually high affinity of marine and terrestrial AOA for ammonia indicates that this group may determine the oxidation state of nitrogen available to associated micro- and macrobiota, altering our current understanding of trophic interactions. Initial comparative genomics and physiological studies have revealed a novel, and as yet unresolved, primarily copper-based pathway for ammonia oxidation and respiration distinct from that of known ammonia-oxidizing bacteria and possibly relevant to the production of atmospherically active nitrogen oxides. Comparative studies also provide compelling evidence that the lineage of Archaea with which the AOA affiliate is sufficiently divergent to justify the creation of a novel phylum, the Thaumarchaeota.},
}
@article {pmid22973261,
year = {2012},
author = {Bustamante, M and Verdejo, V and Zúñiga, C and Espinosa, F and Orlando, J and Carú, M},
title = {Comparison of water availability effect on ammonia-oxidizing bacteria and archaea in microcosms of a Chilean semiarid soil.},
journal = {Frontiers in microbiology},
volume = {3},
number = {},
pages = {282},
pmid = {22973261},
issn = {1664-302X},
abstract = {Water availability is the main limiting factor in arid soils; however, few studies have examined the effects of drying and rewetting on nitrifiers from these environments. The effect of water availability on the diversity of ammonia-oxidizing bacteria (AOB) and archaea (AOA) from a semiarid soil of the Chilean sclerophyllous matorral was determined by microcosm assays. The addition of water every 14 days to reach 60% of the WHC significantly increased nitrate content in rewetted soil microcosms (p < 0.001). This stimulation of net nitrification by water addition was inhibited by acetylene addition at 100 Pa. The composition of AOA and AOB assemblages from the soils microcosms was determined by clone sequencing of amoA genes (A-amoA and B-amoA, respectively), and the 16S rRNA genes specific for β-proteobacteria (beta-amo). Sequencing of beta-amo genes has revealed representatives of Nitrosomonas and Nitrosospira while B-amoA clones consisted only of Nitrosospira sequences. Furthermore, all clones from the archaeal amoA gene library (A-amoA) were related to "mesophilic Crenarchaeota" sequences (actually, reclassified as the phylum Thaumarchaeota). The effect of water availability on both microbial assemblages structure was determined by T-RFLP profiles using the genetic markers amoA for archaea, and beta-amo for bacteria. While AOA showed fluctuations in some T-RFs, AOB structure remained unchanged by water pulses. The relative abundance of AOA and AOB was estimated by the Most Probable Number coupled to Polymerase Chain Reaction (MPN-PCR) assay. AOB was the predominant guild in this soil and higher soil water content did not affect their abundance, in contrast to AOA, which slightly increased under these conditions. Therefore, these results suggest that water addition to these semiarid soil microcosms could favor archaeal contribution to ammonium oxidation.},
}
@article {pmid22972386,
year = {2012},
author = {Yamamoto, N and Oishi, R and Suyama, Y and Tada, C and Nakai, Y},
title = {Ammonia-oxidizing bacteria rather than ammonia-oxidizing archaea were widely distributed in animal manure composts from field-scale facilities.},
journal = {Microbes and environments},
volume = {27},
number = {4},
pages = {519-524},
pmid = {22972386},
issn = {1347-4405},
mesh = {Ammonia/*metabolism ; Animals ; Archaea/enzymology/isolation &amp; purification/*metabolism ; Bacteria/enzymology/isolation &amp; purification/*metabolism ; Cattle ; Chickens ; DNA, Archaeal/analysis ; DNA, Bacterial/analysis ; Manure/*microbiology ; Nitrification ; Oxidation-Reduction ; RNA, Ribosomal, 16S/genetics ; Soil Microbiology ; Swine ; },
abstract = {The distribution of ammonia-oxidizing archaea (AOA) and bacteria (AOB) in cattle, swine, and chicken manure compost was analyzed. PCR-denaturing gradient gel electrophoresis (DGGE) showed that a Candidatus Nitrososphaera gargensis-like sequence dominated in cattle manure compost, while few AOA were detected in other composts. In the case of AOB, Nitrosomonas-like sequences were detected with higher diversity in cattle and swine manure composts. The relative abundance of ammonia oxidizers by real-time PCR revealed that more AOB was present in compost except in one swine manure compost. Our results indicated that AOB rather than AOA are widely distributed in animal manure compost.},
}
@article {pmid22950020,
year = {2012},
author = {Kim, JS and Makama, M and Petito, J and Park, NH and Cohan, FM and Dungan, RS},
title = {Diversity of Bacteria and Archaea in hypersaline sediment from Death Valley National Park, California.},
journal = {MicrobiologyOpen},
volume = {1},
number = {2},
pages = {135-148},
pmid = {22950020},
issn = {2045-8827},
abstract = {The objective of this study was to phylogenetically analyze microorganisms from the domains Bacteria and Archaea in hypersaline sediment from Death Valley National Park. Using domain-specific primers, a region of the 16S rRNA gene was amplified using polymerase chain reaction (PCR), and the product was subsequently used to create a clone library. A total of 243 bacterial clones, 99 archaeal clones, and 209 bacterial isolates were examined. The 243 clones from Bacteria were affiliated with the following groups: the Bacilli (59 clones) and Clostridia (1) of the Firmicutes, Bacteroidetes (90), Proteobacteria (27), Cyanobacteria (18), Gemmatimonadetes (41), candidate division OP1 (5), Actinobacteria (1), and the Deinococcus-Thermus division (1). Within the class Bacilli, 46 of 59 clones were tentatively identified as 10 unclassified species. The majority of bacterial isolates (130 of 209) were more closely related to the Bacillus subtilis-B. licheniformis clade than to any other recognized taxon, and an Ecotype Simulation analysis of B. subtilis relatives identified four previously unknown ecotypes. Several new genera were discovered within the Bacteroidetes (4) and the Gemmatimonadetes (2). Of the 99 archaeal clones, 94 were tentatively identified as belonging to 3 new genera within the Halobacteriaceae; other clones represented novel species within each of 4 established genera.},
}
@article {pmid22940806,
year = {2012},
author = {Ishibashi, T and Tomita, H and Yokooji, Y and Morikita, T and Watanabe, B and Hiratake, J and Kishimoto, A and Kita, A and Miki, K and Imanaka, T and Atomi, H},
title = {A detailed biochemical characterization of phosphopantothenate synthetase, a novel enzyme involved in coenzyme A biosynthesis in the Archaea.},
journal = {Extremophiles : life under extreme conditions},
volume = {16},
number = {6},
pages = {819-828},
pmid = {22940806},
issn = {1433-4909},
mesh = {Adenosine Triphosphate/metabolism ; Alanine/metabolism ; Archaeal Proteins/chemistry/isolation &amp; purification/*metabolism ; Coenzyme A/*biosynthesis ; Kinetics ; Pantothenic Acid/*analogs &amp; derivatives/biosynthesis/chemical synthesis ; Peptide Synthases/chemistry/isolation &amp; purification/*metabolism ; Phosphates/metabolism ; Phosphotransferases (Alcohol Group Acceptor)/metabolism ; Thermococcus/*enzymology ; },
abstract = {We have previously reported that the majority of the archaea utilize a novel pathway for coenzyme A biosynthesis (CoA). Bacteria/eukaryotes commonly use pantothenate synthetase and pantothenate kinase to convert pantoate to 4'-phosphopantothenate. However, in the hyperthermophilic archaeon Thermococcus kodakarensis, two novel enzymes specific to the archaea, pantoate kinase and phosphopantothenate synthetase, are responsible for this conversion. Here, we examined the enzymatic properties of the archaeal phosphopantothenate synthetase, which catalyzes the ATP-dependent condensation of 4-phosphopantoate and β-alanine. The activation energy of the phosphopantothenate synthetase reaction was 82.3 kJ mol(-1). In terms of substrate specificity toward nucleoside triphosphates, the enzyme displayed a strict preference for ATP. Among several amine substrates, activity was detected with β-alanine, but not with γ-aminobutyrate, glycine nor aspartate. The phosphopantothenate synthetase reaction followed Michaelis-Menten kinetics toward β-alanine, whereas substrate inhibition was observed with 4-phosphopantoate and ATP. Feedback inhibition by CoA/acetyl-CoA and product inhibition by 4'-phosphopantothenate were not observed. By contrast, the other archaeal enzyme pantoate kinase displayed product inhibition by 4-phosphopantoate in a non-competitive manner. Based on our results, we discuss the regulation of CoA biosynthesis in the archaea.},
}
@article {pmid22936929,
year = {2012},
author = {Shen, JP and Zhang, LM and Di, HJ and He, JZ},
title = {A review of ammonia-oxidizing bacteria and archaea in Chinese soils.},
journal = {Frontiers in microbiology},
volume = {3},
number = {},
pages = {296},
pmid = {22936929},
issn = {1664-302X},
abstract = {Ammonia (NH(3)) oxidation, the first and rate-limiting step of nitrification, is a key step in the global Nitrogen (N) cycle. Major advances have been made in recent years in our knowledge and understanding of the microbial communities involved in ammonia oxidation in a wide range of habitats, including Chinese agricultural soils. In this mini-review, we focus our attention on the distribution and community diversity of ammonia-oxidizing bacteria (AOB) and ammonia oxidizing archaea (AOA) in Chinese soils with variable soil properties and soil management practices. The niche differentiation of AOB and AOA in contrasting soils have been functionally demonstrated using DNA-SIP (stable isotope probing) methods, which have shown that AOA dominate nitrification processes in acidic soils, while AOB dominated in neutral, alkaline and N-rich soils. Finally, we discuss the composition and activity of ammonia oxidizers in paddy soils, as well as the mitigation of the greenhouse gas nitrous oxide (N(2)O) emissions and nitrate leaching via inhibition of nitrification by both AOB and AOA.},
}
@article {pmid22936928,
year = {2012},
author = {Ceballos, RM and Marceau, CD and Marceau, JO and Morris, S and Clore, AJ and Stedman, KM},
title = {Differential virus host-ranges of the Fuselloviridae of hyperthermophilic Archaea: implications for evolution in extreme environments.},
journal = {Frontiers in microbiology},
volume = {3},
number = {},
pages = {295},
pmid = {22936928},
issn = {1664-302X},
abstract = {An emerging model for investigating virus-host interactions in hyperthermophilic Archaea is the Fusellovirus-Sulfolobus system. The host, Sulfolobus, is a hyperthermophilic acidophile endemic to sulfuric hot springs worldwide. The Fuselloviruses, also known as Sulfolobus Spindle-shaped Viruses (SSVs), are "lemon" or "spindle"-shaped double-stranded DNA viruses, which are also found worldwide. Although a few studies have addressed the host-range for the type virus, Sulfolobus Spindle-shaped Virus 1 (SSV1), using common Sulfolobus strains, a comprehensive host-range study for SSV-Sulfolobus systems has not been performed. Herein, we examine six bona fide SSV strains (SSV1, SSV2, SSV3, SSVL1, SSVK1, SSVRH) and their respective infection characteristics on multiple hosts from the family Sulfolobaceae. A spot-on-lawn or "halo" assay was employed to determine SSV infectivity (and host susceptibility) in parallel challenges of multiple SSVs on a lawn of a single Sulfolobus strain. Different SSVs have different host-ranges with SSV1 exhibiting the narrowest host-range and SSVRH exhibiting the broadest host range. In contrast to previous reports, SSVs can infect hosts beyond the genus Sulfolobus. Furthermore, geography does not appear to be a reliable predictor of Sulfolobus susceptibility to infection by any given SSV. The ability for SSVs to infect susceptible Sulfolobus host does not appear to change between 65°C and 88°C (physiological range); however, very low pH appears to influence infection. Lastly, for the virus-host pairs tested the Fusellovirus-Sulfolobus system appears to exhibit host-advantage. This work provides a foundation for understanding Fusellovirus biology and virus-host coevolution in extreme ecosystems.},
}
@article {pmid22927959,
year = {2012},
author = {Borrel, G and Lehours, AC and Crouzet, O and Jézéquel, D and Rockne, K and Kulczak, A and Duffaud, E and Joblin, K and Fonty, G},
title = {Stratification of Archaea in the deep sediments of a freshwater meromictic lake: vertical shift from methanogenic to uncultured archaeal lineages.},
journal = {PloS one},
volume = {7},
number = {8},
pages = {e43346},
pmid = {22927959},
issn = {1932-6203},
mesh = {Archaea/classification/*genetics/*metabolism ; DNA, Archaeal/genetics ; DNA, Ribosomal/genetics ; *Geologic Sediments/chemistry/microbiology ; *Lakes/chemistry/microbiology ; Methane/*biosynthesis ; Oxygen/analysis ; Polymerase Chain Reaction ; RNA, Archaeal/genetics ; RNA, Ribosomal, 16S/genetics ; },
abstract = {As for lineages of known methanogens, several lineages of uncultured archaea were recurrently retrieved in freshwater sediments. However, knowledge is missing about how these lineages might be affected and structured according to depth. In the present study, the vertical changes of archaeal communities were characterized in the deep sediment of the freshwater meromictic Lake Pavin. For that purpose, an integrated molecular approach was performed to gain information on the structure, composition, abundance and vertical stratification of archaeal communities thriving in anoxic freshwater sediments along a gradient of sediments encompassing 130 years of sedimentation. Huge changes occurred in the structure and composition of archaeal assemblages along the sediment core. Methanogenic taxa (i.e. Methanosaeta and Methanomicrobiales) were progressively replaced by uncultured archaeal lineages (i.e. Marine Benthic Group-D (MBG-D) and Miscellaneous Crenarchaeal Group (MCG)) which are suspected to be involved in the methane cycle.},
}
@article {pmid22927945,
year = {2012},
author = {Naor, A and Thiaville, PC and Altman-Price, N and Cohen-Or, I and Allers, T and de Crécy-Lagard, V and Gophna, U},
title = {A genetic investigation of the KEOPS complex in halophilic Archaea.},
journal = {PloS one},
volume = {7},
number = {8},
pages = {e43013},
pmid = {22927945},
issn = {1932-6203},
support = {R01 GM070641/GM/NIGMS NIH HHS/United States ; R01 GM70641/GM/NIGMS NIH HHS/United States ; },
mesh = {Adenosine/analogs &amp; derivatives/metabolism ; Archaeal Proteins/*genetics/metabolism ; DNA, Archaeal/metabolism ; Gene Fusion ; Glycation End Products, Advanced/metabolism ; Haloferax/*genetics/growth &amp; development/metabolism ; Mutation ; RNA, Archaeal/metabolism ; },
abstract = {KEOPS is an important cellular complex conserved in Eukarya, with some subunits conserved in Archaea and Bacteria. This complex was recently found to play an essential role in formation of the tRNA modification threonylcarbamoyladenosine (t(6)A), and was previously associated with telomere length maintenance and transcription. KEOPS subunits are conserved in Archaea, especially in the Euryarchaea, where they had been studied in vitro. Here we attempted to delete the genes encoding the four conserved subunits of the KEOPS complex in the euryarchaeote Haloferax volcanii and study their phenotypes in vivo. The fused kae1-bud32 gene was shown to be essential as was cgi121, which is dispensable in yeast. In contrast, pcc1 (encoding the putative dimerizing unit of KEOPS) was not essential in H. volcanii. Deletion of pcc1 led to pleiotropic phenotypes, including decreased growth rate, reduced levels of t(6)A modification, and elevated levels of intra-cellular glycation products.},
}
@article {pmid22925153,
year = {2012},
author = {Patra, AK and Stiverson, J and Yu, Z},
title = {Effects of quillaja and yucca saponins on communities and select populations of rumen bacteria and archaea, and fermentation in vitro.},
journal = {Journal of applied microbiology},
volume = {113},
number = {6},
pages = {1329-1340},
doi = {10.1111/j.1365-2672.2012.05440.x},
pmid = {22925153},
issn = {1365-2672},
mesh = {Ammonia/metabolism ; Animal Feed ; Animals ; Archaea/*drug effects ; Bacteria/*drug effects ; Biodiversity ; Cattle ; Fatty Acids, Volatile/analysis/metabolism ; *Fermentation ; Fibrobacter/drug effects ; Methane/biosynthesis ; Prevotella/drug effects ; Quillaja/chemistry ; Quillaja Saponins/pharmacology ; Rumen/*microbiology ; Ruminococcus/drug effects ; Saponins/*pharmacology ; Yucca/chemistry ; },
abstract = {AIMS: The objective of this study was to comprehensively evaluate quillaja (QSP) and yucca saponin (YSP) products with respect to their effects on diversity of rumen bacteria and archaea, abundance of selected microbes, and feed degradability and fermentation.<br><br>METHODS AND RESULTS: Both QSP and YSP at doses 0-0.6 g l(-1) tended to increase degradability of feed substrate in in vitro rumen cultures, but to different extents. Neither one of the saponins affected the concentrations of ammonia, total volatile fatty acids, or molar proportion of acetate. However, QSP increased molar proportion of propionate and decreased that of butyrate, whereas YSP tended to decrease that of butyrate. As determined by qPCR, QSP and YSP did not affect the abundance of total bacteria or Ruminococcus albus. The QSP did not affect the abundances of Fibrobacter succinogenes or genus Prevotella, but tended to decrease that of Ruminococcus flavefaciens, whereas YSP significantly increased the abundance of R. flavefaciens and Prevotella, and numerically increased that of F. succinogenes. Both saponins increased archaeal abundance, although to small magnitudes (0.3-0.4 log). The protozoal populations were decreased significantly by QSP, but not by YSP. Based on DGGE and T-RFLP analysis, both saponins altered the bacterial community and species organization, but less so the archaeal community.<br><br>CONCLUSIONS: This study demonstrated that saponins, although not effective in mitigating methane emission, may improve feed utilization at low doses, and modulate ruminal microbial communities in a dose-dependent manner.<br><br>The results of this study suggest that saponins at low doses may directly stimulate the growth of some rumen bacteria including cellulolytic bacteria, thus improving digestibility of feeds, independent of their defaunation activity. In contrast, saponins at high doses modulate rumen fermentation characteristically similar to defaunation.},
}
@article {pmid22923400,
year = {2012},
author = {Hatzenpichler, R},
title = {Diversity, physiology, and niche differentiation of ammonia-oxidizing archaea.},
journal = {Applied and environmental microbiology},
volume = {78},
number = {21},
pages = {7501-7510},
pmid = {22923400},
issn = {1098-5336},
mesh = {Ammonia/*metabolism ; Archaea/classification/genetics/*physiology ; DNA, Archaeal/genetics ; Metabolic Networks and Pathways ; Nitrification/genetics ; Nitrogen Cycle ; Nitrous Oxide/metabolism ; Oxidation-Reduction ; Oxidoreductases/*genetics ; Soil Microbiology ; },
abstract = {Nitrification, the aerobic oxidation of ammonia to nitrate via nitrite, has been suggested to have been a central part of the global biogeochemical nitrogen cycle since the oxygenation of Earth. The cultivation of several ammonia-oxidizing archaea (AOA) as well as the discovery that archaeal ammonia monooxygenase (amo)-like gene sequences are nearly ubiquitously distributed in the environment and outnumber their bacterial counterparts in many habitats fundamentally revised our understanding of nitrification. Surprising insights into the physiological distinctiveness of AOA are mirrored by the recognition of the phylogenetic uniqueness of these microbes, which fall within a novel archaeal phylum now known as Thaumarchaeota. The relative importance of AOA in nitrification, compared to ammonia-oxidizing bacteria (AOB), is still under debate. This minireview provides a synopsis of our current knowledge of the diversity and physiology of AOA, the factors controlling their ecology, and their role in carbon cycling as well as their potential involvement in the production of the greenhouse gas nitrous oxide. It emphasizes the importance of activity-based analyses in AOA studies and formulates priorities for future research.},
}
@article {pmid22920653,
year = {2012},
author = {Nasir, A and Kim, KM and Caetano-Anolles, G},
title = {Giant viruses coexisted with the cellular ancestors and represent a distinct supergroup along with superkingdoms Archaea, Bacteria and Eukarya.},
journal = {BMC evolutionary biology},
volume = {12},
number = {},
pages = {156},
pmid = {22920653},
issn = {1471-2148},
mesh = {Archaea/virology ; Bacteria/virology ; *Biological Evolution ; Eukaryota/virology ; Gene Transfer, Horizontal ; Mimiviridae ; Models, Molecular ; *Phylogeny ; Protein Biosynthesis ; Protein Folding ; Protein Structure, Tertiary ; Proteome/analysis ; Viral Proteins/analysis ; Viruses/*classification/*genetics ; },
abstract = {BACKGROUND: The discovery of giant viruses with genome and physical size comparable to cellular organisms, remnants of protein translation machinery and virus-specific parasites (virophages) have raised intriguing questions about their origin. Evidence advocates for their inclusion into global phylogenomic studies and their consideration as a distinct and ancient form of life.<br><br>RESULTS: Here we reconstruct phylogenies describing the evolution of proteomes and protein domain structures of cellular organisms and double-stranded DNA viruses with medium-to-very-large proteomes (giant viruses). Trees of proteomes define viruses as a 'fourth supergroup' along with superkingdoms Archaea, Bacteria, and Eukarya. Trees of domains indicate they have evolved via massive and primordial reductive evolutionary processes. The distribution of domain structures suggests giant viruses harbor a significant number of protein domains including those with no cellular representation. The genomic and structural diversity embedded in the viral proteomes is comparable to the cellular proteomes of organisms with parasitic lifestyles. Since viral domains are widespread among cellular species, we propose that viruses mediate gene transfer between cells and crucially enhance biodiversity.<br><br>CONCLUSIONS: Results call for a change in the way viruses are perceived. They likely represent a distinct form of life that either predated or coexisted with the last universal common ancestor (LUCA) and constitute a very crucial part of our planet's biosphere.},
}
@article {pmid22913376,
year = {2012},
author = {Godde, JS},
title = {Breaking through a phylogenetic impasse: a pair of associated archaea might have played host in the endosymbiotic origin of eukaryotes.},
journal = {Cell &amp; bioscience},
volume = {2},
number = {1},
pages = {29},
pmid = {22913376},
issn = {2045-3701},
abstract = {For over a century, the origin of eukaryotes has been a topic of intense debate among scientists. Although it has become widely accepted that organelles such as the mitochondria and chloroplasts arose via endosymbiosis, the origin of the eukaryotic nucleus remains enigmatic. Numerous models for the origin of the nucleus have been proposed over the years, many of which use endosymbiosis to explain its existence. Proposals of microbes whose ancestors may have served as either a host or a guest in various endosymbiotic scenarios abound, none of which have been able to sufficiently incorporate the cell biological as well as phylogenetic data which links these organisms to the nucleus. While it is generally agreed that eukaryotic nuclei share more features in common with archaea rather than with bacteria, different studies have identified either one or the other of the two major groups of archaea as potential ancestors, leading to somewhat of a stalemate. This paper seeks to resolve this impasse by presenting evidence that not just one, but a pair of archaea might have served as host to the bacterial ancestor of the mitochondria. This pair may have consisted of ancestors of both Ignicoccus hospitalis as well as its ectosymbiont/ectoparasite 'Nanoarchaeum equitans'.},
}
@article {pmid22904062,
year = {2012},
author = {Penger, J and Conrad, R and Blaser, M},
title = {Stable carbon isotope fractionation by methylotrophic methanogenic archaea.},
journal = {Applied and environmental microbiology},
volume = {78},
number = {21},
pages = {7596-7602},
pmid = {22904062},
issn = {1098-5336},
mesh = {Carbon Isotopes ; Hydrocarbons, Fluorinated/pharmacology ; Methane/*biosynthesis ; Methanol/*metabolism ; Methanosarcina barkeri/drug effects/*metabolism ; },
abstract = {In natural environments methane is usually produced by aceticlastic and hydrogenotrophic methanogenic archaea. However, some methanogens can use C(1) compounds such as methanol as the substrate. To determine the contributions of individual substrates to methane production, the stable-isotope values of the substrates and the released methane are often used. Additional information can be obtained by using selective inhibitors (e.g., methyl fluoride, a selective inhibitor of acetoclastic methanogenesis). We studied stable carbon isotope fractionation during the conversion of methanol to methane in Methanosarcina acetivorans, Methanosarcina barkeri, and Methanolobus zinderi and generally found large fractionation factors (-83‰ to -72‰). We further tested whether methyl fluoride impairs methylotrophic methanogenesis. Our experiments showed that even though a slight inhibition occurred, the carbon isotope fractionation was not affected. Therefore, the production of isotopically light methane observed in the presence of methyl fluoride may be due to the strong fractionation by methylotrophic methanogens and not only by hydrogenotrophic methanogens as previously assumed.},
}
@article {pmid22897959,
year = {2012},
author = {Sakami, T and Andoh, T and Morita, T and Yamamoto, Y},
title = {Phylogenetic diversity of ammonia-oxidizing archaea and bacteria in biofilters of recirculating aquaculture systems.},
journal = {Marine genomics},
volume = {7},
number = {},
pages = {27-31},
doi = {10.1016/j.margen.2012.04.006},
pmid = {22897959},
issn = {1876-7478},
mesh = {Ammonia/analysis ; Aquaculture/*instrumentation ; Archaea/*enzymology ; Bacteria/*enzymology ; Base Sequence ; Cloning, Molecular ; Cluster Analysis ; DNA Primers/genetics ; Filtration/*instrumentation ; Gene Library ; Molecular Sequence Data ; Oxidoreductases/*genetics ; *Phylogeny ; Protein Subunits/genetics ; Seawater/chemistry/microbiology ; Sequence Analysis, DNA ; *Water Microbiology ; },
abstract = {We constructed ammonia monooxygenase alpha subunit (amoA) gene clone libraries of ammonia-oxidizing archaea (AOA) and bacteria (AOB) from three biofiltration tanks used for closed marine fish culture systems. The number of operational taxonomic units (OTUs) found in any one place was 76%-80% of the total OTUs in each tank for AOA and 100% for AOB when OUTs were defined on the basis of a 5% nucleotide difference. In a phylogenetic tree, all of the AOA amoA sequences fell into a cluster, which contained Candidatus Nitrosopumilus maritimus. All of the AOB amoA sequences were related to the Nitrosospira lineage. These results indicated that different ammonia oxidizers were present in different tanks, but that the dominant phylogenetic types were stable. In a biofiltration tank to which a high concentration of ammonium chloride was added periodically to condition the biofilter materials, most of the AOA amoA sequences were different from the dominant one observed in the fish culture tanks. The AOB amoA sequences were also different, and were similar to those of Nitrosomonas aestuarii. These findings suggest that high concentration ammonia loads have a considerable affect on ammonia-oxidizer community composition.},
}
@article {pmid22897827,
year = {2012},
author = {Dridi, B},
title = {Laboratory tools for detection of archaea in humans.},
journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases},
volume = {18},
number = {9},
pages = {825-833},
doi = {10.1111/j.1469-0691.2012.03952.x},
pmid = {22897827},
issn = {1469-0691},
mesh = {Archaea/genetics/*isolation &amp; purification ; Feces/microbiology ; Humans ; *Metagenome ; Methanobacteriaceae/isolation &amp; purification ; Microbiological Techniques/*methods ; Mucous Membrane/microbiology ; },
abstract = {This work represents an update of knowledge regarding the detection methods for human microbiome-associated archaea. Despite the fact that, during the last three decades, only four methanoarchaeal species have been isolated from the human mucosa, including faeces, subgingival plaque, and vaginal mucosa (Methanobrevibacter smithii, Methanosphaera stadtmanae, Methanobrevibacter oralis and, most recently, 'Methanomassiliicoccus luminyensis'), molecular studies, including PCR and metagenomic analyses, have detected DNA sequences indicative of the presence of additional methanoarchaea, as well as non-methanogenic archaea, in the human intestinal tract. Opinion is divided on the roles (if any) of these organisms in human disease, and certainly the data are still unclear. Future research and recently reported data highlighting the antimicrobial susceptibility of the human methanoarchaea could help in the design of selective media to discover additional human mucosa-associated archaea and ascertain their role in human infections involving complex flora.},
}
@article {pmid22897826,
year = {2012},
author = {Drancourt, M},
title = {Archaea as emerging, fastidious members of the human microbiota.},
journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases},
volume = {18},
number = {9},
pages = {823-824},
doi = {10.1111/j.1469-0691.2012.03904.x},
pmid = {22897826},
issn = {1469-0691},
mesh = {Archaea/genetics/*growth &amp; development ; Humans ; *Metagenome ; },
}
@article {pmid22897363,
year = {2012},
author = {Klieve, AV and Ouwerkerk, D and Maguire, AJ},
title = {Archaea in the foregut of macropod marsupials: PCR and amplicon sequence-based observations.},
journal = {Journal of applied microbiology},
volume = {113},
number = {5},
pages = {1065-1075},
doi = {10.1111/j.1365-2672.2012.05428.x},
pmid = {22897363},
issn = {1365-2672},
mesh = {Animals ; Archaea/classification/genetics/*isolation &amp; purification ; Cattle/microbiology ; DNA, Archaeal/genetics ; Ecosystem ; Female ; Genes, Archaeal ; Macropodidae/*microbiology ; Male ; Methane/metabolism ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sheep/microbiology ; Stomach/*microbiology ; },
abstract = {AIMS: To investigate, using culture-independent techniques, the presence and diversity of methanogenic archaea in the foregut of kangaroos.<br><br>METHODS AND RESULTS: DNA was extracted from forestomach contents of 42 kangaroos (three species), three sheep and three cattle. Four qualitative and quantitative PCR assays targeting the archaeal domain (16S rRNA gene) or the functional methanogenesis gene, mcrA, were used to determine the presence and population density of archaea in kangaroos and whether they were likely to be methanogens. All ruminal samples were positive for archaea, produced PCR product of expected size, contained high numbers of archaea and high numbers of cells with mcrA genes. Kangaroos were much more diverse and contradictory. Fourteen kangaroos had detectable archaea with numbers 10- to 1000-fold fewer than sheep and cattle. Many kangaroos that did not possess archaea were positive for the mcrA gene and had detectable numbers of cells with this gene and vice versa. DNA sequence analysis of kangaroos' archaeal 16S rRNA gene clones show that many methanogens were related to Methanosphaera stadmanae. Other sequences were related to non-methanogenic archaea (Thermoplasma sp.), and a number of kangaroos had mcrA gene sequences related to methane oxidising archaea (ANME).<br><br>CONCLUSIONS: Discrepancies between qualitative and quantitative PCR assays for archaea and the mcrA gene suggest that the archaeal communities are very diverse and it is possible that novel species exist.<br><br>Archaea (in general) were below detectable limits in many kangaroos, especially Red kangaroos; when present they are in lower numbers than in ruminants, and the archaea are not necessarily methanogenic. The determination of why this is the case in the kangaroo foregut could assist in reducing emissions from other ecosystems in the future.},
}
@article {pmid22887657,
year = {2012},
author = {Gorlas, A and Robert, C and Gimenez, G and Drancourt, M and Raoult, D},
title = {Complete genome sequence of Methanomassiliicoccus luminyensis, the largest genome of a human-associated Archaea species.},
journal = {Journal of bacteriology},
volume = {194},
number = {17},
pages = {4745},
pmid = {22887657},
issn = {1098-5530},
mesh = {Base Sequence ; Chromosome Mapping ; Euryarchaeota/classification/*genetics/isolation &amp; purification ; Feces/microbiology ; *Genome, Archaeal ; Humans ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; },
abstract = {The present study describes the complete and annotated genome sequence of Methanomassiliicoccus luminyensis strain B10 (DSM 24529(T), CSUR P135), which was isolated from human feces. The 2.6-Mb genome represents the largest genome of a methanogenic euryarchaeon isolated from humans. The genome data of M. luminyensis reveal unique features and horizontal gene transfer events, which might have occurred during its adaptation and/or evolution in the human ecosystem.},
}
@article {pmid22885352,
year = {2012},
author = {Bouali, M and Zrafi-Nouira, I and Bakhrouf, A and Le Paslier, D and Chaussonnerie, S and Ammar, E and Sghir, A},
title = {The structure and spatio-temporal distribution of the Archaea in a horizontal subsurface flow constructed wetland.},
journal = {The Science of the total environment},
volume = {435-436},
number = {},
pages = {465-471},
doi = {10.1016/j.scitotenv.2012.07.047},
pmid = {22885352},
issn = {1879-1026},
mesh = {Ammonia/metabolism ; Archaea/classification/genetics/*isolation &amp; purification ; Base Sequence ; Biodiversity ; DNA, Archaeal/genetics ; Genes, rRNA ; Molecular Sequence Data ; Oxidation-Reduction ; Phylogeny ; Plant Roots/microbiology ; Sequence Analysis, DNA ; *Soil Microbiology ; Tunisia ; Wastewater/microbiology ; *Wetlands ; },
abstract = {In this study, archaeal community structure and temporal dynamics were monitored, using 16S rRNA clone libraries construction from a horizontal subsurface flow constructed wetland. Phylogenetic assignation of 1026 16S rRNA gene sequences shows that 96.2% of the total operational taxonomic units (OTUs) were affiliated with Thaumarchaeota, a newly proposed archaeal phylum and 3.7% with unclassified Archaea. Among the total sequences, 42% and 40.2% were affiliated with Candidatus Nitrososphaera and unclassified Nitrosopumilus respectively with more than 99% similarity. Results suggest that several dominant and active nitrifiers may benefit from the micro-aerobic conditions around the reed roots to perform ammonia oxidation. The archaeal diversity detected in the rhizosphere zone is clearly different from that detected in the bottom basin. This engineered habitat revealed the reed root and the water composition effects on the archaeal diversity.},
}
@article {pmid22873515,
year = {2012},
author = {Nelson, DK and Lapara, TM and Novak, PJ},
title = {Structure and function of assemblages of Bacteria and Archaea in model anaerobic aquifer columns: can functional instability be practically beneficial?.},
journal = {Environmental science &amp; technology},
volume = {46},
number = {18},
pages = {10137-10144},
doi = {10.1021/es300652z},
pmid = {22873515},
issn = {1520-5851},
mesh = {Archaea/genetics/*metabolism ; Bacteria/genetics/*metabolism ; Biodegradation, Environmental ; DNA, Archaeal/isolation &amp; purification ; DNA, Bacterial/isolation &amp; purification ; Fermentation ; Groundwater/*microbiology ; Molasses/*microbiology ; },
abstract = {Biodegradable organic carbon is often added to aquifers to stimulate microbial reduction of oxidized contaminants. This carbon also stimulates fermenters, which generate important metabolites that can fuel contaminant reduction and may enhance dissolution of hydrophobic compounds. Therefore, understanding how different methods of carbon addition affect the fermentative community will enable design of more effective remediation strategies. Our research objective was to evaluate the microbial communities that developed in model aquifer columns in response to pulsed or continuous molasses input. Results indicated that the continuously fed column produced relatively low concentrations of metabolic intermediates and had a greater proportion of Bacteria and methanogens, as measured by quantitative polymerase chain reaction, near the column inlet. In contrast, the pulsed-fed column generated periodic high concentrations of metabolic intermediates, with Bacteria and methanogens distributed throughout the length of the column. The community structures of Bacteria and Archaea, measured via automated ribosomal intergenic spacer analysis, in the pulsed-fed column were significantly different from those in the control column (not fed). The microbial community composition of the continuously fed column, however, became increasingly similar to the control column along the column length. These results demonstrate that a strategy of pulsed carbon addition leads to activity that is associated with functional instability, in terms of the production of periodic pulses of fermentation products and changing carbon concentration, and may be advantageous for remediation by producing large quantities of beneficial intermediates and resulting in more homogenously distributed biomass.},
}
@article {pmid22865846,
year = {2012},
author = {Tomita, H and Yokooji, Y and Ishibashi, T and Imanaka, T and Atomi, H},
title = {Biochemical characterization of pantoate kinase, a novel enzyme necessary for coenzyme A biosynthesis in the Archaea.},
journal = {Journal of bacteriology},
volume = {194},
number = {19},
pages = {5434-5443},
pmid = {22865846},
issn = {1098-5530},
mesh = {Adenosine Triphosphate/metabolism ; Archaeal Proteins/genetics/*metabolism ; Coenzyme A/*biosynthesis ; Cytidine Triphosphate/metabolism ; Gene Expression Regulation, Archaeal/*physiology ; Guanosine Triphosphate/metabolism ; Hydrogen-Ion Concentration ; Hydroxybutyrates ; Kinetics ; Peptide Synthases ; Phosphotransferases ; Substrate Specificity ; Temperature ; Thermococcus/*enzymology/metabolism ; Uridine Triphosphate/metabolism ; },
abstract = {Although bacteria and eukaryotes share a pathway for coenzyme A (CoA) biosynthesis, we previously clarified that most archaea utilize a distinct pathway for the conversion of pantoate to 4'-phosphopantothenate. Whereas bacteria/eukaryotes use pantothenate synthetase and pantothenate kinase (PanK), the hyperthermophilic archaeon Thermococcus kodakarensis utilizes two novel enzymes: pantoate kinase (PoK) and phosphopantothenate synthetase (PPS). Here, we report a detailed biochemical examination of PoK from T. kodakarensis. Kinetic analyses revealed that the PoK reaction displayed Michaelis-Menten kinetics toward ATP, whereas substrate inhibition was observed with pantoate. PoK activity was not affected by the addition of CoA/acetyl-CoA. Interestingly, PoK displayed broad nucleotide specificity and utilized ATP, GTP, UTP, and CTP with comparable k(cat)/K(m) values. Sequence alignment of 27 PoK homologs revealed seven conserved residues with reactive side chains, and variant proteins were constructed for each residue. Activity was not detected when mutations were introduced to Ser104, Glu134, and Asp143, suggesting that these residues play vital roles in PoK catalysis. Kinetic analysis of the other variant proteins, with mutations S28A, H131A, R155A, and T186A, indicated that all four residues are involved in pantoate recognition and that Arg155 and Thr186 play important roles in PoK catalysis. Gel filtration analyses of the variant proteins indicated that Thr186 is also involved in dimer assembly. A sequence comparison between PoK and other members of the GHMP kinase family suggests that Ser104 and Glu134 are involved in binding with phosphate and Mg(2+), respectively, while Asp143 is the base responsible for proton abstraction from the pantoate hydroxy group.},
}
@article {pmid22860902,
year = {2012},
author = {Mardanov, AV and Ravin, NV},
title = {The impact of genomics on research in diversity and evolution of archaea.},
journal = {Biochemistry. Biokhimiia},
volume = {77},
number = {8},
pages = {799-812},
doi = {10.1134/S0006297912080019},
pmid = {22860902},
issn = {1608-3040},
mesh = {Archaea/*genetics ; *Evolution, Molecular ; *Genetic Research ; *Genomics ; Phylogeny ; },
abstract = {Since the definition of archaea as a separate domain of life along with bacteria and eukaryotes, they have become one of the most interesting objects of modern microbiology, molecular biology, and biochemistry. Sequencing and analysis of archaeal genomes were especially important for studies on archaea because of a limited availability of genetic tools for the majority of these microorganisms and problems associated with their cultivation. Fifteen years since the publication of the first genome of an archaeon, more than one hundred complete genome sequences of representatives of different phylogenetic groups have been determined. Analysis of these genomes has expanded our knowledge of biology of archaea, their diversity and evolution, and allowed identification and characterization of new deep phylogenetic lineages of archaea. The development of genome technologies has allowed sequencing the genomes of uncultivated archaea directly from enrichment cultures, metagenomic samples, and even from single cells. Insights have been gained into the evolution of key biochemical processes in archaea, such as cell division and DNA replication, the role of horizontal gene transfer in the evolution of archaea, and new relationships between archaea and eukaryotes have been revealed.},
}
@article {pmid22857613,
year = {2012},
author = {Jarrell, KF},
title = {Control of archaellation in Sulfolobus acidocaldarius: unravelling of the regulation of surface structure biosynthesis in Archaea begins.},
journal = {Molecular microbiology},
volume = {86},
number = {1},
pages = {1-5},
doi = {10.1111/j.1365-2958.2012.08191.x},
pmid = {22857613},
issn = {1365-2958},
mesh = {Archaeal Proteins/*biosynthesis ; *Gene Expression Regulation, Archaeal ; Repressor Proteins/*metabolism ; Sulfolobus acidocaldarius/*genetics ; },
abstract = {Archaea have a variety of surface appendages including archaella (archaeal flagella), pili, hami and cannulae. While expected to be energetically expensive to express, studies focused on the regulation of such structures are nevertheless lacking. In the current issue of Molecular Microbiology, Reimann et al. (2012) identified a two-partner system called ArnA and ArnB in Sulfolobus acidocaldarius that interact strongly with each other and are repressors of archaella expression while also having an enhancing effect on the appearance of type IV pili. ArnA is a forkhead-associated domain-containing protein while ArnB is a von Willebrand domain-containing protein. Both proteins can be phosphorylated in vitro by S. acidocaldarius protein kinases. The repression of archaella expression is dependent on dephosphorylation of the Arn proteins. Deletions of arnA or arnB resulted in increased levels of archaella operon proteins and cells that were hypermotile due to increased archaellation. Direct effects of ArnA/ArnB on transcription from fla promoters were demonstrated using arnA and arnB deletion strains but only a modest increase in transcription was demonstrated in each mutant suggesting that the repression effect observed may be due to protein-protein interactions. This paper represents a significant step forward in our understanding of archaeal surface structure biogenesis.},
}
@article {pmid22849643,
year = {2012},
author = {Henneke, G},
title = {In vitro reconstitution of RNA primer removal in Archaea reveals the existence of two pathways.},
journal = {The Biochemical journal},
volume = {447},
number = {2},
pages = {271-280},
doi = {10.1042/BJ20120959},
pmid = {22849643},
issn = {1470-8728},
mesh = {DNA/metabolism ; DNA Replication ; Flap Endonucleases/metabolism ; Pyrococcus abyssi/enzymology ; RNA/*metabolism ; RNA Polymerase II/*metabolism ; Ribonuclease H ; },
abstract = {Using model DNA substrates and purified recombinant proteins from Pyrococcus abyssi, I have reconstituted the enzymatic reactions involved in RNA primer elimination in vitro. In my dual-labelled system, polymerase D performed efficient strand displacement DNA synthesis, generating 5'-RNA flaps which were subsequently released by Fen1, before ligation by Lig1. In this pathway, the initial cleavage event by RNase HII facilitated RNA primer removal of Okazaki fragments. In addition, I have shown that polymerase B was able to displace downstream DNA strands with a single ribonucleotide at the 5'-end, a product resulting from a single cut in the RNA initiator by RNase HII. After RNA elimination, the combined activities of strand displacement DNA synthesis by polymerase B and flap cleavage by Fen1 provided a nicked substrate for ligation by Lig1. The unique specificities of Okazaki fragment maturation enzymes and replicative DNA polymerases strongly support the existence of two pathways in the resolution of RNA fragments.},
}
@article {pmid22838837,
year = {2012},
author = {Zeng, J and Zhao, DY and Huang, R and Wu, QL},
title = {Abundance and community composition of ammonia-oxidizing archaea and bacteria in two different zones of Lake Taihu.},
journal = {Canadian journal of microbiology},
volume = {58},
number = {8},
pages = {1018-1026},
doi = {10.1139/w2012-078},
pmid = {22838837},
issn = {1480-3275},
mesh = {Ammonia/analysis ; Archaea/*classification/genetics ; Bacteria/*classification/genetics ; *Biodiversity ; China ; Genes, Archaeal/genetics ; Genes, Bacterial/genetics ; Geologic Sediments/chemistry/*microbiology ; Hydrogen-Ion Concentration ; Lakes/chemistry/*microbiology ; Molecular Sequence Data ; Oxidation-Reduction ; *Phylogeny ; Population Density ; *Water Microbiology ; },
abstract = {The abundance and community composition of ammonia-oxidizing archaea and ammonia-oxidizing bacteria in the surface sediments of 2 different zones (Meiliang Bay and Eastern Lake Taihu) of Lake Taihu were investigated using real-time quantitative polymerase chain reaction and clone libraries. The amoA gene copy numbers in the surface sediment of Meiliang Bay ranged from 4.91 × 10(5) to 8.65 × 10(6) copies/g dry sediment for the archaeal amoA gene and from 3.74 × 10(4) to 3.86 × 10(5) copies/g dry sediment for the bacterial amoA gene, which were significantly higher than those of Eastern Lake Taihu (P < 0.05). Concentrations of ammonia (NH(4)(+)), total nitrogen, organic matter, and pH of the sediments exhibited significantly negative correlations with the abundance of ammonia-oxidizing archaea or ammonia-oxidizing bacteria (P < 0.05 or P < 0.01, respectively). The potential nitrification rates show remarkable correlations with the copy numbers of the archaeal amoA gene. Diversity of the archaeal amoA gene in Eastern Lake Taihu was significantly higher than that of Meiliang Bay, whereas the bacterial amoA gene diversity was comparable for the 2 lake zones. The data obtained in this study would be useful to elucidate the role of ammonia-oxidizing archaea and ammonia-oxidizing bacteria in the nitrogen cycle of freshwater ecosystems.},
}
@article {pmid22837756,
year = {2012},
author = {Beman, JM and Bertics, VJ and Braunschweiler, T and Wilson, JM},
title = {Quantification of ammonia oxidation rates and the distribution of ammonia-oxidizing Archaea and Bacteria in marine sediment depth profiles from Catalina Island, California.},
journal = {Frontiers in microbiology},
volume = {3},
number = {},
pages = {263},
pmid = {22837756},
issn = {1664-302X},
abstract = {Microbial communities present in marine sediments play a central role in nitrogen biogeochemistry at local to global scales. Along the oxidation-reduction gradients present in sediment profiles, multiple nitrogen cycling processes (such as nitrification, denitrification, nitrogen fixation, and anaerobic ammonium oxidation) are active and actively coupled to one another - yet the microbial communities responsible for these transformations and the rates at which they occur are still poorly understood. We report pore water geochemical (O(2), [Formula: see text], and [Formula: see text]) profiles, quantitative profiles of archaeal and bacterial amoA genes, and ammonia oxidation rate measurements, from bioturbated marine sediments of Catalina Island, California. Across triplicate sediment cores collected offshore at Bird Rock (BR) and within Catalina Harbor (CH), oxygen penetration (0.24-0.5 cm depth) and the abundance of amoA genes (up to 9.30 × 10(7) genes g(-) (1)) varied with depth and between cores. Bacterial amoA genes were consistently present at depths of up to 10 cm, and archaeal amoA was readily detected in BR cores, and CH cores from 2008, but not 2007. Although detection of DNA is not necessarily indicative of active growth and metabolism, ammonia oxidation rate measurements made in 2008 (using isotope tracer) demonstrated the production of oxidized nitrogen at depths where amoA was present. Rates varied with depth and between cores, but indicate that active ammonia oxidation occurs at up to 10 cm depth in bioturbated CH sediments, where it may be carried out by either or both ammonia-oxidizing archaea and bacteria.},
}
@article {pmid22827611,
year = {2012},
author = {Matarazzo, F and Ribeiro, AC and Faveri, M and Taddei, C and Martinez, MB and Mayer, MP},
title = {The domain Archaea in human mucosal surfaces.},
journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases},
volume = {18},
number = {9},
pages = {834-840},
doi = {10.1111/j.1469-0691.2012.03958.x},
pmid = {22827611},
issn = {1469-0691},
mesh = {Archaea/*growth &amp; development/isolation &amp; purification ; Humans ; Intestinal Mucosa/*microbiology ; Mouth Mucosa/*microbiology ; },
abstract = {Archaea present distinct features from bacteria and eukaryotes, and thus constitute one of the branches of the phylogenetic tree of life. Members of this domain colonize distinct niches in the human body, arranged in complex communities, especially in the intestines and the oral cavity. The diversity of archaea within these niches is limited to a few phylotypes, constituted in particular by methane-producing archaeal organisms. Although they are possibly symbionts, methanogens may play a role in the establishment of mucosal diseases by favouring the growth of certain bacterial groups.},
}
@article {pmid22826704,
year = {2012},
author = {Biller, SJ and Mosier, AC and Wells, GF and Francis, CA},
title = {Global Biodiversity of Aquatic Ammonia-Oxidizing Archaea is Partitioned by Habitat.},
journal = {Frontiers in microbiology},
volume = {3},
number = {},
pages = {252},
pmid = {22826704},
issn = {1664-302X},
abstract = {Archaea play an important role in nitrification and are, thus, inextricably linked to the global carbon and nitrogen cycles. Since the initial discovery of an ammonia monooxygenase α-subunit (amoA) gene associated with an archaeal metagenomic fragment, archaeal amoA sequences have been detected in a wide variety of nitrifying environments. Recent sequencing efforts have revealed extensive diversity of archaeal amoA sequences within different habitats. In this study, we have examined over 8000 amoA sequences from the literature and public databases in an effort to understand the ecological factors influencing the distribution and diversity of ammonia-oxidizing archaea (AOA), with a particular focus on sequences from aquatic habitats. This broad survey provides strong statistical support for the hypothesis that different environments contain distinct clusters of AOA amoA sequences, as surprisingly few sequences are found in more than one habitat type. Within aquatic environments, salinity, depth in the water column, and temperature were significantly correlated with the distribution of sequence types. These findings support the existence of multiple distinct aquatic AOA populations in the environment and suggest some possible selective pressures driving the partitioning of AOA amoA diversity.},
}
@article {pmid22804926,
year = {2012},
author = {Fendrihan, S and Dornmayr-Pfaffenhuemer, M and Gerbl, FW and Holzinger, A and Grösbacher, M and Briza, P and Erler, A and Gruber, C and Plätzer, K and Stan-Lotter, H},
title = {Spherical particles of halophilic archaea correlate with exposure to low water activity--implications for microbial survival in fluid inclusions of ancient halite.},
journal = {Geobiology},
volume = {10},
number = {5},
pages = {424-433},
pmid = {22804926},
issn = {1472-4669},
mesh = {Geologic Sediments/*microbiology ; Halobacterium/cytology/*drug effects/growth &amp; development/*isolation &amp; purification ; Lithium Chloride/chemistry ; Microbial Viability/drug effects ; Salinity ; Sodium Chloride/metabolism ; Water/chemistry ; },
abstract = {Viable extremely halophilic archaea (haloarchaea) have been isolated from million-year-old salt deposits around the world; however, an explanation of their supposed longevity remains a fundamental challenge. Recently small roundish particles in fluid inclusions of 22 000- to 34 000-year-old halite were identified as haloarchaea capable of proliferation (Schubert BA, Lowenstein TK, Timofeeff MN, Parker MA, 2010, Environmental Microbiology, 12, 440-454). Searching for a method to produce such particles in the laboratory, we exposed rod-shaped cells of Halobacterium species to reduced external water activity (a(w)). Gradual formation of spheres of about 0.4 μm diameter occurred in 4 M NaCl buffer of a(w) ≤ 0.75, but exposure to buffered 4 M LiCl (a(w) ≤ 0.73) split cells into spheres within seconds, with concomitant release of several proteins. From one rod, three or four spheres emerged, which re-grew to normal rods in nutrient media. Biochemical properties of rods and spheres were similar, except for a markedly reduced ATP content (about 50-fold) and an increased lag phase of spheres, as is known from dormant bacteria. The presence of viable particles of similar sizes in ancient fluid inclusions suggested that spheres might represent dormant states of haloarchaea. The easy production of spheres by lowering a(w) should facilitate their investigation and could help to understand the mechanisms for microbial survival over geological times.},
}
@article {pmid22796877,
year = {2012},
author = {Jermy, A},
title = {Archaea: Breaking down the species barrier.},
journal = {Nature reviews. Microbiology},
volume = {10},
number = {8},
pages = {522-523},
pmid = {22796877},
issn = {1740-1534},
}
@article {pmid22787457,
year = {2012},
author = {de Gannes, V and Eudoxie, G and Dyer, DH and Hickey, WJ},
title = {Diversity and abundance of ammonia oxidizing archaea in tropical compost systems.},
journal = {Frontiers in microbiology},
volume = {3},
number = {},
pages = {244},
pmid = {22787457},
issn = {1664-302X},
abstract = {Composting is widely used to transform waste materials into valuable agricultural products. In the tropics, large quantities of agricultural wastes could be potentially useful in agriculture after composting. However, while microbiological processes of composts in general are well established, relatively little is known about microbial communities that may be unique to these in tropical systems, particularly nitrifiers. The recent discovery of ammonia oxidizing archaea (AOA) has changed the paradigm of nitrification being initiated solely by ammonia oxidizing bacteria. In the present study, AOA abundance and diversity was examined in composts produced from combinations of plant waste materials common in tropical agriculture (rice straw, sugar cane bagasse, and coffee hulls), which were mixed with either cow- or sheep-manure. The objective was to determine how AOA abundance and diversity varied as a function of compost system and time, the latter being a contrast between the start of the compost process (mesophilic phase) and the finished product (mature phase). The results showed that AOA were relatively abundant in composts of tropical agricultural wastes, and significantly more so than were the ammonia-oxidizing bacteria. Furthermore, while the AOA communities in the composts were predominatly group I.1b, the communities were diverse and exhibited structures that diverged between compost types and phases. These patterns could be taken as indicators of the ecophysiological diversity in the soil AOA (group I.1b), in that significantly different AOA communties developed when exposed to varying physico-chemical environments. Nitrification patterns and levels differed in the composts which, for the mature material, could have significant effects on its performance as a plant growth medium. Thus, it will also be important to determine the association of AOA (and diversity in their communities) with nitrification in these systems.},
}
@article {pmid22784955,
year = {2012},
author = {Xie, K and Jia, X and Xu, P and Huang, X and Gu, W and Zhang, F and Yang, S and Tang, S},
title = {Improved composting of poultry feces via supplementation with ammonia oxidizing archaea.},
journal = {Bioresource technology},
volume = {120},
number = {},
pages = {70-77},
doi = {10.1016/j.biortech.2012.06.029},
pmid = {22784955},
issn = {1873-2976},
mesh = {Ammonia/*metabolism ; Animals ; Archaea/genetics/growth &amp; development/*metabolism ; Base Sequence ; Biodegradation, Environmental ; Biotechnology/*methods ; Carbon/metabolism ; Denaturing Gradient Gel Electrophoresis ; Feces/*microbiology ; Hydrogen-Ion Concentration ; Molecular Sequence Data ; Nitrogen/metabolism ; Phylogeny ; *Poultry ; Soil/*analysis ; Temperature ; Time Factors ; },
abstract = {Ammonia-oxidizing archaea (AOA) play an important role in the oxidation of ammonia. However, the participation of AOA in the composting process has not been established. The addition of AOA to a compost mix was able to speed up both the onset of the hyperthermic phase and the composting time. The composition of the microflora and the relative abundance were determined by using denaturing gradient gel electrophoresis and quantitative real-time PCR, based on the presence of the archaeal amoA genes. The amplicon profiles allowed some of the major AOA species present in the final compost to be identified, and their relative abundance to be estimated from their amplification intensity. The lower pH during the lower temperature phase of compost served to enhance the nitrogen content of the final compost. The addition of AOA resulted in the expanding diversity of microflora species than that of the natural colonization.},
}
@article {pmid22784022,
year = {2012},
author = {Fredriksson, NJ and Hermansson, M and Wilén, BM},
title = {Diversity and dynamics of Archaea in an activated sludge wastewater treatment plant.},
journal = {BMC microbiology},
volume = {12},
number = {},
pages = {140},
pmid = {22784022},
issn = {1471-2180},
mesh = {Archaea/*classification/genetics/isolation &amp; purification ; DNA, Archaeal/genetics ; Gene Library ; In Situ Hybridization, Fluorescence ; *Phylogeny ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; Sewage/*microbiology ; },
abstract = {BACKGROUND: The activated sludge process is one of the most widely used methods for treatment of wastewater and the microbial community composition in the sludge is important for the process operation. While the bacterial communities have been characterized in various activated sludge systems little is known about archaeal communities in activated sludge. The diversity and dynamics of the Archaea community in a full-scale activated sludge wastewater treatment plant were investigated by fluorescence in situ hybridization, terminal restriction fragment length polymorphism analysis and cloning and sequencing of 16S rRNA genes.<br><br>RESULTS: The Archaea community was dominated by Methanosaeta-like species. During a 15&#x2009;month period major changes in the community composition were only observed twice despite seasonal variations in environmental and operating conditions. Water temperature appeared to be the process parameter that affected the community composition the most. Several terminal restriction fragments also showed strong correlations with sludge properties and effluent water properties. The Archaea were estimated to make up 1.6% of total cell numbers in the activated sludge and were present both as single cells and colonies of varying sizes.<br><br>CONCLUSIONS: The results presented here show that Archaea can constitute a constant and integral part of the activated sludge and that it can therefore be useful to include Archaea in future studies of microbial communities in activated sludge.},
}
@article {pmid22783241,
year = {2012},
author = {Bernick, DL and Dennis, PP and Lui, LM and Lowe, TM},
title = {Diversity of Antisense and Other Non-Coding RNAs in Archaea Revealed by Comparative Small RNA Sequencing in Four Pyrobaculum Species.},
journal = {Frontiers in microbiology},
volume = {3},
number = {},
pages = {231},
pmid = {22783241},
issn = {1664-302X},
abstract = {A great diversity of small, non-coding RNA (ncRNA) molecules with roles in gene regulation and RNA processing have been intensely studied in eukaryotic and bacterial model organisms, yet our knowledge of possible parallel roles for small RNAs (sRNA) in archaea is limited. We employed RNA-seq to identify novel sRNA across multiple species of the hyperthermophilic genus Pyrobaculum, known for unusual RNA gene characteristics. By comparing transcriptional data collected in parallel among four species, we were able to identify conserved RNA genes fitting into known and novel families. Among our findings, we highlight three novel cis-antisense sRNAs encoded opposite to key regulatory (ferric uptake regulator), metabolic (triose-phosphate isomerase), and core transcriptional apparatus genes (transcription factor B). We also found a large increase in the number of conserved C/D box sRNA genes over what had been previously recognized; many of these genes are encoded antisense to protein coding genes. The conserved opposition to orthologous genes across the Pyrobaculum genus suggests similarities to other cis-antisense regulatory systems. Furthermore, the genus-specific nature of these sRNAs indicates they are relatively recent, stable adaptations.},
}
@article {pmid22776796,
year = {2012},
author = {Oishi, R and Hirooka, K and Otawa, K and Tada, C and Nakai, Y},
title = {Ammonia-oxidizing Archaea in laboratory-scale activated sludge systems for wastewater of low- or high-ammonium concentration.},
journal = {Animal science journal = Nihon chikusan Gakkaiho},
volume = {83},
number = {7},
pages = {571-576},
doi = {10.1111/j.1740-0929.2011.00995.x},
pmid = {22776796},
issn = {1740-0929},
mesh = {Ammonia/*analysis/*metabolism ; Archaea/enzymology/genetics/*metabolism ; Denaturing Gradient Gel Electrophoresis ; Oxidation-Reduction ; Oxidoreductases/genetics/metabolism ; Sewage/*chemistry/*microbiology ; Wastewater/*chemistry/*microbiology ; },
abstract = {Ammonia-oxidizing bacteria (AOB) is known as ammonia-oxidizer in wastewater treatment systems. However, ammonia-oxidizing Archaea (AOA) is found from various environments, including wastewater treatment systems. In this study, to investigate the relationships between AOA population and ammonia concentration, AOA was monitored in two laboratory-scale reactors treating artificial wastewater of different ammonium concentrations by denaturing gradient gel electrophoresis targeting ammonia monooxygenase genes. At day 60 of the operation, AOA populations dominant in each reactor differed, suggesting the importance of influent ammonia concentration in dominant AOA selection.},
}
@article {pmid22776323,
year = {2012},
author = {Knappy, CS and Barillà, D and de Blaquiere, JP and Morgan, HW and Nunn, CE and Suleman, M and Tan, CH and Keely, BJ},
title = {Structural complexity in isoprenoid glycerol dialkyl glycerol tetraether lipid cores of Sulfolobus and other archaea revealed by liquid chromatography-tandem mass spectrometry.},
journal = {Chemistry and physics of lipids},
volume = {165},
number = {6},
pages = {648-655},
doi = {10.1016/j.chemphyslip.2012.06.009},
pmid = {22776323},
issn = {1873-2941},
mesh = {Archaea/chemistry ; Chromatography, High Pressure Liquid ; Glyceryl Ethers/chemistry ; Isomerism ; Lipids/*chemistry ; Sulfolobus/*chemistry ; Tandem Mass Spectrometry ; Terpenes/*chemistry ; },
abstract = {Liquid chromatography-tandem mass spectrometry of membrane lipid cores from Sulfolobus species reveals isomeric forms of ring-containing isoprenoid glycerol dialkyl glycerol tetraether components not previously recognised via the use of NMR and liquid chromatography-mass spectrometry techniques. Equivalent isomerism was confirmed for the components in other hyperthermophilic genera and in sediments which contain the lipids of mesophilic archaea. The recognition of the isomeric structures in distinct archaeal clades suggests that profiles of tetraether lipids reported previously may have oversimplified the true lipid complexity in archaeal cultures and natural environments. Accordingly, the extent of variation in tetraether structures revealed by the work should direct more informative interpretations of lipid profiles in the future. Moreover, the results emphasise that tandem mass spectrometry provides a unique capability for assigning the structures of intact tetraether lipid cores for co-eluting species during chromatographic separation.},
}
@article {pmid22775980,
year = {2013},
author = {Brown, MN and Briones, A and Diana, J and Raskin, L},
title = {Ammonia-oxidizing archaea and nitrite-oxidizing nitrospiras in the biofilter of a shrimp recirculating aquaculture system.},
journal = {FEMS microbiology ecology},
volume = {83},
number = {1},
pages = {17-25},
doi = {10.1111/j.1574-6941.2012.01448.x},
pmid = {22775980},
issn = {1574-6941},
mesh = {Ammonia/*metabolism ; Animals ; *Aquaculture ; Archaea/classification/genetics/*metabolism ; Bacteria/classification/genetics/*metabolism ; Biofilms ; Filtration ; Genes, Archaeal ; Genes, Bacterial ; Nitrification ; Nitrites/*metabolism ; Oxidation-Reduction ; Oxidoreductases/genetics ; Penaeidae ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Water Quality ; },
abstract = {This study analysed the nitrifier community in the biofilter of a zero discharge, recirculating aquaculture system (RAS) for the production of marine shrimp in a low density (low ammonium production) system. The ammonia-oxidizing populations were examined by targeting 16S rRNA and amoA genes of ammonia-oxidizing bacteria (AOB) and archaea (AOA). The nitrite-oxidizing bacteria (NOB) were investigated by targeting the 16S rRNA gene. Archaeal amoA genes were more abundant in all compartments of the RAS than bacterial amoA genes. Analysis of bacterial and archaeal amoA gene sequences revealed that most ammonia oxidizers were related to Nitrosomonas marina and Nitrosopumilus maritimus. The NOB detected were related to Nitrospira marina and Nitrospira moscoviensis, and Nitrospira marina-type NOB were more abundant than N. moscoviensis-type NOB. Water quality and biofilm attachment media played a role in the competitiveness of AOA over AOB and Nitrospira marina-over N. moscoviensis-type NOB.},
}
@article {pmid22772895,
year = {2013},
author = {Nishida, H},
title = {Genome DNA Sequence Variation, Evolution, and Function in Bacteria and Archaea.},
journal = {Current issues in molecular biology},
volume = {15},
number = {},
pages = {19-24},
pmid = {22772895},
issn = {1467-3045},
mesh = {Archaea/classification/*genetics/physiology ; Bacteria/classification/*genetics ; Bacterial Physiological Phenomena ; Base Composition ; Clustered Regularly Interspaced Short Palindromic Repeats ; Gene Transfer, Horizontal ; Mutation ; },
abstract = {Comparative genomics has revealed that variations in bacterial and archaeal genome DNA sequences cannot be explained by only neutral mutations. Virus resistance and plasmid distribution systems have resulted in changes in bacterial and archaeal genome sequences during evolution. The restriction-modification system, a virus resistance system, leads to avoidance of palindromic DNA sequences in genomes. Clustered, regularly interspaced, short palindromic repeats (CRISPRs) found in genomes represent yet another virus resistance system. Comparative genomics has shown that bacteria and archaea have failed to gain any DNA with GC content higher than the GC content of their chromosomes. Thus, horizontally transferred DNA regions have lower GC content than the host chromosomal DNA does. Some nucleoid-associated proteins bind DNA regions with low GC content and inhibit the expression of genes contained in those regions. This form of gene repression is another type of virus resistance system. On the other hand, bacteria and archaea have used plasmids to gain additional genes. Virus resistance systems influence plasmid distribution. Interestingly, the restriction-modification system and nucleoid-associated protein genes have been distributed via plasmids. Thus, GC content and genomic signatures do not reflect bacterial and archaeal evolutionary relationships.},
}
@article {pmid22763819,
year = {2012},
author = {Marchfelder, A and Fischer, S and Brendel, J and Stoll, B and Maier, LK and Jäger, D and Prasse, D and Plagens, A and Schmitz, RA and Randau, L},
title = {Small RNAs for defence and regulation in archaea.},
journal = {Extremophiles : life under extreme conditions},
volume = {16},
number = {5},
pages = {685-696},
pmid = {22763819},
issn = {1433-4909},
mesh = {*Archaea/genetics/metabolism ; Gene Expression Regulation, Archaeal/*physiology ; Interspersed Repetitive Sequences ; Protein Biosynthesis/*physiology ; *RNA, Archaeal ; *RNA, Small Untranslated ; },
abstract = {Non-coding RNAs are key players in many cellular processes within organisms from all three domains of life. The range and diversity of small RNA functions beyond their involvement in translation and RNA processing was first recognized for eukaryotes and bacteria. Since then, small RNAs were also found to be abundant in archaea. Their functions include the regulation of gene expression and the establishment of immunity against invading mobile genetic elements. This review summarizes our current knowledge about small RNAs used for regulation and defence in archaea.},
}
@article {pmid22754756,
year = {2012},
author = {Gophna, U and Brodt, A},
title = {CRISPR/Cas systems in archaea: What array spacers can teach us about parasitism and gene exchange in the 3rd domain of life.},
journal = {Mobile genetic elements},
volume = {2},
number = {1},
pages = {63-64},
pmid = {22754756},
issn = {2159-2543},
abstract = {CRISPR (Clustered, Regularly, Interspaced, Short, Palindromic Repeats) loci have been shown to provide prokaryotes with an adaptive immunity against viruses and plasmids. CRISPR arrays are transcribed and processed into small CRISPR RNA molecules, which base-pair with invading DNA or RNA and lead to its degradation by CRISPR-associated (Cas) protein complexes. New spacers can be acquired by active CRISPR/Cas systems, and thus the sequences of these spacers provide a record of the past "infection history" of the organism. Recently we used spacer sequences from archaeal genomes to infer gene exchange events among archaeal species and genera and to demonstrate that at least in this domain of life CRISPR indeed has an anti-viral role.},
}
@article {pmid22753779,
year = {2012},
author = {Bower-Phipps, KR and Taylor, DW and Wang, HW and Baserga, SJ},
title = {The box C/D sRNP dimeric architecture is conserved across domain Archaea.},
journal = {RNA (New York, N.Y.)},
volume = {18},
number = {8},
pages = {1527-1540},
pmid = {22753779},
issn = {1469-9001},
support = {T32 GM007223/GM/NIGMS NIH HHS/United States ; GM052581/GM/NIGMS NIH HHS/United States ; R01 GM052581/GM/NIGMS NIH HHS/United States ; 5 T32 GM008283/GM/NIGMS NIH HHS/United States ; T32 GM008283/GM/NIGMS NIH HHS/United States ; R29 GM052581/GM/NIGMS NIH HHS/United States ; },
mesh = {Archaea/classification/genetics/*metabolism ; Archaeal Proteins/*chemistry/genetics/*metabolism ; Base Sequence ; Methylation ; Molecular Sequence Data ; Mutagenesis ; Protein Binding ; Protein Conformation ; Protein Multimerization ; RNA, Archaeal/genetics/*metabolism ; RNA, Small Nucleolar/genetics/*metabolism ; Ribonucleoproteins, Small Nucleolar/*chemistry/genetics/*metabolism ; },
abstract = {Box C/D small (nucleolar) ribonucleoproteins [s(no)RNPs] catalyze RNA-guided 2'-O-ribose methylation in two of the three domains of life. Recent structural studies have led to a controversy over whether box C/D sRNPs functionally assemble as monomeric or dimeric macromolecules. The archaeal box C/D sRNP from Methanococcus jannaschii (Mj) has been shown by glycerol gradient sedimentation, gel filtration chromatography, native gel analysis, and single-particle electron microscopy (EM) to adopt a di-sRNP architecture, containing four copies of each box C/D core protein and two copies of the Mj sR8 sRNA. Subsequently, investigators used a two-stranded artificial guide sRNA, CD45, to assemble a box C/D sRNP from Sulfolobus solfataricus with a short RNA methylation substrate, yielding a crystal structure of a mono-sRNP. To more closely examine box C/D sRNP architecture, we investigate the role of the omnipresent sRNA loop as a structural determinant of sRNP assembly. We show through sRNA mutagenesis, native gel electrophoresis, and single-particle EM that a di-sRNP is the near exclusive architecture obtained when reconstituting box C/D sRNPs with natural or artificial sRNAs containing an internal loop. Our results span three distantly related archaeal species--Sulfolobus solfataricus, Pyrococcus abyssi, and Archaeoglobus fulgidus--indicating that the di-sRNP architecture is broadly conserved across the entire archaeal domain.},
}
@article {pmid22753131,
year = {2013},
author = {Güven, K and Mutlu, MB and Çırpan, C and Kutlu, HM},
title = {Isolation and identification of selenite reducing archaea from Tuz (salt) Lake In Turkey.},
journal = {Journal of basic microbiology},
volume = {53},
number = {5},
pages = {397-401},
doi = {10.1002/jobm.201200008},
pmid = {22753131},
issn = {1521-4028},
mesh = {Archaea/*isolation &amp; purification/metabolism ; DNA, Ribosomal/chemistry ; Halorubrum/metabolism ; Lakes/*microbiology ; Microscopy, Electron, Transmission ; Oxidation-Reduction ; RNA, Ribosomal, 16S/genetics ; Selenious Acid/*metabolism ; Turkey ; },
abstract = {In this study, Tuz lake brine samples were investigated for isolation and identification of selenite resistant halophilic prokaryotes. Among the 20 strains of extremely halophilic Bacteria and Archaea, a Gram negative rod designated as strain 106, showed high capacity in the resistance to selenite (25 mM) under aerobic conditions. Phenotypic characterizations and phylogenetic analyses based on 16S rDNA sequence comparison indicated that strain 106 was Halorubrum xinjiangense. The ability of strain 106 to deposite selenium-containing particles were investigated by Transmission Electron Microscopy (TEM). Electron micrographs shows intact cells after selenite reduction and large amounts of selenium-containing particles are present in the culture medium indicating that strain 106 is able to efficiently transport elemental selenium out of the cell.},
}
@article {pmid22748314,
year = {2012},
author = {Naor, A and Lapierre, P and Mevarech, M and Papke, RT and Gophna, U},
title = {Low species barriers in halophilic archaea and the formation of recombinant hybrids.},
journal = {Current biology : CB},
volume = {22},
number = {15},
pages = {1444-1448},
doi = {10.1016/j.cub.2012.05.056},
pmid = {22748314},
issn = {1879-0445},
mesh = {Haloferax mediterranei/*genetics ; Haloferax volcanii/*genetics ; *Hybridization, Genetic ; *Recombination, Genetic ; },
abstract = {Speciation of sexually reproducing organisms requires reproductive barriers. Prokaryotes reproduce asexually but often exchange DNA by lateral gene transfer mechanisms and recombination [1], yet distinct lineages are still observed. Thus, barriers to gene flow such as geographic isolation, genetic incompatibility or a physiological inability to transfer DNA represent potential underlying mechanisms behind preferred exchange groups observed in prokaryotes [2-6]. In Bacteria, experimental evidence showed that sequence divergence impedes homologous recombination between bacterial species [7-11]. Here we study interspecies gene exchange in halophilic archaea that possess a parasexual mechanism of genetic exchange that is functional between species [12, 13]. In this process, cells fuse forming a diploid state containing the full genetic repertoire of both parental cells, which facilitates genetic exchange and recombination. Later, cells separate, occasionally resulting in hybrids of the parental strains [14]. We show high recombination frequencies between Haloferax volcanii and Haloferax mediterranei, two species that have an average nucleotide sequence identity of 86.6%. Whole genome sequencing of Haloferax interspecies hybrids revealed the exchange of chromosomal fragments ranging from 310Kb to 530Kb. These results show that recombination barriers may be more permissive in halophilic archaea than they are in bacteria.},
}
@article {pmid22748132,
year = {2012},
author = {Khelaifia, S and Drancourt, M},
title = {Susceptibility of archaea to antimicrobial agents: applications to clinical microbiology.},
journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases},
volume = {18},
number = {9},
pages = {841-848},
doi = {10.1111/j.1469-0691.2012.03913.x},
pmid = {22748132},
issn = {1469-0691},
mesh = {Anti-Infective Agents/*pharmacology ; Archaea/*drug effects ; Humans ; Metagenome/drug effects ; Microbial Sensitivity Tests ; },
abstract = {We herein review the state of knowledge regarding the in vitro and in vivo susceptibility of archaea to antimicrobial agents, including some new molecules. Indeed, some archaea colonizing the human microbiota have been implicated in diseases such as periodontopathy. Archaea are characterized by their broad-spectrum resistance to antimicrobial agents. In particular, their cell wall lacks peptidoglycan, making them resistant to antimicrobial agents interfering with peptidoglycan biosynthesis. Archaea are, however, susceptible to the protein synthesis inhibitor fusidic acid and imidazole derivatives. Also, squalamine, an antimicrobial agent acting on the cell wall, proved effective against human methanogenic archaea. In vitro susceptibility data could be used to design protocols for the decontamination of complex microbiota and the selective isolation of archaea in anaerobic culture.},
}
@article {pmid22747590,
year = {2012},
author = {Mani, K and Salgaonkar, BB and Braganca, JM},
title = {Culturable halophilic archaea at the initial and crystallization stages of salt production in a natural solar saltern of Goa, India.},
journal = {Aquatic biosystems},
volume = {8},
number = {1},
pages = {15},
pmid = {22747590},
issn = {2046-9063},
abstract = {BACKGROUND: Goa is a coastal state in India and salt making is being practiced for many years. This investigation aimed in determining the culturable haloarchaeal diversity during two different phases of salt production in a natural solar saltern of Ribandar, Goa. Water and sediment samples were collected from the saltern during pre-salt harvesting phase and salt harvesting phase. Salinity and pH of the sampling site was determined. Isolates were obtained by plating of the samples on complex and synthetic haloarchaeal media. Morphology of the isolates was determined using Gram staining and electron microscopy. Response of cells to distilled water was studied spectrophotometrically at 600nm. Molecular identification of the isolates was performed by sequencing the 16S rRNA.<br><br>RESULTS: Salinity of salt pans varied from 3-4% (non-salt production phase) to 30% (salt production phase) and pH varied from 7.0-8.0. Seven haloarchaeal strains were isolated from water and sediment samples during non-salt production phase and seventeen haloarchaeal strains were isolated during the salt production phase. All the strains stained uniformly Gram negative. The orange-red acetone extract of the pigments showed similar spectrophotometric profile with absorption maxima at 393, 474, 501 and 535 nm. All isolates obtained from the salt dilute phase were grouped within the genus Halococcus. This was validated using both total lipid profiling and 16S rRNA data sequencing. The isolates obtained from pre-salt harvesting phase were resistant to lysis. 16S rRNA data showed that organisms belonging to Halorubrum, Haloarcula, Haloferax and Halococcus genera were obtained during the salt concentrated phase. The isolates obtained from salt harvesting phase showed varied lysis on suspension in distilled water and /or 3.5% NaCl.<br><br>CONCLUSION: Salterns in Goa are transiently operated during post monsoon season from January to May. During the pre-salt harvesting phase, all the isolates obtained belonged to Halococcus sp. During the salt harvesting phase, isolates belonging to Halorubrum, Haloarcula, Haloferax and Halococcus genera were obtained. This study clearly indicates that Halococcus sp. dominates during the low salinity conditions.},
}
@article {pmid22739494,
year = {2012},
author = {Walker, CB and Redding-Johanson, AM and Baidoo, EE and Rajeev, L and He, Z and Hendrickson, EL and Joachimiak, MP and Stolyar, S and Arkin, AP and Leigh, JA and Zhou, J and Keasling, JD and Mukhopadhyay, A and Stahl, DA},
title = {Functional responses of methanogenic archaea to syntrophic growth.},
journal = {The ISME journal},
volume = {6},
number = {11},
pages = {2045-2055},
pmid = {22739494},
issn = {1751-7370},
mesh = {Desulfovibrio vulgaris/genetics/*growth &amp; development/metabolism ; Energy Metabolism ; Hydrogen/metabolism ; Lactic Acid/metabolism ; Methane/metabolism ; Methanococcus/genetics/*growth &amp; development/metabolism ; Oxidoreductases/genetics/metabolism ; Proteomics ; },
abstract = {Methanococcus maripaludis grown syntrophically with Desulfovibrio vulgaris was compared with M. maripaludis monocultures grown under hydrogen limitation using transcriptional, proteomic and metabolite analyses. These measurements indicate a decrease in transcript abundance for energy-consuming biosynthetic functions in syntrophically grown M. maripaludis, with an increase in transcript abundance for genes involved in the energy-generating central pathway for methanogenesis. Compared with growth in monoculture under hydrogen limitation, the response of paralogous genes, such as those coding for hydrogenases, often diverged, with transcripts of one variant increasing in relative abundance, whereas the other was little changed or significantly decreased in abundance. A common theme was an apparent increase in transcripts for functions using H(2) directly as reductant, versus those using the reduced deazaflavin (coenzyme F(420)). The greater importance of direct reduction by H(2) was supported by improved syntrophic growth of a deletion mutant in an F(420)-dependent dehydrogenase of M. maripaludis. These data suggest that paralogous genes enable the methanogen to adapt to changing substrate availability, sustaining it under environmental conditions that are often near the thermodynamic threshold for growth. Additionally, the discovery of interspecies alanine transfer adds another metabolic dimension to this environmentally relevant mutualism.},
}
@article {pmid22723795,
year = {2012},
author = {Bartossek, R and Spang, A and Weidler, G and Lanzen, A and Schleper, C},
title = {Metagenomic analysis of ammonia-oxidizing archaea affiliated with the soil group.},
journal = {Frontiers in microbiology},
volume = {3},
number = {},
pages = {208},
pmid = {22723795},
issn = {1664-302X},
support = {P 23000/FWF_/Austrian Science Fund FWF/Austria ; },
abstract = {Ammonia-oxidizing archaea (AOA) have recently been recognized as a significant component of many microbial communities and represent one of the most abundant prokaryotic groups in the biosphere. However, only few AOA have been successfully cultivated so far and information on the physiology and genomic content remains scarce. We have performed a metagenomic analysis to extend the knowledge of the AOA affiliated with group I.1b that is widespread in terrestrial habitats and of which no genome sequences has been described yet. A fosmid library was generated from samples of a radioactive thermal cave (46°C) in the Austrian Central Alps in which AOA had been found as a major part of the microbial community. Out of 16 fosmids that possessed either an amoA or 16S rRNA gene affiliating with AOA, 5 were fully sequenced, 4 of which grouped with the soil/I.1b (Nitrososphaera-) lineage, and 1 with marine/I.1a (Nitrosopumilus-) lineage. Phylogenetic analyses of amoBC and an associated conserved gene were congruent with earlier analyses based on amoA and 16S rRNA genes and supported the separation of the soil and marine group. Several putative genes that did not have homologs in currently available marine Thaumarchaeota genomes indicated that AOA of the soil group contain specific genes that are distinct from their marine relatives. Potential cis-regulatory elements around conserved promoter motifs found upstream of the amo genes in sequenced (meta-) genomes differed in marine and soil group AOA. On one fosmid, a group of genes including amoA and amoB were flanked by identical transposable insertion sequences, indicating that amoAB could potentially be co-mobilized in the form of a composite transposon. This might be one of the mechanisms that caused the greater variation in gene order compared to genomes in the marine counterparts. Our findings highlight the genetic diversity within the two major and widespread lineages of Thaumarchaeota.},
}
@article {pmid22718911,
year = {2012},
author = {Lombard, J and López-García, P and Moreira, D},
title = {An ACP-independent fatty acid synthesis pathway in archaea: implications for the origin of phospholipids.},
journal = {Molecular biology and evolution},
volume = {29},
number = {11},
pages = {3261-3265},
doi = {10.1093/molbev/mss160},
pmid = {22718911},
issn = {1537-1719},
mesh = {Acyl Carrier Protein/metabolism ; Archaea/enzymology/*metabolism ; *Biosynthetic Pathways ; Fatty Acid Synthase, Type II/chemistry/metabolism ; Fatty Acids/*biosynthesis ; Likelihood Functions ; Phospholipids/*metabolism ; Phylogeny ; Sequence Homology, Amino Acid ; },
abstract = {Fatty acids (FAs) are major building blocks of membrane phospholipids in bacteria and eukaryotes. Their presumed absence in archaea led to propose a late origin in bacteria and eukaryotes and that the last common ancestor of living organisms (the cenancestor) was devoid of both FA and phospholipid membranes. However, small FA amounts and homologs of bacterial FA biosynthesis enzymes are found in archaea. We have investigated the origin of these archaeal enzymes using phylogenomic analyses of all enzymes of the main bacterial FA biosynthesis pathway. Our results suggest that modern archaea and their last common ancestor possessed a complete pathway except for the acyl carrier protein (ACP) processing machinery, which evolved in the bacterial lineage. This has not only implications for archaeal physiology but also opens the possibility for the presence of ACP-independent FA synthesis in the cenancestor, which may have been endowed with FA-phospholipid membranes.},
}
@article {pmid22713092,
year = {2013},
author = {Schut, GJ and Boyd, ES and Peters, JW and Adams, MW},
title = {The modular respiratory complexes involved in hydrogen and sulfur metabolism by heterotrophic hyperthermophilic archaea and their evolutionary implications.},
journal = {FEMS microbiology reviews},
volume = {37},
number = {2},
pages = {182-203},
doi = {10.1111/j.1574-6976.2012.00346.x},
pmid = {22713092},
issn = {1574-6976},
mesh = {Archaea/*enzymology/genetics/metabolism ; Bacteria/*enzymology/genetics/metabolism ; Energy Metabolism ; Ferredoxins/metabolism ; Hydrogen/*metabolism ; Hydrogenase/genetics/*metabolism ; Metabolic Networks and Pathways/*genetics ; Multigene Family ; Oxidation-Reduction ; Sodium-Hydrogen Exchangers/genetics/metabolism ; Sulfur/*metabolism ; },
abstract = {Hydrogen production is a vital metabolic process for many anaerobic organisms, and the enzyme responsible, hydrogenase, has been studied since the 1930s. A novel subfamily with unique properties was recently recognized, represented by the 14-subunit membrane-bound [NiFe] hydrogenase from the archaeon Pyrococcus furiosus. This so-called energy-converting hydrogenase links the thermodynamically favorable oxidation of ferredoxin with the formation of hydrogen and conserves energy in the form of an ion gradient. It is therefore a simple respiratory system within a single complex. This hydrogenase shows a modular composition represented by a Na(+)/H(+) antiporter domain (Mrp) and a [NiFe] hydrogenase domain (Mbh). An analysis of the large number of microbial genome sequences available shows that homologs of Mbh and Mrp tend to be clustered within the genomes of a limited number of archaeal and bacterial species. In several instances, additional genes are associated with the Mbh and Mrp gene clusters that encode proteins that catalyze the oxidation of formate, CO or NAD(P)H. The Mbh complex also shows extensive homology to a number of subunits within the NADH quinone oxidoreductase or complex I family. The respiratory-type membrane-bound hydrogenase complex appears to be closely related to the common ancestor of complex I and [NiFe] hydrogenases in general.},
}
@article {pmid22706066,
year = {2012},
author = {Trias, R and Ruiz-Rueda, O and García-Lledó, A and Vilar-Sanz, A and López-Flores, R and Quintana, XD and Hallin, S and Bañeras, L},
title = {Emergent macrophytes act selectively on ammonia-oxidizing bacteria and archaea.},
journal = {Applied and environmental microbiology},
volume = {78},
number = {17},
pages = {6352-6356},
pmid = {22706066},
issn = {1098-5336},
mesh = {Ammonia/*metabolism ; Archaea/*classification/*genetics/metabolism ; Bacteria/*classification/*genetics/metabolism ; Biodiversity ; Hydrogen-Ion Concentration ; Metagenome ; Oxidation-Reduction ; Plant Roots/*microbiology ; Wetlands ; },
abstract = {Ammonia-oxidizing bacteria (AOB) and archaea (AOA) were quantified in the sediments and roots of dominant macrophytes in eight neutral to alkaline coastal wetlands. The AOA dominated in most samples, but the bacterial-to-archaeal amoA gene ratios increased with increasing ammonium levels and pH in the sediments. For all plant species, the ratios increased on the root surface relative to the adjacent bulk sediment. This suggests that root surfaces in these environments provide conditions favoring enrichment of AOB.},
}
@article {pmid22695861,
year = {2012},
author = {Taylor, AE and Zeglin, LH and Wanzek, TA and Myrold, DD and Bottomley, PJ},
title = {Dynamics of ammonia-oxidizing archaea and bacteria populations and contributions to soil nitrification potentials.},
journal = {The ISME journal},
volume = {6},
number = {11},
pages = {2024-2032},
pmid = {22695861},
issn = {1751-7370},
mesh = {Ammonia/*metabolism ; Archaea/*metabolism ; Bacteria/*metabolism ; Fertilizers ; Nitrification ; Oxidation-Reduction ; Soil/*chemistry ; *Soil Microbiology ; },
abstract = {It is well known that the ratio of ammonia-oxidizing archaea (AOA) and bacteria (AOB) ranges widely in soils, but no data exist on what might influence this ratio, its dynamism, or how changes in relative abundance influences the potential contributions of AOA and AOB to soil nitrification. By sampling intensively from cropped-to-fallowed and fallowed-to-cropped phases of a 2-year wheat/fallow cycle, and adjacent uncultivated long-term fallowed land over a 15-month period in 2010 and 2011, evidence was obtained for seasonal and cropping phase effects on the soil nitrification potential (NP), and on the relative contributions of AOA and AOB to the NP that recovers after acetylene inactivation in the presence and absence of bacterial protein synthesis inhibitors. AOB community composition changed significantly (P(?)0.0001) in response to cropping phase, and there were both seasonal and cropping phase effects on the amoA gene copy numbers of AOA and AOB. Our study showed that the AOA:AOB shifts were generated by a combination of different phenomena: an increase in AOA amoA abundance in unfertilized treatments, compared with their AOA counterparts in the N-fertilized treatment; a larger population of AOB under the N-fertilized treatment compared with the AOB community under unfertilized treatments; and better overall persistence of AOA than AOB in the unfertilized treatments. These data illustrate the complexity of the factors that likely influence the relative contributions of AOA and AOB to nitrification under the various combinations of soil conditions and NH(4)(+)-availability that exist in the field.},
}
@article {pmid22691113,
year = {2012},
author = {Roy Chowdhury, A and Dutta, C},
title = {A pursuit of lineage-specific and niche-specific proteome features in the world of archaea.},
journal = {BMC genomics},
volume = {13},
number = {},
pages = {236},
pmid = {22691113},
issn = {1471-2164},
mesh = {Amino Acids/metabolism ; Archaea/*genetics/metabolism ; Archaeal Proteins/chemistry/genetics/metabolism ; Cluster Analysis ; Isoelectric Point ; Proteome/*metabolism ; Salts/chemistry ; Sulfur/metabolism ; Temperature ; },
abstract = {BACKGROUND: Archaea evoke interest among researchers for two enigmatic characteristics -a combination of bacterial and eukaryotic components in their molecular architectures and an enormous diversity in their life-style and metabolic capabilities. Despite considerable research efforts, lineage- specific/niche-specific molecular features of the whole archaeal world are yet to be fully unveiled. The study offers the first large-scale in silico proteome analysis of all archaeal species of known genome sequences with a special emphasis on methanogenic and sulphur-metabolising archaea.<br><br>RESULTS: Overall amino acid usage in archaea is dominated by GC-bias. But the environmental factors like oxygen requirement or thermal adaptation seem to play important roles in selection of residues with no GC-bias at the codon level. All methanogens, irrespective of their thermal/salt adaptation, show higher usage of Cys and have relatively acidic proteomes, while the proteomes of sulphur-metabolisers have higher aromaticity and more positive charges. Despite of exhibiting thermophilic life-style, korarchaeota possesses an acidic proteome. Among the distinct trends prevailing in COGs (Cluster of Orthologous Groups of proteins) distribution profiles, crenarchaeal organisms display higher intra-order variations in COGs repertoire, especially in the metabolic ones, as compared to euryarchaea. All methanogens are characterised by a presence of 22 exclusive COGs.<br><br>CONCLUSIONS: Divergences in amino acid usage, aromaticity/charge profiles and COG repertoire among methanogens and sulphur-metabolisers, aerobic and anaerobic archaea or korarchaeota and nanoarchaeota, as elucidated in the present study, point towards the presence of distinct molecular strategies for niche specialization in the archaeal world.},
}
@article {pmid22688860,
year = {2012},
author = {Vasileiadis, S and Coppolecchia, D and Puglisi, E and Balloi, A and Mapelli, F and Hamon, RE and Daffonchio, D and Trevisan, M},
title = {Response of ammonia oxidizing bacteria and archaea to acute zinc stress and different moisture regimes in soil.},
journal = {Microbial ecology},
volume = {64},
number = {4},
pages = {1028-1037},
pmid = {22688860},
issn = {1432-184X},
mesh = {Ammonia/*metabolism ; Archaea/classification/genetics/metabolism/*physiology ; Bacteria/classification/genetics/*metabolism ; Bacterial Physiological Phenomena ; DNA, Archaeal/analysis/genetics ; DNA, Bacterial/analysis/genetics ; Ecosystem ; *Heat-Shock Response ; Nitrification ; Oxidation-Reduction ; Oxidoreductases/genetics ; Polymerase Chain Reaction ; Soil/chemistry ; *Soil Microbiology ; *Water ; Zinc/analysis/*pharmacology ; },
abstract = {Ammonia oxidation has been intensively studied for its sensitivity to environmental shifts and stresses. However, acute stress effects on the occurrence and composition of ammonia oxidizing bacteria (AOB) and archaea (AOA) based on expression of related molecular markers in complex soil environments have been to an extent overlooked, particularly concerning transient but commonly occurring environmental changes like soil moisture shifts. The present study investigates the responses of AOB and AOA to moisture shifts and high Zn soil content. AmoA gene copies and transcripts of AOB and AOA along with potential nitrification activity were measured in a soil microcosm approach for investigating the referred environmental shifts. Moisture change from 87 to 50 % of the water holding capacity caused a ~99 % reduction of AOB but not of AOA amoA transcripts that did not change significantly. Increasing applied zinc concentrations resulted in a reduction of potential nitrification rates and negatively affected studied gene expressions of both AOB and AOA, with AOB being more responsive. Both 16 S rRNA and amoA transcripts of AOB had an inverse relation to the applied zinc, indicating a gradual loss in total cell activity. Our results suggest the existence of pronounced differences between AOB and AOA concerning ammonia oxidation activity.},
}
@article {pmid22685142,
year = {2012},
author = {French, E and Kozlowski, JA and Mukherjee, M and Bullerjahn, G and Bollmann, A},
title = {Ecophysiological characterization of ammonia-oxidizing archaea and bacteria from freshwater.},
journal = {Applied and environmental microbiology},
volume = {78},
number = {16},
pages = {5773-5780},
pmid = {22685142},
issn = {1098-5336},
mesh = {Aerobiosis ; Ammonia/*metabolism ; Archaea/classification/*growth &amp; development/isolation &amp; purification/*metabolism ; Bacteria/classification/*growth &amp; development/isolation &amp; purification/*metabolism ; Fresh Water/*microbiology ; Hydrogen-Ion Concentration ; Light ; Molecular Sequence Data ; Oxidation-Reduction ; Oxygen/metabolism ; Sequence Analysis, DNA ; },
abstract = {Aerobic biological ammonia oxidation is carried out by two groups of microorganisms, ammonia-oxidizing bacteria (AOB) and the recently discovered ammonia-oxidizing archaea (AOA). Here we present a study using cultivation-based methods to investigate the differences in growth of three AOA cultures and one AOB culture enriched from freshwater environments. The strain in the enriched AOA culture belong to thaumarchaeal group I.1a, with the strain in one enrichment culture having the highest identity with "Candidatus Nitrosoarchaeum koreensis" and the strains in the other two representing a new genus of AOA. The AOB strain in the enrichment culture was also obtained from freshwater and had the highest identity to AOB from the Nitrosomonas oligotropha group (Nitrosomonas cluster 6a). We investigated the influence of ammonium, oxygen, pH, and light on the growth of AOA and AOB. The growth rates of the AOB increased with increasing ammonium concentrations, while the growth rates of the AOA decreased slightly. Increasing oxygen concentrations led to an increase in the growth rate of the AOB, while the growth rates of AOA were almost oxygen insensitive. Light exposure (white and blue wavelengths) inhibited the growth of AOA completely, and the AOA did not recover when transferred to the dark. AOB were also inhibited by blue light; however, growth recovered immediately after transfer to the dark. Our results show that the tested AOB have a competitive advantage over the tested AOA under most conditions investigated. Further experiments will elucidate the niches of AOA and AOB in more detail.},
}
@article {pmid22673339,
year = {2012},
author = {Sims, A and Horton, J and Gajaraj, S and McIntosh, S and Miles, RJ and Mueller, R and Reed, R and Hu, Z},
title = {Temporal and spatial distributions of ammonia-oxidizing archaea and bacteria and their ratio as an indicator of oligotrophic conditions in natural wetlands.},
journal = {Water research},
volume = {46},
number = {13},
pages = {4121-4129},
doi = {10.1016/j.watres.2012.05.007},
pmid = {22673339},
issn = {1879-2448},
mesh = {Ammonia/*metabolism ; Archaea/genetics/*metabolism ; Archaeal Proteins/genetics/metabolism ; Bacteria/genetics/*metabolism ; Bacterial Proteins/genetics/metabolism ; Ecosystem ; Gene Dosage ; Nitrification ; Nitrogen Cycle ; Oxidation-Reduction ; Oxidoreductases/genetics/metabolism ; Real-Time Polymerase Chain Reaction ; Seasons ; Soil/analysis ; Soil Microbiology ; Time Factors ; Water Microbiology ; *Wetlands ; },
abstract = {Ammonia-oxidizing organisms play an important role in wetland water purification and nitrogen cycling. We determined soil nitrification rates and investigated the seasonal and spatial distributions of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in three freshwater wetlands by using specific primers targeting the amoA genes of AOA and AOB and real-time quantitative polymerase chain reaction (qPCR). The nitrifying potentials of wetland soils ranged from 1.4 to 4.0 μg g(-1) day(-1). The specific rates of ammonia oxidation activity by AOA and AOB at the Bee Hollow wetlands were 1.9 fmol NH(3) cell(-1) day(-1) and 36.8 fmol NH(3) cell(-1) day(-1), respectively. Soil nitrification potential was positively correlated with both archaeal and bacterial amoA abundance. However, the gene copies of AOA amoA were higher than those of AOB amoA by at least an order of magnitude in wetland soils and water in both summer and winter over a three year study period. AOB were more sensitive to low temperature than AOA. The amoA gene copy ratios of AOA to AOB in top soils (0-10 cm) ranged from 19 ± 4 to 100 ± 11 among the wetland sites. In contrast, the ratio of the wetland boundary soil was 10 ± 2, which was significantly lower than that of the wetland soils (P < 0.001). The NH(4)(+)-N concentrations in wetland water were lower than 2 mg/L throughout the study. The results suggest that ammonium concentration is a major factor influencing AOA and AOB population in wetlands, although other factors such as temperature, dissolved oxygen, and soil organic matter are involved. AOA are more persistent and more abundant than AOB in the nutrient-depleted oligotrophic wetlands. Therefore, ratio of AOA amoA gene copies to AOB amoA gene copies may serve as a new biological indicator for wetland condition assessment and wetland restoration applications.},
}
@article {pmid22666218,
year = {2012},
author = {Durbin, AM and Teske, A},
title = {Archaea in organic-lean and organic-rich marine subsurface sediments: an environmental gradient reflected in distinct phylogenetic lineages.},
journal = {Frontiers in microbiology},
volume = {3},
number = {},
pages = {168},
pmid = {22666218},
issn = {1664-302X},
abstract = {Examining the patterns of archaeal diversity in little-explored organic-lean marine subsurface sediments presents an opportunity to study the association of phylogenetic affiliation and habitat preference in uncultured marine Archaea. Here we have compiled and re-analyzed published archaeal 16S rRNA clone library datasets across a spectrum of sediment trophic states characterized by a wide range of terminal electron-accepting processes. Our results show that organic-lean marine sediments in deep marine basins and oligotrophic open ocean locations are inhabited by distinct lineages of archaea that are not found in the more frequently studied, organic-rich continental margin sediments. We hypothesize that different combinations of electron donor and acceptor concentrations along the organic-rich/organic-lean spectrum result in distinct archaeal communities, and propose an integrated classification of habitat characteristics and archaeal community structure.},
}
@article {pmid22666082,
year = {2012},
author = {Rohlin, L and Leon, DR and Kim, U and Loo, JA and Ogorzalek Loo, RR and Gunsalus, RP},
title = {Identification of the major expressed S-layer and cell surface-layer-related proteins in the model methanogenic archaea: Methanosarcina barkeri Fusaro and Methanosarcina acetivorans C2A.},
journal = {Archaea (Vancouver, B.C.)},
volume = {2012},
number = {},
pages = {873589},
pmid = {22666082},
issn = {1472-3654},
support = {F31 AI061886/AI/NIAID NIH HHS/United States ; R01 GM085402/GM/NIGMS NIH HHS/United States ; GM085402/GM/NIGMS NIH HHS/United States ; 5F31AI61886-02/AI/NIAID NIH HHS/United States ; },
mesh = {DNA, Archaeal/genetics ; Gene Expression ; Genes, Archaeal ; Genome, Archaeal ; Membrane Glycoproteins/*analysis/chemistry/genetics ; Methanosarcina/*chemistry/genetics ; Molecular Weight ; Promoter Regions, Genetic ; Protein Processing, Post-Translational ; Proteomics/methods ; },
abstract = {Many archaeal cell envelopes contain a protein coat or sheath composed of one or more surface exposed proteins. These surface layer (S-layer) proteins contribute structural integrity and protect the lipid membrane from environmental challenges. To explore the species diversity of these layers in the Methanosarcinaceae, the major S-layer protein in Methanosarcina barkeri strain Fusaro was identified using proteomics. The Mbar_A1758 gene product was present in multiple forms with apparent sizes of 130, 120, and 100 kDa, consistent with post-translational modifications including signal peptide excision and protein glycosylation. A protein with features related to the surface layer proteins found in Methanosarcina acetivorans C2A and Methanosarcina mazei Goel was identified in the M. barkeri genome. These data reveal a distinct conserved protein signature with features and implied cell surface architecture in the Methanosarcinaceae that is absent in other archaea. Paralogous gene expression patterns in two Methanosarcina species revealed abundant expression of a single S-layer paralog in each strain. Respective promoter elements were identified and shown to be conserved in mRNA coding and upstream untranslated regions. Prior M. acetivorans genome annotations assigned S-layer or surface layer associated roles of eighty genes: however, of 68 examined none was significantly expressed relative to the experimentally determined S-layer gene.},
}
@article {pmid22654563,
year = {2012},
author = {Yoshinaga, MY and Wörmer, L and Elvert, M and Hinrichs, KU},
title = {Novel cardiolipins from uncultured methane-metabolizing archaea.},
journal = {Archaea (Vancouver, B.C.)},
volume = {2012},
number = {},
pages = {832097},
pmid = {22654563},
issn = {1472-3654},
mesh = {Archaea/*chemistry/isolation &amp; purification/metabolism ; Cardiolipins/chemistry/*isolation &amp; purification ; Cell Membrane/chemistry ; Chromatography, Liquid ; Geologic Sediments/microbiology ; Methane/metabolism ; Pakistan ; Spectrometry, Mass, Electrospray Ionization ; },
abstract = {Novel cardiolipins from Archaea were detected by screening the intact polar lipid (IPL) composition of microbial communities associated with methane seepage in deep-sea sediments from the Pakistan margin by high-performance liquid chromatography electrospray ionization mass spectrometry. A series of tentatively identified cardiolipin analogues (dimeric phospholipids or bisphosphatidylglycerol, BPG) represented 0.5% to 5% of total archaeal IPLs. These molecules are similar to the recently described cardiolipin analogues with four phytanyl chains from extreme halophilic archaea. It is worth noting that cardiolipin analogues from the seep archaeal communities are composed of four isoprenoidal chains, which may contain differences in chain length (20 and 25 carbon atoms) and degrees of unsaturation and the presence of a hydroxyl group. Two novel diether lipids, structurally related to the BPGs, are described and interpreted as degradation products of archaeal cardiolipin analogues. Since archaeal communities in seep sediments are dominated by anaerobic methanotrophs, our observations have implications for characterizing structural components of archaeal membranes, in which BPGs are presumed to contribute to modulation of cell permeability properties. Whether BPGs facilitate interspecies interaction in syntrophic methanotrophic consortia remains to be tested.},
}
@article {pmid22654153,
year = {2011},
author = {Ahmad, N and Johri, S and Sultan, P and Abdin, MZ and Qazi, GN},
title = {Phylogenetic characterization of archaea in saltpan sediments.},
journal = {Indian journal of microbiology},
volume = {51},
number = {2},
pages = {132-137},
pmid = {22654153},
issn = {0973-7715},
abstract = {A study was undertaken to investigate the presence of archaeal diversity in saltpan sediments of Goa, India by 16S rDNA-dependent molecular phylogeny. Small subunit rRNA (16S rDNA) from saltpan sediment metagenome were amplified by polymerase chain reaction (PCR) using primers specific to the domain archaea. 10 unique phylotypes were obtained by PCR based RFLP of 16S rRNA genes using endonuclease Msp 1, which was most suitable to score the genetic diversity. These phylotypes spanned a wide range within the domain archaea including both crenarchaeota and euryarcheaota. None of the retrieved crenarchaeota sequences could be grouped with previously cultured crenarchaeota however; two sequences were related with haloarchaea. Most of the sequences determined were closely related to the sequences that had been previously obtained from metagenome of a variety of marine environments. The phylogenetic study of a site investigated for the first time revealed the presence of low archaeal population but showed yet unclassified species, may specially adapted to the salt pan sediment of Goa.},
}
@article {pmid22646318,
year = {2012},
author = {Goncearenco, A and Berezovsky, IN},
title = {Exploring the evolution of protein function in Archaea.},
journal = {BMC evolutionary biology},
volume = {12},
number = {},
pages = {75},
pmid = {22646318},
issn = {1471-2148},
mesh = {Amino Acyl-tRNA Synthetases/genetics ; Archaea/chemistry/enzymology/*genetics/*metabolism ; Archaeal Proteins/chemistry/*genetics ; *Evolution, Molecular ; Methane/biosynthesis ; Models, Molecular ; Protein Folding ; Protein Structure, Tertiary ; Proteome/chemistry/genetics ; Structure-Activity Relationship ; },
abstract = {BACKGROUND: Despite recent progress in studies of the evolution of protein function, the questions what were the first functional protein domains and what were their basic building blocks remain unresolved. Previously, we introduced the concept of elementary functional loops (EFLs), which are the functional units of enzymes that provide elementary reactions in biochemical transformations. They are presumably descendants of primordial catalytic peptides.<br><br>RESULTS: We analyzed distant evolutionary connections between protein functions in Archaea based on the EFLs comprising them. We show examples of the involvement of EFLs in new functional domains, as well as reutilization of EFLs and functional domains in building multidomain structures and protein complexes.<br><br>CONCLUSIONS: Our analysis of the archaeal superkingdom yields the dominating mechanisms in different periods of protein evolution, which resulted in several levels of the organization of biochemical function. First, functional domains emerged as combinations of prebiotic peptides with the very basic functions, such as nucleotide/phosphate and metal cofactor binding. Second, domain recombination brought to the evolutionary scene the multidomain proteins and complexes. Later, reutilization and de novo design of functional domains and elementary functional loops complemented evolution of protein function.},
}
@article {pmid22645085,
year = {2012},
author = {Dong, X and Chen, Z},
title = {Psychrotolerant methanogenic archaea: diversity and cold adaptation mechanisms.},
journal = {Science China. Life sciences},
volume = {55},
number = {5},
pages = {415-421},
doi = {10.1007/s11427-012-4320-0},
pmid = {22645085},
issn = {1869-1889},
mesh = {*Adaptation, Physiological ; Archaea/*classification/physiology ; *Cold Temperature ; },
abstract = {Because of their diversity and abundance in a wide range of environments, particularly in cold regions, cold-adaptive archaea are expected to play a pivotal role in material recycling in cold environments. Methanogenic archaea are ubiquitous on earth and produce a large amount of methane (CH(4)) as their main carbon metabolite. Methanogens are the most laboratory amendable archaea. The few psychrophilic archaea that have been cultured to date are mainly affiliated with methanogens, thus make them a good model for investigating mechanisms of archaeal cold adaptation. Studies of psychrotolerant methanogens have been ongoing since the 1990s. Using Methanococcoides burtonii, a methanogen isolated from Ace Lake in Antarctica, extensive studies on the genomic characteristics associated with cold adaptation have been carried out by the Cavicchioli laboratory. We recently analyzed the genome of another psychrophilic methanogen and identified the gene repertoire associated with cold adaptation. This review summarizes recent studies of psychroactive methanogens, particularly their diversity, the genomics and proteomics associated with their cold adaptation, and the cellular components and proteins likely involved in their cold protection.},
}
@article {pmid22645083,
year = {2012},
author = {Ishino, Y and Ishino, S},
title = {Rapid progress of DNA replication studies in Archaea, the third domain of life.},
journal = {Science China. Life sciences},
volume = {55},
number = {5},
pages = {386-403},
doi = {10.1007/s11427-012-4324-9},
pmid = {22645083},
issn = {1869-1889},
mesh = {Base Sequence ; *DNA Replication ; DNA, Archaeal/biosynthesis/*genetics ; Molecular Sequence Data ; },
abstract = {Archaea, the third domain of life, are interesting organisms to study from the aspects of molecular and evolutionary biology. Archaeal cells have a unicellular ultrastructure without a nucleus, resembling bacterial cells, but the proteins involved in genetic information processing pathways, including DNA replication, transcription, and translation, share strong similarities with those of Eukaryota. Therefore, archaea provide useful model systems to understand the more complex mechanisms of genetic information processing in eukaryotic cells. Moreover, the hyperthermophilic archaea provide very stable proteins, which are especially useful for the isolation of replisomal multicomplexes, to analyze their structures and functions. This review focuses on the history, current status, and future directions of archaeal DNA replication studies.},
}
@article {pmid22645081,
year = {2012},
author = {Huang, L},
title = {Unveiling the beauty of Archaea.},
journal = {Science China. Life sciences},
volume = {55},
number = {5},
pages = {375-376},
doi = {10.1007/s11427-012-4323-x},
pmid = {22645081},
issn = {1869-1889},
mesh = {Archaea/classification/*physiology ; },
}
@article {pmid22639927,
year = {2012},
author = {Sauder, LA and Peterse, F and Schouten, S and Neufeld, JD},
title = {Low-ammonia niche of ammonia-oxidizing archaea in rotating biological contactors of a municipal wastewater treatment plant.},
journal = {Environmental microbiology},
volume = {14},
number = {9},
pages = {2589-2600},
pmid = {22639927},
issn = {1462-2920},
mesh = {Ammonia/analysis/*metabolism ; Archaea/*classification/genetics/*metabolism ; Genes, Archaeal/genetics ; Genetic Variation ; Lipids/analysis ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Wastewater/chemistry/*microbiology ; *Water Purification ; },
abstract = {The first step of nitrification is catalysed by both ammonia-oxidizing bacteria (AOB) and archaea (AOA), but physicochemical controls on the relative abundance and function of these two groups are not yet fully understood, especially in freshwater environments. This study investigated ammonia-oxidizing populations in nitrifying rotating biological contactors (RBCs) from a municipal wastewater treatment plant. Individual RBC stages are arranged in series, with nitrification at each stage creating an ammonia gradient along the flowpath. This RBC system provides a valuable experimental system for testing the hypothesis that ammonia concentration determines the relative abundance of AOA and AOB. The results demonstrate that AOA increased as ammonium decreased across the RBC flowpath, as indicated by qPCR for thaumarchaeal amoA and 16S rRNA genes, and core lipid (CL) and intact polar lipid (IPL) crenarchaeol abundances. Overall, there was a negative logarithmic relationship (R(2) =0.51) between ammonium concentration and the relative abundance of AOA amoA genes. A single AOA population was detected in the RBC biofilms; this phylotype shared low amoA and 16S rRNA gene homology with existing AOA cultures and enrichments. These results provide evidence that ammonia availability influences the relative abundances of AOA and AOB, and that AOA are abundant in some municipal wastewater treatment systems.},
}
@article {pmid22626264,
year = {2012},
author = {Liu, Y and Beer, LL and Whitman, WB},
title = {Sulfur metabolism in archaea reveals novel processes.},
journal = {Environmental microbiology},
volume = {14},
number = {10},
pages = {2632-2644},
doi = {10.1111/j.1462-2920.2012.02783.x},
pmid = {22626264},
issn = {1462-2920},
mesh = {Aerobiosis ; Anaerobiosis ; Archaea/*metabolism ; Oxidation-Reduction ; Sulfur/*metabolism ; Sulfur Compounds/metabolism ; },
abstract = {Studies on sulfur metabolism in archaea have revealed many novel enzymes and pathways and have advanced our understanding on metabolic processes, not only of the archaea, but of biology in general. A variety of dissimilatory sulfur metabolisms, i.e. reactions used for energy conservation, are found in archaea from both the Crenarchaeota and Euryarchaeota phyla. Although not yet fully characterized, major processes include aerobic elemental sulfur (S(0)) oxidation, anaerobic S(0) reduction, anaerobic sulfate/sulfite reduction and anaerobic respiration of organic sulfur. Assimilatory sulfur metabolism, i.e. reactions used for biosynthesis of sulfur-containing compounds, also possesses some novel features. Cysteine biosynthesis in some archaea uses a unique tRNA-dependent pathway. Fe-S cluster biogenesis in many archaea differs from that in bacteria and eukaryotes and requires unidentified components. The eukaryotic ubiquitin system is conserved in archaea and involved in both protein degradation and biosynthesis of sulfur-containing cofactors. Lastly, specific pathways are utilized for the biosynthesis of coenzyme M and coenzyme B, the sulfur-containing cofactors required for methanogenesis.},
}
@article {pmid22611552,
year = {2012},
author = {Bai, Y and Sun, Q and Wen, D and Tang, X},
title = {Abundance of ammonia-oxidizing bacteria and archaea in industrial and domestic wastewater treatment systems.},
journal = {FEMS microbiology ecology},
volume = {80},
number = {2},
pages = {323-330},
doi = {10.1111/j.1574-6941.2012.01296.x},
pmid = {22611552},
issn = {1574-6941},
mesh = {Ammonia/analysis/*metabolism ; Archaea/genetics/growth &amp; development/*metabolism ; Bacteria/genetics/growth &amp; development/*metabolism ; Base Sequence ; Biodiversity ; Bioreactors/microbiology ; Molecular Sequence Data ; Nitrification/physiology ; Oxidation-Reduction ; Phylogeny ; Real-Time Polymerase Chain Reaction ; Sewage/microbiology ; *Waste Disposal, Fluid ; *Water Microbiology ; Water Pollutants, Chemical/analysis/*metabolism ; },
abstract = {Nitrification plays a significant role in the global nitrogen cycle. Ammonia oxidation, the first step of nitrification, is performed in wastewater treatment by both ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA). Most previous studies focused on their distribution in natural environments. In this study we qualified and quantified AOB, AOA, total bacteria, and total archaea in six different wastewater treatment systems (WTSs) using clone library and real-time PCR techniques. The results revealed that wastewater quality was an essential factor for the distribution of AOB and AOA in aerobic reactors. Although both AOB and AOA were present in all samples and contributed to nitrification simultaneously, AOB were the dominant nitrifiers in the three industrial WTSs, whereas AOA were dominant in the three domestic WTSs. This indicates AOA may be more sensitive to some toxic compounds than AOB. In addition, the dominant groups of AOB in the industrial WTSs were Nitrosomonas and Nitrosospira; the composition of AOA in the domestic WTSs was very similar, possibly due to the same source of raw sewage.},
}
@article {pmid22587395,
year = {2012},
author = {Singh, A and Singh, RS and Upadhyay, SN and Joshi, CG and Tripathi, AK and Dubey, SK},
title = {Community structure of methanogenic archaea and methane production associated with compost-treated tropical rice-field soil.},
journal = {FEMS microbiology ecology},
volume = {82},
number = {1},
pages = {118-134},
doi = {10.1111/j.1574-6941.2012.01411.x},
pmid = {22587395},
issn = {1574-6941},
mesh = {Agriculture/methods ; DNA, Archaeal/genetics ; Methane/*biosynthesis ; Methanomicrobiaceae/*classification/genetics ; Methanosarcinaceae/*classification/genetics ; Methanosarcinales/*classification/genetics ; Oryza/growth &amp; development/*microbiology ; Phylogeny ; Polymorphism, Restriction Fragment Length ; Population Density ; RNA, Ribosomal, 16S/genetics ; Soil/chemistry ; *Soil Microbiology ; },
abstract = {The diversity and density of methanogenic archaea and methane production were investigated ex situ at different growth stages of rice plant cultivated in compost-treated tropical rice fields. The qPCR analysis revealed variation in methanogens population from 3.40 × 10(6) to 1.11 × 10(7) copies g(-1) dws, in the year 2009 and 4.37 × 10(6) to 1.36 × 10(7) copies g(-1) dws in the year 2010. Apart from methanogens, a large number of bacterial (9.60 × 10(9) -1.44 × 10(10) copies g(-1) dws) and archaeal (7.13 × 10(7) -3.02 × 10(8) copies g(-1) dws) communities were also associated with methanogenesis. Methanogen population size varied in the order: flowering > ripening > tillering > postharvest > preplantation stage. The RFLP-based 16S rRNA gene-targeted phylogenetic analysis showed that clones were closely related to diverse group of methanogens comprising members of Methanomicrobiaceae, Methanosarcinaceae, Methanosaetaceae and RC I. Laboratory incubation studies revealed higher amount of cumulative CH(4) at the flowering stage. The integration of methanogenic community structure and CH(4) production potential of soil resulted in a better understanding of the dynamics of CH(4) production in organically treated rice-field soil. The hypothesis that the stages of plant development influence the methanogenic community structure leading to temporal variation in the CH(4) production has been successfully tested.},
}
@article {pmid22585226,
year = {2012},
author = {Bang, C and Schilhabel, A and Weidenbach, K and Kopp, A and Goldmann, T and Gutsmann, T and Schmitz, RA},
title = {Effects of antimicrobial peptides on methanogenic archaea.},
journal = {Antimicrobial agents and chemotherapy},
volume = {56},
number = {8},
pages = {4123-4130},
pmid = {22585226},
issn = {1098-6596},
mesh = {Anti-Infective Agents/*pharmacology ; Antimicrobial Cationic Peptides/*pharmacology ; Escherichia coli/drug effects/growth &amp; development ; Methanobacteriaceae/*drug effects/growth &amp; development ; Methanosarcina/*drug effects/growth &amp; development ; Microbial Sensitivity Tests ; Mucoproteins/pharmacology ; Cathelicidins ; },
abstract = {As members of the indigenous human microbiota found on several mucosal tissues, Methanobrevibacter smithii and Methanosphaera stadtmanae are exposed to the effects of antimicrobial peptides (AMPs) secreted by these epithelia. Although antimicrobial and molecular effects of AMPs on bacteria are well described, data for archaea are not available yet. Besides, it is not clear whether AMPs affect them as the archaeal cell envelope differs profoundly in terms of chemical composition and structure from that of bacteria. The effects of different synthetic AMPs on growth of M. smithii, M. stadtmanae, and Methanosarcina mazei were tested using a microtiter plate assay adapted to their anaerobic growth requirements. All three tested methanoarchaea were highly sensitive against derivatives of human cathelicidin, of porcine lysin, and a synthetic antilipopolysaccharide peptide (Lpep); however, sensitivities differed markedly among the methanoarchaeal strains. The potent AMP concentrations affecting growth were below 10 μM, whereas growth of Escherichia coli WBB01 was not affected at peptide concentrations up to 10 μM under the same anaerobic growth conditions. Atomic force microscopy and transmission electron microscopy revealed that the structural integrity of the methanoarchaeal cells is destroyed within 4 h after incubation with AMPs. The disruption of the cell envelope of M. smithii, M. stadtmanae, and M. mazei within a few minutes of exposure was verified by using LIVE/DEAD staining. Our results strongly suggest that the release of AMPs by eukaryotic epithelial cells is a potent defense mechanism targeting not only bacteria, but also methanoarchaea.},
}
@article {pmid22565329,
year = {2013},
author = {Salvador, AF and Cavaleiro, AJ and Sousa, DZ and Alves, MM and Pereira, MA},
title = {Endurance of methanogenic archaea in anaerobic bioreactors treating oleate-based wastewater.},
journal = {Applied microbiology and biotechnology},
volume = {97},
number = {5},
pages = {2211-2218},
doi = {10.1007/s00253-012-4061-9},
pmid = {22565329},
issn = {1432-0614},
mesh = {Archaea/classification/genetics/growth &amp; development/*metabolism ; Bioreactors/*microbiology ; *Biota ; Cluster Analysis ; DNA, Archaeal/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Denaturing Gradient Gel Electrophoresis ; Methane/*metabolism ; Molecular Sequence Data ; Oleic Acid/*metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Wastewater/*microbiology ; Water Pollutants, Chemical/*metabolism ; },
abstract = {Methanogenic archaea are reported as very sensitive to lipids and long chain fatty acids (LCFA). Therefore, in conventional anaerobic processes, methane recovery during LCFA-rich wastewater treatment is usually low. By applying a start-up strategy, based on a sequence of step feeding and reaction cycles, an oleate-rich wastewater was efficiently treated at an organic loading rate of 21 kg COD m(-3) day(-1) (50 % as oleate), showing a methane recovery of 72 %. In the present work, the archaeal community developed in that reactor is investigated using a 16S rRNA gene approach. This is the first time that methanogens present in a bioreactor converting efficiently high loads of LCFA to methane are monitored. Denaturing gradient gel electrophoresis profiling showed that major changes on the archaeal community took place during the bioreactor start-up, where phases of continuous feeding were alternated with batch phases. After the start-up, a stable archaeal community (similarity higher than 84 %) was observed and maintained throughout the continuous operation. This community exhibited high LCFA tolerance and high acetoclastic and hydrogenotrophic activity. Cloning and sequencing results showed that Methanobacterium- and Methanosaeta-like microorganisms prevailed in the system and were able to tolerate and endure during prolonged exposure to high LCFA loads, despite the previously reported LCFA sensitivity of methanogens.},
}
@article {pmid22561061,
year = {2012},
author = {Horz, HP and Seyfarth, I and Conrads, G},
title = {McrA and 16S rRNA gene analysis suggests a novel lineage of Archaea phylogenetically affiliated with Thermoplasmatales in human subgingival plaque.},
journal = {Anaerobe},
volume = {18},
number = {3},
pages = {373-377},
doi = {10.1016/j.anaerobe.2012.04.006},
pmid = {22561061},
issn = {1095-8274},
mesh = {Aged ; Amino Acid Sequence ; Archaea/genetics/isolation &amp; purification ; Archaeal Proteins/*genetics ; Conserved Sequence ; Dental Plaque/*microbiology ; Evolution, Molecular ; Female ; Humans ; Likelihood Functions ; Male ; Middle Aged ; Molecular Sequence Data ; Molecular Typing ; Periodontitis/microbiology ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Ribosome Subunits, Small, Archaeal/*genetics ; Sequence Analysis, DNA ; Thermoplasmales/*genetics/isolation &amp; purification ; },
abstract = {Based on the molecular analysis of human subgingival plaque samples from 30 periodontitis patients a novel lineage of Archaea within the phylogenetic radiation of Thermoplasmatales was identified in 10% of cases. Co-occurrence of unique 16S rRNA gene and mcrA gene sequences suggests that this lineage corresponds to a hitherto unknown group of methanogens.},
}
@article {pmid22551871,
year = {2012},
author = {Kubo, K and Lloyd, KG and F Biddle, J and Amann, R and Teske, A and Knittel, K},
title = {Archaea of the Miscellaneous Crenarchaeotal Group are abundant, diverse and widespread in marine sediments.},
journal = {The ISME journal},
volume = {6},
number = {10},
pages = {1949-1965},
pmid = {22551871},
issn = {1751-7370},
mesh = {Archaea/*classification/genetics ; *Biodiversity ; DNA, Archaeal/genetics ; Estuaries ; Geologic Sediments/*microbiology ; Methane/metabolism ; *Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sulfates/metabolism ; },
abstract = {Members of the highly diverse Miscellaneous Crenarchaeotal Group (MCG) are globally distributed in various marine and continental habitats. In this study, we applied a polyphasic approach (rRNA slot blot hybridization, quantitative PCR (qPCR) and catalyzed reporter deposition FISH) using newly developed probes and primers for the in situ detection and quantification of MCG crenarchaeota in diverse types of marine sediments and microbial mats. In general, abundance of MCG (cocci, 0.4 μm) relative to other archaea was highest (12-100%) in anoxic, low-energy environments characterized by deeper sulfate depletion and lower microbial respiration rates (P=0.06 for slot blot and P=0.05 for qPCR). When studied in high depth resolution in the White Oak River estuary and Hydrate Ridge methane seeps, changes in MCG abundance relative to total archaea and MCG phylogenetic composition did not correlate with changes in sulfate reduction or methane oxidation with depth. In addition, MCG abundance did not vary significantly (P>0.1) between seep sites (with high rates of methanotrophy) and non-seep sites (with low rates of methanotrophy). This suggests that MCG are likely not methanotrophs. MCG crenarchaeota are highly diverse and contain 17 subgroups, with a range of intragroup similarity of 82 to 94%. This high diversity and widespread distribution in subsurface sediments indicates that this group is globally important in sedimentary processes.},
}
@article {pmid22495069,
year = {2012},
author = {Auguet, JC and Triadó-Margarit, X and Nomokonova, N and Camarero, L and Casamayor, EO},
title = {Vertical segregation and phylogenetic characterization of ammonia-oxidizing Archaea in a deep oligotrophic lake.},
journal = {The ISME journal},
volume = {6},
number = {9},
pages = {1786-1797},
pmid = {22495069},
issn = {1751-7370},
mesh = {Archaea/*classification/genetics/*physiology ; Biodiversity ; Genes, Archaeal/genetics ; Lakes/chemistry/*microbiology ; Molecular Sequence Data ; Oxidation-Reduction ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Freshwater habitats have been identified as one of the largest reservoirs of archaeal genetic diversity, with specific lineages of ammonia-oxidizing archaea (AOA) populations different from soils and seas. The ecology and biology of lacustrine AOA is, however, poorly known. In the present study, vertical changes in archaeal abundance by CARD-FISH, quantitative PCR (qPCR) analyses and identity by clone libraries were correlated with environmental parameters in the deep glacial high-altitude Lake Redon. The lake is located in the central Spanish Pyrenees where atmospheric depositions are the main source of reactive nitrogen. Strong correlations were found between abundance of thaumarchaeotal 16S rRNA gene, archaeal amoA gene and nitrite concentrations, indicating an ammonium oxidation potential by these microorganisms. The bacterial amoA gene was not detected. Three depths with potential ammonia-oxidation activity were unveiled along the vertical gradient, (i) on the top of the lake in winter-spring (that is, the 0 (o)C slush layers above the ice-covered sheet), (ii) at the thermocline and (iii) the bottom waters in summer-autumn. Overall, up to 90% of the 16S rRNA gene sequences matched Thaumarchaeota, mostly from both the Marine Group (MG) 1.1a (Nitrosoarchaeum-like) and the sister clade SAGMGC-1 (Nitrosotalea-like). Clone-libraries analysis showed the two clades changed their relative abundances with water depth being higher in surface and lower in depth for SAGMGC-1 than for MG 1.1a, reflecting a vertical phylogenetic segregation. Overall, the relative abundance and recurrent appearance of SAGMGC-1 suggests a significant environmental role of this clade in alpine lakes. These results expand the set of ecological and thermal conditions where Thaumarchaeota are distributed, unveiling vertical positioning in the water column as a key factor to understand the ecology of different thaumarchaeotal clades in lacustrine environments.},
}
@article {pmid22494458,
year = {2012},
author = {Wang, A and Wu, FZ and Yang, WQ and Wu, ZC and Wang, XX and Tan, B},
title = {Abundance and composition dynamics of soil ammonia-oxidizing archaea in an alpine fir forest on the eastern Tibetan Plateau of China.},
journal = {Canadian journal of microbiology},
volume = {58},
number = {5},
pages = {572-580},
doi = {10.1139/w2012-032},
pmid = {22494458},
issn = {1480-3275},
mesh = {Ammonia/*metabolism ; Archaea/genetics/*growth &amp; development/metabolism ; Bacteria/growth &amp; development/metabolism ; China ; DNA, Archaeal/isolation &amp; purification ; Ecosystem ; Nitrogen Cycle ; Phylogeny ; Seasons ; Soil ; *Soil Microbiology ; Trees/*microbiology ; },
abstract = {Real-time qPCR and clone library sequencing targeting amoA genes were used to investigate the seasonal dynamics of an ammonia-oxidizing archaea (AOA) community in an alpine fir forest in western China. AOA were detected at all sampling dates, and there were significant variations in archaeal amoA gene copy numbers (7.63 × 10(5) to 8.35 × 10(8) per gram of dry soil) throughout the nongrowing season. Compared with ammonia-oxidizing bacteria (AOB), the AOA displayed a higher abundance on the majority of sampling dates during the freeze-thaw period. All of the AOA sequences fell within soil and sediment lineages and were affiliated with 7 clusters. Compared with the other clusters, cluster 1 was more sensitive to low temperature and was the dominant group in August. In contrast, cluster 3 dominated the AOA community in winter and probably represents a group of cold-adapted archaea. Redundancy analysis (RDA) revealed that the seasonality of the AOA community was mainly attributed to changes in soil temperature and nutrient availability (e.g., dissolved organic nitrogen and carbon). Our results indicate that AOA exist in frozen soils in the alpine coniferous forest ecosystem of the eastern Tibetan Plateau. Moreover, soil temperature may directly and (or) indirectly affect AOA abundance and composition and may further influence the soil N cycle during the winter.},
}
@article {pmid22481976,
year = {2012},
author = {Cattani, C},
title = {On the existence of wavelet symmetries in archaea DNA.},
journal = {Computational and mathematical methods in medicine},
volume = {2012},
number = {},
pages = {673934},
pmid = {22481976},
issn = {1748-6718},
mesh = {Algorithms ; DNA, Archaeal/*chemistry/*genetics ; *Sequence Analysis, DNA ; *Wavelet Analysis ; },
abstract = {This paper deals with the complex unit roots representation of archea DNA sequences and the analysis of symmetries in the wavelet coefficients of the digitalized sequence. It is shown that even for extremophile archaea, the distribution of nucleotides has to fulfill some (mathematical) constraints in such a way that the wavelet coefficients are symmetrically distributed, with respect to the nucleotides distribution.},
}
@article {pmid22481885,
year = {2012},
author = {Santana, PB and Junior, RG and Alves, CN and Silva, JL and McCulloch, JA and Schneider, MP and da Costa da Silva, A},
title = {Diversity and three-dimensional structures of the alpha Mcr of the methanogenic Archaea from the anoxic region of Tucuruí Lake, in Eastern Brazilian Amazonia.},
journal = {Genetics and molecular biology},
volume = {35},
number = {1},
pages = {126-133},
pmid = {22481885},
issn = {1678-4685},
abstract = {Methanogenic archaeans are organisms of considerable ecological and biotechnological interest that produce methane through a restricted metabolic pathway, which culminates in the reaction catalyzed by the Methyl-coenzyme M reductase (Mcr) enzyme, and results in the release of methane. Using a metagenomic approach, the gene of the α subunit of mcr (mcrα) was isolated from sediment sample from an anoxic zone, rich in decomposing organic material, obtained from the Tucuruí hydroelectric dam reservoir in eastern Brazilian Amazonia. The partial nucleotide sequences obtained were 83 to 95% similar to those available in databases, indicating a low diversity of archaeans in the reservoir. Two orders were identified - the Methanomicrobiales, and a unique Operational Taxonomic Unit (OTU) forming a clade with the Methanosarcinales according to low bootstrap values. Homology modeling was used to determine the three-dimensional (3D) structures, for this the partial nucleotide sequence of the mcrα were isolated and translated on their partial amino acid sequences. The 3D structures of the archaean Mcrα observed in the present study varied little, and presented approximately 70% identity in comparison with the Mcrα of Methanopyrus klanderi. The results demonstrated that the community of methanogenic archaeans of the anoxic C1 region of the Tucurui reservoir is relatively homogeneous.},
}
@article {pmid22439800,
year = {2012},
author = {Miller, D and Xu, H and White, RH},
title = {A new subfamily of agmatinases present in methanogenic Archaea is Fe(II) dependent.},
journal = {Biochemistry},
volume = {51},
number = {14},
pages = {3067-3078},
doi = {10.1021/bi300039f},
pmid = {22439800},
issn = {1520-4995},
mesh = {Amino Acid Sequence ; Archaea/*enzymology/metabolism ; Archaeal Proteins/*chemistry/metabolism ; Binding Sites ; Disulfides/chemistry/metabolism ; Ferrous Compounds/*chemistry ; Methanococcus/*enzymology/metabolism ; Molecular Sequence Data ; Mutagenesis, Site-Directed ; Oxidation-Reduction ; Phylogeny ; Ureohydrolases/*chemistry/metabolism ; },
abstract = {Here we report that the Methanocaldococcus jannaschii enzyme derived from the MJ0309 gene is an Fe(II) dependent agmatinase (SpeB). This is the first report of an iron-dependent agmatinase. We demonstrate that aerobically isolated recombinant enzyme contains two disulfide bonds and only a trace amount of any metal and requires the presence of both dithiothreitol (DTT) and 4 equiv of Fe(II) for maximum activity. The DTT activation could be indicative of the presence of a redox system, which would regulate the activity of this as well as other enzymes in the methanogens. Site-directed mutagenesis of the four conserved cysteines C71, C136, C151, and C229 to alanine or serine showed that only the C71 and C151 mutants showed a significant drop in activity indicating that the disulfide bond responsible for regulating activity was likely between C136 and C229. We propose that the C71 and C151 cysteine thiols, produced by the DTT-dependent reduction of their disulfide, are two additional metal binding ligands that alter the metal specificity of the M. jannaschii agmatinase from Mn(II) to Fe(II).},
}
@article {pmid22429327,
year = {2012},
author = {Davidova, IA and Duncan, KE and Perez-Ibarra, BM and Suflita, JM},
title = {Involvement of thermophilic archaea in the biocorrosion of oil pipelines.},
journal = {Environmental microbiology},
volume = {14},
number = {7},
pages = {1762-1771},
doi = {10.1111/j.1462-2920.2012.02721.x},
pmid = {22429327},
issn = {1462-2920},
mesh = {Archaea/genetics/*metabolism ; Coculture Techniques ; Corrosion ; DNA, Archaeal/genetics ; Fatty Acids/biosynthesis ; Fermentation ; Ferric Compounds/*metabolism ; Hot Temperature ; Methane/biosynthesis ; Petroleum/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; },
abstract = {Two thermophilic archaea, strain PK and strain MG, were isolated from a culture enriched at 80°C from the inner surface material of a hot oil pipeline. Strain PK could ferment complex organic nitrogen sources (e.g. yeast extract, peptone, tryptone) and was able to reduce elemental sulfur (S°), Fe(3+) and Mn(4+) . Phylogenetic analysis revealed that the organism belonged to the order Thermococcales. Incubations of this strain with elemental iron (Fe°) resulted in the abiotic formation of ferrous iron and the accumulation of volatile fatty acids during yeast extract fermentation. The other isolate, strain MG, was a H(2) :CO(2) -utilizing methanogen, phylogenetically affiliated with the genus Methanothermobacter family. Co-cultures of the strains grew as aggregates that produced CH(4) without exogenous H(2) amendment. The co-culture produced the same suite but greater concentrations of fatty acids from yeast extract than did strain PK alone. Thus, the physiological characteristics of organisms both alone and in combination could conceivably contribute to pipeline corrosion. The Thermococcus strain PK could reduce elemental sulfur to sulfide, produce fatty acids and reduce ferric iron. The hydrogenotrophic methanogen strain MG enhanced fatty acid production by fermentative organisms but could not couple the dissolution Fe° with the consumption of water-derived H(2) like other methanogens.},
}
@article {pmid22409932,
year = {2012},
author = {Deatherage, BL and Cookson, BT},
title = {Membrane vesicle release in bacteria, eukaryotes, and archaea: a conserved yet underappreciated aspect of microbial life.},
journal = {Infection and immunity},
volume = {80},
number = {6},
pages = {1948-1957},
pmid = {22409932},
issn = {1098-5522},
support = {T32 AI055396/AI/NIAID NIH HHS/United States ; U19 AI090882/AI/NIAID NIH HHS/United States ; T32 AI55396/AI/NIAID NIH HHS/United States ; },
mesh = {Animals ; Archaea/*cytology/metabolism ; Bacteria/*cytology/metabolism ; Cell Membrane/physiology ; Eukaryota/*cytology/metabolism ; Exosomes/*physiology ; Fungi/cytology/metabolism ; Host-Pathogen Interactions ; Parasites/cytology/metabolism ; },
abstract = {Interaction of microbes with their environment depends on features of the dynamic microbial surface throughout cell growth and division. Surface modifications, whether used to acquire nutrients, defend against other microbes, or resist the pressures of a host immune system, facilitate adaptation to unique surroundings. The release of bioactive membrane vesicles (MVs) from the cell surface is conserved across microbial life, in bacteria, archaea, fungi, and parasites. MV production occurs not only in vitro but also in vivo during infection, underscoring the influence of these surface organelles in microbial physiology and pathogenesis through delivery of enzymes, toxins, communication signals, and antigens recognized by the innate and adaptive immune systems. Derived from a variety of organisms that span kingdoms of life and called by several names (membrane vesicles, outer membrane vesicles [OMVs], exosomes, shedding microvesicles, etc.), the conserved functions and mechanistic strategies of MV release are similar, including the use of ESCRT proteins and ESCRT protein homologues to facilitate these processes in archaea and eukaryotic microbes. Although forms of MV release by different organisms share similar visual, mechanistic, and functional features, there has been little comparison across microbial life. This underappreciated conservation of vesicle release, and the resulting functional impact throughout the tree of life, explored in this review, stresses the importance of vesicle-mediated processes throughout biology.},
}
@article {pmid22402398,
year = {2012},
author = {Thurber, AR and Levin, LA and Orphan, VJ and Marlow, JJ},
title = {Archaea in metazoan diets: implications for food webs and biogeochemical cycling.},
journal = {The ISME journal},
volume = {6},
number = {8},
pages = {1602-1612},
pmid = {22402398},
issn = {1751-7370},
mesh = {Animals ; Archaea/chemistry/*physiology ; Carbon Radioisotopes/analysis ; *Diet ; Fatty Acids/analysis ; *Food Chain ; Polychaeta/chemistry/growth &amp; development/*metabolism ; },
abstract = {Although the importance of trophic linkages, including 'top-down forcing', on energy flow and ecosystem productivity is recognized, the influence of metazoan grazing on Archaea and the biogeochemical processes that they mediate is unknown. Here, we test if: (1) Archaea provide a food source sufficient to allow metazoan fauna to complete their life cycle; (2) neutral lipid biomarkers (including crocetane) can be used to identify Archaea consumers; and (3) archaeal aggregates are a dietary source for methane seep metazoans. In the laboratory, we demonstrated that a dorvilleid polychaete, Ophryotrocha labronica, can complete its life cycle on two strains of Euryarchaeota with the same growth rate as when fed bacterial and eukaryotic food. Archaea were therefore confirmed as a digestible and nutritious food source sufficient to sustain metazoan populations. Both strains of Euryarchaeota used as food sources had unique lipids that were not incorporated into O. labronica tissues. At methane seeps, sulfate-reducing bacteria that form aggregations and live syntrophically with anaerobic-methane oxidizing Archaea contain isotopically and structurally unique fatty acids (FAs). These biomarkers were incorporated into tissues of an endolithofaunal dorvilleid polychaete species from Costa Rica (mean bulk δ(13)C=-92±4‰; polar lipids -116‰) documenting consumption of archaeal-bacterial aggregates. FA composition of additional soft-sediment methane seep species from Oregon and California provided evidence that consumption of archaeal-bacterial aggregates is widespread at methane seeps. This work is the first to show that Archaea are consumed by heterotrophic metazoans, a trophic process we coin as 'archivory'.},
}
@article {pmid22381407,
year = {2012},
author = {Pech, M and Nierhaus, KH},
title = {Identical binding sites--nonidentical functions in Eukarya and Archaea: the complex of aeIF6 with the large ribosomal subunit.},
journal = {Journal of molecular biology},
volume = {418},
number = {3-4},
pages = {131-133},
doi = {10.1016/j.jmb.2012.02.033},
pmid = {22381407},
issn = {1089-8638},
mesh = {Archaeal Proteins/*chemistry ; Cryoelectron Microscopy/*methods ; Methanobacteriaceae/*metabolism ; Prokaryotic Initiation Factors/*chemistry ; Ribosome Subunits, Large, Archaeal/*ultrastructure ; Ribosomes/*genetics ; },
}
@article {pmid22379100,
year = {2012},
author = {Bolduc, B and Shaughnessy, DP and Wolf, YI and Koonin, EV and Roberto, FF and Young, M},
title = {Identification of novel positive-strand RNA viruses by metagenomic analysis of archaea-dominated Yellowstone hot springs.},
journal = {Journal of virology},
volume = {86},
number = {10},
pages = {5562-5573},
pmid = {22379100},
issn = {1098-5514},
support = {//Intramural NIH HHS/United States ; },
mesh = {Amino Acid Sequence ; Archaea/*virology ; Archaeal Viruses/chemistry/classification/*genetics/*isolation &amp; purification ; Genome, Viral ; Hot Springs/microbiology/*virology ; Metagenomics/*methods ; Molecular Sequence Data ; Phylogeny ; RNA Viruses/chemistry/classification/*genetics/*isolation &amp; purification ; Sequence Alignment ; United States ; Viral Proteins/chemistry/genetics ; },
abstract = {There are no known RNA viruses that infect Archaea. Filling this gap in our knowledge of viruses will enhance our understanding of the relationships between RNA viruses from the three domains of cellular life and, in particular, could shed light on the origin of the enormous diversity of RNA viruses infecting eukaryotes. We describe here the identification of novel RNA viral genome segments from high-temperature acidic hot springs in Yellowstone National Park in the United States. These hot springs harbor low-complexity cellular communities dominated by several species of hyperthermophilic Archaea. A viral metagenomics approach was taken to assemble segments of these RNA virus genomes from viral populations isolated directly from hot spring samples. Analysis of these RNA metagenomes demonstrated unique gene content that is not generally related to known RNA viruses of Bacteria and Eukarya. However, genes for RNA-dependent RNA polymerase (RdRp), a hallmark of positive-strand RNA viruses, were identified in two contigs. One of these contigs is approximately 5,600 nucleotides in length and encodes a polyprotein that also contains a region homologous to the capsid protein of nodaviruses, tetraviruses, and birnaviruses. Phylogenetic analyses of the RdRps encoded in these contigs indicate that the putative archaeal viruses form a unique group that is distinct from the RdRps of RNA viruses of Eukarya and Bacteria. Collectively, our findings suggest the existence of novel positive-strand RNA viruses that probably replicate in hyperthermophilic archaeal hosts and are highly divergent from RNA viruses that infect eukaryotes and even more distant from known bacterial RNA viruses. These positive-strand RNA viruses might be direct ancestors of RNA viruses of eukaryotes.},
}
@article {pmid22363207,
year = {2012},
author = {Cadillo-Quiroz, H and Didelot, X and Held, NL and Herrera, A and Darling, A and Reno, ML and Krause, DJ and Whitaker, RJ},
title = {Patterns of gene flow define species of thermophilic Archaea.},
journal = {PLoS biology},
volume = {10},
number = {2},
pages = {e1001265},
pmid = {22363207},
issn = {1545-7885},
mesh = {Base Sequence ; *Ecosystem ; Gene Flow/*genetics ; *Genetic Speciation ; Genetics, Population ; High-Throughput Nucleotide Sequencing/methods ; Homologous Recombination/genetics ; Likelihood Functions ; Models, Genetic ; Molecular Sequence Data ; *Phenotype ; *Phylogeny ; Russia ; Species Specificity ; Sulfolobus/classification/*genetics ; },
abstract = {Despite a growing appreciation of their vast diversity in nature, mechanisms of speciation are poorly understood in Bacteria and Archaea. Here we use high-throughput genome sequencing to identify ongoing speciation in the thermoacidophilic Archaeon Sulfolobus islandicus. Patterns of homologous gene flow among genomes of 12 strains from a single hot spring in Kamchatka, Russia, demonstrate higher levels of gene flow within than between two persistent, coexisting groups, demonstrating that these microorganisms fit the biological species concept. Furthermore, rates of gene flow between two species are decreasing over time in a manner consistent with incipient speciation. Unlike other microorganisms investigated, we do not observe a relationship between genetic divergence and frequency of recombination along a chromosome, or other physical mechanisms that would reduce gene flow between lineages. Each species has its own genetic island encoding unique physiological functions and a unique growth phenotype that may be indicative of ecological specialization. Genetic differentiation between these coexisting groups occurs in large genomic "continents," indicating the topology of genomic divergence during speciation is not uniform and is not associated with a single locus under strong diversifying selection. These data support a model where species do not require physical barriers to gene flow but are maintained by ecological differentiation.},
}
@article {pmid22358840,
year = {2012},
author = {Becker, T and Franckenberg, S and Wickles, S and Shoemaker, CJ and Anger, AM and Armache, JP and Sieber, H and Ungewickell, C and Berninghausen, O and Daberkow, I and Karcher, A and Thomm, M and Hopfner, KP and Green, R and Beckmann, R},
title = {Structural basis of highly conserved ribosome recycling in eukaryotes and archaea.},
journal = {Nature},
volume = {482},
number = {7386},
pages = {501-506},
pmid = {22358840},
issn = {1476-4687},
support = {R37 GM059425/GM/NIGMS NIH HHS/United States ; T32 GM007445/GM/NIGMS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; R01 GM059425/GM/NIGMS NIH HHS/United States ; U19 AI083025/AI/NIAID NIH HHS/United States ; },
mesh = {ATP-Binding Cassette Transporters/chemistry/metabolism ; Cell Cycle Proteins/chemistry/metabolism ; Cryoelectron Microscopy ; Endoribonucleases/chemistry/metabolism ; *Evolution, Molecular ; Iron-Sulfur Proteins/chemistry/metabolism ; Models, Molecular ; Movement ; Multiprotein Complexes/chemistry/metabolism ; Nuclear Proteins/chemistry/metabolism ; Peptide Termination Factors/chemistry/metabolism ; Protein Binding ; Protein Stability ; Protein Structure, Tertiary ; Pyrococcus furiosus/*chemistry/metabolism ; Ribosomes/*chemistry/*metabolism/ultrastructure ; Saccharomyces cerevisiae/*chemistry/metabolism ; Saccharomyces cerevisiae Proteins/chemistry/metabolism ; },
abstract = {Ribosome-driven protein biosynthesis is comprised of four phases: initiation, elongation, termination and recycling. In bacteria, ribosome recycling requires ribosome recycling factor and elongation factor G, and several structures of bacterial recycling complexes have been determined. In the eukaryotic and archaeal kingdoms, however, recycling involves the ABC-type ATPase ABCE1 and little is known about its structural basis. Here we present cryo-electron microscopy reconstructions of eukaryotic and archaeal ribosome recycling complexes containing ABCE1 and the termination factor paralogue Pelota. These structures reveal the overall binding mode of ABCE1 to be similar to canonical translation factors. Moreover, the iron-sulphur cluster domain of ABCE1 interacts with and stabilizes Pelota in a conformation that reaches towards the peptidyl transferase centre, thus explaining how ABCE1 may stimulate peptide-release activity of canonical termination factors. Using the mechanochemical properties of ABCE1, a conserved mechanism in archaea and eukaryotes is suggested that couples translation termination to recycling, and eventually to re-initiation.},
}
@article {pmid22357279,
year = {2012},
author = {Pietilä, MK and Atanasova, NS and Manole, V and Liljeroos, L and Butcher, SJ and Oksanen, HM and Bamford, DH},
title = {Virion architecture unifies globally distributed pleolipoviruses infecting halophilic archaea.},
journal = {Journal of virology},
volume = {86},
number = {9},
pages = {5067-5079},
pmid = {22357279},
issn = {1098-5514},
mesh = {Archaea/*virology ; Archaeal Viruses/*physiology/ultrastructure ; Molecular Sequence Data ; Peptide Hydrolases/chemistry ; RNA, Ribosomal, 16S/chemistry ; Viral Envelope Proteins/chemistry ; Virion/*chemistry/physiology/ultrastructure ; },
abstract = {Our understanding of the third domain of life, Archaea, has greatly increased since its establishment some 20 years ago. The increasing information on archaea has also brought their viruses into the limelight. Today, about 100 archaeal viruses are known, which is a low number compared to the numbers of characterized bacterial or eukaryotic viruses. Here, we have performed a comparative biological and structural study of seven pleomorphic viruses infecting extremely halophilic archaea. The pleomorphic nature of this novel virion type was established by sedimentation analysis and cryo-electron microscopy. These nonlytic viruses form virions characterized by a lipid vesicle enclosing the genome, without any nucleoproteins. The viral lipids are unselectively acquired from host cell membranes. The virions contain two to three major structural proteins, which either are embedded in the membrane or form spikes distributed randomly on the external membrane surface. Thus, the most important step during virion assembly is most likely the interaction of the membrane proteins with the genome. The interaction can be driven by single-stranded or double-stranded DNA, resulting in the virions having similar architectures but different genome types. Based on our comparative study, these viruses probably form a novel group, which we define as pleolipoviruses.},
}
@article {pmid22355141,
year = {2012},
author = {Kalliomaa-Sanford, AK and Rodriguez-Castañeda, FA and McLeod, BN and Latorre-Roselló, V and Smith, JH and Reimann, J and Albers, SV and Barillà, D},
title = {Chromosome segregation in Archaea mediated by a hybrid DNA partition machine.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {109},
number = {10},
pages = {3754-3759},
pmid = {22355141},
issn = {1091-6490},
support = {BB/F012004/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Adenosine Triphosphatases/chemistry/genetics/*physiology ; Amino Acid Motifs ; Archaea/*genetics ; Archaeal Proteins/genetics/*physiology ; Binding Sites ; Biotinylation ; Chromosomes/*ultrastructure ; Cluster Analysis ; Conserved Sequence ; DNA/*genetics ; DNA-Binding Proteins/chemistry/genetics/*physiology ; Dimerization ; Gene Expression Regulation ; Genes, Archaeal ; Genome, Archaeal ; Protein Structure, Secondary ; Sulfolobus solfataricus/*genetics ; },
abstract = {Eukarya and, more recently, some bacteria have been shown to rely on a cytoskeleton-based apparatus to drive chromosome segregation. In contrast, the factors and mechanisms underpinning this fundamental process are underexplored in archaea, the third domain of life. Here we establish that the archaeon Sulfolobus solfataricus harbors a hybrid segrosome consisting of two interacting proteins, SegA and SegB, that play a key role in genome segregation in this organism. SegA is an ortholog of bacterial, Walker-type ParA proteins, whereas SegB is an archaea-specific factor lacking sequence identity to either eukaryotic or bacterial proteins, but sharing homology with a cluster of uncharacterized factors conserved in both crenarchaea and euryarchaea, the two major archaeal sub-phyla. We show that SegA is an ATPase that polymerizes in vitro and that SegB is a site-specific DNA-binding protein contacting palindromic sequences located upstream of the segAB cassette. SegB interacts with SegA in the presence of nucleotides and dramatically affects its polymerization dynamics. Our data demonstrate that SegB strongly stimulates SegA polymerization, possibly by promoting SegA nucleation and accelerating polymer growth. Increased expression levels of segAB resulted in severe growth and chromosome segregation defects, including formation of anucleate cells, compact nucleoids confined to one half of the cell compartment and fragmented nucleoids. The overall picture emerging from our findings indicates that the SegAB complex fulfills a crucial function in chromosome segregation and is the prototype of a DNA partition machine widespread across archaea.},
}
@article {pmid22352042,
year = {2011},
author = {Kawarabayasi, Y},
title = {[Uniqueness of the metabolic pathway of carbohydrate in thermophilic archaea].},
journal = {Seikagaku. The Journal of Japanese Biochemical Society},
volume = {83},
number = {12},
pages = {1117-1121},
pmid = {22352042},
issn = {0037-1017},
mesh = {Archaea/*enzymology/*metabolism ; *Carbohydrate Metabolism ; Energy Metabolism ; Hot Temperature ; Rhamnose/biosynthesis ; Sulfolobus/enzymology ; },
}
@article {pmid22339687,
year = {2012},
author = {Andrei, A&#x15e; and Banciu, HL and Oren, A},
title = {Living with salt: metabolic and phylogenetic diversity of archaea inhabiting saline ecosystems.},
journal = {FEMS microbiology letters},
volume = {330},
number = {1},
pages = {1-9},
doi = {10.1111/j.1574-6968.2012.02526.x},
pmid = {22339687},
issn = {1574-6968},
mesh = {Archaea/*classification/genetics/*physiology ; *Biodiversity ; Carbon/metabolism ; *Ecosystem ; Energy Metabolism ; Metabolic Networks and Pathways ; *Salinity ; Salts/*metabolism ; },
abstract = {Archaea that live at high salt concentrations are a phylogenetically diverse group of microorganisms. They include the heterotrophic haloarchaea (class Halobacteria) and some methanogenic Archaea, and they inhabit both oxic and anoxic environments. In spite of their common hypersaline environment, halophilic archaea are surprisingly diverse in their nutritional demands, range of carbon sources degraded (including hydrocarbons and aromatic compounds) and metabolic pathways. The recent discovery of a new group of extremely halophilic Euryarchaeota, the yet uncultured Nanohaloarchaea, shows that the archaeal diversity and metabolic variability in hypersaline environments is higher than hitherto estimated.},
}
@article {pmid22339597,
year = {2011},
author = {Murina, VN and Nikulin, AD},
title = {RNA-binding Sm-like proteins of bacteria and archaea. similarity and difference in structure and function.},
journal = {Biochemistry. Biokhimiia},
volume = {76},
number = {13},
pages = {1434-1449},
doi = {10.1134/S0006297911130050},
pmid = {22339597},
issn = {1608-3040},
mesh = {Amino Acid Sequence ; *Archaea ; Archaeal Proteins/chemistry/genetics/*physiology ; *Bacteria ; Bacterial Proteins/chemistry/genetics/*physiology ; Binding Sites ; Conserved Sequence ; Host Factor 1 Protein/chemistry/genetics/physiology ; Molecular Sequence Data ; Protein Conformation ; RNA Stability ; snRNP Core Proteins/chemistry/physiology ; },
abstract = {RNA-binding proteins play a significant role in many processes of RNA metabolism, such as splicing and processing, regulation of DNA transcription and RNA translation, etc. Among the great number of RNA-binding proteins, so-called RNA-chaperones occupy an individual niche; they were named for their ability to assist RNA molecules to gain their accurate native spatial structure. When binding with RNAs, they possess the capability of altering (melting) their secondary structure, thus providing a possibility for formation of necessary intramolecular contacts between individual RNA sites for proper folding. These proteins also have an additional helper function in RNA-RNA and RNA-protein interactions. Members of such class of the RNA-binding protein family are Sm and Sm-like proteins (Sm-Like, LSm). The presence of these proteins in bacteria, archaea, and eukaryotes emphasizes their biological significance. These proteins are now attractive for researchers because of their implication in many processes associated with RNAs in bacterial and archaeal cells. This review is focused on a comparison of architecture of bacterial and archaeal LSm proteins and their interaction with different RNA molecules.},
}
@article {pmid22337052,
year = {2012},
author = {Wiedenheft, B and Sternberg, SH and Doudna, JA},
title = {RNA-guided genetic silencing systems in bacteria and archaea.},
journal = {Nature},
volume = {482},
number = {7385},
pages = {331-338},
pmid = {22337052},
issn = {1476-4687},
support = {//Howard Hughes Medical Institute/United States ; },
mesh = {Archaea/*genetics ; Bacteria/*genetics ; *Gene Expression Regulation, Bacterial ; *Gene Silencing ; Models, Molecular ; RNA Interference ; RNA, Archaeal/biosynthesis/chemistry/genetics/*metabolism ; RNA, Bacterial/biosynthesis/chemistry/genetics/*metabolism ; },
abstract = {Clustered regularly interspaced short palindromic repeat (CRISPR) are essential components of nucleic-acid-based adaptive immune systems that are widespread in bacteria and archaea. Similar to RNA interference (RNAi) pathways in eukaryotes, CRISPR-mediated immune systems rely on small RNAs for sequence-specific detection and silencing of foreign nucleic acids, including viruses and plasmids. However, the mechanism of RNA-based bacterial immunity is distinct from RNAi. Understanding how small RNAs are used to find and destroy foreign nucleic acids will provide new insights into the diverse mechanisms of RNA-controlled genetic silencing systems.},
}
@article {pmid22329974,
year = {2012},
author = {Makarova, KS and Koonin, EV and Kelman, Z},
title = {The CMG (CDC45/RecJ, MCM, GINS) complex is a conserved component of the DNA replication system in all archaea and eukaryotes.},
journal = {Biology direct},
volume = {7},
number = {},
pages = {7},
pmid = {22329974},
issn = {1745-6150},
support = {//Intramural NIH HHS/United States ; },
mesh = {Amino Acid Sequence ; Archaea/*genetics/metabolism ; Archaeal Proteins/genetics/*metabolism ; Chromosomal Proteins, Non-Histone/chemistry/genetics ; DNA Helicases/genetics/*metabolism ; *DNA Replication ; DNA-Binding Proteins/genetics/metabolism ; Eukaryota/*genetics/metabolism ; Evolution, Molecular ; Genes, Archaeal ; Molecular Sequence Data ; Phylogeny ; Protein Structure, Secondary ; Sequence Alignment ; },
abstract = {BACKGROUND: In eukaryotes, the CMG (CDC45, MCM, GINS) complex containing the replicative helicase MCM is a key player in DNA replication. Archaeal homologs of the eukaryotic MCM and GINS proteins have been identified but until recently no homolog of the CDC45 protein was known. Two recent developments, namely the discovery of archaeal GINS-associated nuclease (GAN) that belongs to the RecJ family of the DHH hydrolase superfamily and the demonstration of homology between the DHH domains of CDC45 and RecJ, show that at least some Archaea possess a full complement of homologs of the CMG complex subunits. Here we present the results of in-depth phylogenomic analysis of RecJ homologs in archaea.<br><br>RESULTS: We confirm and extend the recent hypothesis that CDC45 is the eukaryotic ortholog of the bacterial and archaeal RecJ family nucleases. At least one RecJ homolog was identified in all sequenced archaeal genomes, with the single exception of Caldivirga maquilingensis. These proteins include previously unnoticed remote RecJ homologs with inactivated DHH domain in Thermoproteales. Combined with phylogenetic tree reconstruction of diverse eukaryotic, archaeal and bacterial DHH subfamilies, this analysis yields a complex scenario of RecJ family evolution in Archaea which includes independent inactivation of the nuclease domain in Crenarchaeota and Halobacteria, and loss of this domain in Methanococcales.<br><br>CONCLUSIONS: The archaeal complex of a CDC45/RecJ homolog, MCM and GINS is homologous and most likely functionally analogous to the eukaryotic CMG complex, and appears to be a key component of the DNA replication machinery in all Archaea. It is inferred that the last common archaeo-eukaryotic ancestor encoded a CMG complex that contained an active nuclease of the RecJ family. The inactivated RecJ homologs in several archaeal lineages most likely are dedicated structural components of replication complexes.},
}
@article {pmid22327114,
year = {2012},
author = {Urakawa, H and Garcia, JC and Barreto, PD and Molina, GA and Barreto, JC},
title = {A sensitive crude oil bioassay indicates that oil spills potentially induce a change of major nitrifying prokaryotes from the archaea to the bacteria.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {164},
number = {},
pages = {42-45},
doi = {10.1016/j.envpol.2012.01.009},
pmid = {22327114},
issn = {1873-6424},
mesh = {Archaea/growth &amp; development/*metabolism ; Bacteria/growth &amp; development/*metabolism ; Biological Assay ; Environmental Monitoring/*methods ; Nitrogen/analysis/*metabolism ; Petroleum Pollution/*analysis/statistics &amp; numerical data ; Seawater/chemistry/*microbiology ; Water Microbiology ; Water Pollutants, Chemical/analysis ; },
abstract = {The sensitivity of nitrifiers to crude oil released by the BP Deepwater Horizon oil spill in Gulf of Mexico was examined using characterized ammonia-oxidizing bacteria and archaea to develop a bioassay and to gain further insight into the ecological response of these two groups of microorganisms to marine oil spills. Inhibition of nitrite production was observed among all the tested ammonia-oxidizing organisms at 100 ppb crude oil. Nitrosopumilus maritimus, a cultured representative of the abundant Marine Group I Archaea, showed 20% inhibition at 1 ppb, a much greater degree of sensitivity to petroleum than the tested ammonia-oxidizing and heterotrophic bacteria. The differing susceptibility may have ecological significance since a shift to bacterial dominance in response to an oil spill could potentially persist and alter trophic interactions influenced by availability of different nitrogen species.},
}
@article {pmid22326171,
year = {2012},
author = {Mansfield, JM and Campbell, JH and Bhandari, AR and Jesionowski, AM and Vickerman, MM},
title = {Molecular analysis of 16S rRNA genes identifies potentially periodontal pathogenic bacteria and archaea in the plaque of partially erupted third molars.},
journal = {Journal of oral and maxillofacial surgery : official journal of the American Association of Oral and Maxillofacial Surgeons},
volume = {70},
number = {7},
pages = {1507-14.e1-6},
doi = {10.1016/j.joms.2011.09.049},
pmid = {22326171},
issn = {1531-5053},
mesh = {Archaea/*classification/genetics ; Bacteroides/genetics/isolation &amp; purification ; Dental Plaque/*microbiology ; Fusobacterium/genetics/isolation &amp; purification ; Fusobacterium nucleatum/genetics/isolation &amp; purification ; Gram-Negative Anaerobic Straight, Curved, and Helical Rods/classification/genetics/isolation &amp; purification ; Gram-Negative Bacteria/*classification/genetics ; Humans ; Incisor/microbiology ; Methanobrevibacter/genetics/isolation &amp; purification ; Molar, Third/*microbiology ; Pericoronitis/*microbiology ; Phylogeny ; Porphyromonas endodontalis/genetics/isolation &amp; purification ; Prevotella/genetics/isolation &amp; purification ; RNA, Archaeal/*analysis ; RNA, Bacterial/*analysis ; RNA, Ribosomal, 16S/*analysis ; Streptococcus/genetics/isolation &amp; purification ; Tooth Eruption ; Treponema denticola/genetics/isolation &amp; purification ; },
abstract = {PURPOSE: Small subunit rRNA sequencing and phylogenetic analysis were used to identify cultivable and uncultivable microorganisms present in the dental plaque of symptomatic and asymptomatic partially erupted third molars to determine the prevalence of putative periodontal pathogens in pericoronal sites.<br><br>MATERIALS AND METHODS: Template DNA prepared from subgingival plaque collected from partially erupted symptomatic and asymptomatic mandibular third molars and healthy incisors was used in polymerase chain reaction with broad-range oligonucleotide primers to amplify 16S rRNA bacterial and archaeal genes. Amplicons were cloned, sequenced, and compared with known nucleotide sequences in online databases to identify the microorganisms present.<br><br>RESULTS: Two thousand three hundred two clones from the plaque of 12 patients carried bacterial sequences from 63 genera belonging to 11 phyla, including members of the uncultivable TM7, SR1, and Chloroflexi, and difficult-to-cultivate Synergistetes and Spirochaetes. Dialister invisus, Filifactor alocis, Fusobacterium nucleatum, Porphyromonas endodontalis, Prevotella denticola, Tannerella forsythia, and Treponema denticola, which have been associated with periodontal disease, were found in significantly greater abundance in pericoronal compared with incisor sites. Dialister invisus and F nucleatum were found in greater abundance in sites exhibiting clinical symptoms. The archaeal species, Methanobrevibacter oralis, which has been associated with severe periodontitis, was found in 3 symptomatic patients.<br><br>CONCLUSIONS: These findings have provided new insights into the complex microbiota of pericoronitis. Several bacterial and archaeal species implicated in periodontal disease were recovered in greater incidence and abundance from the plaque of partially erupted third molars compared with incisors, supporting the hypothesis that the pericoronal region may provide a favored niche for periodontal pathogens in otherwise healthy mouths.},
}
@article {pmid22303679,
year = {2011},
author = {Shen, JP and Zhang, LM and He, JP},
title = {[Abundance of archaea, crenarchaea and bacteria in selected agricultural soils of China].},
journal = {Ying yong sheng tai xue bao = The journal of applied ecology},
volume = {22},
number = {11},
pages = {2996-3002},
pmid = {22303679},
issn = {1001-9332},
mesh = {Archaea/genetics/*growth &amp; development ; Bacteria/genetics/*growth &amp; development ; China ; Crenarchaeota/genetics/*growth &amp; development ; Crops, Agricultural/*growth &amp; development ; RNA, Ribosomal, 16S/analysis ; Real-Time Polymerase Chain Reaction ; *Soil Microbiology ; },
abstract = {Eukaryota, bacteria and archaea are the three domains of life. As the third domain of life, archaea has been found not only in extreme environments such as high-temperature, high-saline, and extremely acid habitats, but also in moderate environments including ocean, lake and soil, which implies that archaea may contribute greatly to various ecosystems. By targeting the 16S rRNA gene with real-time PCR approaches, this paper studied the abundance of archaea, crenarchaea and bacteria from two agricultural soil profiles and two long-term fertilization stations Qiyang (QY) and Fengqiu (FQ). The 16S rRNA gene copy number of crenarchaea was 1-2 orders of magnitude lower than that of archaea, and the order of these three groups was crenarchaea < archaea < bacteria. The ratios of both archaea and crenarchaea to bacteria increased with soil depth. The abundance of archaea and crenarchaea had significantly different responses to different fertilization treatments. In QY station, the copy numbers of archaeal and bacterial 16S rRNA gene had significant positive correlations with soil pH (r = 0.850, P < 0.01 and r = 0.676, P < 0.05, respectively); in FQ station, all the 16S rRNA gene copy numbers of archaea, crenarchaea and bacteria had no significant correlations with soil pH, but significantly correlated with soil organic matter (r = 0.783, P < 0.05; r = 0. 827, P < 0.05; r = 0.767, P < 0.05, respectively). To understand the distribution of archaea and crenarchaea in agricultural soil could provide important information to evaluate their ecological functions in soil ecosystem and element cycling.},
}
@article {pmid22293502,
year = {2012},
author = {Su, D and Ojo, TT and Söll, D and Hohn, MJ},
title = {Selenomodification of tRNA in archaea requires a bipartite rhodanese enzyme.},
journal = {FEBS letters},
volume = {586},
number = {6},
pages = {717-721},
pmid = {22293502},
issn = {1873-3468},
support = {1RC2GM092602-01/GM/NIGMS NIH HHS/United States ; R37 GM022854/GM/NIGMS NIH HHS/United States ; R01 GM022854/GM/NIGMS NIH HHS/United States ; RC2 GM092602/GM/NIGMS NIH HHS/United States ; GM22854/GM/NIGMS NIH HHS/United States ; R01 GM022854-37/GM/NIGMS NIH HHS/United States ; },
mesh = {Amino Acid Sequence ; Animals ; Archaeal Proteins/chemistry/classification/genetics/*metabolism ; Ligases/chemistry/classification/genetics/metabolism ; Methanococcus/*genetics/metabolism ; Models, Molecular ; Molecular Sequence Data ; Organoselenium Compounds/chemistry/*metabolism ; Phylogeny ; Protein Structure, Tertiary ; RNA, Transfer/classification/genetics/*metabolism ; Selenium/*metabolism ; Sequence Alignment ; Thiosulfate Sulfurtransferase/chemistry/genetics/*metabolism ; Uridine/*analogs &amp; derivatives/chemistry/genetics/metabolism ; },
abstract = {5-Methylaminomethyl-2-selenouridine (mnm(5)Se(2)U) is found in the first position of the anticodon in certain tRNAs from bacteria, archaea and eukaryotes. This selenonucleoside is formed in Escherichia coli from the corresponding thionucleoside mnm(5)S(2)U by the monomeric enzyme YbbB. This nucleoside is present in the tRNA of Methanococcales, yet the corresponding 2-selenouridine synthase is unknown in archaea and eukaryotes. Here we report that a bipartite ybbB ortholog is present in all members of the Methanococcales. Gene deletions in Methanococcus maripaludis and in vitro activity assays confirm that the two proteins act in trans to form in tRNA a selenonucleoside, presumably mnm(5)Se(2)U. Phylogenetic data suggest a primal origin of seleno-modified tRNAs.},
}
@article {pmid22286497,
year = {2012},
author = {Siboni, N and Ben-Dov, E and Sivan, A and Kushmaro, A},
title = {Geographic specific coral-associated ammonia-oxidizing archaea in the northern Gulf of Eilat (Red Sea).},
journal = {Microbial ecology},
volume = {64},
number = {1},
pages = {18-24},
pmid = {22286497},
issn = {1432-184X},
mesh = {Ammonia/*metabolism ; Animals ; Anthozoa/*microbiology ; Archaea/classification/genetics/*isolation &amp; purification/*metabolism ; Archaeal Proteins/genetics ; Biodiversity ; Geography ; Indian Ocean ; Molecular Sequence Data ; Oxidation-Reduction ; Oxidoreductases/genetics ; Phylogeny ; },
abstract = {Coral holobionts are densely populated with microorganisms that are essential for their well-being. Here we compared the diversity of the archaeal ammonia monooxygenase alpha subunit (amoA) gene from three coral genera, Acanthastrea sp., Favia sp., and Fungia granulosa, from the Gulf of Eilat, Red Sea. At 99% similarity, archaeal amoA from the three coral genera shared 71% of their cloned sequences, while the Favia and Acanthastrea presented a few genus-specific clones. In addition, the sequences retrieved in our samples displayed lower similarity to amoA sequences previously found in association with other coral species from different geographic regions. This finding suggests that the populations of ammonia-oxidizing archaea are less host-specific and more geographically dependent.},
}
@article {pmid22267662,
year = {2012},
author = {Xu, M and Schnorr, J and Keibler, B and Simon, HM},
title = {Comparative analysis of 16S rRNA and amoA genes from archaea selected with organic and inorganic amendments in enrichment culture.},
journal = {Applied and environmental microbiology},
volume = {78},
number = {7},
pages = {2137-2146},
pmid = {22267662},
issn = {1098-5336},
mesh = {Archaea/classification/genetics/*isolation &amp; purification/metabolism ; Autotrophic Processes ; Culture Media ; DNA, Archaeal ; DNA, Bacterial/analysis/isolation &amp; purification ; Genes, rRNA ; Inorganic Chemicals/chemistry/metabolism ; Solanum lycopersicum/*microbiology ; Molecular Sequence Data ; Nitrification ; Organic Chemicals/chemistry/metabolism ; Oxidoreductases/*genetics ; Plant Roots/*microbiology ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; },
abstract = {We took advantage of a plant-root enrichment culture system to characterize mesophilic soil archaea selected through the use of organic and inorganic amendments. Comparative analysis of 16S rRNA and amoA genes indicated that specific archaeal clades were selected under different conditions. Three amoA sequence clades were identified, while for a fourth group, identified by 16S rRNA gene analysis alone and referred to as the "root" clade, we detected no corresponding amoA gene. The amoA-containing archaea were present in media with either organic or inorganic amendments, whereas archaea representing the root clade were present only when organic amendment was used. Analysis of amoA gene abundance and expression, together with nitrification-coupled growth assays, indicated potential growth by autotrophic ammonia oxidation for members of two group 1.1b clades. Increased abundance of one of these clades, however, also occurred upon the addition of organic amendment. Finally, although amoA-containing group 1.1a archaea were present in enrichments, we detected neither expression of amoA genes nor evidence for nitrification-coupled growth of these organisms. These data support a model of a diverse metabolic community in mesophilic soil archaea that is just beginning to be characterized.},
}
@article {pmid22263906,
year = {2012},
author = {Krieger, JR and Kourtev, PS},
title = {Detection of methanogenic archaea in the pitchers of the Northern pitcher plant (Sarracenia purpurea).},
journal = {Canadian journal of microbiology},
volume = {58},
number = {2},
pages = {189-194},
doi = {10.1139/w11-117},
pmid = {22263906},
issn = {1480-3275},
mesh = {Animals ; Archaea/*growth &amp; development/isolation &amp; purification ; Base Sequence ; DNA, Archaeal ; Ecosystem ; Methane/*metabolism ; Molecular Sequence Data ; Sarraceniaceae/*microbiology/physiology ; Symbiosis ; },
abstract = {Carnivorous plants of the genus Sarracenia rely on microorganisms in their pitchers to decompose drowned insects. The environment inside pitchers is considered to be aerobic; however, there might be zones, such as at the bottom of the pitcher, where anaerobic conditions develop. Samples of the sediment at the bottom of Sarracenia purpurea pitchers were analyzed for the presence of archaea, using PCR and sequencing of the 16S rRNA gene. Archaeal DNA was detected in 20% of sampled pitchers. All sequences were closely related to Methanobrevibacter . Therefore, pitchers may contain anoxic zones inhabited by methanogens.},
}
@article {pmid22260087,
year = {2012},
author = {Schick, M and Xie, X and Ataka, K and Kahnt, J and Linne, U and Shima, S},
title = {Biosynthesis of the iron-guanylylpyridinol cofactor of [Fe]-hydrogenase in methanogenic archaea as elucidated by stable-isotope labeling.},
journal = {Journal of the American Chemical Society},
volume = {134},
number = {6},
pages = {3271-3280},
doi = {10.1021/ja211594m},
pmid = {22260087},
issn = {1520-5126},
mesh = {Acetates/chemistry ; Archaea/*metabolism ; Carbon/chemistry ; Carbon Dioxide/chemistry ; Carbon Isotopes/chemistry ; Cysteine/chemistry ; Hydrogenase/*chemistry ; Iron/*chemistry ; Iron-Sulfur Proteins/*chemistry ; Isotope Labeling/*methods ; Ligands ; Magnetic Resonance Spectroscopy/methods ; Methane/*chemistry ; Models, Chemical ; Protons ; Spectrometry, Mass, Electrospray Ionization/methods ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods ; Spectrophotometry, Infrared/methods ; },
abstract = {[Fe]-hydrogenase catalyzes the reversible hydride transfer from H(2) to methenyltetrahydromethanoptherin, which is an intermediate in methane formation from H(2) and CO(2) in methanogenic archaea. The enzyme harbors a unique active site iron-guanylylpyridinol (FeGP) cofactor, in which a low-spin Fe(II) is coordinated by a pyridinol-N, an acyl group, two carbon monoxide, and the sulfur of the enzyme's cysteine. Here, we studied the biosynthesis of the FeGP cofactor by following the incorporation of (13)C and (2)H from labeled precursors into the cofactor in growing methanogenic archaea and by subsequent NMR, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS), electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI-FT-ICR-MS) and IR analysis of the isolated cofactor and reference compounds. The pyridinol moiety of the cofactor was found to be synthesized from three C-1 of acetate, two C-2 of acetate, two C-1 of pyruvate, one carbon from the methyl group of l-methionine, and one carbon directly from CO(2). The metabolic origin of the two CO-ligands was CO(2) rather than C-1 or C-2 of acetate or pyruvate excluding that the two CO are derived from dehydroglycine as has previously been shown for the CO-ligands in [FeFe]-hydrogenases. A formation of CO from CO(2) via direct reduction catalyzed by a nickel-dependent CO dehydrogenase or from formate could also be excluded. When the cells were grown in the presence of (13)CO, the two CO-ligands and the acyl group became (13)C-labeled, indicating either that free CO is an intermediate in their synthesis or that free CO can exchange with these iron-bound ligands. Based on these findings, we propose pathways for how the FeGP cofactor might be synthesized.},
}
@article {pmid22247169,
year = {2012},
author = {Herzog, B and Wirth, R},
title = {Swimming behavior of selected species of Archaea.},
journal = {Applied and environmental microbiology},
volume = {78},
number = {6},
pages = {1670-1674},
pmid = {22247169},
issn = {1098-5336},
mesh = {Archaea/*physiology ; *Locomotion ; *Water Microbiology ; },
abstract = {The swimming behavior of Bacteria has been studied extensively, at least for some species like Escherichia coli. In contrast, almost no data have been published for Archaea on this topic. In a systematic study we asked how the archaeal model organisms Halobacterium salinarum, Methanococcus voltae, Methanococcus maripaludis, Methanocaldococcus jannaschii, Methanocaldococcus villosus, Pyrococcus furiosus, and Sulfolobus acidocaldarius swim and which swimming behavior they exhibit. The two Euryarchaeota M. jannaschii and M. villosus were found to be, by far, the fastest organisms reported up to now, if speed is measured in bodies per second (bps). Their swimming speeds, at close to 400 and 500 bps, are much higher than the speed of the bacterium E. coli or of a very fast animal, like the cheetah, each with a speed of ca. 20 bps. In addition, we observed that two different swimming modes are used by some Archaea. They either swim very rapidly, in a more or less straight line, or they exhibit a slower kind of zigzag swimming behavior if cells are in close proximity to the surface of the glass capillary used for observation. We argue that such a "relocate-and-seek" behavior enables the organisms to stay in their natural habitat.},
}
@article {pmid22229263,
year = {2012},
author = {Dridi, B and Raoult, D and Drancourt, M},
title = {Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry identification of Archaea: towards the universal identification of living organisms.},
journal = {APMIS : acta pathologica, microbiologica, et immunologica Scandinavica},
volume = {120},
number = {2},
pages = {85-91},
doi = {10.1111/j.1600-0463.2011.02833.x},
pmid = {22229263},
issn = {1600-0463},
mesh = {Archaea/*chemistry/*classification/genetics/isolation &amp; purification ; Archaeal Proteins/*analysis ; Phylogeny ; Reproducibility of Results ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/*methods ; },
abstract = {Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) identification of Archaea has been limited to some environmental extremophiles belonging to distant taxa. We developed a specific protocol for MALDI-TOF-MS identification of Archaea and applied it to seven environmental human-associated Methanobrevibacter smithii, Methanobrevibacter oralis, Methanosphaera stadtmanae, and the recently described Methanomassiliicoccus luminyensi Archaea. After mechanical lyse, we observed a unique protein profile for each organisms comprising 7-24 peaks ranging from 3,015 to 10,632 Da with a high quality score of 7.38 ± 1.26. Profiles were reproducible over successive experiments performed at 1, 2, and 3-week growth durations and unambiguously distinguished the Archaea from all of the 3,995 bacterial spectra in the Brüker database. After the incorporation of the determined profiles into a local database, archaeal isolates were blindly identified within 10 min with an identification score of 1.9-2.3. The MALDI-TOF-MS-based clustering of these archaeal organisms was consistent with their 16S rDNA sequence-based phylogeny. These data prove that MALDI-TOF-MS profiling could be used as a first-line technique for the identification of human Archaea. In complement to previous reports for animal cells, Bacteria and giant viruses, MALDI-TOF-MS therefore appears as a universal method for the identification of living unicellular and multicellular organisms.},
}
@article {pmid22224831,
year = {2012},
author = {Isobe, K and Koba, K and Suwa, Y and Ikutani, J and Fang, Y and Yoh, M and Mo, J and Otsuka, S and Senoo, K},
title = {High abundance of ammonia-oxidizing archaea in acidified subtropical forest soils in southern China after long-term N deposition.},
journal = {FEMS microbiology ecology},
volume = {80},
number = {1},
pages = {193-203},
doi = {10.1111/j.1574-6941.2011.01294.x},
pmid = {22224831},
issn = {1574-6941},
mesh = {Ammonia/*metabolism ; Archaea/*classification/genetics/metabolism ; Autotrophic Processes ; Bacteria/classification/genetics/metabolism ; Base Sequence ; China ; Climate ; Molecular Sequence Data ; Nitrification ; Nitrites/metabolism ; Oxidation-Reduction ; Oxidoreductases/analysis/genetics/metabolism ; Soil/chemistry ; *Soil Microbiology ; Trees ; },
abstract = {Nitrification has been believed to be performed only by autotrophic ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB) until the recent discovery of ammonia-oxidizing archaea (AOA). Meanwhile, it has been questioned whether AOB are significantly responsible for NH(3) oxidation in acidic forest soils. Here, we investigated nitrifying communities and their activity in highly acidified soils of three subtropical forests in southern China that had received chronic high atmospheric N deposition. Nitrifying communities were analyzed using PCR- and culture (most probable number)-based approaches. Nitrification activity was analyzed by measuring gross soil nitrification rates using a (15) N isotope dilution technique. AOB were not detected in the three forest soils: neither via PCR of 16S rRNA and ammonia monooxygenase (amoA) genes nor via culture-based approaches. In contrast, an extraordinary abundance of the putative archaeal amoA was detected (3.2 × 10(8) -1.2 × 10(9) g soil(-1)). Moreover, this abundance was correlated with gross soil nitrification rates. This indicates that amoA-possessing archaea rather than bacteria were predominantly responsible for nitrification of the soils. Furthermore, sequences of the genus Nitrospira, a dominant group of soil NOB, were detected. Thus, nitrification of acidified subtropical forest soils in southern China could be performed by a combination of AOA and NOB.},
}
@article {pmid22221383,
year = {2012},
author = {St-Pierre, B and Wright, AD},
title = {Molecular analysis of methanogenic archaea in the forestomach of the alpaca (Vicugna pacos).},
journal = {BMC microbiology},
volume = {12},
number = {},
pages = {1},
pmid = {22221383},
issn = {1471-2180},
mesh = {Animals ; Archaea/*classification/genetics/*isolation &amp; purification/metabolism ; *Biota ; Camelids, New World/*microbiology ; Cluster Analysis ; DNA, Archaeal/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Gastrointestinal Tract/*microbiology ; Male ; Methane/*metabolism ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; },
abstract = {BACKGROUND: Methanogens that populate the gastrointestinal tract of livestock ruminants contribute significantly to methane emissions from the agriculture industry. There is a great need to analyze archaeal microbiomes from a broad range of host species in order to establish causal relationships between the structure of methanogen communities and their potential for methane emission. In this report, we present an investigation of methanogenic archaeal populations in the foregut of alpacas.<br><br>RESULTS: We constructed individual 16S rRNA gene clone libraries from five sampled animals and recovered a total of 947 sequences which were assigned to 51 species-level OTUs. Individuals were found to each have between 21 and 27 OTUs, of which two to six OTUs were unique. As reported in other host species, Methanobrevibacter was the dominant genus in the alpaca, representing 88.3% of clones. However, the alpaca archaeal microbiome was different from other reported host species, as clones showing species-level identity to Methanobrevibacter millerae were the most abundant.<br><br>CONCLUSION: From our analysis, we propose a model to describe the population structure of Methanobrevibacter-related methanogens in the alpaca and in previously reported host species, which may contribute in unraveling the complexity of symbiotic archaeal communities in herbivores.},
}
@article {pmid22219037,
year = {2012},
author = {Luque, R and González-Domenech, CM and Llamas, I and Quesada, E and Béjar, V},
title = {Diversity of culturable halophilic archaea isolated from Rambla Salada, Murcia (Spain).},
journal = {Extremophiles : life under extreme conditions},
volume = {16},
number = {2},
pages = {205-213},
pmid = {22219037},
issn = {1433-4909},
mesh = {Archaea/*genetics ; Biodiversity ; DNA, Archaeal/genetics ; Fermentation ; Gene Expression Regulation, Archaeal ; *Genetic Variation ; Halobacteriaceae/genetics ; Halobacteriales/genetics ; Oxygen Consumption ; Phenotype ; Phylogeny ; Polymerase Chain Reaction/methods ; RNA, Ribosomal, 16S/genetics/metabolism ; Sodium Chloride/chemistry ; Spain ; Water Microbiology ; },
abstract = {We have studied the diversity of culturable halophilic Archaea at Rambla Salada, Murcia (south-eastern Spain). We made 8 samplings at different places in this habitat during the years 2006 and 2007 and isolated a total of 49 strains, which were identified by means of phenotypic tests and the hypervariable V1-V3 region of the 16S rRNA gene sequences (around 500 bp). The ribosomal data showed that the isolates belonged to 12 genera within the Halobacteriaceae family, with Haloferax and Natrinema being the most abundant. Five strains showed less than 97% sequence identity with validly described species and may well represent new taxa. All the strains grew best with around 25% w/v salts, required high concentrations of NaCl and magnesium and produced red to pink colonies. They were facultative anaerobes with both respiratory and fermentative metabolisms. The diversity of the archaeal community was analysed with the MOTHUR package. We identified 14 OTUs at the 3% genetic distance level and found quite high diversity. Rarefaction curves of richness estimators and diversity indices demonstrated that our collection of isolates represented the archaeal community at Rambla Salada that can be isolated under the conditions used in this work. This is the first report to be published on the culturable archaea at Rambla Salada, an area of considerable ecological interest.},
}
@article {pmid22218772,
year = {2012},
author = {Liu, D and Ding, W and Jia, Z and Cai, Z},
title = {The impact of dissolved organic carbon on the spatial variability of methanogenic archaea communities in natural wetland ecosystems across China.},
journal = {Applied microbiology and biotechnology},
volume = {96},
number = {1},
pages = {253-263},
doi = {10.1007/s00253-011-3842-x},
pmid = {22218772},
issn = {1432-0614},
mesh = {Archaea/*classification/genetics/*isolation &amp; purification/metabolism ; *Biota ; Carbon/*analysis ; China ; Cluster Analysis ; DNA, Archaeal/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Ecosystem ; Methane/metabolism ; Molecular Sequence Data ; Organic Chemicals/*analysis ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Soil/chemistry ; *Soil Microbiology ; *Wetlands ; },
abstract = {Significant spatial variation in CH(4) emissions is a well-established feature of natural wetland ecosystems. To understand the key factors affecting CH(4) production, the variation in community structure of methanogenic archaea, in relation to substrate and external environmental influences, was investigated in selected wetlands across China, using denaturing gradient gel electrophoresis. Case study areas were the subtropical Poyang wetland, the warm-temperate Hongze wetland, the cold-temperate Sanjiang marshes, and the alpine Ruoergai peatland on the Qinghai-Tibetan Plateau. The topsoil layer in the Hongze wetland exhibited the highest population of methanogens; the lowest was found in the Poyang wetland. Maximum CH(4) production occurred in the topsoil layer of the Sanjiang Carex lasiocarpa marsh, the minimum was observed in the Ruoergai peatland. CH(4) production potential was significantly correlated with the dissolved organic carbon (DOC) concentration but not with the abundance or diversity indices of methanogenic archaea. Phylogenetic analysis and DOC concentration indicated a shift in the dominant methanogen from the hydrogenotrophic Methanobacteriales in DOC-rich wetlands to Methanosarcinaceae with a low affinity in wetlands with relatively high DOC and then to the acetotrophic methanogen Methanosaetaceae with a high affinity in wetlands with low DOC, or with high DOC but rich sulfate-reducing bacteria. Therefore, it is proposed that the dominant methanogen type in wetlands is primarily influenced by available DOC concentration. In turn, the variation in CH(4) production potential in the wetlands of eastern China is attributable to differences in the DOC content and the dominant type of methanogen present.},
}
@article {pmid25371329,
year = {2012},
author = {Oren, A},
title = {The function of gas vesicles in halophilic archaea and bacteria: theories and experimental evidence.},
journal = {Life (Basel, Switzerland)},
volume = {3},
number = {1},
pages = {1-20},
pmid = {25371329},
issn = {2075-1729},
abstract = {A few extremely halophilic Archaea (Halobacterium salinarum, Haloquadratum walsbyi, Haloferax mediterranei, Halorubrum vacuolatum, Halogeometricum borinquense, Haloplanus spp.) possess gas vesicles that bestow buoyancy on the cells. Gas vesicles are also produced by the anaerobic endospore-forming halophilic Bacteria Sporohalobacter lortetii and Orenia sivashensis. We have extensive information on the properties of gas vesicles in Hbt. salinarum and Hfx. mediterranei and the regulation of their formation. Different functions were suggested for gas vesicle synthesis: buoying cells towards oxygen-rich surface layers in hypersaline water bodies to prevent oxygen limitation, reaching higher light intensities for the light-driven proton pump bacteriorhodopsin, positioning the cells optimally for light absorption, light shielding, reducing the cytoplasmic volume leading to a higher surface-area-to-volume ratio (for the Archaea) and dispersal of endospores (for the anaerobic spore-forming Bacteria). Except for Hqr. walsbyi which abounds in saltern crystallizer brines, gas-vacuolate halophiles are not among the dominant life forms in hypersaline environments. There only has been little research on gas vesicles in natural communities of halophilic microorganisms, and the few existing studies failed to provide clear evidence for their possible function. This paper summarizes the current status of the different theories why gas vesicles may provide a selective advantage to some halophilic microorganisms.},
}
@article {pmid22200641,
year = {2012},
author = {Sakami, T},
title = {Distribution of ammonia-oxidizing archaea and bacteria in the surface sediments of Matsushima Bay in relation to environmental variables.},
journal = {Microbes and environments},
volume = {27},
number = {1},
pages = {61-66},
pmid = {22200641},
issn = {1347-4405},
mesh = {Ammonia/*metabolism ; Archaea/classification/genetics/*isolation &amp; purification/metabolism ; Archaeal Proteins/genetics/metabolism ; Bacteria/classification/genetics/*isolation &amp; purification/metabolism ; Bacterial Proteins/genetics/metabolism ; Bays ; *Biodiversity ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; Ecosystem ; Geologic Sediments/*microbiology ; Japan ; Molecular Sequence Data ; Oxidation-Reduction ; Oxidoreductases/genetics/metabolism ; Oxygen/metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Ammonia oxidization is the first and a rate-limiting step of nitrification, which is often a critical process in nitrogen removal from estuarine and coastal environments. To clarify the correlation of environmental conditions with the distribution of ammonia oxidizers in organic matter-rich coastal sediments, ammonia-oxidizing archaea (AOA) and bacteria (AOB) ammonia monooxygenase alpha subunit gene (amoA) abundance was determined in sediments of Matsushima Bay located in northeast Japan. The AOA and AOB amoA copy numbers ranged from 1.1×10(6) to 1.7×10(7) and from 7.1×10(5) to 7.6×10(6) copies g(-1) sediment, respectively. AOA and AOB amoA abundance was negatively correlated with dissolved oxygen levels in the bottom water. AOA amoA abundance was also correlated with total phosphorus levels in the sediments. On the other hand, no significant relationship was observed between the amoA abundance and ammonium, organic matter (ignition loss), or acid volatile sulfide-sulfur levels in the sediments. These results show the heterogeneous distribution of ammonia oxidizers by the difference in environmental conditions within the bay. Moreover, AOA amoA diversity was relatively low in the area of high AOA amoA abundance, suggesting the variability of AOA community composition.},
}
@article {pmid22188759,
year = {2011},
author = {Brodt, A and Lurie-Weinberger, MN and Gophna, U},
title = {CRISPR loci reveal networks of gene exchange in archaea.},
journal = {Biology direct},
volume = {6},
number = {1},
pages = {65},
pmid = {22188759},
issn = {1745-6150},
mesh = {Archaea/*genetics ; Base Sequence ; *Gene Transfer, Horizontal ; *Genetic Loci ; *Genome, Archaeal ; Inverted Repeat Sequences ; },
abstract = {BACKGROUND: CRISPR (Clustered, Regularly, Interspaced, Short, Palindromic Repeats) loci provide prokaryotes with an adaptive immunity against viruses and other mobile genetic elements. CRISPR arrays can be transcribed and processed into small crRNA molecules, which are then used by the cell to target the foreign nucleic acid. Since spacers are accumulated by active CRISPR/Cas systems, the sequences of these spacers provide a record of the past "infection history" of the organism.<br><br>RESULTS: Here we analyzed all currently known spacers present in archaeal genomes and identified their source by DNA similarity. While nearly 50% of archaeal spacers matched mobile genetic elements, such as plasmids or viruses, several others matched chromosomal genes of other organisms, primarily other archaea. Thus, networks of gene exchange between archaeal species were revealed by the spacer analysis, including many cases of inter-genus and inter-species gene transfer events. Spacers that recognize viral sequences tend to be located further away from the leader sequence, implying that there exists a selective pressure for their retention.<br><br>CONCLUSIONS: CRISPR spacers provide direct evidence for extensive gene exchange in archaea, especially within genera, and support the current dogma where the primary role of the CRISPR/Cas system is anti-viral and anti-plasmid defense.<br><br>OPEN PEER REVIEW: This article was reviewed by: Profs. W. Ford Doolittle, John van der Oost, Christa Schleper (nominated by board member Prof. J Peter Gogarten).},
}
@article {pmid22151831,
year = {2011},
author = {Collins, RE and Merz, H and Higgs, PG},
title = {Origin and evolution of gene families in Bacteria and Archaea.},
journal = {BMC bioinformatics},
volume = {12 Suppl 9},
number = {Suppl 9},
pages = {S14},
pmid = {22151831},
issn = {1471-2105},
mesh = {Cluster Analysis ; *Evolution, Molecular ; Gene Duplication ; *Genes, Archaeal ; *Genes, Bacterial ; Genome Size ; Genome, Archaeal ; Genome, Bacterial ; Genomics/methods ; *Multigene Family ; },
abstract = {BACKGROUND: Comparison of complete genomes of Bacteria and Archaea shows that gene content varies considerably and that genomes evolve quite rapidly via gene duplication and deletion and horizontal gene transfer. We analyze a diverse set of 92 Bacteria and 79 Archaea in order to investigate the processes governing the origin and evolution of families of related genes within genomes.<br><br>RESULTS: Genes were clustered into related groups using similarity criteria derived from BLAST. Most clusters contained genes from only one or a small number of genomes, and relatively few core clusters were found that spanned all genomes. Gene clusters found in larger numbers of genomes tended to have larger numbers of genes per genome; however, clusters with unusually large numbers of genes per genome were found among both narrowly and widely distributed clusters. Larger genomes were found to have larger mean gene family sizes and a greater proportion of families of very large size. We used a model of birth, death, and innovation to predict the distribution of gene family sizes. The key parameter is r, the ratio of duplications to deletions. It was found that the model can give a good fit to the observed distribution only if there are several classes of genes with different values of r. The preferred model in most cases had three classes of genes.<br><br>CONCLUSIONS: There appears to be a rapid rate of origination of new gene families within individual genomes. Most of these gene families are deleted before they spread to large numbers of genomes, which suggests that they may not be generally beneficial to the organisms. The family size distribution is best described by a large fraction of families that tend to have only one or two genes and a small fraction of families of multi-copy genes that are highly prone to duplication. Larger families occur more frequently in larger genomes, indicating higher r in these genomes, possibly due to a greater tolerance for non-beneficial gene duplicates. The smallest genomes contain very few multi-copy families, suggesting a high rate of deletion of all but the most beneficial genes in these genomes.},
}
@article {pmid22179255,
year = {2012},
author = {Youssef, NH and Ashlock-Savage, KN and Elshahed, MS},
title = {Phylogenetic diversities and community structure of members of the extremely halophilic Archaea (order Halobacteriales) in multiple saline sediment habitats.},
journal = {Applied and environmental microbiology},
volume = {78},
number = {5},
pages = {1332-1344},
pmid = {22179255},
issn = {1098-5336},
mesh = {*Biota ; Cluster Analysis ; DNA, Archaeal/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Ecosystem ; Geologic Sediments/*microbiology ; Halobacteriales/*classification/*isolation &amp; purification ; *Phylogeny ; Puerto Rico ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; United States ; },
abstract = {We investigated the phylogenetic diversity and community structure of members of the halophilic Archaea (order Halobacteriales) in five distinct sediment habitats that experience various levels of salinity and salinity fluctuations (sediments from Great Salt Plains and Zodletone Spring in Oklahoma, mangrove tree sediments in Puerto Rico, sediment underneath salt heaps in a salt-processing plant, and sediments from the Great Salt Lake northern arm) using Halobacteriales-specific 16S rRNA gene primers. Extremely diverse Halobacteriales communities were encountered in all habitats, with 27 (Zodletone) to 37 (mangrove) different genera identified per sample, out of the currently described 38 Halobacteriales genera. With the exception of Zodletone Spring, where the prevalent geochemical conditions are extremely inhospitable to Halobacteriales survival, habitats with fluctuating salinity levels were more diverse than permanently saline habitats. Sequences affiliated with the recently described genera Halogranum, Halolamina, Haloplanus, Halosarcina, and Halorientalis, in addition to the genera Halorubrum, Haloferax, and Halobacterium, were among the most abundant and ubiquitous genera, suggesting a wide distribution of these poorly studied genera in saline sediments. The Halobacteriales sediment communities analyzed in this study were more diverse than and completely distinct from communities from typical hypersaline water bodies. Finally, sequences unaffiliated with currently described genera represented a small fraction of the total Halobacteriales communities, ranging between 2.5% (Zodletone) to 7.0% (mangrove and Great Salt Lake). However, these novel sequences were characterized by remarkably high levels of alpha and beta diversities, suggesting the presence of an enormous, yet-untapped supply of novel Halobacteriales genera within the rare biosphere of various saline ecosystems.},
}
@article {pmid22176665,
year = {2012},
author = {Radax, R and Hoffmann, F and Rapp, HT and Leininger, S and Schleper, C},
title = {Ammonia-oxidizing archaea as main drivers of nitrification in cold-water sponges.},
journal = {Environmental microbiology},
volume = {14},
number = {4},
pages = {909-923},
doi = {10.1111/j.1462-2920.2011.02661.x},
pmid = {22176665},
issn = {1462-2920},
mesh = {Ammonia/*metabolism ; Animals ; Archaea/classification/genetics/*metabolism ; Base Sequence ; Molecular Sequence Data ; Nitrates/metabolism ; Nitrification/*physiology ; Nitrites/metabolism ; Oxidoreductases/genetics ; Phylogeny ; Porifera/*microbiology ; },
abstract = {The association of archaea with marine sponges was first described 15 years ago and their role in the nitrification process in Mediterranean and tropical sponges has been suggested. Here we explore the occurrence and abundance of potential ammonia-oxidizing archaea (AOA) in four morphologically different cold-water sponges (Phakellia ventilabrum, Geodia barretti, Antho dichotoma and Tentorium semisuberites) from the sublittoral and upper bathyal zone [Correction added on 30 December 2011, after first online publication on 19 December 2011: The term 'mesopelagic zone' has been replaced.] of the Norwegian coast, and relate them to nitrification rates determined in laboratory incubations. Net nitrification rates, calculated from the sum of nitrite and nitrate release during 24 h, were up to 1880 nmol N cm(-3) day(-1); i.e. comparable with those measured in Mediterranean sponges. Furthermore, a high abundance of archaeal cells was determined by fluorescence in situ hybridizations (CARD-FISH) and quantitative PCR, targeting archaeal amoA genes (encoding the alpha subunit of ammonia monooxygenase). AmoA genes as well as amoA transcripts were either exclusively detectable from archaea or were orders of magnitudes higher in abundance than their bacterial counterparts. Phylogenetic analyses of AOA and bacterial nitrite oxidizers (genus Nitrospira) confirmed the presence of specific populations of nitrifying microorganisms in the sponge mesohyl, which either were affiliated with groups detected earlier in marine sponges or were typical inhabitants of cold- and deep-water environments. Estimated cell-specific nitrification rates for P. ventilabrum were 0.6 to 6 fmol N archaeal cell(-1) day(-1), thus comparable with planktonic organisms. Our results identify AOA as the major drivers of nitrification in four cold-water sponges, and indicate that these archaea may be considered as a relevant factor in nitrogen cycling in ocean regions with high sponge biomass.},
}
@article {pmid22174796,
year = {2011},
author = {Halachev, MR and Loman, NJ and Pallen, MJ},
title = {Calculating orthologs in bacteria and Archaea: a divide and conquer approach.},
journal = {PloS one},
volume = {6},
number = {12},
pages = {e28388},
pmid = {22174796},
issn = {1932-6203},
support = {BB/E011179/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBE0111791/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Archaea/*genetics ; Bacteria/*genetics ; Genome, Archaeal/genetics ; Genome, Bacterial/genetics ; Open Reading Frames/genetics ; Sequence Alignment ; *Sequence Homology, Amino Acid ; Time Factors ; },
abstract = {Among proteins, orthologs are defined as those that are derived by vertical descent from a single progenitor in the last common ancestor of their host organisms. Our goal is to compute a complete set of protein orthologs derived from all currently available complete bacterial and archaeal genomes. Traditional approaches typically rely on all-against-all BLAST searching which is prohibitively expensive in terms of hardware requirements or computational time (requiring an estimated 18 months or more on a typical server). Here, we present xBASE-Orth, a system for ongoing ortholog annotation, which applies a "divide and conquer" approach and adopts a pragmatic scheme that trades accuracy for speed. Starting at species level, xBASE-Orth carefully constructs and uses pan-genomes as proxies for the full collections of coding sequences at each level as it progressively climbs the taxonomic tree using the previously computed data. This leads to a significant decrease in the number of alignments that need to be performed, which translates into faster computation, making ortholog computation possible on a global scale. Using xBASE-Orth, we analyzed an NCBI collection of 1,288 bacterial and 94 archaeal complete genomes with more than 4 million coding sequences in 5 weeks and predicted more than 700 million ortholog pairs, clustered in 175,531 orthologous groups. We have also identified sets of highly conserved bacterial and archaeal orthologs and in so doing have highlighted anomalies in genome annotation and in the proposed composition of the minimal bacterial genome. In summary, our approach allows for scalable and efficient computation of the bacterial and archaeal ortholog annotations. In addition, due to its hierarchical nature, it is suitable for incorporating novel complete genomes and alternative genome annotations. The computed ortholog data and a continuously evolving set of applications based on it are integrated in the xBASE database, available at http://www.xbase.ac.uk/.},
}
@article {pmid22168471,
year = {2011},
author = {Brown, AM and Hoopes, SL and White, RH and Sarisky, CA},
title = {Purine biosynthesis in archaea: variations on a theme.},
journal = {Biology direct},
volume = {6},
number = {},
pages = {63},
pmid = {22168471},
issn = {1745-6150},
mesh = {Archaea/chemistry/enzymology/*genetics ; Carbon-Nitrogen Ligases/chemistry/genetics ; Carbon-Nitrogen Ligases with Glutamine as Amide-N-Donor/chemistry/genetics ; Carboxy-Lyases/chemistry/genetics ; Catalytic Domain ; Enzyme Activation ; Gene Duplication ; Gene Transfer, Horizontal ; *Genes, Archaeal ; Peptide Synthases/chemistry/genetics ; Phosphoribosylglycinamide Formyltransferase/chemistry/genetics ; Purines/*biosynthesis/chemistry ; },
abstract = {BACKGROUND: The ability to perform de novo biosynthesis of purines is present in organisms in all three domains of life, reflecting the essentiality of these molecules to life. Although the pathway is quite similar in eukaryotes and bacteria, the archaeal pathway is more variable. A careful manual curation of genes in this pathway demonstrates the value of manual curation in archaea, even in pathways that have been well-studied in other domains.<br><br>RESULTS: We searched the Integrated Microbial Genome system (IMG) for the 17 distinct genes involved in the 11 steps of de novo purine biosynthesis in 65 sequenced archaea, finding 738 predicted proteins with sequence similarity to known purine biosynthesis enzymes. Each sequence was manually inspected for the presence of active site residues and other residues known or suspected to be required for function.Many apparently purine-biosynthesizing archaea lack evidence for a single enzyme, either glycinamide ribonucleotide formyltransferase or inosine monophosphate cyclohydrolase, suggesting that there are at least two more gene variants in the purine biosynthetic pathway to discover. Variations in domain arrangement of formylglycinamidine ribonucleotide synthetase and substantial problems in aminoimidazole carboxamide ribonucleotide formyltransferase and inosine monophosphate cyclohydrolase assignments were also identified.Manual curation revealed some overly specific annotations in the IMG gene product name, with predicted proteins without essential active site residues assigned product names implying enzymatic activity (21 proteins, 2.8% of proteins inspected) or Enzyme Commission (E. C.) numbers (57 proteins, 7.7%). There were also 57 proteins (7.7%) assigned overly generic names and 78 proteins (10.6%) without E.C. numbers as part of the assigned name when a specific enzyme name and E. C. number were well-justified.<br><br>CONCLUSIONS: The patchy distribution of purine biosynthetic genes in archaea is consistent with a pathway that has been shaped by horizontal gene transfer, duplication, and gene loss. Our results indicate that manual curation can improve upon automated annotation for a small number of automatically-annotated proteins and can reveal a need to identify further pathway components even in well-studied pathways.},
}
@article {pmid22159570,
year = {2012},
author = {Molari, M and Manini, E},
title = {Reliability of CARD-FISH procedure for enumeration of Archaea in deep-sea surficial sediments.},
journal = {Current microbiology},
volume = {64},
number = {3},
pages = {242-250},
pmid = {22159570},
issn = {1432-0991},
mesh = {Archaea/*isolation &amp; purification ; Biodiversity ; Cell Count/methods ; Geologic Sediments/*microbiology ; In Situ Hybridization, Fluorescence/*methods ; Oligonucleotide Probes/genetics ; },
abstract = {The enumeration of Archaea in deep-sea sediment samples is still limited, although different methodological procedures have been applied. Among these, catalysed reporter deposition-fluorescence in situ hybridisation (CARD-FISH) technique is a promising tool for estimation of archaeal abundance in deep-sea sediment samples. Comparing different permeabilisation treatments, the best results obtained both on archaeal pure cultures and on natural assemblages were with hydrochloric acid (0.1 M) and proteinase K (0.004 U/ml) treatments. The application of CARD-FISH on deep-sea sediments revealed that Archaea reach up to 41% of total prokaryotic cells. Specific probes for planktonic Archaea showed that marine Crenarchaea dominated archaeal seafloor communities. No clear bathymetric trends were observed for archaeal abundances and the morphology of continental margin (slope vs. canyon) seems not to have a direct influence on archaeal relative abundances. The site-specific sediment habitat-both abiotic environmental setting and sedimentary organic matter quality-explain up to 65% of variance of archaeal, crenarchaeal and euryarchaeal relative abundance, suggesting a wide ecophysiological adaptation to deep-sea benthic ecosystems. The findings demonstrate that Archaea are an important component of benthic microbial assemblages so far neglected, and hence they lay the groundwork for more focused research on their ecological importance in the functioning of deep-sea benthic ecosystems.},
}
@article {pmid22150151,
year = {2012},
author = {Antony, CP and Murrell, JC and Shouche, YS},
title = {Molecular diversity of methanogens and identification of Methanolobus sp. as active methylotrophic Archaea in Lonar crater lake sediments.},
journal = {FEMS microbiology ecology},
volume = {81},
number = {1},
pages = {43-51},
doi = {10.1111/j.1574-6941.2011.01274.x},
pmid = {22150151},
issn = {1574-6941},
mesh = {Archaea/*classification/genetics/*metabolism ; Biodiversity ; Ecosystem ; Euryarchaeota/classification/genetics ; Gene Library ; Genes, rRNA ; Geologic Sediments/*microbiology ; India ; *Lakes ; Methane/*metabolism ; Methanomicrobiaceae/genetics ; Methanomicrobiales/classification/genetics ; Methanosarcinaceae/*classification/genetics/*metabolism ; Methanosarcinales/classification/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Soda lakes constitute extreme aquatic ecosystems with remarkably high primary productivity rates, but information on the diversity and activity of methanogens in such environments is sparse. Using 16S rRNA and functional genes, we investigated the diversity of methanogens in the sediments of Lonar Lake, a unique saline and alkaline ecosystem formed by meteorite impact in the Deccan basalts. Although domain and phylum level 16S rRNA gene libraries were dominated by phylotypes related to Halobacteriales, sequences related to potentially novel Archaea within the orders Methanosarcinales and Methanomicrobiales were obtained together with a significant fraction of sequences representing uncultivated Euryarchaeota [Correction added after online publication 16 April 2012: orders 'Methanosarcina and Methanomicrobiaceae' changed to 'Methanosarcinales and Methanomicrobiales']. To identify the active methylotrophic Archaea involved in methanogenesis, mRNA transcripts of mcrA were retrieved from methanol consuming and methane emitting sediment microcosms at two different time points. Reverse-transcription PCR, qPCR, DGGE fingerprint, and clone library analysis showed that the active Archaea were closely related to Methanolobus oregonensis. To our knowledge, this is the first study identifying active methylotrophic methanogens in such an environment.},
}
@article {pmid22141924,
year = {2012},
author = {Pester, M and Rattei, T and Flechl, S and Gröngröft, A and Richter, A and Overmann, J and Reinhold-Hurek, B and Loy, A and Wagner, M},
title = {amoA-based consensus phylogeny of ammonia-oxidizing archaea and deep sequencing of amoA genes from soils of four different geographic regions.},
journal = {Environmental microbiology},
volume = {14},
number = {2},
pages = {525-539},
pmid = {22141924},
issn = {1462-2920},
support = {P 18836/FWF_/Austrian Science Fund FWF/Austria ; P 20185/FWF_/Austrian Science Fund FWF/Austria ; },
mesh = {Ammonia/*metabolism ; Archaea/classification/*genetics ; Austria ; Biodiversity ; Costa Rica ; *Genes, Archaeal ; Greenland ; High-Throughput Nucleotide Sequencing ; Namibia ; Nitrification ; Phylogeny ; Soil ; *Soil Microbiology ; },
abstract = {Ammonia-oxidizing archaea (AOA) play an important role in nitrification and many studies exploit their amoA genes as marker for their diversity and abundance. We present an archaeal amoA consensus phylogeny based on all publicly available sequences (status June 2010) and provide evidence for the diversification of AOA into four previously recognized clusters and one newly identified major cluster. These clusters, for which we suggest a new nomenclature, harboured 83 AOA species-level OTU (using an inferred species threshold of 85% amoA identity). 454 pyrosequencing of amoA amplicons from 16 soils sampled in Austria, Costa Rica, Greenland and Namibia revealed that only 2% of retrieved sequences had no database representative on the species-level and represented 30-37 additional species-level OTUs. With the exception of an acidic soil from which mostly amoA amplicons of the Nitrosotalea cluster were retrieved, all soils were dominated by amoA amplicons from the Nitrososphaera cluster (also called group I.1b), indicating that the previously reported AOA from the Nitrosopumilus cluster (also called group I.1a) are absent or represent minor populations in soils. AOA richness estimates on the species level ranged from 8-83 co-existing AOAs per soil. Presence/absence of amoA OTUs (97% identity level) correlated with geographic location, indicating that besides contemporary environmental conditions also dispersal limitation across different continents and/or historical environmental conditions might influence AOA biogeography in soils.},
}
@article {pmid22140119,
year = {2012},
author = {Danan, M and Schwartz, S and Edelheit, S and Sorek, R},
title = {Transcriptome-wide discovery of circular RNAs in Archaea.},
journal = {Nucleic acids research},
volume = {40},
number = {7},
pages = {3131-3142},
pmid = {22140119},
issn = {1362-4962},
mesh = {Gene Expression Profiling ; Introns ; RNA/*chemistry/classification/metabolism ; RNA, Archaeal/*chemistry/classification/metabolism ; RNA, Circular ; RNA, Ribosomal/chemistry/metabolism ; RNA, Transfer/chemistry/metabolism ; RNA, Untranslated/chemistry/metabolism ; Sequence Analysis, RNA ; Sulfolobus acidocaldarius/genetics ; Sulfolobus solfataricus/*genetics ; Transcriptome ; },
abstract = {Circular RNA forms had been described in all domains of life. Such RNAs were shown to have diverse biological functions, including roles in the life cycle of viral and viroid genomes, and in maturation of permuted tRNA genes. Despite their potentially important biological roles, discovery of circular RNAs has so far been mostly serendipitous. We have developed circRNA-seq, a combined experimental/computational approach that enriches for circular RNAs and allows profiling their prevalence in a whole-genome, unbiased manner. Application of this approach to the archaeon Sulfolobus solfataricus P2 revealed multiple circular transcripts, a subset of which was further validated independently. The identified circular RNAs included expected forms, such as excised tRNA introns and rRNA processing intermediates, but were also enriched with non-coding RNAs, including C/D box RNAs and RNase P, as well as circular RNAs of unknown function. Many of the identified circles were conserved in Sulfolobus acidocaldarius, further supporting their functional significance. Our results suggest that circular RNAs, and particularly circular non-coding RNAs, are more prevalent in archaea than previously recognized, and might have yet unidentified biological roles. Our study establishes a specific and sensitive approach for identification of circular RNAs using RNA-seq, and can readily be applied to other organisms.},
}
@article {pmid22137029,
year = {2012},
author = {Kurup, R and Kurup, PA},
title = {A cholesterol and actinide dependent shadow biosphere of archaea and viroids in autoimmune diseases.},
journal = {Immunobiology},
volume = {217},
number = {3},
pages = {316-320},
doi = {10.1016/j.imbio.2011.10.005},
pmid = {22137029},
issn = {1878-3279},
mesh = {Actinoid Series Elements/*metabolism ; Archaea/*metabolism ; Autoimmune Diseases/*blood/*etiology/microbiology ; Cholesterol/*metabolism ; Humans ; Viroids/*metabolism ; },
abstract = {Endogenous digoxin has been related to the pathogenesis of multiple sclerosis and other autoimmune diseases like systemic lupus erythematosis and rheumatoid arthritis. The possibility of endogenous digoxin synthesis by archaea with a mevalonate pathway and cholesterol catabolism was considered. 10 cases each of multiple sclerosis and other autoimmune diseases like systemic lupus erythematosis and rheumatoid arthritis before starting treatment and 10 age and sex matched healthy controls from general population were chosen for the study. Cholesterol substrate was added to the plasma of the patients and the generation of cytochrome F420, free RNA, free DNA, polycyclic aromatic hydrocarbon, hydrogen peroxide, serotonin, pyruvate, ammonia, glutamate, cytochrome C, hexokinase, ATP synthase, HMG CoA reductase, digoxin and bile acids were studied. The changes with the addition of antibiotics and cerium to the patient's plasma were also studied. The statistical analysis was done by ANOVA. The parameters mentioned above were increased the patient's plasma with addition of cholesterol substrate. The addition of antibiotics to the patient's plasma caused a decrease in all the parameters while addition of cerium increased their levels. An actinide dependent shadow biosphere of archaea and viroids is described in multiple sclerosis and other autoimmune diseases like systemic lupus erythematosis and rheumatoid arthritis contributing to their pathogenesis.},
}
@article {pmid22134646,
year = {2012},
author = {McDonald, D and Price, MN and Goodrich, J and Nawrocki, EP and DeSantis, TZ and Probst, A and Andersen, GL and Knight, R and Hugenholtz, P},
title = {An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea.},
journal = {The ISME journal},
volume = {6},
number = {3},
pages = {610-618},
pmid = {22134646},
issn = {1751-7370},
support = {UH2/UH3CA140233/CA/NCI NIH HHS/United States ; U01 HG004866/HG/NHGRI NIH HHS/United States ; R01 HG004872/HG/NHGRI NIH HHS/United States ; U01-HG004866/HG/NHGRI NIH HHS/United States ; /HHMI_/Howard Hughes Medical Institute/United States ; },
mesh = {Archaea/*classification/genetics ; Bacteria/*classification/genetics ; Classification/*methods ; *Databases, Genetic ; Metagenomics ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Software ; },
abstract = {Reference phylogenies are crucial for providing a taxonomic framework for interpretation of marker gene and metagenomic surveys, which continue to reveal novel species at a remarkable rate. Greengenes is a dedicated full-length 16S rRNA gene database that provides users with a curated taxonomy based on de novo tree inference. We developed a 'taxonomy to tree' approach for transferring group names from an existing taxonomy to a tree topology, and used it to apply the Greengenes, National Center for Biotechnology Information (NCBI) and cyanoDB (Cyanobacteria only) taxonomies to a de novo tree comprising 408,315 sequences. We also incorporated explicit rank information provided by the NCBI taxonomy to group names (by prefixing rank designations) for better user orientation and classification consistency. The resulting merged taxonomy improved the classification of 75% of the sequences by one or more ranks relative to the original NCBI taxonomy with the most pronounced improvements occurring in under-classified environmental sequences. We also assessed candidate phyla (divisions) currently defined by NCBI and present recommendations for consolidation of 34 redundantly named groups. All intermediate results from the pipeline, which includes tree inference, jackknifing and transfer of a donor taxonomy to a recipient tree (tax2tree) are available for download. The improved Greengenes taxonomy should provide important infrastructure for a wide range of megasequencing projects studying ecosystems on scales ranging from our own bodies (the Human Microbiome Project) to the entire planet (the Earth Microbiome Project). The implementation of the software can be obtained from http://sourceforge.net/projects/tax2tree/.},
}
@article {pmid22134644,
year = {2012},
author = {Zhang, LM and Hu, HW and Shen, JP and He, JZ},
title = {Ammonia-oxidizing archaea have more important role than ammonia-oxidizing bacteria in ammonia oxidation of strongly acidic soils.},
journal = {The ISME journal},
volume = {6},
number = {5},
pages = {1032-1045},
pmid = {22134644},
issn = {1751-7370},
mesh = {Agriculture ; Ammonia/*metabolism ; Archaea/classification/genetics/*metabolism ; Autotrophic Processes ; Bacteria/classification/genetics/*metabolism ; Carbon Isotopes/analysis ; China ; Denaturing Gradient Gel Electrophoresis ; Guanidines/chemistry ; *Nitrification ; Nitrogen Cycle ; Oxidation-Reduction ; Phylogeny ; Soil/chemistry ; *Soil Microbiology ; },
abstract = {Increasing evidence demonstrated the involvement of ammonia-oxidizing archaea (AOA) in the global nitrogen cycle, but the relative contributions of AOA and ammonia-oxidizing bacteria (AOB) to ammonia oxidation are still in debate. Previous studies suggest that AOA would be more adapted to ammonia-limited oligotrophic conditions, which seems to be favored by protonation of ammonia, turning into ammonium in low-pH environments. Here, we investigated the autotrophic nitrification activity of AOA and AOB in five strongly acidic soils (pH<4.50) during microcosm incubation for 30 days. Significantly positive correlations between nitrate concentration and amoA gene abundance of AOA, but not of AOB, were observed during the active nitrification. (13)CO(2)-DNA-stable isotope probing results showed significant assimilation of (13)C-labeled carbon source into the amoA gene of AOA, but not of AOB, in one of the selected soil samples. High levels of thaumarchaeal amoA gene abundance were observed during the active nitrification, coupled with increasing intensity of two denaturing gradient gel electrophoresis bands for specific thaumarchaeal community. Addition of the nitrification inhibitor dicyandiamide (DCD) completely inhibited the nitrification activity and CO(2) fixation by AOA, accompanied by decreasing thaumarchaeal amoA gene abundance. Bacterial amoA gene abundance decreased in all microcosms irrespective of DCD addition, and mostly showed no correlation with nitrate concentrations. Phylogenetic analysis of thaumarchaeal amoA gene and 16S rRNA gene revealed active (13)CO(2)-labeled AOA belonged to groups 1.1a-associated and 1.1b. Taken together, these results provided strong evidence that AOA have a more important role than AOB in autotrophic ammonia oxidation in strongly acidic soils.},
}
@article {pmid22126075,
year = {2011},
author = {Guo, X and Zhang, G and Liu, X and Ma, K and Dong, X},
title = {[Detection of the quorum sensing signals in methanogenic archaea].},
journal = {Wei sheng wu xue bao = Acta microbiologica Sinica},
volume = {51},
number = {9},
pages = {1200-1204},
pmid = {22126075},
issn = {0001-6209},
mesh = {4-Butyrolactone/analogs &amp; derivatives/metabolism/pharmacology ; Methanosarcinales/drug effects/*metabolism ; *Quorum Sensing ; *Signal Transduction ; },
abstract = {UNLABELLED: Methanosaeta harundinacea 6Ac displayed a cell-density dependent cell morphology transition between short rods (3 microm - 5 microm) and filaments (>200 microm), implying a quorum sensing system in this archaeon.<br><br>OBJECTIVE: This study aimed to confirm that cell morphology related quorum sensing exists in Methanosaeta harundinacea.<br><br>METHODS: By using the bioassay of Agrobacterium tumefaciens NTL4, we determined the presence of acyl homoserine lactones (AHLs) in the spent cultures of Methanosaeta harundinacea 6Ac and other three methanogens. A chemical synthetic AHL, N-(beta-Ketooctanoyl)-L-homoserine lactone was added into the culture of short rods to detect the morphology change.<br><br>RESULTS: We determined that AHLs were produced by Methanosaeta harundinacea, Methanosarcina mazei, Methanothermobacter thermautotrophicus and Methanobacterium formicicum. Addition of N-(beta-Ketooctanoyl)-L-homoserine lactone into the culture of Methanosaeta harundinacea 6Ac stimulated the formation of filamentous cells.<br><br>CONCLUSION: This study indicates that AHL-based quorum sensing may be used by several species of methanogenic Archaea.},
}
@article {pmid22117845,
year = {2012},
author = {Li, PY and Xie, BB and Zhang, XY and Qin, QL and Dang, HY and Wang, XM and Chen, XL and Yu, J and Zhang, YZ},
title = {Genetic structure of three fosmid-fragments encoding 16S rRNA genes of the Miscellaneous Crenarchaeotic Group (MCG): implications for physiology and evolution of marine sedimentary archaea.},
journal = {Environmental microbiology},
volume = {14},
number = {2},
pages = {467-479},
doi = {10.1111/j.1462-2920.2011.02637.x},
pmid = {22117845},
issn = {1462-2920},
mesh = {Archaea/classification/*genetics/physiology ; Base Sequence ; China ; DNA, Archaeal/*analysis ; Gene Library ; Genes, rRNA ; Genome, Archaeal ; Geologic Sediments/microbiology ; Metagenomics ; Molecular Sequence Data ; Oceans and Seas ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/microbiology ; },
abstract = {Archaea of the Miscellaneous Crenarchaeotic Group (MCG) exist widely in soil, freshwater and marine sediments of both surface and subsurface. However, current knowledge about this group is limited to its phylogenetic diversity. An archaeal 16S library was constructed from a sediment sample from the South China Sea, which was dominated by MCG and Marine Group I (MG-I). A metagenomic library was constructed from the same sediment sample, and three MCG fosmids (E6-3G, E37-7F and E48-1C) containing 16S rRNA genes were screened. Annotation showed that the three genomic fragments encode a variety of open reading frames (ORFs) that are potentially homologous to important functional genes related to lipid biosynthesis, energy metabolism, and resistance to oxidants. No colinear regions were found between MCG fosmids and reported archaeal genomic fragments or genomes, suggesting that the MCG archaea are quite different from the sequenced archaea in gene arrangement. Analyses of both the phylogenies of 16S rRNA genes and several informational processing genes and nucleotide frequencies showed that MCG archaea are distinct from MG-I plus relatives. In addition, tetranucleotide frequency analysis in combination with phylogenetic analysis suggested that some fragments in the MCG fosmids are probably derived from non-MCG or non-archaeal genomes.},
}
@article {pmid22114679,
year = {2011},
author = {Venter, E and Smith, RD and Payne, SH},
title = {Proteogenomic analysis of bacteria and archaea: a 46 organism case study.},
journal = {PloS one},
volume = {6},
number = {11},
pages = {e27587},
pmid = {22114679},
issn = {1932-6203},
mesh = {Archaea/*physiology ; Archaeal Proteins/genetics/*metabolism ; Bacteria/*genetics/metabolism ; Bacterial Proteins/genetics/*metabolism ; Computational Biology ; *Genome, Archaeal ; *Genome, Bacterial ; Mass Spectrometry ; Open Reading Frames/genetics ; Proteome/*analysis ; },
abstract = {Experimental evidence is increasingly being used to reassess the quality and accuracy of genome annotation. Proteomics data used for this purpose, called proteogenomics, can alleviate many of the problematic areas of genome annotation, e.g. short protein validation and start site assignment. We performed a proteogenomic analysis of 46 genomes spanning eight bacterial and archaeal phyla across the tree of life. These diverse datasets facilitated the development of a robust approach for proteogenomics that is functional across genomes varying in %GC, gene content, proteomic sampling depth, phylogeny, and genome size. In addition to finding evidence for 682 novel proteins, 1336 new start sites, and numerous dubious genes, we discovered sites of post-translational maturation in the form of proteolytic cleavage of 1175 signal peptides. The number of novel proteins per genome is highly variable (median 7, mean 15, stdev 20). Moreover, comparison of novel genes with the current genes did not reveal any consistent abnormalities. Thus, we conclude that proteogenomics fulfills a yet to be understood deficiency in gene prediction. With the adoption of new sequencing technologies which have higher error rates than Sanger-based methods and the advances in proteomics, proteogenomics may become even more important in the future.},
}
@article {pmid22099630,
year = {2011},
author = {Tenorio-Salgado, S and Huerta-Saquero, A and Perez-Rueda, E},
title = {New insights on gene regulation in archaea.},
journal = {Computational biology and chemistry},
volume = {35},
number = {6},
pages = {341-346},
doi = {10.1016/j.compbiolchem.2011.10.006},
pmid = {22099630},
issn = {1476-928X},
mesh = {Archaea/*genetics ; Gene Expression Regulation, Archaeal/*genetics ; Genome, Archaeal ; },
abstract = {Archaea represent an important and vast domain of life. This cellular domain includes a large diversity of organisms characterized as prokaryotes with basal transcriptional machinery similar to eukarya. In this work we explore the most recent findings concerning the transcriptional regulatory organization in archaeal genomes since the perspective of the DNA-binding transcription factors (TFs), such as the high proportion of archaeal TFs homologous to bacteria, the apparent deficit of TFs, only comparable to the proportion of TFs in parasites or intracellular pathogenic bacteria, suggesting a deficit in this class of proteins. We discuss an appealing hypothesis to explain the apparent deficit of TFs in archaea, based on their characteristics, such as their small length sizes. The hypothesis suggests that a large fraction of these small-sized TFs could supply the deficit of TFs in archaea, by forming different combinations of monomers similar to that observed in eukaryotic transcriptional machinery, where a wide diversity of protein-protein interactions could act as mediators of regulatory feedback, indicating a chimera of bacterial and eukaryotic TFs' functionality. Finally, we discuss how global experiments can help to understand in a global context the role of TFs in these organisms.},
}
@article {pmid22092358,
year = {2012},
author = {Staley, BF and de los Reyes, FL and Barlaz, MA},
title = {Comparison of Bacteria and Archaea communities in municipal solid waste, individual refuse components, and leachate.},
journal = {FEMS microbiology ecology},
volume = {79},
number = {2},
pages = {465-473},
doi = {10.1111/j.1574-6941.2011.01239.x},
pmid = {22092358},
issn = {1574-6941},
mesh = {Archaea/*classification/genetics/isolation &amp; purification ; Bacteria/*classification/genetics/isolation &amp; purification ; Cities ; Garbage ; Polymorphism, Restriction Fragment Length ; Refuse Disposal/methods ; Waste Products/*analysis ; Water Pollutants, Chemical/analysis ; },
abstract = {Refuse decomposition in landfills is a microbially mediated process that occurs primarily under anaerobic conditions. Because of limited moisture conditions, hydraulic transport as a means of cellular translocation within the landfill appears limited, especially during the initial stages of decomposition. Thus, microbial communities within the incoming refuse serve as a primary source of facultative and obligate anaerobic microorganisms that initiate refuse decomposition. Fresh residential refuse was collected five times over 26 months, and microbial communities in these samples were compared with those in individual refuse components and decomposed refuse. Bacterial and archaeal community structures were determined using T-RFLP. The Bacterial microbial community richness was correlated (r(2) = 0.91) with seasonal differences in ambient air temperature. Analysis of the results shows that fresh refuse is most likely not the source of methanogens in landfills. Microbial communities in the solid and leachate phases were different, indicating that both matrices must be considered when characterizing microbial diversity within a landfill.},
}
@article {pmid22089387,
year = {2012},
author = {Kawakami, R and Satomura, T and Sakuraba, H and Ohshima, T},
title = {L-proline dehydrogenases in hyperthermophilic archaea: distribution, function, structure, and application.},
journal = {Applied microbiology and biotechnology},
volume = {93},
number = {1},
pages = {83-93},
doi = {10.1007/s00253-011-3682-8},
pmid = {22089387},
issn = {1432-0614},
mesh = {Amino Acid Sequence ; Archaea/*enzymology/genetics ; Coenzymes/metabolism ; Models, Molecular ; Molecular Sequence Data ; Proline/*metabolism ; Proline Oxidase/chemistry/genetics/*metabolism ; Protein Multimerization ; Protein Subunits/metabolism ; Pyrroles/*metabolism ; },
abstract = {Dye-linked L-proline dehydrogenase (ProDH) catalyzes the oxidation of L-proline to ∆(1)-pyrroline-5-carboxylate (P5C) in the presence of artificial electron acceptors. The enzyme is known to be widely distributed in bacteria and eukarya, together with nicotinamide adenine dinucleotide (phosphate)-dependent P5C dehydrogenase, and to function in the metabolism of L-proline to L-glutamate. In addition, over the course of the last decade, three other types of ProDH with molecular compositions completely different from previously known ones have been identified in hyperthermophilic archaea. The first is a heterotetrameric αβγδ-type ProDH, which exhibits both ProDH and reduced nicotinamide adenine dinucleotide dehydrogenase activity and includes two electron transfer proteins. The second is a heterooctameric α(4)β(4)-type ProDH, which uses flavin adenine dinucleotide, flavin mononucleotide, adenosine triphosphate, and Fe as cofactors and creates a new electron transfer pathway. The third is a recently identified homodimeric ProDH, which exhibits the greatest thermostability among these archaeal ProDHs. This minireview focuses on the functional and structural properties of these three types of archaeal ProDH and their distribution in archaea. In addition, we will describe the specific application of hyperthermostable ProDH for use in a biosensor and for DNA sensing.},
}
@article {pmid22080280,
year = {2012},
author = {Sharma, A and Kawarabayasi, Y and Satyanarayana, T},
title = {Acidophilic bacteria and archaea: acid stable biocatalysts and their potential applications.},
journal = {Extremophiles : life under extreme conditions},
volume = {16},
number = {1},
pages = {1-19},
pmid = {22080280},
issn = {1433-4909},
mesh = {Acids/*metabolism ; Archaea/genetics/*metabolism ; Bacteria/genetics/*metabolism ; Biocatalysis ; Directed Molecular Evolution ; Enzymes/metabolism ; Hydrogen-Ion Concentration ; Models, Molecular ; Proteolysis ; },
abstract = {Acidophiles are ecologically and economically important group of microorganisms, which thrive in acidic natural (solfataric fields, sulfuric pools) as well as artificial man-made (areas associated with human activities such as mining of coal and metal ores) environments. They possess networked cellular adaptations to regulate pH inside the cell. Several extracellular enzymes from acidophiles are known to be functional at much lower pH than the cytoplasmic pH. Enzymes like amylases, proteases, ligases, cellulases, xylanases, α-glucosidases, endoglucanases, and esterases stable at low pH are known from various acidophilic microbes. The possibility of improving them by genetic engineering and directed evolution will further boost their industrial applications. Besides biocatalysts, other biomolecules such as plasmids, rusticynin, and maltose-binding protein have also been reported from acidophiles. Some strategies for circumventing the problems encountered in expressing genes encoding proteins from extreme acidophiles have been suggested. The investigations on the analysis of crystal structures of some acidophilic proteins have thrown light on their acid stability. Attempts are being made to use thermoacidophilic microbes for biofuel production from lignocellulosic biomass. The enzymes from acidophiles are mainly used in polymer degradation.},
}
@article {pmid22073040,
year = {2011},
author = {Paramasivam, N and Linke, D},
title = {ClubSub-P: Cluster-Based Subcellular Localization Prediction for Gram-Negative Bacteria and Archaea.},
journal = {Frontiers in microbiology},
volume = {2},
number = {},
pages = {218},
pmid = {22073040},
issn = {1664-302X},
abstract = {The subcellular localization (SCL) of proteins provides important clues to their function in a cell. In our efforts to predict useful vaccine targets against Gram-negative bacteria, we noticed that misannotated start codons frequently lead to wrongly assigned SCLs. This and other problems in SCL prediction, such as the relatively high false-positive and false-negative rates of some tools, can be avoided by applying multiple prediction tools to groups of homologous proteins. Here we present ClubSub-P, an online database that combines existing SCL prediction tools into a consensus pipeline from more than 600 proteomes of fully sequenced microorganisms. On top of the consensus prediction at the level of single sequences, the tool uses clusters of homologous proteins from Gram-negative bacteria and from Archaea to eliminate false-positive and false-negative predictions. ClubSub-P can assign the SCL of proteins from Gram-negative bacteria and Archaea with high precision. The database is searchable, and can easily be expanded using either new bacterial genomes or new prediction tools as they become available. This will further improve the performance of the SCL prediction, as well as the detection of misannotated start codons and other annotation errors. ClubSub-P is available online at http://toolkit.tuebingen.mpg.de/clubsubp/},
}
@article {pmid22072124,
year = {2012},
author = {Oishi, R and Tada, C and Asano, R and Yamamoto, N and Suyama, Y and Nakai, Y},
title = {Growth of ammonia-oxidizing archaea and bacteria in cattle manure compost under various temperatures and ammonia concentrations.},
journal = {Microbial ecology},
volume = {63},
number = {4},
pages = {787-793},
pmid = {22072124},
issn = {1432-184X},
mesh = {Ammonia/*metabolism ; Animals ; Archaea/classification/enzymology/genetics/*growth &amp; development ; Bacteria/classification/enzymology/genetics/*growth &amp; development ; Cattle ; Culture Media ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; Denaturing Gradient Gel Electrophoresis ; Manure/*microbiology ; Nitrosomonas/classification/enzymology/genetics/growth &amp; development ; Oxidation-Reduction ; Oxidoreductases/*genetics/metabolism ; Polymerase Chain Reaction/methods ; Soil/analysis ; *Temperature ; },
abstract = {A recent study showed that ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) coexist in the process of cattle manure composting. To investigate their physiological characteristics, liquid cultures seeded with fermenting cattle manure compost were incubated at various temperatures (37°C, 46°C, or 60°C) and ammonium concentrations (0.5, 1, 4, or 10 mM NH (4) (+) -N). The growth rates of the AOB and AOA were monitored using real-time polymerase chain reaction analysis targeting the bacterial and archaeal ammonia monooxygenase subunit A genes. AOB grew at 37°C and 4 or 10 mM NH (4) (+) -N, whereas AOA grew at 46°C and 10 mM NH (4) (+) -N. Incubation with allylthiourea indicated that the AOB and AOA grew by oxidizing ammonia. Denaturing gradient gel electrophoresis and subsequent sequencing analyses revealed that a bacterium related to Nitrosomonas halophila and an archaeon related to Candidatus Nitrososphaera gargensis were the predominant AOB and AOA, respectively, in the seed compost and in cultures after incubation. This is the first report to demonstrate that the predominant AOA in cattle manure compost can grow and can probably oxidize ammonia under moderately thermophilic conditions.},
}
@article {pmid22071343,
year = {2012},
author = {Angel, R and Claus, P and Conrad, R},
title = {Methanogenic archaea are globally ubiquitous in aerated soils and become active under wet anoxic conditions.},
journal = {The ISME journal},
volume = {6},
number = {4},
pages = {847-862},
pmid = {22071343},
issn = {1751-7370},
mesh = {Carbon Dioxide/metabolism ; DNA, Ribosomal/analysis/genetics ; Euryarchaeota/*classification/genetics/*metabolism ; Methane/*metabolism ; Methanosarcina/classification/genetics/metabolism ; Oxidoreductases/genetics ; Phylogeny ; RNA, Ribosomal, 16S/analysis/genetics ; *Soil Microbiology ; },
abstract = {The prototypical representatives of the Euryarchaeota--the methanogens--are oxygen sensitive and are thought to occur only in highly reduced, anoxic environments. However, we found methanogens of the genera Methanosarcina and Methanocella to be present in many types of upland soils (including dryland soils) sampled globally. These methanogens could be readily activated by incubating the soils as slurry under anoxic conditions, as seen by rapid methane production within a few weeks, without any additional carbon source. Analysis of the archaeal 16S ribosomal RNA gene community profile in the incubated samples through terminal restriction fragment length polymorphism and quantification through quantitative PCR indicated dominance of Methanosarcina, whose gene copy numbers also correlated with methane production rates. Analysis of the δ(13)C of the methane further supported this, as the dominant methanogenic pathway was in most cases aceticlastic, which Methanocella cannot perform. Sequences of the key methanogenic enzyme methyl coenzyme M reductase retrieved from the soil samples before incubation confirmed that Methanosarcina and Methanocella are the dominant methanogens, though some sequences of Methanobrevibacter and Methanobacterium were also detected. The global occurrence of only two active methanogenic archaea supports the hypothesis that these are autochthonous members of the upland soil biome and are well adapted to their environment.},
}
@article {pmid22066608,
year = {2011},
author = {Roux, S and Enault, F and Bronner, G and Debroas, D},
title = {Comparison of 16S rRNA and protein-coding genes as molecular markers for assessing microbial diversity (Bacteria and Archaea) in ecosystems.},
journal = {FEMS microbiology ecology},
volume = {78},
number = {3},
pages = {617-628},
doi = {10.1111/j.1574-6941.2011.01190.x},
pmid = {22066608},
issn = {1574-6941},
mesh = {Archaea/classification/*genetics ; Archaeal Proteins/genetics ; Bacteria/classification/*genetics ; Bacterial Proteins/genetics ; *Biodiversity ; DNA Primers ; Metagenome ; Operon ; Phylogeny ; Polymerase Chain Reaction ; RNA, Archaeal/genetics ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/*genetics ; *Water Microbiology ; },
abstract = {PCR amplification of the rRNA gene is the most popular method for assessing microbial diversity. However, this molecular marker is often present in multiple copies in cells presenting, in addition, an intragenomic heterogeneity. In this context, housekeeping genes may be used as taxonomic markers for ecological studies. However, the efficiency of these protein-coding genes compared to 16S rRNA genes has not been tested on environmental data. For this purpose, five protein marker genes for which primer sets are available, were selected (rplB, pyrG, fusA, leuS and rpoB) and compared with 16S rRNA gene results from PCR amplification or metagenomic data from aquatic ecosystems. Analysis of the major groups found in these ecosystems, such as Actinobacteria, Bacteroides, Proteobacteria and Cyanobacteria, showed good agreement between the protein markers and the results given by 16S rRNA genes from metagenomic reads. However, with the markers it was possible to detect minor groups among the microbial assemblages, providing more details compared to 16S rRNA results from PCR amplification. In addition, the use of a set of protein markers made it possible to deduce a mean copy number of rRNA operons. This average estimate is essentially lower than the one estimated in sequenced genomes.},
}
@article {pmid22060043,
year = {2011},
author = {Bhaya, D and Davison, M and Barrangou, R},
title = {CRISPR-Cas systems in bacteria and archaea: versatile small RNAs for adaptive defense and regulation.},
journal = {Annual review of genetics},
volume = {45},
number = {},
pages = {273-297},
doi = {10.1146/annurev-genet-110410-132430},
pmid = {22060043},
issn = {1545-2948},
mesh = {Adaptive Immunity ; Archaea/chemistry/*genetics/immunology/virology ; Bacteria/chemistry/*genetics/immunology/virology ; Bacterial Proteins/chemistry/genetics/immunology ; Bacteriophages/genetics/immunology ; CRISPR-Associated Proteins ; Computational Biology ; Endodeoxyribonucleases/chemistry/genetics ; Escherichia coli Proteins ; Evolution, Molecular ; Gene Expression Regulation, Archaeal ; Gene Expression Regulation, Bacterial ; Genetic Loci ; Plasmids/immunology ; RNA Interference ; RNA Processing, Post-Transcriptional ; RNA, Archaeal/chemistry/*genetics/immunology ; RNA, Bacterial/chemistry/*genetics/immunology ; RNA, Small Untranslated/chemistry/genetics/immunology ; Transcription, Genetic ; Virus Diseases/genetics/immunology/virology ; },
abstract = {Bacteria and archaea have evolved defense and regulatory mechanisms to cope with various environmental stressors, including virus attack. This arsenal has been expanded by the recent discovery of the versatile CRISPR-Cas system, which has two novel features. First, the host can specifically incorporate short sequences from invading genetic elements (virus or plasmid) into a region of its genome that is distinguished by clustered regularly interspaced short palindromic repeats (CRISPRs). Second, when these sequences are transcribed and precisely processed into small RNAs, they guide a multifunctional protein complex (Cas proteins) to recognize and cleave incoming foreign genetic material. This adaptive immunity system, which uses a library of small noncoding RNAs as a potent weapon against fast-evolving viruses, is also used as a regulatory system by the host. Exciting breakthroughs in understanding the mechanisms of the CRISPR-Cas system and its potential for biotechnological applications and understanding evolutionary dynamics are discussed.},
}
@article {pmid22060041,
year = {2011},
author = {Yamaguchi, Y and Park, JH and Inouye, M},
title = {Toxin-antitoxin systems in bacteria and archaea.},
journal = {Annual review of genetics},
volume = {45},
number = {},
pages = {61-79},
doi = {10.1146/annurev-genet-110410-132412},
pmid = {22060041},
issn = {1545-2948},
support = {1R01GM081567/GM/NIGMS NIH HHS/United States ; },
mesh = {Adenosine Triphosphate/chemistry ; Amino Acid Sequence ; Archaea/*chemistry/genetics/physiology ; Bacteria/*chemistry/genetics ; Bacterial Physiological Phenomena ; Bacterial Toxins/*chemistry/genetics ; Cell Division ; DNA Replication ; Drug Resistance, Bacterial ; *Genome, Bacterial ; Molecular Sequence Data ; Multiprotein Complexes/chemistry/genetics ; Protein Binding ; Protein Structure, Secondary ; RNA Stability ; Ribosomes/chemistry/genetics ; },
abstract = {Almost all bacteria and many archaea contain genes whose expression inhibits cell growth and may lead to cell death when overproduced, reminiscent of apoptotic genes in higher systems. The cellular targets of these toxins are quite diverse and include DNA replication, mRNA stability, protein synthesis, cell-wall biosynthesis, and ATP synthesis. These toxins are co-expressed and neutralized with their cognate antitoxins from a TA (toxin-antitoxin) operon in normally growing cells. Antitoxins are more labile than toxins and are readily degraded under stress conditions, allowing the toxins to exert their toxic effect. Presence of at least 33 TA systems in Escherichia coli and more than 60 TA systems in Mycobacterium tuberculosis suggests that the TA systems are involved not only in normal bacterial physiology but also in pathogenicity of bacteria. The elucidation of their cellular function and regulation is thus crucial for our understanding of bacterial physiology under various stress conditions.},
}
@article {pmid22057919,
year = {2012},
author = {Gao, J and Wang, J},
title = {Re-annotation of two hyperthermophilic archaea Pyrococcus abyssi GE5 and Pyrococcus furiosus DSM 3638.},
journal = {Current microbiology},
volume = {64},
number = {2},
pages = {118-129},
pmid = {22057919},
issn = {1432-0991},
mesh = {Archaeal Proteins/genetics ; Genome, Archaeal ; Molecular Sequence Annotation ; Molecular Sequence Data ; Open Reading Frames ; Pyrococcus abyssi/*genetics ; Pyrococcus furiosus/*genetics ; },
abstract = {Pyrococcus abyssi GE5 (P. aby) and Pyrococcus furiosus DSM 3638 (P. fur) are two model hyperthermophilic archaea. However, their annotations in public databases are unsatisfactory. In this article, the two genomes were re-annotated according to the following steps. (i) All "hypothetical genes" in the original annotation were re-identified based on the Z-curve method, and some of them were recognized as non-coding open reading frames (ORFs). Evidence showed that the recognized non-coding ORFs were highly unlikely to encode proteins. (ii) The translation initiation sites (TISs) of all the annotated genes were re-located, and more than 10% of the TISs were shifted to 5'-upstream or 3'-downstream regions. (iii) The functions of the refined "hypothetical genes" were predicted using sequence alignment tools, more than 200 originally annotated "hypothetical genes" in either of the two hyperthermophiles were assigned functions. A large number of these functions have reference support or experimentally characterized homologues. All the refined information will serve as a valuable resource for research on P. aby and P. fur, which may be helpful in the exploration of thermal adaptation mechanisms. The complete re-annotation files of P. aby and P. fur are available at http://211.69.128.148/download/ .},
}
@article {pmid22029483,
year = {2012},
author = {Galand, PE and Bourrain, M and De Maistre, E and Catala, P and Desdevises, Y and Elifantz, H and Kirchman, DL and Lebaron, P},
title = {Phylogenetic and functional diversity of Bacteria and Archaea in a unique stratified lagoon, the Clipperton atoll (N Pacific).},
journal = {FEMS microbiology ecology},
volume = {79},
number = {1},
pages = {203-217},
doi = {10.1111/j.1574-6941.2011.01209.x},
pmid = {22029483},
issn = {1574-6941},
mesh = {Archaea/classification/*genetics/growth &amp; development ; Bacteria/classification/*genetics/growth &amp; development ; Base Sequence ; Biodiversity ; Ecosystem ; Genes, Archaeal ; Genes, Bacterial ; Molecular Sequence Data ; Pacific Ocean ; Phylogeny ; RNA, Ribosomal, 16S ; Seawater/*microbiology ; },
abstract = {The Clipperton lagoon in the North Pacific Ocean has been isolated from the surrounding sea for c. 160 years. It has a stratified water column that comprises an oxic and brackish upper water layer (mixolimnion) and a deep sulfuric anoxic saline layer (monimolimnion), separated by a steep pycnocline. Here, we test whether the Clipperton lagoon with its distinctive physico-chemical features, geographic isolation, recent water column stratification, and large nutrient input harbors original microbial communities. The combination of capillary electrophoresis single-strand polymorphism (CE-SSCP) fingerprinting and sequencing of cloned bacterial and archaeal 16S rRNA genes, and functional genes for methanogenesis (mcrA), methanotrophy (pmoA), and sulfate reduction (dsrAB), revealed that microbial communities and pathways were highly stratified down the water column. The mixolimnion contained ubiquitous freshwater clades of Alpha- and Betaproteobacteria, while the pycnocline contained mostly green sulfur bacteria (phylum Chlorobi). Sequences of the upper layers were closely related to sequences found in other aquatic ecosystems, suggesting that they have a strong potential for dispersal and colonization. In contrast, the monimolimnion contained new deeply branching bacterial divisions within the OP11 cluster and the Bacteroidetes, and was the most diverse of the layers. The unique environmental conditions characterizing the deep layers of the lagoon may explain the novelty of the microbial communities found at the Clipperton atoll.},
}
@article {pmid22029420,
year = {2012},
author = {Guan, Z and Naparstek, S and Calo, D and Eichler, J},
title = {Protein glycosylation as an adaptive response in Archaea: growth at different salt concentrations leads to alterations in Haloferax volcanii S-layer glycoprotein N-glycosylation.},
journal = {Environmental microbiology},
volume = {14},
number = {3},
pages = {743-753},
pmid = {22029420},
issn = {1462-2920},
support = {U54 GM069338/GM/NIGMS NIH HHS/United States ; GM-069338/GM/NIGMS NIH HHS/United States ; },
mesh = {Archaeal Proteins/genetics/metabolism ; Dolichol Phosphates/metabolism ; Glycoproteins/genetics/*metabolism ; Glycosylation ; Haloferax volcanii/genetics/metabolism/*physiology ; Membrane Glycoproteins ; Oligosaccharides/metabolism ; Polysaccharides/metabolism ; Protein Processing, Post-Translational ; Salinity ; Salt Tolerance/*physiology ; Sodium Chloride/metabolism ; },
abstract = {To cope with life in hypersaline environments, halophilic archaeal proteins are enriched in acidic amino acids. This strategy does not, however, offer a response to transient changes in salinity, as would post-translational modifications. To test this hypothesis, N-glycosylation of the Haloferax volcanii S-layer glycoprotein was compared in cells grown in high (3.4 M NaCl) and low (1.75 M NaCl) salt, as was the glycan bound to dolichol phosphate, the lipid upon which the N-linked glycan is assembled. In high salt, S-layer glycoprotein Asn-13 and Asn-83 are modified by a pentasaccharide, while dolichol phosphate is modified by a tetrasaccharide comprising the first four pentasaccharide residues. When the same targets were considered from cells grown in low salt, substantially less pentasaccharide was detected. At the same time, cells grown at low salinity contain dolichol phosphate modified by a distinct tetrasaccharide absent in cells grown at high salinity. The same tetrasaccharide modified S-layer glycoprotein Asn-498 in cells grown in low salt, whereas no glycan decorated this residue in cells grown in the high-salt medium. Thus, in response to changes in environmental salinity, Hfx. volcanii not only modulates the N-linked glycans decorating the S-layer glycoprotein but also the sites of such post-translational modification.},
}
@article {pmid22028845,
year = {2011},
author = {Shah, V and Shah, S and Kambhampati, MS and Ambrose, J and Smith, N and Dowd, SE and McDonnell, KT and Panigrahi, B and Green, T},
title = {Bacterial and archaea community present in the Pine Barrens Forest of Long Island, NY: unusually high percentage of ammonia oxidizing bacteria.},
journal = {PloS one},
volume = {6},
number = {10},
pages = {e26263},
pmid = {22028845},
issn = {1932-6203},
mesh = {Ammonia/*metabolism ; Archaea/*classification ; Bacteria/*classification/isolation &amp; purification/*metabolism ; *Biodiversity ; Cluster Analysis ; New York ; Oxidation-Reduction ; Soil Microbiology ; Trees/*microbiology ; },
abstract = {Of the few preserved areas in the northeast of United States, the soil in the Pine Barrens Forests presents a harsh environment for the microorganisms to grow and survive. In the current study we report the use of clustering methods to scientifically select the sampling locations that would represent the entire forest and also report the microbial diversity present in various horizons of the soil. Sixty six sampling locations were selected across the forest and soils were collected from three horizons (sampling depths). The three horizons were 0-10 cm (Horizon O); 11-25 cm (Horizon A) and 26-40 cm (Horizon B). Based on the total microbial substrate utilization pattern and K-means clustering analysis, the soil in the Pine Barrens Forest can be classified into four distinct clusters at each of the three horizons. One soil sample from each of the four clusters were selected and archaeal and bacterial populations within the soil studied using pyrosequencing method. The results show the microbial communities present in each of these clusters are different. Within the microbial communities present, microorganisms involved in nitrogen cycle occupy a major fraction of microbial community in the soil. High level of diversity was observed for nitrogen fixing bacteria. In contrast, Nitrosovibrio and Nitrosocaldus spp are the single bacterial and archaeal population respectively carrying out ammonia oxidation in the soil.},
}
@article {pmid22012341,
year = {2011},
author = {Visweswaran, GR and Dijkstra, BW and Kok, J},
title = {Murein and pseudomurein cell wall binding domains of bacteria and archaea--a comparative view.},
journal = {Applied microbiology and biotechnology},
volume = {92},
number = {5},
pages = {921-928},
pmid = {22012341},
issn = {1432-0614},
mesh = {Archaea/chemistry/enzymology/*metabolism ; Archaeal Proteins/chemistry/genetics/*metabolism ; Bacteria/chemistry/enzymology/*metabolism ; Bacterial Proteins/chemistry/genetics/*metabolism ; Cell Wall/*chemistry/enzymology/metabolism ; N-Acetylmuramoyl-L-alanine Amidase/chemistry/genetics/metabolism ; Peptidoglycan/*chemistry/metabolism ; Protein Binding ; },
abstract = {The cell wall, a major barrier protecting cells from their environment, is an essential compartment of both bacteria and archaea. It protects the organism from internal turgor pressure and gives a defined shape to the cell. The cell wall serves also as an anchoring surface for various proteins and acts as an adhesion platform for bacteriophages. The walls of bacteria and archaea are mostly composed of murein and pseudomurein, respectively. Cell wall binding domains play a crucial role in the non-covalent attachment of proteins to cell walls. Here, we give an overview of the similarities and differences in the biochemical and functional properties of the two major murein and pseudomurein cell wall binding domains, i.e., the Lysin Motif (LysM) domain (Pfam PF01476) and the pseudomurein binding (PMB) domain (Pfam PF09373) of bacteria and archaea, respectively.},
}
@article {pmid22007151,
year = {2011},
author = {Poli, A and Di Donato, P and Abbamondi, GR and Nicolaus, B},
title = {Synthesis, production, and biotechnological applications of exopolysaccharides and polyhydroxyalkanoates by archaea.},
journal = {Archaea (Vancouver, B.C.)},
volume = {2011},
number = {},
pages = {693253},
pmid = {22007151},
issn = {1472-3654},
mesh = {Acyltransferases/chemistry ; Archaea/*chemistry/genetics/growth &amp; development/physiology ; Archaeal Proteins/chemistry/physiology ; Bacteria/chemistry/growth &amp; development ; Biofilms/growth &amp; development ; Biological Products/chemistry ; *Biotechnology ; Environmental Microbiology ; Genes, Archaeal ; Polyhydroxyalkanoates/*biosynthesis/chemistry ; Polysaccharides/*biosynthesis/chemistry ; Polysaccharides, Bacterial/biosynthesis/chemistry/physiology ; Salinity ; Temperature ; },
abstract = {Extreme environments, generally characterized by atypical temperatures, pH, pressure, salinity, toxicity, and radiation levels, are inhabited by various microorganisms specifically adapted to these particular conditions, called extremophiles. Among these, the microorganisms belonging to the Archaea domain are of significant biotechnological importance as their biopolymers possess unique properties that offer insights into their biology and evolution. Particular attention has been devoted to two main types of biopolymers produced by such peculiar microorganisms, that is, the extracellular polysaccharides (EPSs), considered as a protection against desiccation and predation, and the endocellular polyhydroxyalkanoates (PHAs) that provide an internal reserve of carbon and energy. Here, we report the composition, biosynthesis, and production of EPSs and PHAs by different archaeal species.},
}
@article {pmid22006072,
year = {2012},
author = {Lentini, V and Gugliandolo, C and Maugeri, TL},
title = {Vertical distribution of Archaea and Bacteria in a meromictic lake as determined by fluorescent in situ hybridization.},
journal = {Current microbiology},
volume = {64},
number = {1},
pages = {66-74},
pmid = {22006072},
issn = {1432-0991},
mesh = {Archaea/classification/genetics/*isolation &amp; purification ; Bacteria/classification/genetics/*isolation &amp; purification ; Biodiversity ; Ecosystem ; In Situ Hybridization, Fluorescence/*methods ; Lakes/*microbiology ; Molecular Sequence Data ; },
abstract = {The prokaryotic cells distribution in the water column of the coastal saline meromictic Lake Faro (Messina, Italy) was investigated by microscopic counting techniques. Water samples were collected at a central station from the surface to the bottom, when waters were characterized by a marked stratification. A "red-water" layer, caused by a dense growth of photosynthetic sulfur bacteria, was present at a depth of 15 m, defining a transition area between oxic (mixolimnion) and anoxic (monimolimnion) layers. Fluorescently labeled 16S rRNA oligonucleotide, group-specific probes were used to determine the abundance of Bacteria and Archaea, and their subgroups, Green Sulfur Bacteria (GSB), Sulfate Reducing Bacteria (SRB), Cyanobacteria and Chromatium okenii, and Crenarchaeota and Euryarchaeota, as key elements of the microbial community. Bacteria decreased from surface to bottom, while Archaea increased with depth and reached the maximum value at 30 m, where they outnumbered the Bacteria. Bacteria and picophytoplankton prevailed in the mixolimnion. At the chemocline high numbers of prokaryotic cells were present, mainly represented by Cyanobacteria, Chromatium okenii and Euryarchaeota. GSB, SRB, and Crenarchaeota prevailed below the chemocline. Although Archaea constitute a minor fraction of microbial community, they could represent active contributors to the meromictic Lake Faro ecosystem.},
}
@article {pmid22002710,
year = {2012},
author = {Murphy, DJ},
title = {The dynamic roles of intracellular lipid droplets: from archaea to mammals.},
journal = {Protoplasma},
volume = {249},
number = {3},
pages = {541-585},
pmid = {22002710},
issn = {1615-6102},
mesh = {Animals ; Archaea/*metabolism ; Bacteria/metabolism ; Fungi/metabolism ; Humans ; *Lipid Metabolism ; Organelles/*metabolism/ultrastructure ; Plants/metabolism ; Polyhydroxyalkanoates/metabolism ; Triglycerides/metabolism ; },
abstract = {During the past decade, there has been a paradigm shift in our understanding of the roles of intracellular lipid droplets (LDs). New genetic, biochemical and imaging technologies have underpinned these advances, which are revealing much new information about these dynamic organelles. This review takes a comparative approach by examining recent work on LDs across the whole range of biological organisms from archaea and bacteria, through yeast and Drosophila to mammals, including humans. LDs probably evolved originally in microorganisms as temporary stores of excess dietary lipid that was surplus to the immediate requirements of membrane formation/turnover. LDs then acquired roles as long-term carbon stores that enabled organisms to survive episodic lack of nutrients. In multicellular organisms, LDs went on to acquire numerous additional roles including cell- and organism-level lipid homeostasis, protein sequestration, membrane trafficking and signalling. Many pathogens of plants and animals subvert their host LD metabolism as part of their infection process. Finally, malfunctions in LDs and associated proteins are implicated in several degenerative diseases of modern humans, among the most serious of which is the increasingly prevalent constellation of pathologies, such as obesity and insulin resistance, which is associated with metabolic syndrome.},
}
@article {pmid21999488,
year = {2011},
author = {Ajon, M and Fröls, S and van Wolferen, M and Stoecker, K and Teichmann, D and Driessen, AJ and Grogan, DW and Albers, SV and Schleper, C},
title = {UV-inducible DNA exchange in hyperthermophilic archaea mediated by type IV pili.},
journal = {Molecular microbiology},
volume = {82},
number = {4},
pages = {807-817},
doi = {10.1111/j.1365-2958.2011.07861.x},
pmid = {21999488},
issn = {1365-2958},
mesh = {Biological Transport ; DNA, Archaeal/*metabolism ; Gene Transfer, Horizontal/*radiation effects ; In Situ Hybridization, Fluorescence ; Recombination, Genetic ; Sulfolobus/*genetics/*radiation effects ; },
abstract = {Archaea, like bacteria and eukaryotes, contain proteins involved in various mechanisms of DNA repair, highlighting the importance of these processes for all forms of life. Species of the order Sulfolobales of hyperthermophilic crenarchaeota are equipped with a strongly UV-inducible type IV pilus system that promotes cellular aggregation. Here we demonstrate by fluorescence in situ hybridization that cellular aggregates are formed based on a species-specific recognition process and that UV-induced cellular aggregation mediates chromosomal marker exchange with high frequency. Recombination rates exceeded those of uninduced cultures by up to three orders of magnitude. Knockout strains of Sulfolobus acidocaldarius incapable of pilus production could not self-aggregate, but were partners in mating experiments with wild-type strains indicating that one cellular partner can mediate the DNA transfer. Since pilus knockout strains showed decreased survival upon UV treatment, we conclude that the UV-inducible DNA transfer process and subsequent homologous recombination represents an important mechanism to maintain chromosome integrity in Sulfolobus. It might also contribute substantially to the frequent chromosomal DNA exchange and horizontal gene transfer in these archaea in their natural habitat.},
}
@article {pmid21998711,
year = {2011},
author = {Takemoto, K and Borjigin, S},
title = {Metabolic network modularity in archaea depends on growth conditions.},
journal = {PloS one},
volume = {6},
number = {10},
pages = {e25874},
pmid = {21998711},
issn = {1932-6203},
mesh = {Adaptation, Physiological ; Archaea/*growth &amp; development/*metabolism/physiology ; Autotrophic Processes ; Ecosystem ; Heterotrophic Processes ; *Metabolic Networks and Pathways ; Oxygen/metabolism ; Temperature ; },
abstract = {Network modularity is an important structural feature in metabolic networks. A previous study suggested that the variability in natural habitat promotes metabolic network modularity in bacteria. However, since many factors influence the structure of the metabolic network, this phenomenon might be limited and there may be other explanations for the change in metabolic network modularity. Therefore, we focus on archaea because they belong to another domain of prokaryotes and show variability in growth conditions (e.g., trophic requirement and optimal growth temperature), but not in habitats because of their specialized growth conditions (e.g., high growth temperature). The relationship between biological features and metabolic network modularity is examined in detail. We first show the absence of a relationship between network modularity and habitat variability in archaea, as archaeal habitats are more limited than bacterial habitats. Although this finding implies the need for further studies regarding the differences in network modularity, it does not contradict previous work. Further investigations reveal alternative explanations. Specifically, growth conditions, trophic requirement, and optimal growth temperature, in particular, affect metabolic network modularity. We have discussed the mechanisms for the growth condition-dependant changes in network modularity. Our findings suggest different explanations for the changes in network modularity and provide new insights into adaptation and evolution in metabolic networks, despite several limitations of data analysis.},
}
@article {pmid21985229,
year = {2011},
author = {Ugalde, JA and Podell, S and Narasingarao, P and Allen, EE},
title = {Xenorhodopsins, an enigmatic new class of microbial rhodopsins horizontally transferred between archaea and bacteria.},
journal = {Biology direct},
volume = {6},
number = {},
pages = {52},
pmid = {21985229},
issn = {1745-6150},
support = {R21HG005107-02/HG/NHGRI NIH HHS/United States ; },
mesh = {Amino Acid Sequence ; Archaea/*chemistry/classification/genetics ; Bacteria/*chemistry/classification/genetics ; *Gene Transfer, Horizontal ; *Genes, Archaeal ; *Genes, Bacterial ; Molecular Sequence Data ; Phylogeny ; Rhodopsins, Microbial/*chemistry/genetics ; Sequence Alignment ; },
abstract = {Based on unique, coherent properties of phylogenetic analysis, key amino acid substitutions and structural modeling, we have identified a new class of unusual microbial rhodopsins related to the Anabaena sensory rhodopsin (ASR) protein, including multiple homologs not previously recognized. We propose the name xenorhodopsin for this class, reflecting a taxonomically diverse membership spanning five different Bacterial phyla as well as the Euryarchaeotal class Nanohaloarchaea. The patchy phylogenetic distribution of xenorhodopsin homologs is consistent with historical dissemination through horizontal gene transfer. Shared characteristics of xenorhodopsin-containing microbes include the absence of flagellar motility and isolation from high light habitats.},
}
@article {pmid21958017,
year = {2012},
author = {Rosselló-Móra, R},
title = {Towards a taxonomy of Bacteria and Archaea based on interactive and cumulative data repositories.},
journal = {Environmental microbiology},
volume = {14},
number = {2},
pages = {318-334},
doi = {10.1111/j.1462-2920.2011.02599.x},
pmid = {21958017},
issn = {1462-2920},
mesh = {Archaea/*classification/genetics ; Bacteria/*classification/genetics ; Genomics/methods ; *Information Storage and Retrieval ; Phylogeny ; },
abstract = {Taxonomy in the second decade of the 21st century is benefiting from technological advances in molecular microbiology, especially those related to genomics. Gene and genome databases are significantly increasing due to intense research activities in the field of molecular ecology and genomics. Taxa, and especially species, are tailored by means of the recognition of a phylogenetic, genomic and phenotypic coherence that reveal their uniqueness in the classification schema. Phylogenetic coherence is mainly revealed by means of 16S rRNA gene analyses for which curated databases such as EzTaxon and LTP provide a valuable tool for tree reconstruction to taxonomy users. On the other hand, in silico full or partial genomic sequence comparisons are called on to substitute cumbersome techniques such as DNA-DNA hybridization (DDH) to genomically circumscribe species. DDH similarity values around 70% would be equivalent to ANI values of 96%. Finally, finding an exclusive phenotypic property for the taxa to be classified is of paramount relevance to producing an operative and predictive classification system. The current methods used for taxonomic classification require significant laboratory experimentation, and generally will not produce interactive databases. The new high-throughput metabolomic technologies, such as ICR-FT and MALDI-TOF mass spectrometry methods, open the door to the construction of metabolic databases for taxonomic purposes. It is to be foreseen that, in the future, taxonomists will benefit significantly from public databases speeding up the classification process. However, serious effort will be needed to harmonize them and to prevent inaccurate material.},
}
@article {pmid21955587,
year = {2011},
author = {Levy, S and Portnoy, V and Admon, J and Schuster, G},
title = {Distinct activities of several RNase J proteins in methanogenic archaea.},
journal = {RNA biology},
volume = {8},
number = {6},
pages = {1073-1083},
doi = {10.4161/rna.8.6.16604},
pmid = {21955587},
issn = {1555-8584},
mesh = {Archaeal Proteins/chemistry/genetics/*metabolism ; Cleavage And Polyadenylation Specificity Factor/chemistry ; DNA, Single-Stranded/metabolism ; Escherichia coli/genetics ; Euryarchaeota/*enzymology/genetics ; Genome, Archaeal ; Phosphorylation ; Recombinant Proteins/genetics/metabolism ; Ribonucleases/*chemistry/genetics/*metabolism ; Sequence Homology, Amino Acid ; Substrate Specificity ; Temperature ; },
abstract = {RNA degradation plays an important role in the control of gene expression in all domains of life, including Archaea. While analyzing RNA degradation in different archaea, we faced an interesting situation. The members of a group of methanogenic archaea, including Methanocaldococcus jannaschii, contain neither the archaeal exosome nor RNase II/R homologs. However, looking for potential ribonucleases revealed proteins related to the recently discovered ribonuclease RNase J. RNase J is unique among known ribonucleases because it may combine endo- and 5'→3' exo-ribonucleolytic activities in a single polypeptide. Here, we report the characterization of the ribonuclease activities of three RNase J homologs encoded in the genome of the methanogenic archaeon Methanocaldococcus jannaschii. The analysis of the recombinant archaeal proteins purified from E. coli revealed an optimal activity at 60°C. Whereas mjRNase J1 and -J3 displayed exclusively 5'→3' exonucleolytic activity, mjRNase J2 is an endonuclease with no apparent exonuclease activity. The exonucleolytic activity of both mjRNase J1 and -J3 is enhanced in molecules harboring monophosphate at the 5' end. mjRNase J3, and to some extent mjRNase J2, degrade ssDNA. Together, these results reveal that in archaea lacking the exosome and RNase II/R, RNA and perhaps also DNA are possibly degraded by the coordinated activities of several RNase J proteins. Unlike bacteria, in archaea RNase J proteins provide separately the exo- and endonucleolytic activities that are probably essential for RNA degradation.},
}
@article {pmid21945597,
year = {2012},
author = {Allocati, N and Federici, L and Masulli, M and Di Ilio, C},
title = {Distribution of glutathione transferases in Gram-positive bacteria and Archaea.},
journal = {Biochimie},
volume = {94},
number = {3},
pages = {588-596},
doi = {10.1016/j.biochi.2011.09.008},
pmid = {21945597},
issn = {1638-6183},
mesh = {Archaea/*enzymology/metabolism ; Glutathione/metabolism ; Glutathione Transferase/genetics/*metabolism ; Gram-Positive Bacteria/*enzymology/metabolism ; },
abstract = {Glutathione transferases (GSTs) have been widely studied in Gram-negative bacteria and the structure and function of several representatives have been elucidated. Conversely, limited information is available about the occurrence, classification and functional features of GSTs both in Gram-positive bacteria and in Archaea. An analysis of 305 fully-sequenced Gram-positive genomes highlights the presence of 49 putative GST genes in the genera of both Firmicutes and Actinobacteria phyla. We also performed an analysis on 81 complete genomes of the Archaea domain. Eleven hits were found in the Halobacteriaceae family of the Euryarchaeota phylum and only one in the Crenarchaeota phylum. A comparison of the identified sequences with well-characterized GSTs belonging to both Gram-negative and eukaryotic GSTs sheds light on their putative function and the evolutionary relationships within the large GST superfamily. This analysis suggests that the identified sequences mainly cluster in the new Xi class, while Beta class GSTs, widely distributed in Gram-negative bacteria, are under-represented in Gram-positive bacteria and absent in Archaea.},
}
@article {pmid21941460,
year = {2011},
author = {Jorda, J and Yeates, TO},
title = {Widespread disulfide bonding in proteins from thermophilic archaea.},
journal = {Archaea (Vancouver, B.C.)},
volume = {2011},
number = {},
pages = {409156},
pmid = {21941460},
issn = {1472-3654},
mesh = {Archaeal Proteins/*chemistry/isolation &amp; purification ; Computational Biology/methods ; Crenarchaeota/*chemistry ; Disulfides/*metabolism ; Euryarchaeota/*chemistry ; Models, Molecular ; Protein Stability ; },
abstract = {Disulfide bonds are generally not used to stabilize proteins in the cytosolic compartments of bacteria or eukaryotic cells, owing to the chemically reducing nature of those environments. In contrast, certain thermophilic archaea use disulfide bonding as a major mechanism for protein stabilization. Here, we provide a current survey of completely sequenced genomes, applying computational methods to estimate the use of disulfide bonding across the Archaea. Microbes belonging to the Crenarchaeal branch, which are essentially all hyperthermophilic, are universally rich in disulfide bonding while lesser degrees of disulfide bonding are found among the thermophilic Euryarchaea, excluding those that are methanogenic. The results help clarify which parts of the archaeal lineage are likely to yield more examples and additional specific data on protein disulfide bonding, as increasing genomic sequencing efforts are brought to bear.},
}
@article {pmid21935454,
year = {2011},
author = {Mao, Y and Yannarell, AC and Mackie, RI},
title = {Changes in N-transforming archaea and bacteria in soil during the establishment of bioenergy crops.},
journal = {PloS one},
volume = {6},
number = {9},
pages = {e24750},
pmid = {21935454},
issn = {1932-6203},
mesh = {Ammonia ; Archaea/classification/genetics/*metabolism ; Archaeal Proteins/genetics/metabolism ; Bacteria/classification/genetics/*metabolism ; Bacterial Proteins/genetics/metabolism ; Biodiversity ; Crops, Agricultural/*microbiology ; Nitrification ; Nitrogen/*metabolism ; Real-Time Polymerase Chain Reaction ; Soil Microbiology ; },
abstract = {Widespread adaptation of biomass production for bioenergy may influence important biogeochemical functions in the landscape, which are mainly carried out by soil microbes. Here we explore the impact of four potential bioenergy feedstock crops (maize, switchgrass, Miscanthus X giganteus, and mixed tallgrass prairie) on nitrogen cycling microorganisms in the soil by monitoring the changes in the quantity (real-time PCR) and diversity (barcoded pyrosequencing) of key functional genes (nifH, bacterial/archaeal amoA and nosZ) and 16S rRNA genes over two years after bioenergy crop establishment. The quantities of these N-cycling genes were relatively stable in all four crops, except maize (the only fertilized crop), in which the population size of AOB doubled in less than 3 months. The nitrification rate was significantly correlated with the quantity of ammonia-oxidizing archaea (AOA) not bacteria (AOB), indicating that archaea were the major ammonia oxidizers. Deep sequencing revealed high diversity of nifH, archaeal amoA, bacterial amoA, nosZ and 16S rRNA genes, with 229, 309, 330, 331 and 8989 OTUs observed, respectively. Rarefaction analysis revealed the diversity of archaeal amoA in maize markedly decreased in the second year. Ordination analysis of T-RFLP and pyrosequencing results showed that the N-transforming microbial community structures in the soil under these crops gradually differentiated. Thus far, our two-year study has shown that specific N-transforming microbial communities develop in the soil in response to planting different bioenergy crops, and each functional group responded in a different way. Our results also suggest that cultivation of maize with N-fertilization increases the abundance of AOB and denitrifiers, reduces the diversity of AOA, and results in significant changes in the structure of denitrification community.},
}
@article {pmid21915180,
year = {2011},
author = {Montoya, L and Lozada-Chávez, I and Amils, R and Rodriguez, N and Marín, I},
title = {The sulfate-rich and extreme saline sediment of the ephemeral tirez lagoon: a biotope for acetoclastic sulfate-reducing bacteria and hydrogenotrophic methanogenic archaea.},
journal = {International journal of microbiology},
volume = {2011},
number = {},
pages = {753758},
pmid = {21915180},
issn = {1687-9198},
abstract = {Our goal was to examine the composition of methanogenic archaea (MA) and sulfate-reducing (SRP) and sulfur-oxidizing (SOP) prokaryotes in the extreme athalassohaline and particularly sulfate-rich sediment of Tirez Lagoon (Spain). Thus, adenosine-5'-phosphosulfate (APS) reductase α (aprA) and methyl coenzyme M reductase α (mcrA) gene markers were amplified given that both enzymes are specific for SRP, SOP, and MA, respectively. Anaerobic populations sampled at different depths in flooded and dry seasons from the anoxic sediment were compared qualitatively via denaturing gradient gel electrophoresis (DGGE) fingerprint analysis. Phylogenetic analyses allowed the detection of SRP belonging to Desulfobacteraceae, Desulfohalobiaceae, and Peptococcaceae in ∂-proteobacteria and Firmicutes and SOP belonging to Chromatiales/Thiotrichales clade and Ectothiorhodospiraceae in γ-proteobacteria as well as MA belonging to methylotrophic species in Methanosarcinaceae and one hydrogenotrophic species in Methanomicrobiaceae. We also estimated amino acid composition, GC content, and preferential codon usage for the AprA and McrA sequences from halophiles, nonhalophiles, and Tirez phylotypes. Even though our results cannot be currently conclusive regarding the halotolerant strategies carried out by Tirez phylotypes, we discuss the possibility of a plausible "salt-in" signal in SRP and SOP as well as of a speculative complementary haloadaptation between salt-in and salt-out strategies in MA.},
}
@article {pmid21906652,
year = {2012},
author = {Merino, F and Rivas-Pardo, JA and Caniuguir, A and García, I and Guixé, V},
title = {Catalytic and regulatory roles of divalent metal cations on the phosphoryl-transfer mechanism of ADP-dependent sugar kinases from hyperthermophilic archaea.},
journal = {Biochimie},
volume = {94},
number = {2},
pages = {516-524},
doi = {10.1016/j.biochi.2011.08.021},
pmid = {21906652},
issn = {1638-6183},
mesh = {ATP Synthetase Complexes/genetics/*metabolism ; Amino Acid Sequence ; Archaea/*enzymology/genetics ; Archaeal Proteins/genetics/*metabolism ; Binding Sites ; Biocatalysis ; Cations, Divalent/metabolism ; Glucokinase/genetics/*metabolism ; Hot Temperature ; Kinetics ; Metals/metabolism ; Molecular Dynamics Simulation ; Molecular Sequence Data ; Nucleotides/metabolism ; Phosphofructokinases/genetics/*metabolism ; Phosphorylation ; Protein Binding ; Protein Structure, Tertiary ; Recombinant Proteins/genetics/metabolism ; Substrate Specificity ; },
abstract = {In some archaea, glucose degradation proceeds through a modified version of the Embden-Meyerhof pathway where glucose and fructose-6-P phosphorylation is carried out by kinases that use ADP as the phosphoryl donor. Unlike their ATP-dependent counterparts these enzymes have been reported as non-regulated. Based on the three dimensional structure determination of several ADP-dependent kinases they can be classified as members of the ribokinase superfamily. In this work, we have studied the role of divalent metal cations on the catalysis and regulation of ADP-dependent glucokinases and phosphofructokinase from hyperthermophilic archaea by means of initial velocity assays as well as molecular dynamics simulations. The results show that a divalent cation is strictly necessary for the activity of these enzymes and they strongly suggest that the true substrate is the metal-nucleotide complex. Also, these enzymes are promiscuous in relation to their metal usage where the only considerations for metal assisted catalysis seem to be related to the ionic radii and coordination geometry of the cations. Molecular dynamics simulations strongly suggest that this metal is bound to the highly conserved NXXE motif, which constitutes one of the signatures of the ribokinase superfamily. Although free ADP cannot act as a phosphoryl donor it still can bind to these enzymes with a reduced affinity, stressing the importance of the metal in the proper binding of the nucleotide at the active site. Also, data show that the binding of a second metal to these enzymes produces a complex with a reduced catalytic constant. On the basis of these findings and considering evolutionary information for the ribokinase superfamily, we propose that the regulatory metal acts by modulating the energy difference between the protein-substrates complex and the reaction transition state, which could constitute a general mechanism for the metal regulation of the enzymes that belong this superfamily.},
}
@article {pmid21894491,
year = {2011},
author = {Abrevaya, XC and Sacco, N and Mauas, PJ and Cortón, E},
title = {Archaea-based microbial fuel cell operating at high ionic strength conditions.},
journal = {Extremophiles : life under extreme conditions},
volume = {15},
number = {6},
pages = {633-642},
pmid = {21894491},
issn = {1433-4909},
mesh = {Archaea/*growth &amp; development/metabolism ; *Bioelectric Energy Sources ; Electrochemistry ; Electrodes ; Osmolar Concentration ; },
abstract = {In this work, two archaea microorganisms (Haloferax volcanii and Natrialba magadii) used as biocatalyst at a microbial fuel cell (MFC) anode were evaluated. Both archaea are able to grow at high salt concentrations. By increasing the media conductivity, the internal resistance was diminished, improving the MFC's performance. Without any added redox mediator, maximum power (P (max)) and current at P (max) were 11.87/4.57/0.12 μW cm(-2) and 49.67/22.03/0.59 μA cm(-2) for H. volcanii, N. magadii and E. coli, respectively. When neutral red was used as the redox mediator, P (max) was 50.98 and 5.39 μW cm(-2) for H. volcanii and N. magadii, respectively. In this paper, an archaea MFC is described and compared with other MFC systems; the high salt concentration assayed here, comparable with that used in Pt-catalyzed alkaline hydrogen fuel cells, will open new options when MFC scaling up is the objective necessary for practical applications.},
}
@article {pmid21889861,
year = {2012},
author = {Cui, HL and Mou, YZ and Yang, X and Zhou, YG and Liu, HC and Zhou, PJ},
title = {Halorubellus salinus gen. nov., sp. nov. and Halorubellus litoreus sp. nov., novel halophilic archaea isolated from a marine solar saltern.},
journal = {Systematic and applied microbiology},
volume = {35},
number = {1},
pages = {30-34},
doi = {10.1016/j.syapm.2011.08.001},
pmid = {21889861},
issn = {1618-0984},
mesh = {Archaea/*classification/genetics/*isolation &amp; purification ; Base Composition ; China ; Cluster Analysis ; DNA, Archaeal/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; DNA-Directed RNA Polymerases/genetics ; Geologic Sediments/*microbiology ; Glycolipids/analysis ; Hydrogen-Ion Concentration ; Magnesium/metabolism ; Molecular Sequence Data ; Nucleic Acid Hybridization ; Phospholipids/analysis ; Phylogeny ; Pigments, Biological/metabolism ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sodium Chloride/metabolism ; Temperature ; },
abstract = {Two extremely halophilic archaeal strains GX3(T) and GX26(T) were isolated from the Gangxi marine solar saltern near the Weihai city of Shandong Province, China. Cells from the two strains were pleomorphic and stained Gram-negative, colonies were red-pigmented. Strains GX3(T) and GX26(T) were able to grow at 25-50 °C (optimum 37 °C), at 1.4-5.1M NaCl (optimum 3.1M), at pH 5.5-9.5 (optimum pH 7.0) and neither strain required Mg(2+) for growth. Cells lyse in distilled water and the minimal NaCl concentration to prevent cell-lysis was 8% (w/v). The major polar lipids of the two strains were PA (phosphatidic acid), PG (phosphatidylglycerol), PGP-Me (phosphatidylglycerol phosphate methyl ester) and three major glycolipids (GL1, GL2 &amp; GL3) chromatographically identical to S-TGD-1 (sulfated galactosyl mannosy glucosyl diether), S-DGD-1 (sulfated mannosyl glucosyl diether), and DGD-1 (mannosyl glucosyl diether) respectively, an unidentified lipid (GL4) was also detected in strain GX26(T). Phylogenetic analysis based on 16S rRNA gene revealed that strain GX3(T) and strain GX26(T) formed a distinct clade with the closest relative, Haladaptatus paucihalophilus (89.9-92.4% and 90.4-92.7, respectively). The rpoB' gene similarities between strains GX3(T) and GX26(T), and between the two strains and the closest relative, Halorussus rarus TBN4(T) are 96.5%, 84.3% and 83.9%, respectively. The DNA G+C contents of strain GX3(T) and strain GX26(T) are 67.3 mol% and 67.2 mol%, respectively. The DNA-DNA hybridization value between strain GX3(T) and strain GX26(T) was 44%. The phenotypic, chemotaxonomic and phylogenetic properties suggest that strain GX3(T) and strain GX26(T) represent two novel species in a new genus within the family Halobacteriaceae, Halorubellus salinus gen. nov., sp. nov. (type strain GX3(T)=CGMCC 1.10384(T)=JCM 17115(T)) and Halorubellus litoreus sp. nov. (type strain GX26(T)=CGMCC 1.10386(T)=JCM 17117(T)).},
}
@article {pmid21880595,
year = {2011},
author = {Fujishima, K and Sugahara, J and Miller, CS and Baker, BJ and Di Giulio, M and Takesue, K and Sato, A and Tomita, M and Banfield, JF and Kanai, A},
title = {A novel three-unit tRNA splicing endonuclease found in ultrasmall Archaea possesses broad substrate specificity.},
journal = {Nucleic acids research},
volume = {39},
number = {22},
pages = {9695-9704},
pmid = {21880595},
issn = {1362-4962},
mesh = {Amino Acid Sequence ; Base Sequence ; Dimerization ; Endoribonucleases/*chemistry/classification/*metabolism ; Euryarchaeota/*enzymology/genetics ; Evolution, Molecular ; Molecular Sequence Data ; Nucleotide Motifs ; Phylogeny ; Protein Subunits/metabolism ; RNA Splicing ; RNA, Transfer/chemistry/genetics/*metabolism ; Substrate Specificity ; },
abstract = {tRNA splicing endonucleases, essential enzymes found in Archaea and Eukaryotes, are involved in the processing of pre-tRNA molecules. In Archaea, three types of splicing endonuclease [homotetrameric: α(4), homodimeric: α(2), and heterotetrameric: (αβ)(2)] have been identified, each representing different substrate specificity during the tRNA intron cleavage. Here, we discovered a fourth type of archaeal tRNA splicing endonuclease (ε(2)) in the genome of the acidophilic archaeon Candidatus Micrarchaeum acidiphilum, referred to as ARMAN-2 and its closely related species, ARMAN-1. The enzyme consists of two duplicated catalytic units and one structural unit encoded on a single gene, representing a novel three-unit architecture. Homodimeric formation was confirmed by cross-linking assay, and site-directed mutagenesis determined that the conserved L10-pocket interaction between catalytic and structural unit is necessary for the assembly. A tRNA splicing assay reveal that ε(2) endonuclease cleaves both canonical and non-canonical bulge-helix-bulge motifs, similar to that of (αβ)(2) endonuclease. Unlike other ARMAN and Euryarchaeota, tRNAs found in ARMAN-2 are highly disrupted by introns at various positions, which again resemble the properties of archaeal species with (αβ)(2) endonuclease. Thus, the discovery of ε(2) endonuclease in an archaeon deeply branched within Euryarchaeota represents a new example of the coevolution of tRNA and their processing enzymes.},
}
@article {pmid21869898,
year = {2011},
author = {Liu, F and Han, M and Zhang, F and Zhang, B and Li, Z},
title = {Distribution and Abundance of Archaea in South China Sea Sponge Holoxea sp. and the Presence of Ammonia-Oxidizing Archaea in Sponge Cells.},
journal = {Evidence-based complementary and alternative medicine : eCAM},
volume = {2011},
number = {},
pages = {723696},
pmid = {21869898},
issn = {1741-4288},
abstract = {Compared with bacterial symbionts, little is known about archaea in sponges especially about their spatial distribution and abundance. Understanding the distribution and abundance of ammonia-oxidizing archaea will help greatly in elucidating the potential function of symbionts in nitrogen cycling in sponges. In this study, gene libraries of 16S rRNA gene and ammonia monooxygenase subunit A (amoA) genes and quantitative real-time PCR were used to study the spatial distribution and abundance of archaea in the South China Sea sponge Holoxea sp. As a result, Holoxea sp. specific AOA, mainly group C1a (marine group I: Crenarchaeota) were identified. The presence of ammonia-oxidizing crenarchaea was observed for the first time within sponge cells. This study suggested a close relationship between sponge host and its archaeal symbionts as well as the archaeal potential contribution to sponge host in the ammonia-oxidizing process of nitrification.},
}
@article {pmid21853327,
year = {2011},
author = {Litchfield, CD},
title = {Potential for industrial products from the halophilic Archaea.},
journal = {Journal of industrial microbiology &amp; biotechnology},
volume = {38},
number = {10},
pages = {1635-1647},
pmid = {21853327},
issn = {1476-5535},
mesh = {Biopolymers/metabolism ; Esterases/metabolism ; Halobacteriales/*enzymology ; Industrial Microbiology ; Lipase/metabolism ; N-Glycosyl Hydrolases/metabolism ; Peptide Hydrolases/metabolism ; Surface-Active Agents/metabolism ; },
abstract = {The halophilic Archaea are a group of microorganisms that have not been extensively considered for biotechnological applications. This review describes some of the enzymes and products and the potential applications of this unique group of microorganisms to various industrial processes. Specifically, the characteristics of the glycosyl hydrolases, lipases and esterases, proteases, biopolymers and surfactants, as well as some miscellaneous other activities will be described.},
}
@article {pmid21848800,
year = {2011},
author = {Guerry, P},
title = {N-linked glycosylation in Archaea: two paths to the same glycan.},
journal = {Molecular microbiology},
volume = {81},
number = {5},
pages = {1133-1135},
doi = {10.1111/j.1365-2958.2011.07782.x},
pmid = {21848800},
issn = {1365-2958},
mesh = {Archaeal Proteins/*metabolism ; Haloarcula marismortui/*metabolism ; Haloferax volcanii/*metabolism ; },
abstract = {N-linked protein glycosylation occurs in all three branches of life, eukaryotes, bacteria and archaea. The simplest system is that of the bacterium, Campylobacter jejuni, in which a heptasaccharide glycan is added to multiple proteins from a single lipid carrier molecule. In the eukaryotic system a conserved tetradecasaccharide modification is first added to target proteins, but is then modified by trimming and addition of other glycans from additional carrier molecules resulting in a diverse array of glycans of distinct functionality. In the halophilic Archaea from the Dead Sea, Haloferax volcanii, the surface array or S-layer protein is glycosylated with a pentasaccharide. This glycan is synthesized from two separate carrier molecules, one that carries a tetrasaccharide and another that carries the terminal mannose, in a process that is analogous to that of eukaryotes. In this issue of Molecular Microbiology the glycosylation of the S-layer of another halophilic Archaea from the Dead Sea, Haloarcula marismortui is characterized (Calo et al., 2011). This S-layer is glycosylated with the same pentasaccharide as that of Hfx. volcanii, but the intact pentasaccharide is synthesized on a single carrier molecule in Har. marismortui in a process that more closely resembles that of the bacterial N-linked system.},
}
@article {pmid21843932,
year = {2011},
author = {Zeng, G and Zhang, J and Chen, Y and Yu, Z and Yu, M and Li, H and Liu, Z and Chen, M and Lu, L and Hu, C},
title = {Relative contributions of archaea and bacteria to microbial ammonia oxidation differ under different conditions during agricultural waste composting.},
journal = {Bioresource technology},
volume = {102},
number = {19},
pages = {9026-9032},
doi = {10.1016/j.biortech.2011.07.076},
pmid = {21843932},
issn = {1873-2976},
mesh = {Agriculture/*methods ; Ammonia/*metabolism ; Archaea/genetics/*metabolism ; Bacteria/genetics/*metabolism ; Denaturing Gradient Gel Electrophoresis ; Oxidation-Reduction ; Oxidoreductases/*genetics ; Polymerase Chain Reaction ; Soil ; Waste Products ; },
abstract = {The aim of this study was to compare the relative contribution of ammonia-oxidizing archaea (AOA) and bacteria (AOB) to nitrification during agricultural waste composting. The AOA and AOB amoA gene abundance and composition were determined by quantitative PCR and denaturing gradient gel electrophoresis (DGGE), respectively. The results showed that the archaeal amoA gene was abundant throughout the composting process, while the bacterial amoA gene abundance decreased to undetectable level during the thermophilic and cooling stages. DGGE showed more diverse archaeal amoA gene composition when the potential ammonia oxidation (PAO) rate reached peak values. A significant positive relationship was observed between the PAO rate and the archaeal amoA gene abundance (R[2]=0.554; P<0.001), indicating that archaea dominated ammonia oxidation during the thermophilic and cooling stages. Bacteria were also related to ammonia oxidation activity (R[2]=0.503; P=0.03) especially during the mesophilic and maturation stages.},
}
@article {pmid21833311,
year = {2011},
author = {Edgcomb, VP and Leadbetter, ER and Bourland, W and Beaudoin, D and Bernhard, JM},
title = {Structured multiple endosymbiosis of bacteria and archaea in a ciliate from marine sulfidic sediments: a survival mechanism in low oxygen, sulfidic sediments?.},
journal = {Frontiers in microbiology},
volume = {2},
number = {},
pages = {55},
pmid = {21833311},
issn = {1664-302X},
abstract = {Marine micro-oxic to sulfidic environments are sites of intensive biogeochemical cycling and elemental sequestration, where prokaryotes are major driving forces mediating carbon, nitrogen, sulfur, phosphorus, and metal cycles, important from both biogeochemical and evolutionary perspectives. Associations between single-celled eukaryotes and bacteria and/or archaea are common in such habitats. Here we describe a ciliate common in the micro-oxic to anoxic, typically sulfidic, sediments of Santa Barbara Basin (CA, USA). The ciliate is 95% similar to Parduzcia orbis (18S rRNA). Transmission electron micrographs reveal clusters of at least three different endobiont types organized within membrane-bound sub-cellular regions. Catalyzed reporter deposition-fluorescent in situ hybridization and 16S rRNA clone libraries confirm the symbionts include up to two sulfate reducers (Desulfobulbaceae, Desulfobacteraceae), a methanogen (Methanobacteriales), and possibly a Bacteroidete (Cytophaga) and a Type I methanotroph, suggesting synergistic metabolisms in this environment. This case study is discussed in terms of implications to biogeochemistry, and benthic ecology.},
}
@article {pmid21821465,
year = {2011},
author = {Snyder, JC and Young, MJ},
title = {Advances in understanding archaea-virus interactions in controlled and natural environments.},
journal = {Current opinion in microbiology},
volume = {14},
number = {4},
pages = {497-503},
doi = {10.1016/j.mib.2011.07.007},
pmid = {21821465},
issn = {1879-0364},
mesh = {Acids/metabolism ; Archaea/genetics/*virology ; Archaeal Viruses/genetics/*pathogenicity/physiology ; *Environment ; *Gene Expression Regulation, Viral ; Genetic Variation ; *Genome, Viral ; *Host-Pathogen Interactions ; Hot Springs/microbiology/virology ; Virus Assembly ; Virus Cultivation ; Virus Replication ; Water Microbiology ; },
abstract = {Our understanding of host-virus interactions in archaeal systems generally lags behind our knowledge of host-virus interactions in bacterial and eukaryotic systems. This is due to the limited number of archaeal host-virus systems available for study under laboratory conditions, as well as the absence of diseases known to be caused by archaea. However, in recent years there has been a rapid expansion of our understanding of archaeal host-virus interactions combining traditional genetic and biochemical approaches with 'omics' based approaches in both laboratory and natural environmental studies. We highlight here the emerging features of host-virus interactions in archaea with a particular emphasis on host-virus interactions gathered from the study of archaeal viruses from high temperature acidic thermal environments.},
}
@article {pmid21815949,
year = {2011},
author = {Calo, D and Guan, Z and Naparstek, S and Eichler, J},
title = {Different routes to the same ending: comparing the N-glycosylation processes of Haloferax volcanii and Haloarcula marismortui, two halophilic archaea from the Dead Sea.},
journal = {Molecular microbiology},
volume = {81},
number = {5},
pages = {1166-1177},
pmid = {21815949},
issn = {1365-2958},
support = {U54 GM069338/GM/NIGMS NIH HHS/United States ; GM-069338/GM/NIGMS NIH HHS/United States ; },
mesh = {Aquatic Organisms/metabolism ; Archaeal Proteins/genetics/*metabolism ; Dolichol Phosphates/metabolism ; Gene Expression Regulation, Archaeal ; Glycosylation ; Haloarcula marismortui/*metabolism ; Haloferax volcanii/*metabolism ; Membrane Glycoproteins ; Protein Processing, Post-Translational ; Seawater ; Sequence Alignment ; },
abstract = {Recent insight into the N-glycosylation pathway of the haloarchaeon, Haloferax volcanii, is helping to bridge the gap between our limited understanding of the archaeal version of this universal post-translational modification and the better-described eukaryal and bacterial processes. To delineate as yet undefined steps of the Hfx. volcanii N-glycosylation pathway, a comparative approach was taken with the initial characterization of N-glycosylation in Haloarcula marismortui, a second haloarchaeon also originating from the Dead Sea. While both species decorate the reporter glycoprotein, the S-layer glycoprotein, with the same N-linked pentasaccharide and employ dolichol phosphate as lipid glycan carrier, species-specific differences in the two N-glycosylation pathways exist. Specifically, Har. marismortui first assembles the complete pentasaccharide on dolichol phosphate and only then transfers the glycan to the target protein, as in the bacterial N-glycosylation pathway. In contrast, Hfx. volcanii initially transfers the first four pentasaccharide subunits from a common dolichol phosphate carrier to the target protein and only then delivers the final pentasaccharide subunit from a distinct dolichol phosphate to the N-linked tetrasaccharide, reminiscent of what occurs in eukaryal N-glycosylation. This study further indicates the extraordinary diversity of N-glycosylation pathways in Archaea, as compared with the relatively conserved parallel processes in Eukarya and Bacteria.},
}
@article {pmid21815108,
year = {2011},
author = {Maezato, Y and Dana, K and Blum, P},
title = {Engineering thermoacidophilic archaea using linear DNA recombination.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {765},
number = {},
pages = {435-445},
doi = {10.1007/978-1-61779-197-0_26},
pmid = {21815108},
issn = {1940-6029},
mesh = {DNA, Recombinant/*genetics ; *Genetic Engineering ; Homologous Recombination/*genetics ; Sulfolobus solfataricus/*genetics ; },
abstract = {Thermoacidophilic archaea comprise one of the major classes of extremophiles. Most belong to the family Sulfolobales within the phylum Crenarchaeota. They are of applied interest as sources of hyperstable enzymes, for biomining of base and precious metals, and for evolutionary studies because of their use of eukaryotic-like subcellular mechanisms. Genetic methods are available for several species particularly Sulfolobus solfataricus. This organism has a considerable number of methods available for the construction of novel cell lines with unique functions. This chapter presents recent developments in the use of homologous recombination and linear DNA for the engineering of site-specific changes in the genome of S. solfataricus.},
}
@article {pmid21814394,
year = {2011},
author = {Zafar, S and Nasir, A and Bokhari, H},
title = {Computational analysis reveals abundance of potential glycoproteins in Archaea, Bacteria and Eukarya.},
journal = {Bioinformation},
volume = {6},
number = {9},
pages = {352-355},
pmid = {21814394},
issn = {0973-2063},
abstract = {Glycosylation is the most common type of post-translational modification (PTM) and is known to affect protein stability, folding and activity. Inactivity of enzymes mediating glycosylation can result in serious disorders including colon cancer and brain disorders. Out of five main types of glycosylation, N-linked glycosylation is most abundant and characterized by the addition of a sugar group to an Asparagine residue at the N-X-S/T motif. Enzyme mediating such transfer is known as oligosaccharyl transferase (OST). It has been hypothesized before that a significant number of proteins serve as glycoproteins. In this study, we used programming implementations of Python to statistically quantify the representation of glycoproteins by scanning all the available proteome sequence data at ExPASy server for the presence of glycoproteins and also the enzyme which plays critical role in glycosylation i.e. OST. Our results suggest that more than 50% of the proteins carry N-X-S/T motif i.e. they could be potential glycoproteins. Furthermore, approximately 28-36% (1/3) of proteins possesses signature motifs which are characteristic features of enzyme OST. Quantifying this bias individually reveals that both the number of proteins tagged with N-X-S/T motif and the average number of motifs per protein is significantly higher in case of eukaryotes when compared to prokaryotes. In the light of these results we conclude that there is a significant bias in the representation of glycoproteins in the proteomes of all species and is manifested substantially in eukaryotes and claim for glycosylation to be the most common and ubiquitous PTM in cells, especially in eukaryotes.},
}
@article {pmid21806748,
year = {2011},
author = {Lloyd, KG and Alperin, MJ and Teske, A},
title = {Environmental evidence for net methane production and oxidation in putative ANaerobic MEthanotrophic (ANME) archaea.},
journal = {Environmental microbiology},
volume = {13},
number = {9},
pages = {2548-2564},
doi = {10.1111/j.1462-2920.2011.02526.x},
pmid = {21806748},
issn = {1462-2920},
mesh = {Anaerobiosis ; Archaea/genetics/isolation &amp; purification/*metabolism ; DNA, Archaeal/genetics ; DNA, Ribosomal/genetics ; Gene Library ; Geologic Sediments/*microbiology ; Methane/*biosynthesis ; Molecular Sequence Data ; North Carolina ; Oxidation-Reduction ; Oxidoreductases/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Water/chemistry ; Water Microbiology ; },
abstract = {Uncultured ANaerobic MEthanotrophic (ANME) archaea are often assumed to be obligate methanotrophs that are incapable of net methanogenesis, and are therefore used as proxies for anaerobic methane oxidation in many environments in spite of uncertainty regarding their metabolic capabilities. Anaerobic methane oxidation regulates methane emissions in marine sediments and appears to occur through a reversal of a methane-producing metabolism. We tested the assumption that ANME are obligate methanotrophs by detecting and quantifying gene transcription of ANME-1 across zones of methane oxidation versus methane production in sediments from the White Oak River estuary, North Carolina. ANME-1 consistently transcribe 16S rRNA and mRNA of methyl coenzyme M reductase (mcrA), the key gene for methanogenesis, up to 45 cm into methanogenic sediments. CARD-FISH shows that ANME-1 exist as single rod-shaped cells or pairs of cells. Integrating normalized depth distributions of 16S rDNA and rRNA (measured with qPCR and RT-qPCR respectively) shows that 26-77% of the rDNA (a proxy for ANME-1 cell numbers), and 18-76% of the rRNA (a proxy for ANME-1 activity) occurs within methane-producing sediments. These results, along with a re-assessment of the published Iiterature, change the perspective to ANME-1 as methanogens that are also capable of methane oxidation.},
}
@article {pmid21803892,
year = {2011},
author = {Kelly, JJ and Policht, K and Grancharova, T and Hundal, LS},
title = {Distinct responses in ammonia-oxidizing archaea and bacteria after addition of biosolids to an agricultural soil.},
journal = {Applied and environmental microbiology},
volume = {77},
number = {18},
pages = {6551-6558},
pmid = {21803892},
issn = {1098-5336},
mesh = {Ammonia/*metabolism ; Anaerobiosis ; Archaea/*growth &amp; development/metabolism ; Bacteria/*growth &amp; development/metabolism ; DNA, Archaeal/chemistry/genetics ; DNA, Bacterial/chemistry/genetics ; *Fertilizers ; *Manure ; Molecular Sequence Data ; Oxidation-Reduction ; Oxidoreductases/genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; },
abstract = {The recently discovered ammonia-oxidizing archaea (AOA) have been suggested as contributors to the first step of nitrification in terrestrial ecosystems, a role that was previously assigned exclusively to ammonia-oxidizing bacteria (AOB). The current study assessed the effects of agricultural management, specifically amendment of soil with biosolids or synthetic fertilizer, on nitrification rates and copy numbers of archaeal and bacterial ammonia monooxygenase (amoA) genes. Anaerobically digested biosolids or synthetic fertilizer was applied annually for three consecutive years to field plots used for corn production. Biosolids were applied at two loading rates, a typical agronomic rate (27 Mg hectare(-1) year(-1)) and double the agronomic rate (54 Mg hectare(-1) year(-1)), while synthetic fertilizer was applied at an agronomic rate typical for the region (291 kg N hectare(-1) year(-1)). Both biosolids amendments and synthetic fertilizer increased soil N and corn yield, but only the biosolids amendments resulted in significant increases in nitrification rates and increases in the copy numbers of archaeal and bacterial amoA genes. In addition, only archaeal amoA gene copy numbers increased in response to biosolids applied at the typical agronomic rate and showed a significant correlation with nitrification rates. Finally, copy numbers of archaeal amoA genes were significantly higher than copy numbers of bacterial amoA genes for all treatments. These results implicate AOA as being primarily responsible for the increased nitrification observed in an agricultural soil amended with biosolids. These results also support the hypothesis that physiological differences between AOA and AOB may enable them to occupy distinct ecological niches.},
}
@article {pmid21798895,
year = {2011},
author = {Santoro, AE and Buchwald, C and McIlvin, MR and Casciotti, KL},
title = {Isotopic signature of N(2)O produced by marine ammonia-oxidizing archaea.},
journal = {Science (New York, N.Y.)},
volume = {333},
number = {6047},
pages = {1282-1285},
doi = {10.1126/science.1208239},
pmid = {21798895},
issn = {1095-9203},
mesh = {Ammonia/*metabolism ; Archaea/enzymology/*metabolism ; Bacteria/metabolism ; Culture Media ; Denitrification ; Linear Models ; Molecular Sequence Data ; Nitrification ; Nitrogen Isotopes ; Nitrous Oxide/*metabolism ; Oxidation-Reduction ; Oxygen Isotopes ; Pacific Ocean ; Seawater/*microbiology ; },
abstract = {The ocean is an important global source of nitrous oxide (N(2)O), a greenhouse gas that contributes to stratospheric ozone destruction. Bacterial nitrification and denitrification are thought to be the primary sources of marine N(2)O, but the isotopic signatures of N(2)O produced by these processes are not consistent with the marine contribution to the global N(2)O budget. Based on enrichment cultures, we report that archaeal ammonia oxidation also produces N(2)O. Natural-abundance stable isotope measurements indicate that the produced N(2)O had bulk δ(15)N and δ(18)O values higher than observed for ammonia-oxidizing bacteria but similar to the δ(15)N and δ(18)O values attributed to the oceanic N(2)O source to the atmosphere. Our results suggest that ammonia-oxidizing archaea may be largely responsible for the oceanic N(2)O source.},
}
@article {pmid21784945,
year = {2011},
author = {Mochizuki, T and Sako, Y and Prangishvili, D},
title = {Provirus induction in hyperthermophilic archaea: characterization of Aeropyrum pernix spindle-shaped virus 1 and Aeropyrum pernix ovoid virus 1.},
journal = {Journal of bacteriology},
volume = {193},
number = {19},
pages = {5412-5419},
pmid = {21784945},
issn = {1098-5530},
mesh = {Aeropyrum/*genetics/ultrastructure/*virology ; Archaeal Proteins/genetics ; Archaeal Viruses/genetics/ultrastructure ; Genome, Archaeal/genetics ; Microscopy, Electron, Transmission ; Molecular Sequence Data ; Proviruses/*genetics/ultrastructure ; Virion/genetics ; },
abstract = {By in silico analysis, we have identified two putative proviruses in the genome of the hyperthermophilic archaeon Aeropyrum pernix, and under special conditions of A. pernix growth, we were able to induce their replication. Both viruses were isolated and characterized. Negatively stained virions of one virus appeared as pleomorphic spindle-shaped particles, 180 to 210 nm by 40 to 55 nm, with tails of heterogeneous lengths in the range of 0 to 300 nm. This virus was named Aeropyrum pernix spindle-shaped virus 1 (APSV1). Negatively stained virions of the other virus appeared as slightly irregular oval particles with one pointed end, while in cryo-electron micrographs, the virions had a regular oval shape and uniform size (70 by 55 nm). The virus was named Aeropyrum pernix ovoid virus 1 (APOV1). Both viruses have circular, double-stranded DNA genomes of 38,049 bp for APSV1 and 13,769 bp for APOV1. Similarities to proteins of other archaeal viruses were limited to the integrase and Dna1-like protein. We propose to classify APOV1 into the family Guttaviridae.},
}
@article {pmid21784917,
year = {2011},
author = {Huffer, S and Clark, ME and Ning, JC and Blanch, HW and Clark, DS},
title = {Role of alcohols in growth, lipid composition, and membrane fluidity of yeasts, bacteria, and archaea.},
journal = {Applied and environmental microbiology},
volume = {77},
number = {18},
pages = {6400-6408},
pmid = {21784917},
issn = {1098-5336},
mesh = {Alcohols/*metabolism/toxicity ; Archaea/drug effects/*physiology ; *Bacterial Physiological Phenomena ; Cell Membrane/chemistry/drug effects/*physiology ; Lipids/*analysis ; Membrane Fluidity/*drug effects ; Yeasts/drug effects/*physiology ; },
abstract = {Increased membrane fluidity, which causes cofactor leakage and loss of membrane potential, has long been documented as a cause for decreased cell growth during exposure to ethanol, butanol, and other alcohols. Reinforcement of the membrane with more complex lipid components is thus thought to be beneficial for the generation of more tolerant organisms. In this study, organisms with more complex membranes, namely, archaea, did not maintain high growth rates upon exposure to alcohols, indicating that more complex lipids do not necessarily fortify the membrane against the fluidizing effects of alcohols. In the presence of alcohols, shifts in lipid composition to more saturated and unbranched lipids were observed in most of the organisms tested, including archaea, yeasts, and bacteria. However, these shifts did not always result in a decrease in membrane fluidity or in greater tolerance of the organism to alcohol exposure. In general, organisms tolerating the highest concentrations of alcohols maintained membrane fluidity after alcohol exposure, whereas organisms that increased membrane rigidity were less tolerant. Altered lipid composition was a common response to alcohol exposure, with the most tolerant organisms maintaining a modestly fluid membrane. Our results demonstrate that increased membrane fluidity is not the sole cause of growth inhibition and that alcohols may also denature proteins within the membrane and cytosol, adversely affecting metabolism and decreasing cell growth.},
}
@article {pmid21780150,
year = {2012},
author = {Schmidt, A and Rzanny, M and Schmidt, A and Hagen, M and Schütze, E and Kothe, E},
title = {GC content-independent amino acid patterns in bacteria and archaea.},
journal = {Journal of basic microbiology},
volume = {52},
number = {2},
pages = {195-205},
doi = {10.1002/jobm.201100067},
pmid = {21780150},
issn = {1521-4028},
mesh = {Amino Acids/*genetics ; Archaea/*genetics ; Bacteria/*genetics ; *Base Composition ; Codon ; Evolution, Molecular ; Genome, Archaeal ; Genome, Bacterial ; Phylogeny ; Proteome/analysis ; Sequence Analysis, Protein ; },
abstract = {Every organism can be characterized by the amino acid composition of its proteome. So far it was assumed that these compositions are determined by the GC content of the DNA or, in some cases, by extreme lifestyles, like thermophily or halophily. Here, we focussed our analysis on eight amino acids, each of which is encoded by both, GC and AT rich codons, to identify finer amino acid patterns beyond the GC dominance. We investigated the conceptually translated proteomes of 1029 bacterial and archaeal strains with sequenced genomes for amino acid composition. Using correspondence analysis, we found that phylogenetic groups within bacteria and archaea generally can be discriminated from other groups due to their amino acid composition. In some cases, single organisms, e.g. Treponema pallidum strains or Mycoplasma penetrans, are characterized by extreme amino acid compositions. We assume that our data could provide a basis for a new approach to analyze evolution of bacterial and archaeal groups. Furthermore, for single organisms, the detailed knowledge of the amino acid composition of the entire proteome encoded in the genome could lead to a better understanding, important for pharmaceutical or biotechnological applications. We recommend that information about amino acid compositions should be provided in databases, comparable to the GC content of genomes.},
}
@article {pmid21776031,
year = {2012},
author = {Chaban, B and Hill, JE},
title = {A 'universal' type II chaperonin PCR detection system for the investigation of Archaea in complex microbial communities.},
journal = {The ISME journal},
volume = {6},
number = {2},
pages = {430-439},
pmid = {21776031},
issn = {1751-7370},
mesh = {Animals ; Archaea/*classification/*genetics/physiology ; Bacteria/classification/genetics ; Biodiversity ; Cattle ; Female ; Group II Chaperonins/*genetics ; Metagenomics/*methods ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Rumen/microbiology ; },
abstract = {Bacteria and Archaea are evolutionarily and biochemically distinct domains found together in many environments. Robust 'universal' PCR primer sets targeting both the bacterial 16S rRNA gene and the type I chaperonin gene have been established. However, 'universal' PCR primers for Archaea are currently limited to the 16S rRNA gene. We investigated the type II chaperonin (known as the thermosome, TF55, CCT or TCP-1) as a potential universal target (UT) for Archaea. Reproducible amplification of thermosome gene sequences from all major phyla tested was achieved through the application of a mixture or 'cocktail' of two forward and two reverse primers. Phylogenies based on the ∼750-bp thermosome UT were congruent with 16S rRNA gene phylogenies while exhibiting longer branch lengths, improving resolution of closely related taxa. 'Universal' thermosome primers were applied to profiling the archaeal community of dairy cow rumen and results compared with profiles based on the 16S rRNA gene and methyl co-enzyme M reductase (methanogen-specific) gene. Clone libraries generated from each target gene, as well as a pyrosequencing profile of one thermosome rumen library, revealed that all three targets consistently detected Methanobrevibacter smithii, Methanobrevibacter ruminantium and Methanosphaera stadtmanae as the dominant constituents; however, thermosome gene sequences were more diverse than either of the other targets providing a higher resolution description of the archaeal community. These findings demonstrate that a 'universal' thermosome PCR protocol is a powerful metagenomic tool for detecting and characterizing Archaea and archaeal communities.},
}
@article {pmid21774172,
year = {2010},
author = {Merkel', AIu and Chernykh, NA and Kanapatskiĭ, TA and Pimenov, NV},
title = {[Methanotrophic archaea detection using sequence analysis of methyl coenzyme M reductase A gene in pockmark sediments(Gdansk Basin, Baltic Sea) ].},
journal = {Mikrobiologiia},
volume = {79},
number = {6},
pages = {852-855},
pmid = {21774172},
issn = {0026-3656},
mesh = {Archaea/*classification/genetics/*isolation &amp; purification ; Geologic Sediments/*microbiology ; Methane/*metabolism ; Oxidoreductases/*genetics ; Seawater/*microbiology ; },
}
@article {pmid21769188,
year = {2011},
author = {Bokhari, H and Anwar, M and Mirza, HB and Gillevet, PM},
title = {Evidences of lateral gene transfer between archaea and pathogenic bacteria.},
journal = {Bioinformation},
volume = {6},
number = {8},
pages = {293-296},
pmid = {21769188},
issn = {0973-2063},
abstract = {Acquisition of new genetic material through horizontal gene transfer has been shown to be an important feature in the evolution of many pathogenic bacteria. Changes in the genetic repertoire, occurring through gene acquisition and deletion, are the major events underlying the emergence and evolution of bacterial pathogens. However, horizontal gene transfer across the domains i.e. archaea and bacteria is not so common. In this context, we explore events of horizontal gene transfer between archaea and bacteria. In order to determine whether the acquisition of archaeal genes by lateral gene transfer is an important feature in the evolutionary history of the pathogenic bacteria, we have developed a scheme of stepwise eliminations that identifies archaeal-like genes in various bacterial genomes. We report the presence of 9 genes of archaeal origin in the genomes of various bacteria, a subset of which is also unique to the pathogenic members and are not found in respective non-pathogenic counterparts. We believe that these genes, having been retained in the respective genomes through selective advantage, have key functions in the organism's biology and may play a role in pathogenesis.},
}
@article {pmid21761520,
year = {2011},
author = {Guldan, H and Matysik, FM and Bocola, M and Sterner, R and Babinger, P},
title = {Functional assignment of an enzyme that catalyzes the synthesis of an archaea-type ether lipid in bacteria.},
journal = {Angewandte Chemie (International ed. in English)},
volume = {50},
number = {35},
pages = {8188-8191},
doi = {10.1002/anie.201101832},
pmid = {21761520},
issn = {1521-3773},
mesh = {Alkyl and Aryl Transferases/chemistry/*metabolism ; Archaea/enzymology ; Archaeal Proteins/chemistry/metabolism ; Bacillales/*enzymology ; Bacterial Proteins/chemistry/*metabolism ; Biocatalysis ; Ether/*chemistry ; Glycerophosphates/biosynthesis ; Lipids/*biosynthesis ; Protein Structure, Tertiary ; },
abstract = {An archaea-type ether lipid in bacteria: PcrB, the bacterial homologue of the archaea-specific geranylgeranylglyceryl phosphate synthase, produces heptaprenylglyceryl phosphate in bacillales. The product becomes dephosphorylated and acetylated in vivo.},
}
@article {pmid21751006,
year = {2012},
author = {Gonzalez-Contreras, P and Weijma, J and Buisman, CJ},
title = {Kinetics of ferrous iron oxidation by batch and continuous cultures of thermoacidophilic Archaea at extremely low pH of 1.1-1.3.},
journal = {Applied microbiology and biotechnology},
volume = {93},
number = {3},
pages = {1295-1303},
pmid = {21751006},
issn = {1432-0614},
mesh = {Arsenicals/metabolism ; Bioreactors ; Biotechnology/methods ; Culture Media/chemistry ; Ferric Compounds/metabolism ; Ferrous Compounds/*metabolism ; Hydrogen-Ion Concentration ; Iron/*metabolism ; Kinetics ; Oxidation-Reduction ; Sulfates/metabolism ; Sulfolobales/*growth &amp; development/*metabolism ; Temperature ; },
abstract = {The extreme acid conditions required for scorodite (FeAsO4·2H2O) biomineralization (pH below 1.3) are suboptimal for growth of most thermoacidophilic Archaea. With the objective to develop a continuous process suitable for biomineral production, this research focuses on growth kinetics of thermoacidophilic Archaea at low pH conditions. Ferrous iron oxidation rates were determined in batch-cultures at pH 1.3 and a temperature of 75°C for Acidianus sulfidivorans, Metallosphaera prunea and a mixed Sulfolobus culture. Ferrous iron and CO2 in air were added as sole energy and carbon source. The highest growth rate (0.066 h[-1]) was found with the mixed Sulfolobus culture. Therefore, this culture was selected for further experiments. Growth was not stimulated by increase of the CO2 concentration or by addition of sulphur as an additional energy source. In a CSTR operated at the suboptimal pH of 1.1, the maximum specific growth rate of the mixed culture was 0.022 h[-1], with ferrous iron oxidation rates of 1.5 g L[-1] d[-1]. Compared to pH 1.3, growth rates were strongly reduced but the ferrous iron oxidation rate remained unaffected. Influent ferrous iron concentrations above 6 g L[-1] caused instability of Fe[2+] oxidation, probably due to product (Fe[3+]) inhibition. Ferric-containing, nano-sized precipitates of K-jarosite were found on the cell surface. Continuous cultivation stimulated the formation of an exopolysaccharide-like substance. This indicates that biofilm formation may provide a means of biomass retention. Our findings showed that stable continuous cultivation of a mixed iron-oxidizing culture is feasible at the extreme conditions required for continuous biomineral formation.},
}
@article {pmid21748268,
year = {2011},
author = {Cao, H and Hong, Y and Li, M and Gu, JD},
title = {Phylogenetic diversity and ecological pattern of ammonia-oxidizing archaea in the surface sediments of the western Pacific.},
journal = {Microbial ecology},
volume = {62},
number = {4},
pages = {813-823},
pmid = {21748268},
issn = {1432-184X},
mesh = {Ammonia/*metabolism ; Archaea/*classification/enzymology/genetics ; *Biodiversity ; Cluster Analysis ; DNA, Archaeal/genetics ; Genes, Archaeal ; Geologic Sediments/*microbiology ; Oxidoreductases/genetics ; Pacific Ocean ; *Phylogeny ; Seawater/microbiology ; Sequence Analysis, DNA ; },
abstract = {The phylogenetic diversity of ammonia-oxidizing archaea (AOA) was surveyed in the surface sediments from the northern part of the South China Sea (SCS). The distribution pattern of AOA in the western Pacific was discussed through comparing the SCS with other areas in the western Pacific including Changjiang Estuary and the adjacent East China Sea where high input of anthropogenic nitrogen was evident, the tropical West Pacific Continental Margins close to the Philippines, the deep-sea methane seep sediments in the Okhotsk Sea, the cold deep sea of Northeastern Japan Sea, and the hydrothermal field in the Southern Okinawa Trough. These various environments provide a wide spectrum of physical and chemical conditions for a better understanding of the distribution pattern and diversities of AOA in the western Pacific. Under these different conditions, the distinct community composition between shallow and deep-sea sediments was clearly delineated based on the UniFrac PCoA and Jackknife Environmental Cluster analyses. Phylogenetic analyses showed that a few ammonia-oxidizing archaeal subclades in the marine water column/sediment clade and endemic lineages were indicative phylotypes for some environments. Higher phylogenetic diversity was observed in the Philippines while lower diversity in the hydrothermal vent habitat. Water depth and possibly with other environmental factors could be the main driving forces to shape the phylogenetic diversity of AOA observed, not only in the SCS but also in the whole western Pacific. The multivariate regression tree analysis also supported this observation consistently. Moreover, the functions of current and other climate factors were also discussed in comparison of phylogenetic diversity. The information collectively provides important insights into the ecophysiological requirements of uncultured ammonia-oxidizing archaeal lineages in the western Pacific Ocean.},
}
@article {pmid21747791,
year = {2011},
author = {Pereira, IA and Ramos, AR and Grein, F and Marques, MC and da Silva, SM and Venceslau, SS},
title = {A comparative genomic analysis of energy metabolism in sulfate reducing bacteria and archaea.},
journal = {Frontiers in microbiology},
volume = {2},
number = {},
pages = {69},
pmid = {21747791},
issn = {1664-302X},
abstract = {The number of sequenced genomes of sulfate reducing organisms (SRO) has increased significantly in the recent years, providing an opportunity for a broader perspective into their energy metabolism. In this work we carried out a comparative survey of energy metabolism genes found in 25 available genomes of SRO. This analysis revealed a higher diversity of possible energy conserving pathways than classically considered to be present in these organisms, and permitted the identification of new proteins not known to be present in this group. The Deltaproteobacteria (and Thermodesulfovibrio yellowstonii) are characterized by a large number of cytochromes c and cytochrome c-associated membrane redox complexes, indicating that periplasmic electron transfer pathways are important in these bacteria. The Archaea and Clostridia groups contain practically no cytochromes c or associated membrane complexes. However, despite the absence of a periplasmic space, a few extracytoplasmic membrane redox proteins were detected in the Gram-positive bacteria. Several ion-translocating complexes were detected in SRO including H(+)-pyrophosphatases, complex I homologs, Rnf, and Ech/Coo hydrogenases. Furthermore, we found evidence that cytoplasmic electron bifurcating mechanisms, recently described for other anaerobes, are also likely to play an important role in energy metabolism of SRO. A number of cytoplasmic [NiFe] and [FeFe] hydrogenases, formate dehydrogenases, and heterodisulfide reductase-related proteins are likely candidates to be involved in energy coupling through electron bifurcation, from diverse electron donors such as H(2), formate, pyruvate, NAD(P)H, β-oxidation, and others. In conclusion, this analysis indicates that energy metabolism of SRO is far more versatile than previously considered, and that both chemiosmotic and flavin-based electron bifurcating mechanisms provide alternative strategies for energy conservation.},
}
@article {pmid21738312,
year = {2011},
author = {Tabish, S and Raza, A and Nasir, A and Zafar, S and Bokhari, H},
title = {Analysis of glycosylation motifs and glycosyltransferases in Bacteria and Archaea.},
journal = {Bioinformation},
volume = {6},
number = {5},
pages = {191-195},
pmid = {21738312},
issn = {0973-2063},
abstract = {The process of glycosylation has been studied extensively in prokaryotes but many questions still remain unanswered. Glycosyltransferase is the enzyme which mediates glycosylation and has its preference for the target glycosylation sites as well as for the type of glycosylation i.e. N-linked and O-linked glycosylation. In this study we carried out the bioinformatics analysis of one of the key enzymes of pgl locus from Campylobacter jejuni, known as PglB, which is distributed widely in bacteria and AglB from archaea. Relatively little sequence similarity was observed in the archaeal AglB(s) as compared to those of the bacterial PglB(s). In addition we tried to the answer the question of as to why not all the sequins Asp-X-Ser/Thr have an equal opportunity to be glycosylated by looking at the influence of the neighboring amino acids but no significant conserved pattern of the flanking sites could be identified. The software tool was developed to predict the potential glycosylation sites in autotransporter protein, the virulence factors of gram negative bacteria, and our results revealed that the frequency of glycosylation sites was higher in adhesins (a subclass of autotransporters) relative to the other classes of autotransporters.},
}
@article {pmid21726564,
year = {2011},
author = {Bhaskaran, H and Perona, JJ},
title = {Two-step aminoacylation of tRNA without channeling in Archaea.},
journal = {Journal of molecular biology},
volume = {411},
number = {4},
pages = {854-869},
pmid = {21726564},
issn = {1089-8638},
support = {R01 GM063713/GM/NIGMS NIH HHS/United States ; R01 GM063713-10/GM/NIGMS NIH HHS/United States ; GM63713/GM/NIGMS NIH HHS/United States ; },
mesh = {Archaea ; Binding Sites ; Crystallography, X-Ray ; Glutamate-tRNA Ligase/*metabolism ; Models, Molecular ; Nitrogenous Group Transferases/*metabolism ; Protein Binding ; Protein Biosynthesis ; RNA, Transfer, Amino Acyl/*metabolism ; *Transfer RNA Aminoacylation ; },
abstract = {Catalysis of sequential reactions is often envisaged to occur by channeling of substrate between enzyme active sites without release into bulk solvent. However, while there are compelling physiological rationales for direct substrate transfer, proper experimental support for the hypothesis is often lacking, particularly for metabolic pathways involving RNA. Here, we apply transient kinetics approaches developed to study channeling in bienzyme complexes to an archaeal protein synthesis pathway featuring the misaminoacylated tRNA intermediate Glu-tRNA(Gln). Experimental and computational elucidation of a kinetic and thermodynamic framework for two-step cognate Gln-tRNA(Gln) synthesis demonstrates that the misacylating aminoacyl-tRNA synthetase (GluRS(ND)) and the tRNA-dependent amidotransferase (GatDE) function sequentially without channeling. Instead, rapid processing of the misacylated tRNA intermediate by GatDE and preferential elongation factor binding to the cognate Gln-tRNA(Gln) together permit accurate protein synthesis without formation of a binary protein-protein complex between GluRS(ND) and GatDE. These findings establish an alternate paradigm for protein quality control via two-step pathways for cognate aminoacyl-tRNA formation.},
}
@article {pmid21716304,
year = {2012},
author = {Narasingarao, P and Podell, S and Ugalde, JA and Brochier-Armanet, C and Emerson, JB and Brocks, JJ and Heidelberg, KB and Banfield, JF and Allen, EE},
title = {De novo metagenomic assembly reveals abundant novel major lineage of Archaea in hypersaline microbial communities.},
journal = {The ISME journal},
volume = {6},
number = {1},
pages = {81-93},
pmid = {21716304},
issn = {1751-7370},
support = {R21 HG005107/HG/NHGRI NIH HHS/United States ; },
mesh = {Australia ; Euryarchaeota/*classification/genetics/*isolation &amp; purification/physiology ; Genome, Archaeal ; Lakes/*microbiology ; *Metagenomics ; Molecular Sequence Data ; Phylogeny ; Salinity ; Victoria ; },
abstract = {This study describes reconstruction of two highly unusual archaeal genomes by de novo metagenomic assembly of multiple, deeply sequenced libraries from surface waters of Lake Tyrrell (LT), a hypersaline lake in NW Victoria, Australia. Lineage-specific probes were designed using the assembled genomes to visualize these novel archaea, which were highly abundant in the 0.1-0.8 μm size fraction of lake water samples. Gene content and inferred metabolic capabilities were highly dissimilar to all previously identified hypersaline microbial species. Distinctive characteristics included unique amino acid composition, absence of Gvp gas vesicle proteins, atypical archaeal metabolic pathways and unusually small cell size (approximately 0.6 μm diameter). Multi-locus phylogenetic analyses demonstrated that these organisms belong to a new major euryarchaeal lineage, distantly related to halophilic archaea of class Halobacteria. Consistent with these findings, we propose creation of a new archaeal class, provisionally named 'Nanohaloarchaea'. In addition to their high abundance in LT surface waters, we report the prevalence of Nanohaloarchaea in other hypersaline environments worldwide. The simultaneous discovery and genome sequencing of a novel yet ubiquitous lineage of uncultivated microorganisms demonstrates that even historically well-characterized environments can reveal unexpected diversity when analyzed by metagenomics, and advances our understanding of the ecology of hypersaline environments and the evolutionary history of the archaea.},
}
@article {pmid21706171,
year = {2011},
author = {Zhang, T and Ye, L and Tong, AH and Shao, MF and Lok, S},
title = {Ammonia-oxidizing archaea and ammonia-oxidizing bacteria in six full-scale wastewater treatment bioreactors.},
journal = {Applied microbiology and biotechnology},
volume = {91},
number = {4},
pages = {1215-1225},
pmid = {21706171},
issn = {1432-0614},
mesh = {Ammonia/*metabolism ; Archaea/*classification/genetics/*metabolism ; Bacteria/*classification/genetics/*metabolism ; *Biodiversity ; Bioreactors/*microbiology ; Cluster Analysis ; DNA, Archaeal/chemistry/genetics ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Genes, rRNA ; Molecular Sequence Data ; Oxidation-Reduction ; Oxidoreductases/genetics ; Phylogeny ; RNA, Archaeal/genetics ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; Water Microbiology ; Water Purification ; },
abstract = {In this study, dideoxy sequencing and 454 high-throughput sequencing were used to analyze diversities of the ammonia monooxygenase (amoA) genes and the 16S rRNA genes of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in six municipal wastewater treatment plants. The results showed that AOB amoA genes were quite diverse in different wastewater treatment plants while the 16S rRNA genes were relatively conserved. Based on the observed complexity of amoA and 16S rRNA genes, most of the AOB can be assigned to the Nitrosomonas genus, with Nitrosomonas ureae, Nitrosomonas oligotropha, Nitrosomonas marina, and Nitrosomonas aestuarii being the four most dominant species. From the sequences of the AOA amoA genes, most AOA observed in this study belong to the CGI.1b group, i.e., the soil lineage. The AOB amoA and 16S rRNA genes were quantified by quantitative PCR and 454 high-throughput pyrosequencing, respectively. Although the results from the two approaches show some disconcordance, they both indicated that the abundance of AOB in activated sludge was very low.},
}
@article {pmid21703550,
year = {2011},
author = {Liu, H and Han, J and Liu, X and Zhou, J and Xiang, H},
title = {Development of pyrF-based gene knockout systems for genome-wide manipulation of the archaea Haloferax mediterranei and Haloarcula hispanica.},
journal = {Journal of genetics and genomics = Yi chuan xue bao},
volume = {38},
number = {6},
pages = {261-269},
doi = {10.1016/j.jgg.2011.05.003},
pmid = {21703550},
issn = {1673-8527},
mesh = {Alkyl and Aryl Transferases/*genetics ; Amino Acid Sequence ; Archaeal Proteins/*genetics ; Culture Media ; Gene Knockout Techniques/*methods ; Genetic Vectors ; Geranylgeranyl-Diphosphate Geranylgeranyltransferase ; Haloarcula/*genetics ; Haloferax mediterranei/*genetics ; Molecular Sequence Data ; Orotic Acid/analogs &amp; derivatives/metabolism ; Plasmids ; Recombination, Genetic/genetics ; Sequence Deletion/genetics ; Uracil/metabolism ; },
abstract = {The haloarchaea Haloferax mediterranei and Haloarcula hispanica are both polyhydroxyalkanoate producers in the domain Archaea, and they are becoming increasingly attractive for research and biotechnology due to their unique genetic and metabolic features. To accelerate their genome-level genetic and metabolic analyses, we have developed specific and highly efficient gene knockout systems for these two haloarchaea. These gene knockout systems consist of a suicide plasmid vector with the pyrF gene as the selection marker and a uracil auxotrophic haloarchaeon (ΔpyrF) as the host. For in-frame deletion of a target gene, the suicide plasmid carrying the flanking region of the target gene was transferred into the corresponding ΔpyrF host. After positive selection of the single-crossover integration recombinants (pop-in) on AS-168SY medium without uracil and counterselection of the double-crossover pyrF-excised recombinants (pop-out) with 5-fluoroorotic acid (5-FOA), the target gene knockout mutants were confirmed by PCR and Southern blot analysis. We have demonstrated the effectiveness of these systems by knocking out the crtB gene which encodes a phytoene synthase in these haloarchaea. In conclusion, these well-developed knockout systems would greatly accelerate the functional genomic research of these halophilic archaea.},
}
@article {pmid21692831,
year = {2011},
author = {Jantzer, K and Zerulla, K and Soppa, J},
title = {Phenotyping in the archaea: optimization of growth parameters and analysis of mutants of Haloferax volcanii.},
journal = {FEMS microbiology letters},
volume = {322},
number = {2},
pages = {123-130},
doi = {10.1111/j.1574-6968.2011.02341.x},
pmid = {21692831},
issn = {1574-6968},
mesh = {Aerobiosis/physiology ; Carbon/metabolism ; Gene Expression Regulation, Archaeal ; Haloferax volcanii/*genetics/*growth &amp; development/metabolism ; Mutation/*genetics ; Osmotic Pressure ; Oxidative Stress ; Phenotype ; RNA, Archaeal/genetics ; Vitamins/metabolism ; },
abstract = {A method to grow the halophilic archaeon Haloferax volcanii in microtiter plates has been optimized and now allows the parallel generation of very reproducible growth curves. The doubling time in a synthetic medium with glucose is around 6 h. The method was used to optimize glucose and casamino acid concentrations, to clarify carbon source usage and to analyze vitamin dependence. The characterization of osmotolerance revealed that after a lag phase of 24 h, H. volcanii is able to grow at salt concentrations as low as 0.7 M NaCl, much lower than the 1.4 M NaCl described as the lowest concentration until now. The application of oxidative stresses showed that H. volcanii exhibits a reaction to paraquat that is delayed by about 10 h. Surprisingly, only one of two amino acid auxotrophic mutants could be fully supplemented by the addition of the respective amino acid. Analysis of eight sRNA gene deletion mutants exemplified that the method can be applied for bona fide phenotyping of mutant collections. This method for the parallel analysis of many cultures contributes towards making H. volcanii an archaeal model species for functional genomic approaches.},
}
@article {pmid21685165,
year = {2011},
author = {Golyshina, OV},
title = {Environmental, biogeographic, and biochemical patterns of archaea of the family Ferroplasmaceae.},
journal = {Applied and environmental microbiology},
volume = {77},
number = {15},
pages = {5071-5078},
pmid = {21685165},
issn = {1098-5336},
mesh = {*Environment ; Hydrogen-Ion Concentration ; Microbial Consortia ; Phylogeography ; RNA, Ribosomal, 16S/genetics ; *Thermoplasmales/chemistry/classification/genetics/physiology ; },
abstract = {About 10 years ago, a new family of cell wall-deficient, iron-oxidizing archaea, Ferroplasmaceae, within the large archaeal phylum Euryarchaeota, was described. In this minireview, I summarize the research progress achieved since then and report on the current status of taxonomy, biogeography, physiological diversity, biochemistry, and other research areas involving this exciting group of acidophilic archaea.},
}
@article {pmid21680581,
year = {2011},
author = {Dridi, B and Fardeau, ML and Ollivier, B and Raoult, D and Drancourt, M},
title = {The antimicrobial resistance pattern of cultured human methanogens reflects the unique phylogenetic position of archaea.},
journal = {The Journal of antimicrobial chemotherapy},
volume = {66},
number = {9},
pages = {2038-2044},
doi = {10.1093/jac/dkr251},
pmid = {21680581},
issn = {1460-2091},
mesh = {Anti-Bacterial Agents/*pharmacology ; Archaea/*drug effects/*genetics/metabolism ; Bacteria/drug effects ; Bacterial Infections/microbiology ; Chloramphenicol O-Acetyltransferase/genetics ; Computational Biology ; Drug Resistance, Bacterial/*genetics ; Humans ; Methane/metabolism ; Methanobacteriaceae/*drug effects/*genetics/metabolism ; Microbial Sensitivity Tests ; Phylogeny ; },
abstract = {OBJECTIVES: Methanogenic archaea are constant members of the human oral and digestive microbiota retrieved, in particular, from periodontitis lesions. The objective of the study was to determine their susceptibility to antimicrobials.<br><br>METHODS: Using the macrodilution method in Hungate tubes with optical microscope observation combined with monitoring methane production, we determined the antibiotic resistance characteristics of eight methanogenic archaea.<br><br>RESULTS: Methanobrevibacter smithii strains were resistant to ampicillin, streptomycin, gentamicin, rifampicin, ofloxacin, tetracycline and amphotericin B, with MICs &#x2265; 100 mg/L; these strains were also highly resistant to vancomycin (MIC &#x2265; 50 mg/L). They were moderately resistant to chloramphenicol (MIC &#x2264; 25 mg/L), and were susceptible to bacitracin (MIC &#x2264; 4 mg/L), metronidazole, ornidazole and squalamine (MIC &#x2264; 1 mg/L). The susceptibility of Methanosphaera stadtmanae was the same as M. smithii, except for chloramphenicol (MIC &#x2264; 4 mg/L), and Methanobrevibacter oralis yielded the same data as M. smithii, except for bacitracin (MIC &#x2264; 25 mg/L). The antibiotic susceptibility pattern of 'Methanomassiliicoccus luminyensis', which was recently isolated from human faeces, was identical to that of M. smithii.<br><br>CONCLUSIONS: Human methanogenic archaea are highly resistant to antibiotics, being susceptible only to molecules that are also effective against both bacteria and eukarya. Methanogenic archaea are good candidates to test for antimicrobial activity against members of this unique domain of life. Further studies to develop new molecules specifically targeting archaea as potential causes of infection are warranted.},
}
@article {pmid21674231,
year = {2011},
author = {Bengtsson, J and Eriksson, KM and Hartmann, M and Wang, Z and Shenoy, BD and Grelet, GA and Abarenkov, K and Petri, A and Rosenblad, MA and Nilsson, RH},
title = {Metaxa: a software tool for automated detection and discrimination among ribosomal small subunit (12S/16S/18S) sequences of archaea, bacteria, eukaryotes, mitochondria, and chloroplasts in metagenomes and environmental sequencing datasets.},
journal = {Antonie van Leeuwenhoek},
volume = {100},
number = {3},
pages = {471-475},
doi = {10.1007/s10482-011-9598-6},
pmid = {21674231},
issn = {1572-9699},
mesh = {Archaea/*genetics/isolation &amp; purification ; Bacteria/*genetics/isolation &amp; purification ; Chloroplasts/*genetics ; Databases, Nucleic Acid ; Eukaryota/*genetics/isolation &amp; purification ; Metagenome ; Metagenomics/instrumentation/*methods ; Mitochondria/*genetics ; Phylogeny ; Ribosome Subunits, Small/*genetics ; Sequence Alignment ; *Software ; },
abstract = {The ribosomal small subunit (SSU) rRNA gene has emerged as an important genetic marker for taxonomic identification in environmental sequencing datasets. In addition to being present in the nucleus of eukaryotes and the core genome of prokaryotes, the gene is also found in the mitochondria of eukaryotes and in the chloroplasts of photosynthetic eukaryotes. These three sets of genes are conceptually paralogous and should in most situations not be aligned and analyzed jointly. To identify the origin of SSU sequences in complex sequence datasets has hitherto been a time-consuming and largely manual undertaking. However, the present study introduces Metaxa (http://microbiology.se/software/metaxa/), an automated software tool to extract full-length and partial SSU sequences from larger sequence datasets and assign them to an archaeal, bacterial, nuclear eukaryote, mitochondrial, or chloroplast origin. Using data from reference databases and from full-length organelle and organism genomes, we show that Metaxa detects and scores SSU sequences for origin with very low proportions of false positives and negatives. We believe that this tool will be useful in microbial and evolutionary ecology as well as in metagenomics.},
}
@article {pmid21665398,
year = {2011},
author = {Cao, H and Li, M and Hong, Y and Gu, JD},
title = {Diversity and abundance of ammonia-oxidizing archaea and bacteria in polluted mangrove sediment.},
journal = {Systematic and applied microbiology},
volume = {34},
number = {7},
pages = {513-523},
doi = {10.1016/j.syapm.2010.11.023},
pmid = {21665398},
issn = {1618-0984},
mesh = {Ammonia/*metabolism ; Archaea/chemistry/classification/genetics/*isolation &amp; purification ; Betaproteobacteria/chemistry/classification/genetics/*isolation &amp; purification ; Biodiversity ; Biomarkers/chemistry ; Biota ; Cloning, Molecular ; Environment ; Environmental Microbiology ; Environmental Pollution ; Genes, Archaeal ; Genes, Bacterial ; Geologic Sediments/analysis/chemistry/*microbiology ; Hong Kong ; Hydrogen-Ion Concentration ; Metals/chemistry ; Multigene Family ; Oxidation-Reduction ; Oxidoreductases/genetics ; Phosphorus/chemistry ; Phylogeny ; Quaternary Ammonium Compounds/chemistry ; Rhizophoraceae ; Seasons ; Species Specificity ; Temperature ; },
abstract = {Ammonia oxidation by microorganisms is a critical process in the nitrogen cycle. Recent research results show that ammonia-oxidizing archaea (AOA) are both abundant and diverse in a range of ecosystems. In this study, we examined the abundance and diversity of AOA and ammonia-oxidizing beta-proteobacteria (AOB) in estuarine sediments in Hong Kong for two seasons using the ammonia monooxygenase A subunit gene (amoA) as molecular biomarker. Relationships between diversity and abundance of AOA and AOB and physicochemical parameters were also explored. AOB were more diverse but less abundant than AOA. A few phylogenetically distinct amoA gene clusters were evident for both AOA and AOB from the mangrove sediment. Pearson moment correlation analysis and canonical correspondence analysis (CCA) were used to explore physicochemical parameters potentially important to AOA and AOB. Metal concentrations were proposed to contribute potentially to the distributions of AOA while total phosphorus (TP) was correlated to the distributions of AOB. Quantitative PCR estimates indicated that AOA were more abundant than AOB in all samples, but the ratio of AOA/AOB (from 1.8 to 6.3) was smaller than most other studies by one to two orders. The abundance of AOA or AOB was correlated with pH and temperature while the AOA/AOB ratio was with the concentrations of ammonium. Several physicochemical factors, rather than any single one, affect the distribution patterns suggesting that a combination of factors is involved in shaping the dynamics of AOA and AOB in the mangrove ecosystem.},
}
@article {pmid21632276,
year = {2011},
author = {Brochier-Armanet, C and Forterre, P and Gribaldo, S},
title = {Phylogeny and evolution of the Archaea: one hundred genomes later.},
journal = {Current opinion in microbiology},
volume = {14},
number = {3},
pages = {274-281},
doi = {10.1016/j.mib.2011.04.015},
pmid = {21632276},
issn = {1879-0364},
mesh = {Archaea/*classification/*genetics ; Biological Evolution ; *Genome, Archaeal ; *Phylogeny ; },
abstract = {Little more than 30 years since the discovery of the Archaea, over one hundred archaeal genome sequences are now publicly available, of which ∼40% have been released in the last two years. Their analysis provides an increasingly complex picture of archaeal phylogeny and evolution with the proposal of new major phyla, such as the Thaumarchaeota, and important information on the evolution of key central cellular features such as cell division. Insights have been gained into the events and processes in archaeal evolution, with a number of additional and unexpected links to the Eukaryotes revealed. Taken together, these results predict that many more surprises will be found as new archaeal genomes are sequenced.},
}
@article {pmid21632226,
year = {2012},
author = {Szukics, U and Hackl, E and Zechmeister-Boltenstern, S and Sessitsch, A},
title = {Rapid and dissimilar response of ammonia oxidizing archaea and bacteria to nitrogen and water amendment in two temperate forest soils.},
journal = {Microbiological research},
volume = {167},
number = {2},
pages = {103-109},
pmid = {21632226},
issn = {1618-0623},
support = {P 16580/FWF_/Austrian Science Fund FWF/Austria ; },
mesh = {Ammonia/*metabolism ; Archaea/*metabolism ; Bacteria/*metabolism ; Biota ; DNA Fingerprinting ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; Nitrates/metabolism ; Nitrification ; Nitrogen/*metabolism ; Oxidation-Reduction ; Oxidoreductases/genetics ; Polymorphism, Restriction Fragment Length ; Real-Time Polymerase Chain Reaction ; *Soil Microbiology ; Trees ; Water/*metabolism ; },
abstract = {Biochemical processes relevant to soil nitrogen (N) cycling are performed by soil microorganisms affiliated with diverse phylogenetic groups. For example, the oxidation of ammonia, representing the first step of nitrification, can be performed by ammonia oxidizing bacteria (AOB) and, as recently reported, also by ammonia oxidizing archaea (AOA). However, the contribution to ammonia oxidation of the phylogenetically separated AOA versus AOB and their respective responsiveness to environmental factors are still poorly understood. The present study aims at comparing the capacity of AOA and AOB to momentarily respond to N input and increased soil moisture in two contrasting forest soils. Soils from the pristine Rothwald forest and the managed Schottenwald forest were amended with either NH(4)(+)-N or NO(3)(-)-N and were incubated at 40% and 70% water-filled pore space (WFPS) for four days. Nitrification rates were measured and AOA and AOB abundance and community composition were determined via quantitative PCR (qPCR) and terminal restriction length fragment polymorphism (T-RFLP) analysis of bacterial and archaeal amoA genes. Our study reports rapid and distinct changes in AOA and AOB abundances in the two forest soils in response to N input and increased soil moisture but no significant effects on net nitrification rates. Functional microbial communities differed significantly in the two soils and responded specifically to the treatments during the short-term incubation. In the Rothwald soil the abundance and community composition of AOA were affected by the water content, whereas AOB communities responded to N amendment. In the Schottenwald soil, by contrast, AOA responded to N addition. These results suggest that AOA and AOB may be selectively influenced by soil and management factors.},
}
@article {pmid21631688,
year = {2011},
author = {Dodsworth, JA and Hungate, BA and Hedlund, BP},
title = {Ammonia oxidation, denitrification and dissimilatory nitrate reduction to ammonium in two US Great Basin hot springs with abundant ammonia-oxidizing archaea.},
journal = {Environmental microbiology},
volume = {13},
number = {8},
pages = {2371-2386},
doi = {10.1111/j.1462-2920.2011.02508.x},
pmid = {21631688},
issn = {1462-2920},
mesh = {Ammonia/*metabolism ; Archaea/classification/genetics/*metabolism ; Bacteria/classification/genetics/metabolism ; Biodiversity ; Biomarkers/analysis ; *Denitrification ; Geologic Sediments/microbiology ; Hot Springs/*microbiology ; Nitrates/metabolism ; Quaternary Ammonium Compounds/analysis ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Many thermophiles catalyse free energy-yielding redox reactions involving nitrogenous compounds; however, little is known about these processes in natural thermal environments. Rates of ammonia oxidation, denitrification and dissimilatory nitrate reduction to ammonium (DNRA) were measured in source water and sediments of two ≈ 80°C springs in the US Great Basin. Ammonia oxidation and denitrification occurred mainly in sediments. Ammonia oxidation rates measured using (15)N-NO(3)(-) pool dilution ranged from 5.5 ± 0.8 to 8.6 ± 0.9 nmol N g(-1) h(-1) and were unaffected or only mildly stimulated by amendment with NH(4) Cl. Denitrification rates measured using acetylene block ranged from 15.8 ± 0.7 to 51 ± 12 nmol N g(-1) h(-1) and were stimulated by amendment with NO(3)(-) and complex organic compounds. The DNRA rate in one spring sediment measured using an (15)N-NO(3)(-) tracer was 315 ± 48 nmol N g(-1) h(-1). Both springs harboured distinct planktonic and sediment microbial communities. Close relatives of the autotrophic, ammonia-oxidizing archaeon 'Candidatus Nitrosocaldus yellowstonii' represented the most abundant OTU in both spring sediments by 16S rRNA gene pyrotag analysis. Quantitative PCR (qPCR) indicated that 'Ca. N. yellowstonii'amoA and 16S rRNA genes were present at 3.5-3.9 × 10(8) and 6.4-9.0 × 10(8) copies g(-1) sediment. Potential denitrifiers included members of the Aquificales and Thermales. Thermus spp. comprised <1% of 16S rRNA gene pyrotags in both sediments and qPCR for T. thermophilus narG revealed sediment populations of 1.3-1.7 × 10(6) copies g(-1) sediment. These data indicate a highly active nitrogen cycle (N-cycle) in these springs and suggest that ammonia oxidation may be a major source of energy fuelling primary production.},
}
@article {pmid21618465,
year = {2011},
author = {Ye, L and Zhang, T},
title = {Ammonia-oxidizing bacteria dominates over ammonia-oxidizing archaea in a saline nitrification reactor under low DO and high nitrogen loading.},
journal = {Biotechnology and bioengineering},
volume = {108},
number = {11},
pages = {2544-2552},
doi = {10.1002/bit.23211},
pmid = {21618465},
issn = {1097-0290},
mesh = {Ammonia/*metabolism ; Archaea/*classification/genetics/*metabolism ; Bacteria/*classification/genetics/*metabolism ; *Biodiversity ; Bioreactors/*microbiology ; Culture Media/chemistry ; DNA Fingerprinting ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; Molecular Sequence Data ; Nitrification ; Nitrogen/metabolism ; Oxidation-Reduction ; Oxygen/metabolism ; Polymorphism, Restriction Fragment Length ; Real-Time Polymerase Chain Reaction ; Salinity ; Sequence Analysis, DNA ; Water Microbiology ; },
abstract = {A continuous nitrification reactor treating saline wastewater was operated for almost 1 year under low dissolved oxygen (DO) levels (0.15-0.5 mg/L) and high nitrogen loadings (0.26-0.52 kg-N/(m(3) day)) in four phases. The diversity and abundance of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) were analyzed by cloning, terminal restriction fragment length polymorphism (T-RFLP) and quantitative polymerase chain reaction (qPCR). The results showed that there were only one dominant AOA species and one dominant AOB species in the reactor in all of the four experimental phases. The amoA gene of the dominant AOA only had a similarity of 89.3% with the cultured AOA species Nitrosopumilus maritimus SCM1. All of the AOB species detected in the reactor belong to Nitrosomonas genus and it was found that the AOB populations changed with the ammonium loadings and DO levels. The abundance of AOB in the reactor was ∼40 times larger than that of AOA, and the ratio of AOB to AOA increased significantly up to ∼2,000 to ∼4,000 with the increase of ammonium loading, indicating that AOB are much more competitive than AOA in high ammonium environments and probably AOA play a less important role than AOB in the nitrification reactors.},
}
@article {pmid21612976,
year = {2011},
author = {Sato, T and Atomi, H},
title = {Novel metabolic pathways in Archaea.},
journal = {Current opinion in microbiology},
volume = {14},
number = {3},
pages = {307-314},
doi = {10.1016/j.mib.2011.04.014},
pmid = {21612976},
issn = {1879-0364},
mesh = {Archaea/*genetics/*metabolism ; Genes, Archaeal ; Genome, Archaeal ; *Metabolic Networks and Pathways ; },
abstract = {The Archaea harbor many metabolic pathways that differ to previously recognized classical pathways. Glycolysis is carried out by modified versions of the Embden-Meyerhof and Entner-Doudoroff pathways. Thermophilic archaea have recently been found to harbor a bi-functional fructose-1,6-bisphosphate aldolase/phosphatase for gluconeogenesis. A number of novel pentose-degrading pathways have also been recently identified. In terms of anabolic metabolism, a pathway for acetate assimilation, the methylaspartate cycle, and two CO2-fixing pathways, the 3-hydroxypropionate/4-hydroxybutyrate cycle and the dicarboxylate/4-hydroxybutyrate cycle, have been elucidated. As for biosynthetic pathways, recent studies have clarified the enzymes responsible for several steps involved in the biosynthesis of inositol phospholipids, polyamine, coenzyme A, flavin adeninedinucleotide and heme. By examining the presence/absence of homologs of these enzymes on genome sequences, we have found that the majority of these enzymes and pathways are specific to the Archaea.},
}
@article {pmid21600187,
year = {2011},
author = {Luo, H and Robb, FT},
title = {A modulator domain controlling thermal stability in the Group II chaperonins of Archaea.},
journal = {Archives of biochemistry and biophysics},
volume = {512},
number = {1},
pages = {111-118},
doi = {10.1016/j.abb.2011.04.017},
pmid = {21600187},
issn = {1096-0384},
mesh = {Adenosine Triphosphate/metabolism ; Amino Acid Motifs ; Amino Acid Sequence ; Enzyme Stability ; Group II Chaperonins/*chemistry/*genetics/metabolism ; Methanosarcinaceae/chemistry/enzymology/genetics ; Molecular Sequence Data ; Mutation ; Protein Multimerization ; Protein Structure, Tertiary ; Pyrococcus furiosus/chemistry/*enzymology/genetics ; Temperature ; },
abstract = {Archaeal Group II chaperonins (Cpns) are strongly conserved, considering that their growth temperatures range from 23 to 122°C. The C-terminal 15-25 residues are hypervariable, and highly charged in thermophilic species. Our hypothesis is that the C-terminal is a key determinant of stabilization of the Cpn complex. The C-terminus of the Cpn from the hyperthermophile Pyrococcus furiosus was mutated to test this hypothesis. C-terminal deletions and replacement of charged residues resulted in destabilization. The stability of ATPase activity declined in proportion to the reduction in charged residues with Ala or Gly. An EK-rich motif ((528)EKEKEKEGEK5(37)) proved to be a key domain for stabilization at or near 100°C. Mutations "tuned" the Cpn for optimal protein folding at lower optimal temperatures, and Glu substitution was more potent than Lys replacement. Pf Cpn stability was enhanced by Ca(2+), especially in the mutant Cpn lacking C-terminal Lys residues. This suggests that Glu-Glu interactions between C termini might be mediated by Ca(2+). The C-terminal of a Cpn from the psychrophilic archaeon Methanococcoides burtonii was replaced by a domain from the hyperthermophile, resulting in increased thermostability and thermoactivity. We conclude that localized evolutionary variation in the C-terminus modulates the temperature range of archaeal Cpns.},
}
@article {pmid21593795,
year = {2011},
author = {Pitcher, A and Villanueva, L and Hopmans, EC and Schouten, S and Reichart, GJ and Sinninghe Damsté, JS},
title = {Niche segregation of ammonia-oxidizing archaea and anammox bacteria in the Arabian Sea oxygen minimum zone.},
journal = {The ISME journal},
volume = {5},
number = {12},
pages = {1896-1904},
pmid = {21593795},
issn = {1751-7370},
mesh = {Ammonia/*metabolism ; Archaea/classification/genetics/*metabolism ; Bacteria/classification/genetics/*metabolism ; DNA, Ribosomal/chemistry/genetics/metabolism ; Glyceryl Ethers/metabolism ; Oceans and Seas ; Oxidation-Reduction ; Oxygen/metabolism ; Phylogeny ; Quaternary Ammonium Compounds/metabolism ; RNA, Ribosomal, 16S/genetics/metabolism ; Seawater/*microbiology ; },
abstract = {Ammonia-oxidizing archaea (AOA) and anaerobic ammonia-oxidizing (anammox) bacteria have emerged as significant factors in the marine nitrogen cycle and are responsible for the oxidation of ammonium to nitrite and dinitrogen gas, respectively. Potential for an interaction between these groups exists; however, their distributions are rarely determined in tandem. Here we have examined the vertical distribution of AOA and anammox bacteria through the Arabian Sea oxygen minimum zone (OMZ), one of the most intense and vertically exaggerated OMZs in the global ocean, using a unique combination of intact polar lipid (IPL) and gene-based analyses, at both DNA and RNA levels. To screen for AOA-specific IPLs, we developed a high-performance liquid chromatography/mass spectrometry/mass spectrometry method targeting hexose-phosphohexose (HPH) crenarchaeol, a common IPL of cultivated AOA. HPH-crenarchaeol showed highest abundances in the upper OMZ transition zone at oxygen concentrations of ca. 5 μM, coincident with peaks in both thaumarchaeotal 16S rDNA and amoA gene abundances and gene expression. In contrast, concentrations of anammox-specific IPLs peaked within the core of the OMZ at 600 m, where oxygen reached the lowest concentrations, and coincided with peak anammox 16S rDNA and the hydrazine oxidoreductase (hzo) gene abundances and their expression. Taken together, the data reveal a unique depth distribution of abundant AOA and anammox bacteria and the segregation of their respective niches by >400 m, suggesting no direct coupling of their metabolisms at the time and site of sampling in the Arabian Sea OMZ.},
}
@article {pmid21576844,
year = {2011},
author = {Morimoto, S and Hayatsu, M and Takada Hoshino, Y and Nagaoka, K and Yamazaki, M and Karasawa, T and Takenaka, M and Akiyama, H},
title = {Quantitative analyses of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in fields with different soil types.},
journal = {Microbes and environments},
volume = {26},
number = {3},
pages = {248-253},
doi = {10.1264/jsme2.me11127},
pmid = {21576844},
issn = {1347-4405},
mesh = {Ammonia/*metabolism ; Archaea/enzymology/genetics/isolation &amp; purification/*metabolism ; Archaeal Proteins/genetics/metabolism ; Bacteria/enzymology/genetics/isolation &amp; purification/*metabolism ; Bacterial Proteins/genetics/metabolism ; Biodiversity ; Nitrification ; Oxidation-Reduction ; Oxidoreductases/genetics/metabolism ; Soil/*chemistry ; *Soil Microbiology ; },
abstract = {Soil type is one of the key factors affecting soil microbial communities. With regard to ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB), however, it has not been determined how soil type affects their community size and soil nitrification activity. Here we quantitatively analyzed the ammonia monooxygenase genes (amoA) of these ammonia oxidizers in fields with three different soil types (Low-humic Andosol [LHA], Gray Lowland Soil [GLS], and Yellow Soil [YS]) under common cropping conditions, and assessed the relationships between soil nitrification activity and the abundance of each amoA. Nitrification activity of LHA was highest, followed by that of GLS and YS; this order was consistent with that for the abundance of AOB amoA. Abundance of AOB amoA showed temporal variation, which was similar to that observed in nitrification activity, and a strong relationship (adjusted R(2)=0.742) was observed between the abundance of AOB amoA and nitrification activity. Abundance of AOA amoA also exhibited a significant relationship (adjusted R(2)=0.228) with nitrification activity, although this relationship was much weaker. Our results indicate that soil type affects the community size of AOA and AOB and the resulting nitrification activity, and that AOB are major contributors to nitrification in soils, while AOA are partially responsible.},
}
@article {pmid21575735,
year = {2011},
author = {Cunha, IS and Barreto, CC and Costa, OY and Bomfim, MA and Castro, AP and Kruger, RH and Quirino, BF},
title = {Bacteria and Archaea community structure in the rumen microbiome of goats (Capra hircus) from the semiarid region of Brazil.},
journal = {Anaerobe},
volume = {17},
number = {3},
pages = {118-124},
doi = {10.1016/j.anaerobe.2011.04.018},
pmid = {21575735},
issn = {1095-8274},
mesh = {Animals ; Archaea/classification/*genetics/isolation &amp; purification ; Bacteria/classification/*genetics/isolation &amp; purification ; Base Sequence ; Biota ; Brazil ; Female ; Gene Library ; Genes, Archaeal ; Genes, Bacterial ; Goats/*microbiology ; *Metagenome ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Rumen/*microbiology ; Sequence Analysis, DNA ; },
abstract = {Most studies present in the literature about the rumen microbiome have focused on cattle and sheep. This is the first report of the characterization of the bacterial and archaeal communities present in the liquid and solid-associated fractions of the rumen from free ranging Moxotó breed goats using 16S rRNA gene libraries. PCR was used to amplify the 16S rRNA gene with bacterial and archaeal universal primers and sequences from each library constructed were obtained. Sequences of Bacteria from the phyla Bacteroidetes and Firmicutes were predominant. The overall dominant classes in the rumen were Clostridia and Bacteroidia, which are known to play a role in plant fiber degradation in other ruminants. Unclassified Bacteria accounted for 4.7% of the liquid fraction sequences and 16.4% of the solid fraction sequences. From the archaeal libraries only sequences from the phylum Euryarcheota were identified and were assigned to the class Methanobacteria of the genera Methanobrevibacter and Methanosphaera. A group of Archaea not previously known to be associated with the rumen was identified: uncultured methanogens belonging to the "uncultured marine bacteria" groups II and III. The local water contained high salt concentrations and this may explain the presence of these groups in the Moxotó goat rumen.},
}
@article {pmid21562601,
year = {2011},
author = {Santoro, AE and Casciotti, KL},
title = {Enrichment and characterization of ammonia-oxidizing archaea from the open ocean: phylogeny, physiology and stable isotope fractionation.},
journal = {The ISME journal},
volume = {5},
number = {11},
pages = {1796-1808},
pmid = {21562601},
issn = {1751-7370},
mesh = {Ammonia/*metabolism ; Archaea/classification/genetics/*isolation &amp; purification/*metabolism ; DNA, Archaeal/chemistry/genetics/metabolism ; DNA, Bacterial/genetics/metabolism ; Molecular Sequence Data ; Nitrites/metabolism ; Nitrogen/metabolism ; Oxidoreductases/genetics ; Pacific Ocean ; Phylogeny ; Proteobacteria/genetics/metabolism ; RNA, Ribosomal, 16S/genetics/metabolism ; Seawater/*microbiology ; },
abstract = {Archaeal genes for ammonia oxidation are widespread in the marine environment, but direct physiological evidence for ammonia oxidation by marine archaea is limited. We report the enrichment and characterization of three strains of pelagic ammonia-oxidizing archaea (AOA) from the North Pacific Ocean that have been maintained in laboratory culture for over 3 years. Phylogenetic analyses indicate the three strains belong to a previously identified clade of water column-associated AOA and possess 16S ribosomal RNA genes and ammonia monooxygenase subunit a (amoA) genes highly similar (98-99% identity) to those recovered in DNA and complementary DNA clone libraries from the open ocean. The strains grow in natural seawater-based liquid medium while stoichiometrically converting ammonia (NH(3)) to nitrite (NO(2)(-)). Ammonia oxidation by the enrichments is only partially inhibited by allylthiourea at concentrations known to completely inhibit cultivated ammonia-oxidizing bacteria. The three strains were used to determine the nitrogen stable isotope effect ((15)ɛ(NH3)) during archaeal ammonia oxidation, an important parameter for interpreting stable isotope ratios in the environment. Archaeal (15)ɛ(NH3) ranged from 13‰ to 41‰, within the range of that previously reported for ammonia-oxidizing bacteria. Despite low amino acid identity between the archaeal and bacterial Amo proteins, their functional diversity as captured by (15)ɛ(NH3) is similar.},
}
@article {pmid21550839,
year = {2011},
author = {Reeve, JN and Schleper, C},
title = {Archaea: very diverse, often different but never bad?.},
journal = {Current opinion in microbiology},
volume = {14},
number = {3},
pages = {271-273},
doi = {10.1016/j.mib.2011.04.011},
pmid = {21550839},
issn = {1879-0364},
mesh = {Archaea/*classification/genetics/*isolation &amp; purification/pathogenicity ; Ecosystem ; *Environmental Microbiology ; *Genetic Variation ; },
}
@article {pmid21546550,
year = {2011},
author = {Hsu, CH and Wang, AH},
title = {The DNA-recognition fold of Sso7c4 suggests a new member of SpoVT-AbrB superfamily from archaea.},
journal = {Nucleic acids research},
volume = {39},
number = {15},
pages = {6764-6774},
pmid = {21546550},
issn = {1362-4962},
mesh = {Amino Acid Sequence ; Archaeal Proteins/*chemistry/classification ; Binding Sites ; DNA/*chemistry ; DNA-Binding Proteins/*chemistry/classification ; Dimerization ; Models, Molecular ; Molecular Sequence Data ; Nuclear Magnetic Resonance, Biomolecular ; Nucleic Acid Conformation ; Protein Folding ; Protein Structure, Secondary ; Sequence Alignment ; Sulfolobus solfataricus ; },
abstract = {Organisms growing at elevated temperatures face the challenge of maintaining the integrity of their genetic materials. Archaea possess unique chromatin proteins for gene organization and information processing. We present the solution structure of Sso7c4 from Sulfolobus solfataricus, which has a homodimeric DNA-binding fold forming a swapped β-loop-β 'Tai-Chi' topology. The fold is reminiscent of the N-terminal DNA-binding domain of AbrB and MazE. In addition, several amide resonances in the heteronuclear single quantum coherence spectra of Sso7c4 are shifted and broadened with the addition of small amounts of duplex DNA oligomers. The locations of the corresponding amides in the Sso7c4 structure define its DNA-interacting surface. NMR spectra of DNA titrated with the protein further indicated that Sso7c4 interacts with DNA in the major groove. Taken together, a plausible model for the Sso7c4-DNA complex is presented, in which the DNA double helix is curved around the protein dimer.},
}
@article {pmid21544103,
year = {2011},
author = {Kan, J and Clingenpeel, S and Macur, RE and Inskeep, WP and Lovalvo, D and Varley, J and Gorby, Y and McDermott, TR and Nealson, K},
title = {Archaea in Yellowstone Lake.},
journal = {The ISME journal},
volume = {5},
number = {11},
pages = {1784-1795},
pmid = {21544103},
issn = {1751-7370},
mesh = {Archaea/*classification/genetics ; DNA, Archaeal/analysis/genetics ; Hydrothermal Vents ; Lakes/*microbiology ; Northwestern United States ; Phylogeny ; Polymerase Chain Reaction ; },
abstract = {The Yellowstone geothermal complex has yielded foundational discoveries that have significantly enhanced our understanding of the Archaea. This study continues on this theme, examining Yellowstone Lake and its lake floor hydrothermal vents. Significant Archaea novelty and diversity were found associated with two near-surface photic zone environments and two vents that varied in their depth, temperature and geochemical profile. Phylogenetic diversity was assessed using 454-FLX sequencing (~51,000 pyrosequencing reads; V1 and V2 regions) and Sanger sequencing of 200 near-full-length polymerase chain reaction (PCR) clones. Automated classifiers (Ribosomal Database Project (RDP) and Greengenes) were problematic for the 454-FLX reads (wrong domain or phylum), although BLAST analysis of the 454-FLX reads against the phylogenetically placed full-length Sanger sequenced PCR clones proved reliable. Most of the archaeal diversity was associated with vents, and as expected there were differences between the vents and the near-surface photic zone samples. Thaumarchaeota dominated all samples: vent-associated organisms corresponded to the largely uncharacterized Marine Group I, and in surface waters, ~69-84% of the 454-FLX reads matched archaeal clones representing organisms that are Nitrosopumilus maritimus-like (96-97% identity). Importance of the lake nitrogen cycling was also suggested by >5% of the alkaline vent phylotypes being closely related to the nitrifier Candidatus Nitrosocaldus yellowstonii. The Euryarchaeota were primarily related to the uncharacterized environmental clones that make up the Deep Sea Euryarchaeal Group or Deep Sea Hydrothermal Vent Group-6. The phylogenetic parallels of Yellowstone Lake archaea to marine microorganisms provide opportunities to examine interesting evolutionary tracks between freshwater and marine lineages.},
}
@article {pmid21543251,
year = {2011},
author = {Samson, RY and Bell, SD},
title = {Cell cycles and cell division in the archaea.},
journal = {Current opinion in microbiology},
volume = {14},
number = {3},
pages = {350-356},
doi = {10.1016/j.mib.2011.04.005},
pmid = {21543251},
issn = {1879-0364},
support = {//Wellcome Trust/United Kingdom ; },
mesh = {Archaea/*physiology ; *Cell Cycle ; Cell Cycle Proteins/genetics/metabolism ; Chromosomes, Archaeal/metabolism ; Models, Biological ; },
abstract = {Until recently little was known about the cell cycle parameters and division mechanisms of archaeal organisms. Although this is still the case for the majority of archaea, significant advances have been made in some model species. The information that has been gleaned thus far points to a remarkable degree of diversity within the archaeal domain of life. More specifically, members of distinct phyla have very different chromosome copy numbers, replication control systems and even employ distinct machineries for cell division.},
}
@article {pmid21541092,
year = {2011},
author = {Horz, HP and Conrads, G},
title = {Methanogenic Archaea and oral infections - ways to unravel the black box.},
journal = {Journal of oral microbiology},
volume = {3},
number = {},
pages = {},
pmid = {21541092},
issn = {2000-2297},
abstract = {Archaea, organisms that make up the third domain of cellular life are members of the human oral microflora. They are strikingly less diverse than oral bacteria and appear to be relatively rare with respect to their numerical abundance. Since they have been exclusively found in association with oral infections such as periodontitis and apical periodontitis and given their unique physiology and energy metabolism, it is highly plausible that they are more than just secondary colonizers of infected areas, but instead are actively involved in the overall poly-microbial infection process. Conversely, it is a highly challenging task to clearly demonstrate their possible active participation - mostly due to the difficulty to grow them in routine microbiology laboratories. This current review points out the importance for understanding the medical impact of methanogens and aims at devising strategies for elucidating the true function of archaea in the oral ecosystem.},
}
@article {pmid21539593,
year = {2011},
author = {Matarazzo, F and Ribeiro, AC and Feres, M and Faveri, M and Mayer, MP},
title = {Diversity and quantitative analysis of Archaea in aggressive periodontitis and periodontally healthy subjects.},
journal = {Journal of clinical periodontology},
volume = {38},
number = {7},
pages = {621-627},
doi = {10.1111/j.1600-051X.2011.01734.x},
pmid = {21539593},
issn = {1600-051X},
mesh = {Adult ; Aggressive Periodontitis/*microbiology ; Archaea/*classification/isolation &amp; purification ; Biofilms ; Colony Count, Microbial ; DNA, Archaeal/analysis ; Dental Plaque/microbiology ; Female ; Gingival Hemorrhage/microbiology ; Humans ; Male ; Methanobacterium/classification/isolation &amp; purification ; Methanobrevibacter/classification/isolation &amp; purification ; Methanosarcina/classification/isolation &amp; purification ; Methanosarcinales/classification/isolation &amp; purification ; Periodontal Attachment Loss/microbiology ; Periodontal Pocket/microbiology ; Periodontium/*microbiology ; Porphyromonas gingivalis/isolation &amp; purification ; RNA, Archaeal/analysis ; RNA, Ribosomal, 16S/analysis ; Young Adult ; },
abstract = {AIM: To investigate the diversity, levels and proportions of Archaea in the subgingival biofilm of generalized aggressive periodontitis (GAgP; n=30) and periodontally healthy (PH; n=30) subjects.<br><br>MATERIALS AND METHODS: Diversity was determined by sequencing archaeal 16S rRNA gene libraries from 20 samples (10/group). The levels and proportions of Archaea were analysed by quantitative PCR (qPCR) in four and two samples/subject in GAgP and PH groups, respectively.<br><br>RESULTS: Archaea were detected in 27/28 subjects and 68% of the sites of the GAgP group, and in 26/30 subjects and 58.3% sites of the PH group. Methanobrevibacter oralis was found in all 20 samples studied, Methanobacterium curvum/congolense in three GAgP and six PH samples, and Methanosarcina mazeii in four samples from each group. The levels and proportions of Archaea were higher in GAgP than in PH, whereas no differences were observed between the two probing depth category sites from the GAgP group.<br><br>CONCLUSION: Archaea were frequently found in subjects with periodontal health and GAgP, especially M. oralis. However, the higher levels and proportions (Archaea/total prokaryotes) of this domain observed in GAgP in comparison with PH subjects indicate a possible role of some of these microorganisms as an environmental modifier in GAgP.},
}
@article {pmid21534268,
year = {2011},
author = {},
title = {Archaea and the tree of life. Proceedings of an international interdisciplinary meeting. 2009. Fondation Des Treilles. France.},
journal = {Research in microbiology},
volume = {162},
number = {1},
pages = {1-98},
pmid = {21534268},
issn = {1769-7123},
mesh = {Archaea/*classification/genetics ; Biological Evolution ; Phylogeny ; },
}
@article {pmid21518817,
year = {2011},
author = {Fernandez-Pol, JA},
title = {Conservation of multifunctional ribosomal protein metallopanstimulin-1 (RPS27) through complex evolution demonstrates its key role in growth regulation in Archaea, eukaryotic cells, DNA repair, translation and viral replication.},
journal = {Cancer genomics &amp; proteomics},
volume = {8},
number = {3},
pages = {105-126},
pmid = {21518817},
issn = {1790-6245},
mesh = {Archaea/*growth &amp; development ; Cell Division/*physiology ; DNA Repair/*physiology ; Eukaryotic Cells/cytology ; Herpesvirus 1, Human/physiology ; Herpesvirus 2, Human/physiology ; Humans ; Metalloproteins/genetics/*physiology ; Nuclear Proteins/genetics/*physiology ; Protein Biosynthesis/*physiology ; RNA-Binding Proteins/genetics/*physiology ; Ribosomal Proteins/genetics/*physiology ; Virus Replication/*physiology ; },
abstract = {BACKGROUND: When the functions of a protein serve a useful survival and unique purpose, the selective pressures of evolutionary laws of nature conserve the DNA sequences encoding such proteins. In many instances, the conservation of these sequences has occurred since the inception of life on earth to the present in phylogenetically related species. The unique function(s) of metallopanstimulin (MPS-1/RPS27) ribosomal protein (RP) and a limited number of other RPs, in growth regulation, and viral infection is further documented here. Based on the correlation of information concerning Genome Context Analysis, and new information presented here, the author proposes that neutralization or elimination of ribosomal MPS-1/S27 DNA, mRNA or translated protein in eukaryote cells, initiated in the process of chemical, viral or radiation carcinogenesis can result in control of most carcinogenic processes by selective elimination of transformed cells which display overexpression of RPMPS-1/S27, and/or non-lethal pathogenic mutations of RPMPS-1/S27 gene. Recently, critical interactions were reported between RPMPS-1/S27 and p53 induced by DNA damage such as ionizing radiation, or chemotherapy drugs, that result in the activation of p53 which in turn represses RPMPS-1/S27 actions. Thus, p53, RPS27L, and RPS27/MPS-1) regulate growth and survival.<br><br>MATERIALS AND METHODS: Antivirals were tested in virus-infected cells using: cell culture, cytotoxicity assays, apoptosis, defined virus strains, cloned cells, and RT-PCR. Purity of antivirals was validated by mass spectroscopy (MS). Disruption of zinc finger peptides (ZFPs), by these agents was determined by NMR.<br><br>RESULTS: The data presented here indicates that anti-ZFP agents can potentially be used to prevent and control viral infections by disrupting viral ZFP motifs. Different DNA/RNA virus-infected cells exposed to the antivirals resulted in distruption of both RPMPS-1/S27 and essential viral ZFPs. Picolinic acid (PA) and fusaric acid (FU) were tested and have been shown to have both antiviral and preventive antiviral activities which have been consistently shown to be mediated, at least in part, via interacting with RPMPS-1/S27. The same antiviral agents simultaneously disrupt essential viral ZFPs. Both antiviral events on ZFPs render the pathogenic virus inactive.<br><br>CONCLUSION: It is demonstrated here that PA and FU exhibit antiviral activity towards several DNA and RNA viruses of human and animal importance. Illustrative evidence of the mechanism of action was obtained via MS, NMR, and molecular modeling that PA and, more potently, FU, bind to a particular site of the viral ZFPs. Similarly, it was previously shown by MS, NMR and molecular modeling with RPMPS-1/S27 that PA and FU disrupts the function of this RP protein, preventing viral replication by formation of ternary complexes. This work is consistent with a critical role of RPMPS-1/S27 in the life cycle of various viruses and shows that disruption of viral ZFPs is potentially important to control and prevent deathly viral diseases.},
}
@article {pmid21517915,
year = {2011},
author = {Llirós, M and Alonso-Sáez, L and Gich, F and Plasencia, A and Auguet, O and Casamayor, EO and Borrego, CM},
title = {Active bacteria and archaea cells fixing bicarbonate in the dark along the water column of a stratified eutrophic lagoon.},
journal = {FEMS microbiology ecology},
volume = {77},
number = {2},
pages = {370-384},
doi = {10.1111/j.1574-6941.2011.01117.x},
pmid = {21517915},
issn = {1574-6941},
mesh = {Acetyl-CoA Carboxylase/genetics ; Archaea/classification/genetics/*metabolism ; Bacteria/classification/genetics/*metabolism ; Bicarbonates/*metabolism ; *Carbon Cycle ; Carbon Dioxide/metabolism ; Carbon Isotopes/analysis ; *Darkness ; Denaturing Gradient Gel Electrophoresis ; Fresh Water/chemistry/microbiology ; Gene Library ; Genes, Archaeal ; Genes, Bacterial ; In Situ Hybridization, Fluorescence ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Water Microbiology ; },
abstract = {We studied the carbon dioxide fixation activity in a stratified hypereutrophic karstic lagoon using a combination of fingerprinting techniques targeting bacterial and archaeal 16S rRNA genes, functional gene cloning [the acetyl-CoA carboxylase (accC)], and isotopic labelling ((14)C-bicarbonate) coupled to single-cell analyses [microautoradiography combined with catalyzed reported deposition-FISH (MAR-CARD-FISH)]. The microbial planktonic community was dominated by bacteria with maximal abundances of archaea just below the oxic/anoxic transition zone (7% of total cells). In situ incubations with radiolabelled bicarbonate showed maximal photoassimilation activity in the oxic epilimnion, whereas dark CO(2) fixation was consistently observed throughout the water column, with a maximum at the oxic/anoxic interface (8.6 mg C m(-3) h(-1)). The contributions of light and dark carbon fixation activities in the whole water column were 69% and 31% of the total C incorporated, respectively. MAR-CARD-FISH incubations corroborated these results and revealed that the highest fraction of bacterial and archaeal cells actively uptaking bicarbonate in the light was found at the surface. The bacterial community was mainly composed of green sulfur bacteria (Chlorobi) and members of the Betaproteobacteria and the Bacteroidetes. The archaeal assemblage was composed of phylotypes of the Miscellaneous Crenarchaeotic Group and a few methanogens. Clone libraries of the accC gene showed an absolute dominance of bacterial carboxylases. Our results suggest that the dark carbon fixation activity measured was mainly related to CO(2) incorporation by heterotrophs rather than to the activity of true chemoautotrophs.},
}
@article {pmid21514476,
year = {2011},
author = {Martens-Habbena, W and Stahl, DA},
title = {Nitrogen metabolism and kinetics of ammonia-oxidizing archaea.},
journal = {Methods in enzymology},
volume = {496},
number = {},
pages = {465-487},
doi = {10.1016/B978-0-12-386489-5.00019-1},
pmid = {21514476},
issn = {1557-7988},
mesh = {Ammonia/analysis/*metabolism ; Archaea/*growth &amp; development/*metabolism ; Kinetics ; Methods ; Nitrification/*physiology ; Nitrogen/analysis/*metabolism ; Nitrogen Cycle/*genetics/physiology ; Nitrosomonas europaea/growth &amp; development/metabolism ; Oxidation-Reduction ; },
abstract = {The discovery of ammonia-oxidizing mesophilic and thermophilic Group I archaea changed the century-old paradigm that aerobic ammonia oxidation is solely mediated by two small clades of Beta- and Gammaproteobacteria. Group I archaea are extremely diverse and ubiquitous in marine and terrestrial environments, accounting for 20-30% of the microbial plankton in the global oceans. Recent studies indicated that many of these organisms carry putative ammonia monooxygenase genes and are more abundant than ammonia-oxidizing bacteria in most natural environments suggesting a potentially significant role in the nitrogen cycle. The isolation of Nitrosopumilus maritimus strain SCM1 provided the first direct evidence that Group I archaea indeed gain energy from ammonia oxidation. To characterize the physiology of this archaeal nitrifier, we developed a respirometry setup particularly suited for activity measurements in dilute microbial cultures with extremely low oxygen uptake rates. Here, we describe the setup and review the kinetic experiments conducted with N. maritimus and other nitrifying microorganisms. These experiments demonstrated that N. maritimus is adapted to grow on ammonia concentrations found in oligotrophic open ocean environments, far below the survival threshold of ammonia-oxidizing bacteria. The described setup and experimental procedures should facilitate physiological studies on other nitrifying archaea and oligotrophic microorganisms in general.},
}
@article {pmid21514472,
year = {2011},
author = {Ward, BB and Bouskill, NJ},
title = {The utility of functional gene arrays for assessing community composition, relative abundance, and distribution of ammonia-oxidizing bacteria and archaea.},
journal = {Methods in enzymology},
volume = {496},
number = {},
pages = {373-396},
doi = {10.1016/B978-0-12-386489-5.00015-4},
pmid = {21514472},
issn = {1557-7988},
mesh = {Ammonia/*metabolism ; Archaea/*classification/genetics/isolation &amp; purification ; Bacteria/*classification/genetics/isolation &amp; purification ; DNA, Archaeal/isolation &amp; purification ; DNA, Bacterial/isolation &amp; purification ; Nitrification/genetics ; Oligonucleotide Array Sequence Analysis/*methods ; Oxidoreductases/*genetics/metabolism ; Seawater/microbiology ; Soil Microbiology ; },
abstract = {Ammonia-oxidizing bacteria (AOB) and archaea (AOA) transform ammonium to nitrite, an essential step in the complete mineralization of organic matter, leading to the accumulation of nitrate in oxic environments. The diversity and community composition of both groups have been extensively explored by sequence analysis of both 16S rRNA and amoA (encoding the critical enzyme, ammonia monooxygenase subunit A) genes. In this chapter, the power of the amoA gene as a phylogenetic marker for both AOB and AOA is extended to the development and application of DNA microarrays. Functional gene microarrays provide high throughput, relatively high resolution data on community composition and relative abundance, which is especially useful for comparisons among environments, and between samples in time and space, targeting the microbial group that is responsible for a biogeochemical transformation of interest, such as nitrification. In this chapter, the basic approaches to the design of probes to represent the target groups AOB and AOA are described, and the protocols for preparing hybridization targets from environmental samples are provided. Factors that influence the hybridization results and determine the sensitivity and specificity of the assays are discussed. A few examples of recent applications of amoA microarrays to explore temporal and spatial patterns in AOB and AOA community composition in estuaries and the ocean are presented. Array data are lower resolution than sequencing, but much higher throughput, thus allowing robust statistics and reproducibility that are not possible with large clone libraries. For specific functional groups, arrays provide more direct information in a more economical format than is possible with next generation sequencing.},
}
@article {pmid21514458,
year = {2011},
author = {Nicol, GW and Prosser, JI},
title = {Strategies to determine diversity, growth, and activity of ammonia-oxidizing archaea in soil.},
journal = {Methods in enzymology},
volume = {496},
number = {},
pages = {3-34},
doi = {10.1016/B978-0-12-386489-5.00001-4},
pmid = {21514458},
issn = {1557-7988},
mesh = {Ammonia/metabolism ; Archaea/classification/enzymology/growth &amp; development/*isolation &amp; purification ; Biodiversity ; DNA Fingerprinting/methods ; Genes, rRNA/genetics ; Oxidoreductases/*analysis/*isolation &amp; purification ; Ribotyping/methods ; Sequence Analysis, DNA ; *Soil Microbiology ; },
abstract = {Ecological studies of soil microorganisms require reliable techniques for assessment of microbial community composition, abundance, growth, and activity. Soil structure and physicochemical properties seriously limit the applicability and value of methods involving direct observation, and ecological studies have focused on communities and populations, rather than single cells or microcolonies. Although ammonia-oxidizing archaea were discovered 5 years ago, there are still no cultured representatives from soil and there remains a lack of knowledge regarding their genomic composition, physiology, or functional diversity. Despite these limitations, however, significant insights into their distribution, growth characteristics, and metabolism have been made through the use of a range of molecular methodologies. As well as the analysis of taxonomic markers such as 16S rRNA genes, the development of PCR primers based on a limited number of (mostly marine) sequences has enabled the analysis of homologues encoding proteins involved in energy and carbon metabolism. This chapter will highlight the range of molecular methodologies available for examining the diversity, growth, and activity of ammonia-oxidizing archaea in the soil environment.},
}
@article {pmid21512891,
year = {2011},
author = {Mardanov, AV and Gumerov, VM and Beletsky, AV and Perevalova, AA and Karpov, GA and Bonch-Osmolovskaya, EA and Ravin, NV},
title = {Uncultured archaea dominate in the thermal groundwater of Uzon Caldera, Kamchatka.},
journal = {Extremophiles : life under extreme conditions},
volume = {15},
number = {3},
pages = {365-372},
pmid = {21512891},
issn = {1433-4909},
mesh = {Acidithiobacillus/classification ; Archaea/*classification/genetics/isolation &amp; purification ; Autotrophic Processes ; Bacteria/*classification/genetics/isolation &amp; purification ; Biodiversity ; Crenarchaeota/classification ; DNA, Archaeal/isolation &amp; purification ; DNA, Bacterial/isolation &amp; purification ; Hot Springs/*microbiology ; Hot Temperature ; Hydrogen-Ion Concentration ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Ribotyping ; Russia ; Thermoplasmales/classification ; *Water Microbiology ; },
abstract = {The thermoacidophilic microbial community inhabiting the groundwater with pH 4.0 and temperature 50°C at the East Thermal Field of Uzon Caldera, Kamchatka, was examined using pyrosequencing of the V3 region of the 16S rRNA gene. Bacteria comprise about 30% of microorganisms and are represented primarily by aerobic lithoautotrophs using the energy sources of volcanic origin--thermoacidophilic methanotrophs of the phylum Verrucomicrobia and Acidithiobacillus spp. oxidising metals and reduced sulfur compounds. More than 70% of microbial population in this habitat were represented by archaea, in majority affiliated with "uncultured" lineages. The most numerous group (39% of all archaea) represented a novel division in the phylum Euryarchaeota related to the order Thermoplasmatales. Another abundant group (33% of all archaea) was related to MCG1 lineage of the phylum Crenarchaeota, originally detected in the Yellowstone hot spring as the environmental clone pJP89. The organisms belonging to these two groups are widely spread in hydrothermal environments worldwide. These data indicate an important environmental role of these two archaeal groups and should stimulate the investigation of their metabolism by cultivation or metagenomic approaches.},
}
@article {pmid21505884,
year = {2011},
author = {Miralles, F},
title = {Compositional and structural features related to thermal stability in the archaea SRP19 and SRP54 signal recognition particle proteins.},
journal = {Journal of molecular evolution},
volume = {72},
number = {5-6},
pages = {450-465},
pmid = {21505884},
issn = {1432-1432},
mesh = {Adaptation, Physiological ; Amino Acid Sequence ; Amino Acids/chemistry ; Archaea/*metabolism ; Archaeal Proteins/*chemistry/*metabolism ; Bacterial Proteins/metabolism ; Molecular Sequence Data ; Protein Stability ; Protein Structure, Secondary ; Signal Recognition Particle/*chemistry/*metabolism ; Thermodynamics ; },
abstract = {To survive at high temperature, thermophile organisms must adapt their biomolecules. In both nucleic acids and proteins, this adaptation involves a vast array of compositional and structural modifications. The archaea stand out as the only group of organisms that have species capable of growing at temperatures ranging from 0 to 110°C. In this study, we have used the archaea genome datasets to identify molecular trends related to thermal adaptation in the protein components (SRP19 and SRP54) of the signal recognition particle (SRP). Using comparative genomics and secondary structure homology modeling we have detected significant differences in the amino acids composition and distribution between the SRP proteins of thermophile and mesophile archaea. These include: a significant increase in the thermophile SRP proteins of the frequency of charged amino acids able to participate in electrostatic interactions which contribute to stabilize proteins; decreased content of both thermolabile and small/tiny amino acids which usually contribute to protein flexibility; and a significant increase in aliphatic and aromatic amino acids providing good covering and masking to produce hydrophobic pockets involved in stabilizing protein structure. Moreover, a detailed analysis of the four structural and functional domains of the SRP54 indicates a particularly robust correlation between the compositional properties of the M domain and the optimal growth temperature (OGT) of the archaea. The analysis of the bacterial SRP54(Ffh) shows similar adaptations to the OGT. Thus, natural selection has adapted the SRP proteins to the OGT of the archaea and bacteria species by modifying both, their amino acids composition and distribution.},
}
@article {pmid21498602,
year = {2011},
author = {Groussin, M and Gouy, M},
title = {Adaptation to environmental temperature is a major determinant of molecular evolutionary rates in archaea.},
journal = {Molecular biology and evolution},
volume = {28},
number = {9},
pages = {2661-2674},
doi = {10.1093/molbev/msr098},
pmid = {21498602},
issn = {1537-1719},
mesh = {*Adaptation, Physiological ; Amino Acids/genetics ; Archaea/*genetics/physiology ; Archaeal Proteins/genetics ; Genome, Archaeal ; *Models, Genetic ; *Mutation Rate ; Phylogeny ; Protein Structure, Tertiary/genetics ; RNA, Ribosomal/genetics ; *Temperature ; },
abstract = {Methods to infer the ancestral conditions of life are commonly based on geological and paleontological analyses. Recently, several studies used genome sequences to gain information about past ecological conditions taking advantage of the property that the G+C and amino acid contents of bacterial and archaeal ribosomal DNA genes and proteins, respectively, are strongly influenced by the environmental temperature. The adaptation to optimal growth temperature (OGT) since the Last Universal Common Ancestor (LUCA) over the universal tree of life was examined, and it was concluded that LUCA was likely to have been a mesophilic organism and that a parallel adaptation to high temperature occurred independently along the two lineages leading to the ancestors of Bacteria on one side and of Archaea and Eukarya on the other side. Here, we focus on Archaea to gain a precise view of the adaptation to OGT over time in this domain. It has been often proposed on the basis of indirect evidence that the last archaeal common ancestor was a hyperthermophilic organism. Moreover, many results showed the influence of environmental temperature on the evolutionary dynamics of archaeal genomes: Thermophilic organisms generally display lower evolutionary rates than mesophiles. However, to our knowledge, no study tried to explain the differences of evolutionary rates for the entire archaeal domain and to investigate the evolution of substitution rates over time. A comprehensive archaeal phylogeny and a non homogeneous model of the molecular evolutionary process allowed us to estimate ancestral base and amino acid compositions and OGTs at each internal node of the archaeal phylogenetic tree. The last archaeal common ancestor is predicted to have been hyperthermophilic and adaptations to cooler environments can be observed for extant mesophilic species. Furthermore, mesophilic species present both long branches and high variation of nucleotide and amino acid compositions since the last archaeal common ancestor. The increase of substitution rates observed in mesophilic lineages along all their branches can be interpreted as an ongoing adaptation to colder temperatures and to new metabolisms. We conclude that environmental temperature is a major factor that governs evolutionary rates in Archaea.},
}
@article {pmid21494271,
year = {2011},
author = {van Ooij, C},
title = {Archaea: Archaea shape up.},
journal = {Nature reviews. Microbiology},
volume = {9},
number = {5},
pages = {312},
pmid = {21494271},
issn = {1740-1534},
}
@article {pmid21489296,
year = {2011},
author = {Chan, PP and Cozen, AE and Lowe, TM},
title = {Discovery of permuted and recently split transfer RNAs in Archaea.},
journal = {Genome biology},
volume = {12},
number = {4},
pages = {R38},
pmid = {21489296},
issn = {1474-760X},
support = {HG004002-01A2/HG/NHGRI NIH HHS/United States ; },
mesh = {Archaea/*genetics ; Base Sequence ; Computational Biology ; Eukaryota/genetics ; Evolution, Molecular ; Genome, Archaeal/*genetics ; Introns/genetics ; Molecular Sequence Data ; Phylogeny ; RNA, Archaeal/classification/*genetics ; RNA, Transfer/classification/*genetics ; Trans-Splicing/*genetics ; },
abstract = {BACKGROUND: As in eukaryotes, precursor transfer RNAs in Archaea often contain introns that are removed in tRNA maturation. Two unrelated archaeal species display unique pre-tRNA processing complexity in the form of split tRNA genes, in which two to three segments of tRNAs are transcribed from different loci, then trans-spliced to form a mature tRNA. Another rare type of pre-tRNA, found only in eukaryotic algae, is permuted, where the 3' half is encoded upstream of the 5' half, and must be processed to be functional.<br><br>RESULTS: Using an improved version of the gene-finding program tRNAscan-SE, comparative analyses and experimental verifications, we have now identified four novel trans-spliced tRNA genes, each in a different species of the Desulfurococcales branch of the Archaea: tRNA(Asp(GUC)) in Aeropyrum pernix and Thermosphaera aggregans, and tRNA(Lys(CUU)) in Staphylothermus hellenicus and Staphylothermus marinus. Each of these includes features surprisingly similar to previously studied split tRNAs, yet comparative genomic context analysis and phylogenetic distribution suggest several independent, relatively recent splitting events. Additionally, we identified the first examples of permuted tRNA genes in Archaea: tRNA(iMet(CAU)) and tRNA(Tyr(GUA)) in Thermofilum pendens, which appear to be permuted in the same arrangement seen previously in red alga.<br><br>CONCLUSIONS: Our findings illustrate that split tRNAs are sporadically spread across a major branch of the Archaea, and that permuted tRNAs are a new shared characteristic between archaeal and eukaryotic species. The split tRNA discoveries also provide new clues to their evolutionary history, supporting hypotheses for recent acquisition via viral or other mobile elements.},
}
@article {pmid21470902,
year = {2011},
author = {Phillips, G and de Crécy-Lagard, V},
title = {Biosynthesis and function of tRNA modifications in Archaea.},
journal = {Current opinion in microbiology},
volume = {14},
number = {3},
pages = {335-341},
doi = {10.1016/j.mib.2011.03.001},
pmid = {21470902},
issn = {1879-0364},
mesh = {Archaea/*genetics/*metabolism ; Biosynthetic Pathways/genetics ; Protein Biosynthesis ; *RNA Processing, Post-Transcriptional ; RNA, Transfer/*biosynthesis ; },
abstract = {tRNA modifications are important for decoding, translation accuracy, and structural integrity of tRNAs. Archaeal tRNAs contain at least 47 different tRNA modifications, some of them, including archaeosine, agmatidine, and mimG, are specific to the archaeal domain. The biosynthetic pathways for these complex signature modifications have recently been elucidated and are extensively described in this review. Archaeal organisms still lag Escherichia coli and Saccharomyces cerevisiae in terms of genetic characterization and in vivo function of tRNA modifications. However, recent advances in the model Haloferax volcanii, described here, should allow closing this gap soon. Consequently, an update on experimental characterizations of archaeal tRNA modification genes and proteins is given to set the stage for future work in this field.},
}
@article {pmid21465792,
year = {2011},
author = {Gao, L and Lin, W},
title = {[Diversity of beta-proteobacterial ammonia-oxidizing bacteria and ammonia-oxidizing archaea in shrimp farm sediment].},
journal = {Wei sheng wu xue bao = Acta microbiologica Sinica},
volume = {51},
number = {1},
pages = {75-82},
pmid = {21465792},
issn = {0001-6209},
mesh = {Ammonia/*metabolism ; Animals ; Archaea/classification/genetics/*isolation &amp; purification/*metabolism ; Archaeal Proteins/genetics/metabolism ; Bacterial Proteins/genetics/metabolism ; Betaproteobacteria/classification/genetics/*isolation &amp; purification/*metabolism ; *Biodiversity ; Crustacea/*microbiology ; Geologic Sediments/*microbiology ; Molecular Sequence Data ; Oxidation-Reduction ; Oxidoreductases/genetics/metabolism ; Phylogeny ; },
abstract = {OBJECTIVE: In order to study the diversity of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) in shrimp farm sediment.<br><br>METHODS: Total microbial DNA was directly extracted from the shrimp farm sediment. The clone library of amoA genes were constructed with beta-Proteobacterial-AOB and AOA specific primers. The library was screened by PCR-restriction fragment length polymorphism (RFLP) analysis and clones with unique RFLP patterns were sequenced.<br><br>RESULTS: Phylogenetic analyses of the amoA gene fragments showed that all AOB sequences from shrimp farm sediment were affiliated with Nitrosomonas (61.54%) or Nitrosomonas-like (38. 46%) species and grouped into Nitrosomonas communis cluster, Nitrosomonas sp. Nm148 cluster, Nitrosomonas oligotropha cluster. All AOA sequences belonged to the kingdom Crenarchaeote except that one Operational Taxa Unit (OTU) sequence was Unclassified-Archaea and fell within cluster S (soil origin). AOB and AOA species composition included 13 OTUs and 9 OTUs. The clone coverage of bacterial and archaeal amoA genes was 73.47% and 90.43%. The Shannon-Wiener index, Evenness index, Simpson index and Richness index of AOB were higher than those of AOA.<br><br>CONCLUSION: These findings represent the first detailed examination of archaeal amoA diversity in shrimp farm sediment and demonstrate that diverse communities of Crenarchaeote capable of ammonia oxidation are present within shrimp farm sediment, where they may be actively involved in nitrification.},
}
@article {pmid21441324,
year = {2011},
author = {Pitcher, A and Hopmans, EC and Mosier, AC and Park, SJ and Rhee, SK and Francis, CA and Schouten, S and Damsté, JS},
title = {Core and intact polar glycerol dibiphytanyl glycerol tetraether lipids of ammonia-oxidizing archaea enriched from marine and estuarine sediments.},
journal = {Applied and environmental microbiology},
volume = {77},
number = {10},
pages = {3468-3477},
pmid = {21441324},
issn = {1098-5336},
mesh = {Ammonia/*metabolism ; Archaea/*chemistry/isolation &amp; purification/*metabolism ; Chromatography, High Pressure Liquid ; Geologic Sediments/microbiology ; Glyceryl Ethers/*chemistry/*isolation &amp; purification ; Hexoses/analysis ; Korea ; Mass Spectrometry ; Membrane Lipids/*chemistry/*isolation &amp; purification ; Oxidation-Reduction ; San Francisco ; Svalbard ; },
abstract = {Glycerol dibiphytanyl glycerol tetraether (GDGT)-based intact membrane lipids are increasingly being used as complements to conventional molecular methods in ecological studies of ammonia-oxidizing archaea (AOA) in the marine environment. However, the few studies that have been done on the detailed lipid structures synthesized by AOA in (enrichment) culture are based on species enriched from nonmarine environments, i.e., a hot spring, an aquarium filter, and a sponge. Here we have analyzed core and intact polar lipid (IPL)-GDGTs synthesized by three newly available AOA enriched directly from marine sediments taken from the San Francisco Bay estuary ("Candidatus Nitrosoarchaeum limnia"), and coastal marine sediments from Svalbard, Norway, and South Korea. Like previously screened AOA, the sedimentary AOA all synthesize crenarchaeol (a GDGT containing a cyclohexane moiety and four cyclopentane moieties) as a major core GDGT, thereby supporting the hypothesis that crenarchaeol is a biomarker lipid for AOA. The IPL headgroups synthesized by sedimentary AOA comprised mainly monohexose, dihexose, phosphohexose, and hexose-phosphohexose moieties. The hexose-phosphohexose headgroup bound to crenarchaeol was common to all enrichments and, in fact, the only IPL common to every AOA enrichment analyzed to date. This apparent specificity, in combination with its inferred lability, suggests that it may be the most suitable biomarker lipid to trace living AOA. GDGTs bound to headgroups with a mass of 180 Da of unknown structure appear to be specific to the marine group I.1a AOA: they were synthesized by all three sedimentary AOA and "Candidatus Nitrosopumilus maritimus"; however, they were absent in the group I.1b AOA "Candidatus Nitrososphaera gargensis."},
}
@article {pmid21435682,
year = {2011},
author = {Kleineidam, K and Košmrlj, K and Kublik, S and Palmer, I and Pfab, H and Ruser, R and Fiedler, S and Schloter, M},
title = {Influence of the nitrification inhibitor 3,4-dimethylpyrazole phosphate (DMPP) on ammonia-oxidizing bacteria and archaea in rhizosphere and bulk soil.},
journal = {Chemosphere},
volume = {84},
number = {1},
pages = {182-186},
doi = {10.1016/j.chemosphere.2011.02.086},
pmid = {21435682},
issn = {1879-1298},
mesh = {Ammonia/analysis/*metabolism ; Archaea/*drug effects/genetics/metabolism ; Bacteria/*drug effects/genetics/metabolism ; Nitrates/analysis/metabolism ; Nitrification/*drug effects ; Pyrazoles/*toxicity ; Rhizosphere ; Soil Microbiology ; Soil Pollutants/analysis/metabolism/*toxicity ; },
abstract = {In agricultural plant production nitrification inhibitors like 3,4-dimethylpyrazole phosphate (DMPP) are used to retard the microbial nitrification process of fertilized ammonium to enhance the nitrogen supply for cultivated crops and to reduce nitrogen losses from the production system. Besides the well-known ammonia-oxidizing bacteria (AOB) it is known for a few years that also ammonia-oxidizing archaea (AOA) are able to perform the first step in nitrification, hence being also a target for a nitrification inhibitor. However, so far no information are available concerning the effectiveness of DMPP and its extent towards AOB and AOA, neither in bulk soil nor in the root-rhizosphere complex. We investigated in a field experiment performed according to agricultural practice the effect of DMPP on the abundance of AOB and AOA two, four and eight weeks after fertilization. We observed impaired abundances of AOB but not of AOA in both soil compartments that were still visible eight weeks after application, possibly indicating a reduced effectiveness of the nitrification inhibitor in our study.},
}
@article {pmid21426367,
year = {2011},
author = {Mirete, S and de Figueras, CG and González-Pastor, JE},
title = {Diversity of Archaea in Icelandic hot springs based on 16S rRNA and chaperonin genes.},
journal = {FEMS microbiology ecology},
volume = {77},
number = {1},
pages = {165-175},
doi = {10.1111/j.1574-6941.2011.01095.x},
pmid = {21426367},
issn = {1574-6941},
mesh = {Archaea/classification/*genetics ; Chaperonin 60/*genetics ; Cloning, Molecular ; DNA, Archaeal/genetics ; Hot Springs/*microbiology ; Iceland ; *Phylogeny ; RNA, Ribosomal, 16S/*genetics ; },
abstract = {The diversity of archaeal communities growing in four hot springs (65-90 °C, pH 6.5) was assessed with 16S rRNA gene primers specific for the domain Archaea. Overall, mainly uncultured members of the Desulfurococcales, the Thermoproteales and the Korarchaeota, were identified. Based on this diversity, a set of chaperonin heat-shock protein (Hsp60) gene sequences from different archaeal species were aligned to design two degenerate primer sets for the amplification of the chaperonin gene: Ths and Kor (which can also detect the korarchaeotal chaperonin gene from one of the samples). A phylogenetic tree was constructed using the chaperonin sequences retrieved and other sequences from cultured representatives. The Alpha and Beta paralogs of the chaperonin gene were observed within the main clades and orthologs among them. Cultivated representatives from these clades were assigned to either paralog in the chaperonin tree. Uncultured representatives observed in the 16S rRNA gene analysis were found to be related to the Desulfurococcales. The topologies of the 16S rRNA gene and chaperonin phylogenetic trees were compared, and similar phylogenetic relationships were observed. Our results suggest that the chaperonin Hsp60 gene may be used as a phylogenetic marker for the clades found in this extreme environment.},
}
@article {pmid21421788,
year = {2011},
author = {Oslowski, DM and Jung, JH and Seo, DH and Park, CS and Holden, JF},
title = {Production of hydrogen from α-1,4- and β-1,4-linked saccharides by marine hyperthermophilic Archaea.},
journal = {Applied and environmental microbiology},
volume = {77},
number = {10},
pages = {3169-3173},
pmid = {21421788},
issn = {1098-5336},
mesh = {Archaea/genetics/growth &amp; development/isolation &amp; purification/*metabolism ; *Carbohydrate Metabolism ; Hot Springs/microbiology ; Hydro-Lyases/genetics ; Hydrogen/*metabolism ; Peptides/metabolism ; Seawater/microbiology ; },
abstract = {Nineteen hyperthermophilic heterotrophs from deep-sea hydrothermal vents, plus the control organism Pyrococcus furiosus, were examined for their ability to grow and produce H2 on maltose, cellobiose, and peptides and for the presence of the genes encoding proteins that hydrolyze starch and cellulose. All of the strains grew on these disaccharides and peptides and converted maltose and peptides to H2 even when elemental sulfur was present as a terminal electron acceptor. Half of the strains had at least one gene for an extracellular starch hydrolase, but only P. furiosus had a gene for an extracellular β-1,4-endoglucanase. P. furiosus was serially adapted for growth on CF11 cellulose and H2 production, which is the first reported instance of hyperthermophilic growth on cellulose, with a doubling time of 64 min. Cell-specific H2 production rates were 29 fmol, 37 fmol, and 54 fmol of H2 produced cell[-1] doubling[-1] on α-1,4-linked sugars, β-1,4-linked sugars, and peptides, respectively. The highest total community H2 production rate came from growth on starch (2.6 mM H2 produced h[-1]). Hyperthermophilic heterotrophs may serve as an important alternate source of H2 for hydrogenotrophic microorganisms in low-H2 hydrothermal environments, and some are candidates for H2 bioenergy production in bioreactors.},
}
@article {pmid21420503,
year = {2011},
author = {Dridi, B and Raoult, D and Drancourt, M},
title = {Archaea as emerging organisms in complex human microbiomes.},
journal = {Anaerobe},
volume = {17},
number = {2},
pages = {56-63},
doi = {10.1016/j.anaerobe.2011.03.001},
pmid = {21420503},
issn = {1095-8274},
mesh = {Anaerobiosis ; *Biodiversity ; Female ; Humans ; Intestinal Mucosa/microbiology ; *Metagenome ; Methanobacteriaceae/classification/*isolation &amp; purification/metabolism ; Methanobrevibacter/classification/*isolation &amp; purification/metabolism ; Mouth Mucosa/microbiology ; Vagina/microbiology ; },
abstract = {In this work, we review the state of knowledge of Archaea associated with the human microbiome. These prokaryotes, initially discovered in extreme environments, were named Archaea because these environments were thought to be the most primitive on Earth. Further research revealed that this terminology is misleading because these organisms were later found in various non-extreme environments, including the human host. Further examination of the human microbiome has enabled the isolation of three archaeal species, Methanobrevibacter smithii, Methanosphaera stadtmanae and Methanobrevibacter oralis, which are associated with oral, intestinal and vaginal mucosae in humans. Moreover, molecular studies including metagenomic analyses detected DNA sequences indicative of the presence of additional methanogenic and non-methanogenic Archaea in the human intestinal tract. All three culturable Archaea are strict anaerobes, although their potential role in human diseases remains to be established. Future research aims to detect and culture additional human mucosa-associated Archaea and to look for their presence in additional human tissues, to establish their role in human infections involving complex flora.},
}
@article {pmid21414041,
year = {2011},
author = {Ettema, TJ and Lindås, AC and Bernander, R},
title = {An actin-based cytoskeleton in archaea.},
journal = {Molecular microbiology},
volume = {80},
number = {4},
pages = {1052-1061},
doi = {10.1111/j.1365-2958.2011.07635.x},
pmid = {21414041},
issn = {1365-2958},
mesh = {Actins/analysis/*genetics ; Cytoskeletal Proteins/genetics/*physiology ; Cytoskeleton/genetics/*physiology ; Microtubules/genetics ; Phylogeny ; Pyrobaculum/*genetics/physiology ; },
abstract = {In eukaryotic and bacterial cells, spatial organization is dependent upon cytoskeletal filaments. Actin is a main eukaryotic cytoskeletal element, involved in key processes such as cell shape determination, mechanical force generation and cytokinesis. We describe an archaeal cytoskeleton which forms helical structures within Pyrobaculum calidifontis cells, as shown by in situ immunostaining. The core components include an archaeal actin homologue, Crenactin, closely related to the eukaryotic counterpart. The crenactin gene belongs to a conserved gene cluster denoted Arcade (actin-related cytoskeleton in Archaea involved in shape determination). The phylogenetic distribution of arcade genes is restricted to the crenarchaeal Thermoproteales lineage, and to Korarchaeota, and correlates with rod-shaped and filamentous cell morphologies. Whereas Arcadin-1, -3 and -4 form helical structures, suggesting cytoskeleton-associated functions, Arcadin-2 was found to be localized between segregated nucleoids in a cell subpopulation, in agreement with possible involvement in cytokinesis. The results support a crenarchaeal origin of the eukaryotic actin cytoskeleton and, as such, have implications for theories concerning the origin of the eukaryotic cell.},
}
@article {pmid21402214,
year = {2011},
author = {Ferguson, DJ and Longstaff, DG and Krzycki, JA},
title = {Assay of methylotrophic methyltransferases from methanogenic archaea.},
journal = {Methods in enzymology},
volume = {494},
number = {},
pages = {139-158},
doi = {10.1016/B978-0-12-385112-3.00008-1},
pmid = {21402214},
issn = {1557-7988},
support = {GM070663/GM/NIGMS NIH HHS/United States ; },
mesh = {Archaea/*enzymology/*metabolism ; Archaeal Proteins/isolation &amp; purification/metabolism ; Mesna/metabolism ; Methane/*metabolism ; Methanosarcina barkeri/enzymology/metabolism ; Methyltransferases/isolation &amp; purification/*metabolism ; },
abstract = {The family Methanosarcinaceae has an expanded repertoire of growth substrates relative to most other methanogenic archaea. Various methylamines, methylated thiols, and methanol can serve as precursors to both methane and carbon dioxide. These compounds are mobilized into metabolism by methyltransferases that use the growth substrate to methylate a cognate corrinoid protein, which in turn is used as a substrate by a second methyltransferase to methylate Coenzyme M (CoM), forming methyl-SCoM, the precursor to both methane and carbon dioxide. Orthologs of the methyltransferases, as well as the small corrinoid proteins, are found in many archaeal and bacterial genomes. Some of these are homologs of the methylamine methyltransferases predicted to require pyrrolysine, an atypical genetically encoded amino acid, for synthesis. As a resource for the study of these sizable families of proteins, we describe here techniques our laboratories have used for the study of methanogen corrinoid-dependent methyltransferases, focusing especially on isolation and assay techniques useful for various activities of components of the methylamine- and methylthiol-dependent CoM methyltransferase systems.},
}
@article {pmid21402213,
year = {2011},
author = {Shima, S and Schick, M and Tamura, H},
title = {Preparation of [Fe]-hydrogenase from methanogenic archaea.},
journal = {Methods in enzymology},
volume = {494},
number = {},
pages = {119-137},
doi = {10.1016/B978-0-12-385112-3.00007-X},
pmid = {21402213},
issn = {1557-7988},
mesh = {Archaea/*enzymology ; Archaeal Proteins/*isolation &amp; purification/*metabolism ; Hydrogenase/*isolation &amp; purification/*metabolism ; Iron-Sulfur Proteins/*isolation &amp; purification/*metabolism ; Methane/*metabolism ; Methanobacteriaceae/enzymology ; },
abstract = {[Fe]-hydrogenase is one of the three types of hydrogenases. This enzyme is found in many hydrogenotrophic methanogenic archaea and catalyzes the reversible hydride transfer from H(2) to methenyl-H(4)MPT(+) in methanogenesis from H(2) and CO(2). The enzyme harbors a unique iron-guanylyl pyridinol (FeGP) cofactor as a prosthetic group. Here, we describe the purification of [Fe]-hydrogenase from Methanothermobacter marburgensis, the isolation of the FeGP cofactor from the native holoenzyme, and the reconstitution of [Fe]-hydrogenase from the isolated FeGP cofactor and the heterologously produced apoenzyme.},
}
@article {pmid21402211,
year = {2011},
author = {Rother, M and Sattler, C and Stock, T},
title = {Studying gene regulation in methanogenic archaea.},
journal = {Methods in enzymology},
volume = {494},
number = {},
pages = {91-110},
doi = {10.1016/B978-0-12-385112-3.00005-6},
pmid = {21402211},
issn = {1557-7988},
mesh = {Archaea/genetics/*metabolism ; Archaeal Proteins/genetics/metabolism ; DNA Transposable Elements/genetics ; Gene Expression Regulation, Archaeal ; Methane/*metabolism ; Methanococcus/genetics/metabolism ; Methanosarcina/genetics/metabolism ; Reverse Transcriptase Polymerase Chain Reaction ; },
abstract = {Methanogenic archaea are a unique group of strictly anaerobic microorganisms characterized by their ability, and dependence, to convert simple C1 and C2 compounds to methane for growth. The major models for studying the biology of methanogens are members of the Methanococcus and Methanosarcina species. Recent development of sophisticated tools for molecular analysis and for genetic manipulation allows investigating not only their metabolism but also their cell cycle, and their interaction with the environment in great detail. One aspect of such analyses is assessment and dissection of methanoarchaeal gene regulation, for which, at present, only a handful of cases have been investigated thoroughly, partly due to the great methodological effort required. However, it becomes more and more evident that many new regulatory paradigms can be unraveled in this unique archaeal group. Here, we report both molecular and physiological/genetic methods to assess gene regulation in Methanococcus maripaludis and Methanosarcina acetivorans, which should, however, be applicable for other methanogens as well.},
}
@article {pmid21375721,
year = {2011},
author = {Narihiro, T and Sekiguchi, Y},
title = {Oligonucleotide primers, probes and molecular methods for the environmental monitoring of methanogenic archaea.},
journal = {Microbial biotechnology},
volume = {4},
number = {5},
pages = {585-602},
pmid = {21375721},
issn = {1751-7915},
mesh = {Archaea/classification/genetics/*isolation &amp; purification/metabolism ; Bacterial Typing Techniques/instrumentation/*methods ; DNA Primers/*genetics ; DNA Probes/genetics ; *Environmental Microbiology ; Methane/*metabolism ; *Molecular Probe Techniques/instrumentation ; Molecular Sequence Data ; Phylogeny ; },
abstract = {For the identification and quantification of methanogenic archaea (methanogens) in environmental samples, various oligonucleotide probes/primers targeting phylogenetic markers of methanogens, such as 16S rRNA, 16S rRNA gene and the gene for the α-subunit of methyl coenzyme M reductase (mcrA), have been extensively developed and characterized experimentally. These oligonucleotides were designed to resolve different groups of methanogens at different taxonomic levels, and have been widely used as hybridization probes or polymerase chain reaction primers for membrane hybridization, fluorescence in situ hybridization, rRNA cleavage method, gene cloning, DNA microarray and quantitative polymerase chain reaction for studies in environmental and determinative microbiology. In this review, we present a comprehensive list of such oligonucleotide probes/primers, which enable us to determine methanogen populations in an environment quantitatively and hierarchically, with examples of the practical applications of the probes and primers.},
}
@article {pmid21368171,
year = {2011},
author = {Miranda, HV and Nembhard, N and Su, D and Hepowit, N and Krause, DJ and Pritz, JR and Phillips, C and Söll, D and Maupin-Furlow, JA},
title = {E1- and ubiquitin-like proteins provide a direct link between protein conjugation and sulfur transfer in archaea.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {108},
number = {11},
pages = {4417-4422},
pmid = {21368171},
issn = {1091-6490},
support = {R01 GM057498/GM/NIGMS NIH HHS/United States ; R37 GM022854/GM/NIGMS NIH HHS/United States ; R01 GM022854/GM/NIGMS NIH HHS/United States ; GM22854/GM/NIGMS NIH HHS/United States ; GM57498/GM/NIGMS NIH HHS/United States ; },
mesh = {Amino Acid Sequence ; Archaeal Proteins/chemistry/*metabolism ; Gene Knockout Techniques ; Genes, Archaeal/genetics ; Haloferax volcanii/genetics/growth &amp; development/*metabolism ; Models, Biological ; Molecular Sequence Data ; Molybdenum/metabolism ; RNA, Transfer/metabolism ; Sulfhydryl Compounds/metabolism ; Sulfur/*metabolism ; Temperature ; Ubiquitin-Activating Enzymes/*metabolism ; Ubiquitination ; Ubiquitins/*metabolism ; },
abstract = {Based on our recent work with Haloferax volcanii, ubiquitin-like (Ubl) proteins (SAMP1 and SAMP2) are known to be covalently attached to proteins in archaea. Here, we investigated the enzymes required for the formation of these Ubl-protein conjugates (SAMPylation) and whether this system is linked to sulfur transfer. Markerless in-frame deletions were generated in H. volcanii target genes. The mutants were examined for: (i) the formation of Ubl protein conjugates, (ii) growth under various conditions, including those requiring the synthesis of the sulfur-containing molybdenum cofactor (MoCo), and (iii) the thiolation of tRNA. With this approach we found that UbaA of the E1/MoeB/ThiF superfamily was required for the formation of both SAMP1- and SAMP2-protein conjugates. In addition, UbaA, SAMP1, and MoaE (a homolog of the large subunit of molybdopterin synthase) were essential for MoCo-dependent dimethyl sulfoxide reductase activity, suggesting that these proteins function in MoCo-biosynthesis. UbaA and SAMP2 were also crucial for optimal growth at high temperature and the thiolation of tRNA. Based on these results, we propose a working model for archaea in which the E1-like UbaA can activate multiple Ubl SAMPs for protein conjugation as well as for sulfur transfer. In sulfur transfer, SAMP1 and SAMP2 appear specific for MoCo biosynthesis and the thiolation of tRNA, respectively. Overall, this study provides a fundamental insight into the diverse cellular functions of the Ubl system.},
}
@article {pmid21368116,
year = {2011},
author = {Pratscher, J and Dumont, MG and Conrad, R},
title = {Ammonia oxidation coupled to CO2 fixation by archaea and bacteria in an agricultural soil.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {108},
number = {10},
pages = {4170-4175},
pmid = {21368116},
issn = {1091-6490},
mesh = {*Agriculture ; Ammonia/*metabolism ; Archaea/genetics/*metabolism ; Bacteria/genetics/*metabolism ; Carbon Dioxide/*metabolism ; In Situ Hybridization, Fluorescence ; Molecular Sequence Data ; Oxidation-Reduction ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Soil ; },
abstract = {Ammonia oxidation is an essential part of the global nitrogen cycling and was long thought to be driven only by bacteria. Recent findings expanded this pathway also to the archaea. However, most questions concerning the metabolism of ammonia-oxidizing archaea, such as ammonia oxidation and potential CO(2) fixation, remain open, especially for terrestrial environments. Here, we investigated the activity of ammonia-oxidizing archaea and bacteria in an agricultural soil by comparison of RNA- and DNA-stable isotope probing (SIP). RNA-SIP demonstrated a highly dynamic and diverse community involved in CO(2) fixation and carbon assimilation coupled to ammonia oxidation. DNA-SIP showed growth of the ammonia-oxidizing bacteria but not of archaea. Furthermore, the analysis of labeled RNA found transcripts of the archaeal acetyl-CoA/propionyl-CoA carboxylase (accA/pccB) to be expressed and labeled. These findings strongly suggest that ammonia-oxidizing archaeal groups in soil autotrophically fix CO(2) using the 3-hydroxypropionate-4-hydroxybutyrate cycle, one of the two pathways recently identified for CO(2) fixation in Crenarchaeota. Catalyzed reporter deposition (CARD)-FISH targeting the gene encoding subunit A of ammonia monooxygenase (amoA) mRNA and 16S rRNA of archaea also revealed ammonia-oxidizing archaea to be numerically relevant among the archaea in this soil. Our results demonstrate a diverse and dynamic contribution of ammonia-oxidizing archaea in soil to nitrification and CO(2) assimilation and that their importance to the overall archaeal community might be larger than previously thought.},
}
@article {pmid21346789,
year = {2011},
author = {Brochier-Armanet, C and Deschamps, P and López-García, P and Zivanovic, Y and Rodríguez-Valera, F and Moreira, D},
title = {Complete-fosmid and fosmid-end sequences reveal frequent horizontal gene transfers in marine uncultured planktonic archaea.},
journal = {The ISME journal},
volume = {5},
number = {8},
pages = {1291-1302},
pmid = {21346789},
issn = {1751-7370},
mesh = {Archaea/classification/*genetics/physiology ; Crenarchaeota/classification/genetics ; Euryarchaeota/classification/genetics ; Gene Library ; *Gene Transfer, Horizontal ; Genes, Archaeal ; Metagenomics ; Oceans and Seas ; Phylogeny ; Plankton/classification/genetics ; RNA, Archaeal/genetics ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The extent of horizontal gene transfer (HGT) among marine pelagic prokaryotes and the role that HGT may have played in their adaptation to this particular environment remain open questions. This is partly due to the paucity of cultured species and genomic information for many widespread groups of marine bacteria and archaea. Molecular studies have revealed a large diversity and relative abundance of marine planktonic archaea, in particular of Thaumarchaeota (also known as group I Crenarchaeota) and Euryarchaeota of groups II and III, but only one species (the thaumarchaeote Candidatus Nitrosopumilus maritimus) has been isolated in pure culture so far. Therefore, metagenomics remains the most powerful approach to study these environmental groups. To investigate the impact of HGT in marine archaea, we carried out detailed phylogenetic analyses of all open reading frames of 21 archaeal 16S rRNA gene-containing fosmids and, to extend our analysis to other genomic regions, also of fosmid-end sequences of 12 774 fosmids from three different deep-sea locations (South Atlantic and Adriatic Sea at 1000 m depth, and Ionian Sea at 3000 m depth). We found high HGT rates in both marine planktonic Thaumarchaeota and Euryarchaeota, with remarkable converging values estimated from complete-fosmid and fosmid-end sequence analysis (25 and 21% of the genes, respectively). Most HGTs came from bacterial donors (mainly from Proteobacteria, Firmicutes and Chloroflexi) but also from other archaea and eukaryotes. Phylogenetic analyses showed that in most cases HGTs are shared by several representatives of the studied groups, implying that they are ancient and have been conserved over relatively long evolutionary periods. This, together with the functions carried out by these acquired genes (mostly related to energy metabolism and transport of metabolites across membranes), suggests that HGT has played an important role in the adaptation of these archaea to the cold and nutrient-depleted deep marine environment.},
}
@article {pmid21340748,
year = {2011},
author = {Bowers, KJ and Wiegel, J},
title = {Temperature and pH optima of extremely halophilic archaea: a mini-review.},
journal = {Extremophiles : life under extreme conditions},
volume = {15},
number = {2},
pages = {119-128},
pmid = {21340748},
issn = {1433-4909},
mesh = {Archaea/*physiology ; Halobacteriales/*physiology ; Haloferax/genetics/physiology ; Hydrogen-Ion Concentration ; Models, Biological ; Sodium/chemistry ; Sodium Chloride/pharmacology ; Species Specificity ; Temperature ; },
abstract = {Archaeal microorganisms that grow optimally at Na(+) concentrations of 1.7 M, or the equivalent of 10% (w/v) NaCl, and greater are considered to be extreme halophiles. This review encompasses extremely halophilic archaea and their growth characteristics with respect to the correlation between the extent of alkaline pH and elevated temperature optima and the extent of salt tolerance. The focus is on poly-extremophiles, i.e., taxa growing optimally at a Na(+) concentration at or above 1.7 M (approximately 10% w/v NaCl); alkaline pH, at or above 8.5; and elevated temperature optima, at or above 50°C. So far, only a very few extreme halophiles that are able to grow optimally under alkaline conditions as well as at elevated temperatures have been isolated. The distribution of extremely halophilic archaea growing optimally at 3.4 M Na(+) (approximately 20% w/v NaCl) is bifurcated with respect to pH optima, either they are neutrophilic, with a pH(opt) of approximately 7, or strongly alkaliphilic, with pH(opt) at or above 8.5. Amongst these extreme halophiles which have elevated pH optima, only four taxa have an optimum temperature above 50°C: Haloarcula quadrata (52°C), Haloferax elongans (53°C), Haloferax mediterranei (51°C) and Natronolimnobius 'aegyptiacus' (55°C).},
}
@article {pmid21338478,
year = {2011},
author = {Calo, D and Guan, Z and Eichler, J},
title = {Glyco-engineering in Archaea: differential N-glycosylation of the S-layer glycoprotein in a transformed Haloferax volcanii strain.},
journal = {Microbial biotechnology},
volume = {4},
number = {4},
pages = {461-470},
pmid = {21338478},
issn = {1751-7915},
support = {U54 GM069338/GM/NIGMS NIH HHS/United States ; },
mesh = {Biotechnology/*methods ; Glucosyltransferases/genetics/metabolism ; *Glycosylation ; Halobacterium salinarum/enzymology/genetics ; Haloferax volcanii/enzymology/genetics/*metabolism ; Membrane Glycoproteins/*metabolism ; *Metabolic Engineering ; Metabolic Networks and Pathways/genetics ; },
abstract = {Archaeal glycoproteins present a variety of N-linked glycans not seen elsewhere. The ability to harness the agents responsible for this unparalleled diversity offers the possibility of generating glycoproteins bearing tailored glycans, optimized for specific functions. With a well-defined N-glycosylation pathway and available genetic tools, the haloarchaeon Haloferax volcanii represents a suitable platform for such glyco-engineering efforts. In Hfx. volcanii, the S-layer glycoprotein is modified by an N-linked pentasaccharide. In the following, S-layer glycoprotein N-glycosylation was considered in cells in which AglD, the dolichol phosphate mannose synthase involved in addition of the final residue of the pentasaccharide, was replaced by a haloarchaeal homologue of AglJ, the enzyme involved in addition of the first residue of the N-linked pentasaccharide. In the engineering strain, the S-layer glycoprotein is modified by a novel N-linked glycan not found on this reporter from the parent strain. Moreover, deletion of AglD alone and introduction of the AglJ homologue from Halobacterium salinarum, OE2528R, into the deletion strain resulted in increased biosynthesis of the novel 894 Da glycan concomitant with reduced biogenesis of the pentasaccharide normally N-linked to the S-layer glycoprotein. These findings justify efforts designed to transform Hfx. volcanii into a glyco-engineering 'workshop'.},
}
@article {pmid21338359,
year = {2011},
author = {Faveri, M and Gonçalves, LF and Feres, M and Figueiredo, LC and Gouveia, LA and Shibli, JA and Mayer, MP},
title = {Prevalence and microbiological diversity of Archaea in peri-implantitis subjects by 16S ribosomal RNA clonal analysis.},
journal = {Journal of periodontal research},
volume = {46},
number = {3},
pages = {338-344},
doi = {10.1111/j.1600-0765.2011.01347.x},
pmid = {21338359},
issn = {1600-0765},
mesh = {Alveolar Bone Loss/microbiology ; Archaea/*classification/genetics ; *Biofilms ; Clone Cells ; Dental Implants/microbiology ; Dental Plaque/microbiology ; Female ; Gingival Hemorrhage/microbiology ; Humans ; Male ; Methanobacterium/classification ; Methanobrevibacter/classification ; Middle Aged ; Peri-Implantitis/*microbiology ; Periodontal Attachment Loss/microbiology ; Periodontal Pocket/microbiology ; Phylogeny ; RNA, Archaeal/*analysis ; RNA, Ribosomal, 16S/*analysis ; Tooth/microbiology ; },
abstract = {BACKGROUND AND OBJECTIVE: This study evaluated the prevalence and the molecular diversity of Archaea in the subgingival biofilm samples of subjects with peri-implantitis.<br><br>MATERIAL AND METHODS: Fifty subjects were assigned into two groups: Control (n = 25), consisting of subjects with healthy implants; and Test (n = 25), consisting of subjects with peri-implantitis sites, as well as a healthy implant. In the Test group, subgingival biofilm samples were taken from the deepest sites of the diseased implant. In both groups, subgingival biofilm was collected from one site with a healthy implant and from one site with a periodontally healthy tooth. DNA was extracted and the 16S ribosomal RNA gene was amplified with universal primer pairs for Archaea. Amplified genes were cloned and sequenced, and the phylotypes were identified by comparison with known 16S ribosomal RNA sequences.<br><br>RESULTS: In the Control group, Archaea were detected in two and three sites of the implant and the tooth, respectively. In the Test group, Archaea were detected in 12, 4 and 2 sites of diseased implants, healthy implants and teeth, respectively. Diseased implants presented a significantly higher prevalence of Archaea in comparison with healthy implants and natural teeth, irrespective of group. Over 90% of the clone libraries were formed by Methanobrevibacter oralis, which was detected in both groups. Methanobacterium congelense/curvum was detected in four subjects from the Test group and in two subjects from the Control group.<br><br>CONCLUSION: Although M. oralis was the main species of Archaea associated with both healthy and diseased implant sites, the data indicated an increased prevalence of Archaea in peri-implantitis sites, and their role in pathogenesis should be further investigated.},
}
@article {pmid21336928,
year = {2011},
author = {Yamamoto, N and Asano, R and Yoshii, H and Otawa, K and Nakai, Y},
title = {Archaeal community dynamics and detection of ammonia-oxidizing archaea during composting of cattle manure using culture-independent DNA analysis.},
journal = {Applied microbiology and biotechnology},
volume = {90},
number = {4},
pages = {1501-1510},
doi = {10.1007/s00253-011-3153-2},
pmid = {21336928},
issn = {1432-0614},
mesh = {Ammonia/*metabolism ; Animals ; Archaea/classification/genetics/*isolation &amp; purification/*metabolism ; Bacterial Typing Techniques ; Biodiversity ; Cattle ; DNA, Archaeal/*genetics ; Electrophoresis, Polyacrylamide Gel ; Manure/*microbiology ; Molecular Sequence Data ; Oxidation-Reduction ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Soil Microbiology ; },
abstract = {The composting process is carried out under aerobic conditions involving bacteria, archaea, and fungi. Little is known about the diversity of archaeal community in compost, although they may play an important role in methane production and ammonia oxidation. In the present study, archaeal community dynamics during cattle manure composting were analyzed using a clone library of the archaeal 16S rRNA gene. The results indicated that methane-producing archaea (methanogen) and ammonia-oxidizing archaea (AOA) may be the dominant microbes throughout the composting. The community consisted primarily of Methanocorpusculum-like and Methanosarcina-like sequences until day 2, while the number of Candidatus Nitrososphaera-like sequences increased from day 6 to day 30. Methanosarcina thermophila-like sequences were dominant from day 2, suggesting that M. thermophila-like species can adapt to increasing temperature or nutrient loss. A denaturant gradient gel electrophoresis analysis of the archaeal amoA genes revealed that the dominant amoA gene sequence with 99% homology to that of Candidatus Nitrososphaera gargensis was identical to those obtained from a different composting facility. These data suggested that AOA may play a role in ammonia oxidation in several composting practices. Our results provide fundamental information regarding archaeal community dynamics that will help in understanding the collective microbial community in compost.},
}
@article {pmid21330437,
year = {2011},
author = {Jarrell, KF and Walters, AD and Bochiwal, C and Borgia, JM and Dickinson, T and Chong, JPJ},
title = {Major players on the microbial stage: why archaea are important.},
journal = {Microbiology (Reading, England)},
volume = {157},
number = {Pt 4},
pages = {919-936},
doi = {10.1099/mic.0.047837-0},
pmid = {21330437},
issn = {1465-2080},
support = {BB/D525056/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/F003099/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Ammonia ; Archaea/*metabolism ; *Ecosystem ; Oxidation-Reduction ; },
abstract = {As microbiology undergoes a renaissance, fuelled in part by developments in new sequencing technologies, the massive diversity and abundance of microbes becomes yet more obvious. The Archaea have traditionally been perceived as a minor group of organisms forced to evolve into environmental niches not occupied by their more 'successful' and 'vigorous' counterparts, the bacteria. Here we outline some of the evidence gathered by an increasingly large and productive group of scientists that demonstrates not only that the Archaea contribute significantly to global nutrient cycling, but also that they compete successfully in 'mainstream' environments. Recent data suggest that the Archaea provide the major routes for ammonia oxidation in the environment. Archaea also have huge economic potential that to date has only been fully realized in the production of thermostable polymerases. Archaea have furnished us with key paradigms for understanding fundamentally conserved processes across all domains of life. In addition, they have provided numerous exemplars of novel biological mechanisms that provide us with a much broader view of the forms that life can take and the way in which micro-organisms can interact with other species. That this information has been garnered in a relatively short period of time, and appears to represent only a small proportion of what the Archaea have to offer, should provide further incentives to microbiologists to investigate the underlying biology of this fascinating domain.},
}
@article {pmid21326901,
year = {2010},
author = {De Carlo, S and Lin, SC and Taatjes, DJ and Hoenger, A},
title = {Molecular basis of transcription initiation in Archaea.},
journal = {Transcription},
volume = {1},
number = {2},
pages = {103-111},
pmid = {21326901},
issn = {2154-1272},
support = {G12-RR03060/RR/NCRR NIH HHS/United States ; RR-000592/RR/NCRR NIH HHS/United States ; P01 CA112181/CA/NCI NIH HHS/United States ; G12 RR003060/RR/NCRR NIH HHS/United States ; P41 RR000592/RR/NCRR NIH HHS/United States ; },
mesh = {Archaeal Proteins/chemistry/*metabolism ; Cryoelectron Microscopy ; Crystallography, X-Ray ; DNA, Archaeal/chemistry/genetics/metabolism ; DNA-Directed RNA Polymerases/chemistry/*metabolism ; Microscopy, Electron, Transmission ; Models, Molecular ; Multiprotein Complexes/chemistry/metabolism ; *Nucleic Acid Conformation ; Protein Binding ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protein Subunits/chemistry/metabolism ; Pyrococcus furiosus/*genetics/metabolism ; TATA-Box Binding Protein/chemistry/metabolism ; Transcription Factor TFIIB/chemistry/*metabolism ; Transcription, Genetic/*genetics ; },
abstract = {Compared with eukaryotes, the archaeal transcription initiation machinery-commonly known as the Pre-Initiation Complex-is relatively simple. The archaeal PIC consists of the TFIIB ortholog TFB, TBP, and an 11-subunit RNA polymerase (RNAP). The relatively small size of the entire archaeal PIC makes it amenable to structural analysis. Using purified RNAP, TFB, and TBP from the thermophile Pyrococcus furiosus, we assembled the biochemically active PIC at 65ºC. The intact archaeal PIC was isolated by implementing a cross-linking technique followed by size-exclusion chromatography, and the structure of this 440 kDa assembly was determined using electron microscopy and single-particle reconstruction techniques. Combining difference maps with crystal structure docking of various sub-domains, TBP and TFB were localized within the macromolecular PIC. TBP/TFB assemble near the large RpoB subunit and the RpoD/L "foot" domain behind the RNAP central cleft. This location mimics that of yeast TBP and TFIIB in complex with yeast RNAP II. Collectively, these results define the structural organization of the archaeal transcription machinery and suggest a conserved core PIC architecture.},
}
@article {pmid21286709,
year = {2011},
author = {Jin, T and Zhang, T and Ye, L and Lee, OO and Wong, YH and Qian, PY},
title = {Diversity and quantity of ammonia-oxidizing Archaea and Bacteria in sediment of the Pearl River Estuary, China.},
journal = {Applied microbiology and biotechnology},
volume = {90},
number = {3},
pages = {1137-1145},
pmid = {21286709},
issn = {1432-0614},
mesh = {Ammonia/*metabolism ; Archaea/classification/genetics/*isolation &amp; purification/*metabolism ; Bacteria/classification/genetics/*isolation &amp; purification/*metabolism ; *Biodiversity ; China ; Geologic Sediments/*microbiology ; Molecular Sequence Data ; Phylogeny ; Rivers/*microbiology ; },
abstract = {The diversity and abundance of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in the sediment of the Pearl River Estuary were investigated by cloning and quantitative real-time polymerase chain reaction (qPCR). From one sediment sample S16, 36 AOA OTUs (3% cutoff) were obtained from three clone libraries constructed using three primer sets for amoA gene. Among the 36 OTUs, six were shared by all three clone libraries, two appeared in two clone libraries, and the other 28 were only recovered in one of the libraries. For AOB, only seven OTUs (based on 16S rRNA gene) and eight OTUs (based on amoA gene) were obtained, showing lower diversity than AOA. The qPCR results revealed that AOA amoA gene copy numbers ranged from 9.6 × 10(6) to 5.1 × 10(7) copies per gram of sediment and AOB amoA gene ranged from 9.5 × 10(4) to 6.2 × 10(5) copies per gram of sediment, indicating that the dominant ammonia-oxidizing microorganisms in the sediment of the Pearl River Estuary were AOA. The terminal restriction fragment length polymorphism results showed that the relative abundance of AOB species in the sediment samples of different salinity were significantly different, indicating that salinity might be a key factor shaping the AOB community composition.},
}
@article {pmid21282609,
year = {2011},
author = {Quax, TE and Lucas, S and Reimann, J and Pehau-Arnaudet, G and Prevost, MC and Forterre, P and Albers, SV and Prangishvili, D},
title = {Simple and elegant design of a virion egress structure in Archaea.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {108},
number = {8},
pages = {3354-3359},
pmid = {21282609},
issn = {1091-6490},
mesh = {Archaea/*virology ; Hot Temperature ; Hydrogen-Ion Concentration ; Rudiviridae/*ultrastructure ; Virion/*chemistry ; Virus Assembly ; *Virus Release ; },
abstract = {Some viruses of Archaea use an unusual egress mechanism that involves the formation of virus-associated pyramids (VAPs) on the host cell surface. At the end of the infection cycle, these structures open outward and create apertures through which mature virions escape from the cell. Here we describe in detail the structure and composition of VAPs formed by the Sulfolobus islandicus rod-shaped virus 2 (SIRV2) in cells of its hyperthermophilic archaeal host. We show that the VAPs are stable and autonomous assemblies that can be isolated from membranes of infected cells and purified without affecting their structure. The purified VAPs are heterogeneous in size, reflecting the dynamics of VAP development in a population of infected cells; however, they have a uniform geometry, consisting of seven isosceles triangular faces forming a baseless pyramid. Biochemical and immunoelectron microscopy analyses revealed that the 10-kDa P98 protein encoded by the SIRV2 virus is the sole component of the VAPs. The VAPs were produced in Sulfolobus acidocaldarius and Escherichia coli by heterologous expression of the SIRV2-P98 gene. The results confirm that P98 is the only constituent of the VAPs and demonstrate that no other viral protein is involved in the assembly of pyramids. P98 was able to produce stable structures under conditions ranging from moderate to extremely high temperatures (80 °C) and from neutral to extremely acidic pH (pH 2), demonstrating another remarkable property of this exceptional viral protein.},
}
@article {pmid21265868,
year = {2011},
author = {Leigh, JA and Albers, SV and Atomi, H and Allers, T},
title = {Model organisms for genetics in the domain Archaea: methanogens, halophiles, Thermococcales and Sulfolobales.},
journal = {FEMS microbiology reviews},
volume = {35},
number = {4},
pages = {577-608},
doi = {10.1111/j.1574-6976.2011.00265.x},
pmid = {21265868},
issn = {1574-6976},
mesh = {Archaea/classification/*genetics ; Biochemistry ; Crenarchaeota/classification/genetics ; Euryarchaeota/classification/genetics ; Gene Expression Regulation, Archaeal ; *Genetic Techniques ; Genetics, Microbial/*methods ; Models, Genetic ; Phylogeny ; },
abstract = {The tree of life is split into three main branches: eukaryotes, bacteria, and archaea. Our knowledge of eukaryotic and bacteria cell biology has been built on a foundation of studies in model organisms, using the complementary approaches of genetics and biochemistry. Archaea have led to some exciting discoveries in the field of biochemistry, but archaeal genetics has been slow to get off the ground, not least because these organisms inhabit some of the more inhospitable places on earth and are therefore believed to be difficult to culture. In fact, many species can be cultivated with relative ease and there has been tremendous progress in the development of genetic tools for both major archaeal phyla, the Euryarchaeota and the Crenarchaeota. There are several model organisms available for methanogens, halophiles, and thermophiles; in the latter group, there are genetic systems for Sulfolobales and Thermococcales. In this review, we present the advantages and disadvantages of working with each archaeal group, give an overview of their different genetic systems, and direct the neophyte archaeologist to the most appropriate model organism.},
}
@article {pmid21265763,
year = {2011},
author = {Soppa, J},
title = {Ploidy and gene conversion in Archaea.},
journal = {Biochemical Society transactions},
volume = {39},
number = {1},
pages = {150-154},
doi = {10.1042/BST0390150},
pmid = {21265763},
issn = {1470-8752},
mesh = {Archaea/classification/*genetics ; *Gene Conversion ; Gene Dosage ; Genome ; *Ploidies ; },
abstract = {The genome copy numbers of seven crenarchaeal species of four genera have been reported. All of them are monoploid and thus this seems to be a characteristic feature of Crenarchaeota. In stark contrast, none of six species representing six euryarchaeal genera is monoploid. Therefore Euryarchaea are typically oligoploid or polyploidy and their genome copy numbers are tightly regulated in response to growth phase and/or growth rate. A theoretical consideration called 'Muller's ratchet' predicts that asexually reproducing polyploid species should not be able to exist. An escape from Muller's ratchet would be a mechanism leading to the equalization of genome copies, such as gene conversion. Using two species of methanogenic and halophilic archaea, it was shown that heterozygous cells containing different genomes simultaneously can be selected, exemplifying gene redundancy as one possible evolutionary advantage of polyploidy. In both cases, the genomes were rapidly equalized in the absence of selection, showing that gene conversion operates at least in halophilic and methanogenic Euryarchaea.},
}
@article {pmid21265752,
year = {2011},
author = {Benelli, D and Londei, P},
title = {Translation initiation in Archaea: conserved and domain-specific features.},
journal = {Biochemical Society transactions},
volume = {39},
number = {1},
pages = {89-93},
doi = {10.1042/BST0390089},
pmid = {21265752},
issn = {1470-8752},
mesh = {Archaea/genetics/*metabolism ; Archaeal Proteins/chemistry/genetics/metabolism ; Bacterial Proteins/chemistry/metabolism ; Eukaryotic Initiation Factor-2/genetics/metabolism ; Models, Molecular ; Nucleic Acid Conformation ; Peptide Initiation Factors/chemistry/genetics/metabolism ; *Protein Biosynthesis ; Protein Conformation ; Protein Subunits/chemistry/metabolism ; RNA, Messenger/chemistry/metabolism ; Ribosomes/metabolism ; },
abstract = {Initiation is a critical step in translation, during which the ribosome lands on the start codon and sets the correct reading frame for mRNA decoding. The rate and efficiency of translation are largely determined by initiation, which is therefore the preferred target of translation regulation mechanisms. Initiation has incurred an extensive evolutionary divergence among the primary domains of cell descent. The Archaea, albeit prokaryotes, have an initiation mechanism and apparatus more complex than those of the Bacteria; the molecular details of archaeal initiation are just beginning to be unravelled. The most notable aspects of archaeal initiation are the presence of two, perhaps three, distinct mechanisms for mRNA-ribosome interaction and the presence of a relatively large set of IFs (initiation factors), several of which are shared exclusively with the Eukarya. Among these, the protein termed a/eIF2 (archaeal/eukaryotic IF2) and aIF6 (archaeal IF6) are of special interest, since they appear to play key regulatory roles in the Eukarya. Studies of the function of these factors in Archaea have uncovered new features that will help to elucidate their conserved and domain-specific functions.},
}
@article {pmid21265751,
year = {2011},
author = {Krupovic, M and Spang, A and Gribaldo, S and Forterre, P and Schleper, C},
title = {A thaumarchaeal provirus testifies for an ancient association of tailed viruses with archaea.},
journal = {Biochemical Society transactions},
volume = {39},
number = {1},
pages = {82-88},
doi = {10.1042/BST0390082},
pmid = {21265751},
issn = {1470-8752},
support = {P 23000/FWF_/Austrian Science Fund FWF/Austria ; },
mesh = {Amino Acid Sequence ; Archaea/*genetics/*virology ; Archaeal Viruses/classification/*genetics ; Biological Evolution ; Genome, Archaeal ; Genome, Viral ; Models, Molecular ; Molecular Sequence Data ; Phylogeny ; Protein Conformation ; Proviruses/*genetics ; Sequence Alignment ; Synteny ; Viral Proteins/genetics ; Virion/genetics ; },
abstract = {Archaeal viruses, or archaeoviruses, display a wide range of virion morphotypes. Whereas the majority of those morphotypes are unique to archaeal viruses, some are more widely distributed across different cellular domains. Tailed double-stranded DNA archaeoviruses are remarkably similar to viruses of the same morphology (order Caudovirales) that infect many bacterial hosts. They have, so far, only been found in one phylum of the archaea, the Euryarchaeota, which has led to controversial hypotheses about their origin. In the present paper, we describe the identification and analysis of a putative provirus present in the genome of a mesophilic thaumarchaeon. We show that the provirus is related to tailed bacterial and euryarchaeal viruses and encodes a full complement of proteins that are required to build a tailed virion. The recently discovered wide distribution of tailed viruses in Euryarchaeota and the identification of a related provirus in Thaumarchaeota, an archaeal phylum which might have branched off before the separation of Crenarchaeota and Euryarchaeota, suggest that an association of these viruses with Archaea might be more ancient than previously anticipated.},
}
@article {pmid21265749,
year = {2011},
author = {Beattie, TR and Bell, SD},
title = {The role of the DNA sliding clamp in Okazaki fragment maturation in archaea and eukaryotes.},
journal = {Biochemical Society transactions},
volume = {39},
number = {1},
pages = {70-76},
doi = {10.1042/BST0390070},
pmid = {21265749},
issn = {1470-8752},
support = {//Biotechnology and Biological Sciences Research Council/United Kingdom ; //Wellcome Trust/United Kingdom ; },
mesh = {Archaea/*genetics ; Archaeal Proteins/chemistry/genetics/metabolism ; DNA/chemistry/*genetics/*metabolism ; DNA Replication ; Eukaryota/*genetics ; Flap Endonucleases/metabolism ; Humans ; Models, Molecular ; Proliferating Cell Nuclear Antigen/chemistry/genetics/metabolism ; Protein Conformation ; Protein Subunits/chemistry/genetics/metabolism ; },
abstract = {Efficient processing of Okazaki fragments generated during discontinuous lagging-strand DNA replication is critical for the maintenance of genome integrity. In eukaryotes, a number of enzymes co-ordinate to ensure the removal of initiating primers from the 5'-end of each fragment and the generation of a covalently linked daughter strand. Studies in eukaryotic systems have revealed that the co-ordination of DNA polymerase δ and FEN-1 (Flap Endonuclease 1) is sufficient to remove the majority of primers. Other pathways such as that involving Dna2 also operate under certain conditions, although, notably, Dna2 is not universally conserved between eukaryotes and archaea, unlike the other core factors. In addition to the catalytic components, the DNA sliding clamp, PCNA (proliferating-cell nuclear antigen), plays a pivotal role in binding and co-ordinating these enzymes at sites of lagging-strand replication. Structural studies in eukaryotic and archaeal systems have revealed that PCNA-binding proteins can adopt different conformations when binding PCNA. This conformational malleability may be key to the co-ordination of these enzymes' activities.},
}
@article {pmid21265740,
year = {2011},
author = {White, MF},
title = {Homologous recombination in the archaea: the means justify the ends.},
journal = {Biochemical Society transactions},
volume = {39},
number = {1},
pages = {15-19},
doi = {10.1042/BST0390015},
pmid = {21265740},
issn = {1470-8752},
mesh = {Archaea/*genetics ; Archaeal Proteins/chemistry/genetics/metabolism ; Congresses as Topic ; *DNA Repair ; DNA Replication ; DNA, Cruciform/genetics ; DNA-Binding Proteins/chemistry/genetics/metabolism ; Models, Molecular ; Protein Conformation ; *Recombination, Genetic ; },
abstract = {The process of information exchange between two homologous DNA duplexes is known as homologous recombination (HR) or double-strand break repair (DSBR), depending on the context. HR is the fundamental process underlying the genome shuffling that expands genetic diversity (for example during meiosis in eukaryotes). DSBR is an essential repair pathway in all three domains of life, and plays a major role in the rescue of stalled or collapsed replication forks, a phenomenon known as recombination-dependent replication (RDR). The process of HR in the archaea is gradually being elucidated, initially from structural and biochemical studies, but increasingly using new genetic systems. The present review focuses on our current understanding of the structures, functions and interactions of archaeal HR proteins, with an emphasis on recent advances. There are still many unknown aspects of archaeal HR, most notably the mechanism of branch migration of Holliday junctions, which is also an open question in eukarya.},
}
@article {pmid21262829,
year = {2011},
author = {Kaster, AK and Moll, J and Parey, K and Thauer, RK},
title = {Coupling of ferredoxin and heterodisulfide reduction via electron bifurcation in hydrogenotrophic methanogenic archaea.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {108},
number = {7},
pages = {2981-2986},
pmid = {21262829},
issn = {1091-6490},
mesh = {Carbon Dioxide/*metabolism ; Chromatography, High Pressure Liquid ; Disulfides/*metabolism ; Ferredoxins/*metabolism ; Hydrogen/*metabolism ; Magnetic Resonance Spectroscopy ; Mesna/metabolism ; Methane/*biosynthesis ; Methanobacteriaceae/*metabolism ; Metronidazole ; Oxidation-Reduction ; Phosphothreonine/analogs &amp; derivatives/metabolism ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; },
abstract = {In methanogenic archaea growing on H(2) and CO(2) the first step in methanogenesis is the ferredoxin-dependent endergonic reduction of CO(2) with H(2) to formylmethanofuran and the last step is the exergonic reduction of the heterodisulfide CoM-S-S-CoB with H(2) to coenzyme M (CoM-SH) and coenzyme B (CoB-SH). We recently proposed that in hydrogenotrophic methanogens the two reactions are energetically coupled via the cytoplasmic MvhADG/HdrABC complex. It is reported here that the purified complex from Methanothermobacter marburgensis catalyzes the CoM-S-S-CoB-dependent reduction of ferredoxin with H(2). Per mole CoM-S-S-CoB added, 1 mol of ferredoxin (Fd) was reduced, indicating an electron bifurcation coupling mechanism: 2H(2) + Fd(OX) + CoM-S-S-CoB-->Fd(red)(2-) + CoM-SH + CoB-SH + 2H(+). This stoichiometry of coupling is consistent with an ATP gain per mole methane from 4 H(2) and CO(2) of near 0.5 deduced from an H(2)-threshold concentration of 8 Pa and a growth yield of up to 3 g/mol methane.},
}
@article {pmid21261623,
year = {2011},
author = {Aquino, AR and Lima, KC and Paiva, MS and Rôças, IN and Siqueira, JF},
title = {Molecular survey of atheromatous plaques for the presence of DNA from periodontal bacterial pathogens, archaea and fungi.},
journal = {Journal of periodontal research},
volume = {46},
number = {3},
pages = {303-309},
doi = {10.1111/j.1600-0765.2010.01343.x},
pmid = {21261623},
issn = {1600-0765},
mesh = {Aged ; Aggregatibacter actinomycetemcomitans/isolation &amp; purification ; Bacteria, Anaerobic/isolation &amp; purification ; Carotid Artery Diseases/microbiology ; Chronic Periodontitis/microbiology ; Coronary Disease/microbiology ; Cross-Sectional Studies ; DNA, Archaeal/*analysis ; DNA, Bacterial/*analysis ; DNA, Fungal/*analysis ; Female ; Femoral Artery/microbiology ; Gingival Hemorrhage/microbiology ; Humans ; Male ; Middle Aged ; Periodontal Attachment Loss/microbiology ; Periodontitis/*microbiology ; Plaque, Atherosclerotic/*microbiology ; Porphyromonas gingivalis/isolation &amp; purification ; RNA, Archaeal/analysis ; RNA, Bacterial/analysis ; RNA, Fungal/analysis ; RNA, Ribosomal, 16S/analysis ; Treponema denticola/isolation &amp; purification ; },
abstract = {BACKGROUND AND OBJECTIVE: Chronic infections, such as periodontitis, have been associated with the development and progression of atherosclerosis. The mechanisms through which this occurs have yet to be elucidated. This study was carried out to detect periodontopathic bacteria as well as archaea and fungi in atheromatous plaques and search for factors associated with their occurrence in atheromas.<br><br>MATERIAL AND METHODS: &#x2002; A cross-sectional study was carried out including 30 patients diagnosed with atherosclerosis in the carotid, coronary or femoral arteries. Plaques were collected during surgery and analysed using PCR to detect Aggregatibacter actinomycetemcomitans, Porphyromonas gingivalis, Treponema denticola and members of the Synergistetes group. Samples were also surveyed with universal primers for bacterial, archaeal and fungal DNA. Patients responded to a questionnaire to determine factors associated with PCR results.<br><br>RESULTS: All dentate individuals (66.7%) had periodontal disease, 95% of which was severe and 65% extensive. None of the targeted periodontopathic bacteria was found in the atheromas. No sample yielded positive results for fungal and archaeal DNA. Four samples (13%) were positive for the presence of bacterial DNA. Of these, three participants were dentate (two with severely chronic generalized periodontitis and one with severely chronic localized periodontitis).<br><br>CONCLUSION: This study did not confirm previous findings of periodontal pathogens in atheromas, making it impossible to establish factors associated with their presence in plaques. Presence of bacterial DNA in some samples indicates that periodontal or nonoral bacterial species other than the ones targeted in this study may be involved with some cases of atherosclerosis.},
}
@article {pmid21255425,
year = {2011},
author = {Atkinson, GC and Hauryliuk, V and Tenson, T},
title = {An ancient family of SelB elongation factor-like proteins with a broad but disjunct distribution across archaea.},
journal = {BMC evolutionary biology},
volume = {11},
number = {},
pages = {22},
pmid = {21255425},
issn = {1471-2148},
mesh = {Amino Acid Sequence ; Archaea/chemistry/classification/*genetics/metabolism ; Archaeal Proteins/chemistry/*genetics/metabolism ; Binding Sites ; Molecular Sequence Data ; *Multigene Family ; Peptide Elongation Factors/chemistry/*genetics/metabolism ; Phylogeny ; Protein Conformation ; Sequence Alignment ; },
abstract = {BACKGROUND: SelB is the dedicated elongation factor for delivery of selenocysteinyl-tRNA to the ribosome. In archaea, only a subset of methanogens utilizes selenocysteine and encodes archaeal SelB (aSelB). A SelB-like (aSelBL) homolog has previously been identified in an archaeon that does not encode selenosysteine, and has been proposed to be a pyrrolysyl-tRNA-specific elongation factor (EF-Pyl). However, elongation factor EF-Tu is capable of binding archaeal Pyl-tRNA in bacteria, suggesting the archaeal ortholog EF1A may also be capable of delivering Pyl-tRNA to the ribosome without the need of a specialized factor.<br><br>RESULTS: We have phylogenetically characterized the aSelB and aSelBL families in archaea. We find the distribution of aSelBL to be wider than both selenocysteine and pyrrolysine usage. The aSelBLs also lack the carboxy terminal domain usually involved in recognition of the selenocysteine insertion sequence in the target mRNA. While most aSelBL-encoding archaea are methanogenic Euryarchaea, we also find aSelBL representatives in Sulfolobales and Thermoproteales of Crenarchaea, and in the recently identified phylum Thaumarchaea, suggesting that aSelBL evolution has involved horizontal gene transfer and/or parallel loss. Severe disruption of the GTPase domain suggests that some family members may employ a hitherto unknown mechanism of nucleotide hydrolysis, or have lost their GTPase ability altogether. However, patterns of sequence conservation indicate that aSelBL is still capable of binding the ribosome and aminoacyl-tRNA.<br><br>CONCLUSIONS: Although it is closely related to SelB, aSelBL appears unlikely to either bind selenocysteinyl-tRNA or function as a classical GTP hydrolyzing elongation factor. We propose that following duplication of aSelB, the resultant aSelBL was recruited for binding another aminoacyl-tRNA. In bacteria, aminoacylation with selenocysteine is essential for efficient thermodynamic coupling of SelB binding to tRNA and GTP. Therefore, change in tRNA specificity of aSelBL could have disrupted its GTPase cycle, leading to relaxation of selective pressure on the GTPase domain and explaining its apparent degradation. While the specific role of aSelBL is yet to be experimentally tested, its broad phylogenetic distribution, surpassing that of aSelB, indicates its importance.},
}
@article {pmid21253721,
year = {2011},
author = {Wang, S and Wang, Y and Feng, X and Zhai, L and Zhu, G},
title = {Quantitative analyses of ammonia-oxidizing Archaea and bacteria in the sediments of four nitrogen-rich wetlands in China.},
journal = {Applied microbiology and biotechnology},
volume = {90},
number = {2},
pages = {779-787},
doi = {10.1007/s00253-011-3090-0},
pmid = {21253721},
issn = {1432-0614},
mesh = {Ammonia/*metabolism ; Archaea/classification/*genetics/growth &amp; development/metabolism ; Bacteria/classification/*genetics/growth &amp; development/metabolism ; Biodiversity ; China ; DNA, Archaeal/genetics/metabolism ; DNA, Bacterial/genetics/metabolism ; Genes, Archaeal ; Genes, Bacterial ; Geologic Sediments/microbiology ; Nitrification ; Nitrogen/metabolism ; Oxidation-Reduction ; Phylogeny ; *Soil Microbiology ; *Wetlands ; },
abstract = {With the rapid development of ammonia-synthesizing industry, the ammonia-nitrogen pollution in wetlands acting as the sink of point and diffuse pollution has been increased dramatically. Most of ammonia-nitrogen is oxidized at least once by ammonia-oxidizing prokaryotes to complete the nitrogen cycle. Current research findings have expanded the known ammonia-oxidizing prokaryotes from the domain Bacteria to Archaea. However, in the complex wetlands environment, it remains unclear whether ammonia oxidation is exclusively or predominantly linked to Archaea or Bacteria as implied by specific high abundance. In this research, the abundance and composition of Archaea and Bacteria in sediments of four kinds of wetlands with different nitrogen concentration were investigated by using quantitative real-time polymerase chain reaction, cloning, and sequencing approaches based on amoA genes. The results indicated that AOA distributed widely in wetland sediments, and the phylogenetic tree revealed that archaeal amoA functional gene sequences from wetlands sediments cluster as two major evolutionary branches: soil/sediment and sediment/water. The bacteria functionally dominated microbial ammonia oxidation in different wetlands sediments on the basis of molecule analysis, potential nitrification rate, and soil chemistry. Moreover, the factors influencing AOA and AOB abundances with environmental indicator were also analyzed, and the results addressed the copy numbers of archaeal and bacterial amoA functional gene having the higher correlation with pH and ammonia concentration. The pH had relatively great negative impact on the abundance of AOA and AOB, while ammonia concentration showed positive impact on AOB abundance only. These findings could be fundamental to improve understanding of the importance of AOB and AOA in nitrogen and other nutrients cycle in wetland ecosystems.},
}
@article {pmid21239545,
year = {2011},
author = {Herrmann, M and Scheibe, A and Avrahami, S and Küsel, K},
title = {Ammonium availability affects the ratio of ammonia-oxidizing bacteria to ammonia-oxidizing archaea in simulated creek ecosystems.},
journal = {Applied and environmental microbiology},
volume = {77},
number = {5},
pages = {1896-1899},
pmid = {21239545},
issn = {1098-5336},
mesh = {Archaea/classification/genetics/*growth &amp; development/*metabolism ; Bacteria/classification/genetics/*growth &amp; development/*metabolism ; *Biodiversity ; Cluster Analysis ; DNA, Archaeal/chemistry/genetics ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; *Ecosystem ; Environmental Microbiology ; Genes, rRNA ; Molecular Sequence Data ; Oxidation-Reduction ; Phylogeny ; Quaternary Ammonium Compounds/*metabolism ; RNA, Archaeal/genetics ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; },
abstract = {The ammonia-oxidizing microbial community colonizing clay tiles in flow channels changed in favor of ammonia-oxidizing bacteria during a 12-week incubation period even at originally high ratios of ammonia-oxidizing archaea to ammonia-oxidizing bacteria (AOB). AOB predominance was established more rapidly in flow channels incubated at 350 μM NH(4)(+) than in those incubated at 50 or 20 μM NH(4)(+). Biofilm-associated potential nitrification activity was first detected after 28 days and was positively correlated with bacterial but not archaeal amoA gene copy numbers.},
}
@article {pmid21239153,
year = {2011},
author = {Wei, B and Yu, X and Zhang, S and Gu, L},
title = {Comparison of the community structures of ammonia-oxidizing bacteria and archaea in rhizoplanes of floating aquatic macrophytes.},
journal = {Microbiological research},
volume = {166},
number = {6},
pages = {468-474},
doi = {10.1016/j.micres.2010.09.001},
pmid = {21239153},
issn = {1618-0623},
mesh = {Ammonia/*metabolism ; Araceae/*microbiology ; Archaea/classification/genetics/isolation &amp; purification/*metabolism ; Archaeal Proteins/genetics/metabolism ; Bacteria/classification/genetics/isolation &amp; purification/*metabolism ; Bacterial Proteins/genetics/metabolism ; Ipomoea/*microbiology ; Magnoliopsida/*microbiology ; Molecular Sequence Data ; Oxidation-Reduction ; Phylogeny ; *Water Microbiology ; },
abstract = {Some common floating aquatic macrophytes could remove nutrients, such as nitrogen, from eutrophic water. However, the relationship between these macrophytes and the ammonia-oxidizing microorganisms on their rhizoplanes is still unknown. In this study, we examined communities of ammonia-oxidizing archaea (AOA) and bacteria (AOB) on the rhizoplanes of common floating aquatic macrophytes (Eichhornia crassipes, Pistia stratiotes and Ipomoea aquatic) in a eutrophic reservoir.The results show that AOB were the predominant ammonia-oxidizer on the three rhizoplanes. The principal AOB were Nitrosomonas europaea and Nitrosomonas ureae clades. The principal group of AOA was most similar to the clone from activated sludge. The ratio of AOB amoA gene copies to AOA varied from 1.36 (on E. crassipes) to 41.90 (on P. stratiotes). Diversity of AOA was much lower than that of AOB in most samples, with the exception of P. stratiotes.},
}
@article {pmid21234384,
year = {2010},
author = {Blaby, IK and Phillips, G and Blaby-Haas, CE and Gulig, KS and El Yacoubi, B and de Crécy-Lagard, V},
title = {Towards a systems approach in the genetic analysis of archaea: Accelerating mutant construction and phenotypic analysis in Haloferax volcanii.},
journal = {Archaea (Vancouver, B.C.)},
volume = {2010},
number = {},
pages = {426239},
pmid = {21234384},
issn = {1472-3654},
support = {R01 GM070641/GM/NIGMS NIH HHS/United States ; },
mesh = {Automation/methods ; Gene Knockout Techniques/*methods ; Genes, Archaeal ; Genes, Essential ; Genetic Engineering/methods ; Genetics, Microbial/*methods ; Haloferax volcanii/*genetics ; High-Throughput Screening Assays/methods ; Phenotype ; Recombination, Genetic ; },
abstract = {With the availability of a genome sequence and increasingly sophisticated genetic tools, Haloferax volcanii is becoming a model for both Archaea and halophiles. In order for H. volcanii to reach a status equivalent to Escherichia coli, Bacillus subtilis, or Saccharomyces cerevisiae, a gene knockout collection needs to be constructed in order to identify the archaeal essential gene set and enable systematic phenotype screens. A streamlined gene-deletion protocol adapted for potential automation was implemented and used to generate 22 H. volcanii deletion strains and identify several potentially essential genes. These gene deletion mutants, generated in this and previous studies, were then analyzed in a high-throughput fashion to measure growth rates in different media and temperature conditions. We conclude that these high-throughput methods are suitable for a rapid investigation of an H. volcanii mutant library and suggest that they should form the basis of a larger genome-wide experiment.},
}
@article {pmid24031614,
year = {2011},
author = {Singh, KM and Pandya, PR and Parnerkar, S and Tripathi, AK and Rank, DN and Kothari, RK and Joshi, CG},
title = {Molecular identification of methanogenic archaea from surti buffaloes (bubalus bubalis), reveals more hydrogenotrophic methanogens phylotypes.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {42},
number = {1},
pages = {132-139},
pmid = {24031614},
issn = {1517-8382},
abstract = {Methane emissions from ruminant livestock are considered to be one of the more potent forms of greenhouses gases contributing to global warming. Many strategies to reduce emissions are targeting the methanogens that inhabit the rumen, but such an approach can only be successful if it targets all the major groups of ruminant methanogens. Therefore, a thorough knowledge of the diversity of these microbes in breeds of buffaloes, as well as in response to geographical location and different diets, is required. Therefore, molecular diversity of rumen methanogens in Surti buffaloes was investigated using 16S rRNA gene libraries prepared from pooled rumen contents from three Surti buffaloes. A total of 171 clones were identified revealing 23 different sequences (phylotypes). Of these 23 sequences, twelve sequences (12 OTUs, 83 clones) and 10 sequences (10 OTUs, 83 clones) were similar to methanogens belonging to the orders Methanomicrobiales and Methanobacteriales, and the remaining 1 phylotype (5 clones) were similar to Methanosarcina barkeri. These unique sequences clustered within a distinct and strongly supported phylogenetic group. Further studies and effective strategies can be made to inhibit the growth of Methanomicrobiales and Methanobacteriales phylotypes to reduce the methane emission from rumen and thus help in preventing global warming.},
}
@article {pmid21966926,
year = {2010},
author = {Muller, F and Brissac, T and Le Bris, N and Felbeck, H and Gros, O},
title = {First description of giant Archaea (Thaumarchaeota) associated with putative bacterial ectosymbionts in a sulfidic marine habitat.},
journal = {Environmental microbiology},
volume = {12},
number = {8},
pages = {2371-2383},
doi = {10.1111/j.1462-2920.2010.02309.x},
pmid = {21966926},
issn = {1462-2920},
mesh = {Archaea/*classification/genetics/growth &amp; development/ultrastructure ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; Ecosystem ; Gammaproteobacteria/genetics/growth &amp; development ; Hydrogen-Ion Concentration ; In Situ Hybridization, Fluorescence ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/microbiology ; Sequence Analysis, DNA ; Sulfides/analysis ; Sulfur-Reducing Bacteria/*genetics/growth &amp; development ; *Symbiosis ; *Water Microbiology ; },
abstract = {Archaea may be involved in global energy cycles, and are known for their ability to interact with eukaryotic species (sponges, corals and ascidians) or as archaeal-bacterial consortia. The recently proposed phylum Thaumarchaeota may represent the deepest branching lineage in the archaeal phylogeny emerging before the divergence between Euryarchaeota and Crenarchaeota. Here we report the first characterization of two marine thaumarchaeal species from shallow waters that consist of multiple giant cells. One species is coated with sulfur-oxidizing γ-Proteobacteria. These new uncultured thaumarchaeal species are able to live in the sulfide-rich environments of a tropical mangrove swamp, either on living tissues such as roots or on various kinds of materials such as stones, sunken woods, etc. These archaea and archaea/bacteria associations have been studied using light microscopy, transmission electron microscopy and scanning electron microscopy. Species identification of archaeons and the putative bacterial symbiont have been assessed by 16S small subunit ribosomal RNA analysis. The sulfur-oxidizing ability of the bacteria has been assessed by genetic investigation on alpha-subunit of the adenosine-5'-phosphosulfate reductase/oxidase's (AprA). Species identifications have been confirmed by fluorescence in situ hybridization using specific probes designed in this study. In this article, we describe two new giant archaeal species that form the biggest archaeal filaments ever observed. One of these species is covered by a specific biofilm of sulfur-oxidizing γ-Proteobacteria. This study highlights an unexpected morphological and genetic diversity of the phylum Thaumarchaeota.},
}
@article {pmid23766082,
year = {2010},
author = {Ying, JY and Zhang, LM and He, JZ},
title = {Putative ammonia-oxidizing bacteria and archaea in an acidic red soil with different land utilization patterns.},
journal = {Environmental microbiology reports},
volume = {2},
number = {2},
pages = {304-312},
doi = {10.1111/j.1758-2229.2009.00130.x},
pmid = {23766082},
issn = {1758-2229},
abstract = {Ammonia-oxidizers play a key role in nitrification, which is important for nitrogen cycling and soil function. However, little is known about how vegetation successions and agricultural practices caused by human activities impact the ammonia-oxidizers and nitrification process. Putative ammonia-oxidizing bacteria (AOB) and archaea (AOA) communities under different land utilization patterns of restoration (forest), degradation (pasture), cropland and pine plantation were analysed in an acidic red soil based on bacterial and archaeal amoA genes together with archaeal 16S rRNA gene. Real-time PCR, terminal restriction fragment length polymorphism (T-RFLP) and sequencing of clone libraries were conducted to study their abundance and community structure. Land utilization pattern showed significant effects on the copy numbers of all these genes, but only the bacterial amoA gene correlated significantly with potential nitrification rates (PNR). The cropland plot possessed the highest bacterial amoA gene copies and PNR, while the degradation plot was opposite to that. There were no significant variations in the bacterial amoA gene structure, which was dominated by Clusters 10 and 11 in Nitrosospira. However, archaeal amoA gene structure varied among different land utilization patterns especially for the cropland. The degradation plot was dominated by Crenarchaea 1.1c-related groups from which the amoA gene could not been amplified in this study, while other plots were dominated by Crenarchaea 1.1a/b group based on archaeal 16S rRNA gene analysis. These results indicated significant effects of land utilization patterns on putative ammonia oxidizers, which were especially obvious in the degradation and cropland plots where frequent human disturbance occurred.},
}
@article {pmid23766074,
year = {2010},
author = {Brazelton, WJ and Sogin, ML and Baross, JA},
title = {Multiple scales of diversification within natural populations of archaea in hydrothermal chimney biofilms.},
journal = {Environmental microbiology reports},
volume = {2},
number = {2},
pages = {236-242},
doi = {10.1111/j.1758-2229.2009.00097.x},
pmid = {23766074},
issn = {1758-2229},
abstract = {Corroborative data collected from 16S rRNA clone libraries, intergenic transcribed spacer (ITS) region clone libraries, and 16S rRNA hypervariable region tag pyrosequencing demonstrate microdiversity within single-species archaeal biofilms of the Lost City Hydrothermal Field. Both 16S rRNA clone libraries and pyrosequencing of the V6 hypervariable region show that Lost City Methanosarcinales (LCMS) biofilms are dominated by a single sequence, but the pyrosequencing data set also reveals the presence of an additional 1654 rare sequences. Clone libraries constructed with DNA spanning the V6 hypervariable region and ITS show that multiple ITS sequences are associated with the same dominant V6 sequence. Furthermore, ITS variability differed among three chimney samples, and the sample with the highest ITS diversity also contained the highest V6 diversity as measured by clone libraries as well as tag pyrosequencing. These results indicate that the extensive microdiversity detected in V6 tag sequences is an underestimate of genetic diversity within the archaeal biofilms.},
}
@article {pmid21576849,
year = {2010},
author = {Onodera, Y and Nakagawa, T and Takahashi, R and Tokuyama, T},
title = {Seasonal change in vertical distribution of ammonia-oxidizing archaea and bacteria and their nitrification in temperate forest soil.},
journal = {Microbes and environments},
volume = {25},
number = {1},
pages = {28-35},
doi = {10.1264/jsme2.me09179},
pmid = {21576849},
issn = {1347-4405},
mesh = {Ammonia/*metabolism ; Archaea/*classification/genetics/isolation &amp; purification/*metabolism ; Bacteria/*classification/genetics/isolation &amp; purification/*metabolism ; *Biodiversity ; Cluster Analysis ; DNA, Archaeal/chemistry/genetics ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Genes, rRNA ; Molecular Sequence Data ; *Nitrification ; Phylogeny ; RNA, Archaeal/genetics ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Seasons ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; Soil Microbiology ; Trees ; },
abstract = {Seasonal change in the vertical distribution of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in temperate forest soil was examined from March 2008 to January 2009 by quantitative PCR of the amoA genes. Abundances of AOA amoA genes (ranging from 2.0×10(8) to 1.2×10(9) copies per gram dry soil) were significantly higher than those of AOB amoA genes (1.9×10(5) to 1.7×10(7) copies). A significant increase in AOB was observed at a depth of 0-5 cm in July when net nitrification was also high in the top soil, while AOA increased significantly at depths of 5-10 cm, 10-15 cm, and over 15 cm in July. Sequencing of the crenarchaeotal amoA gene revealed shifts in major AOA components along the soil depth profile and among sampling dates. Betaproteobacterial amoA clone libraries at 0-5 cm in March, May, and July were dominated by Nitrosospira clusters 1 and 4. A microcosm experiment at 0-5 cm in July revealed a decrease in the ratio of AOA/AOB amoA genes in microcosms. These results suggest that AOB play an important role in net nitrification in the top layer in temperate forest soil.},
}
@article {pmid22058585,
year = {2009},
author = {Fendrihan, S and Musso, M and Stan-Lotter, H},
title = {Raman spectroscopy as a potentialmethod for the detection of extremely halophilic archaea embedded in halite in terrestrial and possibly extraterrestrial samples.},
journal = {Journal of Raman spectroscopy : JRS},
volume = {40},
number = {12},
pages = {1996-2003},
pmid = {22058585},
issn = {0377-0486},
support = {P 18256/FWF_/Austrian Science Fund FWF/Austria ; },
abstract = {Evidence for the widespread occurrence of extraterrestrial halite, particularly on Mars, has led to speculations on the possibility of halophilic microbial forms of life; these ideas have been strengthened by reports of viable haloarchaea from sediments of geological age (millions of years). Raman spectroscopy, being a sensitive detection method for future astrobiological investigations onsite, has been used in the current study for the detection of nine different extremely halophilic archaeal strains which had been embedded in laboratory-made halite crystals in order to simulate evaporitic conditions. The cells accumulated preferentially in tiny fluid inclusions, in simulation of the precipitation of salt in natural brines. FT-Raman spectroscopy using laser excitation at 1064 nm and dispersive micro Raman spectroscopy at 514.5 nm were applied. The spectra showed prominent peaks at 1507, 1152 and 1002 cm(-1) which are attributed to haloarchaeal C(50) carotenoid compounds (mainly bacterioruberins). Their intensity varied from strain to strain at 1064-nm laser excitation. Other distinguishable features were peaks due to peptide bonds (amide I, amide III) and to nucleic acids. No evidence for fatty acids was detected, consistent with their general absence in all archaea.These results contribute to a growing database on Raman spectra of terrestrial microorganisms from hypersaline environments and highlight the influence of the different macromolecular composition of diverse strains on these spectra.},
}
@article {pmid23100763,
year = {2009},
author = {Sharma, KK and Kuhad, RC},
title = {An evidence of laccases in archaea.},
journal = {Indian journal of microbiology},
volume = {49},
number = {2},
pages = {142-150},
pmid = {23100763},
issn = {0046-8991},
abstract = {Laccases (benzenediol:oxygen oxidoreductase, EC 1.10.3.2) are a diverse group of multicopper oxidases that catalyze the oxidation of a variety of aromatic compounds. Here we present evidence for distribution of laccases among archaea and their probable functions. Putative laccase genes have been found in different archaeal groups that might have branched off early during evolution, e.g. Haloarcula marismortui ATCC 43049, Natronomonas pharaonis DSM2160, Pyrobaculum aerophilum IM2, Candidatus Nitrosopumilus maritimus SCM1, Halorubrum lacusprofundi ATCC 49239. Most of the archaeal multicopper oxidases reported here are of Type 1 and Type 2 whereas type 3 copper-binding domain could be found in Pyrobaculum aerophilum IM2 and Halorubrum lacusprofundi ATCC49239. An analysis of the genome sequence database revealed the presence of novel types of two-domain laccases in archaea. ed using this method. CyMVin the positive samples of Phalaenopsis sp. and Arachnis sp. was confirmed by DNA sequencing and cp gene homeology blast. The results showed that CyMV extracted from the leaves of orchid in Hangzhou, Zhejiang Province, China, could be derived from Kunming city (KM), Yunnan Province, China. This method characterized by high sensitivity, specificity, and precision is suitable for early diagnosis and quantitative detection of CyMV.},
}
@article {pmid21566349,
year = {2009},
author = {Ando, Y and Nakagawa, T and Takahashi, R and Yoshihara, K and Tokuyama, T},
title = {Seasonal changes in abundance of ammonia-oxidizing archaea and ammonia-oxidizing bacteria and their nitrification in sand of an eelgrass zone.},
journal = {Microbes and environments},
volume = {24},
number = {1},
pages = {21-27},
doi = {10.1264/jsme2.me08536},
pmid = {21566349},
issn = {1342-6311},
abstract = {Seasonal changes in the abundance of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) within the sand of an eelgrass (Zostera marina) zone were examined by a quantitative PCR of both crenarchaeotal and betaproteobacterial ammonia monooxygenase alpha subunit (amoA) genes together with temperature and concentrations of ammonium, nitrite, and nitrate from May 2007 to June 2008 at Tanoura Bay, Shizuoka, Japan. The abundance of both amoAs in the sand between May and June 2007 and between January and March 2008 was 1.5 to 2 orders of magnitude higher than the 10(4) copies g(-1) of estimated amoA between September and December. Archaeal amoA was more diverse than betaproteobacterial amoA. Betaproteobacterial amoA clone libraries were dominated by Nitrosospira-like sequence types. An incubation experiment was conducted with sands collected in February 2008 and community structure was analyzed based on reverse-transcribed amoAs. RNA was extracted from sand incubated for 12 days at 30°C, 17 days at 20°C, and 80 days at 10°C. Different amoA clones were detected from in situ sand and incubated sand. This study reveals clear evidence of seasonal change in the abundance of AOA and AOB within the sand of an eelgrass zone.},
}
@article {pmid21984879,
year = {2006},
author = {Fendrihan, S and Legat, A and Pfaffenhuemer, M and Gruber, C and Weidler, G and Gerbl, F and Stan-Lotter, H},
title = {Extremely halophilic archaea and the issue of long-term microbial survival.},
journal = {Re/views in environmental science and bio/technology},
volume = {5},
number = {2-3},
pages = {203-218},
pmid = {21984879},
issn = {1572-9826},
support = {P 16260/FWF_/Austrian Science Fund FWF/Austria ; },
abstract = {Halophilic archaebacteria (haloarchaea) thrive in environments with salt concentrations approaching saturation, such as natural brines, the Dead Sea, alkaline salt lakes and marine solar salterns; they have also been isolated from rock salt of great geological age (195-250 million years). An overview of their taxonomy, including novel isolates from rock salt, is presented here; in addition, some of their unique characteristics and physiological adaptations to environments of low water activity are reviewed. The issue of extreme long-term microbial survival is considered and its implications for the search for extraterrestrial life. The development of detection methods for subterranean haloarchaea, which might also be applicable to samples from future missions to space, is presented.},
}
@article {pmid29711354,
year = {1998},
author = {Auzély-Velty, R and Benvegnu, T and Plusquellec, D and Mackenzie, G and Haley, JA and Goodby, JW},
title = {Self-Organization and Formation of Liquid Crystal Phases by Molecular Templates Related to Membrane Components of Archaebacteria.},
journal = {Angewandte Chemie (International ed. in English)},
volume = {37},
number = {18},
pages = {2511-2515},
doi = {10.1002/(SICI)1521-3773(19981002)37:18&lt;2511::AID-ANIE2511&gt;3.0.CO;2-0},
pmid = {29711354},
issn = {1521-3773},
abstract = {Tubular supramolecular aggregates are formed from glycolipids 1, which are closely related to natural components of membranes of archaebacteria. The glycolipids exhibit disordered columnar thermotropic and hexagonal lyotropic liquid crystal phases. Whereas formation of the mesophases is insensitive to stereochemical factors, formation of the tubules is dependent on the configuration of the stereocenters that are shown in the picture but not specified.},
}
@article {pmid21238259,
year = {1998},
author = {Aravalli, RN and She, Q and Garrett, RA},
title = {Archaea and the new age of microorganisms.},
journal = {Trends in ecology &amp; evolution},
volume = {13},
number = {5},
pages = {190-194},
doi = {10.1016/S0169-5347(98)01343-3},
pmid = {21238259},
issn = {0169-5347},
abstract = {Archaea were, until recently, considered to be confined to specialized environments including those at high temperature, high salinity, extremes of pH and ambients that permit methanogenesis. Recently developed molecular methods for studying microbial ecology, which do not necessitate cell culturing, have demonstrated their presence in a wide variety of temperate and cold environments including agricultural and forest soils, fresh water lake sediments, marine picoplankton and deep-sea locations. These discoveries mark the beginning of a new era for investigating the Archaea and in particular their physiological and metabolic properties and their biological roles in complex microbial populations.},
}
@article {pmid28862554,
year = {1997},
author = {Kudo, Y and Shibata, S and Miyaki, T and Aono, T and Oyaizu, H},
title = {Peculiar Archaea Found in Japanese Paddy Soils[†].},
journal = {Bioscience, biotechnology, and biochemistry},
volume = {61},
number = {5},
pages = {917-920},
doi = {10.1271/bbb.61.917},
pmid = {28862554},
issn = {1347-6947},
abstract = {Archaeal 16S rDNA clones retrieved from paddy soil DNA were sequenced. Among 100 clones, 88 clones were assigned to methanogens and nine clones were assigned to crenarchaeota. However, three of the nine clones were phylogenetically far from the cultured crenarchaeota and closely related to marine planktonic archaea. The other three clones showed extremely novel 16S rDNA sequences and were phylogenetically far from both Crenarchaeota and Euryarchaeota. This paper reports the ubiquitous presence of crenarchaeotal and extremely novel clones in paddy soils.},
}
@article {pmid24193491,
year = {1996},
author = {Keltjens, JT and Vogels, GD},
title = {Metabolic regulation in methanogenic archaea during growth on hydrogen and CO2.},
journal = {Environmental monitoring and assessment},
volume = {42},
number = {1-2},
pages = {19-37},
pmid = {24193491},
issn = {0167-6369},
abstract = {Methanogenic Archaea represent a unique group of micro-organisms in their ability to derive their energy for growth from the conversion of their substrates to methane. The common substrates are hydrogen and CO2. The energy obtained in the latter conversion is highly dependent on the hydrogen concentration which may dramatically vary in their natural habitats and under laboratory conditions. In this review the bio-energetic consequences of the variations in hydrogen supply will be investigated. It will be described how the organisms seem to be equipped as to their methanogenic apparatus to cope with extremes in hydrogen availability and how they could respond to hydrogen changes by the regulation of their metabolism.},
}
@article {pmid24414411,
year = {1995},
author = {Speelmans, G and Poolman, B and Konings, WN},
title = {Na(+) as coupling ion in energy transduction in extremophilic Bacteria and Archaea.},
journal = {World journal of microbiology &amp; biotechnology},
volume = {11},
number = {1},
pages = {58-70},
pmid = {24414411},
issn = {0959-3993},
abstract = {For microorganisms to live under extreme physical conditions requires important adaptations of the cells. In many organisms the use of Na(+) instead of protons as coupling ion in energy transduction is associated with such adaptation. This review focuses on the enzymes that are responsible for the generation and utilization of Na(+) gradients in extremophilic microorganisms. Aspects that are dealt with include: bioenergetics and ion homeostasis in extremophilic Bacteria and Archaea; the molecular mechanism of Na(+) translocation; and (dis)advantages of Na(+) as coupling ion in energy transduction.},
}
@article {pmid23196302,
year = {1983},
author = {Zillig, W and Holz, I and Janekovic, D and Schäfer, W and Reiter, WD},
title = {The Archaebacterium Thermococcus celer Represents, a Novel Genus within the Thermophilic Branch of the Archaebacteria.},
journal = {Systematic and applied microbiology},
volume = {4},
number = {1},
pages = {88-94},
doi = {10.1016/S0723-2020(83)80036-8},
pmid = {23196302},
issn = {0723-2020},
abstract = {Thermococcus celer, isolated from a solfataric marine water hole on a beach of Vulcano, Italy, is a spheric organism of about 1 μm diameter, during multiplication often constricted to diploforms. The organism utilizes peptides and protein, which are oxidized to CO(2) by sulfur respiration. Alternatively, though less efficiently, it can exist by an unknown type of fermentation. The optimal growth temperature is 88 °C, the optimal pH 5.8, the optimal NaCl concentration 3.8 g/l. Under these conditions with yeast extract (2 g/l) as carbon source and in the presence of finely distributed sulfur (10 g/1), the generation time is about 50 min. The envelope consists of subunits in two dimensional hexagonal dense packing. The absence of murein, the presence of polyisopranyl alcohols in the membrane, the component pattern and the rifampicin resistance of the DNA dependent RNA polymerase and the insensitivity of the organism towards the antibiotics streptomycin and vancomycin prove the archaebacterial nature of Thermococcus celer. The component pattern of the DNA dependent RNA polymerase conforms with the type pattern of RNA polymerases from thermoacidophilic archaebacteria. The absence of an immunochemical cross-reaction of the enzyme from Thermococcus with those from Thermoproteus, Desulfurococcus, Sulfolobus and Thermoplasma and the extent of cross-hybridization of the 16S rRNA with DNAs of other thermoacidophiles place it into the thermoacidophilic branch of the archaebacteria as a novel isolated genus.},
}
@article {pmid23194811,
year = {1983},
author = {Stetter, KO and König, H and Stackebrandt, E},
title = {Pyrodictium gen. nov., a New Genus of Submarine Disc-Shaped Sulphur Reducing Archaebacteria Growing Optimally at 105°C.},
journal = {Systematic and applied microbiology},
volume = {4},
number = {4},
pages = {535-551},
doi = {10.1016/S0723-2020(83)80011-3},
pmid = {23194811},
issn = {0723-2020},
abstract = {Six isolates of a new genus of anaerobic archaebacteria, named Pyrodictium, were isolated from a submarine solfataric field off Vulcano, Italy. These disc-shaped organisms grew at at least 110°C with an optimum around 105°C, and formed highly unusual networks of fibres. They were hydrogen-sulphur-autotrops. During growth in a fermenter, pyrite was formed. Two species can be distinguished: Pyrodictium occultum - which has a G + C-content of 62 mol%, and, as the dominant component in its cell envelope, a glycoprotein with a molecular weight of 172000 - and Pyrodictium brockii - which has a G + C-content of 51.5 to 56.6 mol%, a protein of molecular weight 150000 as its major cell envelope component, and whose growth yield is greatly increased in the presence of yeast extract.},
}
@article {pmid21228892,
year = {2011},
author = {Verhamme, DT and Prosser, JI and Nicol, GW},
title = {Ammonia concentration determines differential growth of ammonia-oxidising archaea and bacteria in soil microcosms.},
journal = {The ISME journal},
volume = {5},
number = {6},
pages = {1067-1071},
pmid = {21228892},
issn = {1751-7370},
support = {BB/F022646/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/I009647/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Ammonia/*metabolism ; Archaea/genetics/*growth &amp; development/metabolism ; Bacteria/genetics/*growth &amp; development/metabolism ; Denaturing Gradient Gel Electrophoresis ; Ecosystem ; Molecular Sequence Data ; Nitrification ; Nitrites/metabolism ; Oxidation-Reduction ; Sequence Analysis, DNA ; Soil/analysis ; *Soil Microbiology ; },
abstract = {The first step of nitrification, oxidation of ammonia to nitrite, is performed by both ammonia-oxidising archaea (AOA) and ammonia-oxidising bacteria (AOB) in soil, but their relative contributions to ammonia oxidation and existence in distinct ecological niches remain to be determined. To determine whether available ammonia concentration has a differential effect on AOA and AOB growth, soil microcosms were incubated for 28 days with ammonium at three concentrations: native (control), intermediate (20 μg NH(4)(+)-N per gram of soil) and high (200 μg NH(4)(+)-N per gram of soil). Quantitative PCR demonstrated growth of AOA at all concentrations, whereas AOB growth was prominent only at the highest concentration. Similarly, denaturing gradient gel electrophoresis (DGGE) analysis revealed changes in AOA communities at all ammonium concentrations, whereas AOB communities changed significantly only at the highest ammonium concentration. These results provide evidence that ammonia concentration contributes to the definition of distinct ecological niches of AOA and AOB in soil.},
}
@article {pmid21228891,
year = {2011},
author = {Wessén, E and Söderström, M and Stenberg, M and Bru, D and Hellman, M and Welsh, A and Thomsen, F and Klemedtson, L and Philippot, L and Hallin, S},
title = {Spatial distribution of ammonia-oxidizing bacteria and archaea across a 44-hectare farm related to ecosystem functioning.},
journal = {The ISME journal},
volume = {5},
number = {7},
pages = {1213-1225},
pmid = {21228891},
issn = {1751-7370},
mesh = {Agriculture/*methods ; Ammonia/*metabolism ; Archaea/classification/genetics/*growth &amp; development ; Bacteria/classification/genetics/*growth &amp; development ; Betaproteobacteria ; Carbon/analysis ; DNA, Bacterial/genetics ; *Ecosystem ; Genes, Bacterial ; Hydrogen-Ion Concentration ; Nitrates/metabolism ; Nitrites/metabolism ; Nitrogen/analysis ; Oxidation-Reduction ; Phylogeny ; Polymorphism, Restriction Fragment Length ; Sequence Analysis, DNA ; Soil/analysis ; *Soil Microbiology ; },
abstract = {Characterization of spatial patterns of functional microbial communities could facilitate the understanding of the relationships between the ecology of microbial communities, the biogeochemical processes they perform and the corresponding ecosystem functions. Because of the important role the ammonia-oxidizing bacteria (AOB) and archaea (AOA) have in nitrogen cycling and nitrate leaching, we explored the spatial distribution of their activity, abundance and community composition across a 44-ha large farm divided into an organic and an integrated farming system. The spatial patterns were mapped by geostatistical modeling and correlations to soil properties and ecosystem functioning in terms of nitrate leaching were determined. All measured community components for both AOB and AOA exhibited spatial patterns at the hectare scale. The patchy patterns of community structures did not reflect the farming systems, but the AOB community was weakly related to differences in soil pH and moisture, whereas the AOA community to differences in soil pH and clay content. Soil properties related differently to the size of the communities, with soil organic carbon and total nitrogen correlating positively to AOB abundance, while clay content and pH showed a negative correlation to AOA abundance. Contrasting spatial patterns were observed for the abundance distributions of the two groups indicating that the AOB and AOA may occupy different niches in agro-ecosystems. In addition, the two communities correlated differently to community and ecosystem functions. Our results suggest that the AOA, not the AOB, were contributing to nitrate leaching at the site by providing substrate for the nitrite oxidizers.},
}
@article {pmid21227921,
year = {2011},
author = {Dueber, EC and Costa, A and Corn, JE and Bell, SD and Berger, JM},
title = {Molecular determinants of origin discrimination by Orc1 initiators in archaea.},
journal = {Nucleic acids research},
volume = {39},
number = {9},
pages = {3621-3631},
pmid = {21227921},
issn = {1362-4962},
support = {R01 GM071747/GM/NIGMS NIH HHS/United States ; 086045/Z/08/Z/WT_/Wellcome Trust/United Kingdom ; GM07174/GM/NIGMS NIH HHS/United States ; },
mesh = {Archaeal Proteins/chemistry/*metabolism ; DNA, Archaeal/chemistry/metabolism ; Origin Recognition Complex/chemistry/*metabolism ; Protein Binding ; Protein Structure, Tertiary ; *Replication Origin ; Sulfolobus solfataricus/genetics ; },
abstract = {Unlike bacteria, many eukaryotes initiate DNA replication from genomic sites that lack apparent sequence conservation. These loci are identified and bound by the origin recognition complex (ORC), and subsequently activated by a cascade of events that includes recruitment of an additional factor, Cdc6. Archaeal organisms generally possess one or more Orc1/Cdc6 homologs, belonging to the Initiator clade of ATPases associated with various cellular activities (AAA(+)) superfamily; however, these proteins recognize specific sequences within replication origins. Atomic resolution studies have shown that archaeal Orc1 proteins contact double-stranded DNA through an N-terminal AAA(+) domain and a C-terminal winged-helix domain (WHD), but use remarkably few base-specific contacts. To investigate the biochemical effects of these associations, we mutated the DNA-interacting elements of the Orc1-1 and Orc1-3 paralogs from the archaeon Sulfolobus solfataricus, and tested their effect on origin binding and deformation. We find that the AAA(+) domain has an unpredicted role in controlling the sequence selectivity of DNA binding, despite an absence of base-specific contacts to this region. Our results show that both the WHD and ATPase region influence origin recognition by Orc1/Cdc6, and suggest that not only DNA sequence, but also local DNA structure help define archaeal initiator binding sites.},
}
@article {pmid21211965,
year = {2011},
author = {Habouzit, F and Gévaudan, G and Hamelin, J and Steyer, JP and Bernet, N},
title = {Influence of support material properties on the potential selection of Archaea during initial adhesion of a methanogenic consortium.},
journal = {Bioresource technology},
volume = {102},
number = {5},
pages = {4054-4060},
doi = {10.1016/j.biortech.2010.12.023},
pmid = {21211965},
issn = {1873-2976},
mesh = {Archaea/genetics/*metabolism ; Bacteria/genetics/*metabolism ; Bacterial Adhesion/*physiology ; *Biofilms ; *Biota ; DNA Fingerprinting ; DNA Primers/genetics ; Electrophoresis, Capillary ; Polymerase Chain Reaction ; Polymorphism, Single-Stranded Conformational ; Species Specificity ; Surface Properties ; Waste Disposal, Fluid/*methods ; Water Purification/*methods ; },
abstract = {In anaerobic wastewater treatment systems, the complex microbial biomass including Archaea and Bacteria can be retained as a biofilm attached to solid supports. The aim of this study was to evaluate the impact of specific properties of support material on early microbial adhesion. Seven different substrata are described in terms of topography and surface energy. Adhesion of a methanogenic consortium to these substrata was tested, the adhesion was quantified as a percentage of the surface area covered and the bacterial and archaeal community structures was assessed by molecular fingerprinting profiles (CE-SSCP). As expected, the overall adhesion on the supports was influenced mainly by total surface energy. Moreover, the adhered communities were different from the parent inocula, including the Archaea/Bacteria ratio. This could have a significant impact on the start-up of anaerobic digesters for which supports favoring Archaea adhesion, responsible for the limiting reaction of the process, should be preferred.},
}
@article {pmid21197080,
year = {2010},
author = {Storbeck, S and Rolfes, S and Raux-Deery, E and Warren, MJ and Jahn, D and Layer, G},
title = {A novel pathway for the biosynthesis of heme in Archaea: genome-based bioinformatic predictions and experimental evidence.},
journal = {Archaea (Vancouver, B.C.)},
volume = {2010},
number = {},
pages = {175050},
pmid = {21197080},
issn = {1472-3654},
support = {BB/E024203/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Archaea/*genetics/*metabolism ; Archaeal Proteins/genetics/metabolism ; Bacteria/genetics ; Biosynthetic Pathways/*genetics ; Cloning, Molecular ; Computational Biology/methods ; Eukaryota/genetics ; Genes, Archaeal ; Heme/*biosynthesis ; Methanosarcina barkeri/enzymology ; Models, Biological ; Multigene Family ; Recombinant Proteins/genetics/isolation &amp; purification/metabolism ; Sequence Homology, Amino Acid ; },
abstract = {Heme is an essential prosthetic group for many proteins involved in fundamental biological processes in all three domains of life. In Eukaryota and Bacteria heme is formed via a conserved and well-studied biosynthetic pathway. Surprisingly, in Archaea heme biosynthesis proceeds via an alternative route which is poorly understood. In order to formulate a working hypothesis for this novel pathway, we searched 59 completely sequenced archaeal genomes for the presence of gene clusters consisting of established heme biosynthetic genes and colocalized conserved candidate genes. Within the majority of archaeal genomes it was possible to identify such heme biosynthesis gene clusters. From this analysis we have been able to identify several novel heme biosynthesis genes that are restricted to archaea. Intriguingly, several of the encoded proteins display similarity to enzymes involved in heme d(1) biosynthesis. To initiate an experimental verification of our proposals two Methanosarcina barkeri proteins predicted to catalyze the initial steps of archaeal heme biosynthesis were recombinantly produced, purified, and their predicted enzymatic functions verified.},
}
@article {pmid21185720,
year = {2011},
author = {Limpiyakorn, T and Sonthiphand, P and Rongsayamanont, C and Polprasert, C},
title = {Abundance of amoA genes of ammonia-oxidizing archaea and bacteria in activated sludge of full-scale wastewater treatment plants.},
journal = {Bioresource technology},
volume = {102},
number = {4},
pages = {3694-3701},
doi = {10.1016/j.biortech.2010.11.085},
pmid = {21185720},
issn = {1873-2976},
mesh = {Ammonia/*chemistry ; Archaea/*metabolism ; Archaeal Proteins/*genetics ; Bacterial Proteins/*genetics ; *Biodegradation, Environmental ; DNA/chemistry ; Genes, Archaeal ; Genes, Bacterial ; Nitrogen/chemistry ; Oxidoreductases/*genetics ; Oxygen/*chemistry ; Phylogeny ; Reverse Transcriptase Polymerase Chain Reaction ; Sewage ; Water Microbiology ; Water Pollutants, Chemical/analysis ; Water Purification/*methods ; },
abstract = {In this study, the abundance and sequences of amoA genes of ammonia-oxidizing archaea (AOA) and bacteria (AOB) were determined in seven wastewater treatment plants (WWTPs) whose ammonium concentrations in influent and effluent wastewaters varied considerably (5.6-422.3 mgN l(-1) and 0.2-29.2 mgN l(-1), respectively). Quantitative real-time PCR showed that the comparative abundance of AOA and AOB amoA genes differed among the WWTPs. In all three industrial WWTPs, where the influent and effluent contained the higher levels of ammonium (36.1-422.3 mgN l(-1) and 5.3-29.2 mgN l(-1), respectively), more than four orders of magnitude higher numbers of AOB amoA genes than AOA amoA genes arose (with less than the limit of detection of AOA amoA genes). In contrast, significant numbers of AOA amoA genes occurred in all municipal WWTPs (with ammonium levels in the influent and effluent of 5.6-11.0 mgN l(-1) and 0.2-3.0 mgN l(-1), respectively). Statistical analysis suggested that compared to other plants' parameters, the ammonium levels in the plants' effluent showed correlation with the highest p value to the abundance of AOA amoA genes.},
}
@article {pmid21185437,
year = {2011},
author = {Mosier, AC and Francis, CA},
title = {Determining the distribution of marine and coastal ammonia-oxidizing archaea and bacteria using a quantitative approach.},
journal = {Methods in enzymology},
volume = {486},
number = {},
pages = {205-221},
doi = {10.1016/B978-0-12-381294-0.00009-2},
pmid = {21185437},
issn = {1557-7988},
mesh = {Ammonia/*metabolism ; Archaea/*classification/genetics ; Betaproteobacteria/*classification/genetics ; DNA, Archaeal/genetics/isolation &amp; purification ; DNA, Bacterial/genetics/isolation &amp; purification ; Nitrates/metabolism ; Nitrification ; Nitrites/metabolism ; Oxidation-Reduction ; Oxidoreductases/metabolism ; Phylogeny ; Polymerase Chain Reaction ; Seawater/*microbiology ; Sequence Analysis ; },
abstract = {The oxidation of ammonia to nitrite is the first and often rate-limiting step in nitrification and plays an important role in both nitrogen and carbon cycling. This process is carried out by two distinct groups of microorganisms: ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). This chapter describes methods for measuring the abundance of AOA and AOB using ammonia monooxygenase subunit A (amoA) genes, with a particular emphasis on marine and coastal systems. We also describe quantitative measures designed to target two specific clades of marine AOA: the "shallow" (group A) and "deep" (group B) water column AOA.},
}
@article {pmid21185435,
year = {2011},
author = {Adair, K and Schwartz, E},
title = {Stable isotope probing with 18O-water to investigate growth and mortality of ammonia oxidizing bacteria and archaea in soil.},
journal = {Methods in enzymology},
volume = {486},
number = {},
pages = {155-169},
doi = {10.1016/B978-0-12-381294-0.00007-9},
pmid = {21185435},
issn = {1557-7988},
mesh = {Ammonia/*metabolism ; Archaea/genetics/*growth &amp; development ; Arizona ; Bacteria/genetics/*growth &amp; development ; DNA, Bacterial/analysis ; *Microbiological Techniques ; Nitrification ; Nitrites ; Oxygen Isotopes/*metabolism ; *Soil Microbiology ; United States ; Water ; },
abstract = {Ammonia oxidizing bacteria (AOB) and archaea oxidize ammonia to nitrite, the first and rate-limiting step in the important ecosystem process of nitrification. Growth and mortality of ammonia oxidizers in soil are difficult to quantify but accurate measurements would offer important insights into how environmental parameters regulate the population dynamics of these organisms. Stable isotope probing (SIP) is a recently developed technique that can identify microorganisms that assimilate labeled substrates and can be adapted to quantify the growth of organisms in soil. Here, we describe the use of SIP with (18)O-water to investigate the growth and mortality of ammonia oxidizers in a soil taken from a ponderosa pine forest in northern Arizona, USA. Addition of ammonia to soil stimulated the growth of AOB but not ammonia oxidizing archaea (AOA). The mortality of AOA was increased upon addition of ammonia to soil; however, the variance in these measurements was high. The mortality of AOB, in contrast, was not impacted by addition of ammonia to soil. The results suggest that increased ammonia availability in soil favors AOB over AOA.},
}
@article {pmid21185431,
year = {2011},
author = {Bollmann, A and French, E and Laanbroek, HJ},
title = {Isolation, cultivation, and characterization of ammonia-oxidizing bacteria and archaea adapted to low ammonium concentrations.},
journal = {Methods in enzymology},
volume = {486},
number = {},
pages = {55-88},
doi = {10.1016/B978-0-12-381294-0.00003-1},
pmid = {21185431},
issn = {1557-7988},
mesh = {Ammonia/*metabolism ; Archaea/genetics/*growth &amp; development/*isolation &amp; purification ; *Microbiological Techniques ; Nitrosomonas/genetics/*growth &amp; development/*isolation &amp; purification ; Oxidation-Reduction ; },
abstract = {Ammonia-oxidizing microorganisms (AOM) generate their energy by the oxidation of ammonia (NH(3)) to nitrite (NO(2)(-)). This process can be carried out by ammonia-oxidizing bacteria (AOB) as well as by the recently discovered ammonia-oxidizing archaea (AOA). In the past, AOB were enriched in batch cultures, often in the presence of rather high concentrations of NH(4)(+). Here, we describe methods to enrich, isolate, and investigate the basic physiology of AOB and AOA with emphasis on those that are adapted to low NH(4)(+) concentrations. The methods described include enrichment of AOA and AOB in batch cultures and of AOB in continuous cultures, the isolation of AOA by serial dilution and AOB by pour plates or dilution to extinction, and techniques to determine growth and activity of the AOA and AOB. Finally, we incorporated a section with Appendix about the identification of AOA and AOB as well as the measurement of the different inorganic nitrogen species.},
}
@article {pmid21176052,
year = {2011},
author = {Empadinhas, N and da Costa, MS},
title = {Diversity, biological roles and biosynthetic pathways for sugar-glycerate containing compatible solutes in bacteria and archaea.},
journal = {Environmental microbiology},
volume = {13},
number = {8},
pages = {2056-2077},
doi = {10.1111/j.1462-2920.2010.02390.x},
pmid = {21176052},
issn = {1462-2920},
mesh = {Adaptation, Physiological ; Archaea/genetics/*metabolism ; Bacteria/genetics/*metabolism ; *Biosynthetic Pathways/genetics ; Glucosides/biosynthesis/genetics/metabolism ; Glyceric Acids/metabolism ; Mannose/analogs &amp; derivatives/biosynthesis/genetics/metabolism ; },
abstract = {A decade ago the compatible solutes mannosylglycerate (MG) and glucosylglycerate (GG) were considered to be rare in nature. Apart from two species of thermophilic bacteria, Thermus thermophilus and Rhodothermus marinus, and a restricted group of hyperthermophilic archaea, the Thermococcales, MG had only been identified in a few red algae. Glucosylglycerate was considered to be even rarer and had only been detected as an insignificant solute in two halophilic microorganisms, a cyanobacterium, as a component of a polysaccharide and of a glycolipid in two actinobacteria. Unlike the hyper/thermophilic MG-accumulating microorganisms, branching close to the root of the Tree of Life, those harbouring GG shared a mesophilic lifestyle. Exceptionally, the thermophilic bacterium Persephonella marina was reported to accumulate GG. However, and especially owing to the identification of the key-genes for MG and GG synthesis and to the escalating numbers of genomes available, a plethora of new organisms with the resources to synthesize these solutes has been recognized. The accumulation of GG as an 'emergency' compatible solute under combined salt stress and nitrogen-deficient conditions now seems to be a disseminated survival strategy from enterobacteria to marine cyanobacteria. In contrast, the thermophilic and extremely radiation-resistant bacterium Rubrobacter xylanophilus is the only actinobacterium known to accumulate MG, and under all growth conditions tested. This review addresses the environmental factors underlying the accumulation of MG, GG and derivatives in bacteria and archaea and their roles during stress adaptation or as precursors for more elaborated macromolecules. The diversity of pathways for MG and GG synthesis as well as those for some of their derivatives is also discussed. The importance of glycerate-derived organic solutes in the microbial world is only now being recognized. Their stress-dependent accumulation and the molecular aspects of their interactions with biomolecules have already fuelled several emerging applications in biotechnology and biomedicine.},
}
@article {pmid21169435,
year = {2011},
author = {Wirth, R and Bellack, A and Bertl, M and Bilek, Y and Heimerl, T and Herzog, B and Leisner, M and Probst, A and Rachel, R and Sarbu, C and Schopf, S and Wanner, G},
title = {The mode of cell wall growth in selected archaea is similar to the general mode of cell wall growth in bacteria as revealed by fluorescent dye analysis.},
journal = {Applied and environmental microbiology},
volume = {77},
number = {5},
pages = {1556-1562},
pmid = {21169435},
issn = {1098-5336},
mesh = {Archaea/*growth &amp; development/metabolism/ultrastructure ; Cell Wall/*metabolism/ultrastructure ; Fluorescent Dyes/metabolism ; Microscopy, Electron ; Organelles/metabolism/ultrastructure ; Staining and Labeling/methods ; },
abstract = {The surfaces of 8 bacterial and 23 archaeal species, including many hyperthermophilic Archaea, could be stained using succinimidyl esters of fluorescent dyes. This allowed us for the first time to analyze the mode of cell wall growth in Archaea by subculturing stained cells. The data obtained show that incorporation of new cell wall material in Archaea follows the pattern observed for Bacteria: in the coccoid species Pyrococcus furiosus incorporation was in the region of septum formation while for the rod-shaped species Methanopyrus kandleri and Methanothermus sociabilis, a diffuse incorporation of cell wall material over the cell length was observed. Cell surface appendages like fimbriae/pili, fibers, or flagella were detectable by fluorescence staining only in a very few cases although their presence was proven by electron microscopy. Our data in addition prove that Alexa Fluor dyes can be used for in situ analyses at temperatures up to 100°C.},
}
@article {pmid21169198,
year = {2011},
author = {Nunoura, T and Takaki, Y and Kakuta, J and Nishi, S and Sugahara, J and Kazama, H and Chee, GJ and Hattori, M and Kanai, A and Atomi, H and Takai, K and Takami, H},
title = {Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group.},
journal = {Nucleic acids research},
volume = {39},
number = {8},
pages = {3204-3223},
pmid = {21169198},
issn = {1362-4962},
mesh = {Amino Acid Sequence ; Archaea/classification/genetics/metabolism ; Archaeal Proteins/chemistry/*genetics ; Base Sequence ; Cell Cycle/genetics ; DNA Repair ; DNA Replication ; Energy Metabolism/genetics ; Evolution, Molecular ; Genes, Archaeal ; *Genome, Archaeal ; Genomic Library ; Heat-Shock Proteins/genetics ; Metagenome ; Molecular Sequence Data ; Phylogeny ; Protein Biosynthesis ; Sequence Alignment ; Transcription, Genetic ; Ubiquitins/chemistry/*genetics ; },
abstract = {The domain Archaea has historically been divided into two phyla, the Crenarchaeota and Euryarchaeota. Although regarded as members of the Crenarchaeota based on small subunit rRNA phylogeny, environmental genomics and efforts for cultivation have recently revealed two novel phyla/divisions in the Archaea; the 'Thaumarchaeota' and 'Korarchaeota'. Here, we show the genome sequence of Candidatus 'Caldiarchaeum subterraneum' that represents an uncultivated crenarchaeotic group. A composite genome was reconstructed from a metagenomic library previously prepared from a microbial mat at a geothermal water stream of a sub-surface gold mine. The genome was found to be clearly distinct from those of the known phyla/divisions, Crenarchaeota (hyperthermophiles), Euryarchaeota, Thaumarchaeota and Korarchaeota. The unique traits suggest that this crenarchaeotic group can be considered as a novel archaeal phylum/division. Moreover, C. subterraneum harbors an ubiquitin-like protein modifier system consisting of Ub, E1, E2 and small Zn RING finger family protein with structural motifs specific to eukaryotic system proteins, a system clearly distinct from the prokaryote-type system recently identified in Haloferax and Mycobacterium. The presence of such a eukaryote-type system is unprecedented in prokaryotes, and indicates that a prototype of the eukaryotic protein modifier system is present in the Archaea.},
}
@article {pmid21164034,
year = {2010},
author = {McClain, WH},
title = {Discovery of a mini-RNase P in archaea.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {107},
number = {52},
pages = {22371-22372},
pmid = {21164034},
issn = {1091-6490},
mesh = {Archaeal Proteins/chemistry/*genetics ; Biocatalysis ; Models, Molecular ; Pyrobaculum/enzymology/*genetics ; RNA Precursors/chemistry/genetics/metabolism ; RNA, Archaeal/chemistry/*genetics/metabolism ; RNA, Catalytic/chemistry/genetics/metabolism ; RNA, Transfer/chemistry/genetics/metabolism ; Ribonuclease P/chemistry/*genetics/metabolism ; Substrate Specificity ; },
}
@article {pmid21151646,
year = {2010},
author = {Peeters, E and Charlier, D},
title = {The Lrp family of transcription regulators in archaea.},
journal = {Archaea (Vancouver, B.C.)},
volume = {2010},
number = {},
pages = {750457},
pmid = {21151646},
issn = {1472-3654},
mesh = {Archaea/chemistry/*metabolism ; Gene Expression Regulation, Archaeal ; Leucine-Responsive Regulatory Protein/chemistry/genetics/*metabolism ; Metabolic Networks and Pathways ; Phylogeny ; },
abstract = {Archaea possess a eukaryotic-type basal transcription apparatus that is regulated by bacteria-like transcription regulators. A universal and abundant family of transcription regulators are the bacterial/archaeal Lrp-like regulators. The Lrp family is one of the best studied regulator families in archaea, illustrated by investigations of proteins from the archaeal model organisms: Sulfolobus, Pyrococcus, Methanocaldococcus, and Halobacterium. These regulators are extremely versatile in their DNA-binding properties, response to effector molecules, and molecular regulatory mechanisms. Besides being involved in the regulation of the amino acid metabolism, they also regulate central metabolic processes. It appears that these regulatory proteins are also involved in large regulatory networks, because of hierarchical regulations and the possible combinatorial use of different Lrp-like proteins. Here, we discuss the recent developments in our understanding of this important class of regulators.},
}
@article {pmid21148697,
year = {2011},
author = {Wu, SY and Lai, MC},
title = {Methanogenic archaea isolated from Taiwan's Chelungpu fault.},
journal = {Applied and environmental microbiology},
volume = {77},
number = {3},
pages = {830-838},
pmid = {21148697},
issn = {1098-5336},
mesh = {Archaeal Proteins/analysis ; Base Composition ; Culture Media ; *Earthquakes ; Genes, rRNA ; Geologic Sediments/*microbiology ; Methane/*metabolism ; Methanobacterium/*classification/genetics/*isolation &amp; purification/physiology ; Methanosarcinaceae/*classification/genetics/*isolation &amp; purification/physiology ; Molecular Sequence Data ; Nucleic Acid Hybridization ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Taiwan ; },
abstract = {Terrestrial rocks, petroleum reservoirs, faults, coal seams, and subseafloor gas hydrates contain an abundance of diverse methanoarchaea. However, reports on the isolation, purification, and characterization of methanoarchaea in the subsurface environment are rare. Currently, no studies investigating methanoarchaea within fault environments exist. In this report, we succeeded in obtaining two new methanogen isolates, St545Mb(T) of newly proposed species Methanolobus chelungpuianus and Methanobacterium palustre FG694aF, from the Chelungpu fault, which is the fault that caused a devastating earthquake in central Taiwan in 1999. Strain FG694aF was isolated from a fault gouge sample obtained at 694 m below land surface (mbls) and is an autotrophic, mesophilic, nonmotile, thin, filamentous-rod-shaped organism capable of using H(2)-CO(2) and formate as substrates for methanogenesis. The morphological, biochemical, and physiological characteristics and 16S rRNA gene sequence analysis revealed that this isolate belongs to Methanobacterium palustre. The mesophilic strain St545Mb(T), isolated from a sandstone sample at 545 mbls, is a nonmotile, irregular, coccoid organism that uses methanol and trimethylamine as substrates for methanogenesis. The 16S rRNA gene sequence of strain St545Mb(T) was 99.0% similar to that of Methanolobus psychrophilus strain R15 and was 96 to 97.5% similar to the those of other Methanolobus species. However, the optimal growth temperature and total cell protein profile of strain St545Mb(T) were different from those of M. psychrophilus strain R15, and whole-genome DNA-DNA hybridization revealed less than 20% relatedness between these two strains. On the basis of these observations, we propose that strain St545Mb(T) (DSM 19953(T); BCRC AR10030; JCM 15159) be named Methanolobus chelungpuianus sp. nov. Moreover, the environmental DNA database survey indicates that both Methanolobus chelungpuianus and Methanobacterium palustre are widespread in the subsurface environment.},
}
@article {pmid21145391,
year = {2011},
author = {Gribaldo, S and Forterre, P and Brochier-Armanet, C},
title = {Archaea and the tree of life.},
journal = {Research in microbiology},
volume = {162},
number = {1},
pages = {1-4},
doi = {10.1016/j.resmic.2010.11.007},
pmid = {21145391},
issn = {1769-7123},
mesh = {Archaea/*classification/genetics/physiology ; Biological Evolution ; *Phylogeny ; },
}
@article {pmid21132019,
year = {2011},
author = {Cavicchioli, R},
title = {Archaea--timeline of the third domain.},
journal = {Nature reviews. Microbiology},
volume = {9},
number = {1},
pages = {51-61},
pmid = {21132019},
issn = {1740-1534},
mesh = {Amino Acyl-tRNA Synthetases/genetics/metabolism ; Archaea/cytology/*genetics/*physiology ; *Evolution, Molecular ; Gene Expression Regulation, Archaeal/physiology ; Gene Expression Regulation, Enzymologic ; Phylogeny ; },
abstract = {The Archaea evolved as one of the three primary lineages several billion years ago, but the first archaea to be discovered were described in the scientific literature about 130 years ago. Moreover, the Archaea were formally proposed as the third domain of life only 20 years ago. Over this very short period of investigative history, the scientific community has learned many remarkable things about the Archaea--their unique cellular components and pathways, their abundance and critical function in diverse natural environments, and their quintessential role in shaping the evolutionary path of life on Earth. This Review charts the 'archaea movement', from its genesis through to key findings that, when viewed together, illustrate just how strongly the field has built on new knowledge to advance our understanding not only of the Archaea, but of biology as a whole.},
}
@article {pmid21097629,
year = {2011},
author = {Hildenbrand, C and Stock, T and Lange, C and Rother, M and Soppa, J},
title = {Genome copy numbers and gene conversion in methanogenic archaea.},
journal = {Journal of bacteriology},
volume = {193},
number = {3},
pages = {734-743},
pmid = {21097629},
issn = {1098-5530},
mesh = {*Gene Conversion ; *Gene Dosage ; *Genome, Archaeal ; Methane/metabolism ; Methanococcus/*genetics/growth &amp; development/metabolism ; Methanosarcina/*genetics/growth &amp; development/metabolism ; Ploidies ; },
abstract = {Previous studies revealed that one species of methanogenic archaea, Methanocaldococcus jannaschii, is polyploid, while a second species, Methanothermobacter thermoautotrophicus, is diploid. To further investigate the distribution of ploidy in methanogenic archaea, species of two additional genera-Methanosarcina acetivorans and Methanococcus maripaludis-were investigated. M. acetivorans was found to be polyploid during fast growth (t(D) = 6 h; 17 genome copies) and oligoploid during slow growth (doubling time = 49 h; 3 genome copies). M. maripaludis has the highest ploidy level found for any archaeal species, with up to 55 genome copies in exponential phase and ca. 30 in stationary phase. A compilation of archaeal species with quantified ploidy levels reveals a clear dichotomy between Euryarchaeota and Crenarchaeota: none of seven euryarchaeal species of six genera is monoploid (haploid), while, in contrast, all six crenarchaeal species of four genera are monoploid, indicating significant genetic differences between these two kingdoms. Polyploidy in asexual species should lead to accumulation of inactivating mutations until the number of intact chromosomes per cell drops to zero (called "Muller's ratchet"). A mechanism to equalize the genome copies, such as gene conversion, would counteract this phenomenon. Making use of a previously constructed heterozygous mutant strain of the polyploid M. maripaludis we could show that in the absence of selection very fast equalization of genomes in M. maripaludis took place probably via a gene conversion mechanism. In addition, it was shown that the velocity of this phenomenon is inversely correlated to the strength of selection.},
}
@article {pmid21094181,
year = {2011},
author = {Capes, MD and Coker, JA and Gessler, R and Grinblat-Huse, V and DasSarma, SL and Jacob, CG and Kim, JM and DasSarma, P and DasSarma, S},
title = {The information transfer system of halophilic archaea.},
journal = {Plasmid},
volume = {65},
number = {2},
pages = {77-101},
doi = {10.1016/j.plasmid.2010.11.005},
pmid = {21094181},
issn = {1095-9890},
mesh = {Chromatin/chemistry/metabolism ; DNA Repair ; DNA Replication ; Gene Expression Regulation, Archaeal ; Genome, Archaeal/genetics ; Halobacteriales/*genetics/*metabolism ; Recombination, Genetic ; Replication Origin ; Transcription, Genetic ; },
abstract = {Information transfer is fundamental to all life forms. In the third domain of life, the archaea, many of the genes functioning in these processes are similar to their eukaryotic counterparts, including DNA replication and repair, basal transcription, and translation genes, while many transcriptional regulators and the overall genome structure are more bacterial-like. Among halophilic (salt-loving) archaea, the genomes commonly include extrachromosomal elements, many of which are large megaplasmids or minichromosomes. With the sequencing of genomes representing ten different genera of halophilic archaea and the availability of genetic systems in two diverse models, Halobacterium sp. NRC-1 and Haloferax volcanii, a large number of genes have now been annotated, classified, and studied. Here, we review the comparative genomic, genetic, and biochemical work primarily aimed at the information transfer system of halophilic archaea, highlighting gene conservation and differences in the chromosomes and the large extrachromosomal elements among these organisms.},
}
@article {pmid21079939,
year = {2011},
author = {Di Giulio, M},
title = {The last universal common ancestor (LUCA) and the ancestors of archaea and bacteria were progenotes.},
journal = {Journal of molecular evolution},
volume = {72},
number = {1},
pages = {119-126},
pmid = {21079939},
issn = {1432-1432},
mesh = {Archaea/*genetics/metabolism ; Bacteria/*genetics/metabolism ; *Biological Evolution ; Evolution, Molecular ; *Genes ; Genes, Archaeal ; Genes, Bacterial ; Introns ; Nanoarchaeota/*genetics ; Phylogeny ; RNA, Transfer, Met/*genetics ; },
abstract = {The tRNA split genes of Nanoarchaeum equitans and the Met-tRNA(fMet) → fMet-tRNA(fMet) pathway, identifiable as ancestral traits, and the late appearance of DNA are used to understand the evolutionary stage at which the progenote → genote transition took place. The arguments are such as to impose that not only was the last universal common ancestor (LUCA) a progenote, but the ancestors of Archaea and Bacteria were too. Therefore, the progenote → genote transition took place in a very advanced stage of the evolution of the tree of life, and only when the ancestors of Archaea and Bacteria were already defined. These conclusions are in disagreement with commonly held beliefs.},
}
@article {pmid21078440,
year = {2010},
author = {Schleper, C and Nicol, GW},
title = {Ammonia-oxidising archaea--physiology, ecology and evolution.},
journal = {Advances in microbial physiology},
volume = {57},
number = {},
pages = {1-41},
doi = {10.1016/B978-0-12-381045-8.00001-1},
pmid = {21078440},
issn = {2162-5468},
mesh = {Ammonia/*metabolism ; Archaea/genetics/*physiology ; *Biological Evolution ; *Ecosystem ; *Environmental Microbiology ; *Nitrification ; Nitrites/metabolism ; Oxidation-Reduction ; },
abstract = {Nitrification is a microbially mediated process that plays a central role in the global cycling of nitrogen and is also of economic importance in agriculture and wastewater treatment. The first step in nitrification is performed by ammonia-oxidising microorganisms, which convert ammonia into nitrite ions. Ammonia-oxidising bacteria (AOB) have been known for more than 100 years. However, metagenomic studies and subsequent cultivation efforts have recently demonstrated that microorganisms of the domain archaea are also capable of performing this process. Astonishingly, members of this group of ammonia-oxidising archaea (AOA), which was overlooked for so long, are present in almost every environment on Earth and typically outnumber the known bacterial ammonia oxidisers by orders of magnitudes in common environments such as the marine plankton, soils, sediments and estuaries. Molecular studies indicate that AOA are amongst the most abundant organisms on this planet, adapted to the most common environments, but are also present in those considered extreme, such as hot springs. The ecological distribution and community dynamics of these archaea are currently the subject of intensive study by many research groups who are attempting to understand the physiological diversity and the ecosystem function of these organisms. The cultivation of a single marine isolate and two enrichments from hot terrestrial environments has demonstrated a chemolithoautotrophic mode of growth. Both pure culture-based and environmental studies indicate that at least some AOA have a high substrate affinity for ammonia and are able to grow under extremely oligotrophic conditions. Information from the first available genomes of AOA indicate that their metabolism is fundamentally different from that of their bacterial counterparts, involving a highly copper-dependent system for ammonia oxidation and electron transport, as well as a novel carbon fixation pathway that has recently been discovered in hyperthermophilic archaea. A distinct set of informational processing genes of AOA indicates that they are members of a distinct and novel phylum within the archaea, the 'Thaumarchaeota', which may even be a more ancient lineage than the established Cren- and Euryarchaeota lineages, raising questions about the evolutionary origins of archaea and the origins of ammonia-oxidising metabolism.},
}
@article {pmid21077120,
year = {2011},
author = {Ivanova, I and Atanassov, I and Lyutskanova, D and Stoilova-Disheva, M and Dimitrova, D and Tomova, I and Derekova, A and Radeva, G and Buchvarova, V and Kambourova, M},
title = {High Archaea diversity in Varvara hot spring, Bulgaria.},
journal = {Journal of basic microbiology},
volume = {51},
number = {2},
pages = {163-172},
doi = {10.1002/jobm.201000160},
pmid = {21077120},
issn = {1521-4028},
mesh = {Amino Acid Sequence ; Archaea/classification/genetics/*isolation &amp; purification ; Base Sequence ; Bulgaria ; DNA, Bacterial/chemistry/genetics ; Genetic Variation ; Hot Springs/*microbiology ; Molecular Sequence Data ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal/chemistry/genetics ; Sequence Alignment ; *Water Microbiology ; },
abstract = {The phylogeny of the latest recognized domain, Archaea, is still complicated and it is largely based on environmental sequences. A culture independent molecular phylogenetic analysis revealed high Archaea diversity in a terrestrial hot spring, village Varvara, Bulgaria. A total of 35 archaeal operational taxonomic units (OTUs) belonging to three of the classified five Archaea phyla were identified. Most of the sequences were affiliated with the phylum Crenarchaeota (23), grouped in four branches. The rest of the sequences showed highest similarity to the unidentified archaeal clones (9), Euryarchaeota (2), and "Korarchaeota " (1). Eight (23%) of the sequenced 16S rDNAs didn't have known close relatives and represented new and diverse OTUs, four of them forming a new archaeal subgroup without close described sequences or culturable relatives. A sequence affiliated with "Korarchaeota " showed low similarity (90%) to the closest neighbor and both sequences formed unique branch in this phylum. Consequently, the constructed archaeal libraries are characterized by (1) high proportion of OTUs representing uncultivated archaeal phylogroups, (2) the abundance of novel phylotype sequences, (3) the presence of high proportions of Crenarchaeota phylotypes unrelated to cultivated organisms and (4) the presence of a sequence only distantly related to "Korarchaeota " phylum.},
}
@article {pmid21071402,
year = {2011},
author = {Yu, NY and Laird, MR and Spencer, C and Brinkman, FS},
title = {PSORTdb--an expanded, auto-updated, user-friendly protein subcellular localization database for Bacteria and Archaea.},
journal = {Nucleic acids research},
volume = {39},
number = {Database issue},
pages = {D241-4},
pmid = {21071402},
issn = {1362-4962},
mesh = {Archaeal Proteins/*analysis ; Bacterial Proteins/*analysis ; Computational Biology ; *Databases, Protein ; Intracellular Space/chemistry ; Membrane Proteins/analysis ; Proteome/analysis ; User-Computer Interface ; },
abstract = {The subcellular localization (SCL) of a microbial protein provides clues about its function, its suitability as a drug, vaccine or diagnostic target and aids experimental design. The first version of PSORTdb provided a valuable resource comprising a data set of proteins of known SCL (ePSORTdb) as well as pre-computed SCL predictions for proteomes derived from complete bacterial genomes (cPSORTdb). PSORTdb 2.0 (http://db.psort.org) extends user-friendly functionalities, significantly expands ePSORTdb and now contains pre-computed SCL predictions for all prokaryotes--including Archaea and Bacteria with atypical cell wall/membrane structures. cPSORTdb uses the latest version of the SCL predictor PSORTb (version 3.0), with higher genome prediction coverage and functional improvements over PSORTb 2.0, which has been the most precise bacterial SCL predictor available. PSORTdb 2.0 is the first microbial protein SCL database reported to have an automatic updating mechanism to regularly generate SCL predictions for deduced proteomes of newly sequenced prokaryotic organisms. This updating approach uses a novel sequence analysis we developed that detects whether the microbe being analyzed has an outer membrane. This identification of membrane structure permits appropriate SCL prediction in an auto-updated fashion and allows PSORTdb to serve as a practical resource for genome annotation and prokaryotic research.},
}
@article {pmid21061007,
year = {2011},
author = {Ziganshin, AM and Schmidt, T and Scholwin, F and Il'inskaya, ON and Harms, H and Kleinsteuber, S},
title = {Bacteria and archaea involved in anaerobic digestion of distillers grains with solubles.},
journal = {Applied microbiology and biotechnology},
volume = {89},
number = {6},
pages = {2039-2052},
doi = {10.1007/s00253-010-2981-9},
pmid = {21061007},
issn = {1432-0614},
mesh = {Archaea/*classification/genetics/*metabolism ; Bacteria/*classification/genetics/*metabolism ; *Biodiversity ; Biofuels ; Cluster Analysis ; Culture Media/chemistry ; DNA, Archaeal/chemistry/genetics ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Edible Grain/*metabolism ; Ethanol/*metabolism ; Genes, rRNA ; Iron/metabolism ; Molecular Sequence Data ; Phylogeny ; RNA, Archaeal/genetics ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; Sulfides/metabolism ; },
abstract = {Cereal distillers grains, a by-product from bioethanol industry, proved to be a suitable feedstock for biogas production in laboratory scale anaerobic digesters. Five continuously stirred tank reactors were run under constant conditions and monitored for biogas production and composition along with other process parameters. Iron additives for sulfide precipitation significantly improved the process stability and efficiency, whereas aerobic pretreatment of the grains had no effect. The microbial communities in the reactors were investigated for their phylogenetic composition by terminal restriction fragment length polymorphism analysis and sequencing of 16S rRNA genes. The bacterial subcommunities were highly diverse, and their composition did not show any correlation with reactor performance. The dominant phylotypes were affiliated to the Bacteroidetes. The archaeal subcommunities were less diverse and correlated with the reactor performance. The well-performing reactors operated at lower organic loading rates and amended with iron chloride were dominated by aceticlastic methanogens of the genus Methanosaeta. The well-performing reactor operated at a high organic loading rate and supplemented with iron hydroxide was dominated by Methanosarcina ssp. The reactor without iron additives was characterized by propionate and acetate accumulation and high hydrogen sulfide content and was dominated by hydrogenotrophic methanogens of the genus Methanoculleus.},
}
@article {pmid21060738,
year = {2010},
author = {Lessner, DJ and Lhu, L and Wahal, CS and Ferry, JG},
title = {An engineered methanogenic pathway derived from the domains Bacteria and Archaea.},
journal = {mBio},
volume = {1},
number = {5},
pages = {},
pmid = {21060738},
issn = {2150-7511},
support = {F32 ES013114/ES/NIEHS NIH HHS/United States ; FES013114-02//PHS HHS/United States ; },
mesh = {Acetates/metabolism ; Carbon/metabolism ; Energy Metabolism ; Esterases/genetics/metabolism ; Genetic Engineering/methods ; Genetic Vectors ; Metabolic Networks and Pathways/*genetics ; Methane/*metabolism ; Methanol/metabolism ; Methanosarcina/*genetics/growth &amp; development/*metabolism ; Plasmids ; Promoter Regions, Genetic ; Propionates/metabolism ; Pseudomonas/*enzymology/*genetics ; },
abstract = {A plasmid-based expression system wherein mekB was fused to a constitutive Methanosarcina acetivorans promoter was used to express MekB, a broad-specificity esterase from Pseudomonas veronii, in M. acetivorans. The engineered strain had 80-fold greater esterase activity than wild-type M. acetivorans. Methyl acetate and methyl propionate esters served as the sole carbon and energy sources, resulting in robust growth and methane formation, with consumption of >97% of the substrates. Methanol was undetectable at the end of growth with methyl acetate, whereas acetate accumulated, a result consistent with methanol as the more favorable substrate. Acetate was consumed, and growth continued after a period of adaptation. Similar results were obtained with methyl propionate, except propionate was not metabolized.},
}
@article {pmid21054448,
year = {2010},
author = {Aponte, M and Blaiotta, G and Francesca, N and Moschetti, G},
title = {Could halophilic archaea improve the traditional salted anchovies (Engraulis encrasicholus L.) safety and quality?.},
journal = {Letters in applied microbiology},
volume = {51},
number = {6},
pages = {697-703},
doi = {10.1111/j.1472-765X.2010.02956.x},
pmid = {21054448},
issn = {1472-765X},
mesh = {Animals ; Bacteria/isolation &amp; purification ; Colony Count, Microbial ; Fishes ; Food Contamination/prevention &amp; control ; *Food Microbiology ; Food Preservation/*methods ; *Halobacteriales ; Histamine/analysis ; Seafood/*microbiology ; Sodium Chloride ; },
abstract = {AIMS: The positive influence of two selected extremely halophilic archaea strains in the production of salted anchovies (Engraulis encrasicolus, L., 1758) was highlighted.<br><br>METHODS AND RESULTS: Anchovies produced with salt artificially contaminated with halophiles exhibited lower loads of staphylococci, Enterobacteriaceae and lactic acid bacteria, and a reduced content of histamine as well as an improved organoleptic acceptance.<br><br>CONCLUSIONS: The findings of this survey are expected to enhance the safety of salted anchovies, with regard to the histamine formation during ripening, and to improve the sensory attributes of this product.<br><br>This study represents the first report on the positive influence of halophilic archaea in traditional salted anchovies production, thus suggesting new perspectives about a conscious employment of properly selected haloarchaea strains in this traditional manufacture.},
}
@article {pmid21051361,
year = {2011},
author = {Rao, BS and Maris, EL and Jackman, JE},
title = {tRNA 5'-end repair activities of tRNAHis guanylyltransferase (Thg1)-like proteins from Bacteria and Archaea.},
journal = {Nucleic acids research},
volume = {39},
number = {5},
pages = {1833-1842},
pmid = {21051361},
issn = {1362-4962},
support = {R01 GM087543/GM/NIGMS NIH HHS/United States ; GM087543/GM/NIGMS NIH HHS/United States ; },
mesh = {Bacillus thuringiensis/*enzymology ; Genetic Complementation Test ; Kinetics ; Methanosarcina/*enzymology ; Nucleotides/metabolism ; Nucleotidyltransferases/genetics/*metabolism ; RNA, Transfer, His/chemistry/*metabolism ; RNA, Transfer, Phe/metabolism ; Yeasts/enzymology/genetics ; },
abstract = {The tRNA(His) guanylyltransferase (Thg1) family comprises a set of unique 3'-5' nucleotide addition enzymes found ubiquitously in Eukaryotes, where they function in the critical G(-1) addition reaction required for tRNA(His) maturation. However, in most Bacteria and Archaea, G(-1) is genomically encoded; thus post-transcriptional addition of G(-1) to tRNA(His) is not necessarily required. The presence of highly conserved Thg1-like proteins (TLPs) in more than 40 bacteria and archaea therefore suggests unappreciated roles for TLP-catalyzed 3'-5' nucleotide addition. Here, we report that TLPs from Bacillus thuringiensis (BtTLP) and Methanosarcina acetivorans (MaTLP) display biochemical properties consistent with a prominent role in tRNA 5'-end repair. Unlike yeast Thg1, BtTLP strongly prefers addition of missing N(+1) nucleotides to 5'-truncated tRNAs over analogous additions to full-length tRNA (k(cat)/K(M) enhanced 5-160-fold). Moreover, unlike for -1 addition, BtTLP-catalyzed additions to truncated tRNAs are not biased toward addition of G, and occur with tRNAs other than tRNA(His). Based on these distinct biochemical properties, we propose that rather than functioning solely in tRNA(His) maturation, bacterial and archaeal TLPs are well-suited to participate in tRNA quality control pathways. These data support more widespread roles for 3'-5' nucleotide addition reactions in biology than previously expected.},
}
@article {pmid21050804,
year = {2010},
author = {Bernander, R and Ettema, TJ},
title = {FtsZ-less cell division in archaea and bacteria.},
journal = {Current opinion in microbiology},
volume = {13},
number = {6},
pages = {747-752},
doi = {10.1016/j.mib.2010.10.005},
pmid = {21050804},
issn = {1879-0364},
mesh = {Archaea/genetics/*physiology ; Bacteria/genetics ; *Bacterial Physiological Phenomena ; Bacterial Proteins/*genetics/*metabolism ; *Cell Division ; Cytoskeletal Proteins/*genetics/*metabolism ; },
abstract = {A dedicated cell division machinery is needed for efficient proliferation of an organism. The eukaryotic actin-myosin based mechanism and the bacterial FtsZ-dependent machinery have both been characterized in detail, and a third division mechanism, the Cdv system, was recently discovered in archaea from the Crenarchaeota phylum. Despite these findings, division mechanisms remain to be identified in, for example, organisms belonging to the bacterial PVC superphylum, bacteria with extremely reduced genomes, wall-less archaea and bacteria, and in archaea that carry out the division process without cell constriction. Cytokinesis mechanisms in these clades and individual taxa are likely to include adaptation of host functions to division of bacterial symbionts, transfer of bacterial division genes into the host genome, vesicle formation without a dedicated constriction machinery, cross-wall formation without invagination, as well as entirely novel division mechanisms.},
}
@article {pmid21050470,
year = {2010},
author = {von Mandach, C and Merkl, R},
title = {Genes optimized by evolution for accurate and fast translation encode in Archaea and Bacteria a broad and characteristic spectrum of protein functions.},
journal = {BMC genomics},
volume = {11},
number = {},
pages = {617},
pmid = {21050470},
issn = {1471-2164},
mesh = {Archaea/*genetics/growth &amp; development/metabolism ; Archaeal Proteins/*genetics ; Bacteria/*genetics/growth &amp; development/metabolism ; Bacterial Proteins/*genetics ; Codon/genetics ; Ecosystem ; *Evolution, Molecular ; Genome, Archaeal/genetics ; Genome, Bacterial/genetics ; Metabolic Networks and Pathways/genetics ; Protein Biosynthesis/*genetics ; RNA, Transfer/genetics ; Species Specificity ; Time Factors ; },
abstract = {BACKGROUND: In many microbial genomes, a strong preference for a small number of codons can be observed in genes whose products are needed by the cell in large quantities. This codon usage bias (CUB) improves translational accuracy and speed and is one of several factors optimizing cell growth. Whereas CUB and the overrepresentation of individual proteins have been studied in detail, it is still unclear which high-level metabolic categories are subject to translational optimization in different habitats.<br><br>RESULTS: In a systematic study of 388 microbial species, we have identified for each genome a specific subset of genes characterized by a marked CUB, which we named the effectome. As expected, gene products related to protein synthesis are abundant in both archaeal and bacterial effectomes. In addition, enzymes contributing to energy production and gene products involved in protein folding and stabilization are overrepresented. The comparison of genomes from eleven habitats shows that the environment has only a minor effect on the composition of the effectomes. As a paradigmatic example, we detailed the effectome content of 37 bacterial genomes that are most likely exposed to strongest selective pressure towards translational optimization. These effectomes accommodate a broad range of protein functions like enzymes related to glycolysis/gluconeogenesis and the TCA cycle, ATP synthases, aminoacyl-tRNA synthetases, chaperones, proteases that degrade misfolded proteins, protectants against oxidative damage, as well as cold shock and outer membrane proteins.<br><br>CONCLUSIONS: We made clear that effectomes consist of specific subsets of the proteome being involved in several cellular functions. As expected, some functions are related to cell growth and affect speed and quality of protein synthesis. Additionally, the effectomes contain enzymes of central metabolic pathways and cellular functions sustaining microbial life under stress situations. These findings indicate that cell growth is an important but not the only factor modulating translational accuracy and speed by means of CUB.},
}
@article {pmid21043129,
year = {2010},
author = {Liu, JJ and Wu, WX and Ding, Y and Shi, DZ and Chen, YX},
title = {[Ammonia-oxidizing archaea and their important roles in nitrogen biogeochemical cycling: a review].},
journal = {Ying yong sheng tai xue bao = The journal of applied ecology},
volume = {21},
number = {8},
pages = {2154-2160},
pmid = {21043129},
issn = {1001-9332},
mesh = {Ammonia/*metabolism ; Archaea/classification/genetics/*metabolism ; Bacteria/classification/genetics/metabolism ; *Ecosystem ; Nitrogen/metabolism ; Nitrogen Cycle/*physiology ; Oxidation-Reduction ; Oxidoreductases/genetics/metabolism ; },
abstract = {As the first step of nitrification, ammonia oxidation is the key process in global nitrogen biogeochemical cycling. So far, the autotrophic ammonia-oxidizing bacteria (AOB) in the beta- and gamma-subgroups of proteobacteria have been considered as the most important contributors to ammonia oxidation, but the recent researches indicated that ammonia-oxidizing archaea (AOA) are widely distributed in various kinds of ecosystems and quantitatively predominant, playing important roles in the global nitrogen biogeochemical cycling. This paper reviewed the morphological, physiological, and ecological characteristics and the molecular phylogenies of AOA, and compared and analyzed the differences and similarities of the ammonia monooxygenase (AMO) and its encoding genes between AOA and AOB. In addition, the potential significant roles of AOA in nitrogen biogeochemical cycling in aquatic and terrestrial ecosystems were summarized, and the future research directions of AOA in applied ecology and environmental protection were put forward.},
}
@article {pmid21039653,
year = {2010},
author = {Gubry-Rangin, C and Nicol, GW and Prosser, JI},
title = {Archaea rather than bacteria control nitrification in two agricultural acidic soils.},
journal = {FEMS microbiology ecology},
volume = {74},
number = {3},
pages = {566-574},
doi = {10.1111/j.1574-6941.2010.00971.x},
pmid = {21039653},
issn = {1574-6941},
mesh = {Acetylene/metabolism ; Agriculture ; Ammonia/metabolism ; Archaea/genetics/growth &amp; development/*metabolism ; Bacteria/genetics/growth &amp; development/*metabolism ; DNA, Complementary/genetics ; Ecosystem ; Genes, Archaeal ; Genes, Bacterial ; Hydrogen-Ion Concentration ; *Nitrification ; Nitrogen Cycle ; Oxidation-Reduction ; Scotland ; Sequence Analysis, DNA ; Soil/analysis ; *Soil Microbiology ; Transcription, Genetic ; },
abstract = {Nitrification is a central component of the global nitrogen cycle. Ammonia oxidation, the first step of nitrification, is performed in terrestrial ecosystems by both ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA). Published studies indicate that soil pH may be a critical factor controlling the relative abundances of AOA and AOB communities. In order to determine the relative contributions of AOA and AOB to ammonia oxidation in two agricultural acidic Scottish soils (pH 4.5 and 6), the influence of acetylene (a nitrification inhibitor) was investigated during incubation of soil microcosms at 20 °C for 1 month. High rates of nitrification were observed in both soils in the absence of acetylene. Quantification of respective amoA genes (a key functional gene for ammonia oxidizers) demonstrated significant growth of AOA, but not AOB. A significant positive relationship was found between nitrification rate and AOA, but not AOB growth. AOA growth was inhibited in the acetylene-containing microcosms. Moreover, AOA transcriptional activity decreased significantly in the acetylene-containing microcosms compared with the control, whereas no difference was observed for the AOB transcriptional activity. Consequently, growth and activity of only archaeal but not bacterial ammonia oxidizer communities strongly suggest that AOA, but not AOB, control nitrification in these two acidic soils.},
}
@article {pmid21034818,
year = {2011},
author = {Fournier, GP and Dick, AA and Williams, D and Gogarten, JP},
title = {Evolution of the Archaea: emerging views on origins and phylogeny.},
journal = {Research in microbiology},
volume = {162},
number = {1},
pages = {92-98},
doi = {10.1016/j.resmic.2010.09.016},
pmid = {21034818},
issn = {1769-7123},
mesh = {Archaea/*genetics ; *Biological Evolution ; Eukaryota/genetics ; *Phylogeny ; Ribosomes/genetics ; },
abstract = {Of the three domains of life, the Archaea are the most recently discovered and, from the perspective of systematics, perhaps the least understood. More than three decades after their discovery, there is still no overwhelming consensus as to their phylogenetic status, with diverse evidence supporting in varying degrees their monophyly, paraphyly, or even polyphyly. As a further complication, their evolutionary history is inextricably linked to the origin of Eukarya, one of the most challenging problems in evolutionary biology. This exclusive relationship between the eukaryal nucleocytoplasm and the Archaea is further supported by a new methodology for rooting the ribosomal Tree of Life based on amino acid composition. Novel approaches such as utilizing horizontal gene transfers as synchronizing events and branch length analysis of deep paralogs will help to clarify temporal relationships between these lineages, and may prove useful in evaluating the numerous conflicting hypotheses related to the evolution of the Archaea and Eukarya.},
}
@article {pmid21034816,
year = {2011},
author = {Matsumi, R and Atomi, H and Driessen, AJ and van der Oost, J},
title = {Isoprenoid biosynthesis in Archaea--biochemical and evolutionary implications.},
journal = {Research in microbiology},
volume = {162},
number = {1},
pages = {39-52},
doi = {10.1016/j.resmic.2010.10.003},
pmid = {21034816},
issn = {1769-7123},
mesh = {Archaea/enzymology/genetics/*metabolism ; Bacteria/metabolism ; Biosynthetic Pathways/genetics ; Eukaryota/metabolism ; Membrane Lipids/metabolism ; Terpenes/*metabolism ; },
abstract = {Isoprenoids are indispensable for all types of cellular life in the Archaea, Bacteria, and Eucarya. These membrane-associated molecules are involved in a wide variety of vital biological functions, ranging from compartmentalization and stability, to protection and energy-transduction. In Archaea, isoprenoid compounds constitute the hydrophobic moiety of the typical ether-linked membrane lipids. With respect to stereochemistry and composition, these archaeal lipids are very different from the ester-linked, fatty acid-based phospholipids in bacterial and eukaryotic membranes. This review provides an update on isoprenoid biosynthesis pathways, with a focus on the archaeal enzymes. The black-and-white distribution of fundamentally distinct membrane lipids in Archaea on the one hand, and Bacteria and Eucarya on the other, has previously been used as a basis for hypothetical evolutionary scenarios, a selection of which will be discussed here.},
}
@article {pmid20976295,
year = {2010},
author = {Jarrell, KF and Jones, GM and Nair, DB},
title = {Biosynthesis and role of N-linked glycosylation in cell surface structures of archaea with a focus on flagella and s layers.},
journal = {International journal of microbiology},
volume = {2010},
number = {},
pages = {470138},
pmid = {20976295},
issn = {1687-9198},
abstract = {The genetics and biochemistry of the N-linked glycosylation system of Archaea have been investigated over the past 5 years using flagellins and S layers as reporter proteins in the model organisms, Methanococcus voltae, Methanococcus maripaludis, and Haloferax volcanii. Structures of archaeal N-linked glycans have indicated a variety of linking sugars as well as unique sugar components. In M. voltae, M. maripaludis, and H. volcanii, a number of archaeal glycosylation genes (agl) have been identified by deletion and complementation studies. These include many of the glycosyltransferases and the oligosaccharyltransferase needed to assemble the glycans as well as some of the genes encoding enzymes required for the biosynthesis of the sugars themselves. The N-linked glycosylation system is not essential for any of M. voltae, M. maripaludis, or H. volcanii, as demonstrated by the successful isolation of mutants carrying deletions in the oligosaccharyltransferase gene aglB (a homologue of the eukaryotic Stt3 subunit of the oligosaccharyltransferase complex). However, mutations that affect the glycan structure have serious effects on both flagellation and S layer function.},
}
@article {pmid20975945,
year = {2010},
author = {Cortez, D and Quevillon-Cheruel, S and Gribaldo, S and Desnoues, N and Sezonov, G and Forterre, P and Serre, MC},
title = {Evidence for a Xer/dif system for chromosome resolution in archaea.},
journal = {PLoS genetics},
volume = {6},
number = {10},
pages = {e1001166},
pmid = {20975945},
issn = {1553-7404},
mesh = {Amino Acid Sequence ; Archaea/enzymology/*genetics ; Archaeal Proteins/*genetics/metabolism ; Binding Sites/genetics ; Chromosomes, Archaeal/*genetics ; Cloning, Molecular ; DNA Nucleotidyltransferases/classification/*genetics/metabolism ; DNA Replication ; DNA, Archaeal/genetics/metabolism ; DNA, Circular/genetics/metabolism ; Electrophoretic Mobility Shift Assay ; Molecular Sequence Data ; Phylogeny ; Plasmids/genetics ; Protein Binding ; Pyrococcus abyssi/enzymology/genetics ; Recombination, Genetic ; Sequence Homology, Amino Acid ; },
abstract = {Homologous recombination events between circular chromosomes, occurring during or after replication, can generate dimers that need to be converted to monomers prior to their segregation at cell division. In Escherichia coli, chromosome dimers are converted to monomers by two paralogous site-specific tyrosine recombinases of the Xer family (XerC/D). The Xer recombinases act at a specific dif site located in the replication termination region, assisted by the cell division protein FtsK. This chromosome resolution system has been predicted in most Bacteria and further characterized for some species. Archaea have circular chromosomes and an active homologous recombination system and should therefore resolve chromosome dimers. Most archaea harbour a single homologue of bacterial XerC/D proteins (XerA), but not of FtsK. Therefore, the role of XerA in chromosome resolution was unclear. Here, we have identified dif-like sites in archaeal genomes by using a combination of modeling and comparative genomics approaches. These sites are systematically located in replication termination regions. We validated our in silico prediction by showing that the XerA protein of Pyrococcus abyssi specifically recombines plasmids containing the predicted dif site in vitro. In contrast to the bacterial system, XerA can recombine dif sites in the absence of protein partners. Whereas Archaea and Bacteria use a completely different set of proteins for chromosome replication, our data strongly suggest that XerA is most likely used for chromosome resolution in Archaea.},
}
@article {pmid20953601,
year = {2011},
author = {Li, M and Cao, H and Hong, Y and Gu, JD},
title = {Spatial distribution and abundances of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in mangrove sediments.},
journal = {Applied microbiology and biotechnology},
volume = {89},
number = {4},
pages = {1243-1254},
pmid = {20953601},
issn = {1432-0614},
mesh = {Ammonia/*metabolism ; Archaea/*classification/*isolation &amp; purification ; Bacteria/*classification/*isolation &amp; purification ; *Biodiversity ; Cluster Analysis ; DNA, Archaeal/chemistry/genetics ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Genes, rRNA ; Hong Kong ; Hydrogen-Ion Concentration ; Molecular Sequence Data ; Oxidation-Reduction ; Phylogeny ; RNA, Archaeal/genetics ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Rhizophoraceae/growth &amp; development ; Salinity ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; Soil/analysis ; *Soil Microbiology ; Wetlands ; },
abstract = {We investigated the diversity, spatial distribution, and abundances of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in sediment samples of different depths collected from a transect with different distances to mangrove forest in the territories of Hong Kong. Both the archaeal and bacterial amoA genes (encoding ammonia monooxygenase subunit A) from all samples supported distinct phylogenetic groups, indicating the presences of niche-specific AOA and AOB in mangrove sediments. The higher AOB abundances than AOA in mangrove sediments, especially in the vicinity of the mangrove trees, might indicate the more important role of AOB on nitrification. The spatial distribution showed that AOA had higher diversity and abundance in the surface layer sediments near the mangrove trees (0 and 10 m) but lower away from the mangrove trees (1,000 m), and communities of AOA could be clustered into surface and bottom sediment layer groups. In contrast, AOB showed a reverse distributed pattern, and its communities were grouped by the distances between sites and mangrove trees, indicating mangrove trees might have different influences on AOA and AOB community structures. Furthermore, the strong correlations among archaeal and bacterial amoA gene abundances and their ratio with NH (4) (+) , salinity, and pH of sediments indicated that these environmental factors have strong influences on AOA and AOB distributions in mangrove sediments. In addition, AOA diversity and abundances were significantly correlated with hzo gene abundances, which encodes the key enzyme for transformation of hydrazine into N(2) in anaerobic ammonium-oxidizing (anammox) bacteria, indicating AOA and anammox bacteria may interact with each other or they are influenced by the same controlling factors, such as NH (4) (+) . The results provide a better understanding on using mangrove wetlands as biological treatment systems for removal of nutrients.},
}
@article {pmid20952548,
year = {2011},
author = {Shimane, Y and Hatada, Y and Minegishi, H and Echigo, A and Nagaoka, S and Miyazaki, M and Ohta, Y and Maruyama, T and Usami, R and Grant, WD and Horikoshi, K},
title = {Salarchaeum japonicum gen. nov., sp. nov., an aerobic, extremely halophilic member of the Archaea isolated from commercial salt.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {61},
number = {Pt 9},
pages = {2266-2270},
doi = {10.1099/ijs.0.025064-0},
pmid = {20952548},
issn = {1466-5034},
mesh = {Aerobiosis ; Base Composition ; Cluster Analysis ; DNA, Archaeal/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; DNA-Directed RNA Polymerases/genetics ; *Food Microbiology ; Genes, rRNA ; Halobacteriaceae/*classification/genetics/*isolation &amp; purification/physiology ; Hydrogen-Ion Concentration ; Japan ; Magnesium/metabolism ; Molecular Sequence Data ; Phospholipids/analysis ; Phylogeny ; RNA, Archaeal/genetics ; RNA, Ribosomal, 16S/genetics ; *Salts ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; Sodium Chloride/metabolism ; Temperature ; },
abstract = {Strain YSM-79(T) was isolated from commercial salt made from seawater in Yonaguni island, Okinawa, Japan. The strain is an aerobic, Gram-negative, chemo-organotrophic and extremely halophilic archaeon. Cells are short rods that lyse in distilled water. Growth occurs at 1.5-5.3 M NaCl (optimum 2.5-3.0 M), pH 5.0-8.8 (optimum pH 5.2-6.3) and 20-55 °C (optimum 40 °C). Mg[2+] is required for growth, with maximum growth at 200-300 mM Mg[2+]. Polar lipid analysis revealed the presence of phosphatidylglycerol, phosphatidylglycerophosphate methyl ester, sulfated diglycosyl diether-1 and five unidentified glycolipids. The G+C content of the DNA was 64 mol%. On the basis of 16S rRNA gene sequence analysis, strain YSM-79(T) was determined to be a member of the family Halobacteriaceae, with the closest related genus being Halobacterium (94 % sequence identity). In addition, the rpoB' gene sequence of strain YSM-79(T) had <88 % sequence similarity to those of other members of the family Halobacteriaceae. The results of phenotypic, chemotaxonomic and phylogenetic analysis suggested that strain YSM-79(T) should be placed in a new genus, Salarchaeum gen. nov., as a representative of Salarchaeum japonicum sp. nov. The type strain is YSM-79(T) (= JCM 16327(T) = CECT 7563(T)).},
}
@article {pmid20942947,
year = {2010},
author = {Zafrilla, B and Martínez-Espinosa, RM and Alonso, MA and Bonete, MJ},
title = {Biodiversity of Archaea and floral of two inland saltern ecosystems in the Alto Vinalopó Valley, Spain.},
journal = {Saline systems},
volume = {6},
number = {},
pages = {10},
pmid = {20942947},
issn = {1746-1448},
abstract = {BACKGROUND: The extraction of salt from seawater by means of coastal solar salterns is a very well-described process. Moreover, the characterization of these environments from ecological, biochemical and microbiological perspectives has become a key focus for many research groups all over the world over the last 20 years. In countries such as Spain, there are several examples of coastal solar salterns (mainly on the Mediterranean coast) and inland solar salterns, from which sodium chloride is obtained for human consumption. However, studies focused on the characterization of inland solar salterns are scarce and both the archaeal diversity and the plant communities inhabiting these environments remain poorly described.<br><br>RESULTS: Two of the inland solar salterns (termed Redonda and Penalva), located in the Alto Vinalop&#xf3; Valley (Alicante, Spain), were characterized regarding their geological and physico-chemical characteristics and their archaeal and botanical biodiversity. A preliminary eukaryotic diversity survey was also performed using saline water. The chemical characterization of the brine has revealed that the salted groundwater extracted to fill these inland solar salterns is thalassohaline. The plant communities living in this environment are dominated by Sarcocornia fruticosa (L.) A.J. Scott, Arthrocnemum macrostachyum (Moris) K. Koch, Suaeda vera Forsk. ex Gmelin (Amaranthaceae) and several species of Limonium (Mill) and Tamarix (L). Archaeal diversity was analyzed and compared by polymerase chain reaction (PCR)-based molecular phylogenetic techniques. Most of the sequences recovered from environmental DNA samples are affiliated with haloarchaeal genera such as Haloarcula, Halorubrum, Haloquadratum and Halobacterium, and with an unclassified member of the Halobacteriaceae. The eukaryote Dunaliella was also present in the samples.<br><br>CONCLUSIONS: To our knowledge, this study constitutes the first analysis centered on inland solar salterns located in the southeastern region of Spain. The results obtained revealed that the salt deposits of this region have marine origins. Plant communities typical of salt marshes are present in this ecosystem and members of the Halobacteriaceae family can be easily detected in the microbial populations of these habitats. Possible origins of the haloarchaea detected in this study are discussed.},
}
@article {pmid20929871,
year = {2011},
author = {Shao, Y and Harrison, EM and Bi, D and Tai, C and He, X and Ou, HY and Rajakumar, K and Deng, Z},
title = {TADB: a web-based resource for Type 2 toxin-antitoxin loci in bacteria and archaea.},
journal = {Nucleic acids research},
volume = {39},
number = {Database issue},
pages = {D606-11},
pmid = {20929871},
issn = {1362-4962},
mesh = {Archaea/genetics ; Archaeal Proteins/*genetics ; Bacteria/genetics ; Bacterial Proteins/*genetics ; Bacterial Toxins/*genetics ; *Databases, Genetic ; Genetic Loci ; Genome, Archaeal ; Genome, Bacterial ; Internet ; Toxins, Biological/genetics ; },
abstract = {TADB (http://bioinfo-mml.sjtu.edu.cn/TADB/) is an integrated database that provides comprehensive information about Type 2 toxin-antitoxin (TA) loci, genetic features that are richly distributed throughout bacterial and archaeal genomes. Two-gene and much less frequently three-gene Type 2 TA loci code for cognate partners that have been hypothesized or demonstrated to play key roles in stress response, bacterial physiology and stabilization of horizontally acquired genetic elements. TADB offers a unique compilation of both predicted and experimentally supported Type 2 TA loci-relevant data and currently contains 10,753 Type 2 TA gene pairs identified within 1240 prokaryotic genomes, and details of over 240 directly relevant scientific publications. A broad range of similarity search, sequence alignment, genome context browser and phylogenetic tools are readily accessible via TADB. We propose that TADB will facilitate efficient, multi-disciplinary and innovative exploration of the bacteria and archaea Type 2 TA space, better defining presently recognized TA-related phenomena and potentially even leading to yet-to-be envisaged frontiers. The TADB database, envisaged as a one-stop shop for Type 2 TA-related research, will be maintained, updated and improved regularly to ensure its ongoing maximum utility to the research community.},
}
@article {pmid20889792,
year = {2010},
author = {Taylor, AE and Zeglin, LH and Dooley, S and Myrold, DD and Bottomley, PJ},
title = {Evidence for different contributions of archaea and bacteria to the ammonia-oxidizing potential of diverse Oregon soils.},
journal = {Applied and environmental microbiology},
volume = {76},
number = {23},
pages = {7691-7698},
pmid = {20889792},
issn = {1098-5336},
mesh = {Ammonia/*metabolism ; Archaea/*metabolism ; Bacteria/*metabolism ; Nitrification ; Oregon ; Oxidation-Reduction ; *Soil Microbiology ; },
abstract = {A method was developed to determine the contributions of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) to the nitrification potentials (NPs) of soils taken from forest, pasture, cropped, and fallowed (19 years) lands. Soil slurries were exposed to acetylene to irreversibly inactivate ammonia monooxygenase, and upon the removal of acetylene, the recovery of nitrification potential (RNP) was monitored in the presence and absence of bacterial or eukaryotic protein synthesis inhibitors. For unknown reasons, and despite measureable NPs, RNP did not occur consistently in forest soil samples; however, pasture, cropped, and fallowed soil RNPs commenced after lags that ranged from 12 to 30 h after acetylene removal. Cropped soil RNP was completely prevented by the bacterial protein synthesis inhibitor kanamycin (800 μg/ml), whereas a combination of kanamycin plus gentamicin (800 μg/ml each) only partially prevented the RNP (60%) of fallowed soils. Pasture soil RNP was completely insensitive to either kanamycin, gentamicin, or a combination of the two. Unlike cropped soil, pasture and fallowed soil RNPs occurred at both 30°C and 40°C and without supplemental NH(4)(+) (≤ 10 μM NH(4)(+) in solution), and pasture soil RNP demonstrated ∼ 50% insensitivity to 100 μM allyl thiourea (ATU). In addition, fallowed and pasture soil RNPs were insensitive to the fungal inhibitors nystatin and azoxystrobin. This combination of properties suggests that neither fungi nor AOB contributed to pasture soil RNP and that AOA were responsible for the RNP of the pasture soils. Both AOA and AOB may contribute to RNP in fallowed soil, while RNP in cropped soils was dominated by AOB.},
}
@article {pmid20889776,
year = {2010},
author = {Han, J and Hou, J and Liu, H and Cai, S and Feng, B and Zhou, J and Xiang, H},
title = {Wide distribution among halophilic archaea of a novel polyhydroxyalkanoate synthase subtype with homology to bacterial type III synthases.},
journal = {Applied and environmental microbiology},
volume = {76},
number = {23},
pages = {7811-7819},
pmid = {20889776},
issn = {1098-5336},
mesh = {Acyltransferases/*genetics/*metabolism ; Blotting, Western ; Cluster Analysis ; DNA, Archaeal/chemistry/genetics ; Fermentation ; Haloarcula marismortui/enzymology/immunology ; Halobacteriaceae/*enzymology/*genetics ; Hydroxybutyrates/metabolism ; Molecular Sequence Data ; Phylogeny ; Polyesters/metabolism ; Sequence Analysis, DNA ; Sequence Homology ; },
abstract = {Polyhydroxyalkanoates (PHAs) are accumulated as intracellular carbon and energy storage polymers by various bacteria and a few haloarchaea. In this study, 28 strains belonging to 15 genera in the family Halobacteriaceae were investigated with respect to their ability to synthesize PHAs and the types of their PHA synthases. Fermentation results showed that 18 strains from 12 genera could synthesize polyhydroxybutyrate (PHB) or poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV). For most of these haloarchaea, selected regions of the phaE and phaC genes encoding PHA synthases (type III) were cloned via PCR with consensus-degenerate hybrid oligonucleotide primers (CODEHOPs) and were sequenced. The PHA synthases were also examined by Western blotting using haloarchaeal Haloarcula marismortui PhaC (PhaC(Hm)) antisera. Phylogenetic analysis showed that the type III PHA synthases from species of the Halobacteriaceae and the Bacteria domain clustered separately. Comparison of their amino acid sequences revealed that haloarchaeal PHA synthases differed greatly in both molecular weight and certain conserved motifs. The longer C terminus of haloarchaeal PhaC was found to be indispensable for its enzymatic activity, and two additional amino acid residues (C143 and C190) of PhaC(Hm) were proved to be important for its in vivo function. Thus, we conclude that a novel subtype (IIIA) of type III PHA synthase with unique features that distinguish it from the bacterial subtype (IIIB) is widely distributed in haloarchaea and appears to be involved in PHA biosynthesis.},
}
@article {pmid20886337,
year = {2010},
author = {Wang, P and Li, T and Hu, A and Wei, Y and Guo, W and Jiao, N and Zhang, C},
title = {Community structure of archaea from deep-sea sediments of the South China Sea.},
journal = {Microbial ecology},
volume = {60},
number = {4},
pages = {796-806},
pmid = {20886337},
issn = {1432-184X},
mesh = {Archaea/*classification/genetics/*isolation &amp; purification ; Biodiversity ; China ; DNA, Archaeal/genetics ; Geologic Sediments/*microbiology ; Molecular Sequence Data ; Oceans and Seas ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; },
abstract = {Using the archaeal 16S rRNA gene, we determined the community structures of archaea of subseafloor sediments (∼9-11 m below seafloor) from two geographically distant cores (MD05-2896, south, water depth 1,657 m; MD05-2902, north, water depth 3,697 m) in the South China Sea. Euryarchaeota accounted for 61.4% of total archaeal clone libraries at MD05-2896 and 56.2% at MD05-2902. At both locations, the Euryarchaeota-related sequences were dominated by Marine Benthic Group D, Terrestrial Miscellaneous Eryarchaeotal Group, and South African GoldMine Euryarchaeotal Group; the Crenarchaeota-related sequences were dominated by Marine Benthic Group B, Marine Group I, pSL12, and C3. The community structure showed no significant difference with depth at each location, suggesting the lack of stratification of archaeal populations in the deep-sea marine sediments in the South China Sea. On the other hand, the community structure is significantly different between the two sites, which may be related to geographical difference in the South China Sea.},
}
@article {pmid20885971,
year = {2010},
author = {Soppa, J},
title = {Protein acetylation in archaea, bacteria, and eukaryotes.},
journal = {Archaea (Vancouver, B.C.)},
volume = {2010},
number = {},
pages = {},
pmid = {20885971},
issn = {1472-3654},
mesh = {Acetylation ; Acetyltransferases/genetics/*metabolism ; Archaea/genetics/*metabolism ; Archaeal Proteins/genetics/metabolism ; Escherichia coli/genetics/*metabolism ; Eukaryota/*metabolism/ultrastructure ; *Protein Processing, Post-Translational ; },
abstract = {Proteins can be acetylated at the alpha-amino group of the N-terminal amino acid (methionine or the penultimate amino acid after methionine removal) or at the epsilon-amino group of internal lysines. In eukaryotes the majority of proteins are N-terminally acetylated, while this is extremely rare in bacteria. A variety of studies about N-terminal acetylation in archaea have been reported recently, and it was revealed that a considerable fraction of proteins is N-terminally acetylated in haloarchaea and Sulfolobus, while this does not seem to apply for methanogenic archaea. Many eukaryotic proteins are modified by differential internal acetylation, which is important for a variety of processes. Until very recently, only two bacterial proteins were known to be acetylation targets, but now 125 acetylation sites are known for E. coli. Knowledge about internal acetylation in archaea is extremely limited; only two target proteins are known, only one of which--Alba--was used to study differential acetylation. However, indications accumulate that the degree of internal acetylation of archaeal proteins might be underestimated, and differential acetylation has been shown to be essential for the viability of haloarchaea. Focused proteomic approaches are needed to get an overview of the extent of internal protein acetylation in archaea.},
}
@article {pmid20885930,
year = {2010},
author = {Iwasaki, T},
title = {Iron-sulfur world in aerobic and hyperthermoacidophilic archaea Sulfolobus.},
journal = {Archaea (Vancouver, B.C.)},
volume = {2010},
number = {},
pages = {},
pmid = {20885930},
issn = {1472-3654},
mesh = {Aerobiosis ; Archaeal Proteins/*metabolism ; Biosynthetic Pathways ; Ferredoxins/metabolism ; Iron/chemistry ; Iron-Sulfur Proteins/*metabolism ; Models, Molecular ; Sulfolobus/*metabolism ; Sulfur/chemistry ; },
abstract = {The general importance of the Fe-S cluster prosthetic groups in biology is primarily attributable to specific features of iron and sulfur chemistry, and the assembly and interplay of the Fe-S cluster core with the surrounding protein is the key to in-depth understanding of the underlying mechanisms. In the aerobic and thermoacidophilic archaea, zinc-containing ferredoxin is abundant in the cytoplasm, functioning as a key electron carrier, and many Fe-S enzymes are produced to participate in the central metabolic and energetic pathways. De novo formation of intracellular Fe-S clusters does not occur spontaneously but most likely requires the operation of a SufBCD complex of the SUF machinery, which is the only Fe-S cluster biosynthesis system conserved in these archaea. In this paper, a brief introduction to the buildup and maintenance of the intracellular Fe-S world in aerobic and hyperthermoacidophilic crenarchaeotes, mainly Sulfolobus, is given in the biochemical, genetic, and evolutionary context.},
}
@article {pmid20880885,
year = {2011},
author = {Kelly, S and Wickstead, B and Gull, K},
title = {Archaeal phylogenomics provides evidence in support of a methanogenic origin of the Archaea and a thaumarchaeal origin for the eukaryotes.},
journal = {Proceedings. Biological sciences},
volume = {278},
number = {1708},
pages = {1009-1018},
pmid = {20880885},
issn = {1471-2954},
support = {/WT_/Wellcome Trust/United Kingdom ; /BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Amino Acid Sequence ; Archaea/*classification/genetics ; Artificial Intelligence ; Bacteria/*classification/genetics ; Base Sequence ; Bayes Theorem ; Classification/*methods ; Eukaryota/*classification/genetics ; Evolution, Molecular ; *Genome, Archaeal ; Likelihood Functions ; Markov Chains ; Phylogeny ; },
abstract = {We have developed a machine-learning approach to identify 3537 discrete orthologue protein sequence groups distributed across all available archaeal genomes. We show that treating these orthologue groups as binary detection/non-detection data is sufficient to capture the majority of archaeal phylogeny. We subsequently use the sequence data from these groups to infer a method and substitution-model-independent phylogeny. By holding this phylogeny constrained and interrogating the intersection of this large dataset with both the Eukarya and the Bacteria using Bayesian and maximum-likelihood approaches, we propose and provide evidence for a methanogenic origin of the Archaea. By the same criteria, we also provide evidence in support of an origin for Eukarya either within or as sisters to the Thaumarchaea.},
}
@article {pmid20870784,
year = {2010},
author = {Park, BJ and Park, SJ and Yoon, DN and Schouten, S and Sinninghe Damsté, JS and Rhee, SK},
title = {Cultivation of autotrophic ammonia-oxidizing archaea from marine sediments in coculture with sulfur-oxidizing bacteria.},
journal = {Applied and environmental microbiology},
volume = {76},
number = {22},
pages = {7575-7587},
pmid = {20870784},
issn = {1098-5336},
mesh = {Ammonia/*metabolism ; Archaea/classification/*growth &amp; development/isolation &amp; purification/metabolism ; Bacteria/classification/*growth &amp; development/isolation &amp; purification/metabolism ; Cluster Analysis ; Coculture Techniques ; DNA, Archaeal/chemistry/genetics ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; Genes, rRNA ; Geologic Sediments/*microbiology ; Molecular Sequence Data ; Oxidation-Reduction ; Phylogeny ; RNA, Archaeal/genetics ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; Sulfur/*metabolism ; },
abstract = {The role of ammonia-oxidizing archaea (AOA) in nitrogen cycling in marine sediments remains poorly characterized. In this study, we enriched and characterized AOA from marine sediments. Group I.1a crenarchaea closely related to those identified in marine sediments and "Candidatus Nitrosopumilus maritimus" (99.1 and 94.9% 16S rRNA and amoA gene sequence identities to the latter, respectively) were substantially enriched by coculture with sulfur-oxidizing bacteria (SOB). The selective enrichment of AOA over ammonia-oxidizing bacteria (AOB) is likely due to the reduced oxygen levels caused by the rapid initial growth of SOB. After biweekly transfers for ca. 20 months, archaeal cells became the dominant prokaryotes (>80%), based on quantitative PCR and fluorescence in situ hybridization analysis. The increase of archaeal 16S rRNA gene copy numbers was coincident with the amount of ammonia oxidized, and expression of the archaeal amoA gene was observed during ammonia oxidation. Bacterial amoA genes were not detected in the enrichment culture. The affinities of these AOA to oxygen and ammonia were substantially higher than those of AOB. [(13)C]bicarbonate incorporation and the presence and activation of genes of the 3-hydroxypropionate/4-hydroxybutyrate cycle indicated autotrophy during ammonia oxidation. In the enrichment culture, ammonium was oxidized to nitrite by the AOA and subsequently to nitrate by Nitrospina-like bacteria. Our experiments suggest that AOA may be important nitrifiers in low-oxygen environments, such as oxygen-minimum zones and marine sediments.},
}
@article {pmid20869518,
year = {2010},
author = {Rachel, R and Meyer, C and Klingl, A and Gürster, S and Heimerl, T and Wasserburger, N and Burghardt, T and Küper, U and Bellack, A and Schopf, S and Wirth, R and Huber, H and Wanner, G},
title = {Analysis of the ultrastructure of archaea by electron microscopy.},
journal = {Methods in cell biology},
volume = {96},
number = {},
pages = {47-69},
doi = {10.1016/S0091-679X(10)96003-2},
pmid = {20869518},
issn = {0091-679X},
mesh = {Archaea/physiology/*ultrastructure ; Cell Culture Techniques ; Freeze Etching/methods ; Freeze Substitution/methods ; Microscopy, Electron/instrumentation/*methods ; Negative Staining/methods ; },
abstract = {The ultrastructural characterization of archaeal cells is done with both types of electron microscopy, transmission electron microscopy, and scanning electron microscopy. Depending on the scientific question, different preparation methods have to be employed and need to be optimized, according to the special cultivation conditions of these-in many cases extreme-microorganisms. Recent results using various electron microscopy techniques show that archaeal cells have a variety of cell appendages, used for motility as well as for establishing cell-cell and cell-surface contacts. Cryo-preparation methods, in particular high-pressure freezing and freeze-substitution, are crucial for obtaining results: (1) showing the cells in ultrathin sections in a good structural preservation, often with unusual shapes and subcellular complexity, and (2) enabling us to perform immunolocalization studies. This is an important tool to make a link between biochemical and ultrastructural studies.},
}
@article {pmid20869216,
year = {2011},
author = {Liu, Z and Huang, S and Sun, G and Xu, Z and Xu, M},
title = {Diversity and abundance of ammonia-oxidizing archaea in the Dongjiang River, China.},
journal = {Microbiological research},
volume = {166},
number = {5},
pages = {337-345},
doi = {10.1016/j.micres.2010.08.002},
pmid = {20869216},
issn = {1618-0623},
mesh = {Ammonia/*metabolism ; Archaea/*classification/genetics/isolation &amp; purification/*metabolism ; Bacteria/classification/genetics/isolation &amp; purification/metabolism ; *Biodiversity ; China ; Cluster Analysis ; DNA, Archaeal/chemistry/genetics ; DNA, Bacterial/genetics ; Fresh Water/*microbiology ; Molecular Sequence Data ; Oxidation-Reduction ; Oxidoreductases/genetics ; Phylogeny ; Polymerase Chain Reaction ; Rivers ; Sequence Analysis, DNA ; },
abstract = {Nitrification in aquatic ecosystems plays a crucial role in the global nitrogen cycling. It has been widely accepted that ammonia-oxidizing bacteria (AOB) are responsible for nitrification. However, this concept is currently challenged by the ubiquity of ammonia-oxidizing archaea (AOA) in various environments, such as in aquatic and terrestrial ecosystems. In this study, the presence of AOA in the Dongjiang River was documented via archaeal amoA amplification; the abundance of archaeal and bacterial amoA genes were estimated by quantitative polymerase chain reaction (qPCR), and the diversity was investigated by sequencing of archaeal amoA gene. Based on retrieved sequences and phylogenetic analysis, the majority of sequences obtained were different from Crenarchaeota phylum of marine and soil, affiliated with Freshwater Cluster 1 crenarchaeota. The results showed that the AOA detected fell into clusters which are specifically associated with freshwater habitats, and AOA was more abundance than AOB by around 2-4 orders of magnitude. Furthermore, it was found that AOA was more prefer to aerobic and relative low-ammonia concentrations in fresh water. Our finding provides a vital supplement to the distribution of AOA in global pattern, and offers implications for further understanding of the potential role of ammonia oxidizers in river ecosystems.},
}
@article {pmid20847933,
year = {2010},
author = {Rother, M and Krzycki, JA},
title = {Selenocysteine, pyrrolysine, and the unique energy metabolism of methanogenic archaea.},
journal = {Archaea (Vancouver, B.C.)},
volume = {2010},
number = {},
pages = {},
pmid = {20847933},
issn = {1472-3654},
support = {R01 GM070663/GM/NIGMS NIH HHS/United States ; GM070663/GM/NIGMS NIH HHS/United States ; },
mesh = {Archaeal Proteins/*genetics/metabolism ; Codon, Terminator/metabolism ; Energy Metabolism/*genetics ; Euryarchaeota/genetics/*metabolism ; Lysine/*analogs &amp; derivatives/metabolism ; Methane/metabolism ; Phylogeny ; Selenocysteine/*metabolism ; },
abstract = {Methanogenic archaea are a group of strictly anaerobic microorganisms characterized by their strict dependence on the process of methanogenesis for energy conservation. Among the archaea, they are also the only known group synthesizing proteins containing selenocysteine or pyrrolysine. All but one of the known archaeal pyrrolysine-containing and all but two of the confirmed archaeal selenocysteine-containing protein are involved in methanogenesis. Synthesis of these proteins proceeds through suppression of translational stop codons but otherwise the two systems are fundamentally different. This paper highlights these differences and summarizes the recent developments in selenocysteine- and pyrrolysine-related research on archaea and aims to put this knowledge into the context of their unique energy metabolism.},
}
@article {pmid20844558,
year = {2010},
author = {Gribaldo, S and Poole, AM and Daubin, V and Forterre, P and Brochier-Armanet, C},
title = {The origin of eukaryotes and their relationship with the Archaea: are we at a phylogenomic impasse?.},
journal = {Nature reviews. Microbiology},
volume = {8},
number = {10},
pages = {743-752},
pmid = {20844558},
issn = {1740-1534},
mesh = {Archaea/*classification/*genetics ; Bacteria/classification/genetics ; *Biological Evolution ; Classification/methods ; Eukaryota/*classification/*genetics ; Genome/*genetics ; },
abstract = {The origin of eukaryotes and their evolutionary relationship with the Archaea is a major biological question and the subject of intense debate. In the context of the classical view of the universal tree of life, the Archaea and the Eukarya have a common ancestor, the nature of which remains undetermined. Alternative views propose instead that the Eukarya evolved directly from a bona fide archaeal lineage. Several recent large-scale phylogenomic studies using an array of approaches are divided in supporting either one or the other scenario, despite analysing largely overlapping data sets of universal genes. We examine the reasons for such a lack of consensus and consider how alternative approaches may enable progress in answering this fascinating and as-yet-unresolved question.},
}
@article {pmid20818414,
year = {2010},
author = {Makarova, KS and Yutin, N and Bell, SD and Koonin, EV},
title = {Evolution of diverse cell division and vesicle formation systems in Archaea.},
journal = {Nature reviews. Microbiology},
volume = {8},
number = {10},
pages = {731-741},
pmid = {20818414},
issn = {1740-1534},
support = {ZIA LM000073/ImNIH/Intramural NIH HHS/United States ; ZIA LM000073-16/ImNIH/Intramural NIH HHS/United States ; },
mesh = {Archaea/*classification/cytology/genetics/*physiology ; Archaeal Proteins/genetics/metabolism ; Bacteria/cytology/genetics/metabolism ; *Biological Evolution ; Cell Division/genetics/physiology ; Cell Membrane/metabolism ; Cytoplasmic Vesicles/genetics/*physiology ; Endosomal Sorting Complexes Required for Transport/genetics/metabolism ; Eukaryota/cytology/genetics/metabolism ; Genome, Archaeal/genetics ; },
abstract = {Recently a novel cell division system comprised of homologues of eukaryotic ESCRT-III (endosomal sorting complex required for transport III) proteins was discovered in the hyperthermophilic crenarchaeote Sulfolobus acidocaldarius. On the basis of this discovery, we undertook a comparative genomic analysis of the machineries for cell division and vesicle formation in Archaea. Archaea possess at least three distinct membrane remodelling systems: the FtsZ-based bacterial-type system, the ESCRT-III-based eukaryote-like system and a putative novel system that uses an archaeal actin-related protein. Many archaeal genomes encode assortments of components from different systems. Evolutionary reconstruction from these findings suggests that the last common ancestor of the extant Archaea possessed a complex membrane remodelling apparatus, different components of which were lost during subsequent evolution of archaeal lineages. By contrast, eukaryotes seem to have inherited all three ancestral systems.},
}
@article {pmid20816382,
year = {2010},
author = {Li, Y and Liu, X and Huang, L and Guo, H and Wang, XJ},
title = {Potential coexistence of both bacterial and eukaryotic small RNA biogenesis and functional related protein homologs in Archaea.},
journal = {Journal of genetics and genomics = Yi chuan xue bao},
volume = {37},
number = {8},
pages = {493-503},
doi = {10.1016/S1673-8527(09)60069-2},
pmid = {20816382},
issn = {1673-8527},
mesh = {Archaeal Proteins/*chemistry/genetics/metabolism ; Conserved Sequence ; Eukaryota/*metabolism ; Evolution, Molecular ; Genomics ; Phylogeny ; Protein Structure, Tertiary ; RNA Helicases/chemistry/genetics/metabolism ; RNA Interference ; RNA, Bacterial/*biosynthesis/*genetics ; RNA, Untranslated/*biosynthesis/*genetics ; Ribonuclease H/chemistry/genetics/metabolism ; Ribonuclease III/chemistry/genetics/metabolism ; *Sequence Homology, Amino Acid ; Species Specificity ; },
abstract = {RNA silencing plays crucial roles in both bacteria and eukaryotes, yet its machinery appears to differ in these two kingdoms. A couple of Argonaute protein homologs have been reported in some archaeal species in recent years. As Argonaute protein is the key component of eukaryotic RNA silencing pathways, such findings suggested the possibility of existence of eukaryotic RNA silencing like pathways in Archaea, which present the life forms between prokaryotes and eukaryotes. To further explore such hypothesis, we systematically screened 71 fully sequenced archaeal genomes, and identified some proteins containing homologous regions to the functional domains of eukaryotic RNA silencing pathway key proteins. The phylogenetic relationships of these proteins were analyzed. The conserved functional amino acids between archaeal and eukaryotic Piwi domains suggested their functional similarity. Our results provide new clues to the evolution of RNA silencing pathways.},
}
@article {pmid20736170,
year = {2010},
author = {Nunn, CE and Johnsen, U and Schönheit, P and Fuhrer, T and Sauer, U and Hough, DW and Danson, MJ},
title = {Metabolism of pentose sugars in the hyperthermophilic archaea Sulfolobus solfataricus and Sulfolobus acidocaldarius.},
journal = {The Journal of biological chemistry},
volume = {285},
number = {44},
pages = {33701-33709},
pmid = {20736170},
issn = {1083-351X},
support = {BB/E020704/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Acetyl Coenzyme A/chemistry ; Alcohol Oxidoreductases/chemistry ; Archaea/metabolism ; Carbohydrates/*chemistry ; Citric Acid Cycle ; Gene Expression Regulation, Archaeal ; Hydro-Lyases/chemistry ; Isocitrate Lyase/chemistry ; Malate Synthase/chemistry ; Models, Biological ; Oxygen/chemistry ; Phosphorylation ; Recombinant Proteins/chemistry ; Sulfolobus acidocaldarius/*metabolism ; Sulfolobus solfataricus/*metabolism ; },
abstract = {We have previously shown that the hyperthermophilic archaeon, Sulfolobus solfataricus, catabolizes d-glucose and d-galactose to pyruvate and glyceraldehyde via a non-phosphorylative version of the Entner-Doudoroff pathway. At each step, one enzyme is active with both C6 epimers, leading to a metabolically promiscuous pathway. On further investigation, the catalytic promiscuity of the first enzyme in this pathway, glucose dehydrogenase, has been shown to extend to the C5 sugars, D-xylose and L-arabinose. In the current paper we establish that this promiscuity for C6 and C5 metabolites is also exhibited by the third enzyme in the pathway, 2-keto-3-deoxygluconate aldolase, but that the second step requires a specific C5-dehydratase, the gluconate dehydratase being active only with C6 metabolites. The products of this pathway for the catabolism of D-xylose and L-arabinose are pyruvate and glycolaldehyde, pyruvate entering the citric acid cycle after oxidative decarboxylation to acetyl-coenzyme A. We have identified and characterized the enzymes, both native and recombinant, that catalyze the conversion of glycolaldehyde to glycolate and then to glyoxylate, which can enter the citric acid cycle via the action of malate synthase. Evidence is also presented that similar enzymes for this pentose sugar pathway are present in Sulfolobus acidocaldarius, and metabolic tracer studies in this archaeon demonstrate its in vivo operation in parallel with a route involving no aldol cleavage of the 2-keto-3-deoxy-pentanoates but direct conversion to the citric acid cycle C5-metabolite, 2-oxoglutarate.},
}
@article {pmid20703318,
year = {2011},
author = {Moissl-Eichinger, C},
title = {Archaea in artificial environments: their presence in global spacecraft clean rooms and impact on planetary protection.},
journal = {The ISME journal},
volume = {5},
number = {2},
pages = {209-219},
pmid = {20703318},
issn = {1751-7370},
mesh = {Archaea/classification/genetics/isolation &amp; purification/*physiology ; Biodiversity ; Crenarchaeota/classification/genetics/isolation &amp; purification/physiology ; *Environment, Controlled ; *Environmental Microbiology ; Europe ; Genes, Archaeal/genetics ; In Situ Hybridization, Fluorescence ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; South America ; Spacecraft ; },
abstract = {The presence and role of Archaea in artificial, human-controlled environments is still unclear. The search for Archaea has been focused on natural biotopes where they have been found in overwhelming numbers, and with amazing properties. However, they are considered as one of the major group of microorganisms that might be able to survive a space flight, or even to thrive on other planets. Although still concentrating on aerobic, bacterial spores as a proxy for spacecraft cleanliness, space agencies are beginning to consider Archaea as a possible contamination source that could affect future searches for life on other planets. This study reports on the discovery of archaeal 16S rRNA gene signatures not only in US American spacecraft assembly clean rooms but also in facilities in Europe and South America. Molecular methods revealed the presence of Crenarchaeota in all clean rooms sampled, while signatures derived from methanogens and a halophile appeared only sporadically. Although no Archaeon was successfully enriched in our multiassay cultivation approach thus far, samples from a European clean room revealed positive archaeal fluorescence in situ hybridization (FISH) signals of rod-shaped microorganisms, representing the first visualization of Archaea in clean room environments. The molecular and visual detection of Archaea was supported by the first quantitative PCR studies of clean rooms, estimating the overall quantity of Archaea therein. The significant presence of Archaea in these extreme environments in distinct geographical locations suggests a larger role for these microorganisms not only in natural biotopes, but also in human controlled and rigorously cleaned environments.},
}
@article {pmid20697707,
year = {2010},
author = {Cárdenas, JP and Valdés, J and Quatrini, R and Duarte, F and Holmes, DS},
title = {Lessons from the genomes of extremely acidophilic bacteria and archaea with special emphasis on bioleaching microorganisms.},
journal = {Applied microbiology and biotechnology},
volume = {88},
number = {3},
pages = {605-620},
doi = {10.1007/s00253-010-2795-9},
pmid = {20697707},
issn = {1432-0614},
mesh = {Archaea/*classification/*genetics/metabolism ; Bacteria/classification/*genetics ; Chromosome Mapping/methods ; Computational Biology/methods ; DNA, Bacterial/economics/genetics/isolation &amp; purification ; Energy Metabolism/genetics ; *Genome, Bacterial ; Sequence Analysis, DNA/instrumentation/methods ; Viruses/classification/*genetics ; },
abstract = {This mini-review describes the current status of recent genome sequencing projects of extremely acidophilic microorganisms and highlights the most current scientific advances emerging from their analysis. There are now at least 56 draft or completely sequenced genomes of acidophiles including 30 bacteria and 26 archaea. There are also complete sequences for 38 plasmids, 29 viruses, and additional DNA sequence information of acidic environments is available from eight metagenomic projects. A special focus is provided on the genomics of acidophiles from industrial bioleaching operations. It is shown how this initial information provides a rich intellectual resource for microbiologists that has potential to open innovative and efficient research avenues. Examples presented illustrate the use of genomic information to construct preliminary models of metabolism of individual microorganisms. Most importantly, access to multiple genomes allows the prediction of metabolic and genetic interactions between members of the bioleaching microbial community (ecophysiology) and the investigation of major evolutionary trends that shape genome architecture and evolution. Despite these promising beginnings, a major conclusion is that the genome projects help focus attention on the tremendous effort still required to understand the biological principles that support life in extremely acidic environments, including those that might allow engineers to take appropriate action designed to improve the efficiency and rate of bioleaching and to protect the environment.},
}
@article {pmid20687344,
year = {2010},
author = {Dong, L and Li, B and Yuan, H and Scow, KM},
title = {[Effect of lignite humic acid on soil ammonia oxidizing archaea community].},
journal = {Wei sheng wu xue bao = Acta microbiologica Sinica},
volume = {50},
number = {6},
pages = {780-787},
pmid = {20687344},
issn = {0001-6209},
mesh = {Ammonia/*metabolism ; Archaea/genetics/growth &amp; development/isolation &amp; purification/*metabolism ; Humic Substances/*analysis ; Soil/*analysis ; *Soil Microbiology ; Urea/metabolism ; },
abstract = {OBJECTIVE: To illuminate the impact of humic acid (HA) on soil ammonia oxidizing archaea and then reveal the effect of HA on soil nitrogen cycle.<br><br>METHODS: Two humic acids (cHA and bHA) were added into the soil amended with urea. Community changes of ammonia oxidizing archaea (AOA) and total archaea were studied with terminal restricted fragment length polymorphism (T-RFLP) and real time PCR in the microcosm experiment.<br><br>RESULTS: We found that the AOA population size increased significantly and AOA community changed greatly in the urea only treatment. However, HA could inhibit the increase of AOA population, moreover, HA could buffer the change in AOA community showed by canonical correspondence analysis (CCA) result. On the other hand, the total archaeal population decreased significantly in the urea only treatment, but stabilized in the urea with HA treatments, which indicated HA could eliminate the toxicity of urea to total archaea. CCA results showed that incubation time was the most important factor for the total archaeal community, and partial CCA (pCCA, when time as a covariable) result demonstrated that cHA was the most important environmental variable for total archaeal community.<br><br>CONCLUSION: These results showed that HA diminished ammonia loss by inhibiting the increase of AOA competing with plant for ammonia, thus HA can increase the urea efficiency.},
}
@article {pmid20673944,
year = {2010},
author = {Kasuga, I and Nakagaki, H and Kurisu, F and Furumai, H},
title = {Predominance of ammonia-oxidizing archaea on granular activated carbon used in a full-scale advanced drinking water treatment plant.},
journal = {Water research},
volume = {44},
number = {17},
pages = {5039-5049},
doi = {10.1016/j.watres.2010.07.015},
pmid = {20673944},
issn = {1879-2448},
mesh = {Ammonia/*metabolism ; Archaea/genetics/*metabolism ; Bacteria/genetics/metabolism ; Charcoal/*metabolism ; Genetic Variation ; Halogenation ; Molecular Sequence Data ; Nitrates/metabolism ; Oxidation-Reduction ; Phylogeny ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Time Factors ; Waste Disposal, Fluid ; Water Purification/*methods ; Water Supply/*analysis ; },
abstract = {Ozonation followed by granular activated carbon (GAC) is one of the advanced drinking water treatments. During GAC treatment, ammonia can be oxidized by ammonia-oxidizing microorganisms associated with GAC. However, there is little information on the abundance and diversity of ammonia-oxidizing microorganisms on GAC. In this study, the nitrification activity of GAC and the settlement of ammonia-oxidizing archaea (AOA) and bacteria (AOB) in GAC were monitored at a new full-scale advanced drinking water treatment plant in Japan for 1 year after plant start-up. Prechlorination was implemented at the receiving well for the first 10 months of operation to treat ammonia in raw water. During this prechlorination period, levels of both AOA and AOB associated with GAC were below the quantification limit. After prechlorination was stopped, 10(5) copies g-dry(-1) of AOA amoA genes were detected within 3 weeks and the quantities ultimately reached 10(6)-10(7) copies g-dry(-1), while levels of AOB amoA genes still remained below the quantification limit. This observation indicates that AOA can settle in GAC rapidly without prechlorination. The nitrification activity of GAC increased concurrently with the settlement of AOA after prechlorination was stopped. Estimation of in situ cell-specific ammonia-oxidation activity for AOA on the assumption that only AOA and AOB determined can contribute to nitrification suggests that AOA may account for most of the ammonia-oxidation. However, further validation on AOB contribution is required.},
}
@article {pmid20672053,
year = {2010},
author = {Zwieb, C and Bhuiyan, S},
title = {Archaea signal recognition particle shows the way.},
journal = {Archaea (Vancouver, B.C.)},
volume = {2010},
number = {},
pages = {485051},
pmid = {20672053},
issn = {1472-3654},
mesh = {Archaea/*enzymology ; Archaeal Proteins/chemistry/*genetics/*metabolism ; Base Sequence ; Models, Biological ; Molecular Sequence Data ; Nucleic Acid Conformation ; Protein Binding ; Protein Structure, Tertiary ; RNA, Archaeal/chemistry/*genetics/*metabolism ; RNA, Small Cytoplasmic/chemistry/genetics ; Signal Recognition Particle/chemistry/*genetics/*metabolism ; },
abstract = {Archaea SRP is composed of an SRP RNA molecule and two bound proteins named SRP19 and SRP54. Regulated by the binding and hydrolysis of guanosine triphosphates, the RNA-bound SRP54 protein transiently associates not only with the hydrophobic signal sequence as it emerges from the ribosomal exit tunnel, but also interacts with the membrane-associated SRP receptor (FtsY). Comparative analyses of the archaea genomes and their SRP component sequences, combined with structural and biochemical data, support a prominent role of the SRP RNA in the assembly and function of the archaea SRP. The 5e motif, which in eukaryotes binds a 72 kilodalton protein, is preserved in most archaea SRP RNAs despite the lack of an archaea SRP72 homolog. The primary function of the 5e region may be to serve as a hinge, strategically positioned between the small and large SRP domain, allowing the elongated SRP to bind simultaneously to distant ribosomal sites. SRP19, required in eukaryotes for initiating SRP assembly, appears to play a subordinate role in the archaea SRP or may be defunct. The N-terminal A region and a novel C-terminal R region of the archaea SRP receptor (FtsY) are strikingly diverse or absent even among the members of a taxonomic subgroup.},
}
@article {pmid20662387,
year = {2010},
author = {Verhaart, MR and Bielen, AA and van der Oost, J and Stams, AJ and Kengen, SW},
title = {Hydrogen production by hyperthermophilic and extremely thermophilic bacteria and archaea: mechanisms for reductant disposal.},
journal = {Environmental technology},
volume = {31},
number = {8-9},
pages = {993-1003},
doi = {10.1080/09593331003710244},
pmid = {20662387},
issn = {0959-3330},
mesh = {Archaea/*metabolism ; Bacteria/*metabolism ; *Biomass ; Hydrogen/*metabolism ; Industrial Microbiology/*methods ; Oxidation-Reduction ; Thermodynamics ; },
abstract = {Hydrogen produced from biomass by bacteria and archaea is an attractive renewable energy source. However, to make its application more feasible, microorganisms are needed with high hydrogen productivities. For several reasons, hyperthermophilic and extremely thermophilic bacteria and archaea are promising is this respect. In addition to the high polysaccharide-hydrolysing capacities of many of these organisms, an important advantage is their ability to use most of the reducing equivalents (e.g. NADH, reduced ferredoxin) formed during glycolysis for the production of hydrogen, enabling H2/hexose ratios of between 3.0 and 4.0. So, despite the fact that the hydrogen-yielding reactions, especially the one from NADH, are thermodynamically unfavourable, high hydrogen yields are obtained. In this review we focus on three different mechanisms that are employed by a few model organisms, viz. Caldicellulosiruptor saccharolyticus and Thermoanaerobacter tengcongensis, Thermotoga maritima, and Pyrococcus furiosus, to efficiently produce hydrogen. In addition, recent developments to improve hydrogen production by hyperthermophilic and extremely thermophilic bacteria and archaea are discussed.},
}
@article {pmid20662380,
year = {2010},
author = {Ding, JY and Lai, MC},
title = {The biotechnological potential of the extreme halophilic archaea Haloterrigena sp. H13 in xenobiotic metabolism using a comparative genomics approach.},
journal = {Environmental technology},
volume = {31},
number = {8-9},
pages = {905-914},
doi = {10.1080/09593331003734210},
pmid = {20662380},
issn = {0959-3330},
mesh = {Amino Acid Sequence ; Base Sequence ; DNA, Archaeal/chemistry/genetics ; Gene Expression Profiling ; Genome, Archaeal/*genetics ; Halobacteriales/*metabolism ; Molecular Sequence Data ; Polymerase Chain Reaction ; Sequence Alignment ; Sequence Analysis, DNA ; Xenobiotics/*metabolism ; },
abstract = {Extreme halophilic archaea are thriving and dominant populations within hypersaline environments. Because of the extreme properties of the enzymes of halophilic archaea and similar metabolic abilities to their bacterial counterparts, our interests focus on their potential biotechnological applications. In this study, the partial genome of a newly isolated extreme halophilic archaeon, Haloterrigena sp. H13, was investigated. The genome size was estimated to be about 3.9 MB, and a genomic shotgun library was constructed. A total of 1479 clones from the library were sequenced once, and 1186 contigs were obtained. From these contigs, 580 open reading frames (ORFs) were identified, and 394 ORFs were annotated. From the partial genome of strain H13, we identified genes that may be involved in 1,2-dichloroethane degradation, naphthalene/anthracene degradation, gamma-hexachlorocyclohexane degradation, 1-/2-methylnaphthalene degradation and benzoate degradation via CoA ligation. Among the identified ORFs, gene homologs of (S)-2-haloacid dehalogenase (EC 3.8.1.2) and salicylate hydroxylase (EC 1.14.13.1), which might be involved in the degradation of dichloroethane, gamma-hexachlorocyclohexane and naphthalene, were found in the partial genome sequence of strain H13. According to the current genome annotation of peripheral metabolic pathways and the putative xenobiotic-degrading enzymes, the potential of extreme haloarchaea in bioremediation applications is proposed.},
}
@article {pmid20631805,
year = {2010},
author = {Schleper, C},
title = {Ammonia oxidation: different niches for bacteria and archaea?.},
journal = {The ISME journal},
volume = {4},
number = {9},
pages = {1092-1094},
doi = {10.1038/ismej.2010.111},
pmid = {20631805},
issn = {1751-7370},
mesh = {Ammonia/*metabolism ; Archaea/*growth &amp; development/*metabolism ; Bacteria/*growth &amp; development/*metabolism ; *Environmental Microbiology ; Oxidation-Reduction ; },
}
@article {pmid20627124,
year = {2010},
author = {Orell, A and Navarro, CA and Arancibia, R and Mobarec, JC and Jerez, CA},
title = {Life in blue: copper resistance mechanisms of bacteria and archaea used in industrial biomining of minerals.},
journal = {Biotechnology advances},
volume = {28},
number = {6},
pages = {839-848},
doi = {10.1016/j.biotechadv.2010.07.003},
pmid = {20627124},
issn = {1873-1899},
mesh = {Archaea/*drug effects/metabolism/ultrastructure ; Bacteria/*drug effects/metabolism/ultrastructure ; Copper/*toxicity ; *Industry ; Minerals/*chemistry ; *Mining ; },
abstract = {Industrial biomining processes to extract copper, gold and other metals involve the use of extremophiles such as the acidophilic Acidithiobacillus ferrooxidans (Bacteria), and the thermoacidophilic Sulfolobus metallicus (Archaea). Together with other extremophiles these microorganisms subsist in habitats where they are exposed to copper concentrations higher than 100mM. Herein we review the current knowledge on the Cu-resistance mechanisms found in these microorganisms. Recent information suggests that biomining extremophiles respond to extremely high Cu concentrations by using simultaneously all or most of the following key elements: 1) a wide repertoire of Cu-resistance determinants; 2) duplication of some of these Cu-resistance determinants; 3) existence of novel Cu chaperones; 4) a polyP-based Cu-resistance system, and 5) an oxidative stress defense system. Further insight of the biomining community members and their individual response to copper is highly relevant, since this could provide key information to the mining industry. In turn, this information could be used to select the more fit members of the bioleaching community to attain more efficient industrial biomining processes.},
}
@article {pmid20607531,
year = {2010},
author = {Yamamoto, N and Otawa, K and Nakai, Y},
title = {Diversity and abundance of ammonia-oxidizing bacteria and ammonia-oxidizing archaea during cattle manure composting.},
journal = {Microbial ecology},
volume = {60},
number = {4},
pages = {807-815},
pmid = {20607531},
issn = {1432-184X},
mesh = {Ammonia/*metabolism ; Animals ; Archaea/classification/genetics/isolation &amp; purification/*metabolism ; Bacteria/classification/genetics/isolation &amp; purification/*metabolism ; Bacterial Proteins/genetics/metabolism ; *Biodiversity ; Cattle ; Manure/analysis/*microbiology ; Molecular Sequence Data ; Oxidation-Reduction ; Soil/analysis ; *Soil Microbiology ; },
abstract = {Ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) play important roles in nitrification in various environments. They may also be key communities for ammonia oxidation in composting systems, although few studies have discussed their presence. We investigated the relative diversity and abundance of AOB and AOA using cloning procedures, denaturing gradient gel electrophoresis analysis, and real-time PCR during several stages in the process of cattle manure composting. Our results revealed that the AOB community structure changed during the process. At the high-temperature stage (>60°C), a member of the Nitrosomonas europaea/eutropha cluster dominated while the uncultured Nitrosomonas spp. cluster appeared after the temperature decreased. Additionally, our analysis indicated that AOA sequences, which were classified into a soil/sediment cluster, were present after the temperature decreased during the composting process. At these stages, the number of the archaeal amoA gene copies (3.2 or 3.9 × 10(7) copies per gram freeze-dried compost) was significantly higher than that of bacterial amoA gene copies (2.2-7.2 × 10(6) copies per gram freeze-dried compost). Our results suggest that both AOB and AOA are actively involved in nitrification of composting systems.},
}
@article {pmid20601508,
year = {2010},
author = {Calo, D and Eilam, Y and Lichtenstein, RG and Eichler, J},
title = {Towards glycoengineering in archaea: replacement of Haloferax volcanii AglD with homologous glycosyltransferases from other halophilic archaea.},
journal = {Applied and environmental microbiology},
volume = {76},
number = {17},
pages = {5684-5692},
pmid = {20601508},
issn = {1098-5336},
mesh = {Archaeal Proteins/genetics/metabolism ; *Genetic Engineering ; Glycosylation ; Glycosyltransferases/genetics/*metabolism ; Halobacterium salinarum/*enzymology/genetics ; Haloferax volcanii/*enzymology/genetics/*metabolism ; Hexoses/analysis/metabolism ; Mass Spectrometry ; Membrane Glycoproteins/chemistry/metabolism ; Metabolic Networks and Pathways/*genetics ; Oligosaccharides/metabolism ; Recombinant Proteins/genetics/metabolism ; *Recombination, Genetic ; },
abstract = {Like eukarya and bacteria, archaea also perform N-glycosylation. However, the N-linked glycans of archaeal glycoproteins present a variety not seen elsewhere. Archaea accordingly rely on N-glycosylation pathways likely involving a broad range of species-specific enzymes. To harness the enormous applied potential of such diversity for the generation of glycoproteins bearing tailored N-linked glycans, the development of an appropriate archaeal glycoengineering platform is required. With a sequenced genome, a relatively well-defined N-glycosylation pathway, and molecular tools for gene manipulation, the haloarchaeon Haloferax volcanii (Hfx. volcanii) represents a promising candidate. Accordingly, cells lacking AglD, a glycosyltransferase involved in adding the final hexose of a pentasaccharide N-linked to the surface (S)-layer glycoprotein, were transformed to express AglD homologues from other haloarchaea. The introduction of nonnative versions of AglD led to the appearance of an S-layer glycoprotein similar to the protein from the native strain. Indeed, mass spectrometry confirmed that AglD and its homologues introduce the final hexose to the N-linked S-layer glycoprotein pentasaccharide. Heterologously expressed haloarchaeal AglD homologues contributed to N-glycosylation in Hfx. volcanii despite an apparent lack of AglD function in those haloarchaea from where the introduced homologues came. For example, although functional in Hfx. volcanii, no transcription of the Halobacterium salinarum aglD homologue, OE1482, was detected in cells of the native host grown under various conditions. Thus, at least one AglD homologue works more readily in Hfx. volcanii than in the native host. These results warrant the continued assessment of Hfx. volcanii as a glycosylation "workshop."},
}
@article {pmid20598889,
year = {2010},
author = {Spang, A and Hatzenpichler, R and Brochier-Armanet, C and Rattei, T and Tischler, P and Spieck, E and Streit, W and Stahl, DA and Wagner, M and Schleper, C},
title = {Distinct gene set in two different lineages of ammonia-oxidizing archaea supports the phylum Thaumarchaeota.},
journal = {Trends in microbiology},
volume = {18},
number = {8},
pages = {331-340},
doi = {10.1016/j.tim.2010.06.003},
pmid = {20598889},
issn = {1878-4380},
mesh = {Ammonia/*metabolism ; Archaea/classification/*genetics/metabolism ; Archaeal Proteins/chemistry/*genetics/metabolism ; Cell Division/genetics ; Conserved Sequence ; Crenarchaeota/*classification/genetics/metabolism ; DNA Topoisomerases, Type I/chemistry/genetics/metabolism ; DNA-Binding Proteins/chemistry/genetics/metabolism ; DNA-Directed RNA Polymerases/chemistry/genetics/metabolism ; Euryarchaeota/classification/*genetics ; *Genome, Archaeal ; Oxidation-Reduction ; Phylogeny ; RNA, Archaeal/genetics ; RNA, Ribosomal, 16S/genetics ; Ribosomal Proteins/chemistry/genetics/metabolism ; Sequence Analysis, DNA ; },
abstract = {Globally distributed archaea comprising ammonia oxidizers of moderate terrestrial and marine environments are considered the most abundant archaeal organisms on Earth. Based on 16S rRNA phylogeny, initial assignment of these archaea was to the Crenarchaeota. By contrast, features of the first genome sequence from a member of this group suggested that they belong to a novel phylum, the Thaumarchaeota. Here, we re-investigate the Thaumarchaeota hypothesis by including two newly available genomes, that of the marine ammonia oxidizer Nitrosopumilus maritimus and that of Nitrososphaera gargensis, a representative of another evolutionary lineage within this group predominantly detected in terrestrial environments. Phylogenetic studies based on r-proteins and other core genes, as well as comparative genomics, confirm the assignment of these organisms to a separate phylum and reveal a Thaumarchaeota-specific set of core informational processing genes, as well as potentially ancestral features of the archaea.},
}
@article {pmid20584082,
year = {2011},
author = {Mulligan, C and Fischer, M and Thomas, GH},
title = {Tripartite ATP-independent periplasmic (TRAP) transporters in bacteria and archaea.},
journal = {FEMS microbiology reviews},
volume = {35},
number = {1},
pages = {68-86},
doi = {10.1111/j.1574-6976.2010.00236.x},
pmid = {20584082},
issn = {1574-6976},
support = {BBF0147591//Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Archaea/*metabolism ; Archaeal Proteins/chemistry/genetics/*metabolism ; Bacteria/*metabolism ; Bacterial Proteins/chemistry/genetics/*metabolism ; Membrane Transport Proteins/chemistry/genetics/*metabolism ; Models, Biological ; Models, Molecular ; Periplasmic Proteins/chemistry/genetics/*metabolism ; },
abstract = {The tripartite ATP-independent periplasmic (TRAP) transporters are the best-studied family of substrate-binding protein (SBP)-dependent secondary transporters and are ubiquitous in prokaryotes, but absent from eukaryotes. They are comprised of an SBP of the DctP or TAXI families and two integral membrane proteins of unequal sizes that form the DctQ and DctM protein families, respectively. The SBP component has a structure comprised of two domains connected by a hinge that closes upon substrate binding. In DctP-TRAP transporters, substrate binding is mediated through a conserved and specific arginine/carboxylate interaction in the SBP. While the SBP component has now been relatively well characterized, the membrane components of TRAP transporters are still poorly understood both in terms of their structure and function. We review the expanding repertoire of substrates and physiological roles for experimentally characterized TRAP transporters in bacteria and discuss mechanistic aspects of these transporters using data primarily from the sialic acid-specific TRAP transporter SiaPQM from Haemophilus influenzae, which suggest that TRAP transporters are high-affinity, Na(+)-dependent unidirectional secondary transporters.},
}
@article {pmid20582317,
year = {2010},
author = {Thibodeaux, GN and Liang, X and Moncivais, K and Umeda, A and Singer, O and Alfonta, L and Zhang, ZJ},
title = {Transforming a pair of orthogonal tRNA-aminoacyl-tRNA synthetase from Archaea to function in mammalian cells.},
journal = {PloS one},
volume = {5},
number = {6},
pages = {e11263},
pmid = {20582317},
issn = {1932-6203},
support = {R01 CA120168/CA/NCI NIH HHS/United States ; },
mesh = {Amino Acyl-tRNA Synthetases/genetics/*metabolism ; Animals ; Archaea/*enzymology ; Base Sequence ; Blotting, Western ; Cell Line ; Humans ; Mammals ; Molecular Sequence Data ; Nucleic Acid Conformation ; RNA, Transfer/chemistry/*genetics ; },
abstract = {A previously engineered Methanocaldococcus jannaschii tRNA(CUA Tyr)-tyrosyl-tRNA synthetase pair orthogonal to Escherichia coli was modified to become orthogonal in mammalian cells. The resulting tRNA(CUA Tyr)-tyrosyl-tRNA synthetase pair was able to suppress an amber codon in the green fluorescent protein, GFP, and in a foldon protein in mammalian cells. The methodology reported here will allow rapid transformation of the much larger collection of existing tyrosyl-tRNA synthetases that were already evolved for the incorporation of an array of over 50 unnatural amino acids into proteins in Escherichia coli into proteins in mammalian cells. Thus we will be able to introduce a large array of possibilities for protein modifications in mammalian cells.},
}
@article {pmid20581182,
year = {2010},
author = {Dodsworth, JA and Li, L and Wei, S and Hedlund, BP and Leigh, JA and de Figueiredo, P},
title = {Interdomain conjugal transfer of DNA from bacteria to archaea.},
journal = {Applied and environmental microbiology},
volume = {76},
number = {16},
pages = {5644-5647},
pmid = {20581182},
issn = {1098-5336},
support = {R24 GM074783/GM/NIGMS NIH HHS/United States ; },
mesh = {*Conjugation, Genetic ; DNA, Bacterial/chemistry/*genetics ; Escherichia coli/*genetics ; Gene Transfer Techniques ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Genetic Vectors ; Methanococcus/*genetics ; Molecular Sequence Data ; Plasmids ; Sequence Analysis, DNA ; },
abstract = {Escherichia coli transforms the methanogenic archaeon Methanococcus maripaludis at frequencies ranging from 0.2 x 10(-6) to 2 x 10(-6) per recipient cell. Transformation requires cell-to-cell contact, oriT, and tra functions, is insensitive to DNase I, and otherwise displays hallmarks of conjugation.},
}
@article {pmid20555406,
year = {2010},
author = {Bergmann, I and Nettmann, E and Mundt, K and Klocke, M},
title = {Determination of methanogenic Archaea abundance in a mesophilic biogas plant based on 16S rRNA gene sequence analysis.},
journal = {Canadian journal of microbiology},
volume = {56},
number = {5},
pages = {440-444},
doi = {10.1139/w10-021},
pmid = {20555406},
issn = {1480-3275},
mesh = {Archaea/*genetics/growth &amp; development/*isolation &amp; purification ; Databases, Genetic ; Methanomicrobiales/genetics/growth &amp; development/isolation &amp; purification ; Nucleic Acid Amplification Techniques ; Plants/*microbiology ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/*genetics ; },
abstract = {Energy production of renewable raw material is of increasing importance for sustainable energy production. As an indispensable prerequirement for further upgrading of technical equipment and operation modes of biogas plants, a deeper knowledge of the microbial community responsible for methane formation is crucial. To overcome these limitations a mesophilic biogas plant converting pig manure, maize silage, and grains of crop was sampled and subsequently analysed by construction of a methanogenic Archaea specific 16S rRNA gene clone library combined with PCR-RFLP analysis and group-specific quantitative real-time PCR (qPCR). Seventy percent of all analysed clones belonged to the order Methanomicrobiales, whereas 13% belonged to Methanosarcinales, 6% belonged to the Methanobacteriales group, and 11% of all detected clones were assigned to the CA11 and Arch1 cluster. Comparable percentages were obtained with qPCR: 84% of all detected 16S rRNA gene copy numbers were affiliated with the Methanomicrobiales, while only 14% belonged to the Methanosarcinales and 2% to the Methanobacteriales order. In conclusion, both approaches detected similar archaeal groups and revealed nearly the same abundance, pointing to a predominance of hydrogenotrophic methanogens in the biogas plant.},
}
@article {pmid20555203,
year = {2010},
author = {Kasuga, I and Nakagaki, H and Kurisu, F and Furumai, H},
title = {Abundance and diversity of ammonia-oxidizing archaea and bacteria on biological activated carbon in a pilot-scale drinking water treatment plant with different treatment processes.},
journal = {Water science and technology : a journal of the International Association on Water Pollution Research},
volume = {61},
number = {12},
pages = {3070-3077},
doi = {10.2166/wst.2010.204},
pmid = {20555203},
issn = {0273-1223},
mesh = {Ammonia/*metabolism ; Archaea/genetics/*metabolism ; Bacteria/genetics/*metabolism ; Filtration/methods ; Halogenation ; Humans ; Nitrates/metabolism ; Oxidation-Reduction ; Pilot Projects ; Polymorphism, Restriction Fragment Length ; Silicon Dioxide ; Water Purification/*methods ; Water Supply/*standards ; },
abstract = {The effects of different placements of rapid sand filtration on nitrification performance of BAC treatment in a pilot-scale plant were evaluated. In this plant, rapid sand filtration was placed after ozonation-BAC treatment in Process (A), while it preceded ozonation-BAC treatment in Process (B). Analysis of amoA genes of ammonia-oxidizing archaea (AOA) and bacteria (AOB) combined with nitrification potential test was conducted. BAC from Process (A) demonstrated slightly higher nitrification potential at every sampling occasion. This might be due to higher abundances of AOB on BAC from Process (A) than those on BAC from Process (B). However, AOA rather than AOB could be predominant ammonia-oxidizers in BAC treatment regardless of the position of rapid sand filtration. The highest nitrification potential was observed for BAC from both processes in February when the highest abundances of AOA-amoA and AOB-amoA genes were detected. Since rapid sand filtration was placed after BAC treatment in Process (A), residual aluminum concentration in BAC influent was higher in Process (A). However, adverse effects of aluminum on nitrification activity were not observed. These results suggest that factors other than aluminum concentration in different treatment processes could possibly have some influence on abundances of ammonia-oxidizing microorganisms on BAC.},
}
@article {pmid20547064,
year = {2010},
author = {Darwin, KH and Hofmann, K},
title = {SAMPyling proteins in archaea.},
journal = {Trends in biochemical sciences},
volume = {35},
number = {6},
pages = {348-351},
pmid = {20547064},
issn = {0968-0004},
support = {R01 HL092774/HL/NHLBI NIH HHS/United States ; R01 HL092774-03/HL/NHLBI NIH HHS/United States ; HL092774/HL/NHLBI NIH HHS/United States ; },
mesh = {Archaea/*metabolism ; Archaeal Proteins/*metabolism ; *Protein Processing, Post-Translational ; Ubiquitins/metabolism ; },
abstract = {For some time, post-translational small protein modifications were found only in eukaryotes; much later, such modifications were identified in some species of bacteria. The recent discovery of ubiquitin-like proteins that form polymeric chains and covalently modify proteins in archaea finally closes the evolutionary gap among the domains of life.},
}
@article {pmid20522251,
year = {2010},
author = {Xue, B and Williams, RW and Oldfield, CJ and Dunker, AK and Uversky, VN},
title = {Archaic chaos: intrinsically disordered proteins in Archaea.},
journal = {BMC systems biology},
volume = {4 Suppl 1},
number = {Suppl 1},
pages = {S1},
pmid = {20522251},
issn = {1752-0509},
support = {GM071714-01A2/GM/NIGMS NIH HHS/United States ; R01 LM007688-01A1/LM/NLM NIH HHS/United States ; },
mesh = {Amino Acid Sequence ; Archaea/*chemistry/genetics ; Archaeal Proteins/*chemistry/genetics/metabolism ; Ecosystem ; Evolution, Molecular ; Models, Molecular ; Molecular Sequence Data ; Phylogeny ; Protein Conformation ; *Proteomics ; Species Specificity ; },
abstract = {BACKGROUND: Many proteins or their regions known as intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) lack unique 3D structure in their native states under physiological conditions yet fulfill key biological functions. Earlier bioinformatics studies showed that IDPs and IDRs are highly abundant in different proteomes and carry out mostly regulatory functions related to molecular recognition and signal transduction. Archaea belong to an intriguing domain of life whose members, being microbes, are characterized by a unique mosaic-like combination of bacterial and eukaryotic properties and include inhabitants of some of the most extreme environments on the planet. With the expansion of the archaea genome data (more than fifty archaea species from five different phyla are known now), and with recent improvements in the accuracy of intrinsic disorder prediction, it is time to re-examine the abundance of IDPs and IDRs in the archaea domain.<br><br>RESULTS: The abundance of IDPs and IDRs in 53 archaea species is analyzed. The amino acid composition profiles of these species are generally quite different from each other. The disordered content is highly species-dependent. Thermoproteales proteomes have 14% of disordered residues, while in Halobacteria, this value increases to 34%. In proteomes of these two phyla, proteins containing long disordered regions account for 12% and 46%, whereas 4% and 26% their proteins are wholly disordered. These three measures of disorder content are linearly correlated with each other at the genome level. There is a weak correlation between the environmental factors (such as salinity, pH and temperature of the habitats) and the abundance of intrinsic disorder in Archaea, with various environmental factors possessing different disorder-promoting strengths. Harsh environmental conditions, especially those combining several hostile factors, clearly favor increased disorder content. Intrinsic disorder is highly abundant in functional Pfam domains of the archaea origin. The analysis based on the disordered content and phylogenetic tree indicated diverse evolution of intrinsic disorder among various classes and species of Archaea.<br><br>CONCLUSIONS: Archaea proteins are rich in intrinsic disorder. Some of these IDPs and IDRs likely evolve to help archaea to accommodate to their hostile habitats. Other archaean IDPs and IDRs possess crucial biological functions similar to those of the bacterial and eukaryotic IDPs/IDRs.},
}
@article {pmid20532250,
year = {2010},
author = {Chia, N and Cann, I and Olsen, GJ},
title = {Evolution of DNA replication protein complexes in eukaryotes and Archaea.},
journal = {PloS one},
volume = {5},
number = {6},
pages = {e10866},
pmid = {20532250},
issn = {1932-6203},
mesh = {Archaea/*genetics ; *DNA Replication ; DNA, Archaeal/*genetics ; Eukaryotic Cells ; *Evolution, Molecular ; Phylogeny ; Proliferating Cell Nuclear Antigen/genetics ; Replication Protein C/genetics ; },
abstract = {BACKGROUND: The replication of DNA in Archaea and eukaryotes requires several ancillary complexes, including proliferating cell nuclear antigen (PCNA), replication factor C (RFC), and the minichromosome maintenance (MCM) complex. Bacterial DNA replication utilizes comparable proteins, but these are distantly related phylogenetically to their archaeal and eukaryotic counterparts at best.<br><br>While the structures of each of the complexes do not differ significantly between the archaeal and eukaryotic versions thereof, the evolutionary dynamic in the two cases does. The number of subunits in each complex is constant across all taxa. However, they vary subtly with regard to composition. In some taxa the subunits are all identical in sequence, while in others some are homologous rather than identical. In the case of eukaryotes, there is no phylogenetic variation in the makeup of each complex-all appear to derive from a common eukaryotic ancestor. This is not the case in Archaea, where the relationship between the subunits within each complex varies taxon-to-taxon. We have performed a detailed phylogenetic analysis of these relationships in order to better understand the gene duplications and divergences that gave rise to the homologous subunits in Archaea.<br><br>CONCLUSION/SIGNIFICANCE: This domain level difference in evolution suggests that different forces have driven the evolution of DNA replication proteins in each of these two domains. In addition, the phylogenies of all three gene families support the distinctiveness of the proposed archaeal phylum Thaumarchaeota.},
}
@article {pmid20491927,
year = {2010},
author = {Dorador, C and Vila, I and Remonsellez, F and Imhoff, JF and Witzel, KP},
title = {Unique clusters of Archaea in Salar de Huasco, an athalassohaline evaporitic basin of the Chilean Altiplano.},
journal = {FEMS microbiology ecology},
volume = {73},
number = {2},
pages = {291-302},
doi = {10.1111/j.1574-6941.2010.00891.x},
pmid = {20491927},
issn = {1574-6941},
mesh = {Archaea/classification/*genetics/*isolation &amp; purification ; Bacteria/classification/genetics/isolation &amp; purification ; Chile ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; Fresh Water/microbiology ; Geologic Sediments/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Water Microbiology ; Wetlands ; },
abstract = {Analyses of clone libraries from water and sediments of different sites from Salar de Huasco, a high-altitude athalassohaline wetland in the Chilean Altiplano, revealed the presence of five unique clusters of uncultured Archaea that have not been previously reported or specifically assigned. These sequences were distantly related (83-96% sequence identity) to a limited number of other clone sequences and revealed no identity to cultured Archaea. The abundance of Archaea and Bacteria was estimated using qPCR and community composition was examined through the construction of clone libraries of archaeal 16S rRNA gene. Archaea were found to be dominant over Bacteria in sediments from two saline sites (sites H4: 6.31 x 10(4) and site H6: 1.37 x 10(4) microS cm(-1)) and in one of the water samples (freshwater from site H0: 607 muS cm(-1)). Euryarchaeotal sequences were more abundant than crenarchaeotal sequences. Many of the clone sequences (52%) were similar to uncultured archaeal groups found in marine ecosystems having identity values between 99% and 97%. A major fraction of the sequences (40%) were members of Methanobacteria, while others were included in the Marine Benthic Groups B and D, the Miscellaneous Crenarchaeotic Group, the Terrestrial Miscellaneous Euryarchaeotal Group, Marine Group I and Halobacteria. The presence of uncultured archaeal groups in Salar de Huasco extends their known distribution in inland waters, providing new clues about their possible function in the environment.},
}
@article {pmid20488501,
year = {2010},
author = {Quax, TE and Krupovic, M and Lucas, S and Forterre, P and Prangishvili, D},
title = {The Sulfolobus rod-shaped virus 2 encodes a prominent structural component of the unique virion release system in Archaea.},
journal = {Virology},
volume = {404},
number = {1},
pages = {1-4},
doi = {10.1016/j.virol.2010.04.020},
pmid = {20488501},
issn = {1096-0341},
mesh = {Amino Acid Sequence ; Molecular Sequence Data ; Rudiviridae/genetics/*growth &amp; development ; Sequence Homology ; Sulfolobus/*virology ; Viral Proteins/genetics/*metabolism ; *Virus Release ; },
abstract = {Recently a unique mechanism of virion release was discovered in Archaea, different from lysis and egress systems of bacterial and eukaryotic viruses. It involves formation of pyramidal structures on the host cell surface that rupture the S-layer and by opening outwards, create apertures through which mature virions escape the cell. Here we present results of a protein analysis of Sulfolobus islandicus cells infected with the rudivirus SIRV2, which enable us to postulate SIRV2-encoded protein P98 as the major constituent of these exceptional cellular ultrastructures.},
}
@article {pmid20487296,
year = {2010},
author = {Yurist-Doutsch, S and Magidovich, H and Ventura, VV and Hitchen, PG and Dell, A and Eichler, J},
title = {N-glycosylation in Archaea: on the coordinated actions of Haloferax volcanii AglF and AglM.},
journal = {Molecular microbiology},
volume = {75},
number = {4},
pages = {1047-1058},
doi = {10.1111/j.1365-2958.2009.07045.x},
pmid = {20487296},
issn = {1365-2958},
support = {B19088//Biotechnology and Biological Sciences Research Council/United Kingdom ; BBC5196701//Biotechnology and Biological Sciences Research Council/United Kingdom ; SF19107//Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Archaeal Proteins/*metabolism ; Glycoproteins/genetics/*metabolism ; Glycosylation ; Haloferax volcanii/genetics/growth &amp; development/*metabolism ; Multigene Family ; Transcription, Genetic ; },
abstract = {Like Eukarya and Bacteria, Archaea are also capable of performing N-glycosylation. In the halophilic archaeon Haloferax volcanii, N-glycosylation is mediated by the products of the agl gene cluster. In the present report, this gene cluster was expanded to include an additional sequence, aglM, shown to participate in the biosynthesis of hexuronic acids contained within a pentasaccharide decorating the S-layer glycoprotein, a reporter H. volcanii glycoprotein. In response to different growth conditions, changes in the transcription profile of aglM mirrored changes in the transcription profiles of aglF, aglG and aglI, genes encoding confirmed participants in the H. volcanii N-glycosylation pathway, thus offering support to the hypothesis that in H. volcanii, N-glycosylation serves an adaptive role. Following purification, biochemical analysis revealed AglM to function as a UDP-glucose dehydrogenase. In a scoupled reaction with AglF, a previously identified glucose-1-phosphate uridyltransferase, UDP-glucuronic acid was generated from glucose-1-phosphate and UTP in a NAD(+)-dependent manner. These experiments thus represent the first step towards in vitro reconstitution of the archaeal N-glycosylation process.},
}
@article {pmid20459678,
year = {2010},
author = {Makarova, KS and Koonin, EV},
title = {Two new families of the FtsZ-tubulin protein superfamily implicated in membrane remodeling in diverse bacteria and archaea.},
journal = {Biology direct},
volume = {5},
number = {},
pages = {33},
pmid = {20459678},
issn = {1745-6150},
support = {//Intramural NIH HHS/United States ; },
mesh = {Archaea/*metabolism ; Archaeal Proteins/chemistry/classification/*metabolism ; Bacteria/*metabolism ; Bacterial Proteins/chemistry/classification/*metabolism ; Cell Membrane/classification/*metabolism ; Phylogeny ; Tubulin/chemistry/*metabolism ; },
abstract = {Several recent discoveries reveal unexpected versatility of the bacterial and archaeal cytoskeleton systems that are involved in cell division and other processes based on membrane remodeling. Here we apply methods for distant protein sequence similarity detection, phylogenetic approaches, and genome context analysis to described two previously unnoticed families of the FtsZ-tubulin superfamily. One of these families is limited in its spread to Proteobacteria whereas the other is represented in diverse bacteria and archaea, and might be the key component of a novel, multicomponent membrane remodeling system that also includes a Von Willebrand A domain-containing protein, a distinct GTPase and membrane transport proteins of the OmpA family.},
}
@article {pmid20453874,
year = {2010},
author = {Berg, IA and Kockelkorn, D and Ramos-Vera, WH and Say, RF and Zarzycki, J and Hügler, M and Alber, BE and Fuchs, G},
title = {Autotrophic carbon fixation in archaea.},
journal = {Nature reviews. Microbiology},
volume = {8},
number = {6},
pages = {447-460},
pmid = {20453874},
issn = {1740-1534},
mesh = {Acetyl Coenzyme A/metabolism ; Archaea/classification/*metabolism ; *Autotrophic Processes ; Carbon/*metabolism ; Dicarboxylic Acid Transporters/metabolism ; Ecosystem ; Glucose/metabolism ; Hydroxybutyrates/metabolism ; Metabolic Networks and Pathways ; Phylogeny ; },
abstract = {The acquisition of cellular carbon from inorganic carbon is a prerequisite for life and marked the transition from the inorganic to the organic world. Recent theories of the origins of life assume that chemo-evolution took place in a hot volcanic flow setting through a transition metal-catalysed, autocatalytic carbon fixation cycle. Many archaea live in volcanic habitats under such constraints, in high temperatures with only inorganic substances and often under anoxic conditions. In this Review, we describe the diverse carbon fixation mechanisms that are found in archaea. These reactions differ fundamentally from those of the well-known Calvin cycle, and their distribution mirrors the phylogenetic positions of the archaeal lineages and the needs of the ecological niches that they occupy.},
}
@article {pmid20438582,
year = {2010},
author = {Oxley, AP and Lanfranconi, MP and Würdemann, D and Ott, S and Schreiber, S and McGenity, TJ and Timmis, KN and Nogales, B},
title = {Halophilic archaea in the human intestinal mucosa.},
journal = {Environmental microbiology},
volume = {12},
number = {9},
pages = {2398-2410},
doi = {10.1111/j.1462-2920.2010.02212.x},
pmid = {20438582},
issn = {1462-2920},
mesh = {Adult ; Aged ; DNA, Archaeal/genetics ; Feces/microbiology ; Female ; Halobacteriaceae/classification/genetics/*isolation &amp; purification ; Humans ; Inflammatory Bowel Diseases/*microbiology ; Intestinal Mucosa/*microbiology ; Male ; Middle Aged ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Salinity ; Sequence Analysis, DNA ; Sodium Chloride/analysis ; },
abstract = {The human gastrointestinal tract microbiota, despite its key roles in health and disease, remains a diverse, variable and poorly understood entity. Current surveys reveal a multitude of undefined bacterial taxa and a low diversity of methanogenic archaea. In an analysis of the microbiota in colonic mucosal biopsies from patients with inflammatory bowel disease we found 16S rDNA sequences representing a phylogenetically rich diversity of halophilic archaea from the Halobacteriaceae (haloarchaea), including novel phylotypes. As the human colon is not considered a salty environment and haloarchaea are described as extreme halophiles, we evaluated and further discarded the possibility that these sequences originated from pre-colonoscopy saline lavage solutions. Furthermore, aerobic enrichment cultures prepared from a patient biopsy at low salinity (2.5% NaCl) yielded haloarchaeal sequence types. Microscopic observation after fluorescence in situ hybridization provided evidence of the presence of viable archaeal cells in these cultures. These results prove the survival of haloarchaea in the digestive system and suggest that they may be members of the mucosal microbiota, even if present in low numbers in comparison with methanogenic archaea. Investigation of a potential physiological basis of this association may lead to new insights into gastrointestinal health and disease.},
}
@article {pmid20435758,
year = {2010},
author = {Jiang, H and Huang, Q and Dong, H and Wang, P and Wang, F and Li, W and Zhang, C},
title = {RNA-based investigation of ammonia-oxidizing archaea in hot springs of Yunnan Province, China.},
journal = {Applied and environmental microbiology},
volume = {76},
number = {13},
pages = {4538-4541},
pmid = {20435758},
issn = {1098-5336},
mesh = {Ammonia/*metabolism ; Archaea/*enzymology/genetics/isolation &amp; purification/metabolism ; Archaeal Proteins/genetics/metabolism ; China ; Hot Springs/chemistry/*microbiology ; Hot Temperature ; Molecular Sequence Data ; Oxidation-Reduction ; Oxidoreductases/genetics/*metabolism ; *RNA, Archaeal/analysis/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; },
abstract = {Using RNA-based techniques and hot spring samples collected from Yunnan Province, China, we show that the amoA gene of aerobic ammonia-oxidizing archaea can be transcribed at temperatures higher than 74 degrees C and up to 94 degrees C, suggesting that archaeal nitrification can potentially occur at near boiling temperatures.},
}
@article {pmid20421484,
year = {2010},
author = {Baker, BJ and Comolli, LR and Dick, GJ and Hauser, LJ and Hyatt, D and Dill, BD and Land, ML and Verberkmoes, NC and Hettich, RL and Banfield, JF},
title = {Enigmatic, ultrasmall, uncultivated Archaea.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {107},
number = {19},
pages = {8806-8811},
pmid = {20421484},
issn = {1091-6490},
mesh = {Archaea/*cytology/*genetics/metabolism/ultrastructure ; Archaeal Proteins/classification/genetics ; Biofilms ; Cell Cycle ; DNA Replication ; Genome, Archaeal/genetics ; Genome, Bacterial/genetics ; Molecular Sequence Data ; Protein Biosynthesis ; Proteomics ; Species Specificity ; Transcription, Genetic ; },
abstract = {Metagenomics has provided access to genomes of as yet uncultivated microorganisms in natural environments, yet there are gaps in our knowledge-particularly for Archaea-that occur at relatively low abundance and in extreme environments. Ultrasmall cells (<500 nm in diameter) from lineages without cultivated representatives that branch near the crenarchaeal/euryarchaeal divide have been detected in a variety of acidic ecosystems. We reconstructed composite, near-complete approximately 1-Mb genomes for three lineages, referred to as ARMAN (archaeal Richmond Mine acidophilic nanoorganisms), from environmental samples and a biofilm filtrate. Genes of two lineages are among the smallest yet described, enabling a 10% higher coding density than found genomes of the same size, and there are noncontiguous genes. No biological function could be inferred for up to 45% of genes and no more than 63% of the predicted proteins could be assigned to a revised set of archaeal clusters of orthologous groups. Some core metabolic genes are more common in Crenarchaeota than Euryarchaeota, up to 21% of genes have the highest sequence identity to bacterial genes, and 12 belong to clusters of orthologous groups that were previously exclusive to bacteria. A small subset of 3D cryo-electron tomographic reconstructions clearly show penetration of the ARMAN cell wall and cytoplasmic membranes by protuberances extended from cells of the archaeal order Thermoplasmatales. Interspecies interactions, the presence of a unique internal tubular organelle [Comolli, et al. (2009) ISME J 3:159-167], and many genes previously only affiliated with Crenarchaea or Bacteria indicate extensive unique physiology in organisms that branched close to the time that Cren- and Euryarchaeotal lineages diverged.},
}
@article {pmid20409658,
year = {2010},
author = {Klenk, HP and Göker, M},
title = {En route to a genome-based classification of Archaea and Bacteria?.},
journal = {Systematic and applied microbiology},
volume = {33},
number = {4},
pages = {175-182},
doi = {10.1016/j.syapm.2010.03.003},
pmid = {20409658},
issn = {1618-0984},
mesh = {Archaea/*classification/*genetics ; Bacteria/*classification/*genetics ; *Genome, Archaeal ; *Genome, Bacterial ; *Phylogeny ; },
abstract = {Given the considerable promise whole-genome sequencing offers for phylogeny and classification, it is surprising that microbial systematics and genomics have not yet been reconciled. This might be due to the intrinsic difficulties in inferring reasonable phylogenies from genomic sequences, particularly in the light of the significant amount of lateral gene transfer in prokaryotic genomes. However, recent studies indicate that the species tree and the hierarchical classification based on it are still meaningful concepts, and that state-of-the-art phylogenetic inference methods are able to provide reliable estimates of the species tree to the benefit of taxonomy. Conversely, we suspect that the current lack of completely sequenced genomes for many of the major lineages of prokaryotes and for most type strains is a major obstacle in progress towards a genome-based classification of microorganisms. We conclude that phylogeny-driven microbial genome sequencing projects such as the Genomic Encyclopaedia of Archaea and Bacteria (GEBA) project are likely to rectify this situation.},
}
@article {pmid20406296,
year = {2010},
author = {Molina, V and Belmar, L and Ulloa, O},
title = {High diversity of ammonia-oxidizing archaea in permanent and seasonal oxygen-deficient waters of the eastern South Pacific.},
journal = {Environmental microbiology},
volume = {12},
number = {9},
pages = {2450-2465},
doi = {10.1111/j.1462-2920.2010.02218.x},
pmid = {20406296},
issn = {1462-2920},
mesh = {Ammonia/*metabolism ; Archaea/classification/*genetics/metabolism ; Betaproteobacteria/genetics ; Chile ; DNA, Archaeal/genetics ; Genes, Archaeal ; Genotype ; Nitrogen/analysis ; Oxidoreductases/genetics ; Oxygen/analysis ; Pacific Ocean ; Peru ; Phylogeny ; Seawater/analysis/*microbiology ; *Water Microbiology ; },
abstract = {The community structure of putative aerobic ammonia-oxidizing archaea (AOA) was explored in two oxygen-deficient ecosystems of the eastern South Pacific: the oxygen minimum zone off Peru and northern Chile (11°S-20°S), where permanent suboxic and low-ammonium conditions are found at intermediate depths, and the continental shelf off central Chile (36°S), where seasonal oxygen-deficient and relatively high-ammonium conditions develop in the water column, particularly during the upwelling season. The AOA community composition based on the ammonia monooxygenase subunit A (amoA) genes changed according to the oxygen concentration in the water column and the ecosystem studied, showing a higher diversity in the seasonal low-oxygen waters. The majority of the archaeal amoA genotypes was affiliated to the uncultured clusters A (64%) and B (35%), with Cluster A AOA being mainly associated with higher oxygen and ammonium concentrations and Cluster B AOA with permanent oxygen- and ammonium-poor waters. Q-PCR assays revealed that AOA are an abundant community (up to 10(5) amoA copies ml(-1)), while bacterial amoA genes from β proteobacteria were undetected. Our results thus suggest that a diverse uncultured AOA community, for which, therefore, we do not have any physiological information, to date, is an important component of the nitrifying community in oxygen-deficient marine ecosystems, and particularly in rich coastal upwelling ones.},
}
@article {pmid20405121,
year = {2010},
author = {Jin, T and Zhang, T and Yan, Q},
title = {Characterization and quantification of ammonia-oxidizing archaea (AOA) and bacteria (AOB) in a nitrogen-removing reactor using T-RFLP and qPCR.},
journal = {Applied microbiology and biotechnology},
volume = {87},
number = {3},
pages = {1167-1176},
pmid = {20405121},
issn = {1432-0614},
mesh = {Ammonia/*metabolism ; Archaea/classification/*genetics/*isolation &amp; purification/metabolism ; Archaeal Proteins/genetics ; Bacteria/classification/*genetics/*isolation &amp; purification/metabolism ; Bacterial Proteins/genetics ; Bioreactors/*microbiology ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Molecular Sequence Data ; Nitrogen/*metabolism ; Oxidoreductases/genetics ; Phylogeny ; Polymerase Chain Reaction ; *Polymorphism, Restriction Fragment Length ; },
abstract = {Using ammonia monooxygenase alpha-subunit (amoA) gene and 16S rRNA gene, the community structure and abundance of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in a nitrogen-removing reactor, which was operated for five phases, were characterized and quantified by cloning, terminal restriction fragment length polymorphism (T-RFLP), and quantitative polymerase chain reaction (qPCR). The results suggested that the dominant AOB in the reactor fell to the genus Nitrosomonas, while the dominant AOA belonged to Crenarchaeotal Group I.1a in phylum Crenarchaeota. Real-time PCR results demonstrated that the levels of AOB amoA varied from 2.9 x 10(3) to 2.3 x 10(5) copies per nanogram DNA, greatly (about 60 times) higher than those of AOA, which ranged from 1.7 x 10(2) to 3.8 x 10(3) copies per nanogram DNA. This indicated the possible leading role of AOB in the nitrification process in this study. T-RFLP results showed that the AOB community structure significantly shifted in different phases while AOA only showed one major peak for all the phases. The analyses also suggested that the AOB community was more sensitive than that of AOA to operational conditions, such as ammonia loading and dissolved oxygen.},
}
@article {pmid20403814,
year = {2010},
author = {Soler, N and Marguet, E and Cortez, D and Desnoues, N and Keller, J and van Tilbeurgh, H and Sezonov, G and Forterre, P},
title = {Two novel families of plasmids from hyperthermophilic archaea encoding new families of replication proteins.},
journal = {Nucleic acids research},
volume = {38},
number = {15},
pages = {5088-5104},
pmid = {20403814},
issn = {1362-4962},
mesh = {Archaeal Proteins/classification/*genetics ; Base Sequence ; DNA Replication ; Methanococcales/genetics ; Molecular Sequence Data ; Plasmids/classification/*genetics/isolation &amp; purification ; Pyrococcus/*genetics ; Thermococcus/*genetics ; },
abstract = {Thermococcales (phylum Euryarchaeota) are model organisms for physiological and molecular studies of hyperthermophiles. Here we describe three new plasmids from Thermococcales that could provide new tools and model systems for genetic and molecular studies in Archaea. The plasmids pTN2 from Thermococcus nautilus sp. 30-1 and pP12-1 from Pyrococcus sp. 12-1 belong to the same family. They have similar size (approximately 12 kb) and share six genes, including homologues of genes encoded by the virus PAV1 from Pyrococcus abyssi. The plasmid pT26-2 from Thermococcus sp. 26-2 (21.5 kb), that corresponds to another plasmid family, encodes many proteins having homologues in virus-like elements integrated in several genomes of Thermococcales and Methanococcales. Our analyses confirm that viruses and plasmids are evolutionary related and co-evolve with their hosts. Whereas all plasmids previously isolated from Thermococcales replicate by the rolling circle mechanism, the three plasmids described here probably replicate by the theta mechanism. The plasmids pTN2 and pP12-1 encode a putative helicase of the SFI superfamily and a new family of DNA polymerase, whose activity was demonstrated in vitro, whereas pT26-2 encodes a putative new type of helicase. This strengthens the idea that plasmids and viruses are a reservoir of novel protein families involved in DNA replication.},
}
@article {pmid20402778,
year = {2010},
author = {Dang, H and Luan, XW and Chen, R and Zhang, X and Guo, L and Klotz, MG},
title = {Diversity, abundance and distribution of amoA-encoding archaea in deep-sea methane seep sediments of the Okhotsk Sea.},
journal = {FEMS microbiology ecology},
volume = {72},
number = {3},
pages = {370-385},
doi = {10.1111/j.1574-6941.2010.00870.x},
pmid = {20402778},
issn = {1574-6941},
mesh = {Archaea/classification/enzymology/genetics/*isolation &amp; purification ; *Biodiversity ; DNA, Archaeal/genetics ; Gene Library ; Genes, Archaeal ; Geologic Sediments/*microbiology ; Methane ; Oxidoreductases/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; Sequence Analysis, DNA ; *Water Microbiology ; },
abstract = {The ecological characteristics of amoA-encoding archaea (AEA) in deep-sea sediments are largely unsolved. This paper aimed to study the diversity, structure, distribution and abundance of the archaeal community and especially its AEA components in the cold seep surface sediments of the Okhotsk Sea, a marginal sea harboring one of the largest methane hydrate reservoirs in the world. Diverse archaeal 16S rRNA gene sequences were identified, with the majority being related to sequences from other cold seep and methane-rich sediment environments. However, the AEA diversity and abundance were quite low as revealed by amoA gene analyses. Correlation analysis indicates that the abundance of the archaeal amoA genes was correlated with the sediment organic matter content. Thus, it is possible that the amoA-carrying archaea here might utilize organic matter for a living. The affiliation of certain archaeal amoA sequences to the GenBank sequences originally obtained from deep-sea hydrothermal vent environments indicated that the related AEA either have a wide range of temperature adaptation or they have a thermophilic evolutionary history in the modern cold deep-sea sediments of the Okhotsk Sea. The dominance of ammonia-oxidizing bacteria over AEA may indicate that bacteria play a significant role in nitrification in the Okhotsk Sea cold seep sediments.},
}
@article {pmid20390264,
year = {2010},
author = {López-Legentil, S and Erwin, PM and Pawlik, JR and Song, B},
title = {Effects of sponge bleaching on ammonia-oxidizing Archaea: distribution and relative expression of ammonia monooxygenase genes associated with the barrel sponge Xestospongia muta.},
journal = {Microbial ecology},
volume = {60},
number = {3},
pages = {561-571},
pmid = {20390264},
issn = {1432-184X},
mesh = {Ammonia/*metabolism ; Animals ; Archaeal Proteins/genetics ; Crenarchaeota/*enzymology/genetics ; Gene Library ; Genes, Archaeal ; Oxidation-Reduction ; Oxidoreductases/*genetics ; Phylogeny ; Polymorphism, Restriction Fragment Length ; RNA, Archaeal/genetics ; Xestospongia/*microbiology ; },
abstract = {Sponge-mediated nitrification is an important process in the nitrogen cycle, however, nothing is known about how nitrification and symbiotic Archaea may be affected by sponge disease and bleaching events. The giant barrel sponge Xestospongia muta is a prominent species on Caribbean reefs that contains cyanobacterial symbionts, the loss of which results in two types of bleaching: cyclic, a recoverable condition; and fatal, a condition associated with the disease-like sponge orange band (SOB) syndrome and sponge death. Terminal restriction fragment length polymorphism (TRFLP) analyses, clone libraries, and relative mRNA quantification of ammonia monooxygenase genes (amoA) were performed using a RNA transcript-based approach to characterize the active ammonia-oxidizing Archaea (AOA) community present in bleached, non-bleached, and SOB tissues of cyclically and fatally bleached sponges. We found that non-bleached and cyclically bleached tissues of X. muta harbored a unique Crenarchaeota community closely related to those reported for other sponges. In contrast, bleached tissue from the most degraded sponge contained a Crenarchaeota community that was more similar to those found in sediment and sand. Although there were no significant differences in amoA expression among the different tissues, amoA expression was higher in the most deteriorated tissues. Results suggest that a shift in the Crenarchaeota community precedes an increase in amoA gene expression in fatally bleached sponges, while cyclic bleaching did not alter the AOA community structure and its amoA gene expression.},
}
@article {pmid20382657,
year = {2010},
author = {de Crécy-Lagard, V and Brochier-Armanet, C and Urbonavicius, J and Fernandez, B and Phillips, G and Lyons, B and Noma, A and Alvarez, S and Droogmans, L and Armengaud, J and Grosjean, H},
title = {Biosynthesis of wyosine derivatives in tRNA: an ancient and highly diverse pathway in Archaea.},
journal = {Molecular biology and evolution},
volume = {27},
number = {9},
pages = {2062-2077},
pmid = {20382657},
issn = {1537-1719},
mesh = {Archaea/classification/genetics/*metabolism ; Chromatography, Liquid ; Guanosine/*analogs &amp; derivatives/chemistry/metabolism ; Mass Spectrometry ; Phylogeny ; RNA, Transfer/*metabolism ; Signal Transduction/*physiology ; },
abstract = {Wyosine (imG) and its derivatives such as wybutosine (yW) are found at position 37 of phenylalanine-specific transfer RNA (tRNA(Phe)), 3' adjacent to the anticodon in Eucarya and Archaea. In Saccharomyces cerevisiae, formation of yW requires five enzymes acting in a strictly sequential order: Trm5, Tyw1, Tyw2, Tyw3, and Tyw4. Archaea contain wyosine derivatives, but their diversity is greater than in eukaryotes and the corresponding biosynthesis pathways still unknown. To identify these pathways, we analyzed the phylogenetic distribution of homologues of the yeast wybutosine biosynthesis proteins in 62 archaeal genomes and proposed a scenario for the origin and evolution of wyosine derivatives biosynthesis in Archaea that was partly experimentally validated. The key observations were 1) that four of the five wybutosine biosynthetic enzymes are ancient and may have been present in the last common ancestor of Archaea and Eucarya, 2) that the variations in the distribution pattern of biosynthesis enzymes reflect the diversity of the wyosine derivatives found in different Archaea. We also identified 7-aminocarboxypropyl-demethylwyosine (yW-86) and its N4-methyl derivative (yW-72) as final products in tRNAs of several Archaea when these were previously thought to be only intermediates of the eukaryotic pathway. We confirmed that isowyosine (imG2) and 7-methylwyosine (mimG) are two archaeal-specific guanosine-37 derivatives found in tRNA of both Euryarchaeota and Crenarchaeota. Finally, we proposed that the duplication of the trm5 gene in some Archaea led to a change in function from N1 methylation of guanosine to C7 methylation of 4-demethylwyosine (imG-14).},
}
@article {pmid20371619,
year = {2010},
author = {Deidda, G and Rossi, N and Putti, S and Tocchini-Valentini, GP},
title = {ARCHAEA-ExPRESs targeting of alpha-tubulin 4 mRNA: a model for high-specificity trans-splicing.},
journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology},
volume = {24},
number = {8},
pages = {2976-2984},
doi = {10.1096/fj.10-154658},
pmid = {20371619},
issn = {1530-6860},
mesh = {Animals ; Archaea/enzymology ; Endonucleases ; *Genetic Techniques ; Liver/metabolism ; Methods ; Mice ; RNA, Messenger/*genetics ; *Trans-Splicing ; Tubulin/*genetics ; },
abstract = {Effectiveness of trans-splicing-mediated mRNA reprogramming depends on specificity and efficiency. We have previously developed a new strategy (ARCHAEA-ExPRESs) that uses a tRNA endonuclease derived from Archaea and its natural substrate, the bulge-helix-bulge (BHB) structure. ARCHAEA-ExPRESs provides increased specificity in functional targeting. In fact, this system is based on a double check, the base pairing and the formation of a BHB structure between the target mRNA and the targeting RNA. In this study, we demonstrate the high specificity of ARCHAEA-ExPRESs by tagging the endogenous alpha-tubulin 4 via trans-splicing. Alpha-tubulin 4 belongs to a gene family sharing high degree of nucleotide sequence homology. The formation of a perfect BHB structure between targeting RNAs and the isotype alpha-tubulin 4 enables selective trans-splicing. Most important, ARCHAEA-ExPRESs functionality is conserved in vivo following transient expression of archaeal tRNA endonuclease in mouse liver. Production of the recombinant protein is strictly dependent on the expression of the archaeal endonuclease, and the efficiency of the system depends on the relative amount of the target and targeting mRNAs. These data prove the effectiveness of ARCHAEA-ExPRESs in an endogenous highly demanding context and disclose the possibility to utilize this system in a variety of technological or therapeutic applications.},
}
@article {pmid20371512,
year = {2010},
author = {Calo, D and Kaminski, L and Eichler, J},
title = {Protein glycosylation in Archaea: sweet and extreme.},
journal = {Glycobiology},
volume = {20},
number = {9},
pages = {1065-1076},
doi = {10.1093/glycob/cwq055},
pmid = {20371512},
issn = {1460-2423},
mesh = {Archaea/*metabolism ; Carbohydrate Metabolism ; Carbohydrate Sequence ; Carbohydrates/chemistry ; *Ecosystem ; Glycosylation ; Molecular Sequence Data ; *Protein Processing, Post-Translational ; Proteins/*metabolism ; },
abstract = {While each of the three domains of life on Earth possesses unique traits and relies on characteristic biological strategies, some processes are common to Eukarya, Bacteria and Archaea. Once believed to be restricted to Eukarya, it is now clear that Bacteria and Archaea are also capable of performing N-glycosylation. However, in contrast to Bacteria, where this posttranslational modification is still considered a rare event, numerous species of Archaea, isolated from a wide range of environments, have been reported to contain proteins bearing Asn-linked glycan moieties. Analysis of the chemical composition of the Asn-linked polysaccharides decorating archaeal proteins has, moreover, revealed the use of a wider variety of sugar subunits than seen in either eukaryal or bacterial glycoproteins. Still, although first reported some 30 years ago, little had been known of the steps or components involved in the archaeal version of this universal posttranslational modification. Now, with the availability of sufficient numbers of genome sequences and the development of appropriate experimental tools, molecular analysis of archaeal N-glycosylation pathways has become possible. Accordingly using halophilic, methanogenic and thermophilic model species, insight into the biosynthesis and attachment of N-linked glycans decorating archaeal glycoproteins is starting to amass. In this review, current understanding of N-glycosylation in Archaea is described.},
}
@article {pmid20370827,
year = {2010},
author = {Di, HJ and Cameron, KC and Shen, JP and Winefield, CS and O'Callaghan, M and Bowatte, S and He, JZ},
title = {Ammonia-oxidizing bacteria and archaea grow under contrasting soil nitrogen conditions.},
journal = {FEMS microbiology ecology},
volume = {72},
number = {3},
pages = {386-394},
doi = {10.1111/j.1574-6941.2010.00861.x},
pmid = {20370827},
issn = {1574-6941},
mesh = {Ammonia/*metabolism ; Archaea/*growth &amp; development/isolation &amp; purification/metabolism ; Bacteria/*growth &amp; development/isolation &amp; purification/metabolism ; Ecosystem ; New Zealand ; Nitrogen/*analysis ; Oxidoreductases/genetics ; Soil/analysis ; *Soil Microbiology ; Transcription, Genetic ; },
abstract = {Nitrification is a key process of the nitrogen (N) cycle in soil with major environmental implications. The recent discovery of ammonia-oxidizing archaea (AOA) questions the traditional assumption of the dominant role of ammonia-oxidizing bacteria (AOB) in nitrification. We investigated AOB and AOA growth and nitrification rate in two different layers of three grassland soils treated with animal urine substrate and a nitrification inhibitor [dicyandiamide (DCD)]. We show that AOB were more abundant in the topsoils than in the subsoils, whereas AOA were more abundant in one of the subsoils. AOB grew substantially when supplied with a high dose of urine substrate, whereas AOA only grew in the Controls without the urine-N substrate. AOB growth and the amoA gene transcription activity were significantly inhibited by DCD. Nitrification rates were much higher in the topsoils than in the subsoils and were significantly related to AOB abundance, but not to AOA abundance. These results suggest that AOB and AOA prefer different soil N conditions to grow: AOB under high ammonia (NH(3)) substrate and AOA under low NH(3) substrate conditions.},
}
@article {pmid20364355,
year = {2010},
author = {Al-Mailem, DM and Sorkhoh, NA and Al-Awadhi, H and Eliyas, M and Radwan, SS},
title = {Biodegradation of crude oil and pure hydrocarbons by extreme halophilic archaea from hypersaline coasts of the Arabian Gulf.},
journal = {Extremophiles : life under extreme conditions},
volume = {14},
number = {3},
pages = {321-328},
pmid = {20364355},
issn = {1433-4909},
mesh = {Alkanes/chemistry ; Archaea/*physiology ; Biodegradation, Environmental ; Geologic Sediments/microbiology ; Halobacterium/*metabolism ; Halococcus/*metabolism ; Hydrocarbons/*chemistry ; *Petroleum ; Phenanthrenes/chemistry ; Seawater/microbiology ; Temperature ; Water Pollutants, Chemical/metabolism ; },
abstract = {Two extreme halophilic Haloferax strains and one strain each of Halobacterium and Halococcus were isolated from a hypersaline coastal area of the Arabian Gulf on a mineral salt medium with crude oil vapor as a sole source of carbon and energy. These archaea needed at least 1 M NaCl for growth in culture, and grew best in the presence of 4 M NaCl or more. Optimum growth temperatures lied between 40 and 45 degrees C. The four archaea were resistant to the antibiotics chloramphenicol, cycloheximide, nalidixic acid, penicillin, streptomycin and tetracycline. The strains could grow on a wide scope of aliphatic and aromatic (both mono-and polynuclear) hydrocarbons, as sole sources of carbon and energy. Quantitative measurements revealed that these extreme halophilic prokaryotes could biodegrade crude oil (13-47%, depending on the strain and medium salinity), n-octadecane (28-67%) and phenanthrene (13-30%) in culture after 3 weeks of incubation. The rates of biodegradation by all strains were enhanced with increasing NaCl concentration in the medium. Optimal concentration was 3 M NaCl, but even with 4 M NaCl the hydrocarbon-biodegradation rates were higher than with 1 and 2 M NaCl. It was concluded that these archaea could contribute to self-cleaning and bioremediation of oil-polluted hypersaline environments.},
}
@article {pmid20347718,
year = {2011},
author = {Calo, D and Eichler, J},
title = {Crossing the membrane in Archaea, the third domain of life.},
journal = {Biochimica et biophysica acta},
volume = {1808},
number = {3},
pages = {885-891},
doi = {10.1016/j.bbamem.2010.03.020},
pmid = {20347718},
issn = {0006-3002},
mesh = {Archaea/*physiology ; Archaeal Proteins/*metabolism ; Cell Membrane/*physiology ; Protein Transport/*physiology ; },
abstract = {Many of the recent advancements in the field of protein translocation, particularly from the structural perspective, have relied on Archaea. For instance, the solved structures of the translocon from the methanoarchaeon Methanocaldococcus jannaschii of the ribosomal large subunit from the haloarchaeon Haloarcula marismortui and of components of the SRP pathway from several archaeal species have provided novel insight into various aspects of the translocation event. Given the major contribution that Archaea have made to our understanding of how proteins enter and traverse membranes, it is surprising that relatively little is known of protein translocation in Archaea in comparison to the well-defined translocation pathways of Eukarya and Bacteria. What is known, however, points to archaeal translocation as comprising a mosaic of eukaryal and bacterial traits together with aspects of the process seemingly unique to this, the third domain of life. Here, current understanding of archaeal protein translocation is considered. This article is part of a Special Issue entitled Protein translocation across or insertion into membranes.},
}
@article {pmid20345944,
year = {2010},
author = {Santoro, AE and Casciotti, KL and Francis, CA},
title = {Activity, abundance and diversity of nitrifying archaea and bacteria in the central California Current.},
journal = {Environmental microbiology},
volume = {12},
number = {7},
pages = {1989-2006},
doi = {10.1111/j.1462-2920.2010.02205.x},
pmid = {20345944},
issn = {1462-2920},
mesh = {Ammonia/metabolism ; Archaea/*classification/isolation &amp; purification/*metabolism ; Archaeal Proteins/genetics ; Bacteria/*classification/isolation &amp; purification/*metabolism ; Bacterial Proteins/genetics ; *Biodiversity ; California ; Cluster Analysis ; DNA, Archaeal/chemistry/genetics ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Genes, rRNA ; Molecular Sequence Data ; Nitrates/metabolism ; Nitrites/metabolism ; Nitrogen/*metabolism ; Oxidoreductases/genetics ; Phylogeny ; RNA, Archaeal/genetics ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; },
abstract = {A combination of stable isotope and molecular biological approaches was used to determine the activity, abundance and diversity of nitrifying organisms in the central California Current. Using (15)NH(4)(+) incubations, nitrification was detectable in the upper water column down to 500 m; maximal rates were observed just below the euphotic zone. Crenarchaeal and betaproteobacterial ammonia monooxygenase subunit A genes (amoA), and 16S ribosomal RNA (rRNA) genes of Marine Group I Crenarchaeota and a putative nitrite-oxidizing genus, Nitrospina, were quantified using quantitative PCR. Crenarchaeal amoA abundance ranged from three to six genes ml(-1) in oligotrophic surface waters to > 8.7 x 10(4) genes ml(-1) just below the core of the California Current at 200 m depth. Bacterial amoA abundance was lower than archaeal amoA and ranged from below detection levels to 400 genes ml(-1). Nitrification rates were not directly correlated to bacterial or archaeal amoA abundance. Archaeal amoA and Marine Group I crenarchaeal 16S rRNA gene abundances were correlated with Nitrospina 16S rRNA gene abundance at all stations, indicating that similar factors may control the distribution of these two groups. Putatively shallow water-associated archaeal amoA types ('Cluster A') decreased in relative abundance with depth, while a deep water-associated amoA type ('Cluster B') increased with depth. Although some Cluster B amoA sequences were found in surface waters, expressed amoA gene sequences were predominantly from Cluster A. Cluster B amoA transcripts were detected between 100 and 500 m depths, suggesting an active role in ammonia oxidation in the mesopelagic. Expression of marine Nitrosospira-like bacterial amoA genes was detected throughout the euphotic zone down to 200 m. Natural abundance stable isotope ratios (delta(15)N and delta(18)O) in nitrate (NO(3)(-)) and nitrous oxide (N(2)O) were used to evaluate the importance of nitrification over longer time scales. Using an isotope mass balance model, we calculate that nitrification could produce between 0.45 and 2.93 micromol m(-2) day(-1) N(2)O in the central California Current, or approximately 1.5-4 times the local N(2)O flux from deep water.},
}
@article {pmid20334683,
year = {2010},
author = {Sun, FJ and Caetano-Anollés, G},
title = {The ancient history of the structure of ribonuclease P and the early origins of Archaea.},
journal = {BMC bioinformatics},
volume = {11},
number = {},
pages = {153},
pmid = {20334683},
issn = {1471-2105},
mesh = {Archaea/enzymology/*genetics ; *Evolution, Molecular ; Genetic Variation ; Genomics/*methods ; Phylogeny ; Protein Conformation ; Protein Structure, Tertiary ; RNA, Archaeal/metabolism ; RNA, Transfer/chemistry ; Ribonuclease P/*chemistry ; },
abstract = {BACKGROUND: Ribonuclease P is an ancient endonuclease that cleaves precursor tRNA and generally consists of a catalytic RNA subunit (RPR) and one or more proteins (RPPs). It represents an important macromolecular complex and model system that is universally distributed in life. Its putative origins have inspired fundamental hypotheses, including the proposal of an ancient RNA world.<br><br>RESULTS: To study the evolution of this complex, we constructed rooted phylogenetic trees of RPR molecules and substructures and estimated RPP age using a cladistic method that embeds structure directly into phylogenetic analysis. The general approach was used previously to study the evolution of tRNA, SINE RNA and 5S rRNA, the origins of metabolism, and the evolution and complexity of the protein world, and revealed here remarkable evolutionary patterns. Trees of molecules uncovered the tripartite nature of life and the early origin of archaeal RPRs. Trees of substructures showed molecules originated in stem P12 and were accessorized with a catalytic P1-P4 core structure before the first substructure was lost in Archaea. This core currently interacts with RPPs and ancient segments of the tRNA molecule. Finally, a census of protein domain structure in hundreds of genomes established RPPs appeared after the rise of metabolic enzymes at the onset of the protein world.<br><br>CONCLUSIONS: The study provides a detailed account of the history and early diversification of a fundamental ribonucleoprotein and offers further evidence in support of the existence of a tripartite organismal world that originated by the segregation of archaeal lineages from an ancient community of primordial organisms.},
}
@article {pmid20235826,
year = {2010},
author = {Thauer, RK and Kaster, AK and Goenrich, M and Schick, M and Hiromoto, T and Shima, S},
title = {Hydrogenases from methanogenic archaea, nickel, a novel cofactor, and H2 storage.},
journal = {Annual review of biochemistry},
volume = {79},
number = {},
pages = {507-536},
doi = {10.1146/annurev.biochem.030508.152103},
pmid = {20235826},
issn = {1545-4509},
mesh = {Archaea/*enzymology/metabolism ; Hydrogen/*metabolism ; Hydrogenase/chemistry/genetics/*metabolism ; *Nickel ; },
abstract = {Most methanogenic archaea reduce CO(2) with H(2) to CH(4). For the activation of H(2), they use different [NiFe]-hydrogenases, namely energy-converting [NiFe]-hydrogenases, heterodisulfide reductase-associated [NiFe]-hydrogenase or methanophenazine-reducing [NiFe]-hydrogenase, and F(420)-reducing [NiFe]-hydrogenase. The energy-converting [NiFe]-hydrogenases are phylogenetically related to complex I of the respiratory chain. Under conditions of nickel limitation, some methanogens synthesize a nickel-independent [Fe]-hydrogenase (instead of F(420)-reducing [NiFe]-hydrogenase) and by that reduce their nickel requirement. The [Fe]-hydrogenase harbors a unique iron-guanylylpyridinol cofactor (FeGP cofactor), in which a low-spin iron is ligated by two CO, one C(O)CH(2)-, one S-CH(2)-, and a sp(2)-hybridized pyridinol nitrogen. Ligation of the iron is thus similar to that of the low-spin iron in the binuclear active-site metal center of [NiFe]- and [FeFe]-hydrogenases. Putative genes for the synthesis of the FeGP cofactor have been identified. The formation of methane from 4 H(2) and CO(2) catalyzed by methanogenic archaea is being discussed as an efficient means to store H(2).},
}
@article {pmid20230605,
year = {2010},
author = {Weinberg, Z and Wang, JX and Bogue, J and Yang, J and Corbino, K and Moy, RH and Breaker, RR},
title = {Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea, and their metagenomes.},
journal = {Genome biology},
volume = {11},
number = {3},
pages = {R31},
pmid = {20230605},
issn = {1474-760X},
support = {RR19895-02/RR/NCRR NIH HHS/United States ; //Howard Hughes Medical Institute/United States ; },
mesh = {Amino Acid Motifs/*genetics ; Archaea/*genetics ; Bacteria/*genetics ; Base Pairing ; Computational Biology ; DNA Mutational Analysis/methods ; Genome, Archaeal/*genetics ; Genome, Bacterial/*genetics ; Genomics/*methods ; Nucleic Acid Conformation ; RNA, Untranslated/*genetics ; },
abstract = {BACKGROUND: Structured noncoding RNAs perform many functions that are essential for protein synthesis, RNA processing, and gene regulation. Structured RNAs can be detected by comparative genomics, in which homologous sequences are identified and inspected for mutations that conserve RNA secondary structure.<br><br>RESULTS: By applying a comparative genomics-based approach to genome and metagenome sequences from bacteria and archaea, we identified 104 candidate structured RNAs and inferred putative functions for many of these. Twelve candidate metabolite-binding RNAs were identified, three of which were validated, including one reported herein that binds the coenzyme S-adenosylmethionine. Newly identified cis-regulatory RNAs are implicated in photosynthesis or nitrogen regulation in cyanobacteria, purine and one-carbon metabolism, stomach infection by Helicobacter, and many other physiological processes. A candidate riboswitch termed crcB is represented in both bacteria and archaea. Another RNA motif may control gene expression from 3'-untranslated regions of mRNAs, which is unusual for bacteria. Many noncoding RNAs that likely act in trans are also revealed, and several of the noncoding RNA candidates are found mostly or exclusively in metagenome DNA sequences.<br><br>CONCLUSIONS: This work greatly expands the variety of highly structured noncoding RNAs known to exist in bacteria and archaea and provides a starting point for biochemical and genetic studies needed to validate their biologic functions. Given the sustained rate of RNA discovery over several similar projects, we expect that far more structured RNAs remain to be discovered from bacterial and archaeal organisms.},
}
@article {pmid20222453,
year = {2009},
author = {Shi, Y and Zhang, Y and Yang, H},
title = {[Phylogenetic analysis of symbiotic archaea in the gut of Reticulitermes chinensis Snyder].},
journal = {Wei sheng wu xue bao = Acta microbiologica Sinica},
volume = {49},
number = {12},
pages = {1655-1659},
pmid = {20222453},
issn = {0001-6209},
mesh = {Animals ; Archaea/*classification/genetics/*isolation &amp; purification/physiology ; DNA, Archaeal/genetics ; DNA, Ribosomal/genetics ; Intestines/microbiology ; Isoptera/*microbiology/physiology ; Molecular Sequence Data ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Symbiosis ; },
abstract = {OBJECTIVE: To analyze the phylotypes of symbiotic archaea in the gut of Reticulitermes chinensis Snyder by using non-cultivating method.<br><br>METHODS: We amplified 16S rRNA genes of the symbiotic archaea from the DNA extract of the whole gut with the universal archaeal 16S rDNA primer. A clone library of archaeal 16S rDNA was established and selected clones were sequenced and phylogeneticly analyzed.<br><br>RESULTS: Five 16S rDNA sequences with the similarity between 93.2% and 99.2% to each other were obtained from Reticulitermes chinensis Snyder. Phylogenetic analysis showed that the five clones were clustered with Methanobrevibacter clones or isolates obtained from Reticulitermes speratus and Reticulitermes flavipes.<br><br>CONCLUSION: The results showed that symbiotic archaea in the gut of Reticulitermes chinensis were affiliated with Methanobrevibacter.},
}
@article {pmid20195901,
year = {2010},
author = {Taketani, RG and Yoshiura, CA and Dias, AC and Andreote, FD and Tsai, SM},
title = {Diversity and identification of methanogenic archaea and sulphate-reducing bacteria in sediments from a pristine tropical mangrove.},
journal = {Antonie van Leeuwenhoek},
volume = {97},
number = {4},
pages = {401-411},
doi = {10.1007/s10482-010-9422-8},
pmid = {20195901},
issn = {1572-9699},
mesh = {Archaea/*classification/metabolism ; Archaeal Proteins/genetics ; Bacteria/*classification/metabolism ; Bacterial Proteins/genetics ; *Biodiversity ; Electrophoresis, Polyacrylamide Gel ; Methane/*metabolism ; Molecular Sequence Data ; Nucleic Acid Denaturation ; Oxidation-Reduction ; Rhizophoraceae/*microbiology ; Sequence Analysis, DNA ; Sulfates/*metabolism ; },
abstract = {Mangrove sediments are anaerobic ecosystems rich in organic matter. This environment is optimal for anaerobic microorganisms, such as sulphate-reducing bacteria and methanogenic archaea, which are responsible for nutrient cycling. In this study, the diversity of these two functional guilds was evaluated in a pristine mangrove forest using denaturing gradient gel electrophoresis (DGGE) and clone library sequencing in a 50 cm vertical profile sampled every 5.0 cm. DGGE profiles indicated that both groups presented higher richness in shallow samples (0-30 cm) with a steep decrease in richness beyond that depth. According to redundancy analysis, this alteration significantly correlated with a decrease in the amount of organic matter. Clone library sequencing indicated that depth had a strong effect on the selection of dissimilatory sulphate reductase (dsrB) operational taxonomic units (OTUs), as indicated by the small number of shared OTUs found in shallow (0.0 cm) and deep (40.0 cm) libraries. On the other hand, methyl coenzyme-M reductase (mcrA) libraries indicated that most of the OTUs found in the shallow library were present in the deep library. These results show that these two guilds co-exist in these mangrove sediments and indicate important roles for these organisms in nutrient cycling within this ecosystem.},
}
@article {pmid20192962,
year = {2010},
author = {Beman, JM and Sachdeva, R and Fuhrman, JA},
title = {Population ecology of nitrifying archaea and bacteria in the Southern California Bight.},
journal = {Environmental microbiology},
volume = {12},
number = {5},
pages = {1282-1292},
doi = {10.1111/j.1462-2920.2010.02172.x},
pmid = {20192962},
issn = {1462-2920},
mesh = {Ammonia/metabolism ; Betaproteobacteria/classification/genetics/*isolation &amp; purification/metabolism ; California ; Crenarchaeota/classification/genetics/*isolation &amp; purification/metabolism ; DNA, Archaeal/analysis ; DNA, Bacterial/analysis ; *Ecosystem ; Nitrites/*metabolism ; Oxidoreductases/genetics/*metabolism ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; Sequence Analysis, DNA ; Time Factors ; },
abstract = {Marine Crenarchaeota are among the most abundant microbial groups in the ocean, and although relatively little is currently known about their biogeochemical roles in marine ecosystems, recognition that Crenarchaeota posses ammonia monooxygenase (amoA) genes and may act as ammonia-oxidizing archaea (AOA) offers another means of probing the ecology of these microorganisms. Here we use a time series approach combining quantification of archaeal and bacterial ammonia oxidizers with bacterial community fingerprints and biogeochemistry, to explore the population and community ecology of nitrification. At multiple depths (150, 500 and 890 m) in the Southern California Bight sampled monthly from 2003 to 2006, AOA were enumerated via quantitative PCR of archaeal amoA and marine group 1 Crenarchaeota 16S rRNA genes. Based on amoA genes, AOA were highly variable in time - a consistent feature of marine Crenarchaeota- however, average values were similar at different depths and ranged from 2.20 to 2.76 x 10(4) amoA copies ml(-1). Archaeal amoA genes were correlated with Crenarchaeota 16S rRNA genes (r(2) = 0.79) and the slope of this relationship was 1.02, demonstrating that the majority of marine group 1 Crenarchaeota present over the dates and depths sampled possessed amoA. Two AOA clades were specifically quantified and compared with betaproteobacterial ammonia-oxidizing bacteria (beta-AOB) amoA genes at 150 m; these AOA groups were found to strongly co-vary in time (r(2) = 0.70, P < 0.001) whereas AOA : beta-AOB ratios ranged from 13 to 5630. Increases in the AOA : beta-AOB ratio correlated with the accumulation of nitrite (r(2) = 0.87, P < 0.001), and may be indicative of differences in substrate affinities and activities leading to periodic decoupling between ammonia and nitrite oxidation. These data capture a dynamic nitrogen cycle in which multiple microbial groups appear to be active participants.},
}
@article {pmid20157750,
year = {2010},
author = {Tapilatu, YH and Grossi, V and Acquaviva, M and Militon, C and Bertrand, JC and Cuny, P},
title = {Isolation of hydrocarbon-degrading extremely halophilic archaea from an uncontaminated hypersaline pond (Camargue, France).},
journal = {Extremophiles : life under extreme conditions},
volume = {14},
number = {2},
pages = {225-231},
pmid = {20157750},
issn = {1433-4909},
mesh = {Base Sequence ; Biodegradation, Environmental ; Crystallization ; DNA Primers/genetics ; France ; Fresh Water/*microbiology ; Fuel Oils ; Haloarcula/classification/genetics/*isolation &amp; purification/*metabolism ; Haloferax/classification/genetics/*isolation &amp; purification/*metabolism ; Hydrocarbons/*metabolism ; Molecular Sequence Data ; Phylogeny ; RNA, Archaeal/genetics ; RNA, Ribosomal, 16S/genetics ; Salinity ; Water Pollutants, Chemical/*metabolism ; },
abstract = {Little information exists about the ability of halophilic archaea present in hypersaline environments to degrade hydrocarbons. In order to identify the potential actors of hydrocarbon degradation in these environments, enrichment cultures were prepared using samples collected from a shallow crystallizer pond with no known contamination history in Camargue, France, with n-alkanes provided as source of carbon and energy. Five alkane-degrading halophilic archaeal strains were isolated: one (strain MSNC 2) was closely related to Haloarcula and three (strains MSNC 4, MSNC 14, and MSNC 16) to Haloferax. Biodegradation assays showed that depending on the strain, 32 to 95% (0.5 g/l) of heptadecane was degraded after 30 days of incubation at 40 degrees C in 225 g/l NaCl artificial medium. One of the strains (MSNC 14) was also able to degrade phenanthrene. This work clearly shows for the first time the potential role of halophilic archaea belonging to the genera Haloarcula and Haloferax in the degradation of hydrocarbons in both pristine and hydrocarbon-contaminated hypersaline environments.},
}
@article {pmid20139989,
year = {2010},
author = {Ikeuchi, Y and Kimura, S and Numata, T and Nakamura, D and Yokogawa, T and Ogata, T and Wada, T and Suzuki, T and Suzuki, T},
title = {Agmatine-conjugated cytidine in a tRNA anticodon is essential for AUA decoding in archaea.},
journal = {Nature chemical biology},
volume = {6},
number = {4},
pages = {277-282},
pmid = {20139989},
issn = {1552-4469},
mesh = {Agmatine/*chemistry/metabolism ; Anticodon/*chemistry/*genetics/metabolism ; Archaea/cytology/*genetics/*metabolism ; Catalysis ; Cytidine/*chemistry/metabolism ; Ligases/metabolism ; RNA, Transfer/*chemistry/*genetics/metabolism ; },
abstract = {A modified base at the first (wobble) position of some tRNA anticodons is critical for deciphering the genetic code. In eukaryotes and eubacteria, AUA codons are decoded by tRNAsIle with modified bases pseudouridine (and/or inosine) and lysidine, respectively. The mechanism by which archaeal species translate AUA codons is unclear. We describe a polyamine-conjugated modified base, 2-agmatinylcytidine (agm(2)C or agmatidine), at the wobble position of archaeal tRNA(Ile) that decodes AUA codons specifically. We demonstrate that archaeal cells use agmatine to synthesize agm(2)C of tRNA(Ile). We also identified a new enzyme, tRNA(Ile)-agm(2)C synthetase (TiaS), that catalyzes agm(2)C formation in the presence of agmatine and ATP. Although agm(2)C is chemically similar to lysidine, TiaS constitutes a distinct class of enzyme from tRNA(Ile)-lysidine synthetase (TilS), suggesting that the decoding systems evolved convergently across domains.},
}
@article {pmid20139592,
year = {2010},
author = {Yamauchi, N},
title = {The pathway of leucine to mevalonate in halophilic archaea: efficient incorporation of leucine into isoprenoidal lipid with the involvement of isovaleryl-CoA dehydrogenase in Halobacterium salinarum.},
journal = {Bioscience, biotechnology, and biochemistry},
volume = {74},
number = {2},
pages = {443-446},
doi = {10.1271/bbb.90814},
pmid = {20139592},
issn = {1347-6947},
mesh = {Halobacteriales/genetics/*metabolism ; Halobacterium salinarum/genetics/*metabolism ; Isovaleryl-CoA Dehydrogenase/genetics/*metabolism ; Leucine/genetics/*metabolism ; Lipids/genetics ; Mevalonic Acid/*metabolism ; },
abstract = {The pathway of leucine to mevalonate, which has attracted attention in the study of the biosynthesis of isoprenoid in parasitic protozoa and myxobacterium, was observed in the biosynthesis of the lipid core in halophilic archaea. The involvement of isovaleryl-CoA dehydrogenase was strongly suggested, with stereospecific conversion of the diastereotopic methyl group of leucine to isoprenoidal lipid.},
}
@article {pmid20139321,
year = {2010},
author = {Pereyra, LP and Hiibel, SR and Prieto Riquelme, MV and Reardon, KF and Pruden, A},
title = {Detection and quantification of functional genes of cellulose- degrading, fermentative, and sulfate-reducing bacteria and methanogenic archaea.},
journal = {Applied and environmental microbiology},
volume = {76},
number = {7},
pages = {2192-2202},
pmid = {20139321},
issn = {1098-5336},
mesh = {Archaea/*enzymology/genetics/metabolism ; Archaeal Proteins/genetics ; Bacteria/*enzymology/genetics/metabolism ; Bacterial Proteins/genetics ; Bioreactors/microbiology ; Cellulose/*metabolism ; DNA Primers/genetics ; DNA, Archaeal/chemistry/genetics ; DNA, Bacterial/chemistry/genetics ; Fermentation ; Metagenomics/*methods ; Methane/*metabolism ; Molecular Sequence Data ; Oxidation-Reduction ; Sensitivity and Specificity ; Sequence Analysis, DNA ; Sulfates/*metabolism ; },
abstract = {Cellulose degradation, fermentation, sulfate reduction, and methanogenesis are microbial processes that coexist in a variety of natural and engineered anaerobic environments. Compared to the study of 16S rRNA genes, the study of the genes encoding the enzymes responsible for these phylogenetically diverse functions is advantageous because it provides direct functional information. However, no methods are available for the broad quantification of these genes from uncultured microbes characteristic of complex environments. In this study, consensus degenerate hybrid oligonucleotide primers were designed and validated to amplify both sequenced and unsequenced glycoside hydrolase genes of cellulose-degrading bacteria, hydA genes of fermentative bacteria, dsrA genes of sulfate-reducing bacteria, and mcrA genes of methanogenic archaea. Specificity was verified in silico and by cloning and sequencing of PCR products obtained from an environmental sample characterized by the target functions. The primer pairs were further adapted to quantitative PCR (Q-PCR), and the method was demonstrated on samples obtained from two sulfate-reducing bioreactors treating mine drainage, one lignocellulose based and the other ethanol fed. As expected, the Q-PCR analysis revealed that the lignocellulose-based bioreactor contained higher numbers of cellulose degraders, fermenters, and methanogens, while the ethanol-fed bioreactor was enriched in sulfate reducers. The suite of primers developed represents a significant advance over prior work, which, for the most part, has targeted only pure cultures or has suffered from low specificity. Furthermore, ensuring the suitability of the primers for Q-PCR provided broad quantitative access to genes that drive critical anaerobic catalytic processes.},
}
@article {pmid20132282,
year = {2010},
author = {Bidle, KA and Haramaty, L and Baggett, N and Nannen, J and Bidle, KD},
title = {Tantalizing evidence for caspase-like protein expression and activity in the cellular stress response of Archaea.},
journal = {Environmental microbiology},
volume = {12},
number = {5},
pages = {1161-1172},
doi = {10.1111/j.1462-2920.2010.02157.x},
pmid = {20132282},
issn = {1462-2920},
mesh = {Archaea/drug effects/enzymology/genetics/*physiology ; Archaeal Proteins/genetics/metabolism ; Caspase 8/*metabolism ; Caspase Inhibitors ; Haloferax volcanii/drug effects/enzymology/genetics/*physiology ; *Heat-Shock Response ; Osmotic Pressure ; Proteome ; Sodium Chloride/*pharmacology ; },
abstract = {An enigmatic feature of microbial evolution is the emergence of programmed cell death (PCD), a genetically controlled form of cell suicide triggered by environmental stimuli. Archaea, the second major prokaryotic domain of life, have been notably absent from the PCD inheritance discussion, due to a lack of genetic homologues. Using the model haloarchaeon Haloferax volcanii, we document extremely high caspase-specific activity and expression of immunoreactive proteins to human caspase 8 antisera, both of which were induced by salt stress and death and were abolished by in vivo addition of a broad-spectrum caspase inhibitor. Caspase inhibition severely impaired cell growth under low and high salt stress, demonstrating a critical role in the cellular stress response. In silico analysis of the H. volcanii proteome identified a subset of 18 potential target proteins containing a signature tetrapeptide caspase cleavage motif (IETD), some with putative roles in allosteric regulation, signal transduction, osmotic stress and cell communication. Detection of similarly high activity and expression in other haloarchaea (Halorubrum and Haloarcula) and in diverse members of Euryarchaeota (the methanogen Methanosarcina acetivorans and the hyperthermophile Pyrococcus furiosus) and Crenarchaeota (the acidophile Sulfolobus solfataricus) argue for a broad representation within the archaeal domain. By playing a role in normal cell function, caspase-like proteases in Archaea appear to have co-evolved with other metabolic pathways, broadening their biological roles beyond apoptosis and cell death.},
}
@article {pmid20132279,
year = {2010},
author = {Bartossek, R and Nicol, GW and Lanzen, A and Klenk, HP and Schleper, C},
title = {Homologues of nitrite reductases in ammonia-oxidizing archaea: diversity and genomic context.},
journal = {Environmental microbiology},
volume = {12},
number = {4},
pages = {1075-1088},
doi = {10.1111/j.1462-2920.2010.02153.x},
pmid = {20132279},
issn = {1462-2920},
mesh = {Amino Acid Sequence ; Ammonia/*metabolism ; Archaea/classification/*enzymology/genetics ; Bacteria/enzymology/genetics ; DNA, Archaeal/genetics ; Genome, Archaeal ; Genomic Library ; *Metagenomics ; Molecular Sequence Data ; Nitrite Reductases/*genetics ; Oxidation-Reduction ; Oxidoreductases/genetics ; Phylogeny ; Polymerase Chain Reaction ; Sequence Alignment ; Sequence Analysis, DNA ; },
abstract = {Ammonia-oxidizing archaea are frequent and ubiquitous inhabitants of terrestrial and marine environments. As they have only recently been detected, most aspects of their metabolism are yet unknown. Here we report on the occurrence of genes encoding potential homologues of copper-dependent nitrite reductases (NirK) in ammonia-oxidizing archaea of soils and other environments using metagenomic approaches and PCR amplification. Two pairs of highly overlapping 40 kb genome fragments, each containing nirK genes of archaea, were isolated from a metagenomic soil library. Between 68% and 85% of the open reading frames on these genome fragments had homologues in the genomes of the marine archaeal ammonia oxidizers Nitrosopumilus maritimus and Cenarchaeum symbiosum. Extensions of NirK homologues with C-terminal fused amicyanin domains were deduced from two of the four fosmids indicating structural variation of these multicopper proteins in archaea. Phylogenetic analyses including all major groups of currently known NirK homologues revealed that the deduced protein sequences of marine and soil archaea were separated into two highly divergent lineages that did not contain bacterial homologues. In contrast, another separated lineage contained potential multicopper oxidases of both domains, archaea and bacteria. More nirK gene variants directly amplified by PCR from several environments indicated further diversity of the gene and a widespread occurrence in archaea. Transcription of the potential archaeal nirK in soil was demonstrated at different water contents, but no significant increase in transcript copy number was observed with increased denitrifying activity.},
}
@article {pmid20129051,
year = {2010},
author = {Karginov, FV and Hannon, GJ},
title = {The CRISPR system: small RNA-guided defense in bacteria and archaea.},
journal = {Molecular cell},
volume = {37},
number = {1},
pages = {7-19},
pmid = {20129051},
issn = {1097-4164},
support = {P01 CA013106/CA/NCI NIH HHS/United States ; P01 CA013106-370027/CA/NCI NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; },
mesh = {Archaea/*genetics/virology ; Bacteria/*genetics/virology ; Bacteriophages/genetics ; Evolution, Molecular ; Inverted Repeat Sequences/*physiology ; *Models, Genetic ; RNA, Archaeal/metabolism/*physiology ; RNA, Bacterial/metabolism/*physiology ; Sequence Analysis, DNA ; },
abstract = {All cellular systems evolve ways to combat predators and genomic parasites. In bacteria and archaea, numerous resistance mechanisms have developed against phage. Our understanding of this defensive repertoire has recently been expanded to include the CRISPR system of clustered, regularly interspaced short palindromic repeats. In this remarkable pathway, short sequence tags from invading genetic elements are actively incorporated into the host's CRISPR locus to be transcribed and processed into a set of small RNAs that guide the destruction of foreign genetic material. Here we review the inner workings of this adaptable and heritable immune system and draw comparisons to small RNA-guided defense mechanisms in eukaryotic cells.},
}
@article {pmid20125085,
year = {2010},
author = {Marraffini, LA and Sontheimer, EJ},
title = {CRISPR interference: RNA-directed adaptive immunity in bacteria and archaea.},
journal = {Nature reviews. Genetics},
volume = {11},
number = {3},
pages = {181-190},
pmid = {20125085},
issn = {1471-0064},
support = {R03 AI079722/AI/NIAID NIH HHS/United States ; R03 AI079722-02/AI/NIAID NIH HHS/United States ; },
mesh = {Adaptive Immunity/genetics ; Archaea/*genetics/immunology/metabolism ; Bacteria/*genetics/immunology/metabolism/pathogenicity ; Bacteriophages/genetics/immunology ; Evolution, Molecular ; Inverted Repeat Sequences ; Models, Genetic ; RNA Interference ; RNA, Archaeal/genetics/metabolism ; RNA, Bacterial/genetics/metabolism ; Virulence/genetics/immunology ; },
abstract = {Sequence-directed genetic interference pathways control gene expression and preserve genome integrity in all kingdoms of life. The importance of such pathways is highlighted by the extensive study of RNA interference (RNAi) and related processes in eukaryotes. In many bacteria and most archaea, clustered, regularly interspaced short palindromic repeats (CRISPRs) are involved in a more recently discovered interference pathway that protects cells from bacteriophages and conjugative plasmids. CRISPR sequences provide an adaptive, heritable record of past infections and express CRISPR RNAs - small RNAs that target invasive nucleic acids. Here, we review the mechanisms of CRISPR interference and its roles in microbial physiology and evolution. We also discuss potential applications of this novel interference pathway.},
}
@article {pmid20122937,
year = {2010},
author = {Zuo, Z and Rodgers, CJ and Mikheikin, AL and Trakselis, MA},
title = {Characterization of a functional DnaG-type primase in archaea: implications for a dual-primase system.},
journal = {Journal of molecular biology},
volume = {397},
number = {3},
pages = {664-676},
doi = {10.1016/j.jmb.2010.01.057},
pmid = {20122937},
issn = {1089-8638},
mesh = {Amino Acid Sequence ; Animals ; Archaeal Proteins/*metabolism ; DNA Primase/genetics/*metabolism ; DNA, Archaeal/genetics/*metabolism ; Electrophoretic Mobility Shift Assay ; Eukaryota/enzymology ; Fluorescence Polarization ; Glutamic Acid/chemistry/genetics ; Molecular Sequence Data ; Mutagenesis, Site-Directed ; Mutation/genetics ; Sulfolobus solfataricus/*enzymology/genetics/growth &amp; development ; },
abstract = {We have biochemically characterized the bacterial-like DnaG primase contained within the hyperthermophilic crenarchaeon Sulfolobus solfataricus (Sso) and compared in vitro priming kinetics with those of the eukaryotic-type primase (PriSL) also found in Sso. SsoDnaG exhibited metal- and temperature-dependent profiles consistent with priming at high temperatures. The distribution of primer products was discrete but highly similar to the distribution of primer products produced by the homologous Escherichia coli DnaG. The predominate primer length was 13 bases, although less abundant products are present. SsoDnaG was found to bind DNA cooperatively as a dimer with a moderate dissociation constant. Mutation of the conserved glutamate in the active site severely inhibited priming activity, suggesting a functional homology with E. coli DnaG. SsoDnaG was also found to have a greater than fourfold faster rate of DNA priming over that of SsoPriSL under optimal in vitro conditions. The presence of both enzymatically functional primase families in archaea suggests that the DNA priming role may be shared on leading or lagging strands during DNA replication.},
}
@article {pmid20118363,
year = {2010},
author = {Urakawa, H and Martens-Habbena, W and Stahl, DA},
title = {High abundance of ammonia-oxidizing Archaea in coastal waters, determined using a modified DNA extraction method.},
journal = {Applied and environmental microbiology},
volume = {76},
number = {7},
pages = {2129-2135},
pmid = {20118363},
issn = {1098-5336},
mesh = {Ammonia/*metabolism ; Archaea/genetics/*isolation &amp; purification/*metabolism ; DNA, Archaeal/genetics/*isolation &amp; purification ; Molecular Biology/*methods ; Oxidation-Reduction ; Polymerase Chain Reaction/methods ; Seawater/*microbiology ; Sensitivity and Specificity ; },
abstract = {Molecular characterizations of environmental microbial populations based on recovery and analysis of DNA generally assume efficient or unbiased extraction of DNA from different sample matrices and microbial groups. Appropriate controls to verify this basic assumption are rarely included. Here three different DNA extractions, performed with two commercial kits (FastDNA and UltraClean) and a standard phenol-chloroform method, and two alternative filtration methods (Sterivex and 25-mm-diameter polycarbonate filters) were evaluated, using the addition of Nitrosopumilus maritimus cells to track the recovery of DNA from marine Archaea. After the comparison, a simplified phenol-chloroform extraction method was developed and shown to be significantly superior, in terms of both the recovery and the purity of DNA, to other protocols now generally applied to environmental studies. The simplified and optimized method was used to quantify ammonia-oxidizing Archaea at different depth intervals in a fjord (Hood Canal) by quantitative PCR. The numbers of Archaea increased with depth, often constituting as much as 20% of the total bacterial community.},
}
@article {pmid20117082,
year = {2010},
author = {Wang, L and Hu, ZJ and Luo, YM and Huo, YW and Ma, Q and He, YZ and Zhang, YY and Sun, F and Dong, ZY},
title = {Distinct symmetry and limited peptide refolding activity of the thermosomes from the acidothermophilic archaea Acidianus tengchongensis S5(T).},
journal = {Biochemical and biophysical research communications},
volume = {393},
number = {2},
pages = {228-234},
doi = {10.1016/j.bbrc.2010.01.106},
pmid = {20117082},
issn = {1090-2104},
mesh = {Acidianus/*metabolism ; Adenosine Triphosphate/metabolism ; Hydrolysis ; Microscopy, Electron ; Peptides/chemistry/genetics/*metabolism ; Phylogeny ; Protein Folding ; Protein Subunits/chemistry/genetics/metabolism ; Recombinant Proteins/chemistry/genetics/metabolism ; Sulfolobus/metabolism ; Sulfolobus acidocaldarius/metabolism ; Thermosomes/chemistry/genetics/*metabolism ; },
abstract = {Recombinant thermosomes from the Acidianus tengchongensis strain S5(T) were purified to homogeneity and assembled in vitro into homo-oligomers (rATcpnalpha or rATcpnbeta) and hetero-oligomers (rATcpnalphabeta). The symmetries of these complexes were determined by electron microscopy and image analysis. The rATcpnalpha homo-oligomer was shown to possess 8-fold symmetry while both rATcpnbeta and rATcpnalphabeta oligomers adopted 9-fold symmetry. rATcpnalphabeta oligomers were shown to contain the alpha and beta subunits in a 1:2 ratio. All of the complexes prevented the irreversible inactivation of yeast alcohol dehydrogenase at 55 degrees C and completely prevented the formation of aggregates during thermal inactivation of citrate synthase at 45 degrees C. All rATcpn complexes showed trace ATP hydrolysis activity. Furthermore, rATcpnbeta sequestered fully chemically denatured substrates (GFP and thermophilic malic dehydrogenase) in vitro without refolding them in an ATP-dependent manner. This property is similar to previously reported properties of chaperonins from Sulfolobus tokodaii and Sulfolobus acidocaldarius. These features are consistent with the slow growth rates of these species of archaea in their native environment.},
}
@article {pmid20116227,
year = {2011},
author = {Zhu, C and Zhang, J and Tang, Y and Zhengkai, X and Song, R},
title = {Diversity of methanogenic archaea in a biogas reactor fed with swine feces as the mono-substrate by mcrA analysis.},
journal = {Microbiological research},
volume = {166},
number = {1},
pages = {27-35},
doi = {10.1016/j.micres.2010.01.004},
pmid = {20116227},
issn = {1618-0623},
mesh = {Animals ; *Biodiversity ; Biofuels ; Biomass ; Bioreactors ; DNA, Archaeal/analysis ; Euryarchaeota/*genetics/*metabolism ; Feces ; Methane/biosynthesis ; Methanobacteriales/*genetics/metabolism ; Methanomicrobiales/genetics/metabolism ; Methanosarcinales/genetics/metabolism ; Molecular Sequence Data ; Oxidoreductases/*genetics ; Phylogeny ; Swine ; },
abstract = {Methanogenesis from the biomass in the anoxic biogas reactors is catalyzed by syntrophic cooperation between anaerobic bacteria, syntrophic acetogenic bacteria and methanogenic archaea. Understanding of microbial community composition within the biogas reactors may improve the methane production from biomass fermentation. In this study, methanogenic archaea diverity of a biogas reactor supplied with swine feces as mono-substrate under mesophilic conditions was investigated. Community composition was determined by analysis of methyl coenzyme reductase subunit A gene (mcrA) clone library consisting of 123 clones. Statistical analysis of mcrA library indicated that all major groups of methanogens from our biogas reactor were detected. In the library, 57.7% clones were affiliated to Methanobacteriales, 34.2% to Methanomicrobiales, 2.4% to Methanosarcinales and about 5.7% clones belonged to unclassified euryarchaeota. Over 90% of the methanogenic archaea from our biogas reactor were postulated to be hydrogenotrophic methanogens. Comparing with other previous studies reporting that hydrogenotrophic methanogens are dominant species in the biogas plants, this study firstly reported that Methanobacteriales instead of Methanomicrobiales are the most predominant methanogenic archaea in the biogas reactor fed with swine feces as sole substrate.},
}
@article {pmid20112671,
year = {2009},
author = {Zhang, F and Zhang, B and Xiang, H and Hu, S},
title = {[Comparative analysis of clustered regularly interspaced short palindromic repeats (CRISPRs) loci in the genomes of halophilic archaea].},
journal = {Wei sheng wu xue bao = Acta microbiologica Sinica},
volume = {49},
number = {11},
pages = {1445-1453},
pmid = {20112671},
issn = {0001-6209},
mesh = {Archaea/chemistry/*genetics/metabolism ; Base Sequence ; Chlorides/*metabolism ; Computational Biology ; DNA, Archaeal/chemistry/genetics ; *Genome, Archaeal ; *Inverted Repeat Sequences ; Molecular Sequence Data ; Nucleic Acid Conformation ; Sequence Alignment ; },
abstract = {OBJECTIVE: Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) is a widespread system that provides acquired resistance against phages in bacteria and archaea. Here we aim to genome-widely analyze the CRISPR in extreme halophilic archaea, of which the whole genome sequences are available at present time.<br><br>METHODS: We used bioinformatics methods including alignment, conservation analysis, GC content and RNA structure prediction to analyze the CRISPR structures of 7 haloarchaeal genomes.<br><br>RESULTS: We identified the CRISPR structures in 5 halophilic archaea and revealed a conserved palindromic motif in the flanking regions of these CRISPR structures. In addition, we found that the repeat sequences of large CRISPR structures in halophilic archaea were greatly conserved, and two types of predicted RNA secondary structures derived from the repeat sequences were likely determined by the fourth base of the repeat sequence.<br><br>CONCLUSION: Our results support the proposal that the leader sequence may function as recognition site by having palindromic structures in flanking regions, and the stem-loop secondary structure formed by repeat sequences may function in mediating the interaction between foreign genetic elements and CAS-encoded proteins.},
}
@article {pmid20112667,
year = {2009},
author = {Wang, F and Zhang, S and Huang, Q and Shen, Y and Ni, J},
title = {[Advance in genetic manipulation systems of hyperthermophilic archaea--a review].},
journal = {Wei sheng wu xue bao = Acta microbiologica Sinica},
volume = {49},
number = {11},
pages = {1418-1423},
pmid = {20112667},
issn = {0001-6209},
mesh = {Archaea/*genetics/metabolism ; Gene Expression Regulation, Archaeal ; Genetic Engineering/*methods ; Hot Temperature ; },
abstract = {Genetic manipulation systems play an important role in the functional analysis of genes and gene products. The development of genetic system in hyperthermophilic archaea is lagging behind those in methanogenic and halophilic archaea. The main problem is the unavailability of efficient selective markers. However, in the past 10 years, researchers have made great progress in the development of genetic systems in the genus Sulfolobus and Thermococcus kodakaraensis, representatives of hyperthermophilic archaea. Here we summarize the latest progress in genetic systems and their application for hyperthermophilic archaea.},
}
@article {pmid20097028,
year = {2010},
author = {Bergmann, I and Mundt, K and Sontag, M and Baumstark, I and Nettmann, E and Klocke, M},
title = {Influence of DNA isolation on Q-PCR-based quantification of methanogenic Archaea in biogas fermenters.},
journal = {Systematic and applied microbiology},
volume = {33},
number = {2},
pages = {78-84},
doi = {10.1016/j.syapm.2009.11.004},
pmid = {20097028},
issn = {1618-0984},
mesh = {Archaea/*isolation &amp; purification ; DNA, Archaeal/genetics/*isolation &amp; purification ; *Environmental Microbiology ; Gene Dosage ; Methane/*metabolism ; Polymerase Chain Reaction/*methods ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Quantitative real-time PCR (Q-PCR) is commonly applied for the detection of certain microorganisms in environmental samples. However, some environments, like biomass-degrading biogas fermenters, are enriched with PCR-interfering substances. To study the impact of the DNA extraction protocol on the results of Q-PCR-based analysis of the methane-producing archaeal community in biogas fermenters, nine different protocols with varying cell disruption and DNA purification approaches were tested. Differences in the quantities of the isolated DNA and the purity parameters were found, with the best cell lysis efficiencies being obtained by a combined lysozyme/SDS-based lysis. When DNA was purified by sephacryl columns, the amount of DNA decreased by one log cycle but PCR inhibitors were eliminated sufficiently. In the case of detection of methanogenic Archaea, the chosen DNA isolation protocol strongly influenced the Q-PCR-based determination of 16S rDNA copy numbers. For example, with protocols including mechanical cell disruption, the 16S rDNA of Methanobacteriales were predominantly amplified (81-90% of the total 16S rDNA copy numbers), followed by the 16S rDNA of Methanomicrobiales (9-18%). In contrast, when a lysozyme/SDS-based cell lysis was applied, the 16S rDNA copy numbers determined for these two orders were the opposite (Methanomicrobiales 82-95%, Methanobacteriales 4-18%). In extreme cases, the DNA isolation method led to discrimination of some groups of methanogens (e.g. members of the Methanosaetaceae). In conclusion, for extraction of high amounts of microbial DNA with high purity from samples of biogas plants, a combined lysozyme/SDS-based cell lysis followed by a purification step with sephacryl columns is recommended.},
}
@article {pmid20080711,
year = {2010},
author = {Singh, BK},
title = {Archaea in a hyper-arid polar desert.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {107},
number = {2},
pages = {E1; author reply E2},
pmid = {20080711},
issn = {1091-6490},
mesh = {Archaea/*classification/genetics/physiology ; DNA/genetics ; DNA Primers ; *Desert Climate ; Ecosystem ; Environment ; Phylogeny ; Polymerase Chain Reaction ; },
}
@article {pmid20080654,
year = {2010},
author = {Brazelton, WJ and Ludwig, KA and Sogin, ML and Andreishcheva, EN and Kelley, DS and Shen, CC and Edwards, RL and Baross, JA},
title = {Archaea and bacteria with surprising microdiversity show shifts in dominance over 1,000-year time scales in hydrothermal chimneys.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {107},
number = {4},
pages = {1612-1617},
pmid = {20080654},
issn = {1091-6490},
mesh = {Archaea/classification/*genetics ; Bacteria/classification/*genetics ; *Biodiversity ; Evolution, Molecular ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Temperature ; Time Factors ; Water ; },
abstract = {The Lost City Hydrothermal Field, an ultramafic-hosted system located 15 km west of the Mid-Atlantic Ridge, has experienced at least 30,000 years of hydrothermal activity. Previous studies have shown that its carbonate chimneys form by mixing of approximately 90 degrees C, pH 9-11 hydrothermal fluids and cold seawater. Flow of methane and hydrogen-rich hydrothermal fluids in the porous interior chimney walls supports archaeal biofilm communities dominated by a single phylotype of Methanosarcinales. In this study, we have extensively sampled the carbonate-hosted archaeal and bacterial communities by obtaining sequences of >200,000 amplicons of the 16S rRNA V6 region and correlated the results with isotopic ((230)Th) ages of the chimneys over a 1,200-year period. Rare sequences in young chimneys were commonly more abundant in older chimneys, indicating that members of the rare biosphere can become dominant members of the ecosystem when environmental conditions change. These results suggest that a long history of selection over many cycles of chimney growth has resulted in numerous closely related species at Lost City, each of which is preadapted to a particular set of reoccurring environmental conditions. Because of the unique characteristics of the Lost City Hydrothermal Field, these data offer an unprecedented opportunity to study the dynamics of a microbial ecosystem's rare biosphere over a thousand-year time scale.},
}
@article {pmid20077005,
year = {2011},
author = {Plasencia, A and Bañeras, L and Llirós, M and Casamayor, EO and Borrego, C},
title = {Maintenance of previously uncultured freshwater archaea from anoxic waters under laboratory conditions.},
journal = {Antonie van Leeuwenhoek},
volume = {99},
number = {2},
pages = {403-408},
doi = {10.1007/s10482-010-9412-x},
pmid = {20077005},
issn = {1572-9699},
mesh = {Anaerobiosis ; Archaea/classification/genetics/*growth &amp; development/*isolation &amp; purification ; Biodiversity ; Cluster Analysis ; Culture Media/chemistry ; DNA Fingerprinting ; DNA, Archaeal/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Electrophoresis, Polyacrylamide Gel ; Fresh Water/*microbiology ; Hypoxia ; Microbiological Techniques/*methods ; Molecular Sequence Data ; Nucleic Acid Denaturation ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; },
abstract = {Culture conditions for the maintenance of previously uncultured members of the Archaea thriving in anoxic water layers of stratified freshwater lakes are described. The proposed enrichment conditions, based on the use of defined medium composition and the maintenance of anoxia, have been proven effective for the maintenance of the archaeal community with virtually no changes over time for periods up to 6 months as revealed by a PCR-DGGE analysis. Phylotypes belonging to groups poorly represented in culture collections such as the Deep-Sea Hydrothermal Vent Euryarchaeota (DHVE) and the Miscellaneous Crenarchaeotic Group (MCG) were maintained and selectively enriched when compared to the correspondent indigenous planktonic archaeal community.},
}
@article {pmid20069373,
year = {2010},
author = {Pollack, JD and Pan, X and Pearl, DK},
title = {Concentration of specific amino acids at the catalytic/active centers of highly-conserved "housekeeping" enzymes of central metabolism in archaea, bacteria and Eukaryota: is there a widely conserved chemical signal of prebiotic assembly?.},
journal = {Origins of life and evolution of the biosphere : the journal of the International Society for the Study of the Origin of Life},
volume = {40},
number = {3},
pages = {273-302},
pmid = {20069373},
issn = {1573-0875},
mesh = {Amino Acid Sequence ; Amino Acids/*chemistry ; Archaea/*enzymology ; Archaeal Proteins/chemistry/genetics/metabolism ; Bacteria/*enzymology ; Bacterial Proteins/chemistry/genetics/metabolism ; Catalytic Domain ; Enzymes/*chemistry/genetics/metabolism ; Eukaryota/*enzymology ; Evolution, Molecular ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Origin of Life ; Protein Structure, Tertiary/genetics ; Sequence Alignment ; },
abstract = {In alignments of 1969 protein sequences the amino acid glycine and others were found concentrated at most-conserved sites within approximately 15 A of catalytic/active centers (C/AC) of highly conserved kinases, dehydrogenases or lyases of Archaea, Bacteria and Eukaryota. Lysine and glutamic acid were concentrated at least-conserved sites furthest from their C/ACs. Logistic-regression analyses corroborated the "movement" of glycine towards and lysine away from their C/ACs: the odds of a glycine occupying a site were decreased by 19%, while the odds for a lysine were increased by 53%, for every 10 A moving away from the C/AC. Average conservation of MSA consensus sites was highest surrounding the C/AC and directly decreased in transition toward model's peripheries. Findings held with statistical confidence using sequences restricted to individual Domains or enzyme classes or to both. Our data describe variability in the rate of mutation and likelihoods for phylogenetic trees based on protein sequence data and endorse the extension of substitution models by incorporating data on conservation and distance to C/ACs rather than only using cumulative levels. The data support the view that in the most-conserved environment immediately surrounding the C/AC of taxonomically distant and highly conserved essential enzymes of central metabolism there are amino acids whose identity and degree of occupancy is similar to a proposed amino acid set and frequency associated with prebiotic evolution.},
}
@article {pmid20069286,
year = {2010},
author = {Miralles, F},
title = {Compositional properties and thermal adaptation of SRP-RNA in bacteria and archaea.},
journal = {Journal of molecular evolution},
volume = {70},
number = {2},
pages = {181-189},
pmid = {20069286},
issn = {1432-1432},
mesh = {Adaptation, Biological/*genetics ; Archaea/*genetics ; Bacteria/*genetics ; Base Composition/genetics ; Hot Temperature ; Nucleic Acid Conformation ; RNA, Archaeal/chemistry/*genetics ; RNA, Bacterial/chemistry/*genetics ; Signal Recognition Particle/chemistry/*genetics ; Statistics, Nonparametric ; },
abstract = {Previous studies have reported a positive correlation between the GC content of the double-stranded regions of structural RNAs and the optimal growth temperature (OGT) in prokaryotes. These observations led to the hypothesis that natural selection favors an increase in GC content to ensure the correct folding and the structural stability of the molecule at high temperature. To date these studies have focused mainly on ribosomal and transfer RNAs. Therefore, we addressed the question of the relationship between GC content and OGT in a different and universally conserved structural RNA, the RNA component of the signal recognition particle (SRP). To this end we generated the secondary structures of SRP-RNAs for mesophilic, thermophilic, and hyperthermophilic bacterial and archaeal species. The analysis of the GC content in the stems and loops of the SRP-RNA of these organisms failed to detect a relationship between the GC contents in the stems of this structural RNA and the growth temperature of bacteria. By contrast, we found that in archaea the GC content in the stem regions of SRP-RNA is highest in hyperthermophiles, intermediate in thermophiles, and lower in mesophiles. In these organisms, we demonstrated a clear positive correlation between the GC content of the stem regions of their SRP-RNAs and their OGT. This correlation was confirmed by a phylogenetic nonindependence analysis. Thus we conclude that in archaea the increase in GC content in the stem regions of SRP-RNA is an adaptation response to environmental temperature.},
}
@article {pmid20056882,
year = {2010},
author = {Horvath, P and Barrangou, R},
title = {CRISPR/Cas, the immune system of bacteria and archaea.},
journal = {Science (New York, N.Y.)},
volume = {327},
number = {5962},
pages = {167-170},
doi = {10.1126/science.1179555},
pmid = {20056882},
issn = {1095-9203},
mesh = {Archaea/*genetics/immunology/virology ; Archaeal Proteins/metabolism ; Bacteria/*genetics/immunology/virology ; Bacterial Proteins/metabolism ; Bacteriophages/genetics/physiology ; Base Sequence ; Conserved Sequence ; Gene Transfer, Horizontal ; Genes, Archaeal ; Genes, Bacterial ; *Genetic Loci ; *Genome, Archaeal ; *Genome, Bacterial ; Genome, Viral ; Mutation ; Plasmids ; RNA Interference ; RNA, Archaeal/genetics/metabolism ; RNA, Bacterial/genetics/metabolism ; *Repetitive Sequences, Nucleic Acid ; },
abstract = {Microbes rely on diverse defense mechanisms that allow them to withstand viral predation and exposure to invading nucleic acid. In many Bacteria and most Archaea, clustered regularly interspaced short palindromic repeats (CRISPR) form peculiar genetic loci, which provide acquired immunity against viruses and plasmids by targeting nucleic acid in a sequence-specific manner. These hypervariable loci take up genetic material from invasive elements and build up inheritable DNA-encoded immunity over time. Conversely, viruses have devised mutational escape strategies that allow them to circumvent the CRISPR/Cas system, albeit at a cost. CRISPR features may be exploited for typing purposes, epidemiological studies, host-virus ecological surveys, building specific immunity against undesirable genetic elements, and enhancing viral resistance in domesticated microbes.},
}
@article {pmid20042074,
year = {2009},
author = {Gunbin, KV and Afonnikov, DA and Kolchanov, NA},
title = {Molecular evolution of the hyperthermophilic archaea of the Pyrococcus genus: analysis of adaptation to different environmental conditions.},
journal = {BMC genomics},
volume = {10},
number = {},
pages = {639},
pmid = {20042074},
issn = {1471-2164},
mesh = {Adaptation, Biological ; *Evolution, Molecular ; *Genome, Archaeal ; Multigene Family ; Phylogeny ; Pressure ; Proteome/genetics/metabolism ; Pyrococcus/*genetics/physiology ; Selection, Genetic ; },
abstract = {BACKGROUND: Prokaryotic microorganisms are able to survive and proliferate in severe environmental conditions. The increasing number of complete sequences of prokaryotic genomes has provided the basis for studying the molecular mechanisms of their adaptation at the genomic level. We apply here a computer-based approach to compare the genomes and proteomes from P. furiosus, P. horikoshii, and P. abyssi to identify features of their molecular evolution related to adaptation strategy to diverse environmental conditions.<br><br>RESULTS: Phylogenetic analysis of rRNA genes from 26 Pyrococcus strains suggested that the divergence of P. furiosus, P. horikoshii and P. abyssi might have occurred from ancestral deep-sea organisms. It was demonstrated that the function of genes that have been subject to positive Darwinian selection is closely related to abiotic and biotic conditions to which archaea managed to become adapted. Divergence of the P. furiosus archaea might have been due to loss of some genes involved in cell motility or signal transduction, and/or to evolution under positive selection of the genes for translation machinery. In the course of P. horikoshii divergence, positive selection was found to operate mainly on the transcription machinery; divergence of P. abyssi was related with positive selection for the genes mainly involved in inorganic ion transport. Analysis of radical amino acid replacement rate in evolving P. furiosus, P. horikoshii and P. abyssi showed that the fixation rate was higher for radical substitutions relative to the volume of amino acid side-chain.<br><br>CONCLUSIONS: The current results give due credit to the important role of hydrostatic pressure as a cause of variability in the P. furiosus, P. horikoshii and P. abyssi genomes evolving in different habitats. Nevertheless, adaptation to pressure does not appear to be the sole factor ensuring adaptation to environment. For example, at the stage of the divergence of P. horikoshii and P. abyssi, an essential evolutionary role may be assigned to changes in the trophic chain, namely, acquisition of a consumer status at a high (P. horikoshii) or low level (P. abyssi).},
}
@article {pmid20038706,
year = {2010},
author = {Bernhard, AE and Landry, ZC and Blevins, A and de la Torre, JR and Giblin, AE and Stahl, DA},
title = {Abundance of ammonia-oxidizing archaea and bacteria along an estuarine salinity gradient in relation to potential nitrification rates.},
journal = {Applied and environmental microbiology},
volume = {76},
number = {4},
pages = {1285-1289},
pmid = {20038706},
issn = {1098-5336},
mesh = {Ammonia/*metabolism ; Archaea/classification/genetics/*isolation &amp; purification/*metabolism ; Bacteria/classification/genetics/*isolation &amp; purification/*metabolism ; Betaproteobacteria/classification/genetics/isolation &amp; purification/metabolism ; Ecosystem ; Fresh Water/microbiology ; Genes, Archaeal ; Genes, Bacterial ; Geologic Sediments/microbiology ; Molecular Sequence Data ; Nitrogen/*metabolism ; Oxidation-Reduction ; Phylogeny ; Salinity ; Seawater/microbiology ; *Water Microbiology ; },
abstract = {Abundance of ammonia-oxidizing Archaea (AOA) was found to be always greater than that of ammonia-oxidizing Bacteria along an estuarine salinity gradient, and AOA abundance was highest at intermediate salinity. However, AOA abundance did not correlate with potential nitrification rates. This lack of correlation may be due to methodological limitations or alternative energy sources.},
}
@article {pmid20033070,
year = {2010},
author = {Angel, R and Soares, MI and Ungar, ED and Gillor, O},
title = {Biogeography of soil archaea and bacteria along a steep precipitation gradient.},
journal = {The ISME journal},
volume = {4},
number = {4},
pages = {553-563},
doi = {10.1038/ismej.2009.136},
pmid = {20033070},
issn = {1751-7370},
mesh = {Archaea/*classification/*isolation &amp; purification ; Bacteria/*classification/*isolation &amp; purification ; *Biodiversity ; Cluster Analysis ; DNA Fingerprinting ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Geography ; Israel ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; },
abstract = {For centuries, biodiversity has spellbound biologists focusing mainly on macroorganism's diversity and almost neglecting the geographic mediated dynamics of microbial communities. We surveyed the diversity of soil bacteria and archaea along a steep precipitation gradient ranging from the Negev Desert in the south of Israel (<100 mm annual rain) to the Mediterranean forests in the north (>900 mm annual rain). Soil samples were retrieved from triplicate plots at five long-term ecological research stations, collected from two types of patches: plant interspaces and underneath the predominant perennial at each site. The molecular fingerprint of each soil sample was taken using terminal restriction length polymorphism of the 16S rRNA gene to evaluate the bacterial and archaeal community composition and diversity within and across sites. The difference in community compositions was not statistically significant within sites (P=0.33 and 0.77 for bacteria and archaea, respectively), but it differed profoundly by ecosystem type. These differences could largely be explained by the precipitation gradient combined with the vegetation cover: the archaeal and bacterial operational taxonomic units were unique to each climatic region, that is, arid, semiarid and Mediterranean (P=0.0001, for both domains), as well as patch type (P=0.009 and 0.02 for bacteria and archaea, respectively). Our results suggest that unlike macroorganisms that are more diverse in the Mediterranean ecosystems compared with the desert sites, archaeal and bacterial diversities are not constrained by precipitation. However, the community composition is unique to the climate and vegetation cover that delineates each ecosystem.},
}
@article {pmid20033048,
year = {2009},
author = {Wu, D and Hugenholtz, P and Mavromatis, K and Pukall, R and Dalin, E and Ivanova, NN and Kunin, V and Goodwin, L and Wu, M and Tindall, BJ and Hooper, SD and Pati, A and Lykidis, A and Spring, S and Anderson, IJ and D'haeseleer, P and Zemla, A and Singer, M and Lapidus, A and Nolan, M and Copeland, A and Han, C and Chen, F and Cheng, JF and Lucas, S and Kerfeld, C and Lang, E and Gronow, S and Chain, P and Bruce, D and Rubin, EM and Kyrpides, NC and Klenk, HP and Eisen, JA},
title = {A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea.},
journal = {Nature},
volume = {462},
number = {7276},
pages = {1056-1060},
pmid = {20033048},
issn = {1476-4687},
support = {R01 GM054592/GM/NIGMS NIH HHS/United States ; R01 GM054592-09/GM/NIGMS NIH HHS/United States ; R01 GM067012/GM/NIGMS NIH HHS/United States ; R01 GM067012-04/GM/NIGMS NIH HHS/United States ; },
mesh = {Actins/chemistry ; Amino Acid Sequence ; Archaea/*classification/*genetics ; Bacteria/*classification/*genetics ; Bacterial Proteins/chemistry ; Biodiversity ; Databases, Genetic ; Genes, rRNA/genetics ; Genome, Archaeal/*genetics ; Genome, Bacterial/*genetics ; Models, Molecular ; Molecular Sequence Data ; *Phylogeny ; Protein Structure, Tertiary ; Sequence Alignment ; },
abstract = {Sequencing of bacterial and archaeal genomes has revolutionized our understanding of the many roles played by microorganisms. There are now nearly 1,000 completed bacterial and archaeal genomes available, most of which were chosen for sequencing on the basis of their physiology. As a result, the perspective provided by the currently available genomes is limited by a highly biased phylogenetic distribution. To explore the value added by choosing microbial genomes for sequencing on the basis of their evolutionary relationships, we have sequenced and analysed the genomes of 56 culturable species of Bacteria and Archaea selected to maximize phylogenetic coverage. Analysis of these genomes demonstrated pronounced benefits (compared to an equivalent set of genomes randomly selected from the existing database) in diverse areas including the reconstruction of phylogenetic history, the discovery of new protein families and biological properties, and the prediction of functions for known genes from other organisms. Our results strongly support the need for systematic 'phylogenomic' efforts to compile a phylogeny-driven 'Genomic Encyclopedia of Bacteria and Archaea' in order to derive maximum knowledge from existing microbial genome data as well as from genome sequences to come.},
}
@article {pmid20024684,
year = {2010},
author = {Cadillo-Quiroz, H and Yavitt, JB and Zinder, SH and Thies, JE},
title = {Diversity and community structure of Archaea inhabiting the rhizoplane of two contrasting plants from an acidic bog.},
journal = {Microbial ecology},
volume = {59},
number = {4},
pages = {757-767},
pmid = {20024684},
issn = {1432-184X},
mesh = {Archaea/classification/*genetics ; *Biodiversity ; DNA, Archaeal/genetics ; Gene Library ; Magnoliopsida/*microbiology ; New York ; Phylogeny ; Plant Roots/microbiology ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Soil ; *Soil Microbiology ; *Wetlands ; },
abstract = {Plant root exudates increase nutrient availability and influence microbial communities including archaeal members. We examined the archaeal community inhabiting the rhizoplane of two contrasting vascular plants, Dulichium arundinaceum and Sarracenia purpurea, from an acidic bog in upstate NY. Multiple archaeal 16S rRNA gene libraries showed that methanogenic Archaea were dominant in the rhizoplane of both plants. In addition, the community structure (evenness) of the rhizoplane was found markedly different from the bulk peat. The archaeal community in peat from the same site has been found dominated by the E2 group, meanwhile the rhizoplane communities on both plants were co-dominated by Methanosarcinaceae (MS), rice cluster (RC)-I, and E2. Complementary T-RFLP analysis confirmed the difference between bulk peat and rhizoplane, and further characterized the dominance pattern of MS, RC-I, and E2. In the rhizoplane, MS was dominant on both plants although as a less variable fraction in S. purpurea. RC-I was significantly more abundant than E2 on S. purpurea, while the opposite was observed on D. arundinaceum, suggesting a plant-specific enrichment. Also, the statistical analyses of T-RFLP data showed that although both plants overlap in their community structure, factors such as plant type, patch location, and time could explain nearly a third of the variability in the dataset. Other factors such as water table, plant replicate, and root depth had a low contribution to the observed variance. The results of this study illustrate the general effects of roots and the specific effects of plant types on their nearby archaeal communities which in bog-inhabiting plants were mainly composed by methanogenic groups.},
}
@article {pmid20024655,
year = {2010},
author = {Zhang, W and Saren, G and Li, T and Yu, X and Zhang, L},
title = {Diversity and community structure of archaea in deep subsurface sediments from the tropical Western pacific.},
journal = {Current microbiology},
volume = {60},
number = {6},
pages = {439-445},
pmid = {20024655},
issn = {1432-0991},
mesh = {Base Sequence ; Biodiversity ; Crenarchaeota/*classification/genetics ; DNA, Archaeal/genetics ; DNA, Ribosomal/genetics ; Euryarchaeota/*classification/genetics ; Gene Library ; Geologic Sediments/*microbiology ; Pacific Ocean ; Peru ; Phylogeny ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Tropical Climate ; },
abstract = {Archaeal 16S rRNA gene clone libraries using PCR amplicons from eight different layers of the MD06-3051 core were obtained from the tropical Western Pacific sediments. A total of 768 clones were randomly selected, and 264 representative clones were sequenced by restriction fragment length polymorphism. Finally, 719 valid clones and 104 operational taxonomic units were identified after chimera-check and > or =97% similarity analysis. The phylogenetic analysis of 16S rDNA sequences obtained from sediment samples were very diverse and showed stratification with depth. Majority of the members were most closely related to uncultivated groups and physiologically uncharacterized assemblages. All phylotypes were affiliated with Crenarchaeota (76%) and Euryarchaeota (24%), respectively. Deep-sea archaeal group (DSAG, 41% of total clones) and miscellaneous crenarchaeotic group (MCG, 29% of total clones) belonging to Crenarchaeota were the most predominant archaeal 16S rDNA phylotypes in clone libraries. Phylotypes in this study shared high similarity with those in subsurface sediments from Peru Margin sites, which indicated that different geographical zones might host similar members of archaeal populations based on similar sedimentary environments. In our study, members of DSAG and MCG seemed to dominate certain layers of the nonhydrate sediments, suggesting a wide ecophysiological adaptation than previously appreciated. The spatial distribution and community structure of these groups might vary with the different geochemical gradients of the environment.},
}
@article {pmid20013262,
year = {2010},
author = {Lins-de-Barros, MM and Vieira, RP and Cardoso, AM and Monteiro, VA and Turque, AS and Silveira, CB and Albano, RM and Clementino, MM and Martins, OB},
title = {Archaea, Bacteria, and algal plastids associated with the reef-building corals Siderastrea stellata and Mussismilia hispida from Búzios, South Atlantic Ocean, Brazil.},
journal = {Microbial ecology},
volume = {59},
number = {3},
pages = {523-532},
pmid = {20013262},
issn = {1432-184X},
mesh = {Animals ; Anthozoa/*microbiology ; Archaea/*classification/genetics/isolation &amp; purification ; Atlantic Ocean ; Bacteria/*classification/genetics/isolation &amp; purification ; Brazil ; DNA, Algal/genetics ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; *Ecosystem ; Eukaryota/*classification/genetics/isolation &amp; purification ; Gene Library ; Phylogeny ; Plastids/*genetics/microbiology ; RNA, Ribosomal, 16S/genetics ; Seawater/microbiology ; Sequence Analysis, DNA ; Symbiosis ; Water Microbiology ; },
abstract = {Reef-building corals may be seen as holobiont organisms, presenting diverse associated microbial communities. Best known is the symbiotic relationship with zooxanthellae, but Archaea, Bacteria, fungi, viruses, and algal plastids are also abundant. Until now, there is little information concerning microbial communities associated with Brazilian corals. The present study aims to describe the diversity of Archaea, Bacteria, and eukaryotic algal plastid communities associated with two sympatric species, Siderastrea stellata and Mussismilia hispida, from Southeastern Brazil, using 16S rRNA gene libraries. Since corals present a high number of other associated invertebrates, coral barcoding (COI) was performed to confirm the exclusive occurrence of coral DNA in our samples. Our analysis yielded 354 distinct microbial OTUs, represented mainly by novel phylotypes. Richness (Chao1 and ACE) and diversity (H') estimations of the microbial communities associated with both species were high and comparable to other studies. Rarefaction analyses showed that microbial diversity of S. stellata is higher than that of M. hispida. Libshuff comparative analyses showed that the highest microbial community similarity between the two coral species occurred in the bacterial libraries, while archaeal and plastidial communities were significantly different. Crenarchaeota dominated archaeal communities, while Proteobacteria was the most abundant bacterial phylum, dominated by alpha-Proteobacteria. Plastids were also represented by novel phylotypes and did not match with any 16S rRNA sequences of Cyanobacteria and zooxanthellae from GenBank. Our data improves the pool of available information on Brazilian coral microbes and shows corals as sources of diverse prokaryotic and picoeukaryotic communities.},
}
@article {pmid19940386,
year = {2009},
author = {Kawai, Y and Maeda, Y},
title = {GC-content of tRNA genes classifies archaea into two groups.},
journal = {The Journal of general and applied microbiology},
volume = {55},
number = {5},
pages = {403-408},
doi = {10.2323/jgam.55.403},
pmid = {19940386},
issn = {0022-1260},
mesh = {Archaea/genetics/*isolation &amp; purification ; *Base Composition ; RNA, Transfer/*analysis/genetics ; },
}
@article {pmid19919669,
year = {2010},
author = {Stock, T and Selzer, M and Rother, M},
title = {In vivo requirement of selenophosphate for selenoprotein synthesis in archaea.},
journal = {Molecular microbiology},
volume = {75},
number = {1},
pages = {149-160},
doi = {10.1111/j.1365-2958.2009.06970.x},
pmid = {19919669},
issn = {1365-2958},
mesh = {Archaeal Proteins/genetics ; DNA, Archaeal/chemistry/genetics ; Gene Deletion ; Genes, Essential ; Genetic Complementation Test ; Methanococcus/*metabolism ; Molecular Sequence Data ; Phosphates/*metabolism ; Phosphotransferases/genetics/metabolism ; Selenium Compounds/*metabolism ; Selenoproteins/*biosynthesis ; Sequence Analysis, DNA ; },
abstract = {Biosynthesis of selenocysteine, the 21st proteinogenic amino acid, occurs bound to a dedicated tRNA in all three domains of life, Bacteria, Eukarya and Archaea, but differences exist between the mechanism employed by bacteria and eukaryotes/archaea. The role of selenophosphate and the enzyme providing it, selenophosphate synthetase, in archaeal selenoprotein synthesis was addressed by mutational analysis. Surprisingly, MMP0904, encoding a homologue of eukaryal selenophosphate synthetase in Methanococcus maripaludis S2, could not be deleted unless selD, encoding selenophosphate synthetase of Escherichia coli, was present in trans, demonstrating that the factor is essential for the organism. In contrast, the homologous gene of M. maripaludis JJ could be readily deleted, obviating the strain's ability to synthesize selenoproteins. Complementing with selD restored selenoprotein synthesis, demonstrating that the deleted gene encodes selenophosphate synthetase and that selenophosphate is the in vivo selenium donor for selenoprotein synthesis of this organism. We also showed that this enzyme is a selenoprotein itself and that M. maripaludis contains another, HesB-like selenoprotein previously only predicted from genome analyses. The data highlight the use of genetic methods in archaea for a causal analysis of their physiology and, by comparing two closely related strains of the same species, illustrate the evolution of the selenium-utilizing trait.},
}
@article {pmid19912381,
year = {2009},
author = {Jiang, YT and Xia, WW and Li, CL and Jiang, W and Liang, JP},
title = {Preliminary study of the presence and association of bacteria and archaea in teeth with apical periodontitis.},
journal = {International endodontic journal},
volume = {42},
number = {12},
pages = {1096-1103},
doi = {10.1111/j.1365-2591.2009.01639.x},
pmid = {19912381},
issn = {1365-2591},
mesh = {Archaea/genetics/*isolation &amp; purification/physiology ; Bacteria/genetics/*isolation &amp; purification ; Colony Count, Microbial ; DNA, Archaeal/analysis ; DNA, Bacterial/analysis ; Dental Pulp Cavity/*microbiology ; Dental Pulp Necrosis/*microbiology ; Dental Restoration Failure ; Ecosystem ; Humans ; Microbial Interactions ; Periapical Periodontitis/*microbiology ; RNA, Ribosomal, 16S/analysis ; Treatment Failure ; },
abstract = {AIM: To investigate, by reverse transcription polymerase chain reaction (RT-PCR), the presence and association of bacteria and archaea in primary and secondary root canal infections.<br><br>METHODOLOGY: A total of 77 root canal samples from 77 Chinese patients, 42 with necrotic pulp tissues (primary infection) and 35 with failed prior conventional root canal treatment (secondary infection), aseptically exposed at the first patient visit, were studied. Total RNA was isolated directly from each sample, and 16S rRNA gene-based RT-PCR assays were used to determine the presence of bacteria and archaea, respectively.<br><br>RESULTS: Bacteria were detected in 39/42 (93%) of root canal samples from teeth with primary infections, and archaea in 16/42 (38%). In the cases diagnosed as secondary root-infected canals, bacteria were detected in 30/35 (86%), whilst archaea were detected in 6/35 (17%) of cases. Amongst the canals, which were positive for bacteria, archaea were always found in combination with bacteria. The incidence of symptomatic cases positive for both bacteria and archaea (16/22, 73%) were significantly higher than those positive for bacteria alone (21/47, 45%) (P < 0.05).<br><br>CONCLUSIONS: This study confirms the presence of archaea in root canal infections and further implicates them in an association with clinical symptoms. The nature of this association requires further study.},
}
@article {pmid19888544,
year = {2009},
author = {Fondi, M and Emiliani, G and Liò, P and Gribaldo, S and Fani, R},
title = {The evolution of histidine biosynthesis in archaea: insights into the his genes structure and organization in LUCA.},
journal = {Journal of molecular evolution},
volume = {69},
number = {5},
pages = {512-526},
pmid = {19888544},
issn = {1432-1432},
mesh = {Archaea/enzymology/*genetics/*metabolism ; Archaeal Proteins/*genetics/metabolism ; *Evolution, Molecular ; Histidine/*biosynthesis/genetics ; Operon/*genetics ; Phylogeny ; },
abstract = {The available sequences of genes encoding the enzymes associated with histidine biosynthesis suggest that this is an ancient metabolic pathway that was assembled prior to the diversification of Bacteria, Archaea, and Eucarya. Paralogous duplication, gene elongation, and fusion events of several different his genes have played a major role in shaping this biosynthetic route. We have analyzed the structure and organization of histidine biosynthetic genes from 55 complete archaeal genomes and combined it with phylogenetic inference in order to investigate the mechanisms responsible for the assembly of the his pathway and the origin of his operons. We show that a wide variety of different organizations of his genes exists in Archaea and that some his genes or entire his (sub-)operons have been likely transferred horizontally between Archaea and Bacteria. However, we show that, in most Archaea, his genes are monofunctional (except for hisD) and scattered throughout the genome, suggesting that his operons might have been assembled multiple times during evolution and that in some cases they are the result of recent evolutionary events. An evolutionary model for the structure and organization of his genes in LUCA is proposed.},
}
@article {pmid19878676,
year = {2010},
author = {Heinemann, IU and Söll, D and Randau, L},
title = {Transfer RNA processing in archaea: unusual pathways and enzymes.},
journal = {FEBS letters},
volume = {584},
number = {2},
pages = {303-309},
pmid = {19878676},
issn = {1873-3468},
support = {R01 GM022854/GM/NIGMS NIH HHS/United States ; R01 GM022854-34S1/GM/NIGMS NIH HHS/United States ; },
mesh = {Archaea/*enzymology/genetics ; Endoribonucleases/chemistry/metabolism ; Nucleic Acid Conformation ; Protein Conformation ; *RNA Processing, Post-Transcriptional ; *RNA Splicing ; RNA, Archaeal/chemistry/genetics/*metabolism ; RNA, Transfer/chemistry/genetics/*metabolism ; Ribonuclease P/genetics/metabolism ; },
abstract = {Transfer RNA (tRNA) molecules are highly conserved in length, sequence and structure in order to be functional in the ribosome. However, mostly in archaea, the short genes encoding tRNAs can be found disrupted, fragmented, with permutations or with non-functional mutations of conserved nucleotides. Here, we give an overview of recently discovered tRNA maturation pathways that require intricate processing steps to finally generate the standard tRNA from these unusual tRNA genes.},
}
@article {pmid19878267,
year = {2010},
author = {Meyerdierks, A and Kube, M and Kostadinov, I and Teeling, H and Glöckner, FO and Reinhardt, R and Amann, R},
title = {Metagenome and mRNA expression analyses of anaerobic methanotrophic archaea of the ANME-1 group.},
journal = {Environmental microbiology},
volume = {12},
number = {2},
pages = {422-439},
doi = {10.1111/j.1462-2920.2009.02083.x},
pmid = {19878267},
issn = {1462-2920},
mesh = {Base Sequence ; Cytochromes c/genetics ; Euryarchaeota/classification/*genetics/*metabolism ; Hydrogenase/genetics ; Iron-Sulfur Proteins/genetics ; *Metagenome ; Metagenomics ; Methane/metabolism ; Molecular Sequence Data ; Oceans and Seas ; Oxidation-Reduction ; RNA, Messenger/*metabolism ; },
abstract = {Microbial consortia mediating the anaerobic oxidation of methane with sulfate are composed of methanotrophic Archaea (ANME) and Bacteria related to sulfate-reducing Deltaproteobacteria. Cultured representatives are not available for any of the three ANME clades. Therefore, a metagenomic approach was applied to assess the genetic potential of ANME-1 archaea. In total, 3.4 Mbp sequence information was generated based on metagenomic fosmid libraries constructed directly from a methanotrophic microbial mat in the Black Sea. These sequence data represent, in 30 contigs, about 82-90% of a composite ANME-1 genome. The dataset supports the hypothesis of a reversal of the methanogenesis pathway. Indications for an assimilatory, but not for a dissimilatory sulfate reduction pathway in ANME-1, were found. Draft genome and expression analyses are consistent with acetate and formate as putative electron shuttles. Moreover, the dataset points towards downstream electron-accepting redox components different from the ones known from methanogenic archaea. Whereas catalytic subunits of [NiFe]-hydrogenases are lacking in the dataset, genes for an [FeFe]-hydrogenase homologue were identified, not yet described to be present in methanogenic archaea. Clustered genes annotated as secreted multiheme c-type cytochromes were identified, which have not yet been correlated with methanogenesis-related steps. The genes were shown to be expressed, suggesting direct electron transfer as an additional possible mode to shuttle electrons from ANME-1 to the bacterial sulfate-reducing partner.},
}
@article {pmid19847207,
year = {2010},
author = {Auguet, JC and Barberan, A and Casamayor, EO},
title = {Global ecological patterns in uncultured Archaea.},
journal = {The ISME journal},
volume = {4},
number = {2},
pages = {182-190},
doi = {10.1038/ismej.2009.109},
pmid = {19847207},
issn = {1751-7370},
mesh = {Archaea/classification/genetics/*physiology ; DNA, Ribosomal/genetics ; *Ecosystem ; Multivariate Analysis ; Phylogeny ; Plankton/classification/genetics ; RNA, Ribosomal/genetics ; RNA, Ribosomal, 16S/genetics ; },
abstract = {We have applied a global analytical approach to uncultured Archaea that for the first time reveals well-defined community patterns along broad environmental gradients and habitat types. Phylogenetic patterns and the environmental factors governing the creation and maintenance of these patterns were analyzed for c. 2000 archaeal 16S rRNA gene sequences from 67 globally distributed studies. The sequences were dereplicated at 97% identity, grouped into seven habitat types, and analyzed with both Unifrac (to explore shared phylogenetic history) and multivariate regression tree (that considers the relative abundance of the lineages or taxa) approaches. Both phylogenetic and taxon-based approaches showed salinity and not temperature as one of the principal driving forces at the global scale. Hydrothermal vents and planktonic freshwater habitats emerged as the largest reservoirs of archaeal diversity and consequently are promising environments for the discovery of new archaeal lineages. Conversely, soils were more phylogenetically clustered and archaeal diversity was the result of a high number of closely related phylotypes rather than different lineages. Applying the ecological concept of 'indicator species', we detected up to 13 indicator archaeal lineages for the seven habitats prospected. Some of these lineages (that is, hypersaline MSBL1, marine sediment FCG1 and freshwater plSA1), for which ecological importance has remained unseen to date, deserve further attention as they represent potential key archaeal groups in terms of distribution and ecological processes. Hydrothermal vents held the highest number of indicator lineages, suggesting it would be the earliest habitat colonized by Archaea. Overall, our approach provided ecological support for the often arbitrary nomenclature within uncultured Archaea, as well as phylogeographical clues on key ecological and evolutionary aspects of archaeal biology.},
}
@article {pmid19843187,
year = {2009},
author = {Blank, CE},
title = {Not so old Archaea - the antiquity of biogeochemical processes in the archaeal domain of life.},
journal = {Geobiology},
volume = {7},
number = {5},
pages = {495-514},
doi = {10.1111/j.1472-4669.2009.00219.x},
pmid = {19843187},
issn = {1472-4669},
mesh = {Archaea/*genetics ; *Evolution, Molecular ; Fossils ; *Genetic Variation ; Geologic Sediments/microbiology ; *Phylogeny ; },
abstract = {Since the archaeal domain of life was first recognized, it has often been assumed that Archaea are ancient, and harbor primitive traits. In fact, the names of the major archaeal lineages reflect our assumptions regarding the antiquity of their traits. Ancestral state reconstruction and relaxed molecular clock analyses using newly articulated oxygen age constraints show that although the archaeal domain itself is old, tracing back to the Archean eon, many clades and traits within the domain are not ancient or primitive. Indeed many clades and traits, particularly in the Euryarchaeota, were inferred to be Neoproterozoic or Phanerozoic in age. Both Eury- and Crenarchaeota show increasing metabolic and physiological diversity through time. Early archaeal microbial communities were likely limited to sulfur reduction and hydrogenotrophic methanogenesis, and were confined to high-temperature geothermal environments. However, after the appearance of atmospheric oxygen, nodes containing a wide variety of traits (sulfate and thiosulfate reduction, sulfur oxidation, sulfide oxidation, aerobic respiration, nitrate reduction, mesophilic methanogenesis in sedimentary environments) appear, first in environments containing terrestrial Crenarchaeota in the Meso/Neoproterozoic followed by environments containing marine Euryarchaeota in the Neoproterozoic and Phanerozoic. This provides phylogenetic evidence for increasing complexity in the biogeochemical cycling of C, N, and S through geologic time, likely as a consequence of microbial evolution and the gradual oxygenation of various compartments within the biosphere. This work has implications not only for the large-scale evolution of microbial communities and biogeochemical processes, but also for the interpretation of microbial biosignatures in the ancient rock record.},
}
@article {pmid19841214,
year = {2009},
author = {Bhatta, R and Uyeno, Y and Tajima, K and Takenaka, A and Yabumoto, Y and Nonaka, I and Enishi, O and Kurihara, M},
title = {Difference in the nature of tannins on in vitro ruminal methane and volatile fatty acid production and on methanogenic archaea and protozoal populations.},
journal = {Journal of dairy science},
volume = {92},
number = {11},
pages = {5512-5522},
doi = {10.3168/jds.2008-1441},
pmid = {19841214},
issn = {1525-3198},
mesh = {Animals ; Archaea/drug effects/genetics/*physiology ; *Cattle ; Ciliophora/drug effects/*physiology ; Fatty Acids, Volatile/*metabolism ; Female ; Methane/*metabolism ; Polyethylene Glycols/pharmacology ; RNA, Ribosomal, 16S/genetics ; *Rumen/metabolism/microbiology/parasitology ; Surface-Active Agents/pharmacology ; Tannins/*metabolism ; },
abstract = {Six plant sources of hydrolyzable tannins (HT) or HT and condensed tannins (CT; designated as HT1, HT2, HT3, HT + CT1, HT + CT2, and HT + CT3) were evaluated to determine their effects in vitro on CH(4) production and on ruminal archaeal and protozoa populations, and to assess potential differences in biological activities between sources containing HT only or HT and CT. Samples HT1, HT2, and HT3 contained only HT, whereas samples HT + CT1, HT + CT2, and HT + CT3 contained HT and CT. In experiment 1, in vitro incubations with samples containing HT or HT + CT resulted in a decrease in CH(4) production of 0.6 and 5.5%, respectively, compared with that produced by incubations containing the added tannin binder polyethylene glycol-6000. Tannin also suppressed the population of methanogenic archaea in all incubations except those with HT2, with an average decrease of 11.6% in HT incubations (15.8, 7.09, and 12.0 in HT1, HT2, and HT3) and 28.6% in incubations containing HT + CT (35.0, 40.1, and 10.8 in HT + CT1, HT + CT2, and HT + CT3) when compared with incubations containing added polyethylene glycol-6000. The mean decrease in protozoal counts was 12.3% in HT and 36.2% in HT + CT incubations. Tannins increased in vitro pH, reduced total VFA concentrations, increased propionate concentrations, and decreased concentrations of iso-acids. In experiment 2, when a basal diet was incubated with graded levels of HT + CT1, HT + CT2, and HT + CT3, the total gas and CH4 production and archaeal and protozoal populations decreased as the concentration of tannins increased. Our results confirm that tannins suppress methanogenesis by reducing methanogenic populations in the rumen either directly or by reducing the protozoal population, thereby reducing methanogens symbiotically associated with the protozoal population. In addition, tannin sources containing both HT and CT were more potent in suppressing methanogenesis than those containing only HT.},
}
@article {pmid19840101,
year = {2010},
author = {Schubert, BA and Lowenstein, TK and Timofeeff, MN and Parker, MA},
title = {Halophilic Archaea cultured from ancient halite, Death Valley, California.},
journal = {Environmental microbiology},
volume = {12},
number = {2},
pages = {440-454},
doi = {10.1111/j.1462-2920.2009.02086.x},
pmid = {19840101},
issn = {1462-2920},
mesh = {Base Sequence ; Biodiversity ; California ; Halobacteriaceae/genetics/growth &amp; development/*isolation &amp; purification ; Minerals ; Salts ; Seawater ; Sodium Chloride/chemistry ; },
abstract = {Halophilic Archaea cultured from ancient fluid inclusions in a 90-m-long (0- to 100,000-year-old) salt core from Death Valley, California, demonstrate survival of bacterial cells in subsurface halite for up to 34,000 years. Five enrichment cultures, representing three genera of halophilic Archaea (Halorubrum, Natronomonas and Haloterrigena), were obtained from five surface-sterilized halite crystals exclusively in one section of the core (13.0-17.8 m; 22,000-34,000 years old) containing perennial saline lake deposits. Prokaryote cells were observed microscopically in situ within fluid inclusions from every layer that produced culturable cells. Another 876 crystals analysed from depths of 8.1-86.7 m (10,000-100,000 years old) failed to yield live halophilic Archaea. Considering the number of halite crystals tested (culturing success of 0.6%), microbial survival in fluid inclusions in halite is rare and related to the paleoenvironment, which controls the distribution and abundance of trapped microorganisms. Two cultures from two crystals at 17.8 m that yielded identical 16S rRNA sequences (genus: Haloterrigena) demonstrate intra-laboratory reproducibility. Inter-laboratory reproducibility is shown by two halophilic Archaea (genus: Natronomonas), with 99.3% similarity of 16S rRNA sequences, cultured from the same core interval, but at separate laboratories.},
}
@article {pmid19835159,
year = {2009},
author = {Meng, X and Mao, Z and Chen, G and Yang, Y and Xie, B},
title = {[Diversity of soil archaea in Tibetan Mila Mountains].},
journal = {Wei sheng wu xue bao = Acta microbiologica Sinica},
volume = {49},
number = {8},
pages = {994-1002},
pmid = {19835159},
issn = {0001-6209},
mesh = {Ammonia/metabolism ; Archaea/classification/*genetics/*isolation &amp; purification ; Archaeal Proteins/genetics ; *Biodiversity ; DNA, Archaeal/genetics ; DNA, Ribosomal/genetics ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; Tibet ; },
abstract = {OBJECTIVE: In order to study the diversity of archaea and ammonia-oxidizing archaea (AOA) of the alp prairie soil in Mila Mountain of Tibet.<br><br>METHODS: Total microbial DNA was directly extracted from the alp prairie of Mila Mountain. The clone library of 16S rRNA genes and amoA genes were amplified by PCR with universal primer sets. The sequences of archaea and AOA were defined into operational taxonomic units (OTUs) according to the 97% similarity threshold for OTU assignment was performed using the software program DOTUR.<br><br>RESULTS: Phylogenetic analysis revealed archaea in the soil of Mila Mountain including the Crenarchaeota (71.7%) and unclassified-Archaea (28.3%) phyla. All the Crenarchaeota belong to the Thermoprotei. Phylogenetic analysis revealed AOA in the alp prairie soil of Mila Mountain belonged to the kingdom Crenarchaeota. Archaea and AOA species composition from Mila Mountain included 64 OTUs and 75 OTUs.<br><br>CONCLUSION: These findings show prolific archaeal diversity in the alp prairie soil of Mila Mountain, where they may be actively involved in nitrification.},
}
@article {pmid19833965,
year = {2009},
author = {Dekas, AE and Poretsky, RS and Orphan, VJ},
title = {Deep-sea archaea fix and share nitrogen in methane-consuming microbial consortia.},
journal = {Science (New York, N.Y.)},
volume = {326},
number = {5951},
pages = {422-426},
doi = {10.1126/science.1178223},
pmid = {19833965},
issn = {1095-9203},
mesh = {Anaerobiosis ; Archaea/genetics/growth &amp; development/*metabolism ; Bacteria, Anaerobic/genetics/growth &amp; development/metabolism ; Deltaproteobacteria/genetics/growth &amp; development/*metabolism ; *Ecosystem ; Genes, Archaeal ; Genes, Bacterial ; Geologic Sediments/*microbiology ; Mass Spectrometry/methods ; Methane/*metabolism ; *Nitrogen Fixation/genetics ; Nitrogen Isotopes/metabolism ; Operon ; Oxidation-Reduction ; Oxidoreductases/genetics ; Seawater/microbiology ; Sulfates/metabolism ; *Symbiosis ; },
abstract = {Nitrogen-fixing (diazotrophic) microorganisms regulate productivity in diverse ecosystems; however, the identities of diazotrophs are unknown in many oceanic environments. Using single-cell-resolution nanometer secondary ion mass spectrometry images of 15N incorporation, we showed that deep-sea anaerobic methane-oxidizing archaea fix N2, as well as structurally similar CN-, and share the products with sulfate-reducing bacterial symbionts. These archaeal/bacterial consortia are already recognized as the major sink of methane in benthic ecosystems, and we now identify them as a source of bioavailable nitrogen as well. The archaea maintain their methane oxidation rates while fixing N2 but reduce their growth, probably in compensation for the energetic burden of diazotrophy. This finding extends the demonstrated lower limits of respiratory energy capable of fueling N2 fixation and reveals a link between the global carbon, nitrogen, and sulfur cycles.},
}
@article {pmid19828044,
year = {2009},
author = {Blombach, F and Makarova, KS and Marrero, J and Siebers, B and Koonin, EV and van der Oost, J},
title = {Identification of an ortholog of the eukaryotic RNA polymerase III subunit RPC34 in Crenarchaeota and Thaumarchaeota suggests specialization of RNA polymerases for coding and non-coding RNAs in Archaea.},
journal = {Biology direct},
volume = {4},
number = {},
pages = {39},
pmid = {19828044},
issn = {1745-6150},
support = {//Intramural NIH HHS/United States ; },
mesh = {Amino Acid Sequence ; Crenarchaeota/*enzymology/genetics ; Eukaryotic Cells/*enzymology ; Genome, Archaeal/genetics ; Molecular Sequence Data ; Phylogeny ; Protein Subunits/*chemistry ; RNA Polymerase III/*chemistry ; RNA, Archaeal/*metabolism ; RNA, Untranslated/*metabolism ; Sequence Alignment ; *Sequence Homology, Amino Acid ; Transcription, Genetic ; },
abstract = {One of the hallmarks of eukaryotic information processing is the co-existence of 3 distinct, multi-subunit RNA polymerase complexes that are dedicated to the transcription of specific classes of coding or non-coding RNAs. Archaea encode only one RNA polymerase that resembles the eukaryotic RNA polymerase II with respect to the subunit composition. Here we identify archaeal orthologs of the eukaryotic RNA polymerase III subunit RPC34. Genome context analysis supports a function of this archaeal protein in the transcription of non-coding RNAs. These findings suggest that functional separation of RNA polymerases for protein-coding genes and non-coding RNAs might predate the origin of the Eukaryotes.},
}
@article {pmid19823765,
year = {2010},
author = {Yuan, J and Zweers, JC and van Dijl, JM and Dalbey, RE},
title = {Protein transport across and into cell membranes in bacteria and archaea.},
journal = {Cellular and molecular life sciences : CMLS},
volume = {67},
number = {2},
pages = {179-199},
pmid = {19823765},
issn = {1420-9071},
support = {R01 GM063862/GM/NIGMS NIH HHS/United States ; GM63862/GM/NIGMS NIH HHS/United States ; },
mesh = {Adenosine Triphosphatases/chemistry/*metabolism ; Archaea/*enzymology ; Archaeal Proteins/chemistry/*metabolism ; Bacteria/*enzymology ; Bacterial Proteins/chemistry/*metabolism ; Cell Membrane/*metabolism ; Membrane Transport Proteins/chemistry/*metabolism ; Protein Transport ; SEC Translocation Channels ; SecA Proteins ; },
abstract = {In the three domains of life, the Sec, YidC/Oxa1, and Tat translocases play important roles in protein translocation across membranes and membrane protein insertion. While extensive studies have been performed on the endoplasmic reticular and Escherichia coli systems, far fewer studies have been done on archaea, other Gram-negative bacteria, and Gram-positive bacteria. Interestingly, work carried out to date has shown that there are differences in the protein transport systems in terms of the number of translocase components and, in some cases, the translocation mechanisms and energy sources that drive translocation. In this review, we will describe the different systems employed to translocate and insert proteins across or into the cytoplasmic membrane of archaea and bacteria.},
}
@article {pmid19819658,
year = {2009},
author = {Schleifer, KH},
title = {Classification of Bacteria and Archaea: past, present and future.},
journal = {Systematic and applied microbiology},
volume = {32},
number = {8},
pages = {533-542},
doi = {10.1016/j.syapm.2009.09.002},
pmid = {19819658},
issn = {1618-0984},
mesh = {Archaea/chemistry/*classification/genetics ; Bacteria/chemistry/*classification/genetics ; Classification/*methods ; Genome, Archaeal ; Genome, Bacterial ; },
abstract = {The late 19th century was the beginning of bacterial taxonomy and bacteria were classified on the basis of phenotypic markers. The distinction of prokaryotes and eukaryotes was introduced in the 1960s. Numerical taxonomy improved phenotypic identification but provided little information on the phylogenetic relationships of prokaryotes. Later on, chemotaxonomic and genotypic methods were widely used for a more satisfactory classification. Archaea were first classified as a separate group of prokaryotes in 1977. The current classification of Bacteria and Archaea is based on an operational-based model, the so-called polyphasic approach, comprised of phenotypic, chemotaxonomic and genotypic data, as well as phylogenetic information. The provisional status Candidatus has been established for describing uncultured prokaryotic cells for which their phylogenetic relationship has been determined and their authenticity revealed by in situ probing. The ultimate goal is to achieve a theory-based classification system based on a phylogenetic/evolutionary concept. However, there are currently two contradictory opinions about the future classification of Bacteria and Archaea. A group of mostly molecular biologists posits that the yet-unclear effect of gene flow, in particular lateral gene transfer, makes the line of descent difficult, if not impossible, to describe. However, even in the face of genomic fluidity it seems that the typical geno- and phenotypic characteristics of a taxon are still maintained, and are sufficient for reliable classification and identification of Bacteria and Archaea. There are many well-defined genotypic clusters that are congruent with known species delineated by polyphasic approaches. Comparative sequence analysis of certain core genes, including rRNA genes, may be useful for the characterization of higher taxa, whereas various character genes may be suitable as phylogenetic markers for the delineation of lower taxa. Nevertheless, there may still be a few organisms which escape a reliable classification.},
}
@article {pmid19805277,
year = {2009},
author = {Dreyfus, C and Lemaire, D and Mari, S and Pignol, D and Arnoux, P},
title = {Crystallographic snapshots of iterative substrate translocations during nicotianamine synthesis in Archaea.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {106},
number = {38},
pages = {16180-16184},
pmid = {19805277},
issn = {1091-6490},
mesh = {Alkyl and Aryl Transferases/chemistry/genetics/*metabolism ; Amino Acid Sequence ; Archaeal Proteins/chemistry/genetics/*metabolism ; Azetidinecarboxylic Acid/*analogs &amp; derivatives/chemistry/metabolism ; Binding Sites/genetics ; Catalysis ; Crystallography, X-Ray ; Cyclization ; Hydrogen Bonding ; Mass Spectrometry ; Methanobacteriaceae/*enzymology/genetics ; Models, Chemical ; Models, Molecular ; Molecular Sequence Data ; Molecular Structure ; Mutation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; S-Adenosylmethionine/chemistry/metabolism ; Sequence Homology, Amino Acid ; Substrate Specificity ; },
abstract = {Nicotianamine (NA), a small molecule ubiquitous in plants, is an important divalent metal chelator and the main precursor of phytosiderophores. Nicotianamine synthase (NAS) is the enzyme catalyzing NA synthesis by the condensation of three aminopropyl moieties of S-adenosylmethionine (SAM) and the cyclization of one of them to form an azetidine ring. Here we report five crystal structures of an archaeal NAS from Methanothermobacter thermautotrophicus, either free or in complex with its product(s) and substrate(s). These structures reveal a two-domains fold arrangement of MtNAS, a small molecule related to NA (named here thermoNicotianamine or tNA), and an original mechanism of synthesis in a buried reaction chamber. This reaction chamber is open to the solvent through a small inlet, and a single active site allows the selective entrance of only one substrate at a time that is then processed and translocated stepwise.},
}
@article {pmid19796638,
year = {2009},
author = {Alkalaeva, E and Eliseev, B and Ambrogelly, A and Vlasov, P and Kondrashov, FA and Gundllapalli, S and Frolova, L and Söll, D and Kisselev, L},
title = {Translation termination in pyrrolysine-utilizing archaea.},
journal = {FEBS letters},
volume = {583},
number = {21},
pages = {3455-3460},
pmid = {19796638},
issn = {1873-3468},
support = {R01 GM022854/GM/NIGMS NIH HHS/United States ; R01 GM022854-33/GM/NIGMS NIH HHS/United States ; },
mesh = {Amino Acid Sequence ; Archaeal Proteins/chemistry/metabolism ; Codon, Terminator/genetics/metabolism ; Genome, Archaeal ; Humans ; Lysine/*analogs &amp; derivatives/metabolism ; Methanosarcinaceae/*genetics/*metabolism ; Molecular Sequence Data ; Peptide Termination Factors/chemistry/metabolism ; Phylogeny ; *Protein Biosynthesis ; },
abstract = {Although some data link archaeal and eukaryotic translation, the overall mechanism of protein synthesis in archaea remains largely obscure. Both archaeal (aRF1) and eukaryotic (eRF1) single release factors recognize all three stop codons. The archaeal genus Methanosarcinaceae contains two aRF1 homologs, and also uses the UAG stop to encode the 22nd amino acid, pyrrolysine. Here we provide an analysis of the last stage of archaeal translation in pyrrolysine-utilizing species. We demonstrated that only one of two Methanosarcina barkeri aRF1 homologs possesses activity and recognizes all three stop codons. The second aRF1 homolog may have another unknown function. The mechanism of pyrrolysine incorporation in the Methanosarcinaceae is discussed.},
}
@article {pmid19794413,
year = {2009},
author = {Martens-Habbena, W and Berube, PM and Urakawa, H and de la Torre, JR and Stahl, DA},
title = {Ammonia oxidation kinetics determine niche separation of nitrifying Archaea and Bacteria.},
journal = {Nature},
volume = {461},
number = {7266},
pages = {976-979},
pmid = {19794413},
issn = {1476-4687},
mesh = {Ammonia/*chemistry/*metabolism ; Archaea/*metabolism ; Bacteria/*metabolism ; Kinetics ; Models, Biological ; Nitrogen/metabolism ; Nitrosomonas/metabolism ; Oxidation-Reduction ; Plankton/metabolism ; Quaternary Ammonium Compounds/metabolism ; Seawater/chemistry ; },
abstract = {The discovery of ammonia oxidation by mesophilic and thermophilic Crenarchaeota and the widespread distribution of these organisms in marine and terrestrial environments indicated an important role for them in the global nitrogen cycle. However, very little is known about their physiology or their contribution to nitrification. Here we report oligotrophic ammonia oxidation kinetics and cellular characteristics of the mesophilic crenarchaeon 'Candidatus Nitrosopumilus maritimus' strain SCM1. Unlike characterized ammonia-oxidizing bacteria, SCM1 is adapted to life under extreme nutrient limitation, sustaining high specific oxidation rates at ammonium concentrations found in open oceans. Its half-saturation constant (K(m) = 133 nM total ammonium) and substrate threshold (<or=10 nM) closely resemble kinetics of in situ nitrification in marine systems and directly link ammonia-oxidizing Archaea to oligotrophic nitrification. The remarkably high specific affinity for reduced nitrogen (68,700 l per g cells per h) of SCM1 suggests that Nitrosopumilus-like ammonia-oxidizing Archaea could successfully compete with heterotrophic bacterioplankton and phytoplankton. Together these findings support the hypothesis that nitrification is more prevalent in the marine nitrogen cycle than accounted for in current biogeochemical models.},
}
@article {pmid19784923,
year = {2009},
author = {Nercessian, D and Marino Buslje, C and Ordóñez, MV and De Castro, RE and Conde, RD},
title = {Presence of structural homologs of ubiquitin in haloalkaliphilic Archaea.},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {12},
number = {3},
pages = {167-173},
pmid = {19784923},
issn = {1618-1905},
mesh = {Amino Acid Sequence ; Antibodies/immunology ; Archaeal Proteins/*genetics/immunology ; Cloning, Molecular ; Escherichia coli/genetics ; Gene Expression ; Halobacteriaceae/*genetics ; Models, Molecular ; Molecular Sequence Data ; Protein Binding ; Protein Structure, Tertiary ; *Proteomics ; Sequence Homology, Amino Acid ; Ubiquitin/*genetics/immunology ; },
abstract = {Ubiquitin, a protein widely conserved in eukaryotes, is involved in many cellular processes, including proteolysis. While sequences encoding ubiquitin-like proteins have not been identified in prokaryotic genomes sequenced so far, they have revealed the presence of structural and functional homologs of ubiquitin in Bacteria and Archaea. This work describes the amplification and proteomic analysis of a 400-bp DNA fragment from the haloalkaliphilic archaeon Natrialba magadii. The encoded polypeptide, P400, displayed structural homology to ubiquitin-like proteins such as those of the ThiS family and Urm1. Expression of the P400 DNA sequence in Escherichia coli cells yielded a recombinant polypeptide that reacted with anti-ubiquitin antibodies. In addition, a putative open reading frame encoding P400 was identified in the recently sequenced genome of N. magadii. Together, these results evidence the presence in Archaea of structural homologs of ubiquitin- related proteins.},
}
@article {pmid19783748,
year = {2009},
author = {Miyazaki, J and Higa, R and Toki, T and Ashi, J and Tsunogai, U and Nunoura, T and Imachi, H and Takai, K},
title = {Molecular characterization of potential nitrogen fixation by anaerobic methane-oxidizing archaea in the methane seep sediments at the number 8 Kumano Knoll in the Kumano Basin, offshore of Japan.},
journal = {Applied and environmental microbiology},
volume = {75},
number = {22},
pages = {7153-7162},
pmid = {19783748},
issn = {1098-5336},
mesh = {Anaerobiosis ; Archaea/classification/enzymology/*genetics/*metabolism ; Cloning, Molecular ; DNA, Archaeal/genetics ; Genes, Archaeal/genetics ; Genetic Variation ; Geologic Sediments/*microbiology ; Japan ; Methane/metabolism ; Molecular Sequence Data ; Multigene Family/genetics ; *Nitrogen Fixation/genetics ; Oxidoreductases/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/chemistry ; Sequence Alignment ; },
abstract = {The potential for microbial nitrogen fixation in the anoxic methane seep sediments in a mud volcano, the number 8 Kumano Knoll, was characterized by molecular phylogenetic analyses. A total of 111 of the nifH (a gene coding a nitrogen fixation enzyme, Fe protein) clones were obtained from different depths of the core sediments, and the phylogenetic analysis of the clones indicated the genetic diversity of nifH genes. The predominant group detected (methane seep group 2), representing 74% of clonal abundance, was phylogenetically related to the nifH sequences obtained from the Methanosarcina species but was most closely related to the nifH sequences potentially derived from the anoxic methanotrophic archaea (ANME-2 archaea). The recovery of the nif gene clusters including the nifH sequences of the methane seep group 2 and the subsequent reverse transcription-PCR detection of the nifD and nifH genes strongly suggested that the genetic components of the gene clusters would be operative for the in situ assimilation of molecular nitrogen (N(2)) by the host microorganisms. DNA-based quantitative PCR of the archaeal 16S rRNA gene, the group-specific mcrA (a gene encoding the methyl-coenzyme M reductase alpha subunit) gene, and the nifD and nifH genes demonstrated the similar distribution patterns of the archaeal 16S rRNA gene, the mcrA groups c-d and e, and the nifD and nifH genes through the core sediments. These results supported the idea that the anoxic methanotrophic archaea ANME-2c could be the microorganisms hosting the nif gene clusters and could play an important role in not only the in situ carbon (methane) cycle but also the nitrogen cycle in subseafloor sediments.},
}
@article {pmid19780828,
year = {2009},
author = {Zhang, LM and Wang, M and Prosser, JI and Zheng, YM and He, JZ},
title = {Altitude ammonia-oxidizing bacteria and archaea in soils of Mount Everest.},
journal = {FEMS microbiology ecology},
volume = {70},
number = {2},
pages = {52-61},
doi = {10.1111/j.1574-6941.2009.00775.x},
pmid = {19780828},
issn = {1574-6941},
mesh = {Altitude ; Ammonia/*metabolism ; Archaea/classification/*genetics ; Bacteria/classification/*genetics ; Biodiversity ; Cloning, Molecular ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; Ecosystem ; Genes, Archaeal ; Genes, Bacterial ; Oxidoreductases/genetics ; Sequence Analysis, DNA ; Soil/analysis ; *Soil Microbiology ; },
abstract = {To determine the abundance and distribution of bacterial and archaeal ammonia oxidizers in alpine and permafrost soils, 12 soils at altitudes of 4000-6550 m above sea level (m a.s.l.) were collected from the northern slope of the Mount Everest (Tibetan Plateau), where the permanent snow line is at 5800-6000 m a.s.l. Communities were characterized by real-time PCR and clone sequencing by targeting on amoA genes, which putatively encode ammonia monooxygenase subunit A. Archaeal amoA abundance was greater than bacterial amoA abundance in lower altitude soils (<or=5400 m a.s.l.), but this situation was reversed in higher altitude soils (>or=5700 m a.s.l.). Both archaeal and bacterial amoA abundance decreased abruptly in higher altitude soils. Communities shifted from a Nitrosospira amoA cluster 3a-dominated ammonia-oxidizing bacteria community in lower altitude soils to communities dominated by a newly designated Nitrosospira ME and cluster 2-related groups and Nitrosomonas cluster 6 in higher altitude soils. All archaeal amoA sequences fell within soil and sediment clusters, and the proportions of the major archaeal amoA clusters changed between the lower altitude and the higher altitude soils. These findings imply that the shift in the relative abundance and community structure of archaeal and bacterial ammonia oxidizers may result from selection of organisms adapted to altitude-dependent environmental factors in elevated soils.},
}
@article {pmid19777304,
year = {2010},
author = {Saia, F and Domingues, M and Pellizari, V and Vazoller, R},
title = {Occurrence of methanogenic Archaea in highly polluted sediments of tropical Santos-São Vicente Estuary (São Paulo, Brazil).},
journal = {Current microbiology},
volume = {60},
number = {1},
pages = {66-70},
pmid = {19777304},
issn = {1432-0991},
mesh = {Brazil ; Methane/*biosynthesis ; Methanobacteriaceae/genetics/growth &amp; development/*metabolism ; Methanosarcina/genetics/growth &amp; development/*metabolism ; *Water Microbiology ; *Water Pollutants ; },
abstract = {Little is known about the ability of methanogens to grow and produce methane in estuarine environments. In this study, traditional methods for cultivating strictly anaerobic microorganisms were combined with Fluorescence in situ hybridization (FISH) technique to enrich and identify methanogenic Archaea cultures occurring in highly polluted sediments of tropical Santos-São Vicente Estuary (São Paulo, Brazil). Sediment samples were enriched at 30 degrees C under strict anaerobic and halophilic conditions, using a basal medium containing 2% of sodium chloride and amended with glucose, methanol, and sodium salts of acetate, formate and lactate. High methanogenic activity was detected, as evidenced by the biogas containing 11.5 mmol of methane at 20 days of incubation time and methane yield of 0.138-mmol CH(4)/g organic matter/g volatile suspense solids. Cells of methanogenic Archaea were selected by serial dilution in medium amended separately with sodium acetate, sodium formate, or methanol. FISH analysis revealed the presence of Methanobacteriaceae and Methanosarcina sp. cells.},
}
@article {pmid19753475,
year = {2009},
author = {Higuchi, Mde L and Kawakami, J and Ikegami, R and Clementino, MB and Kawamoto, FM and Reis, MM and Bocchi, E},
title = {Do Archaea and bacteria co-infection have a role in the pathogenesis of chronic chagasic cardiopathy?.},
journal = {Memorias do Instituto Oswaldo Cruz},
volume = {104 Suppl 1},
number = {},
pages = {199-207},
doi = {10.1590/s0074-02762009000900026},
pmid = {19753475},
issn = {1678-8060},
mesh = {Antigens, Bacterial/analysis ; Archaea/*isolation &amp; purification ; Biopsy ; Chagas Cardiomyopathy/*microbiology/pathology ; Chlamydophila pneumoniae/*isolation &amp; purification ; Chronic Disease ; Complement Membrane Attack Complex/*analysis ; Humans ; In Situ Hybridization ; Microscopy, Electron ; Mycoplasma pneumoniae/*isolation &amp; purification ; Polymerase Chain Reaction ; },
abstract = {UNLABELLED: Chronic cardiopathy (CC) in Chagas disease is a fibrotic myocarditis with C5b-9 complement deposition. Mycoplasma and Chlamydia may interfere with the complement response. Proteolytic enzymes and archaeal genes that have been described in Trypanosoma cruzi may increase its virulence. Here we tested the hypothesis that different ratios of Mycoplasma, Chlamydia and archaeal organisms, which are frequent symbionts, may be associated with chagasic clinical forms.<br><br>MATERIALS AND METHODS: eight indeterminate form (IF) and 20 CC chagasic endomyocardial biopsies were submitted to in situ hybridization, electron and immunoelectron microscopy and PCR techniques for detection of Mycoplasma pneumoniae (MP), Chlamydia pneumoniae(CP), C5b-9 and archaeal-like bodies.<br><br>RESULTS: MP and CP-DNA were always present at lower levels in CC than in IF (p < 0.001) and were correlated with each other only in CC. Electron microscopy revealed Mycoplasma, Chlamydia and two types of archaeal-like bodies. One had electron dense lipid content (EDL) and was mainly present in IF. The other had electron lucent content (ELC) and was mainly present in CC. In this group, ELC correlated negatively with the other microbes and EDL and positively with C5b-9. The CC group was positive for Archaea and T. cruzi DNA. In conclusion, different amounts of Mycoplasma, Chlamydia and archaeal organisms may be implicated in complement activation and may have a role in Chagas disease outcome.},
}
@article {pmid19767464,
year = {2009},
author = {Callieri, C and Corno, G and Caravati, E and Rasconi, S and Contesini, M and Bertoni, R},
title = {Bacteria, archaea, and crenarchaeota in the epilimnion and hypolimnion of a deep holo-oligomictic lake.},
journal = {Applied and environmental microbiology},
volume = {75},
number = {22},
pages = {7298-7300},
pmid = {19767464},
issn = {1098-5336},
mesh = {Archaea/genetics/*physiology ; Bacteria/genetics ; *Bacterial Physiological Phenomena ; Biodiversity ; Chlorophyll/analysis ; Chlorophyll A ; Colony Count, Microbial ; Crenarchaeota/genetics/*physiology ; Fresh Water/chemistry/*microbiology ; Oligonucleotide Probes ; Oxygen/analysis ; Temperature ; *Water Microbiology ; Water Pollutants, Chemical ; },
abstract = {In a deep, subalpine holo-oligomictic lake, the relative abundance of Archaea and Crenarchaeota, but not that of Bacteria, increases significantly with depth and varies seasonally. Cell-specific prokaryotic productivity is homogeneous along the water column. The concept of active Archaea observed in the deep ocean can therefore be extended to a deep oxic lake.},
}
@article {pmid19765088,
year = {2009},
author = {Magidovich, H and Eichler, J},
title = {Glycosyltransferases and oligosaccharyltransferases in Archaea: putative components of the N-glycosylation pathway in the third domain of life.},
journal = {FEMS microbiology letters},
volume = {300},
number = {1},
pages = {122-130},
doi = {10.1111/j.1574-6968.2009.01775.x},
pmid = {19765088},
issn = {1574-6968},
mesh = {Archaea/classification/*enzymology/genetics ; Archaeal Proteins/genetics/*metabolism ; Gene Expression Regulation, Archaeal ; Glycosylation ; Glycosyltransferases/genetics/*metabolism ; Hexosyltransferases/genetics/*metabolism ; Membrane Proteins/genetics/*metabolism ; Molecular Sequence Data ; Phylogeny ; },
abstract = {The ability of Eukarya, Bacteria and Archaea to perform N-glycosylation underlies the importance and possible antiquity of this post-translational protein modification. However, in contrast to the relatively well-studied eukaryal and bacterial pathways, the archaeal N-glycosylation process is less understood. To remedy this disparity, the following study has examined 56 available archaeal genomes with the aim of identifying glycosyltransferases and oligosaccharyltransferases, including those putatively catalyzing this post-translational processing event. This analysis reveals that while oligosaccharyltransferases, central components of the N-glycosylation pathway, are found across the range of archaeal phenotypes, the N-glycosylation machinery of hyperthermophilic Archaea may well rely on fewer components than do the parallel systems of nonhyperthermophilic Archaea. Moreover, genes encoding predicted glycosyltransferases of hyperthermophilic Archaea tend to be far more scattered within the genome than is the case with nonhyperthermophilic species, where putative glycosyltransferase genes are often clustered around identified oligosaccharyltransferase-encoding sequences.},
}
@article {pmid19755115,
year = {2009},
author = {Shimada, Y and Fukuda, W and Akada, Y and Ishida, M and Nakayama, J and Imanaka, T and Fujiwara, S},
title = {Property of cold inducible DEAD-box RNA helicase in hyperthermophilic archaea.},
journal = {Biochemical and biophysical research communications},
volume = {389},
number = {4},
pages = {622-627},
doi = {10.1016/j.bbrc.2009.09.038},
pmid = {19755115},
issn = {1090-2104},
mesh = {Base Sequence ; *Cold Temperature ; DEAD-box RNA Helicases/chemistry/genetics/*metabolism ; Gene Expression Regulation, Archaeal ; Molecular Sequence Data ; Protein Conformation ; Thermococcus/*enzymology/genetics ; },
abstract = {TK0306 (Tk-DeaD) of hyperthermophilic archaeon Thermococcus kodakaraensis is annotated as the DEAD-box helicase gene; nevertheless, its ortholog has not been identified in closely related genera, Pyrococcus spp., which generally grow at higher temperature than T. kodakaraensis, suggesting that the cold-inducible RNA helicase of Tk-DeaD functions under cold stress conditions. Quantitative RT-PCR revealed that Tk-deaD was more dominantly transcribed at 60 degrees C than at 85 degrees C and 93 degrees C in both logarithmic and stationary phases. Immunoblot analyses revealed that Tk-DeaD was detected only in logarithmic-phase cells cultivated at 60 degrees C but hardly detected at 85 degrees C and 93 degrees C in both phases. Tk-DeaD expression is, hence, post-transcriptionally regulated and appears under vigorous growth conditions at 60 degrees C. Recombinant Tk-DeaD purified to homogeneity started to unfold at 20 degrees C, fully unfolded at 70 degrees C, and exhibited maximal ATPase activity and unwinding activity specific for single-strand paired RNA at 50 degrees C, which is lower than the growth limit of T. kodakaraensis.},
}
@article {pmid19740110,
year = {2009},
author = {Cacciapuoti, G and Peluso, I and Fuccio, F and Porcelli, M},
title = {Purine nucleoside phosphorylases from hyperthermophilic Archaea require a CXC motif for stability and folding.},
journal = {The FEBS journal},
volume = {276},
number = {20},
pages = {5799-5805},
doi = {10.1111/j.1742-4658.2009.07247.x},
pmid = {19740110},
issn = {1742-4658},
mesh = {Amino Acid Motifs/genetics/physiology ; Amino Acid Sequence ; Archaea/*enzymology ; Archaeal Proteins/*chemistry/genetics/*metabolism ; Molecular Sequence Data ; Protein Folding ; Protein Stability ; Purine-Nucleoside Phosphorylase/*chemistry/genetics/*metabolism ; Sequence Homology, Amino Acid ; },
abstract = {5'-Deoxy-5'-methylthioadenosine phosphorylase II from Sulfolobus solfataricus (SsMTAPII) and purine nucleoside phosphorylase from Pyrococcus furiosus (PfPNP) are hyperthermophilic purine nucleoside phosphorylases stabilized by intrasubunit disulfide bonds. In their C-terminus, both enzymes harbour a CXC motif analogous to the CXXC motif present at the active site of eukaryotic protein disulfide isomerase. By monitoring the refolding of SsMTAPII, PfPNP and their mutants lacking the C-terminal cysteine pair after guanidine-induced unfolding, we demonstrated that the CXC motif is required for the folding of these enzymes. Moreover, two synthesized CXC-containing peptides with the same amino acid sequences present in the C-terminal regions of SsMTAPII and PfPNP were found to act as in vitro catalysts of oxidative folding. These small peptides are involved in the folding of partially refolded SsMTAPII, PfPNP and their CXC-lacking mutants, with a concomitant recovery of their catalytic activity, thus indicating that the CXC motif is necessary to obtain complete reversibility from the unfolded state of the two proteins. The two CXC-containing peptides are also able to reactivate scrambled RNaseA. The data obtained in the present study represent the first example of how the CXC motif improves both stability and folding in hyperthermophilic proteins with disulfide bonds.},
}
@article {pmid19717742,
year = {2009},
author = {Godoy, PD and Nogueira-Junior, LA and Paes, LS and Cornejo, A and Martins, RM and Silber, AM and Schenkman, S and Elias, MC},
title = {Trypanosome prereplication machinery contains a single functional orc1/cdc6 protein, which is typical of archaea.},
journal = {Eukaryotic cell},
volume = {8},
number = {10},
pages = {1592-1603},
pmid = {19717742},
issn = {1535-9786},
mesh = {Amino Acid Sequence ; Archaea/*genetics/metabolism ; Archaeal Proteins/*genetics/metabolism ; Cell Cycle Proteins/genetics/metabolism ; *DNA Replication ; Molecular Sequence Data ; Origin Recognition Complex/*genetics/metabolism ; Protozoan Proteins/*genetics/metabolism ; RNA Interference ; Saccharomyces cerevisiae Proteins/genetics/metabolism ; },
abstract = {In unicellular eukaryotes, such as Saccharomyces cerevisiae, and in multicellular organisms, the replication origin is recognized by the heterohexamer origin recognition complex (ORC) containing six proteins, Orc1 to Orc6, while in members of the domain Archaea, the replication origin is recognized by just one protein, Orc1/Cdc6; the sequence of Orc1/Cdc6 is highly related to those of Orc1 and Cdc6. Similar to Archaea, trypanosomatid genomes contain only one gene encoding a protein named Orc1. Since trypanosome Orc1 is also homologous to Cdc6, in this study we named the Orc1 protein from trypanosomes Orc1/Cdc6. Here we show that the recombinant Orc1/Cdc6 from Trypanosoma cruzi (TcOrc1/Cdc6) and from Trypanosoma brucei (TbOrc1/Cdc6) present ATPase activity, typical of prereplication machinery components. Also, TcOrc1/Cdc6 and TbOrc1/Cdc6 replaced yeast Cdc6 but not Orc1 in a phenotypic complementation assay. The induction of Orc1/Cdc6 silencing by RNA interference in T. brucei resulted in enucleated cells, strongly suggesting the involvement of Orc1/Cdc6 in DNA replication. Orc1/Cdc6 is expressed during the entire cell cycle in the nuclei of trypanosomes, remaining associated with chromatin in all stages of the cell cycle. These results allowed us to conclude that Orc1/Cdc6 is indeed a member of the trypanosome prereplication machinery and point out that trypanosomes carry a prereplication machinery that is less complex than other eukaryotes and closer to archaea.},
}
@article {pmid19704896,
year = {2009},
author = {Ettema, TJ and Bernander, R},
title = {Cell division and the ESCRT complex: A surprise from the archaea.},
journal = {Communicative &amp; integrative biology},
volume = {2},
number = {2},
pages = {86-88},
pmid = {19704896},
issn = {1942-0889},
abstract = {The Archaea constitute the third domain of life, a separate evolutionary lineage together with the Bacteria and the Eukarya.1 Species belonging to the Archaea contain a surprising mix of bacterial (metabolism, life style, genomic organization) and eukaryotic (replication, transcription, translation) features.2 The archaeal kingdom comprises two main phyla, the Crenarchaeota and the Euryarchaeota. Regarding the cell division process in archaeal species (reviewed in ref. 3), members of the Euryarchaeota rely on an FtsZ-based cell division mechanism4 whereas, previously, no division genes had been detected in the crenarchaea. However, we recently reported the discovery of the elusive cell division machinery in crenarchaea from the genus Sulfolobus.5 The minimal machinery consists of three genes, which we designated cdvA, B and C (for cell division), organized into an operon that is widely conserved among crenarchaea. The gene products polymerize between segregating nucleoids at the early mitotic stage, forming a complex that remains associated with the leading edge of constriction throughout cytokinesis. Interestingly, CdvB and CdvC were shown to be related to the eukaryotic ESCRT-III protein sorting machinery (reviewed in ref. 6), indicating shared common ancestry and mechanistic similarities to endosomal vesicle formation and viral (HIV) budding in eukaryotes. We also demonstrated that the cdv operon is subject to checkpoint-like regulation, and that the genes display a complementary phylogenetic distribution within the Archaea domain relative to FtsZ-dependent division systems.5 Here, the findings are further explored and discussed, and topics for further investigation are suggested.},
}
@article {pmid19702957,
year = {2009},
author = {Vianna, ME and Conrads, G and Gomes, BP and Horz, HP},
title = {T-RFLP-based mcrA gene analysis of methanogenic archaea in association with oral infections and evidence of a novel Methanobrevibacter phylotype.},
journal = {Oral microbiology and immunology},
volume = {24},
number = {5},
pages = {417-422},
doi = {10.1111/j.1399-302X.2009.00539.x},
pmid = {19702957},
issn = {1399-302X},
mesh = {Bacteroides/isolation &amp; purification ; Colony Count, Microbial ; Dental Plaque/microbiology ; Dental Pulp Cavity/microbiology ; Dental Pulp Necrosis/*microbiology ; Deoxyribonuclease HpaII/genetics ; Deoxyribonucleases, Type II Site-Specific/genetics ; Gram-Negative Anaerobic Bacteria/isolation &amp; purification ; Humans ; Methanobrevibacter/*classification/genetics/isolation &amp; purification ; Oxidoreductases/analysis/*genetics ; Periapical Periodontitis/microbiology ; Periodontal Pocket/microbiology ; Phylogeny ; Polymorphism, Restriction Fragment Length/*genetics ; Porphyromonas gingivalis/isolation &amp; purification ; Prevotella intermedia/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Reverse Transcriptase Polymerase Chain Reaction ; Treponema/isolation &amp; purification ; },
abstract = {INTRODUCTION: Increasing evidence suggests a role for methanogenic archaea (methanogens) in human health and disease via syntrophic interactions with bacteria. Here we assessed the prevalence and distribution of methanogens and possible associations with bacteria in oral biofilms.<br><br>METHODS: Forty-four periodontal and 32 endodontic samples from necrotic teeth with radiographic evidence of apical periodontitis were analysed. Terminal restriction fragment length polymorphism analysis based on the mcrA gene, specific to methanogens, was applied. The prevalence and amounts of methanogens in endodontic samples were compared with those of Porphyromonas gingivalis, Prevotella intermedia, Tannerella forsythia, Treponema spp. and Synergistes spp. based on real-time quantitative polymerase chain reactions.<br><br>RESULTS: Besides dominance of the mcrA gene corresponding to Methanobrevibacter oralis, one mcrA gene type, for which no cultivated member has been reported previously, was identified in five periodontal samples and one endodontic sample. Rates of non-synonymous vs. synonymous nucleotide substitutions suggest that this mcrA gene type codes for a functionally active methyl-coenzyme M reductase. Methanobrevibacter smithii, the prominent methanogen in the human gut system, was not detected. Mean proportions of methanogens were comparable to Synergistes spp. ranging from 0.5 to 1.0% of the total microbial community. Treponema spp. dominated with a mean proportion of 10%, while the mean proportions of the other endodontic pathogens were below 0.1%. A positive association between methanogens and Synergistes spp. was found.<br><br>CONCLUSION: Our data provide evidence of a novel, as yet uncultured methanogenic phylotype in association with oral infections, and indicate possible interactions between methanogens and Synergistes spp., the nature of which deserves further investigation.},
}
@article {pmid19702875,
year = {2009},
author = {Sundset, MA and Edwards, JE and Cheng, YF and Senosiain, RS and Fraile, MN and Northwood, KS and Praesteng, KE and Glad, T and Mathiesen, SD and Wright, AD},
title = {Rumen microbial diversity in Svalbard reindeer, with particular emphasis on methanogenic archaea.},
journal = {FEMS microbiology ecology},
volume = {70},
number = {3},
pages = {553-562},
doi = {10.1111/j.1574-6941.2009.00750.x},
pmid = {19702875},
issn = {1574-6941},
support = {BBS/E/W/00003135A/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/W/00003135B/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Alveolata/classification/genetics/isolation &amp; purification ; Animals ; Archaea/classification/genetics/*isolation &amp; purification ; Bacteria/classification/genetics/isolation &amp; purification ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; DNA, Protozoan/genetics ; Female ; Gene Library ; RNA, Ribosomal, 16S/genetics ; Reindeer/*microbiology ; Rumen/*microbiology ; Sequence Analysis, DNA ; },
abstract = {Ruminal methanogens, bacteria and ciliate protozoa of Svalbard reindeer grazing natural pastures in October (late fall) and April (late winter) were investigated using molecular-based approaches. The appetite of the Svalbard reindeer peaks in August (summer) and is at its lowest in March (winter). Microbial numbers, quantified by real-time PCR, did not change significantly between October and April, when food intakes are at similar levels, although the numbers of methanogens tended to be higher in October (P=0.074), and ciliate numbers tended to be higher in April (P=0.055). Similarly, no change was detected in the bacterial and protozoal population composition by rRNA gene-based denaturing gradient gel electrophoresis analysis. Dominant methanogens were identified using a 16S rRNA gene library (97 clones) prepared from pooled PCR products from reindeer on October pasture (n=5). Eleven of the 22 distinct operational taxonomic units (OTUs) generated exhibited a high degree of sequence similarity to methanogens affiliated with Methanobacteriales (eight OTUs), Methanomicrobiales (one OTU) and Methanosarcinales (two OTUs). The remaining 11 OTUs (53% of the clones) were associated with a cluster of uncultivated ruminal archaea. This study has provided important insights into the rumen microbiome of a high-arctic herbivorous animal living under harsh nutritional conditions, and evidence suggesting that host type affects the population size of ruminal methanogens.},
}
@article {pmid19671178,
year = {2009},
author = {Goldman, AD and Leigh, JA and Samudrala, R},
title = {Comprehensive computational analysis of Hmd enzymes and paralogs in methanogenic Archaea.},
journal = {BMC evolutionary biology},
volume = {9},
number = {},
pages = {199},
pmid = {19671178},
issn = {1471-2148},
mesh = {Amino Acid Sequence ; Archaea/enzymology/*genetics ; Archaeal Proteins/*genetics ; Computational Biology/methods ; Evolution, Molecular ; Genes, Archaeal ; Methane/metabolism ; Models, Molecular ; Molecular Sequence Data ; Oxidoreductases Acting on CH-NH Group Donors/*genetics ; *Phylogeny ; Protein Structure, Tertiary ; Sequence Alignment ; Sequence Analysis, Protein ; Structure-Activity Relationship ; },
abstract = {BACKGROUND: Methanogenesis is the sole means of energy production in methanogenic Archaea. H2-forming methylenetetrahydromethanopterin dehydrogenase (Hmd) catalyzes a step in the hydrogenotrophic methanogenesis pathway in class I methanogens. At least one hmd paralog has been identified in nine of the eleven complete genome sequences of class I hydrogenotrophic methanogens. The products of these paralog genes have thus far eluded any detailed functional characterization.<br><br>RESULTS: Here we present a thorough computational analysis of Hmd enzymes and paralogs that includes state of the art phylogenetic inference, structure prediction, and functional site prediction techniques. We determine that the Hmd enzymes are phylogenetically distinct from Hmd paralogs but share a common overall structure. We predict that the active site of the Hmd enzyme is conserved as a functional site in Hmd paralogs and use this observation to propose possible molecular functions of the paralog that are consistent with previous experimental evidence. We also identify an uncharacterized site in the N-terminal domains of both proteins that is predicted by our methods to directly impart function.<br><br>CONCLUSION: This study contributes to our understanding of the evolutionary history, structural conservation, and functional roles, of the Hmd enzymes and paralogs. The results of our phylogenetic and structural analysis constitute datasets that will aid in the future study of the Hmd protein family. Our functional site predictions generate several testable hypotheses that will guide further experimental characterization of the Hmd paralog. This work also represents a novel approach to protein function prediction in which multiple computational methods are integrated to achieve a detailed characterization of proteins that are not well understood.},
}
@article {pmid19671140,
year = {2009},
author = {Yokobori, S and Itoh, T and Yoshinari, S and Nomura, N and Sako, Y and Yamagishi, A and Oshima, T and Kita, K and Watanabe, Y},
title = {Gain and loss of an intron in a protein-coding gene in Archaea: the case of an archaeal RNA pseudouridine synthase gene.},
journal = {BMC evolutionary biology},
volume = {9},
number = {},
pages = {198},
pmid = {19671140},
issn = {1471-2148},
mesh = {Archaea/enzymology/*genetics ; Archaeal Proteins/genetics ; Base Sequence ; Evolution, Molecular ; Genes, Archaeal ; Intramolecular Transferases/*genetics ; *Introns ; Molecular Sequence Data ; Phylogeny ; RNA Precursors/genetics ; RNA, Archaeal/*genetics ; Sequence Alignment ; Sequence Analysis, RNA ; },
abstract = {BACKGROUND: We previously found the first examples of splicing of archaeal pre-mRNAs for homologs of the eukaryotic CBF5 protein (also known as dyskerin in humans) in Aeropyrum pernix, Sulfolobus solfataricus, S. tokodaii, and S. acidocaldarirus, and also showed that crenarchaeal species in orders Desulfurococcales and Sulfolobales, except for Hyperthermus butylicus, Pyrodictium occultum, Pyrolobus fumarii, and Ignicoccus islandicus, contain the (putative) cbf5 intron. However, the exact timing of the intron insertion was not determined and verification of the putative secondary loss of the intron in some lineages was not performed.<br><br>RESULTS: In the present study, we determined approximately two-thirds of the entire coding region of crenarchaeal Cbf5 sequences from 43 species. A phylogenetic analysis of our data and information from the available genome sequences suggested that the (putative) cbf5 intron existed in the common ancestor of the orders Desulfurococcales and Sulfolobales and that probably at least two independent lineages in the order Desulfurococcales lost the (putative) intron.<br><br>CONCLUSION: This finding is the first observation of a lineage-specific loss of a pre-mRNA intron in Archaea. As the insertion or deletion of introns in protein-coding genes in Archaea has not yet been seriously considered, our finding suggests the possible difficulty of accurately and completely predicting protein-coding genes in Archaea.},
}
@article {pmid19666462,
year = {2009},
author = {Yokooji, Y and Tomita, H and Atomi, H and Imanaka, T},
title = {Pantoate kinase and phosphopantothenate synthetase, two novel enzymes necessary for CoA biosynthesis in the Archaea.},
journal = {The Journal of biological chemistry},
volume = {284},
number = {41},
pages = {28137-28145},
pmid = {19666462},
issn = {1083-351X},
mesh = {Archaeal Proteins/genetics/*metabolism ; Coenzyme A/*biosynthesis ; Gene Targeting ; Genes, Archaeal ; Hydroxybutyrates/*metabolism ; Molecular Structure ; Peptide Synthases/genetics/*metabolism ; Phosphotransferases/genetics/*metabolism ; Recombinant Proteins/metabolism ; Thermococcus/*enzymology/genetics/growth &amp; development ; },
abstract = {Bacteria/eukaryotes share a common pathway for coenzyme A (CoA) biosynthesis. Although archaeal genomes harbor homologs for most of these enzymes, homologs of bacterial/eukaryotic pantothenate synthetase (PS) and pantothenate kinase (PanK) are missing. PS catalyzes the ATP-dependent condensation of pantoate and beta-alanine to produce pantothenate, whereas PanK catalyzes the ATP-dependent phosphorylation of pantothenate to produce 4'-phosphopantothenate. When we examined the cell-free extracts of the hyperthermophilic archaeon Thermococcus kodakaraensis, PanK activity could not be detected. A search for putative kinase-encoding genes widely distributed in Archaea, but not present in bacteria/eukaryotes, led to four candidate genes. Among these genes, TK2141 encoded a protein with relatively low PanK activity. However, higher levels of activity were observed when pantothenate was replaced with pantoate. V(max) values were 7-fold higher toward pantoate, indicating that TK2141 encoded a novel enzyme, pantoate kinase (PoK). A search for genes with a distribution similar to TK2141 led to the identification of TK1686. The protein product catalyzed the ATP-dependent conversion of phosphopantoate and beta-alanine to produce 4'-phosphopantothenate and did not exhibit PS activity, indicating that TK1686 also encoded a novel enzyme, phosphopantothenate synthetase (PPS). Although the classic PS/PanK system performs condensation with beta-alanine prior to phosphorylation, the PoK/PPS system performs condensation after phosphorylation of pantoate. Gene disruption of TK2141 and TK1686 led to CoA auxotrophy, indicating that both genes are necessary for CoA biosynthesis in T. kodakaraensis. Homologs of both genes are widely distributed among the Archaea, suggesting that the PoK/PPS system represents the pathway for 4'-phosphopantothenate biosynthesis in the Archaea.},
}
@article {pmid19663931,
year = {2009},
author = {Kenward, PA and Goldstein, RH and González, LA and Roberts, JA},
title = {Precipitation of low-temperature dolomite from an anaerobic microbial consortium: the role of methanogenic Archaea.},
journal = {Geobiology},
volume = {7},
number = {5},
pages = {556-565},
doi = {10.1111/j.1472-4669.2009.00210.x},
pmid = {19663931},
issn = {1472-4669},
mesh = {Anaerobiosis ; Archaea/genetics/*metabolism/ultrastructure ; Bacteria/genetics/metabolism ; Calcium Carbonate/*metabolism ; Cold Temperature ; DNA Fingerprinting ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Electrophoresis, Polyacrylamide Gel ; Iron/metabolism ; Magnesium/*metabolism ; Methane/*metabolism ; Microscopy, Electron, Scanning ; Microscopy, Electron, Transmission ; Minnesota ; Nucleic Acid Denaturation ; Oxidation-Reduction ; RNA, Ribosomal, 16S/genetics ; Soil Microbiology ; X-Ray Diffraction ; },
abstract = {Here we report precipitation of dolomite at low temperature (30 degrees C) mediated by a mixed anaerobic microbial consortium composed of dissimilatory iron-reducing bacteria (DIRB), fermenters, and methanogens. Initial solution geochemistry is controlled by DIRB, but after 90 days shifts to a system dominated by methanogens. In live experiments conditions are initially saturated with respect to dolomite (Omega(dol) = 19.40) and increase by two orders of magnitude (Omega(dol) = 2 330.77) only after the onset of methanogenesis, as judged by the increasing [CH(4)] and the detection of methanogenic micro-organisms. We identify ordered dolomite in live microcosms after 90 days via powder X-ray diffraction, while sterile controls precipitate only calcite. Scanning electron microscopy and transmitted electron microscopy demonstrate that the precipitated dolomite is closely associated with cell walls and putative extra-cellular polysaccharides. Headspace gas measurements and denaturing gradient gel electrophoresis confirm the presence of both autotrophic and acetoclastic methanogens and exclude the presence of DIRB and sulfate-reducing bacteria after dolomite begins forming. Furthermore, the absence of dolomite in the controls and prior to methanogenesis confirm that methanogenic Archaea are necessary for the low-temperature precipitation of dolomite under the experimental conditions tested.},
}
@article {pmid19656214,
year = {2009},
author = {Orange, F and Westall, F and Disnar, JR and Prieur, D and Bienvenu, N and Le Romancer, M and Défarge, Ch},
title = {Experimental silicification of the extremophilic Archaea Pyrococcus abyssi and Methanocaldococcus jannaschii: applications in the search for evidence of life in early Earth and extraterrestrial rocks.},
journal = {Geobiology},
volume = {7},
number = {4},
pages = {403-418},
doi = {10.1111/j.1472-4669.2009.00212.x},
pmid = {19656214},
issn = {1472-4669},
mesh = {*Fossils ; Methanococcales/*metabolism ; Pyrococcus abyssi/*metabolism ; Silicon Dioxide/*metabolism ; *Soil Microbiology ; },
abstract = {Hydrothermal activity was common on the early Earth and associated micro-organisms would most likely have included thermophilic to hyperthermophilic species. 3.5-3.3 billion-year-old, hydrothermally influenced rocks contain silicified microbial mats and colonies that must have been bathed in warm to hot hydrothermal emanations. Could they represent thermophilic or hyperthermophilic micro-organisms and if so, how were they preserved? We present the results of an experiment to silicify anaerobic, hyperthermophilic micro-organisms from the Archaea Domain Pyrococcus abyssi and Methanocaldococcus jannaschii, that could have lived on the early Earth. The micro-organisms were placed in a silica-saturated medium for periods up to 1 year. Pyrococcus abyssi cells were fossilized but the M. jannaschii cells lysed naturally after the exponential growth phase, apart from a few cells and cell remains, and were not silicified although their extracellular polymeric substances were. In this first simulated fossilization of archaeal strains, our results suggest that differences between species have a strong influence on the potential for different micro-organisms to be preserved by fossilization and that those found in the fossil record represent probably only a part of the original diversity. Our results have important consequences for biosignatures in hydrothermal or hydrothermally influenced deposits on Earth, as well as on early Mars, as environmental conditions were similar on the young terrestrial planets and traces of early Martian life may have been similarly preserved as silicified microfossils.},
}
@article {pmid19656195,
year = {2009},
author = {Offre, P and Prosser, JI and Nicol, GW},
title = {Growth of ammonia-oxidizing archaea in soil microcosms is inhibited by acetylene.},
journal = {FEMS microbiology ecology},
volume = {70},
number = {1},
pages = {99-108},
doi = {10.1111/j.1574-6941.2009.00725.x},
pmid = {19656195},
issn = {1574-6941},
mesh = {Acetylene/*metabolism ; Ammonia/*metabolism ; Archaea/genetics/*growth &amp; development/metabolism ; Bacteria/genetics ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; Genes, Archaeal ; Genes, Bacterial ; Oxidation-Reduction ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Soil/analysis ; *Soil Microbiology ; },
abstract = {Autotrophic ammonia-oxidizing bacteria were considered to be responsible for the majority of ammonia oxidation in soil until the recent discovery of the autotrophic ammonia-oxidizing archaea. To assess the relative contributions of bacterial and archaeal ammonia oxidizers to soil ammonia oxidation, their growth was analysed during active nitrification in soil microcosms incubated for 30 days at 30 degrees C, and the effect of an inhibitor of ammonia oxidation (acetylene) on their growth and soil nitrification kinetics was determined. Denaturing gradient gel electrophoresis (DGGE) analysis of bacterial ammonia oxidizer 16S rRNA genes did not detect any change in their community composition during incubation, and quantitative PCR (qPCR) analysis of bacterial amoA genes indicated a small decrease in abundance in control and acetylene-containing microcosms. DGGE fingerprints of archaeal amoA and 16S rRNA genes demonstrated changes in the relative abundance of specific crenarchaeal phylotypes during active nitrification. Growth was also indicated by increases in crenarchaeal amoA gene copy number, determined by qPCR. In microcosms containing acetylene, nitrification and growth of the crenarchaeal phylotypes were suppressed, suggesting that these crenarchaea are ammonia oxidizers. Growth of only archaeal but not bacterial ammonia oxidizers occurred in microcosms with active nitrification, indicating that ammonia oxidation was mostly due to archaea in the conditions of the present study.},
}
@article {pmid19645821,
year = {2009},
author = {Ghosh, W and Dam, B},
title = {Biochemistry and molecular biology of lithotrophic sulfur oxidation by taxonomically and ecologically diverse bacteria and archaea.},
journal = {FEMS microbiology reviews},
volume = {33},
number = {6},
pages = {999-1043},
doi = {10.1111/j.1574-6976.2009.00187.x},
pmid = {19645821},
issn = {1574-6976},
mesh = {Animals ; Archaea/chemistry/classification/genetics/*metabolism ; *Autotrophic Processes ; Bacteria/chemistry/classification/genetics/*metabolism ; *Ecosystem ; Humans ; Oxidation-Reduction ; Sulfur/chemistry/*metabolism ; },
abstract = {Lithotrophic sulfur oxidation is an ancient metabolic process. Ecologically and taxonomically diverged prokaryotes have differential abilities to utilize different reduced sulfur compounds as lithotrophic substrates. Different phototrophic or chemotrophic species use different enzymes, pathways and mechanisms of electron transport and energy conservation for the oxidation of any given substrate. While the mechanisms of sulfur oxidation in obligately chemolithotrophic bacteria, predominantly belonging to Beta- (e.g. Thiobacillus) and Gammaproteobacteria (e.g. Thiomicrospira), are not well established, the Sox system is the central pathway in the facultative bacteria from Alphaproteobacteria (e.g. Paracoccus). Interestingly, photolithotrophs such as Rhodovulum belonging to Alphaproteobacteria also use the Sox system, whereas those from Chromatiaceae and Chlorobi use a truncated Sox complex alongside reverse-acting sulfate-reducing systems. Certain chemotrophic magnetotactic Alphaproteobacteria allegedly utilize such a combined mechanism. Sulfur-chemolithotrophic metabolism in Archaea, largely restricted to Sulfolobales, is distinct from those in Bacteria. Phylogenetic and biomolecular fossil data suggest that the ubiquity of sox genes could be due to horizontal transfer, and coupled sulfate reduction/sulfide oxidation pathways, originating in planktonic ancestors of Chromatiaceae or Chlorobi, could be ancestral to all sulfur-lithotrophic processes. However, the possibility that chemolithotrophy, originating in deep sea, is the actual ancestral form of sulfur oxidation cannot be ruled out.},
}
@article {pmid19640276,
year = {2009},
author = {Daniels, JP and Kelly, S and Wickstead, B and Gull, K},
title = {Identification of a crenarchaeal orthologue of Elf1: implications for chromatin and transcription in Archaea.},
journal = {Biology direct},
volume = {4},
number = {},
pages = {24},
pmid = {19640276},
issn = {1745-6150},
support = {/WT_/Wellcome Trust/United Kingdom ; /BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Archaea/*genetics ; Archaeal Proteins/*genetics/*metabolism ; Chromatin/*genetics ; Crenarchaeota/*genetics ; Evolution, Molecular ; *Gene Expression Regulation, Archaeal/genetics ; Transcription Factors/*genetics ; },
abstract = {The transcription machineries of Archaea and eukaryotes are similar in many aspects, but little is understood about archaeal chromatin and its role in transcription. Here, we describe the identification in hyperthermophilic Crenarchaeota and a Korarchaeon of an orthologue of the eukaryotic transcription elongation factor Elf1, which has been shown to function in chromatin structure maintenance of actively transcribed templates. Our discovery has implications for the relationship of chromatin and transcription in Archaea and the evolution of these processes in eukaryotes.},
}
@article {pmid19609258,
year = {2009},
author = {Stams, AJ and Plugge, CM},
title = {Electron transfer in syntrophic communities of anaerobic bacteria and archaea.},
journal = {Nature reviews. Microbiology},
volume = {7},
number = {8},
pages = {568-577},
pmid = {19609258},
issn = {1740-1534},
mesh = {Anaerobiosis ; Archaea/growth &amp; development/*metabolism ; Bacteria, Anaerobic/growth &amp; development/*metabolism ; Electron Transport ; Formates/metabolism ; Hydrogen/*metabolism ; Methane/*metabolism ; *Protons ; },
abstract = {Interspecies electron transfer is a key process in methanogenic and sulphate-reducing environments. Bacteria and archaea that live in syntrophic communities take advantage of the metabolic abilities of their syntrophic partner to overcome energy barriers and break down compounds that they cannot digest by themselves. Here, we review the transfer of hydrogen and formate between bacteria and archaea that helps to sustain growth in syntrophic methanogenic communities. We also describe the process of reverse electron transfer, which is a key requirement in obligately syntrophic interactions. Anaerobic methane oxidation coupled to sulphate reduction is also carried out by syntrophic communities of bacteria and archaea but, as we discuss, the exact mechanism of this syntrophic interaction is not yet understood.},
}
@article {pmid19601959,
year = {2009},
author = {Kalanetra, KM and Bano, N and Hollibaugh, JT},
title = {Ammonia-oxidizing Archaea in the Arctic Ocean and Antarctic coastal waters.},
journal = {Environmental microbiology},
volume = {11},
number = {9},
pages = {2434-2445},
doi = {10.1111/j.1462-2920.2009.01974.x},
pmid = {19601959},
issn = {1462-2920},
mesh = {Ammonia/*metabolism ; Antarctic Regions ; Archaea/genetics/*metabolism ; Arctic Regions ; Base Sequence ; Genes, Archaeal ; Molecular Sequence Data ; Oceans and Seas ; Oxidation-Reduction ; Oxidoreductases/genetics/metabolism ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/analysis ; Seawater/chemistry/*microbiology ; },
abstract = {We compared abundance, distributions and phylogenetic composition of Crenarchaeota and ammonia-oxidizing Archaea (AOA) in samples collected from coastal waters west of the Antarctic Peninsula during the summers of 2005 and 2006, with samples from the central Arctic Ocean collected during the summer of 1997. Ammonia-oxidizing Archaea and Crenarchaeota abundances were estimated from quantitative PCR measurements of amoA and 16S rRNA gene abundances. Crenarchaeota and AOA were approximately fivefold more abundant at comparable depths in the Antarctic versus the Arctic Ocean. Crenarchaeota and AOA were essentially absent from the Antarctic Summer Surface Water (SSW) water mass (0-45 m depth). The ratio of Crenarchaeota 16S rRNA to archaeal amoA gene abundance in the Winter Water (WW) water mass (45-105 m depth) of the Southern Ocean was much lower (0.15) than expected and in sharp contrast to the ratio (2.0) in the Circumpolar Deep Water (CDW) water mass (105-3500 m depth) immediately below it. We did not observe comparable segregation of this ratio by depth or water mass in Arctic Ocean samples. A ubiquitous, abundant and polar-specific crenarchaeote was the dominant ribotype in the WW and important in the upper halocline of the Arctic Ocean. Our data suggest that this organism does not contain an ammonia monooxygenase gene. In contrast to other studies where Crenarchaeota populations apparently lacking amoA genes are found in bathypelagic waters, this organism appears to dominate in well-defined, ammonium-rich, near-surface water masses in polar oceans.},
}
@article {pmid19594830,
year = {2009},
author = {Posner, MG and Upadhyay, A and Bagby, S and Hough, DW and Danson, MJ},
title = {A unique lipoylation system in the Archaea. Lipoylation in Thermoplasma acidophilum requires two proteins.},
journal = {The FEBS journal},
volume = {276},
number = {15},
pages = {4012-4022},
doi = {10.1111/j.1742-4658.2009.07110.x},
pmid = {19594830},
issn = {1742-4658},
mesh = {Archaeal Proteins/genetics/*metabolism ; Base Sequence ; Catalytic Domain ; Cloning, Molecular ; Dihydrolipoyllysine-Residue Acetyltransferase/*genetics/metabolism ; Escherichia coli/genetics ; Lipoylation/*physiology ; Molecular Sequence Data ; Protein Processing, Post-Translational ; TATA Box/genetics ; Thermoplasma/enzymology/*genetics/metabolism ; },
abstract = {Members of the 2-oxoacid dehydrogenase multienzyme complex family play a key role in the pathways of central metabolism. Post-translational lipoylation of the dihydrolipoyl acyltransferase component of these complexes is essential for their activity, the lipoyllysine moiety performing the transfer of substrates and intermediates between the different active sites within these multienzyme systems. We have previously shown that the thermophilic archaeon, Thermoplasma acidophilum, has a four-gene cluster encoding the components of such a complex, which, when recombinantly expressed in Escherichia coli, can be assembled into an active multienzyme in vitro. Crucially, the E. coli host carries out the required lipoylation of the archaeal dihydrolipoyl acyltransferase component. Because active 2-oxoacid dehydrogenase multienzyme complexes have never been detected in any archaeon, the question arises as to whether Archaea possess a functional lipoylation system. In this study, we report the cloning and heterologous expression of two genes from Tp. acidophilum whose protein products together show significant sequence identity with the single lipoate protein ligase enzyme of bacteria. We demonstrate that both recombinantly expressed Tp. acidophilum proteins are required for lipoylation of the acyltransferase, and that the two proteins associate together to carry out this post-translational modification. From the published DNA sequences, we suggest the presence of functional transcriptional and translational regulatory elements, and furthermore we present preliminary evidence that lipoylation occurs in vivo in Tp. acidophilum. This is the first report of the lipoylation machinery in the Archaea, which is unique in that the catalytic activity is dependent on two separate gene products.},
}
@article {pmid19593595,
year = {2009},
author = {Martínez-Espinosa, RM and Lledó, B and Marhuenda-Egea, FC and Díaz, S and Bonete, MJ},
title = {NO3-/NO2- assimilation in halophilic archaea: physiological analysis, nasA and nasD expressions.},
journal = {Extremophiles : life under extreme conditions},
volume = {13},
number = {5},
pages = {785-792},
pmid = {19593595},
issn = {1433-4909},
mesh = {Archaeal Proteins/*genetics/*metabolism ; Base Sequence ; DNA Primers/genetics ; DNA, Archaeal/genetics ; Gene Expression ; *Genes, Archaeal ; Haloferax mediterranei/*genetics/growth &amp; development/*metabolism ; Nitrate Reductase/*genetics/*metabolism ; Nitrates/metabolism ; Nitrite Reductases/*genetics/*metabolism ; Nitrites/metabolism ; Salinity ; },
abstract = {The haloarchaeon Haloferax mediterranei is able to assimilate nitrate or nitrite using the assimilatory nitrate pathway. An assimilatory nitrate reductase (Nas) and an assimilatory nitrite reductase (NiR) catalyze the first and second reactions, respectively. The genes involved in this process are transcribed as two messengers, one polycistronic (nasABC; nasA encodes Nas) and one monocistronic (nasD; codes for NiR). Here we report the Hfx mediterranei growth as well as the Nas and NiR activities in presence of high nitrate, nitrite and salt concentrations, using different approaches such as physiological experiments and enzymatic activities assays. The nasA and nasD expression profiles are also analysed by real-time quantitative PCR. The results presented reveal that the assimilatory nitrate/nitrite pathway in Hfx mediterranei takes place even if the salt concentration is higher than those usually present in the environments where this microorganism inhabits. This haloarchaeon grows in presence of 2 M nitrate or 50 mM nitrite, which are the highest nitrate and nitrite concentrations described from a prokaryotic microorganism. Therefore, it could be attractive for bioremediation applications in sewage plants where high salt, nitrate and nitrite concentrations are detected in wastewaters and brines.},
}
@article {pmid19590870,
year = {2009},
author = {Ulrih, NP and Gmajner, D and Raspor, P},
title = {Structural and physicochemical properties of polar lipids from thermophilic archaea.},
journal = {Applied microbiology and biotechnology},
volume = {84},
number = {2},
pages = {249-260},
doi = {10.1007/s00253-009-2102-9},
pmid = {19590870},
issn = {1432-0614},
mesh = {Archaea/classification/*metabolism ; Biotechnology ; *Lipid Metabolism ; Lipids/biosynthesis/*chemistry ; },
abstract = {The essential general features required for lipid membranes of extremophilic archaea to fulfill biological functions are that they are in the liquid crystalline phase and have extremely low permeability of solutes that is much less temperature sensitive due to a lack of lipid-phase transition and highly branched isoprenoid chains. Many accumulated data indicate that the organism's response to extremely low pH is the opposite of that to high temperature. The high temperature adaptation does not require the tetraether lipids, while the adaptation of thermophiles to acidic environment requires the tetraether polar lipids. The presence of cyclopentane rings and the role of polar heads are not so straightforward regarding the correlations between fluidity and permeability of the lipid membrane. Due to the unique lipid structures and properties of archaeal lipids, they are a valuable resource in the development of novel biotechnological processes. This microreview focuses primarily on structural and physicochemical properties of polar lipids of (hyper)thermophilic archaea.},
}
@article {pmid19587059,
year = {2009},
author = {Jalasvuori, M and Jaatinen, ST and Laurinavicius, S and Ahola-Iivarinen, E and Kalkkinen, N and Bamford, DH and Bamford, JK},
title = {The closest relatives of icosahedral viruses of thermophilic bacteria are among viruses and plasmids of the halophilic archaea.},
journal = {Journal of virology},
volume = {83},
number = {18},
pages = {9388-9397},
pmid = {19587059},
issn = {1098-5514},
mesh = {Adenosine Triphosphatases/genetics ; Bacterial Proteins/*genetics ; Base Sequence ; Capsid Proteins/genetics ; Genes, Bacterial ; Genome, Bacterial/*genetics ; Lipids ; Membrane Proteins/genetics ; Phylogeny ; Thermus thermophilus/*genetics ; },
abstract = {We have sequenced the genome and identified the structural proteins and lipids of the novel membrane-containing, icosahedral virus P23-77 of Thermus thermophilus. P23-77 has an approximately 17-kb circular double-stranded DNA genome, which was annotated to contain 37 putative genes. Virions were subjected to dissociation analysis, and five protein species were shown to associate with the internal viral membrane, while three were constituents of the protein capsid. Analysis of the bacteriophage genome revealed it to be evolutionarily related to another Thermus phage (IN93), archaeal Halobacterium plasmid (pHH205), a genetic element integrated into Haloarcula genome (designated here as IHP for integrated Haloarcula provirus), and the Haloarcula virus SH1. These genetic elements share two major capsid proteins and a putative packaging ATPase. The ATPase is similar with the ATPases found in the PRD1-type viruses, thus providing an evolutionary link to these viruses and furthering our knowledge on the origin of viruses.},
}
@article {pmid19583788,
year = {2009},
author = {Ionescu, D and Penno, S and Haimovich, M and Rihtman, B and Goodwin, A and Schwartz, D and Hazanov, L and Chernihovsky, M and Post, AF and Oren, A},
title = {Archaea in the Gulf of Aqaba.},
journal = {FEMS microbiology ecology},
volume = {69},
number = {3},
pages = {425-438},
doi = {10.1111/j.1574-6941.2009.00721.x},
pmid = {19583788},
issn = {1574-6941},
mesh = {Crenarchaeota/classification/*genetics ; DNA, Archaeal/genetics ; Euryarchaeota/classification/*genetics ; Genes, rRNA ; In Situ Hybridization, Fluorescence ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/microbiology ; Sequence Analysis, DNA ; *Water Microbiology ; },
abstract = {Using a polyphasic approach, we examined the presence of Archaea in the Gulf of Aqaba, a warm marine ecosystem, isolated from major ocean currents and subject to pronounced seasonal changes in hydrography. Catalyzed reported deposition FISH analyses showed that Archaea make up to >20% of the prokaryotic community in the Gulf. A spatial separation between the two major phyla of Archaea was observed during summer stratification. Euryarchaeota were found exclusively in the upper 200 m, whereas Crenarchaeota were present in greater numbers in layers below the summer thermocline. 16S rRNA gene-based denaturing gradient gel electrophoresis confirmed this depth partitioning and revealed further diversity of Crenarchaeota and Euryarchaeota populations along depth profiles. Phylogenetic analysis showed pelagic Crenarchaeota and Euryarchaeota to differ from coral-associated Archaea from the Gulf, forming distinct clusters within the Marine Archaea Groups I and II. Endsequencing of fosmid libraries of environmental DNA provided a tentative identification of some members of the archaeal community and their role in the microbial community of the Gulf. Incorporation studies of radiolabeled leucine and bicarbonate in the presence of different inhibitors suggest that the archaeal community participates in autotrophic CO(2) uptake and contributes little to the heterotrophic activity.},
}
@article {pmid19583437,
year = {2009},
author = {Qu, G and Wang, W and Chen, LL and Qian, SS and Zhang, HY},
title = {tRNA-dependent cysteine biosynthetic pathway represents a strategy to increase cysteine contents by preventing it from thermal degradation: thermal adaptation of methanogenic archaea ancestor.},
journal = {Journal of biomolecular structure &amp; dynamics},
volume = {27},
number = {2},
pages = {111-114},
doi = {10.1080/07391102.2009.10507301},
pmid = {19583437},
issn = {1538-0254},
mesh = {*Adaptation, Physiological ; *Archaea/genetics/metabolism ; Asparagine/metabolism ; Cysteine/*metabolism ; Glutamine/metabolism ; *Hot Temperature ; Methane/metabolism ; RNA, Transfer, Amino Acyl/*metabolism ; },
abstract = {Although cysteine (Cys) is beneficial to stabilize protein structures, it is not prevalent in thermophiles. For instance, the Cys contents in most thermophilic archaea are only around 0.7%. However, methanogenic archaea, no matter thermophilic or not, contain relatively abundant Cys, which remains elusive for a long time. Recently, Klipcan et al. correlated this intriguing property of methanogenic archaea with their unique tRNA-dependent Cys biosynthetic pathway. But, the deep reasons underlying the correlation are ambiguous. Considering the facts that free Cys is thermally labile and the tRNA-dependent Cys biosynthesis avoids the use of free Cys, we speculate that the unique Cys biosynthetic pathway represents a strategy to increase Cys contents by preventing it from thermal degradation, which may be relevant to the thermal adaptation of methanogenic archaea ancestor.},
}
@article {pmid19573695,
year = {2009},
author = {Slonczewski, JL and Fujisawa, M and Dopson, M and Krulwich, TA},
title = {Cytoplasmic pH measurement and homeostasis in bacteria and archaea.},
journal = {Advances in microbial physiology},
volume = {55},
number = {},
pages = {1-79, 317},
doi = {10.1016/S0065-2911(09)05501-5},
pmid = {19573695},
issn = {2162-5468},
support = {R01 GM028454/GM/NIGMS NIH HHS/United States ; GM28454/GM/NIGMS NIH HHS/United States ; },
mesh = {Archaea/*physiology ; *Bacterial Physiological Phenomena ; Cytoplasm/*chemistry ; *Homeostasis ; Hydrogen-Ion Concentration ; },
abstract = {Of all the molecular determinants for growth, the hydronium and hydroxide ions are found naturally in the widest concentration range, from acid mine drainage below pH 0 to soda lakes above pH 13. Most bacteria and archaea have mechanisms that maintain their internal, cytoplasmic pH within a narrower range than the pH outside the cell, termed "pH homeostasis." Some mechanisms of pH homeostasis are specific to particular species or groups of microorganisms while some common principles apply across the pH spectrum. The measurement of internal pH of microbes presents challenges, which are addressed by a range of techniques under varying growth conditions. This review compares and contrasts cytoplasmic pH homeostasis in acidophilic, neutralophilic, and alkaliphilic bacteria and archaea under conditions of growth, non-growth survival, and biofilms. We present diverse mechanisms of pH homeostasis including cell buffering, adaptations of membrane structure, active ion transport, and metabolic consumption of acids and bases.},
}
@article {pmid19572899,
year = {2009},
author = {Li, CL and Liu, DL and Jiang, YT and Zhou, YB and Zhang, MZ and Jiang, W and Liu, B and Liang, JP},
title = {Prevalence and molecular diversity of Archaea in subgingival pockets of periodontitis patients.},
journal = {Oral microbiology and immunology},
volume = {24},
number = {4},
pages = {343-346},
doi = {10.1111/j.1399-302X.2009.00514.x},
pmid = {19572899},
issn = {1399-302X},
mesh = {Adult ; Case-Control Studies ; Chronic Periodontitis/*microbiology ; DNA, Archaeal/analysis ; DNA, Ribosomal/analysis ; Dental Plaque/*microbiology ; Female ; Genetic Variation ; Humans ; Male ; Methanobrevibacter/*isolation &amp; purification ; Middle Aged ; Molecular Sequence Data ; Thermoplasma/*isolation &amp; purification ; },
abstract = {INTRODUCTION: The aim of this study was to investigate the prevalence and molecular diversity of Archaea in the subgingival crevices of patients with chronic periodontitis.<br><br>METHODS: Subgingival plaque was collected from 41 patients with chronic periodontitis and 15 healthy subjects. The prevalence of Archaea in those plaque samples was tested by polymerase chain reaction with two broad-range archaeal primer sets. Amplicons from eight Archaea-positive plaque samples were cloned and sequenced for molecular diversity analysis using one of these two primer sets and a novel third primer set.<br><br>RESULTS: Archaea were detected in the subgingival plaque of patients with chronic periodontitis at a prevalence of 70.7-73.2%, but were not detected in healthy subjects. Using one primer set, all sequences of the archaeal amplicons were identified as Methanobrevibacter oralis-like species. With another primer set, the amplicons were also found to be identical to the uncultured M. oralis-like species except one phylotype was found to belong to the class Thermoplasmata.<br><br>CONCLUSION: Archaea might be correlated with periodontal diseases. The diversity of Archaea associated with periodontitis was limited. Almost all sequenced amplicons fell into the genus Methanobrevibacter of the Euryarcheota phylum. M. oralis-like species was the predominant but non-exclusive archaeon in the subgingival dental plaque of patients with periodontitis.},
}
@article {pmid19570746,
year = {2009},
author = {Csurös, M and Miklós, I},
title = {Streamlining and large ancestral genomes in Archaea inferred with a phylogenetic birth-and-death model.},
journal = {Molecular biology and evolution},
volume = {26},
number = {9},
pages = {2087-2095},
pmid = {19570746},
issn = {1537-1719},
mesh = {Amino Acid Substitution/genetics ; Archaea/*genetics ; Base Sequence ; Computational Biology ; Evolution, Molecular ; Genes, Archaeal ; Genome, Archaeal/*genetics ; *Models, Genetic ; *Phylogeny ; },
abstract = {Homologous genes originate from a common ancestor through vertical inheritance, duplication, or horizontal gene transfer. Entire homolog families spawned by a single ancestral gene can be identified across multiple genomes based on protein sequence similarity. The sequences, however, do not always reveal conclusively the history of large families. To study the evolution of complete gene repertoires, we propose here a mathematical framework that does not rely on resolved gene family histories. We show that so-called phylogenetic profiles, formed by family sizes across multiple genomes, are sufficient to infer principal evolutionary trends. The main novelty in our approach is an efficient algorithm to compute the likelihood of a phylogenetic profile in a model of birth-and-death processes acting on a phylogeny. We examine known gene families in 28 archaeal genomes using a probabilistic model that involves lineage- and family-specific components of gene acquisition, duplication, and loss. The model enables us to consider all possible histories when inferring statistics about archaeal evolution. According to our reconstruction, most lineages are characterized by a net loss of gene families. Major increases in gene repertoire have occurred only a few times. Our reconstruction underlines the importance of persistent streamlining processes in shaping genome composition in Archaea. It also suggests that early archaeal genomes were as complex as typical modern ones, and even show signs, in the case of the methanogenic ancestor, of an extremely large gene repertoire.},
}
@article {pmid19558674,
year = {2009},
author = {Zivanovic, Y and Armengaud, J and Lagorce, A and Leplat, C and Guérin, P and Dutertre, M and Anthouard, V and Forterre, P and Wincker, P and Confalonieri, F},
title = {Genome analysis and genome-wide proteomics of Thermococcus gammatolerans, the most radioresistant organism known amongst the Archaea.},
journal = {Genome biology},
volume = {10},
number = {6},
pages = {R70},
pmid = {19558674},
issn = {1474-760X},
mesh = {Archaeal Proteins/metabolism ; Biological Transport/radiation effects ; Cell Membrane/enzymology/radiation effects ; Chromosomes/metabolism ; Codon, Initiator/genetics ; DNA Repair/radiation effects ; DNA Transposable Elements/genetics ; Gamma Rays ; Genome, Archaeal/*genetics ; Hydrogenase/metabolism ; Mass Spectrometry ; Microbial Viability/radiation effects ; Protein Biosynthesis/genetics/radiation effects ; Protein Processing, Post-Translational/radiation effects ; Proteome/genetics ; *Proteomics ; Radiation Tolerance/*genetics/radiation effects ; Reproducibility of Results ; Sequence Analysis, DNA ; Thermococcus/*genetics/growth &amp; development/metabolism/virology ; },
abstract = {BACKGROUND: Thermococcus gammatolerans was isolated from samples collected from hydrothermal chimneys. It is one of the most radioresistant organisms known amongst the Archaea. We report the determination and annotation of its complete genome sequence, its comparison with other Thermococcales genomes, and a proteomic analysis.<br><br>RESULTS: T. gammatolerans has a circular chromosome of 2.045 Mbp without any extra-chromosomal elements, coding for 2,157 proteins. A thorough comparative genomics analysis revealed important but unsuspected genome plasticity differences between sequenced Thermococcus and Pyrococcus species that could not be attributed to the presence of specific mobile elements. Two virus-related regions, tgv1 and tgv2, are the only mobile elements identified in this genome. A proteogenome analysis was performed by a shotgun liquid chromatography-tandem mass spectrometry approach, allowing the identification of 10,931 unique peptides corresponding to 951 proteins. This information concurrently validates the accuracy of the genome annotation. Semi-quantification of proteins by spectral count was done on exponential- and stationary-phase cells. Insights into general catabolism, hydrogenase complexes, detoxification systems, and the DNA repair toolbox of this archaeon are revealed through this genome and proteome analysis.<br><br>CONCLUSIONS: This work is the first archaeal proteome investigation done at the stage of primary genome annotation. This archaeon is shown to use a large variety of metabolic pathways even under a rich medium growth condition. This proteogenomic study also indicates that the high radiotolerance of T. gammatolerans is probably due to proteins that remain to be characterized rather than a larger arsenal of known DNA repair enzymes.},
}
@article {pmid19549825,
year = {2009},
author = {Bize, A and Karlsson, EA and Ekefjärd, K and Quax, TE and Pina, M and Prevost, MC and Forterre, P and Tenaillon, O and Bernander, R and Prangishvili, D},
title = {A unique virus release mechanism in the Archaea.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {106},
number = {27},
pages = {11306-11311},
pmid = {19549825},
issn = {1091-6490},
mesh = {Archaeal Viruses/pathogenicity/*physiology ; Cell Proliferation ; Chromosomes/metabolism ; Flow Cytometry ; Kinetics ; Sulfolobus/cytology/ultrastructure/*virology ; Time Factors ; },
abstract = {Little is known about the infection cycles of viruses infecting cells from Archaea, the third domain of life. Here, we demonstrate that the virions of the archaeal Sulfolobus islandicus rod-shaped virus 2 (SIRV2) are released from the host cell through a mechanism, involving the formation of specific cellular structures. Large pyramidal virus-induced protrusions transect the cell envelope at several positions, rupturing the S-layer; they eventually open out, thus creating large apertures through which virions escape the cell. We also demonstrate that massive degradation of the host chromosomes occurs because of virus infection, and that virion assembly occurs in the cytoplasm. Furthermore, intracellular viral DNA is visualized by flow cytometry. The results show that SIRV2 is a lytic virus, and that the host cell dies as a consequence of elaborated mechanisms orchestrated by the virus. The generation of specific cellular structures for a distinct step of virus life cycle is known in eukaryal virus-host systems but is unprecedented in cells from other domains.},
}
@article {pmid19519870,
year = {2009},
author = {Kropinski, AM and Prangishvili, D and Lavigne, R},
title = {Position paper: the creation of a rational scheme for the nomenclature of viruses of Bacteria and Archaea.},
journal = {Environmental microbiology},
volume = {11},
number = {11},
pages = {2775-2777},
doi = {10.1111/j.1462-2920.2009.01970.x},
pmid = {19519870},
issn = {1462-2920},
mesh = {Archaea/*virology ; Archaeal Viruses/*classification ; Bacteria/*virology ; Bacteriophages/*classification ; *Terminology as Topic ; },
}
@article {pmid19499931,
year = {2009},
author = {Leitch, J and Kunze, J and Goddard, JD and Schwan, AL and Faragher, RJ and Naumann, R and Knoll, W and Dutcher, JR and Lipkowski, J},
title = {In situ PM-IRRAS studies of an archaea analogue thiolipid assembled on a au(111) electrode surface.},
journal = {Langmuir : the ACS journal of surfaces and colloids},
volume = {25},
number = {17},
pages = {10354-10363},
doi = {10.1021/la900907d},
pmid = {19499931},
issn = {0743-7463},
abstract = {Polarization modulation infrared reflection absorption spectroscopy (PM-IRRAS) has been applied to determine the conformation, orientation, and hydration of a monolayer of 2,3-di-O-phytanyl-sn-glycerol-1-tetraethylene glycol-dl-alpha-lipoic acid ester (DPTL) self-assembled at a gold electrode surface. This Archaea analogue thiolipid has been recently employed to build tethered lipid bilayers. By synthesizing DPT(d16)L, a DPTL molecule with a deuterium substituted tetraethylene glycol spacer, it was possible to differentiate the C-H stretch vibrations of the phytanyl chains from the tetraethylene glycol spacer and acquire the characteristic IR spectra for the chains, spacer, and lipoic acid headgroup separately. Our results show that the structure of the monolayer displays remarkable stability in a broad range of electrode potentials and that the phytanyl chains remain in a liquid crystalline state. The tetraethylene glycol chains are coiled, and the IR spectrum for this region shows that it is in the disordered state. The most significant result of this study is the information that in contrast to expectations the spacer region is poorly hydrated. Our results have implications for the design of a tethered lipid membrane based on this thiolipid.},
}
@article {pmid19496330,
year = {2009},
author = {Gunbin, KV and Afonnikov, DA and Boldyreva, EV and Kolchanov, NA},
title = {Adaptive evolution of genes of archaea belonging to the genus Pyrococcus associated with adaptation to life under high-pressure conditions.},
journal = {Doklady. Biochemistry and biophysics},
volume = {425},
number = {},
pages = {91-93},
pmid = {19496330},
issn = {1607-6729},
mesh = {Adaptation, Biological/*genetics ; Archaeal Proteins/genetics ; *Evolution, Molecular ; *Genes, Archaeal ; Multigene Family ; Phylogeny ; *Pressure ; Pyrococcus/*genetics/*physiology ; Selection, Genetic ; },
}
@article {pmid19486399,
year = {2009},
author = {Zhang, T and Jin, T and Yan, Q and Shao, M and Wells, G and Criddle, C and P Fang, HH},
title = {Occurrence of ammonia-oxidizing Archaea in activated sludges of a laboratory scale reactor and two wastewater treatment plants.},
journal = {Journal of applied microbiology},
volume = {107},
number = {3},
pages = {970-977},
doi = {10.1111/j.1365-2672.2009.04283.x},
pmid = {19486399},
issn = {1365-2672},
mesh = {Ammonia/*metabolism ; Archaea/enzymology/*genetics/*isolation &amp; purification ; Archaeal Proteins/genetics ; Bioreactors/*microbiology ; DNA Primers ; DNA, Archaeal/analysis ; Genetic Variation ; Hong Kong ; Molecular Sequence Data ; Oxidoreductases/*genetics ; Sequence Analysis, DNA ; Sewage/*microbiology ; Waste Disposal, Fluid ; Water Microbiology ; },
abstract = {AIMS: Characterization of the ammonia-oxidizing archaea (AOA) community in activated sludge from a nitrogen removal bioreactor and wastewater treatment plants (WWTPs).<br><br>METHODS AND RESULTS: Three primer sets specific for ammonia mono-oxygenase alpha-subunit (amoA) were used to construct clone libraries for activated sludge sample from a nitrogen removal bioreactor. One primer set resulted in strong nonspecific PCR products. The other two clone libraries retrieved both shared and unique AOA amoA sequences. One primer set was chosen to study the AOA communities of activated sludge samples from Shatin and Stanley WWTPs. In total, 18 AOA amoA sequences were recovered and compared to the previous reported sequences. A phylogenetic analysis indicated that sequences found in this study fell into three clusters.<br><br>CONCLUSIONS: Different primers resulted in varied AOA communities from the same sample. The AOA found from Hong Kong WWTPs were closely similar to those from sediment and soil, but distinct from those from activated sludge in other places. A comparison of clone libraries between Shatin WWTP and bioreactor indicated the AOA community significantly shifted only after 30-day enrichment.<br><br>This study confirmed the occurrence of AOA in a laboratory scale nitrogen removal bioreactor and Hong Kong WWTPs treating saline or freshwater wastewater. AOA communities found in this study were significantly different from those found in other places. To retrieve diverse AOA communities from environmental samples, a combination of different primers for the amoA gene is needed.},
}
@article {pmid19465520,
year = {2009},
author = {van der Wielen, PW and Voost, S and van der Kooij, D},
title = {Ammonia-oxidizing bacteria and archaea in groundwater treatment and drinking water distribution systems.},
journal = {Applied and environmental microbiology},
volume = {75},
number = {14},
pages = {4687-4695},
pmid = {19465520},
issn = {1098-5336},
mesh = {Ammonia/*metabolism ; Archaea/*classification/genetics/*isolation &amp; purification/metabolism ; Archaeal Proteins/genetics ; Bacteria/*classification/genetics/*isolation &amp; purification/metabolism ; Bacterial Proteins/genetics ; Cluster Analysis ; DNA, Archaeal/chemistry/genetics ; DNA, Bacterial/chemistry/genetics ; Molecular Sequence Data ; Oxidation-Reduction ; Phylogeny ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; *Water Microbiology ; },
abstract = {The ammonia-oxidizing prokaryote (AOP) community in three groundwater treatment plants and connected distribution systems was analyzed by quantitative real-time PCR and sequence analysis targeting the amoA gene of ammonia-oxidizing bacteria (AOB) and archaea (AOA). Results demonstrated that AOB and AOA numbers increased during biological filtration of ammonia-rich anoxic groundwater, and AOP were responsible for ammonium removal during treatment. In one of the treatment trains at plant C, ammonia removal correlated significantly with AOA numbers but not with AOB numbers. Thus, AOA were responsible for ammonia removal in water treatment at one of the studied plants. Furthermore, an observed negative correlation between the dissolved organic carbon (DOC) concentration in the water and AOA numbers suggests that high DOC levels might reduce growth of AOA. AOP entered the distribution system in numbers ranging from 1.5 x 10(3) to 6.5 x 10(4) AOPs ml(-1). These numbers did not change during transport in the distribution system despite the absence of a disinfectant residual. Thus, inactive AOP biomass does not seem to be degraded by heterotrophic microorganisms in the distribution system. We conclude from our results that AOA can be commonly present in distribution systems and groundwater treatment, where they can be responsible for the removal of ammonia.},
}
@article {pmid19464258,
year = {2009},
author = {Corcelli, A},
title = {The cardiolipin analogues of Archaea.},
journal = {Biochimica et biophysica acta},
volume = {1788},
number = {10},
pages = {2101-2106},
doi = {10.1016/j.bbamem.2009.05.010},
pmid = {19464258},
issn = {0006-3002},
mesh = {Archaea/*metabolism ; Archaeal Proteins/*metabolism ; Cardiolipins/*chemistry/*metabolism ; Phospholipids/*metabolism ; },
abstract = {The present article reviews studies of the structure and functional roles of the cardiolipin analogues of extremely halophilic prokaryotes belonging to the Archaea domain. Analogies and differences between the archaeal bisphosphatidylglycerol and the mitochondrial cardiolipin are presented. Furthermore the structure of archaeal glycophospholipid dimers is illustrated together with the available information on their function. The studies on the function of cardiolipin analogues in archaebacteria point out the tight interaction established by these phospholipids with membrane proteins and their role as bioactive lipids in the adaptation of microorganisms to osmotic stress.},
}
@article {pmid19453522,
year = {2009},
author = {Erguder, TH and Boon, N and Wittebolle, L and Marzorati, M and Verstraete, W},
title = {Environmental factors shaping the ecological niches of ammonia-oxidizing archaea.},
journal = {FEMS microbiology reviews},
volume = {33},
number = {5},
pages = {855-869},
doi = {10.1111/j.1574-6976.2009.00179.x},
pmid = {19453522},
issn = {1574-6976},
mesh = {Ammonia/metabolism ; Archaea/*enzymology/growth &amp; development ; Crenarchaeota/enzymology/growth &amp; development ; *Ecosystem ; *Hot Springs/chemistry/microbiology ; Hydrogen-Ion Concentration ; Oxidation-Reduction ; Oxidoreductases/*metabolism ; Phosphates/analysis ; Seawater/chemistry/microbiology ; Sulfides/analysis ; },
abstract = {For more than 100 years it was believed that bacteria were the only group responsible for the oxidation of ammonia. However, recently, a new strain of archaea bearing a putative ammonia monooxygenase subunit A (amoA) gene and able to oxidize ammonia was isolated from a marine aquarium tank. Ammonia-oxidizing archaea (AOA) were subsequently discovered in many ecosystems of varied characteristics and even found as the predominant causal organisms in some environments. Here, we summarize the current knowledge on the environmental conditions related to the presence of AOA and discuss the possible site-related properties. Considering these data, we deduct the possible niches of AOA based on pH, sulfide and phosphate levels. It is proposed that the AOA might be important actors within the nitrogen cycle in low-nutrient, low-pH, and sulfide-containing environments.},
}
@article {pmid19428289,
year = {2009},
author = {Kopitz, A and Soppa, J and Krejtschi, C and Hauser, K},
title = {Differential stability of TATA box binding proteins from archaea with different optimal growth temperatures.},
journal = {Spectrochimica acta. Part A, Molecular and biomolecular spectroscopy},
volume = {73},
number = {5},
pages = {799-804},
doi = {10.1016/j.saa.2009.04.002},
pmid = {19428289},
issn = {1873-3557},
mesh = {*Acclimatization ; Arabidopsis/chemistry/growth &amp; development/physiology ; Archaeal Proteins/*chemistry/genetics/isolation &amp; purification ; Cloning, Molecular ; Escherichia coli/genetics ; Methanobacteriaceae/chemistry/growth &amp; development/*physiology ; Methanosarcina/chemistry/growth &amp; development/*physiology ; Models, Molecular ; Plant Proteins/chemistry ; Potassium Chloride/chemistry ; Protein Folding ; Protein Stability ; Spectrophotometry, Infrared ; TATA-Box Binding Protein/*chemistry/genetics/isolation &amp; purification ; Temperature ; Transition Temperature ; },
abstract = {The TATA box binding protein (TBP) is involved in promoter recognition, the first step of transcription initiation. TBP is universally conserved and essential in archaea and eukaryotes. In archaea, TBPs have to be stable and to function in species that cover an extremely wide range of optimal growth temperatures (OGTs), from below 0 degrees C to more than 100 degrees C. Thus, the archaeal TBP family is ideally suited to study the evolutionary adaptation of proteins to an extremely wide range of temperatures. We characterized the thermostability of one mesophilic and one thermophilic TBP by infrared spectroscopy. Transition temperatures (T(m)s) of thermal unfolding have been determined using TBPs from Methanosarcina mazei (OGT 37 degrees C) and from Methanothermobacter thermautotrophicus (OGT 65 degrees C). Furthermore, the influence of protein and salt concentration on thermostability has been characterized. Together with previous studies, our results reveal that the T(m)s of archaeal TBPs are closely correlated with the OGTs of the respective species. Noteworthy, this is also true for the TBP from M. mazei representing the first characterized TBP from a mesophilic archaeon. In contrast, the only characterized eukaryotic TBP of the mesophilic plant Arabidopsis thaliana has a T(m) more than 40 degrees C above the OGT.},
}
@article {pmid19424498,
year = {2009},
author = {Whitehead, K and Pan, M and Masumura, K and Bonneau, R and Baliga, NS},
title = {Diurnally entrained anticipatory behavior in archaea.},
journal = {PloS one},
volume = {4},
number = {5},
pages = {e5485},
pmid = {19424498},
issn = {1932-6203},
support = {P50 GM076547/GM/NIGMS NIH HHS/United States ; R01 GM077398/GM/NIGMS NIH HHS/United States ; 1R01GM077398-01A2/GM/NIGMS NIH HHS/United States ; P50GM076547/GM/NIGMS NIH HHS/United States ; },
mesh = {*Circadian Rhythm/drug effects/genetics ; Gene Expression Regulation, Archaeal/drug effects ; Genes, Archaeal ; Halobacterium salinarum/drug effects/genetics/growth &amp; development/*physiology ; Oxygen/pharmacology ; },
abstract = {By sensing changes in one or few environmental factors biological systems can anticipate future changes in multiple factors over a wide range of time scales (daily to seasonal). This anticipatory behavior is important to the fitness of diverse species, and in context of the diurnal cycle it is overall typical of eukaryotes and some photoautotrophic bacteria but is yet to be observed in archaea. Here, we report the first observation of light-dark (LD)-entrained diurnal oscillatory transcription in up to 12% of all genes of a halophilic archaeon Halobacterium salinarum NRC-1. Significantly, the diurnally entrained transcription was observed under constant darkness after removal of the LD stimulus (free-running rhythms). The memory of diurnal entrainment was also associated with the synchronization of oxic and anoxic physiologies to the LD cycle. Our results suggest that under nutrient limited conditions halophilic archaea take advantage of the causal influence of sunlight (via temperature) on O(2) diffusivity in a closed hypersaline environment to streamline their physiology and operate oxically during nighttime and anoxically during daytime.},
}
@article {pmid19416460,
year = {2009},
author = {Cheng, YF and Mao, SY and Liu, JX and Zhu, WY},
title = {Molecular diversity analysis of rumen methanogenic Archaea from goat in eastern China by DGGE methods using different primer pairs.},
journal = {Letters in applied microbiology},
volume = {48},
number = {5},
pages = {585-592},
doi = {10.1111/j.1472-765X.2009.02583.x},
pmid = {19416460},
issn = {1472-765X},
mesh = {Animals ; Archaea/classification/*genetics/*isolation &amp; purification/metabolism ; *Biodiversity ; China ; DNA Primers/*genetics ; DNA, Archaeal/genetics ; DNA, Ribosomal/genetics ; Electrophoresis, Polyacrylamide Gel ; Goats/*microbiology ; Methane/*metabolism ; Molecular Sequence Data ; RNA, Ribosomal, 16S/genetics ; Rumen/microbiology ; },
abstract = {AIMS: To screen a pair of primers suitable for denaturing gradient gel electrophoretic (DGGE) analysis of ruminal methanogenic Archaea and to detect the archaeal communities in the rumen of goat.<br><br>METHODS AND RESULTS: Nine primer pairs for 16S rDNA of methanogenic Archaea, including six for directed polymerase chain reaction (PCR) and three for nested PCR were first evaluated by PCR amplification of the total DNA from rumen fluids and bacteria. The DGGE analysis of rumen fluids was then conducted with three primer sets (344fGC/915r, 1106fGC/1378r and 519f/915rGC) of the nine pairs tested. Good separation and quality of patterns were obtained in DGGE analysis with primer pairs 1106fGC/1378r and 519f/915rGC. A total of 40 DNA fragments were excised from the DGGE gels and their sequences were determined. All fragments belonged to methanogenic Archaea while primer pair 519f/915rGC had better amplification ranges than the other two primer pairs.<br><br>CONCLUSIONS: The procedure of DGGE analysis with primer pair 519f/915rGC was more suitable for investigating methanogenic archaeal community in the rumen. The dominant methanogenic Archaea in the rumen of goat was Methanobrevibacter sp. and an unidentified methanogenic Archaea.<br><br>One pair of primers suitable for DGGE analysis of ruminal methanogenic Archaea was obtained and the molecular diversity of ruminal methanogenic Archaea in goat was investigated by PCR-DGGE.},
}
@article {pmid19407206,
year = {2009},
author = {Randau, L and Stanley, BJ and Kohlway, A and Mechta, S and Xiong, Y and Söll, D},
title = {A cytidine deaminase edits C to U in transfer RNAs in Archaea.},
journal = {Science (New York, N.Y.)},
volume = {324},
number = {5927},
pages = {657-659},
pmid = {19407206},
issn = {1095-9203},
support = {R33 AI078831/AI/NIAID NIH HHS/United States ; R37 GM022854/GM/NIGMS NIH HHS/United States ; R01 GM022854/GM/NIGMS NIH HHS/United States ; AI078831/AI/NIAID NIH HHS/United States ; GM22854/GM/NIGMS NIH HHS/United States ; R21 AI078831/AI/NIAID NIH HHS/United States ; R01 GM022854-33/GM/NIGMS NIH HHS/United States ; },
mesh = {Amino Acid Motifs ; Catalytic Domain ; Crystallography, X-Ray ; Cytidine Deaminase/*chemistry/*metabolism ; Deamination ; Euryarchaeota/enzymology/genetics/*metabolism ; Genes, Archaeal ; Models, Chemical ; Models, Molecular ; Nucleic Acid Conformation ; Protein Multimerization ; Protein Structure, Tertiary ; *RNA Editing ; RNA, Archaeal/chemistry/genetics/*metabolism ; RNA, Transfer/chemistry/genetics/*metabolism ; },
abstract = {All canonical transfer RNAs (tRNAs) have a uridine at position 8, involved in maintaining tRNA tertiary structure. However, the hyperthermophilic archaeon Methanopyrus kandleri harbors 30 (out of 34) tRNA genes with cytidine at position 8. Here, we demonstrate C-to-U editing at this location in the tRNA's tertiary core, and present the crystal structure of a tRNA-specific cytidine deaminase, CDAT8, which has the cytidine deaminase domain linked to a tRNA-binding THUMP domain. CDAT8 is specific for C deamination at position 8, requires only the acceptor stem hairpin for activity, and belongs to a unique family within the "cytidine deaminase-like" superfamily. The presence of this C-to-U editing enzyme guarantees the proper folding and functionality of all M. kandleri tRNAs.},
}
@article {pmid19395559,
year = {2009},
author = {Wang, S and Xiao, X and Jiang, L and Peng, X and Zhou, H and Meng, J and Wang, F},
title = {Diversity and abundance of ammonia-oxidizing archaea in hydrothermal vent chimneys of the juan de fuca ridge.},
journal = {Applied and environmental microbiology},
volume = {75},
number = {12},
pages = {4216-4220},
pmid = {19395559},
issn = {1098-5336},
mesh = {Ammonia/*metabolism ; Archaea/*classification/genetics/isolation &amp; purification/*metabolism ; Archaeal Proteins/genetics ; Cluster Analysis ; DNA, Archaeal/chemistry/genetics ; Hot Springs/*microbiology ; Molecular Sequence Data ; Oxidation-Reduction ; Phylogeny ; Seawater/*microbiology ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; },
abstract = {The abundance and diversity of archaeal ammonia monooxygenase subunit A (amoA) genes from hydrothermal vent chimneys at the Juan de Fuca Ridge were investigated. The majority of the retrieved archaeal amoA sequences exhibited identities of less than 95% to those in the GenBank database. Novel ammonia-oxidizing archaea may exist in the hydrothermal vent environments.},
}
@article {pmid19387487,
year = {2009},
author = {Mertens, J and Broos, K and Wakelin, SA and Kowalchuk, GA and Springael, D and Smolders, E},
title = {Bacteria, not archaea, restore nitrification in a zinc-contaminated soil.},
journal = {The ISME journal},
volume = {3},
number = {8},
pages = {916-923},
doi = {10.1038/ismej.2009.39},
pmid = {19387487},
issn = {1751-7370},
mesh = {Ammonia/*metabolism ; Archaea/classification/genetics/isolation &amp; purification/*metabolism ; Archaeal Proteins/genetics ; Bacteria/classification/genetics/isolation &amp; purification/*metabolism ; Bacterial Proteins/genetics ; Cluster Analysis ; Colony Count, Microbial ; DNA, Archaeal/chemistry/genetics ; DNA, Bacterial/chemistry/genetics ; Ecosystem ; Gene Expression Profiling ; Molecular Sequence Data ; Oxidation-Reduction ; Phylogeny ; Sequence Analysis, DNA ; Sequence Homology ; *Soil Microbiology ; Soil Pollutants/*metabolism ; Zinc/*metabolism ; },
abstract = {Biological ammonia oxidation had long been thought to be mediated solely by discrete clades of beta- and gamma-proteobacteria (ammonia-oxidizing bacteria; AOB). However, ammonia-oxidizing Crenarchaeota (ammonia-oxidizing archaea; AOA) have recently been identified and proposed to be the dominant agents of ammonia oxidation in soils. Nevertheless, the dynamics of AOB versus AOA, and their relative contribution to soil ammonia oxidation and ecosystem functioning on stress and environmental perturbation, remain unknown. Using a 3-year longitudinal field study and the amoA gene as a molecular marker, we demonstrate that AOB, but not AOA, mediate recovery of nitrification after zinc (Zn) contamination. Pristine soils showed approximately equal amoA gene copy numbers and transcript levels for AOB and AOA. At an intermediate Zn dose (33.7 mmol Zn per kg), ammonia oxidation was completely inhibited, and the numbers of AOB and AOA amoA gene copies and gene transcripts were reduced. After 2 years, ammonia oxidation in the field soils was fully restored to preexposure levels, and this restoration of function was concomitant with an increase of AOB amoA gene copy and gene transcript numbers. Analysis of the restored community revealed domination by a phylogenetically distinct Zn-tolerant Nitrosospira sp. community. In contrast, the numbers of AOA amoA gene copies and gene transcripts remained 3- and 10(4)-fold lower than recovered AOB values, respectively. Thus, although recent findings have emphasized a dominant role of archaea in soil-borne ammonia oxidation, we demonstrate that a phylogenetic shift within the AOB community drives recovery of nitrification from Zn contamination in this soil.},
}
@article {pmid19383036,
year = {2009},
author = {Orphan, VJ and Turk, KA and Green, AM and House, CH},
title = {Patterns of 15N assimilation and growth of methanotrophic ANME-2 archaea and sulfate-reducing bacteria within structured syntrophic consortia revealed by FISH-SIMS.},
journal = {Environmental microbiology},
volume = {11},
number = {7},
pages = {1777-1791},
doi = {10.1111/j.1462-2920.2009.01903.x},
pmid = {19383036},
issn = {1462-2920},
mesh = {Archaea/chemistry/genetics/*growth &amp; development/*metabolism ; Bacteria/chemistry/genetics/*growth &amp; development/*metabolism ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; In Situ Hybridization, Fluorescence ; Methane/*metabolism ; Nitrogen Isotopes/metabolism ; Oxidation-Reduction ; Seawater/microbiology ; Spectrometry, Mass, Secondary Ion ; Sulfates ; *Symbiosis ; },
abstract = {Methane release from the oceans is controlled in large part by syntrophic interactions between anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria (DSS), frequently found as organized consortia. An understanding of the specifics of this symbiotic relationship and the metabolic heterogeneity existing between and within individual methane-oxidizing aggregates is currently lacking. Here, we use the microanalytical method FISH-SIMS (fluorescence in situ hybridization-secondary ion mass spectrometry) to describe the physiological traits and anabolic activity of individual methanotrophic consortia, specifically tracking (15)N-labelled protein synthesis to examine the effects of organization and size on the metabolic activity of the syntrophic partners. Patterns of (15)N distribution within individual aggregates showed enhanced (15)N assimilation in ANME-2 cells relative to the co-associated DSS revealing a decoupling in anabolic activity between the partners. Protein synthesis in ANME-2 cells was sustained throughout the core of individual ANME-2/DSS consortia ranging in size range from 4 to 20 μm. This indicates that metabolic activity of the methane-oxidizing archaea is not limited to, or noticeably enhanced at the ANME-2/DSS boundary. Overall, the metabolic activity of both syntrophic partners within consortia was greater than activity measured in representatives of the ANME-2 and DSS observed alone, with smaller ANME-2/DSS aggregates displaying a tendency for greater (15)N uptake and doubling times ranging from 3 to 5 months. The combination of (15)N-labelling and FISH-SIMS provides an important perspective on the extent of heterogeneity within methanotrophic aggregates and may aid in constraining predictive models of activity and growth by these syntrophic consortia.},
}
@article {pmid19344749,
year = {2009},
author = {Stock, T and Rother, M},
title = {Selenoproteins in Archaea and Gram-positive bacteria.},
journal = {Biochimica et biophysica acta},
volume = {1790},
number = {11},
pages = {1520-1532},
doi = {10.1016/j.bbagen.2009.03.022},
pmid = {19344749},
issn = {0006-3002},
mesh = {Archaea/genetics/*metabolism ; Gram-Positive Bacteria/genetics/*metabolism ; Methane/biosynthesis ; Models, Biological ; Selenoproteins/*metabolism/*physiology ; },
abstract = {Selenium is an essential trace element for many organisms by serving important catalytic roles in the form of the 21st co-translationally inserted amino acid selenocysteine. It is mostly found in redox-active proteins in members of all three domains of life and analysis of the ever-increasing number of genome sequences has facilitated identification of the encoded selenoproteins. Available data from biochemical, sequence, and structure analyses indicate that Gram-positive bacteria synthesize and incorporate selenocysteine via the same pathway as enterobacteria. However, recent in vivo studies indicate that selenocysteine-decoding is much less stringent in Gram-positive bacteria than in Escherichia coli. For years, knowledge about the pathway of selenocysteine synthesis in Archaea and Eukarya was only fragmentary, but genetic and biochemical studies guided by analysis of genome sequences of Sec-encoding archaea has not only led to the characterization of the pathways but has also shown that they are principally identical. This review summarizes current knowledge about the metabolic pathways of Archaea and Gram-positive bacteria where selenium is involved, about the known selenoproteins, and about the respective pathways employed in selenoprotein synthesis.},
}
@article {pmid19326145,
year = {2009},
author = {Luo, J and Teng, M and Zhang, GP and Lun, ZR and Zhou, H and Qu, LH},
title = {Evaluating the evolution of G. lamblia based on the small nucleolar RNAs identified from Archaea and unicellular eukaryotes.},
journal = {Parasitology research},
volume = {104},
number = {6},
pages = {1543-1546},
pmid = {19326145},
issn = {1432-1955},
mesh = {Animals ; *Evolution, Molecular ; Giardia lamblia/*classification/*genetics ; Models, Molecular ; RNA, Protozoan/*genetics ; RNA, Small Nucleolar/*genetics ; Sequence Homology ; },
abstract = {The evolutionary position of Giardia lamblia has been challenged in recent years. Comparison of the snoRNAs identified from Archaea and unicellular eukaryotes shows that G. lamblia snoRNAs are more similar in most respects to the counterparts identified from Dictyostelium discoideum, Plasmodium falciparum, fungi, and some metazoans, remarkably differently from those of Euglenozoa protozoans. We propose that G. lamblia emerged somewhat later than Trypanosoma and Euglena during the early evolution of "excavata" eukaryotes.},
}
@article {pmid19306569,
year = {2008},
author = {Chen, H and Zhang, C and Ma, X and Zhang, Y},
title = {[Heat shock proteins of the hyperthermophilic archaea].},
journal = {Sheng wu gong cheng xue bao = Chinese journal of biotechnology},
volume = {24},
number = {12},
pages = {2011-2021},
pmid = {19306569},
issn = {1000-3061},
mesh = {Archaea/classification/*metabolism ; Archaeal Proteins/*metabolism ; Chaperonin 60/*metabolism ; Heat-Shock Proteins/genetics/*metabolism ; Molecular Chaperones/metabolism ; },
abstract = {As thermostable enzymes and organisms are much more needed, researches on heat shock proteins(HSPs) of hyperthermophilic archaea have drawn more concerns. HSPs from hyperthermophilic archaea are concise only with HSP60, sHSP, prefoldin and AAA+proteins, but without HSP100s, HSP90s, HSP70 (DnaK), HSP40 (DnaJ) and GrpE which are common in mesophilic or thermophilic archaea. Accordingly, studies on the structure, function and operation mechanism of these four groups are much more important and meaningful. This review focuses on the recent progress in the researchs on the structure, function, operation mechanism and cooperation of the HSPs from hyperthermophilic archaea. The problems and obfuscations in these HSPs are analyzed, and farther research direction and key points are put out.},
}
@article {pmid19303051,
year = {2009},
author = {Müller-Santos, M and de Souza, EM and Pedrosa, Fde O and Mitchell, DA and Longhi, S and Carrière, F and Canaan, S and Krieger, N},
title = {First evidence for the salt-dependent folding and activity of an esterase from the halophilic archaea Haloarcula marismortui.},
journal = {Biochimica et biophysica acta},
volume = {1791},
number = {8},
pages = {719-729},
doi = {10.1016/j.bbalip.2009.03.006},
pmid = {19303051},
issn = {0006-3002},
mesh = {Amino Acid Sequence ; Circular Dichroism ; Cloning, Molecular ; Computational Biology ; Electrophoresis, Polyacrylamide Gel ; Enzyme Activation/drug effects ; Enzyme Inhibitors/pharmacology ; Enzyme Stability/drug effects ; Esterases/*chemistry/isolation &amp; purification/*metabolism ; Haloarcula marismortui/drug effects/*enzymology ; Hydrogen-Ion Concentration ; Models, Molecular ; Molecular Sequence Data ; Potassium Chloride/pharmacology ; Protein Folding/*drug effects ; Protein Structure, Secondary ; Sequence Alignment ; Sodium Chloride/*pharmacology ; Static Electricity ; Substrate Specificity/drug effects ; Surface Properties/drug effects ; Temperature ; Time Factors ; },
abstract = {A gene encoding an esterase from Haloarcula marismortui, a halophilic archaea from the Dead Sea, was cloned, expressed in Escherichia coli, and the recombinant protein (Hm EST) was biochemically characterized. The enzymatic activity of Hm EST was shown to exhibit salt dependence through salt-dependent folding. Hm EST exhibits a preference for short chain fatty acids and monoesters. It is inhibited by phenylmethylsulfonyl fluoride, diethyl-p-nitrophenyl phosphate, and 5-methoxy-3-(4-phenoxyphenyl)-3H-[1,3,4]oxadiazol-2-one, confirming the conclusion from sequence alignments that Hm EST is a serine carboxylesterase belonging to the hormone-sensitive lipase family. The activity of Hm EST is optimum in the presence of 3 M KCl and no activity was detected in the absence of salts. Far-UV circular dichroism showed that Hm EST is totally unfolded in salt-free medium and secondary structure appears in the presence of 0.25-0.5 M KCl. After salt depletion, the protein was able to recover 60% of its initial activity when 2 M KCl was added. A 3D model of Hm EST was built and its surface properties were analyzed, pointing to an enrichment in acidic residues paralleled by a depletion in basic residues. This peculiar charge repartition at the protein surface supports a better stability of the protein in a high salt environment.},
}
@article {pmid19298823,
year = {2009},
author = {Di Fiore, A and Fiorentino, G and Vitale, RM and Ronca, R and Amodeo, P and Pedone, C and Bartolucci, S and De Simone, G},
title = {Structural analysis of BldR from Sulfolobus solfataricus provides insights into the molecular basis of transcriptional activation in Archaea by MarR family proteins.},
journal = {Journal of molecular biology},
volume = {388},
number = {3},
pages = {559-569},
doi = {10.1016/j.jmb.2009.03.030},
pmid = {19298823},
issn = {1089-8638},
mesh = {Amino Acid Sequence ; Archaeal Proteins/*chemistry/metabolism ; Crystallography, X-Ray ; DNA, Archaeal/metabolism ; Models, Molecular ; Molecular Sequence Data ; Protein Binding ; Protein Structure, Tertiary ; Sequence Alignment ; Sulfolobus solfataricus/*chemistry/physiology ; Trans-Activators/*chemistry/metabolism ; Transcriptional Activation ; },
abstract = {The multiple antibiotic resistance regulator (MarR) family constitutes a significant class of transcriptional regulators whose members control a variety of important biological functions such as regulation of response to environmental stress, control of virulence factor production, resistance to antimicrobial agents, and regulation of aromatic catabolic pathways. Although the majority of MarR family members have been characterized as transcriptional repressors, a few examples of transcriptional activators have also been reported. BldR is a newly identified member of this family that has been demonstrated to act as a transcriptional activator in stress response to aromatic compounds in the crenarchaeon Sulfolobus solfataricus. In this work, we report findings on the BldR X-ray crystal structure and present a molecular modeling study on the complex that this protein forms with its cognate DNA sequence, thus providing the first detailed description of the DNA-binding mechanism of an archaeal activator belonging to the MarR family. Two residues responsible for the high binding specificity of this transcriptional regulator were also identified. Our studies demonstrated that, in Archaea, the capability of MarR family members to act as activators or repressors is not related to a particular DNA-binding mechanism but rather could be due to the position of the binding site on the target DNA. Moreover, since genes encoding MarR proteins often control transcription of operons that encode for multisubstrate efflux pumps, our results also provided important insights for the identification of new tools to overcome the microorganism's multidrug resistance.},
}
@article {pmid19298373,
year = {2009},
author = {Pietilä, MK and Roine, E and Paulin, L and Kalkkinen, N and Bamford, DH},
title = {An ssDNA virus infecting archaea: a new lineage of viruses with a membrane envelope.},
journal = {Molecular microbiology},
volume = {72},
number = {2},
pages = {307-319},
doi = {10.1111/j.1365-2958.2009.06642.x},
pmid = {19298373},
issn = {1365-2958},
mesh = {Archaeal Viruses/classification/*genetics/isolation &amp; purification/ultrastructure ; DNA Viruses/classification/*genetics/isolation &amp; purification/ultrastructure ; DNA, Single-Stranded/genetics ; DNA, Viral/genetics ; Genome, Viral ; Halorubrum/*virology ; Microscopy, Electron ; Sequence Analysis, DNA ; Viral Envelope Proteins/metabolism ; Virion/genetics ; },
abstract = {Archaeal organisms are generally known as diverse extremophiles, but they play a crucial role also in moderate environments. So far, only about 50 archaeal viruses have been described in some detail. Despite this, unusual viral morphotypes within this group have been reported. Interestingly, all isolated archaeal viruses have a double-stranded DNA (dsDNA) genome. To further characterize the diversity of archaeal viruses, we screened highly saline water samples for archaea and their viruses. Here, we describe a new haloarchaeal virus, Halorubrum pleomorphic virus 1 (HRPV-1) that was isolated from a solar saltern and infects an indigenous host belonging to the genus Halorubrum. Infection does not cause cell lysis, but slightly retards growth of the host and results in high replication of the virus. The sequenced genome (7048 nucleotides) of HRPV-1 is single-stranded DNA (ssDNA), which makes HRPV-1 the first characterized archaeal virus that does not have a dsDNA genome. In spite of this, similarities to another archaeal virus were observed. Two major structural proteins were recognized in protein analyses, and by lipid analyses it was shown that the virion contains a membrane. Electron microscopy studies indicate that the enveloped virion is pleomorphic (approximately 44 x 55 nm). HRPV-1 virion may represent commonly used virion architecture, and it seems that structure-based virus lineages may be extended to non-icosahedral viruses.},
}
@article {pmid19291314,
year = {2009},
author = {Schlesner, M and Miller, A and Streif, S and Staudinger, WF and Müller, J and Scheffer, B and Siedler, F and Oesterhelt, D},
title = {Identification of Archaea-specific chemotaxis proteins which interact with the flagellar apparatus.},
journal = {BMC microbiology},
volume = {9},
number = {},
pages = {56},
pmid = {19291314},
issn = {1471-2180},
mesh = {Amino Acid Motifs ; Amino Acid Sequence ; Archaeal Proteins/chemistry/genetics/*metabolism ; Bacterial Proteins/biosynthesis/genetics ; *Chemotaxis ; Consensus Sequence ; Flagella/*metabolism ; Gene Deletion ; Halobacterium salinarum/genetics/*metabolism ; Membrane Proteins/biosynthesis/genetics ; Methyl-Accepting Chemotaxis Proteins ; Molecular Motor Proteins/chemistry/genetics/*metabolism ; Molecular Sequence Data ; Phylogeny ; Reverse Transcriptase Polymerase Chain Reaction ; Rotation ; Sequence Alignment ; Sequence Homology, Amino Acid ; Signal Transduction ; },
abstract = {BACKGROUND: Archaea share with bacteria the ability to bias their movement towards more favorable locations, a process known as taxis. Two molecular systems drive this process: the motility apparatus and the chemotaxis signal transduction system. The first consists of the flagellum, the flagellar motor, and its switch, which allows cells to reverse the rotation of flagella. The second targets the flagellar motor switch in order to modulate the switching frequency in response to external stimuli. While the signal transduction system is conserved throughout archaea and bacteria, the archaeal flagellar apparatus is different from the bacterial one. The proteins constituting the flagellar motor and its switch in archaea have not yet been identified, and the connection between the bacterial-like chemotaxis signal transduction system and the archaeal motility apparatus is unknown.<br><br>RESULTS: Using protein-protein interaction analysis, we have identified three proteins in Halobacterium salinarum that interact with the chemotaxis (Che) proteins CheY, CheD, and CheC2, as well as the flagella accessory (Fla) proteins FlaCE and FlaD. Two of the proteins belong to the protein family DUF439, the third is a HEAT_PBS family protein. In-frame deletion strains for all three proteins were generated and analyzed as follows: a) photophobic responses were measured by a computer-based cell tracking system b) flagellar rotational bias was determined by dark-field microscopy, and c) chemotactic behavior was analyzed by a swarm plate assay. Strains deleted for the HEAT_PBS protein or one of the DUF439 proteins proved unable to switch the direction of flagellar rotation. In these mutants, flagella rotate only clockwise, resulting in exclusively forward swimming cells that are unable to respond to tactic signals. Deletion of the second DUF439 protein had only minimal effects. HEAT_PBS proteins could be identified in the chemotaxis gene regions of all motile haloarchaea sequenced so far, but not in those of other archaeal species. Genes coding for DUF439 proteins, however, were found to be integral parts of chemotaxis gene regions across the archaeal domain, and they were not detected in other genomic context.<br><br>CONCLUSION: Altogether, these results demonstrate that, in the archaeal domain, previously unrecognized archaea-specific Che proteins are essential for relaying taxis signaling to the flagellar apparatus.},
}
@article {pmid19291145,
year = {2009},
author = {Durá, MA and Rosenbaum, E and Larabi, A and Gabel, F and Vellieux, FM and Franzetti, B},
title = {The structural and biochemical characterizations of a novel TET peptidase complex from Pyrococcus horikoshii reveal an integrated peptide degradation system in hyperthermophilic Archaea.},
journal = {Molecular microbiology},
volume = {72},
number = {1},
pages = {26-40},
doi = {10.1111/j.1365-2958.2009.06600.x},
pmid = {19291145},
issn = {1365-2958},
mesh = {Amino Acid Sequence ; Aminopeptidases/genetics/isolation &amp; purification/*metabolism ; Archaeal Proteins/genetics/isolation &amp; purification/*metabolism ; Cobalt/metabolism ; Hot Temperature ; Hydrogen-Ion Concentration ; Molecular Sequence Data ; Protein Multimerization ; Protein Stability ; Protein Structure, Quaternary ; Pyrococcus horikoshii/*enzymology/genetics ; },
abstract = {The structure of a 468 kDa peptidase complex from the hyperthermophile Pyrococcus horikoshii has been solved at 1.9 A resolution. The monomer contains the M42 peptidase typical catalytic domain, and a dimerization domain that allows the formation of dimers that assemble as a 12-subunit self-compartmentalized tetrahedron, similar to those described for the TET peptidases. The biochemical analysis shows that the enzyme is cobalt-activated and cleaves peptides by a non-processive mechanism. Consequently, this protein represents the third TET peptidase complex described in P. horikoshii, thereby called PhTET3. It is a lysyl aminopeptidase with a strong preference for basic residues, which are poorly cleaved by PhTET1 and PhTET2. The structural analysis of PhTET3 and its comparison with PhTET1 and PhTET2 unravels common features explaining the general mode of action of the TET molecular machines as well as differences that can be associated with strong substrate discriminations. The question of the stability of the TET assemblies under extreme temperatures has been addressed. PhTET3 displays its maximal activity at 95 degrees C and small-angle neutron scattering experiments at 90 degrees C demonstrate the absence of quaternary structure alterations after extensive incubation times. In conclusion, PhTETs are complementary peptide destruction machines that may play an important role in the metabolism of P. horikoshii.},
}
@article {pmid19274727,
year = {2009},
author = {Kang, HJ and Kubota, K and Ming, H and Miyazono, K and Tanokura, M},
title = {Crystal structure of KaiC-like protein PH0186 from hyperthermophilic archaea Pyrococcus horikoshii OT3.},
journal = {Proteins},
volume = {75},
number = {4},
pages = {1035-1039},
doi = {10.1002/prot.22367},
pmid = {19274727},
issn = {1097-0134},
mesh = {Amino Acid Sequence ; Archaeal Proteins/*chemistry ; Bacterial Proteins/chemistry ; Circadian Rhythm Signaling Peptides and Proteins ; Crystallography, X-Ray ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Pyrococcus horikoshii/*chemistry ; Sequence Alignment ; },
}
@article {pmid19266223,
year = {2009},
author = {Kebbouche-Gana, S and Gana, ML and Khemili, S and Fazouane-Naimi, F and Bouanane, NA and Penninckx, M and Hacene, H},
title = {Isolation and characterization of halophilic Archaea able to produce biosurfactants.},
journal = {Journal of industrial microbiology &amp; biotechnology},
volume = {36},
number = {5},
pages = {727-738},
pmid = {19266223},
issn = {1476-5535},
mesh = {DNA, Archaeal/genetics ; DNA, Ribosomal/genetics ; Halobacteriaceae/classification/genetics/*isolation &amp; purification/metabolism ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sodium Chloride/*metabolism ; Surface-Active Agents/*metabolism ; },
abstract = {Halotolerant microorganisms able to live in saline environments offer a multitude of actual or potential applications in various fields of biotechnology. This is why some strains of Halobacteria from an Algerian culture collection were screened for biosurfactant production in a standard medium using the qualitative drop-collapse test and emulsification activity assay. Five of the Halobacteria strains reduced the growth medium surface tension below 40 mN m(-1), and two of them exhibited high emulsion-stabilizing capacity. Diesel oil-in-water emulsions were stabilized over a broad range of conditions, from pH 2 to 11, with up to 35% sodium chloride or up to 25% ethanol in the aqueous phase. Emulsions were stable to three cycles of freezing and thawing. The components of the biosurfactant were determined; it contained sugar, protein and lipid. The two Halobacteria strains with enhanced biosurfactant producers, designated strain A21 and strain D21, were selected to identify by phenotypic, biochemical characteristics and by partial 16S rRNA gene sequencing. The strains have Mg(2+), and salt growth requirements are always above 15% (w/v) salts with an optimal concentration of 15-25%. Analyses of partial 16S rRNA gene sequences of the two strains suggested that they were halophiles belonging to genera of the family Halobacteriaceae, Halovivax (strain A21) and Haloarcula (strain D21). To our knowledge, this is the first report of biosurfactant production at such a high salt concentration.},
}
@article {pmid19258281,
year = {2009},
author = {de Souza, LM and Müller-Santos, M and Iacomini, M and Gorin, PA and Sassaki, GL},
title = {Positive and negative tandem mass spectrometric fingerprints of lipids from the halophilic Archaea Haloarcula marismortui.},
journal = {Journal of lipid research},
volume = {50},
number = {7},
pages = {1363-1373},
pmid = {19258281},
issn = {1539-7262},
mesh = {Ethers/chemistry ; Glyceryl Ethers/*analysis ; Haloarcula marismortui/*chemistry ; Lipids/*analysis ; Molecular Structure ; Phospholipids/*analysis ; Spectrometry, Mass, Electrospray Ionization/methods ; Tandem Mass Spectrometry/*methods ; },
abstract = {Lipids from the extremely halophilic Archaea, Haloarcula marismortui, contain abundant phytanyl diether phospholipids, namely archaetidic acid (AA), archaetidylglycerol (AG), archaetidylglycerosulfate (AGS), with mainly archaetidylglycerophosphate methyl ester (AGP-Me). These were accompanied by a triglycosyl archaeol (TGA), lacking characteristic sulfate groups. Tandem-mass spectrometry was employed to provide fingerprints for identifying these known lipids, as well as small amounts of unsaturated phospholipids. These contained 3 and 6 double bonds in their archaeol moiety, suggested by negative tandem-MS of intact phospholipids, as indicated by differences between their pseudo-molecular ion and specific fragment ions designated as pi(2). The core ether lipids were confirmed by electrospray ionization mass spectrometry (ESI-MS) as 2,3-di-O-phytanyl-sn-glycerol (C20, C20), which gave rise to a precursor-ion at m/z 660 [M+Li](+), and its fragment ion at m/z 379 [M+Li](+), consistent with mono-O-phytanyl-glycerol. Furthermore, lithiated ions at m/z 654 (MS(1)), 379 (MS(2)) and m/z 648 (MS(1)), 373 (MS(2)), combined with (1)H/(13)C NMR chemical shifts at delta 5.31-121.6 (C2/2'-H2/2'), 5.08-124.9 (C6/6'-H6/6') and 5.10-126.0 (10/10'-H10/10') confirmed the presence of unsaturated homologs of archaeol. We carried out a comprehensive study on the lipids present in cells of H. marismortui. We used positive and negative ESI-MS with tandem-MS, which served as a fingerprint analysis for identifying the majority of component lipids.},
}
@article {pmid19243935,
year = {2009},
author = {Manikandan, M and Pasić, L and Kannan, V},
title = {Optimization of growth media for obtaining high-cell density cultures of halophilic archaea (family Halobacteriaceae) by response surface methodology.},
journal = {Bioresource technology},
volume = {100},
number = {12},
pages = {3107-3112},
doi = {10.1016/j.biortech.2009.01.033},
pmid = {19243935},
issn = {1873-2976},
mesh = {*Algorithms ; Bioreactors/*microbiology ; Cell Count ; Cell Culture Techniques/*methods ; Cell Proliferation ; Computer Simulation ; Culture Media/*chemistry/*metabolism ; Halobacteriaceae/*growth &amp; development ; *Models, Biological ; Quality Control ; },
abstract = {Optimization of media components for the growth and biomass production of Halobacterium salinarum VKMM 013 was carried out using response surface methodology. A second order quadratic model was estimated and media components were determined based on quadratic regression equation generated by model. These were 6.35 g L(-1) of KCl, 9.70 g L(-1) of MgSO(4), 13.38 g L(-1) of gelatin and 12.00 g L(-1) of soluble starch in nutrient broth supplemented with artificial seawater with 20% (w/v) of NaCl. In these optimal conditions, the obtained cell concentration of 0.746 g L(-1) dry weight was in agreement with the predicted cell concentration. The optimized media significantly shortened the time required for cell culture to reach the stationary phase while providing a nearly 2.4-fold increase in biomass production. Furthermore, in cell cultures of three other halophilic archaea the use of optimized media enhanced growth rate and provided high-cell density.},
}
@article {pmid19236445,
year = {2009},
author = {Jia, Z and Conrad, R},
title = {Bacteria rather than Archaea dominate microbial ammonia oxidation in an agricultural soil.},
journal = {Environmental microbiology},
volume = {11},
number = {7},
pages = {1658-1671},
doi = {10.1111/j.1462-2920.2009.01891.x},
pmid = {19236445},
issn = {1462-2920},
mesh = {Ammonia/*metabolism ; Archaea/*classification/genetics/isolation &amp; purification/*metabolism ; Bacteria/*classification/genetics/isolation &amp; purification/*metabolism ; Carbon Dioxide/metabolism ; Carbon Isotopes/metabolism ; DNA, Archaeal/chemistry/genetics ; DNA, Bacterial/chemistry/genetics ; Ecosystem ; Molecular Sequence Data ; Oxidation-Reduction ; Oxidoreductases/genetics ; Polymorphism, Genetic ; Sequence Analysis, DNA ; *Soil Microbiology ; Staining and Labeling/methods ; },
abstract = {Agricultural ecosystems annually receive approximately 25% of the global nitrogen input, much of which is oxidized at least once by ammonia-oxidizing prokaryotes to complete the nitrogen cycle. Recent discoveries have expanded the known ammonia-oxidizing prokaryotes from the domain Bacteria to Archaea. However, in the complex soil environment it remains unclear whether ammonia oxidation is exclusively or predominantly linked to Archaea as implied by their exceptionally high abundance. Here we show that Bacteria rather than Archaea functionally dominate ammonia oxidation in an agricultural soil, despite the fact that archaeal versus bacterial amoA genes are numerically more dominant. In soil microcosms, in which ammonia oxidation was stimulated by ammonium and inhibited by acetylene, activity change was paralleled by abundance change of bacterial but not of archaeal amoA gene copy numbers. Molecular fingerprinting of amoA genes also coupled ammonia oxidation activity with bacterial but not archaeal amoA gene patterns. DNA-stable isotope probing demonstrated CO(2) assimilation by Bacteria rather than Archaea. Our results indicate that Archaea were not important for ammonia oxidation in the agricultural soil tested.},
}
@article {pmid19232671,
year = {2009},
author = {You, J and Das, A and Dolan, EM and Hu, Z},
title = {Ammonia-oxidizing archaea involved in nitrogen removal.},
journal = {Water research},
volume = {43},
number = {7},
pages = {1801-1809},
doi = {10.1016/j.watres.2009.01.016},
pmid = {19232671},
issn = {0043-1354},
mesh = {Ammonia/*metabolism ; Archaea/*metabolism ; Nitrogen/*isolation &amp; purification ; Oxidation-Reduction ; },
abstract = {Ammonia oxidation is critical to global nitrogen cycling and is often thought to be driven only by ammonia-oxidizing bacteria. The recent finding of new ammonia-oxidizing organisms belonging to the archaeal domain challenges this perception. Two major microbial groups are now believed to be involved in ammonia oxidation: chemolithotrophic ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA). Candidatus "Nitrosopumilus maritimus", the first isolated ammonia-oxidizing archaeon from a tropical marine aquarium tank, representative of the ubiquitous marine group 1 Crenarchaeota, contains putative genes for all three subunits (amoA, amoB, and amoC) of ammonia monooxygenase, the key enzyme responsible for ammonia oxidation. In this article, important concepts of the nitrogen cycle, ammonia oxidation processes, ammonia-oxidizing organisms, and their physiology are described. AOA are found to thrive in various habitats including hot/thermal springs, marine and fresh waters, soils, and wastewater treatment systems, where they may outnumber their counterpart, AOB. Various molecular tools have been applied to study AOB and AOA and determine their abundance and community structure changes from natural and engineered systems. The presence of AOA in activated sludge opens new opportunities for elucidating its role of ammonia removal in wastewater treatment plants and wetlands. Several significant questions related to AOA research have been raised to evoke reader involvement for broadening future studies.},
}
@article {pmid19224924,
year = {2009},
author = {Grininger, M and Staudt, H and Johansson, P and Wachtveitl, J and Oesterhelt, D},
title = {Dodecin is the key player in flavin homeostasis of archaea.},
journal = {The Journal of biological chemistry},
volume = {284},
number = {19},
pages = {13068-13076},
pmid = {19224924},
issn = {0021-9258},
mesh = {Archaeal Proteins/*chemistry/genetics/*metabolism ; Binding Sites ; Blotting, Western ; Carrier Proteins/*chemistry/genetics/*metabolism ; Crystallography, X-Ray ; Flavins/*metabolism ; Halobacterium salinarum/genetics/growth &amp; development/*metabolism ; Light ; Membrane Transport Proteins/chemistry/*metabolism ; RNA, Messenger/genetics/metabolism ; Reverse Transcriptase Polymerase Chain Reaction ; },
abstract = {Flavins are employed to transform physical input into biological output signals. In this function, flavins catalyze a variety of light-induced reactions and redox processes. However, nature also provides flavoproteins with the ability to uncouple the mediation of signals. Such proteins are the riboflavin-binding proteins (RfBPs) with their function to store riboflavin for fast delivery of FMN and FAD. Here we present in vitro and in vivo data showing that the recently discovered archaeal dodecin is an RfBP, and we reveal that riboflavin storage is not restricted to eukaryotes. However, the function of the prokaryotic RfBP dodecin seems to be adapted to the requirement of a monocellular organism. While in eukaryotes RfBPs are involved in trafficking riboflavin, and dodecin is responsible for the flavin homeostasis of the cell. Although only 68 amino acids in length, dodecin is of high functional versatility in neutralizing riboflavin to protect the cellular environment from uncontrolled flavin reactivity. Besides the predominant ultrafast quenching of excited states, dodecin prevents light-induced riboflavin reactivity by the selective degradation of riboflavin to lumichrome. Coordinated with the high affinity for lumichrome, the directed degradation reaction is neutral to the cellular environment and provides an alternative pathway for suppressing uncontrolled riboflavin reactivity. Intriguingly, the different structural and functional properties of a homologous bacterial dodecin suggest that dodecin has different roles in different kingdoms of life.},
}
@article {pmid19223325,
year = {2009},
author = {Hooper, SD and Anderson, IJ and Pati, A and Dalevi, D and Mavromatis, K and Kyrpides, NC},
title = {Integration of phenotypic metadata and protein similarity in Archaea using a spectral bipartitioning approach.},
journal = {Nucleic acids research},
volume = {37},
number = {7},
pages = {2096-2104},
pmid = {19223325},
issn = {1362-4962},
mesh = {*Algorithms ; Archaeal Proteins/chemistry/*classification/genetics ; Cluster Analysis ; Phenotype ; Phylogeny ; Sequence Analysis, Protein ; Software ; },
abstract = {In order to simplify and meaningfully categorize large sets of protein sequence data, it is commonplace to cluster proteins based on the similarity of those sequences. However, it quickly becomes clear that the sequence flexibility allowed a given protein varies significantly among different protein families. The degree to which sequences are conserved not only differs for each protein family, but also is affected by the phylogenetic divergence of the source organisms. Clustering techniques that use similarity thresholds for protein families do not always allow for these variations and thus cannot be confidently used for applications such as automated annotation and phylogenetic profiling. In this work, we applied a spectral bipartitioning technique to all proteins from 53 archaeal genomes. Comparisons between different taxonomic levels allowed us to study the effects of phylogenetic distances on cluster structure. Likewise, by associating functional annotations and phenotypic metadata with each protein, we could compare our protein similarity clusters with both protein function and associated phenotype. Our clusters can be analyzed graphically and interactively online.},
}
@article {pmid19218417,
year = {2009},
author = {Goberna, M and Insam, H and Franke-Whittle, IH},
title = {Effect of biowaste sludge maturation on the diversity of thermophilic bacteria and archaea in an anaerobic reactor.},
journal = {Applied and environmental microbiology},
volume = {75},
number = {8},
pages = {2566-2572},
pmid = {19218417},
issn = {1098-5336},
support = {P 20001/FWF_/Austrian Science Fund FWF/Austria ; },
mesh = {Anaerobiosis ; Archaea/*classification/genetics/isolation &amp; purification ; Bacteria/*classification/genetics/isolation &amp; purification ; *Biodiversity ; Bioreactors/*microbiology ; DNA, Archaeal/chemistry/genetics ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Fatty Acids, Volatile/metabolism ; Genes, rRNA ; Hydrogen-Ion Concentration ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; Sewage/*microbiology ; },
abstract = {Prokaryotic diversity was investigated near the inlet and outlet of a plug-flow reactor. After analyzing 800 clones, 50 bacterial and 3 archaeal phylogenetic groups were defined. Clostridia (>92%) dominated among bacteria and Methanoculleus (>90%) among archaea. Significant changes in pH and volatile fatty acids did not invoke a major shift in the phylogenetic groups. We suggest that the environmental filter imposed by the saline conditions (20 g liter(-1)) selected a stable community of halotolerant and halophilic prokaryotes.},
}
@article {pmid19215775,
year = {2009},
author = {Evguenieva-Hackenberg, E and Klug, G},
title = {RNA degradation in Archaea and Gram-negative bacteria different from Escherichia coli.},
journal = {Progress in molecular biology and translational science},
volume = {85},
number = {},
pages = {275-317},
doi = {10.1016/S0079-6603(08)00807-6},
pmid = {19215775},
issn = {1877-1173},
mesh = {Archaea/*genetics/metabolism ; Archaeal Proteins/metabolism ; Bacterial Proteins/metabolism ; Base Sequence ; Escherichia coli/*genetics/metabolism ; Exosomes/metabolism ; Molecular Sequence Data ; *RNA Stability ; },
abstract = {Exoribonucleolytic and endoribonucleolytic activities are important for controlled degradation of RNA and contribute to the regulation of gene expression at the posttranscriptional level by influencing the half-lives of specific messenger RNAs. The RNA half-lives are determined by the characteristics of the RNA substrates and by the availability and the properties of the involved proteins-ribonucleases and assisting polypeptides. Much is known about RNA degradation in Eukarya and Bacteria, but there is limited information about RNA-degrading enzymes and RNA destabilizing or stabilizing elements in the domain of the Archaea. The recent progress in the understanding of the structure and function of the archaeal exosome, a protein complex with RNA-degrading and RNA-tailing capabilities, has given some first insights into the mechanisms of RNA degradation in the third domain of life and into the evolution of RNA-degrading enzymes. Moreover, other archaeal RNases with degrading potential have been described and a new mechanism for protection of the 5'-end of RNA in Archaea was discovered. Here, we summarize the current knowledge on RNA degradation in the Archaea. Additionally, RNA degradation mechanisms in Rhodobacter capsulatus and Pseudomonas syringae are compared to those in the major model organism for Gram-negatives, Escherichia coli, which dominates our view on RNA degradation in Bacteria.},
}
@article {pmid19215203,
year = {2009},
author = {Fendrihan, S and Bérces, A and Lammer, H and Musso, M and Rontó, G and Polacsek, TK and Holzinger, A and Kolb, C and Stan-Lotter, H},
title = {Investigating the effects of simulated martian ultraviolet radiation on Halococcus dombrowskii and other extremely halophilic archaebacteria.},
journal = {Astrobiology},
volume = {9},
number = {1},
pages = {104-112},
pmid = {19215203},
issn = {1557-8070},
support = {P 16260/FWF_/Austrian Science Fund FWF/Austria ; P 18256/FWF_/Austrian Science Fund FWF/Austria ; },
mesh = {Archaea/cytology/*radiation effects/ultrastructure ; Crystallization ; Culture Media ; Dose-Response Relationship, Radiation ; *Extraterrestrial Environment ; Geologic Sediments/microbiology ; Halococcus/cytology/*radiation effects/ultrastructure ; *Mars ; Microbial Viability/radiation effects ; Salts/chemistry ; *Space Simulation ; *Ultraviolet Rays ; },
abstract = {The isolation of viable extremely halophilic archaea from 250-million-year-old rock salt suggests the possibility of their long-term survival under desiccation. Since halite has been found on Mars and in meteorites, haloarchaeal survival of martian surface conditions is being explored. Halococcus dombrowskii H4 DSM 14522(T) was exposed to UV doses over a wavelength range of 200-400 nm to simulate martian UV flux. Cells embedded in a thin layer of laboratory-grown halite were found to accumulate preferentially within fluid inclusions. Survival was assessed by staining with the LIVE/DEAD kit dyes, determining colony-forming units, and using growth tests. Halite-embedded cells showed no loss of viability after exposure to about 21 kJ/m(2), and they resumed growth in liquid medium with lag phases of 12 days or more after exposure up to 148 kJ/m(2). The estimated D(37) (dose of 37 % survival) for Hcc. dombrowskii was > or = 400 kJ/m(2). However, exposure of cells to UV flux while in liquid culture reduced D(37) by 2 orders of magnitude (to about 1 kJ/m(2)); similar results were obtained with Halobacterium salinarum NRC-1 and Haloarcula japonica. The absorption of incoming light of shorter wavelength by color centers resulting from defects in the halite crystal structure likely contributed to these results. Under natural conditions, haloarchaeal cells become embedded in salt upon evaporation; therefore, dispersal of potential microscopic life within small crystals, perhaps in dust, on the surface of Mars could resist damage by UV radiation.},
}
@article {pmid19212429,
year = {2009},
author = {Narihiro, T and Terada, T and Ohashi, A and Wu, JH and Liu, WT and Araki, N and Kamagata, Y and Nakamura, K and Sekiguchi, Y},
title = {Quantitative detection of culturable methanogenic archaea abundance in anaerobic treatment systems using the sequence-specific rRNA cleavage method.},
journal = {The ISME journal},
volume = {3},
number = {5},
pages = {522-535},
doi = {10.1038/ismej.2009.4},
pmid = {19212429},
issn = {1751-7370},
mesh = {Anaerobiosis ; Archaea/*classification/*isolation &amp; purification/metabolism ; Cluster Analysis ; DNA, Archaeal/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Genes, rRNA ; Methane/*metabolism ; Molecular Sequence Data ; Oligonucleotide Probes/genetics ; Phylogeny ; RNA, Archaeal/genetics/*metabolism ; RNA, Ribosomal/*metabolism ; RNA, Ribosomal, 16S/genetics ; Ribonuclease H/metabolism ; Sensitivity and Specificity ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; Sewage/*microbiology ; },
abstract = {A method based on sequence-specific cleavage of rRNA with ribonuclease H was used to detect almost all known cultivable methanogens in anaerobic biological treatment systems. To do so, a total of 40 scissor probes in different phylogeny specificities were designed or modified from previous studies, optimized for their specificities under digestion conditions with 32 methanogenic reference strains, and then applied to detect methanogens in sludge samples taken from 6 different anaerobic treatment processes. Among these processes, known aceticlastic and hydrogenotrophic groups of methanogens from the families Methanosarcinaceae, Methanosaetaceae, Methanobacteriaceae, Methanothermaceae and Methanocaldococcaceae could be successfully detected and identified down to the genus level. Within the aceticlastic methanogens, the abundances of mesophilic Methanosaeta accounted for 5.7-48.5% of the total archaeal populations in mesophilic anaerobic processes, and those of Methanosarcina represented 41.7% of the total archaeal populations in thermophilic processes. For hydrogenotrophic methanogens, members of the Methanomicrobiales, Methanobrevibacter and Methanobacterium were detected in mesophilic processes (1.2-17.2%), whereas those of Methanothermobacter, Methanothermaceae and Methanocaldococcaceae were detected in thermophilic process (2.0-4.8%). Overall results suggested that those hierarchical scissor probes developed could be effective for rapid and possibly on-site monitoring of targeted methanogens in different microbial environments.},
}
@article {pmid19205349,
year = {2009},
author = {Ishino, S and Ishino, Y},
title = {[DNA transactions in Archaea].},
journal = {Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme},
volume = {54},
number = {2},
pages = {141-147},
pmid = {19205349},
issn = {0039-9450},
mesh = {Archaea/*genetics ; Archaeal Proteins/physiology ; *DNA Repair ; *DNA Replication ; DNA, Cruciform ; DNA-Binding Proteins/physiology ; DNA-Directed DNA Polymerase ; Genome, Archaeal/genetics ; Origin Recognition Complex/physiology ; },
}
@article {pmid19205348,
year = {2009},
author = {Ohshima, T and Sakuraba, H},
title = {[Unique sugar metabolism of hyperthermophilic Archaea].},
journal = {Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme},
volume = {54},
number = {2},
pages = {134-140},
pmid = {19205348},
issn = {0039-9450},
mesh = {Adenosine Diphosphate/metabolism ; Adenosine Triphosphate/biosynthesis ; Archaea/genetics/*metabolism ; Energy Metabolism ; Glucokinase/genetics/physiology ; *Glycolysis/genetics ; Phosphofructokinases/genetics/physiology ; },
}
@article {pmid19205347,
year = {2009},
author = {Koga, Y},
title = {[Unique characteristics of membrane lipids of Archaea and evolution of two domains of life].},
journal = {Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme},
volume = {54},
number = {2},
pages = {127-133},
pmid = {19205347},
issn = {0039-9450},
mesh = {Archaea/*cytology/metabolism ; *Evolution, Molecular ; Glycerophosphates ; Isomerism ; *Membrane Lipids/biosynthesis/chemistry ; Molecular Conformation ; Protein Structure, Tertiary ; },
}
@article {pmid19205345,
year = {2009},
author = {Nunoura, T and Takai, K},
title = {[Archaea plays important roles in global material circulation].},
journal = {Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme},
volume = {54},
number = {2},
pages = {114-119},
pmid = {19205345},
issn = {0039-9450},
mesh = {Aerobiosis ; Ammonia/metabolism ; Anaerobiosis ; Archaea/metabolism/*physiology ; Biomass ; Geologic Sediments/microbiology ; Methane/metabolism ; Oxidation-Reduction ; Soil Microbiology ; },
}
@article {pmid19205344,
year = {2009},
author = {Yamagishi, A},
title = {[Domain Archaea and evolution of life].},
journal = {Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme},
volume = {54},
number = {2},
pages = {108-113},
pmid = {19205344},
issn = {0039-9450},
mesh = {*Archaea/genetics ; *Biological Evolution ; Genome, Archaeal ; RNA, Ribosomal, 16S ; },
}
@article {pmid19205343,
year = {2009},
author = {Ishino, Y},
title = {[Archaea].},
journal = {Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme},
volume = {54},
number = {2},
pages = {101-107},
pmid = {19205343},
issn = {0039-9450},
mesh = {*Archaea/enzymology/genetics/physiology ; Biological Evolution ; DNA Polymerase I ; Genome, Archaeal ; },
}
@article {pmid19196275,
year = {2009},
author = {Schauss, K and Focks, A and Leininger, S and Kotzerke, A and Heuer, H and Thiele-Bruhn, S and Sharma, S and Wilke, BM and Matthies, M and Smalla, K and Munch, JC and Amelung, W and Kaupenjohann, M and Schloter, M and Schleper, C},
title = {Dynamics and functional relevance of ammonia-oxidizing archaea in two agricultural soils.},
journal = {Environmental microbiology},
volume = {11},
number = {2},
pages = {446-456},
doi = {10.1111/j.1462-2920.2008.01783.x},
pmid = {19196275},
issn = {1462-2920},
mesh = {Ammonia/*metabolism ; Animals ; Anti-Infective Agents/pharmacology ; Archaea/*growth &amp; development/*metabolism ; Bacteria/drug effects/growth &amp; development/metabolism ; Manure/microbiology ; Oxidation-Reduction ; *Soil Microbiology ; Sulfadiazine/pharmacology ; Swine ; },
abstract = {Crucial steps in geochemical cycles are in many cases performed by more than one group of microorganisms, but the significance of this functional redundancy with respect to ecosystem functioning is poorly understood. Ammonia-oxidizing archaea (AOA) and their bacterial counterparts (AOB) are a perfect system to address this question: although performing the same transformation step, they belong to well-separated phylogenetic groups. Using pig manure amended with different concentrations of sulfadiazine (SDZ), an antibiotic that is frequently used in veterinary medicine, it was possible to affect AOB and AOA to different degrees. Addition of manure stimulated growth of AOB in both soils and, interestingly, also growth of AOA was considerably stimulated in one of the soils. The antibiotic treatments decreased the manure effect notably on AOB, whereas AOA were affected to a lower extent. Model calculations concerning the respective proportions of AOA and AOB in ammonia oxidation indicate a substantial contribution of AOA in one of the soils that further increased under the influence of SDZ, hence indicating functional redundancy between AOA and AOB.},
}
@article {pmid19190180,
year = {2009},
author = {Fujishima, K and Sugahara, J and Kikuta, K and Hirano, R and Sato, A and Tomita, M and Kanai, A},
title = {Tri-split tRNA is a transfer RNA made from 3 transcripts that provides insight into the evolution of fragmented tRNAs in archaea.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {106},
number = {8},
pages = {2683-2687},
pmid = {19190180},
issn = {1091-6490},
mesh = {Alternative Splicing ; Archaea/*genetics ; Base Sequence ; *Evolution, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; RNA, Transfer/chemistry/*genetics ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Homology, Nucleic Acid ; },
abstract = {Transfer RNA (tRNA) is essential for decoding the genome sequence into proteins. In Archaea, previous studies have revealed unique multiple intron-containing tRNAs and tRNAs that are encoded on 2 separate genes, so-called split tRNAs. Here, we discovered 10 fragmented tRNA genes in the complete genome of the hyperthermoacidophilic Archaeon Caldivirga maquilingensis that are individually transcribed and further trans-spliced to generate all of the missing tRNAs encoding glycine, alanine, and glutamate. Notably, the 3 mature tRNA(Gly)'s with synonymous codons are created from 1 constitutive 3' half transcript and 4 alternatively switching transcripts, representing tRNA made from a total of 3 transcripts named a "tri-split tRNA." Expression and nucleotide sequences of 10 split tRNA genes and their joined tRNA products were experimentally verified. The intervening sequences of split tRNA have high identity to tRNA intron sequences located at the same positions in intron-containing tRNAs in related Thermoproteales species. This suggests that an evolutionary relationship between intron-containing and split tRNAs exists. Our findings demonstrate the first example of split tRNA genes in a free-living organism and a unique tri-split tRNA gene that provides further insight into the evolution of fragmented tRNAs.},
}
@article {pmid19187134,
year = {2009},
author = {Dang, H and Li, J and Zhang, X and Li, T and Tian, F and Jin, W},
title = {Diversity and spatial distribution of amoA-encoding archaea in the deep-sea sediments of the tropical West Pacific Continental Margin.},
journal = {Journal of applied microbiology},
volume = {106},
number = {5},
pages = {1482-1493},
doi = {10.1111/j.1365-2672.2008.04109.x},
pmid = {19187134},
issn = {1365-2672},
mesh = {Archaea/*genetics/*metabolism ; Archaeal Proteins/*genetics/metabolism ; Base Sequence ; DNA, Archaeal/chemistry/isolation &amp; purification ; Demography ; Gene Expression Regulation, Archaeal/*physiology ; Gene Library ; Genetic Variation ; Geologic Sediments/*microbiology ; Molecular Sequence Data ; Pacific Ocean ; Phylogeny ; Tropical Climate ; },
abstract = {AIMS: The ecological characteristics of the deep-sea amoA-encoding archaea (AEA) are largely unsolved. Our aim was to study the diversity, structure and distribution of the AEA community in the sediments of the tropical West Pacific Continental Margin, to develop a general view of the AEA biogeography in the deep-sea extreme environment.<br><br>METHODS AND RESULTS: Archaeal amoA clone libraries were constructed. Diverse and novel amoA sequences were identified, with the Bohol Sea, Bashi Strait and Sibuyan Sea harbouring the highest and the Bicol Shelf the lowest AEA diversity. Phylogenetic and statistical analyses illustrate a heterogeneous distribution of the AEA community, probably caused by the differential distribution of the terrestrial or estuarine AEA in the various sampling sites.<br><br>CONCLUSIONS: The deep-sea sedimentary environments potentially harbour diverse and novel AEA in the tropical West Pacific Continental Margin. The stations in the Philippine inland seas (including station 3043) may represent AEA assemblages with various terrestrial influences and the stations connected directly to the open Philippine Sea may represent marine environment-dominant AEA assemblages.<br><br>Our study indicates the potential importance of geological and climatic events in the transport of terrestrial micro-organisms to the deep-sea sedimentary environments, almost totally neglected previously.},
}
@article {pmid19161858,
year = {2008},
author = {Slomovic, S and Portnoy, V and Schuster, G},
title = {Detection and characterization of polyadenylated RNA in Eukarya, Bacteria, Archaea, and organelles.},
journal = {Methods in enzymology},
volume = {447},
number = {},
pages = {501-520},
doi = {10.1016/S0076-6879(08)02224-6},
pmid = {19161858},
issn = {1557-7988},
mesh = {Archaea/genetics ; Bacteria/*genetics ; Cloning, Molecular ; DNA, Complementary ; Eukaryotic Cells ; Humans ; Organelles/*genetics ; RNA, Messenger/chemistry/*isolation &amp; purification ; Reverse Transcriptase Polymerase Chain Reaction ; },
abstract = {The posttranscriptional addition of poly(A) extensions to RNA is a phenomenon common to almost all organisms. In eukaryotes, a stable poly(A) tail is added to the 3'-end of most nucleus-encoded mRNAs, as well as to mitochondrion-encoded transcripts in animal cells. In prokaryotes and organelles, RNA molecules are polyadenylated as part of a polyadenylation-stimulated RNA degradation pathway. In addition, polyadenylation of nucleus-encoded transcripts in yeast and human cells was recently reported to promote RNA degradation. Not only homopolymeric poly(A) tails, composed exclusively of adenosines, but also heteropolymeric poly(A)-rich extensions, which include the other three nucleotides as well, have been observed in bacteria, archaea, chloroplasts, and human cells. In most instances, the detection of nonabundant truncated transcripts with posttranscriptionally added poly(A) or poly(A)-rich extensions serves as a telltale sign of the presence of a polyadenylation-stimulated RNA degradation pathway. In this chapter, we describe several methods found to be efficient in detecting and characterizing polyadenylated transcripts in bacteria, archaea, organelles, and nucleus-encoded RNAs. Detailed protocols for the oligo(dT)- and circularized reverse transcription (cRT) PCR methods, as well as the ribonuclease digestion method, are outlined, along with examples of results obtained with these techniques.},
}
@article {pmid19161853,
year = {2008},
author = {Evguenieva-Hackenberg, E and Wagner, S and Klug, G},
title = {In vivo and in vitro studies of RNA degrading activities in Archaea.},
journal = {Methods in enzymology},
volume = {447},
number = {},
pages = {381-416},
doi = {10.1016/S0076-6879(08)02219-2},
pmid = {19161853},
issn = {1557-7988},
mesh = {Archaea/genetics/*metabolism ; Blotting, Northern ; Dactinomycin/pharmacology ; Immunoprecipitation ; Molecular Weight ; RNA, Archaeal/genetics/isolation &amp; purification/*metabolism ; Recombination, Genetic ; Sulfolobus solfataricus/*genetics ; Transcription, Genetic/drug effects ; },
abstract = {Controlled degradation of RNA is important for the regulation of gene expression in Bacteria and Eukarya, but information about these processes is limited in the domain of Archaea. To address this, we studied the half-life of different mRNAs in halophilic Archaea after blocking transcription with actinomycin D. We found that the stability of mRNAs of the gvp operons in Haloferax mediterranei varies under different growth conditions. To understand regulated mRNA decay in Archaea, we need to identify stability determinants within mRNAs and proteins, mainly ribonucleases (RNases), which recognize these determinants. First, we wanted to identify archaeal RNases independently of their sequence similarity to known RNases from Bacteria and Eukarya. To this end we performed fractionation of proteins from Halobacterium salinarum and tested the fractions for RNase activity with an internally labeled in vitro-synthesized mRNA. After three purification steps, we isolated an endoribonucleolytically active protein with similarities to the eukaryotic initiation factor 5A. Further characterization was performed with recombinant halobacterial IF-5A, which was purified from H. salinarum or Escherichia coli. Mutational analysis confirmed unambiguously its RNase activity. In another study, we aimed to purify a double-strand-specific endoribonuclease from Sulfolobus solfataricus. Seven purification steps led to the isolation of two different dehydrogenases with RNase properties. Interestingly, their RNase activity resembled that of aIF-5A and of highly diluted RNase A. RNA was cleaved preferentially between C and A nucleotides in single-stranded regions, and the activity was inhibited at MgCl(2) concentrations >5 mM and at KCl concentrations >200 mM. However, it was possible to distinguish the activity of the archaeal proteins from the activity of RNase A. In a different approach, we used a bioinformatics prediction of the archaeal exosome to purify this protein complex from S. solfataricus. Isolation by coimmunoprecipitation revealed the presence of four orthologs of eukaryotic exosomal subunits and at least one archaea-specific subunit. We characterized the S. solfataricus exosome as a major enzyme involved in phosphorolytic RNA degradation and in RNA polyadenylation. Here we describe in detail the techniques used to achieve these results.},
}
@article {pmid19161834,
year = {2008},
author = {Maquat, LE and Arraiano, CM},
title = {RNA turnover in prokaryotes, archaea and organelles. Preface.},
journal = {Methods in enzymology},
volume = {447},
number = {},
pages = {xxiii-xxiv},
doi = {10.1016/S0076-6879(08)02229-5},
pmid = {19161834},
issn = {1557-7988},
mesh = {Archaea/*metabolism ; Electrophoresis, Gel, Two-Dimensional ; Oligonucleotide Array Sequence Analysis ; Organelles/*metabolism ; Prokaryotic Cells/*metabolism ; RNA/*metabolism ; Tandem Mass Spectrometry ; },
}
@article {pmid19146579,
year = {2009},
author = {Lyimo, TJ and Pol, A and Jetten, MS and den Camp, HJ},
title = {Diversity of methanogenic archaea in a mangrove sediment and isolation of a new Methanococcoides strain.},
journal = {FEMS microbiology letters},
volume = {291},
number = {2},
pages = {247-253},
doi = {10.1111/j.1574-6968.2008.01464.x},
pmid = {19146579},
issn = {1574-6968},
mesh = {Archaea/*classification/genetics/isolation &amp; purification/metabolism ; *Biodiversity ; DNA, Archaeal/genetics ; DNA, Ribosomal/genetics ; Geologic Sediments/*microbiology ; Methanol/*metabolism ; Methanosarcinaceae/classification/genetics/*isolation &amp; purification/metabolism ; Methylamines/metabolism ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Mangrove forest sediments produce significant amounts of methane, but the diversity of methanogenic archaea is not well known at present. Therefore, 16S rRNA gene libraries were made using archaea-specific primers and DNA extracted directly from Tanzanian mangrove sediment samples as a template. Analysis of sequence data showed phylotypes closely related to cultivated methylotrophic methanogenic archaea from the marine environment, or distantly related to acetoclastic and hydrogenotrophic methanogenic archaea. In an attempt to isolate relevant methanogenic archaea, we succeeded in obtaining a new mesophilic methylotrophic methanogenic archaeon (strain MM1) capable of utilizing methanol and methylated amines as the only substrates. Under optimum conditions, the cells of strain MM1 exhibited a high specific growth rate (mu) of 0.21+/-0.03 (i.e. doubling time of 3.2 h) on both methanol and trimethylamine. The 16S rRNA gene sequence of strain MM1 clustered with five environmental clones, indicating that MM1 is an important methanogenic methylotroph in mangrove sediments. Based on physiological and phylogenetic analyses, strain MM1 is proposed to be included in the species of Methanococcoides methylutens.},
}
@article {pmid19143611,
year = {2009},
author = {Haldenby, S and White, MF and Allers, T},
title = {RecA family proteins in archaea: RadA and its cousins.},
journal = {Biochemical Society transactions},
volume = {37},
number = {Pt 1},
pages = {102-107},
doi = {10.1042/BST0370102},
pmid = {19143611},
issn = {1470-8752},
support = {BB/C501641/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Archaea/*metabolism ; Archaeal Proteins/chemistry/genetics/*metabolism ; DNA-Binding Proteins/chemistry/genetics/*metabolism ; Phylogeny ; Rad51 Recombinase/chemistry/metabolism ; Rec A Recombinases/chemistry/*metabolism ; Sequence Homology, Amino Acid ; },
abstract = {Recombinases of the RecA family are essential for homologous recombination and underpin genome stability, by promoting the repair of double-stranded DNA breaks and the rescue of collapsed DNA replication forks. Until now, our understanding of homologous recombination has relied on studies of bacterial and eukaryotic model organisms. Archaea provide new opportunities to study how recombination operates in a lineage distinct from bacteria and eukaryotes. In the present paper, we focus on RadA, the archaeal RecA family recombinase, and its homologues in archaea and other domains. On the basis of phylogenetic analysis, we propose that a family of archaeal proteins with a single RecA domain, which are currently annotated as KaiC, be renamed aRadC.},
}
@article {pmid19143605,
year = {2009},
author = {Woodman, IL and Bolt, EL},
title = {Molecular biology of Hel308 helicase in archaea.},
journal = {Biochemical Society transactions},
volume = {37},
number = {Pt 1},
pages = {74-78},
doi = {10.1042/BST0370074},
pmid = {19143605},
issn = {1470-8752},
support = {BB/D526602/1IW//Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Amino Acid Sequence ; Archaea/*enzymology ; DNA Helicases/chemistry/*genetics/metabolism ; DNA Repair ; DNA Replication ; Molecular Sequence Data ; Recombination, Genetic/genetics ; Sequence Homology, Amino Acid ; },
abstract = {Hel308 is an SF2 (superfamily 2) helicase with clear homologues in metazoans and archaea, but not in fungi or bacteria. Evidence from biochemistry and genetics implicates Hel308 in remodelling compromised replication forks. In the last 4 years, significant advances have been made in understanding the biochemistry of archaeal Hel308, most recently through atomic structures from cren- and eury-archaea. These are good templates for SF2 helicase function more generally, highlighting co-ordinated actions of accessory domains around RecA folds. We review the emerging molecular biology of Hel308, drawing together ideas of how it may contribute to genome stability through the control of recombination, with reference to paradigms developed in bacteria.},
}
@article {pmid19143601,
year = {2009},
author = {de Koning, B and Blombach, F and Wu, H and Brouns, SJ and van der Oost, J},
title = {Role of multiprotein bridging factor 1 in archaea: bridging the domains?.},
journal = {Biochemical Society transactions},
volume = {37},
number = {Pt 1},
pages = {52-57},
doi = {10.1042/BST0370052},
pmid = {19143601},
issn = {1470-8752},
mesh = {Archaea/genetics/*metabolism ; Archaeal Proteins/*chemistry/genetics/*metabolism ; Phylogeny ; Protein Structure, Tertiary ; Stress, Physiological ; Transcriptional Activation ; },
abstract = {MBF1 (multiprotein bridging factor 1) is a highly conserved protein in archaea and eukaryotes. It was originally identified as a mediator of the eukaryotic transcription regulator BmFTZ-F1 (Bombyx mori regulator of fushi tarazu). MBF1 was demonstrated to enhance transcription by forming a bridge between distinct regulatory DNA-binding proteins and the TATA-box-binding protein. MBF1 consists of two parts: a C-terminal part that contains a highly conserved helix-turn-helix, and an N-terminal part that shows a clear divergence: in eukaryotes, it is a weakly conserved flexible domain, whereas, in archaea, it is a conserved zinc-ribbon domain. Although its function in archaea remains elusive, its function as a transcriptional co-activator has been deduced from thorough studies of several eukaryotic proteins, often indicating a role in stress response. In addition, MBF1 was found to influence translation fidelity in yeast. Genome context analysis of mbf1 in archaea revealed conserved clustering in the crenarchaeal branch together with genes generally involved in gene expression. It points to a role of MBF1 in transcription and/or translation. Experimental data are required to allow comparison of the archaeal MBF1 with its eukaryotic counterpart.},
}
@article {pmid19143600,
year = {2009},
author = {Large, AT and Goldberg, MD and Lund, PA},
title = {Chaperones and protein folding in the archaea.},
journal = {Biochemical Society transactions},
volume = {37},
number = {Pt 1},
pages = {46-51},
doi = {10.1042/BST0370046},
pmid = {19143600},
issn = {1470-8752},
support = {BB/F002483/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Archaea/*metabolism ; Archaeal Proteins/chemistry/genetics/metabolism ; Chaperonins/chemistry/genetics/metabolism ; HSP70 Heat-Shock Proteins/metabolism ; Molecular Chaperones/chemistry/genetics/*metabolism ; Protein Binding ; *Protein Folding ; },
abstract = {A survey of archaeal genomes for the presence of homologues of bacterial and eukaryotic chaperones reveals several interesting features. All archaea contain chaperonins, also known as Hsp60s (where Hsp is heat-shock protein). These are more similar to the type II chaperonins found in the eukaryotic cytosol than to the type I chaperonins found in bacteria, mitochondria and chloroplasts, although some archaea also contain type I chaperonin homologues, presumably acquired by horizontal gene transfer. Most archaea contain several genes for these proteins. Our studies on the type II chaperonins of the genetically tractable archaeon Haloferax volcanii have shown that only one of the three genes has to be present for the organisms to grow, but that there is some evidence for functional specialization between the different chaperonin proteins. All archaea also possess genes for prefoldin proteins and for small heat-shock proteins, but they generally lack genes for Hsp90 and Hsp100 homologues. Genes for Hsp70 (DnaK) and Hsp40 (DnaJ) homologues are only found in a subset of archaea. Thus chaperone-assisted protein folding in archaea is likely to display some unique features when compared with that in eukaryotes and bacteria, and there may be important differences in the process between euryarchaea and crenarchaea.},
}
@article {pmid19143597,
year = {2009},
author = {Hecker, A and Graille, M and Madec, E and Gadelle, D and Le Cam, E and van Tilbergh, H and Forterre, P},
title = {The universal Kae1 protein and the associated Bud32 kinase (PRPK), a mysterious protein couple probably essential for genome maintenance in Archaea and Eukarya.},
journal = {Biochemical Society transactions},
volume = {37},
number = {Pt 1},
pages = {29-35},
doi = {10.1042/BST0370029},
pmid = {19143597},
issn = {1470-8752},
mesh = {Amino Acid Sequence ; Archaea/*genetics/*metabolism ; Archaeal Proteins/*metabolism ; DNA-(Apurinic or Apyrimidinic Site) Lyase/metabolism ; DNA-Binding Proteins/metabolism ; Eukaryotic Cells/*metabolism ; Genome, Archaeal/*genetics ; Molecular Sequence Data ; Protein Kinases/chemistry/*metabolism ; Protein Structure, Secondary ; Pyrococcus abyssi/enzymology ; },
abstract = {The similarities between essential molecular mechanisms in Archaea and Eukarya make it possible to discover, using comparative genomics, new fundamental mechanisms conserved between these two domains. We are studying a complex of two proteins conserved in Archaea and Eukarya whose precise biological role and biochemical function remain unknown. One of them is a universal protein known as Kae1 (kinase-asociated endopeptidase 1). The second protein is a serine/threonine kinase corresponding to the proteins Bud32 in Saccharomyces cerevisiae and PRPK (p53-related protein kinase) in humans. The genes encoding the archaeal orthologues of Kae1 and PRPK are either contiguous or even fused in many archaeal genomes. In S. cerevisiae, Kae1 and Bud32 (PRPK) belong to a chromatin-associated complex [KEOPS (kinase, endopeptidase and other proteins of small size)/EKC (endopeptidase-like kinase chromatin-associated)] that is essential for telomere elongation and transcription of essential genes. Although Kae1 is annotated as O-sialoglycoprotein endopeptidase in most genomes, we found that the Kae1 protein from Pyrococcus abyssi has no protease activity, but is an atypical DNA-binding protein with an AP (apurinic) lyase activity. The structure of the fusion protein from Methanocaldococcus jannaschii revealed that Kae1 maintains the ATP-binding site of Bud32 [corrected] in an inactive configuration. We have in fact found that Kae1 inhibits the kinase activity of Bud32 (PRPK) in vitro. Understanding the precise biochemical function and biological role of these two proteins (which are probably essential for genome maintenance) remains a major challenge.},
}
@article {pmid19139072,
year = {2009},
author = {Muller, S and Urban, A and Hecker, A and Leclerc, F and Branlant, C and Motorin, Y},
title = {Deficiency of the tRNATyr:Psi 35-synthase aPus7 in Archaea of the Sulfolobales order might be rescued by the H/ACA sRNA-guided machinery.},
journal = {Nucleic acids research},
volume = {37},
number = {4},
pages = {1308-1322},
pmid = {19139072},
issn = {1362-4962},
mesh = {Amino Acid Motifs ; Amino Acid Sequence ; Base Sequence ; Intramolecular Transferases/*chemistry/genetics/metabolism ; Molecular Sequence Data ; Pyrococcus abyssi/enzymology ; RNA Precursors/chemistry/metabolism ; RNA, Archaeal/*chemistry/metabolism ; RNA, Small Nucleolar/chemistry ; RNA, Transfer, Tyr/*chemistry/metabolism ; Recombinant Proteins/metabolism ; Ribonucleoproteins/metabolism ; Sulfolobales/*enzymology/genetics ; Sulfolobus solfataricus/enzymology ; RNA, Small Untranslated ; },
abstract = {Up to now, Psi formation in tRNAs was found to be catalysed by stand-alone enzymes. By computational analysis of archaeal genomes we detected putative H/ACA sRNAs, in four Sulfolobales species and in Aeropyrum pernix, that might guide Psi 35 formation in pre-tRNA(Tyr)(GUA). This modification is achieved by Pus7p in eukarya. The validity of the computational predictions was verified by in vitro reconstitution of H/ACA sRNPs using the identified Sulfolobus solfataricus H/ACA sRNA. Comparison of Pus7-like enzymes encoded by archaeal genomes revealed amino acid substitutions in motifs IIIa and II in Sulfolobales and A. pernix Pus7-like enzymes. These conserved RNA:Psi-synthase- motifs are essential for catalysis. As expected, the recombinant Pyrococcus abyssi aPus7 was fully active and acted at positions 35 and 13 and other positions in tRNAs, while the recombinant S. solfataricus aPus7 was only found to have a poor activity at position 13. We showed that the presence of an A residue 3' to the target U residue is required for P. abyssi aPus7 activity, and that this is not the case for the reconstituted S. solfataricus H/ACA sRNP. In agreement with the possible formation of Psi 35 in tRNA(Tyr)(GUA) by aPus7 in P. abyssi and by an H/ACA sRNP in S. solfataricus, the A36G mutation in the P. abyssi tRNA(Tyr)(GUA) abolished Psi 35 formation when using P. abyssi extract, whereas the A36G substitution in the S. solfataricus pre-tRNA(Tyr) did not affect Psi 35 formation in this RNA when using an S. solfataricus extract.},
}
@article {pmid19138688,
year = {2009},
author = {Barnwal, RP and Jobby, MK and Devi, KM and Sharma, Y and Chary, KV},
title = {Solution structure and calcium-binding properties of M-crystallin, a primordial betagamma-crystallin from archaea.},
journal = {Journal of molecular biology},
volume = {386},
number = {3},
pages = {675-689},
doi = {10.1016/j.jmb.2008.12.058},
pmid = {19138688},
issn = {1089-8638},
mesh = {Amino Acid Sequence ; Archaeal Proteins/*chemistry/*metabolism ; Calcium/*metabolism ; Cations, Divalent/*metabolism ; Crystallins/*chemistry/*metabolism ; Magnetic Resonance Spectroscopy ; Methanosarcina/chemistry ; Models, Molecular ; Molecular Sequence Data ; Protein Binding ; Protein Structure, Tertiary ; Sequence Alignment ; },
abstract = {The lens betagamma-crystallin superfamily has many diverse but topologically related members belonging to various taxa. Based on structural topology, these proteins are considered to be evolutionarily related to lens crystallins, suggesting their origin from a common ancestor. Proteins with betagamma-crystallin domains, although found in some eukaryotes and eubacteria, have not yet been reported in archaea. Sequence searches in the genome of the archaebacterium Methanosarcina acetivorans revealed the presence of a protein annotated as a betagamma-crystallin family protein, named M-crystallin. Solution structure of this protein indicates a typical betagamma-crystallin fold with a paired Greek-key motif. Among the known structures of betagamma-crystallin members, M-crystallin was found to be structurally similar to the vertebrate lens betagamma-crystallins. The Ca(2+)-binding properties of this primordial protein are somewhat more similar to those of vertebrate betagamma-crystallins than to those of bacterial homologues. These observations, taken together, suggest that amphibian and vertebrate betagamma-crystallin domains are evolutionarily more related to archaeal homologues than to bacterial homologues. Additionally, identification of a betagamma-crystallin homologue in archaea allows us to demonstrate the presence of this domain in all the three domains of life.},
}
@article {pmid19124572,
year = {2009},
author = {Nesbø, CL and Bapteste, E and Curtis, B and Dahle, H and Lopez, P and Macleod, D and Dlutek, M and Bowman, S and Zhaxybayeva, O and Birkeland, NK and Doolittle, WF},
title = {The genome of Thermosipho africanus TCF52B: lateral genetic connections to the Firmicutes and Archaea.},
journal = {Journal of bacteriology},
volume = {191},
number = {6},
pages = {1974-1978},
pmid = {19124572},
issn = {1098-5530},
mesh = {Archaea/classification/*genetics ; Bacteria/classification/*genetics/isolation &amp; purification ; *Gene Transfer, Horizontal ; *Genome, Bacterial ; Molecular Sequence Data ; Phylogeny ; },
abstract = {Lateral gene transfers (LGT) (also called horizontal gene transfers) have been a major force shaping the Thermosipho africanus TCF52B genome, whose sequence we describe here. Firmicutes emerge as the principal LGT partner. Twenty-six percent of phylogenetic trees suggest LGT with this group, while 13% of the open reading frames indicate LGT with Archaea.},
}
@article {pmid19120632,
year = {2008},
author = {Nettmann, E and Bergmann, I and Mundt, K and Linke, B and Klocke, M},
title = {Archaea diversity within a commercial biogas plant utilizing herbal biomass determined by 16S rDNA and mcrA analysis.},
journal = {Journal of applied microbiology},
volume = {105},
number = {6},
pages = {1835-1850},
doi = {10.1111/j.1365-2672.2008.03949.x},
pmid = {19120632},
issn = {1365-2672},
mesh = {Animals ; Archaea/*classification/genetics/isolation &amp; purification ; Biodiversity ; *Bioreactors ; Cattle ; DNA Primers ; DNA, Archaeal/analysis/isolation &amp; purification ; DNA, Ribosomal/analysis/genetics ; Gene Library ; Manure/*microbiology ; Oxidoreductases/*genetics ; Polymerase Chain Reaction/methods ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Zea mays ; },
abstract = {AIMS: The Archaea diversity was evaluated in an agricultural biogas plant supplied with cattle liquid manure and maize silage under mesophilic conditions.<br><br>METHODS AND RESULTS: Two different genes (16S rRNA; methyl-coenzyme-M-reductase, MCR) targeted by three different PCR primer sets were selected and used for the construction of three clone libraries comprising between 104 and 118 clones. The clone libraries were analysed by restriction fragment polymorphism (RFLP). Between 11 and 31 operational taxonomic units (OTUs) were detected and assigned to orders Methanomicrobiales, Methanosarcinales and Methanobacteriales. Over 70% of all Archaea OTUs belong to the order Methanomicrobiales which mostly include hydrogenotrophic methanogens. Acetotrophic methanogens were detected in minor rates. Similar relative values were obtained by a quantitative real-time PCR analysis.<br><br>CONCLUSIONS: The results implied that in this biogas plant the most of the methane formation resulted from the conversion of H(2) and CO(2).<br><br>This study reports, for the first time, a molecular analysis of the archaeal community in this type of agricultural biogas plants. Therein the hydrogenotrophic methanogenesis seems to be the major pathway of methane formation. These results are in contrast with the common thesis that in biogas fermentations the primary substrate for methanogenesis is acetate.},
}
@article {pmid19114531,
year = {2009},
author = {Robertson, CE and Spear, JR and Harris, JK and Pace, NR},
title = {Diversity and stratification of archaea in a hypersaline microbial mat.},
journal = {Applied and environmental microbiology},
volume = {75},
number = {7},
pages = {1801-1810},
pmid = {19114531},
issn = {1098-5336},
mesh = {Archaea/*classification/genetics/*isolation &amp; purification ; *Biodiversity ; DNA, Archaeal/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Genes, rRNA ; Geologic Sediments/*microbiology ; Mexico ; Molecular Sequence Data ; Pacific Ocean ; Phylogeny ; RNA, Archaeal/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; },
abstract = {The Guerrero Negro (GN) hypersaline microbial mats have become one focus for biogeochemical studies of stratified ecosystems. The GN mats are found beneath several of a series of ponds of increasing salinity that make up a solar saltern fed from Pacific Ocean water pumped from the Laguna Ojo de Liebre near GN, Baja California Sur, Mexico. Molecular surveys of the laminated photosynthetic microbial mat below the fourth pond in the series identified an enormous diversity of bacteria in the mat, but archaea have received little attention. To determine the bulk contribution of archaeal phylotypes to the pond 4 study site, we determined the phylogenetic distribution of archaeal rRNA gene sequences in PCR libraries based on nominally universal primers. The ratios of bacterial/archaeal/eukaryotic rRNA genes, 90%/9%/1%, suggest that the archaeal contribution to the metabolic activities of the mat may be significant. To explore the distribution of archaea in the mat, sequences derived using archaeon-specific PCR primers were surveyed in 10 strata of the 6-cm-thick mat. The diversity of archaea overall was substantial albeit less than the diversity observed previously for bacteria. Archaeal diversity, mainly euryarchaeotes, was highest in the uppermost 2 to 3 mm of the mat and decreased rapidly with depth, where crenarchaeotes dominated. Only 3% of the sequences were specifically related to known organisms including methanogens. While some mat archaeal clades corresponded with known chemical gradients, others did not, which is likely explained by heretofore-unrecognized gradients. Some clades did not segregate by depth in the mat, indicating broad metabolic repertoires, undersampling, or both.},
}
@article {pmid19107199,
year = {2008},
author = {Wang, F and Xiao, J and Pan, L and Yang, M and Zhang, G and Jin, S and Yu, J},
title = {A systematic survey of mini-proteins in bacteria and archaea.},
journal = {PloS one},
volume = {3},
number = {12},
pages = {e4027},
pmid = {19107199},
issn = {1932-6203},
mesh = {Archaea/*metabolism ; Archaeal Proteins/*analysis/chemistry/metabolism ; Bacteria/*metabolism ; Bacterial Proteins/*analysis/chemistry/metabolism ; Computational Biology ; Conserved Sequence ; Databases, Protein ; Evolution, Molecular ; Models, Biological ; Phylogeny ; Protein Structure, Tertiary ; Sequence Alignment ; },
abstract = {BACKGROUND: Mini-proteins, defined as polypeptides containing no more than 100 amino acids, are ubiquitous in prokaryotes and eukaryotes. They play significant roles in various biological processes, and their regulatory functions gradually attract the attentions of scientists. However, the functions of the majority of mini-proteins are still largely unknown due to the constraints of experimental methods and bioinformatic analysis.<br><br>In this article, we extracted a total of 180,879 mini-proteins from the annotations of 532 sequenced genomes, including 491 strains of Bacteria and 41 strains of Archaea. The average proportion of mini-proteins among all genomic proteins is approximately 10.99%, but different strains exhibit remarkable fluctuations. These mini-proteins display two notable characteristics. First, the majority are species-specific proteins with an average proportion of 58.79% among six representative phyla. Second, an even larger proportion (70.03% among all strains) is hypothetical proteins. However, a fraction of highly conserved hypothetical proteins potentially play crucial roles in organisms. Among mini-proteins with known functions, it seems that regulatory and metabolic proteins are more abundant than essential structural proteins. Furthermore, domains in mini-proteins seem to have greater distributions in Bacteria than Eukarya. Analysis of the evolutionary progression of these domains reveals that they have diverged to new patterns from a single ancestor.<br><br>CONCLUSIONS/SIGNIFICANCE: Mini-proteins are ubiquitous in bacterial and archaeal species and play significant roles in various functions. The number of mini-proteins in each genome displays remarkable fluctuation, likely resulting from the differential selective pressures that reflect the respective life-styles of the organisms. The answers to many questions surrounding mini-proteins remain elusive and need to be resolved experimentally.},
}
@article {pmid19105819,
year = {2008},
author = {Brochier-Armanet, C and Gribaldo, S and Forterre, P},
title = {A DNA topoisomerase IB in Thaumarchaeota testifies for the presence of this enzyme in the last common ancestor of Archaea and Eucarya.},
journal = {Biology direct},
volume = {3},
number = {},
pages = {54},
pmid = {19105819},
issn = {1745-6150},
mesh = {Archaea/*enzymology ; Bacteria/enzymology ; DNA Topoisomerases, Type I/chemistry/*genetics ; Eukaryotic Cells/*enzymology ; Likelihood Functions ; *Phylogeny ; Protein Structure, Tertiary ; Sequence Alignment ; Viruses/enzymology ; },
abstract = {DNA topoisomerase IB (TopoIB) was thought for a long time to be a eukaryotic specific enzyme. A shorter version was then found in viruses and later on in several bacteria, but not in archaea. Here, we show that a eukaryotic-like TopoIB is present in the recently sequenced genomes of two archaea of the newly proposed phylum Thaumarchaeota. Phylogenetic analyses suggest that a TopoIB was present in the last common ancestor of Archaea and Eucarya. This finding indicates that the last common ancestor of Archaea and Eucarya may have harboured a DNA genome.},
}
@article {pmid19091507,
year = {2009},
author = {Wang, Y and Ke, X and Wu, L and Lu, Y},
title = {Community composition of ammonia-oxidizing bacteria and archaea in rice field soil as affected by nitrogen fertilization.},
journal = {Systematic and applied microbiology},
volume = {32},
number = {1},
pages = {27-36},
doi = {10.1016/j.syapm.2008.09.007},
pmid = {19091507},
issn = {0723-2020},
mesh = {Ammonia/metabolism ; Archaea/classification/enzymology/genetics/*growth &amp; development ; Bacteria/classification/enzymology/genetics/*growth &amp; development ; Electrophoresis/methods ; *Fertilizers ; Molecular Sequence Data ; Nitrogen/metabolism/pharmacology ; Nitrosomonadaceae/enzymology/genetics/isolation &amp; purification ; Nitrosomonas/enzymology/genetics/isolation &amp; purification ; Oryza/*growth &amp; development ; Oxidation-Reduction ; Oxidoreductases/*genetics/metabolism ; Polymorphism, Restriction Fragment Length ; Sequence Analysis, DNA ; *Soil Microbiology ; Urea/metabolism/*pharmacology ; },
abstract = {Little information is available on the ecology of ammonia-oxidizing bacteria (AOB) and archaea (AOA) in flooded rice soils. Consequently, a microcosm experiment was conducted to determine the effect of nitrogen fertilizer on the composition of AOB and AOA communities in rice soil by using molecular analyses of ammonia monooxygenase gene (amoA) fragments. Experimental treatments included three levels of N (urea) fertilizer, i.e. 50, 100 and 150 mgNkg(-1) soil. Soil samples were operationally divided into four fractions: surface soil, bulk soil deep layer, rhizosphere and washed root material. NH(4)(+)-N was the dominant form of N in soil porewater and increased with N fertilization. Cloning and sequencing of amoA gene fragments showed that the AOB community in the rice soil consisted of three major groups, i.e. Nitrosomonas communis cluster, Nitrosospira cluster 3a and cluster 3b. The sequences related to Nitrosomonas were predominant. There was a clear effect of N fertilizer and soil depth on AOB community composition based on terminal restriction fragment length polymorphism fingerprinting. Nitrosomonas appeared to be more abundant in the potentially oxic or micro-oxic fractions, including surface soil, rhizosphere and washed root material, than the deep layer of anoxic bulk soil. Furthermore, Nitrosomonas increased relatively in the partially oxic fractions and that of Nitrosospira decreased with the increasing application of N fertilizer. However, AOA community composition remained unchanged according to the denaturing gradient gel electrophoresis analyses.},
}
@article {pmid19087619,
year = {2008},
author = {Li, CL and Jiang, YT and Zhang, MZ and Liang, JP},
title = {[Identification and quantitative analysis of Archaea involved in periodontal disease].},
journal = {Zhonghua kou qiang yi xue za zhi = Zhonghua kouqiang yixue zazhi = Chinese journal of stomatology},
volume = {43},
number = {10},
pages = {589-591},
pmid = {19087619},
issn = {1002-0098},
mesh = {Aggressive Periodontitis/microbiology ; Archaea/classification/genetics/*isolation &amp; purification ; Case-Control Studies ; Chronic Periodontitis/microbiology ; DNA, Bacterial/genetics ; Dental Plaque/*microbiology ; Humans ; Periodontal Diseases/*microbiology ; RNA, Ribosomal, 16S/genetics ; },
abstract = {OBJECTIVE: To make qualitative and quantitative analysis of Archaea in subgingival plaque sample and to investigate the relationship between periodontal disease and Archaea.<br><br>METHODS: Subgingival plaque was collected from 23 patients with aggressive periodontitis, 29 with chronic periodontitis, 35 with plaque-induced gingivitis and 38 healthy controls. Qualitative and quantitative analysis of methanogenic archaea was performed by amplification of the 16S rRNA genes in the DNA extracted from the plaque samples.<br><br>RESULTS: Archaea were found in 65% of aggressive periodontitis patients, 72% of chronic periodontitis, 26% of gingivitis and zero of healthy subjects. Quantitative analysis showed the average abundance of archaeal 16S rRNA gene in Archaea-positive patients was different among the three groups. The average 16S rRNA gene copy number from per microg wet plaque was 6.66 x 10(6) in aggressive periodontitis sufferers, 4.47 x 10(6) in chronic periodontitis and 1.78 x 10(6) in gingivitis groups. The prevalence of Archaea and the average Archaea 16S rRNA gene numbers in periodontitis groups were higher than those in gingivitis group (P < 0.05).<br><br>CONCLUSIONS: This suggests that Archaea may be implicated as causative agents for periodontitis.},
}
@article {pmid19060138,
year = {2009},
author = {Jørgensen, MG and Pandey, DP and Jaskolska, M and Gerdes, K},
title = {HicA of Escherichia coli defines a novel family of translation-independent mRNA interferases in bacteria and archaea.},
journal = {Journal of bacteriology},
volume = {191},
number = {4},
pages = {1191-1199},
pmid = {19060138},
issn = {1098-5530},
support = {/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Archaea/*enzymology ; Escherichia coli/genetics/*metabolism ; Escherichia coli Proteins/genetics/*metabolism ; Gene Expression Regulation, Bacterial/physiology ; Multigene Family ; Protein Biosynthesis ; RNA, Messenger/metabolism ; },
abstract = {Toxin-antitoxin (TA) loci are common in free-living bacteria and archaea. TA loci encode a stable toxin that is neutralized by a metabolically unstable antitoxin. The antitoxin can be either a protein or an antisense RNA. So far, six different TA gene families, in which the antitoxins are proteins, have been identified. Recently, Makarova et al. (K. S. Makarova, N. V. Grishin, and E. V. Koonin, Bioinformatics 22:2581-2584, 2006) suggested that the hicAB loci constitute a novel TA gene family. Using the hicAB locus of Escherichia coli K-12 as a model system, we present evidence that supports this inference: expression of the small HicA protein (58 amino acids [aa]) induced cleavage in three model mRNAs and tmRNA. Concomitantly, the global rate of translation was severely reduced. Using tmRNA as a substrate, we show that HicA-induced cleavage does not require the target RNA to be translated. Expression of HicB (145 aa) prevented HicA-mediated inhibition of cell growth. These results suggest that HicB neutralizes HicA and therefore functions as an antitoxin. As with other antitoxins (RelB and MazF), HicB could resuscitate cells inhibited by HicA, indicating that ectopic production of HicA induces a bacteriostatic rather than a bactericidal condition. Nutrient starvation induced strong hicAB transcription that depended on Lon protease. Mining of 218 prokaryotic genomes revealed that hicAB loci are abundant in bacteria and archaea.},
}
@article {pmid19054742,
year = {2008},
author = {Dyer, BD and Kahn, MJ and Leblanc, MD},
title = {Classification and regression tree (CART) analyses of genomic signatures reveal sets of tetramers that discriminate temperature optima of archaea and bacteria.},
journal = {Archaea (Vancouver, B.C.)},
volume = {2},
number = {3},
pages = {159-167},
pmid = {19054742},
issn = {1472-3646},
mesh = {*Archaea/classification/genetics ; *Bacteria/classification/genetics ; Computational Biology/*methods ; Evolution, Molecular ; Genome, Archaeal ; Genome, Bacterial ; Genomics ; Hot Temperature ; *Regression Analysis ; Repetitive Sequences, Nucleic Acid/*genetics ; *Temperature ; },
abstract = {Classification and regression tree (CART) analysis was applied to genome-wide tetranucleotide frequencies (genomic signatures) of 195 archaea and bacteria. Although genomic signatures have typically been used to classify evolutionary divergence, in this study, convergent evolution was the focus. Temperature optima for most of the organisms examined could be distinguished by CART analyses of tetranucleotide frequencies. This suggests that pervasive (nonlinear) qualities of genomes may reflect certain environmental conditions (such as temperature) in which those genomes evolved. The predominant use of GAGA and AGGA as the discriminating tetramers in CART models suggests that purine-loading and codon biases of thermophiles may explain some of the results.},
}
@article {pmid19043046,
year = {2009},
author = {Ferguson, T and Soares, JA and Lienard, T and Gottschalk, G and Krzycki, JA},
title = {RamA, a protein required for reductive activation of corrinoid-dependent methylamine methyltransferase reactions in methanogenic archaea.},
journal = {The Journal of biological chemistry},
volume = {284},
number = {4},
pages = {2285-2295},
pmid = {19043046},
issn = {0021-9258},
support = {GM070663/GM/NIGMS NIH HHS/United States ; },
mesh = {Adenosine Triphosphate/metabolism ; Archaeal Proteins/genetics/isolation &amp; purification/*metabolism ; Corrinoids/*metabolism ; Enzyme Activation ; Ferredoxins/genetics/metabolism ; Genome, Archaeal/genetics ; Methanosarcina barkeri/*metabolism ; Methylation ; Methyltransferases/*metabolism ; Time Factors ; },
abstract = {Archaeal methane formation from methylamines is initiated by distinct methyltransferases with specificity for monomethylamine, dimethylamine, or trimethylamine. Each methylamine methyltransferase methylates a cognate corrinoid protein, which is subsequently demethylated by a second methyltransferase to form methyl-coenzyme M, the direct methane precursor. Methylation of the corrinoid protein requires reduction of the central cobalt to the highly reducing and nucleophilic Co(I) state. RamA, a 60-kDa monomeric iron-sulfur protein, was isolated from Methanosarcina barkeri and is required for in vitro ATP-dependent reductive activation of methylamine:CoM methyl transfer from all three methylamines. In the absence of the methyltransferases, highly purified RamA was shown to mediate the ATP-dependent reductive activation of Co(II) corrinoid to the Co(I) state for the monomethylamine corrinoid protein, MtmC. The ramA gene is located near a cluster of genes required for monomethylamine methyltransferase activity, including MtbA, the methylamine-specific CoM methylase and the pyl operon required for co-translational insertion of pyrrolysine into the active site of methylamine methyltransferases. RamA possesses a C-terminal ferredoxin-like domain capable of binding two tetranuclear iron-sulfur proteins. Mutliple ramA homologs were identified in genomes of methanogenic Archaea, often encoded near methyltrophic methyltransferase genes. RamA homologs are also encoded in a diverse selection of bacterial genomes, often located near genes for corrinoid-dependent methyltransferases. These results suggest that RamA mediates reductive activation of corrinoid proteins and that it is the first functional archetype of COG3894, a family of redox proteins of unknown function.},
}
@article {pmid19037758,
year = {2008},
author = {Luijsterburg, MS and White, MF and van Driel, R and Dame, RT},
title = {The major architects of chromatin: architectural proteins in bacteria, archaea and eukaryotes.},
journal = {Critical reviews in biochemistry and molecular biology},
volume = {43},
number = {6},
pages = {393-418},
doi = {10.1080/10409230802528488},
pmid = {19037758},
issn = {1549-7798},
support = {//Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Animals ; Archaea/chemistry/genetics/*metabolism ; Bacteria/chemistry/genetics/*metabolism ; *Chromatin Assembly and Disassembly ; Chromosomes, Bacterial ; DNA/*metabolism ; DNA-Binding Proteins/chemistry/*metabolism ; Eukaryotic Cells/chemistry/*metabolism ; Genome ; Histones/metabolism ; Nucleosomes/metabolism ; },
abstract = {The genomic DNA of all organisms across the three kingdoms of life needs to be compacted and functionally organized. Key players in these processes are DNA supercoiling, macromolecular crowding and architectural proteins that shape DNA by binding to it. The architectural proteins in bacteria, archaea and eukaryotes generally do not exhibit sequence or structural conservation especially across kingdoms. Instead, we propose that they are functionally conserved. Most of these proteins can be classified according to their architectural mode of action: bending, wrapping or bridging DNA. In order for DNA transactions to occur within a compact chromatin context, genome organization cannot be static. Indeed chromosomes are subject to a whole range of remodeling mechanisms. In this review, we discuss the role of (i) DNA supercoiling, (ii) macromolecular crowding and (iii) architectural proteins in genome organization, as well as (iv) mechanisms used to remodel chromosome structure and to modulate genomic activity. We conclude that the underlying mechanisms that shape and remodel genomes are remarkably similar among bacteria, archaea and eukaryotes.},
}
@article {pmid19037244,
year = {2008},
author = {Agogué, H and Brink, M and Dinasquet, J and Herndl, GJ},
title = {Major gradients in putatively nitrifying and non-nitrifying Archaea in the deep North Atlantic.},
journal = {Nature},
volume = {456},
number = {7223},
pages = {788-791},
doi = {10.1038/nature07535},
pmid = {19037244},
issn = {1476-4687},
mesh = {Archaea/classification/enzymology/genetics/*physiology ; Atlantic Ocean ; *Biodiversity ; Carbon Dioxide/metabolism ; Crenarchaeota/physiology ; Gene Dosage ; Genetic Variation ; Molecular Sequence Data ; Nitrogen/*metabolism ; Oxidoreductases/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; },
abstract = {Aerobic nitrification of ammonia to nitrite and nitrate is a key process in the oceanic nitrogen cycling mediated by prokaryotes. Apart from Bacteria belonging to the beta- and gamma-Proteobacteria involved in the first nitrification step, Crenarchaeota have recently been recognized as main drivers of the oxidation of ammonia to nitrite in soil as well as in the ocean, as indicated by the dominance of archaeal ammonia monooxygenase (amoA) genes over bacterial amoA. Evidence is accumulating that archaeal amoA genes are common in a wide range of marine systems. Essentially, all these reports focused on surface and mesopelagic (200-1,000 m depth) waters, where ammonia concentrations are higher than in waters below 1,000 m depth. However, Crenarchaeota are also abundant in the water column below 1,000 m, where ammonia concentrations are extremely low. Here we show that, throughout the North Atlantic Ocean, the abundance of archaeal amoA genes decreases markedly from subsurface waters to 4,000 m depth, and from subpolar to equatorial deep waters, leading to pronounced vertical and latitudinal gradients in the ratio of archaeal amoA to crenarchaeal 16S ribosomal RNA (rRNA) genes. The lack of significant copy numbers of amoA genes and the very low fixation rates of dark carbon dioxide in the bathypelagic North Atlantic suggest that most bathypelagic Crenarchaeota are not autotrophic ammonia oxidizers: most likely, they utilize organic matter and hence live heterotrophically.},
}
@article {pmid19036786,
year = {2009},
author = {Benelli, D and Marzi, S and Mancone, C and Alonzi, T and la Teana, A and Londei, P},
title = {Function and ribosomal localization of aIF6, a translational regulator shared by archaea and eukarya.},
journal = {Nucleic acids research},
volume = {37},
number = {1},
pages = {256-267},
pmid = {19036786},
issn = {1362-4962},
mesh = {Archaeal Proteins/analysis/chemistry/*metabolism ; Base Sequence ; Binding Sites ; Cell Cycle ; Cloning, Molecular ; Eukaryotic Initiation Factors/chemistry ; Models, Molecular ; Molecular Sequence Data ; Prokaryotic Initiation Factors/analysis/chemistry/*metabolism ; *Protein Biosynthesis ; RNA, Ribosomal, 23S/chemistry/metabolism ; Ribosomal Proteins/metabolism ; Ribosome Subunits, Large, Archaeal/*metabolism ; Ribosomes/metabolism ; Sulfolobus solfataricus/*genetics/metabolism ; },
abstract = {The translation factor IF6 is shared by the Archaea and the Eukarya, but is not found in Bacteria. The properties of eukaryal IF6 (eIF6) have been extensively studied, but remain somewhat elusive. eIF6 behaves as a ribosome-anti-association factor and is involved in miRNA-mediated gene silencing; however, it also seems to participate in ribosome synthesis and export. Here we have determined the function and ribosomal localization of the archaeal (Sulfolobus solfataricus) IF6 homologue (aIF6). We find that aIF6 binds specifically to the 50S ribosomal subunits, hindering the formation of 70S ribosomes and strongly inhibiting translation. aIF6 is uniformly expressed along the cell cycle, but it is upregulated following both cold- and heat shock. The aIF6 ribosomal binding site lies in the middle of the 30-S interacting surface of the 50S subunit, including a number of critical RNA and protein determinants involved in subunit association. The data suggest that the IF6 protein evolved in the archaeal-eukaryal lineage to modulate translational efficiency under unfavourable environmental conditions, perhaps acquiring additional functions during eukaryotic evolution.},
}
@article {pmid19008417,
year = {2008},
author = {Samson, RY and Obita, T and Freund, SM and Williams, RL and Bell, SD},
title = {A role for the ESCRT system in cell division in archaea.},
journal = {Science (New York, N.Y.)},
volume = {322},
number = {5908},
pages = {1710-1713},
pmid = {19008417},
issn = {1095-9203},
support = {/WT_/Wellcome Trust/United Kingdom ; MC_U105184308/MRC_/Medical Research Council/United Kingdom ; 083639/Z/07/Z/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Adenosine Triphosphatases/chemistry/*metabolism ; Amino Acid Sequence ; Archaeal Proteins/chemistry/*metabolism ; Biological Evolution ; Cell Cycle ; *Cell Division ; Crystallography, X-Ray ; Molecular Sequence Data ; Peptides/chemistry/metabolism ; Protein Structure, Tertiary ; Sequence Alignment ; Sulfolobus/*cytology/genetics/*metabolism ; Sulfolobus acidocaldarius/*cytology/genetics/*metabolism ; Vesicular Transport Proteins/chemistry/metabolism ; },
abstract = {Archaea are prokaryotic organisms that lack endomembrane structures. However, a number of hyperthermophilic members of the Kingdom Crenarchaea, including members of the Sulfolobus genus, encode homologs of the eukaryotic endosomal sorting system components Vps4 and ESCRT-III (endosomal sorting complex required for transport-III). We found that Sulfolobus ESCRT-III and Vps4 homologs underwent regulation of their expression during the cell cycle. The proteins interacted and we established the structural basis of this interaction. Furthermore, these proteins specifically localized to the mid-cell during cell division. Overexpression of a catalytically inactive mutant Vps4 in Sulfolobus resulted in the accumulation of enlarged cells, indicative of failed cell division. Thus, the archaeal ESCRT system plays a key role in cell division.},
}
@article {pmid19007418,
year = {2009},
author = {Hechler, T and Pfeifer, F},
title = {Anaerobiosis inhibits gas vesicle formation in halophilic Archaea.},
journal = {Molecular microbiology},
volume = {71},
number = {1},
pages = {132-145},
doi = {10.1111/j.1365-2958.2008.06517.x},
pmid = {19007418},
issn = {1365-2958},
mesh = {*Anaerobiosis ; Archaeal Proteins/genetics/metabolism ; Culture Media ; Cytoplasmic Vesicles/*metabolism ; Gene Expression Regulation, Archaeal ; Haloferax mediterranei/genetics/*metabolism ; Haloferax volcanii/genetics/*metabolism ; Proteins/genetics/metabolism ; RNA, Archaeal/metabolism ; Transcription, Genetic ; },
abstract = {The effect of anaerobiosis on the gas vesicle formation was investigated in three Halobacterium salinarum strains, Haloferax mediterranei and in Haloferax volcanii transformants. All these strains significantly reduced gas vesicle formation or lacked these structures under anoxic conditions. When grown by arginine fermentation, Hbt. salinarum PHH4 lacked gas vesicles, whereas Hbt. salinarum PHH1 and NRC-1 contained 5-20 small gas vesicles arranged in two to three aggregates per cell instead of the 30-80 gas vesicles present under oxic conditions. The enlargement presumably stopped due to a depletion of Gvp proteins. Also Hfx. mediterranei and Hfx. volcanii transformants lacked gas vesicles under anoxic growth and yielded a 10-fold reduced gvp transcription. Even the gas vesicle-overproducing DeltaD transformants did not form gas vesicles under anoxic conditions, demonstrating that the repressing protein GvpD was not involved. The presence of large amounts of GvpA implied that the assembly of the gas vesicles was inhibited. When Hbt. salinarum PHH1 and NRC-1 were grown with dimethyl sulphoxide or trimethylamine N-oxid under anoxic conditions the number but not the size of gas vesicles was reduced. This was in contrast to the previously reported overproduction of gas vesicles in NRC-1 that turned out to depend on the citrate-containing medium used for growth.},
}
@article {pmid18988691,
year = {2009},
author = {Bagos, PG and Tsirigos, KD and Plessas, SK and Liakopoulos, TD and Hamodrakas, SJ},
title = {Prediction of signal peptides in archaea.},
journal = {Protein engineering, design &amp; selection : PEDS},
volume = {22},
number = {1},
pages = {27-35},
doi = {10.1093/protein/gzn064},
pmid = {18988691},
issn = {1741-0134},
mesh = {Archaea/genetics/*metabolism ; Archaeal Proteins/*chemistry/genetics ; Computational Biology/*methods ; Genome, Archaeal ; Markov Chains ; *Protein Sorting Signals/genetics ; Sensitivity and Specificity ; Sequence Analysis, Protein/*methods ; Software ; },
abstract = {Computational prediction of signal peptides (SPs) and their cleavage sites is of great importance in computational biology; however, currently there is no available method capable of predicting reliably the SPs of archaea, due to the limited amount of experimentally verified proteins with SPs. We performed an extensive literature search in order to identify archaeal proteins having experimentally verified SP and managed to find 69 such proteins, the largest number ever reported. A detailed analysis of these sequences revealed some unique features of the SPs of archaea, such as the unique amino acid composition of the hydrophobic region with a higher than expected occurrence of isoleucine, and a cleavage site resembling more the sequences of gram-positives with almost equal amounts of alanine and valine at the position-3 before the cleavage site and a dominant alanine at position-1, followed in abundance by serine and glycine. Using these proteins as a training set, we trained a hidden Markov model method that predicts the presence of the SPs and their cleavage sites and also discriminates such proteins from cytoplasmic and transmembrane ones. The method performs satisfactorily, yielding a 35-fold cross-validation procedure, a sensitivity of 100% and specificity 98.41% with the Matthews' correlation coefficient being equal to 0.964. This particular method is currently the only available method for the prediction of secretory SPs in archaea, and performs consistently and significantly better compared with other available predictors that were trained on sequences of eukaryotic or bacterial origin. Searching 48 completely sequenced archaeal genomes we identified 9437 putative SPs. The method, PRED-SIGNAL, and the results are freely available for academic users at http://bioinformatics.biol.uoa.gr/PRED-SIGNAL/ and we anticipate that it will be a valuable tool for the computational analysis of archaeal genomes.},
}
@article {pmid18987308,
year = {2008},
author = {Lindås, AC and Karlsson, EA and Lindgren, MT and Ettema, TJ and Bernander, R},
title = {A unique cell division machinery in the Archaea.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {105},
number = {48},
pages = {18942-18946},
pmid = {18987308},
issn = {1091-6490},
mesh = {Anti-Bacterial Agents/pharmacology ; Archaea/classification/*cytology/genetics/*physiology ; *Archaeal Proteins/genetics/metabolism ; Cell Division/drug effects/*physiology ; Microarray Analysis ; *Operon ; Sulfolobus acidocaldarius/cytology/drug effects/physiology ; Tunicamycin/pharmacology ; },
abstract = {In contrast to the cell division machineries of bacteria, euryarchaea, and eukaryotes, no division components have been identified in the second main archaeal phylum, Crenarchaeota. Here, we demonstrate that a three-gene operon, cdv, in the crenarchaeon Sulfolobus acidocaldarius, forms part of a unique cell division machinery. The operon is induced at the onset of genome segregation and division, and the Cdv proteins then polymerize between segregating nucleoids and persist throughout cell division, forming a successively smaller structure during constriction. The cdv operon is dramatically down-regulated after UV irradiation, indicating division inhibition in response to DNA damage, reminiscent of eukaryotic checkpoint systems. The cdv genes exhibit a complementary phylogenetic range relative to FtsZ-based archaeal division systems such that, in most archaeal lineages, either one or the other system is present. Two of the Cdv proteins, CdvB and CdvC, display homology to components of the eukaryotic ESCRT-III sorting complex involved in budding of luminal vesicles and HIV-1 virion release, suggesting mechanistic similarities and a common evolutionary origin.},
}
@article {pmid18984620,
year = {2008},
author = {Nomura, N and Nomura, Y and Sussman, D and Klein, D and Stoddard, BL},
title = {Recognition of a common rDNA target site in archaea and eukarya by analogous LAGLIDADG and His-Cys box homing endonucleases.},
journal = {Nucleic acids research},
volume = {36},
number = {22},
pages = {6988-6998},
pmid = {18984620},
issn = {1362-4962},
support = {R01 GM049857/GM/NIGMS NIH HHS/United States ; RL1 CA133833/CA/NCI NIH HHS/United States ; R01 GM49857/GM/NIGMS NIH HHS/United States ; },
mesh = {Archaea/*enzymology ; Archaeal Proteins/*chemistry ; Crystallography, X-Ray ; DNA, Ribosomal/*chemistry ; Endodeoxyribonucleases/*chemistry ; Models, Molecular ; },
abstract = {The presence of a homing endonuclease gene (HEG) within a microbial intron or intein empowers the entire element with the ability to invade genomic targets. The persistence of a homing endonuclease lineage depends in part on conservation of its DNA target site. One such rDNA sequence has been invaded both in archaea and in eukarya, by LAGLIDADG and His-Cys box homing endonucleases, respectively. The bases encoded by this target include a universally conserved ribosomal structure, termed helix 69 (H69) in the large ribosomal subunit. This region forms the 'B2a' intersubunit bridge to the small ribosomal subunit, contacts bound tRNA in the A- and P-sites, and acts as a trigger for ribosome disassembly through its interactions with ribosome recycling factor. We have determined the DNA-bound structure and specificity profile of an archaeal LAGLIDADG homing endonuclease (I-Vdi141I) that recognizes this target site, and compared its specificity with the analogous eukaryal His-Cys box endonuclease I-PpoI. These homodimeric endonuclease scaffolds have arrived at similar specificity profiles across their common biological target and analogous solutions to the problem of accommodating conserved asymmetries within the DNA sequence, but with differences at individual base pairs that are fine-tuned to the sequence conservation of archaeal versus eukaryal ribosomes.},
}
@article {pmid18973621,
year = {2008},
author = {Mosier, AC and Francis, CA},
title = {Relative abundance and diversity of ammonia-oxidizing archaea and bacteria in the San Francisco Bay estuary.},
journal = {Environmental microbiology},
volume = {10},
number = {11},
pages = {3002-3016},
doi = {10.1111/j.1462-2920.2008.01764.x},
pmid = {18973621},
issn = {1462-2920},
mesh = {Ammonia/*metabolism ; Archaea/*classification/genetics/isolation &amp; purification/*metabolism ; Archaeal Proteins/genetics ; Bacterial Proteins/genetics ; Betaproteobacteria/*classification/genetics/isolation &amp; purification/*metabolism ; *Biodiversity ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; Geologic Sediments/*microbiology ; Molecular Sequence Data ; Oxidation-Reduction ; Oxidoreductases/genetics ; Phylogeny ; Salts ; San Francisco ; Seawater/microbiology ; Sequence Analysis, DNA ; },
abstract = {Ammonia oxidation in marine and estuarine sediments plays a pivotal role in the cycling and removal of nitrogen. Recent reports have shown that the newly discovered ammonia-oxidizing archaea can be both abundant and diverse in aquatic and terrestrial ecosystems. In this study, we examined the abundance and diversity of ammonia-oxidizing archaea (AOA) and betaproteobacteria (beta-AOB) across physicochemical gradients in San Francisco Bay--the largest estuary on the west coast of the USA. In contrast to reports that AOA are far more abundant than beta-AOB in both terrestrial and marine systems, our quantitative PCR estimates indicated that beta-AOB amoA (encoding ammonia monooxygenase subunit A) copy numbers were greater than AOA amoA in most of the estuary. Ammonia-oxidizing archaea were only more pervasive than beta-AOB in the low-salinity region of the estuary. Both AOA and beta-AOB communities exhibited distinct spatial structure within the estuary. AOA amoA sequences from the north part of the estuary formed a large and distinct low-salinity phylogenetic group. The majority of the beta-AOB sequences were closely related to other marine/estuarine Nitrosomonas-like and Nitrosospira-like sequences. Both ammonia-oxidizer community composition and abundance were strongly correlated with salinity. Ammonia-oxidizing enrichment cultures contained AOA and beta-AOB amoA sequences with high similarity to environmental sequences. Overall, this study significantly enhances our understanding of estuarine ammonia-oxidizing microbial communities and highlights the environmental conditions and niches under which different AOA and beta-AOB phylotypes may thrive.},
}
@article {pmid18973620,
year = {2008},
author = {Prosser, JI and Nicol, GW},
title = {Relative contributions of archaea and bacteria to aerobic ammonia oxidation in the environment.},
journal = {Environmental microbiology},
volume = {10},
number = {11},
pages = {2931-2941},
doi = {10.1111/j.1462-2920.2008.01775.x},
pmid = {18973620},
issn = {1462-2920},
mesh = {Ammonia/*metabolism ; Archaea/genetics/*metabolism ; Bacteria/genetics/*metabolism ; *Environmental Microbiology ; Oxidation-Reduction ; },
abstract = {Traditionally, organisms responsible for major biogeochemical cycling processes have been determined by physiological characterization of environmental isolates in laboratory culture. Molecular techniques have, however, confirmed the widespread occurrence of abundant bacterial and archaeal groups with no cultivated representative, making it difficult to determine their ecosystem function. Until recently, ammonia oxidation, the first step in the globally important process of nitrification, was thought to be performed almost exclusively by bacteria. Metagenome studies, followed by laboratory isolation, then demonstrated the potential for significant ammonia oxidation by mesophilic crenarchaea, whose ecosystem function was previously unknown. Re-assessment of the role of bacteria in ammonia oxidation is now required and this article reviews the current evidence for the relative importance of bacteria and archaea. Much of this evidence is based on metagenomic analysis and molecular techniques for estimation of gene and gene transcript abundance, changes in ammonia oxidizer community structure during active nitrification and phylogeny of natural communities. These studies have been complemented by physiological characterization of a laboratory isolate and by incorporation of labelled substrates. Data from these studies provide increasingly convincing evidence for the importance of archaeal ammonia oxidizers in the global nitrogen cycle. They also highlight the need to re-assess the importance of ammonia-oxidizing bacteria, the requirement and limitations of molecular techniques in linking specific microbial groups to ecosystem function and the limitations of reliance on laboratory cultures.},
}
@article {pmid18956766,
year = {2008},
author = {Liu, T and Shen, Y and Liu, Q and Liu, B},
title = {[The unique Entner-Doudoroff (ED) glycolysis pathway of glucose in archaea--a review].},
journal = {Wei sheng wu xue bao = Acta microbiologica Sinica},
volume = {48},
number = {8},
pages = {1126-1131},
pmid = {18956766},
issn = {0001-6209},
mesh = {Archaea/enzymology/*metabolism ; Energy Metabolism ; Glucose/*metabolism ; *Glycolysis ; *Metabolic Networks and Pathways ; Phosphorylation ; },
abstract = {Glucose is degraded to pyruvate via the so called "central metabolic pathways" that play vital roles in the carbohydrate and energy metabolism of organisms. Some variances to the classical glycolytic pathways in bacteria and eukarya are presented in the glycolysis of archaea. Results from biochemical, genomic and metabolomic studies indicate that some novel and characteristic enzymes are involved in the archaeal Embden-Meyerhof (EM) and Entner-Doudoroff (ED) glycolysis pathway. The ED pathway in archaea is divided into two sub-routes-the semi-phosphorylative and non-hosphorylative Entner-Doudoroff pathways. The unique glycolysis pathway in archaea is different from those in bacteria and eukarya in metabolic route, enzyme, regulation site, and energy transformation. These characteristics show the ability of these extremophiles to evolve flexible metabolic pathways in the extreme life environment. We reviewed recent advances in the ED glycolytic pathway of archaeon concerning enzymes, regulation and energy transformation. The potentials of glycolysis pathway in archaea were also discussed.},
}
@article {pmid18956233,
year = {2009},
author = {Melkikh, AV and Seleznev, VD},
title = {Model of active transport of ions in archaea cells.},
journal = {Bulletin of mathematical biology},
volume = {71},
number = {2},
pages = {383-398},
doi = {10.1007/s11538-008-9366-6},
pmid = {18956233},
issn = {1522-9602},
mesh = {Archaea/*metabolism ; Biological Transport, Active/*physiology ; Cell Membrane Permeability/physiology ; Cytoplasm/microbiology/physiology ; Ion Transport/*physiology ; Membrane Potentials/physiology ; *Models, Biological ; },
abstract = {A mathematical model of the active transport of main ions in cells of archaebacteria has been constructed. A set of equations has been developed and solved for ion fluxes through the bacterium membrane. The model is based on the principle "one ion-one transport system." Considering experimental data, the major transport mechanism was determined for each ion and the balance equation was written on the basis of this mechanism in the stationary state. This allowed calculating values of the membrane potential and intracellular concentrations of the ions independently. The calculated values of the intracellular concentrations and resting potential are in qualitative agreement with the corresponding experimental values for cells of extremely halophilic archaea.},
}
@article {pmid18948295,
year = {2008},
author = {Koonin, EV and Wolf, YI},
title = {Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world.},
journal = {Nucleic acids research},
volume = {36},
number = {21},
pages = {6688-6719},
pmid = {18948295},
issn = {1362-4962},
support = {//Intramural NIH HHS/United States ; },
mesh = {Archaea/metabolism ; Bacteria/metabolism ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genes, Archaeal ; Genes, Bacterial ; *Genome, Archaeal ; *Genome, Bacterial ; Genomics ; Signal Transduction ; },
abstract = {The first bacterial genome was sequenced in 1995, and the first archaeal genome in 1996. Soon after these breakthroughs, an exponential rate of genome sequencing was established, with a doubling time of approximately 20 months for bacteria and approximately 34 months for archaea. Comparative analysis of the hundreds of sequenced bacterial and dozens of archaeal genomes leads to several generalizations on the principles of genome organization and evolution. A crucial finding that enables functional characterization of the sequenced genomes and evolutionary reconstruction is that the majority of archaeal and bacterial genes have conserved orthologs in other, often, distant organisms. However, comparative genomics also shows that horizontal gene transfer (HGT) is a dominant force of prokaryotic evolution, along with the loss of genetic material resulting in genome contraction. A crucial component of the prokaryotic world is the mobilome, the enormous collection of viruses, plasmids and other selfish elements, which are in constant exchange with more stable chromosomes and serve as HGT vehicles. Thus, the prokaryotic genome space is a tightly connected, although compartmentalized, network, a novel notion that undermines the 'Tree of Life' model of evolution and requires a new conceptual framework and tools for the study of prokaryotic evolution.},
}
@article {pmid18948294,
year = {2009},
author = {Lee, ZM and Bussema, C and Schmidt, TM},
title = {rrnDB: documenting the number of rRNA and tRNA genes in bacteria and archaea.},
journal = {Nucleic acids research},
volume = {37},
number = {Database issue},
pages = {D489-93},
pmid = {18948294},
issn = {1362-4962},
mesh = {Database Management Systems ; *Databases, Nucleic Acid ; *Genes, Archaeal ; *Genes, Bacterial ; *Genes, rRNA ; Genomics ; RNA, Ribosomal, 16S/genetics ; },
abstract = {A dramatic exception to the general pattern of single-copy genes in bacterial and archaeal genomes is the presence of 1-15 copies of each ribosomal RNA encoding gene. The original version of the Ribosomal RNA Database (rrnDB) cataloged estimates of the number of 16S rRNA-encoding genes; the database now includes the number of genes encoding each of the rRNAs (5S, 16S and 23S), an internally transcribed spacer region, and the number of tRNA genes. The rrnDB has been used largely by microbiologists to predict the relative rate at which microbial populations respond to favorable growth conditions, and to interpret 16S rRNA-based surveys of microbial communities. To expand the functionality of the rrnDB (http://ribosome.mmg.msu.edu/rrndb/index.php), the search engine has been redesigned to allow database searches based on 16S rRNA gene copy number, specific organisms or taxonomic subsets of organisms. The revamped database also computes average gene copy numbers for any collection of entries selected. Curation tools now permit rapid updates, resulting in an expansion of the database to include data for 785 bacterial and 69 archaeal strains. The rrnDB continues to serve as the authoritative, curated source that documents the phylogenetic distribution of rRNA and tRNA genes in microbial genomes.},
}
@article {pmid18844986,
year = {2008},
author = {Grosjean, H and Gaspin, C and Marck, C and Decatur, WA and de Crécy-Lagard, V},
title = {RNomics and Modomics in the halophilic archaea Haloferax volcanii: identification of RNA modification genes.},
journal = {BMC genomics},
volume = {9},
number = {},
pages = {470},
pmid = {18844986},
issn = {1471-2164},
support = {R01 GM019351/GM/NIGMS NIH HHS/United States ; GM19351/GM/NIGMS NIH HHS/United States ; },
mesh = {Genes, rRNA ; *Genomics ; Haloferax volcanii/*genetics ; Protein Biosynthesis ; RNA, Archaeal/*genetics ; RNA, Ribosomal, 5S/genetics ; RNA, Transfer/genetics ; },
abstract = {BACKGROUND: Naturally occurring RNAs contain numerous enzymatically altered nucleosides. Differences in RNA populations (RNomics) and pattern of RNA modifications (Modomics) depends on the organism analyzed and are two of the criteria that distinguish the three kingdoms of life. If the genomic sequences of the RNA molecules can be derived from whole genome sequence information, the modification profile cannot and requires or direct sequencing of the RNAs or predictive methods base on the presence or absence of the modifications genes.<br><br>RESULTS: By employing a comparative genomics approach, we predicted almost all of the genes coding for the t+rRNA modification enzymes in the mesophilic moderate halophile Haloferax volcanii. These encode both guide RNAs and enzymes. Some are orthologous to previously identified genes in Archaea, Bacteria or in Saccharomyces cerevisiae, but several are original predictions.<br><br>CONCLUSION: The number of modifications in t+rRNAs in the halophilic archaeon is surprisingly low when compared with other Archaea or Bacteria, particularly the hyperthermophilic organisms. This may result from the specific lifestyle of halophiles that require high intracellular salt concentration for survival. This salt content could allow RNA to maintain its functional structural integrity with fewer modifications. We predict that the few modifications present must be particularly important for decoding, accuracy of translation or are modifications that cannot be functionally replaced by the electrostatic interactions provided by the surrounding salt-ions. This analysis also guides future experimental validation work aiming to complete the understanding of the function of RNA modifications in Archaeal translation.},
}
@article {pmid18832371,
year = {2008},
author = {Meskauskas, A and Dinman, JD},
title = {Ribosomal protein L3 functions as a 'rocker switch' to aid in coordinating of large subunit-associated functions in eukaryotes and Archaea.},
journal = {Nucleic acids research},
volume = {36},
number = {19},
pages = {6175-6186},
pmid = {18832371},
issn = {1362-4962},
support = {R01 GM058859/GM/NIGMS NIH HHS/United States ; GM058859/GM/NIGMS NIH HHS/United States ; },
mesh = {Archaeal Proteins/*chemistry/genetics/physiology ; Base Sequence ; Drug Resistance ; Escherichia coli/genetics ; Models, Molecular ; Molecular Sequence Data ; Mutation ; *Peptide Chain Elongation, Translational ; Peptide Elongation Factor 2/metabolism ; Peptidyl Transferases/metabolism ; Protein Subunits/chemistry/genetics/physiology ; RNA, Transfer, Amino Acyl/chemistry ; Ribosomal Protein L3 ; Ribosomal Proteins/*chemistry/genetics/physiology ; Saccharomyces cerevisiae/genetics/virology ; Saccharomyces cerevisiae Proteins/chemistry/genetics ; },
abstract = {Although ribosomal RNAs (rRNAs) comprise the bulk of the ribosome and carry out its main functions, ribosomal proteins also appear to play important structural and functional roles. Many ribosomal proteins contain long, nonglobular domains that extend deep into the rRNA cores. In eukaryotes and Archaea, ribosomal protein L3 contains two such extended domains tethered to a common globular hub, thus providing an excellent model to address basic questions relating to ribosomal protein structure/function relationships. Previous work in our laboratory identified the central 'W-finger' extension of yeast L3 in helping to coordinate ribosomal functions. New studies on the 'N-terminal' extension in yeast suggest that it works with the W-finger to coordinate opening and closing of the corridor through which the 3' end of aa-tRNA moves during the process of accommodation. Additionally, the effect of one of the L3 N-terminal extension mutants on the interaction between C75 of the aa-tRNA and G2921 (Escherichia coli G2553) of 25S rRNA provides the first evidence of the effect of a ribosomal protein on aa-tRNA positioning and peptidyltransfer, possibly through the induced fit model. A model is presented describing how all three domains of L3 may function together as a 'rocker switch' to coordinate the stepwise processes of translation elongation.},
}
@article {pmid18831724,
year = {2008},
author = {Large, AT and Lund, PA},
title = {Archaea at St Andrews.},
journal = {Genome biology},
volume = {9},
number = {9},
pages = {321},
doi = {10.1186/gb-2008-9-9-321},
pmid = {18831724},
issn = {1474-760X},
support = {BB/F002483/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Archaea/*genetics/physiology ; DNA Repair ; DNA Replication ; RNA/physiology ; Recombination, Genetic ; },
abstract = {A report of the Biochemical Society meeting 'The Molecular Biology of Archaea', St Andrews, UK, 19-21 August 2008.},
}
@article {pmid18831045,
year = {2009},
author = {Miyazono, K and Shirokane, M and Sawano, Y and Tanokura, M},
title = {Crystal structure of the DUF54 family protein PH1010 from hyperthermophilic archaea Pyrococcus horikoshii OT3.},
journal = {Proteins},
volume = {74},
number = {1},
pages = {256-260},
doi = {10.1002/prot.22255},
pmid = {18831045},
issn = {1097-0134},
mesh = {Amino Acid Sequence ; Animals ; Archaeal Proteins/*chemistry ; Crystallography, X-Ray ; Models, Molecular ; Molecular Sequence Data ; Protein Structure, Tertiary ; Pyrococcus horikoshii/*chemistry ; Ribosomal Proteins/*chemistry ; Sequence Alignment ; },
}
@article {pmid18831030,
year = {2008},
author = {Miyazono, K and Nishimura, Y and Sawano, Y and Makino, T and Tanokura, M},
title = {Crystal structure of hypothetical protein PH0734.1 from hyperthermophilic archaea Pyrococcus horikoshii OT3.},
journal = {Proteins},
volume = {73},
number = {4},
pages = {1068-1071},
doi = {10.1002/prot.22231},
pmid = {18831030},
issn = {1097-0134},
mesh = {Archaeal Proteins/*chemistry ; Crystallography, X-Ray ; Models, Molecular ; Protein Structure, Secondary ; Pyrococcus horikoshii/*chemistry ; Structural Homology, Protein ; },
}
@article {pmid18830278,
year = {2009},
author = {Vos, M and Didelot, X},
title = {A comparison of homologous recombination rates in bacteria and archaea.},
journal = {The ISME journal},
volume = {3},
number = {2},
pages = {199-208},
doi = {10.1038/ismej.2008.93},
pmid = {18830278},
issn = {1751-7370},
mesh = {Archaea/*physiology ; *Bacterial Physiological Phenomena ; DNA, Archaeal/chemistry/genetics ; DNA, Bacterial/chemistry/genetics ; *Recombination, Genetic ; Sequence Analysis, DNA ; },
abstract = {It is a standard practice to test for the signature of homologous recombination in studies examining the genetic diversity of bacterial populations. Although it has emerged that homologous recombination rates can vary widely between species, comparing the results from different studies is made difficult by the diversity of estimation methods used. Here, Multi Locus Sequence Typing (MLST) datasets from a wide variety of bacteria and archaea are analyzed using the ClonalFrame method. This enables a direct comparison between species and allows for a first exploration of the question whether phylogeny or ecology is the primary determinant of homologous recombination rate.},
}
@article {pmid18822770,
year = {2008},
author = {Smagin, VA and Mardanov, AV and Bonch-Osmolovskaia, EA and Ravin, NV},
title = {[Isolation and characteristics of new thermostable DNA ligase from archaea of the genus Thermococcus].},
journal = {Prikladnaia biokhimiia i mikrobiologiia},
volume = {44},
number = {5},
pages = {523-528},
pmid = {18822770},
issn = {0555-1099},
mesh = {Archaeal Proteins/*chemistry/genetics/*isolation &amp; purification ; DNA Breaks, Single-Stranded ; DNA Ligase ATP ; DNA Ligases/*chemistry/genetics/*isolation &amp; purification ; Gene Expression ; Hot Temperature ; Recombinant Proteins/chemistry/genetics/isolation &amp; purification ; Thermococcus/*enzymology/genetics ; },
abstract = {The DNA ligase gene from thermophilic archaea of the genus Thermococcus (strain 1519) was identified and sequenced in the polymerase chain reaction. The recombinant enzyme LigTh1519 was expressed in Escherichia coli, purified, and characterized. LigTh1519 was capable of ligating the cohesive ends and single-strand breaks in double-stranded DNA (ATP as a cofactor). The optimum conditions for the ligase reaction appeared as follows: 100 mM NaCl, 50 mM MgCl2, pH 7.0-10.5, and temperature 70 degrees C. More than 50% Lig1519 activity were preserved after incubation of the enzyme at 80 degrees C for 30 min. New thermostable DNA ligase LihTh1519 may be used for basic and applied researches in molecular biology and genetic engineering.},
}
@article {pmid18818711,
year = {2009},
author = {De Corte, D and Yokokawa, T and Varela, MM and Agogué, H and Herndl, GJ},
title = {Spatial distribution of Bacteria and Archaea and amoA gene copy numbers throughout the water column of the Eastern Mediterranean Sea.},
journal = {The ISME journal},
volume = {3},
number = {2},
pages = {147-158},
doi = {10.1038/ismej.2008.94},
pmid = {18818711},
issn = {1751-7370},
mesh = {Ammonia/*metabolism ; Archaea/enzymology/genetics/*isolation &amp; purification/*metabolism ; Archaeal Proteins/genetics ; Bacteria/enzymology/genetics/*isolation &amp; purification/*metabolism ; Bacterial Proteins/genetics ; Cluster Analysis ; DNA Fingerprinting ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; Genotype ; Mediterranean Sea ; Nitrites/analysis ; Oxidation-Reduction ; Oxidoreductases/genetics ; Polymerase Chain Reaction/methods ; Polymorphism, Restriction Fragment Length ; Seawater/chemistry/*microbiology ; },
abstract = {Until recently, ammonia oxidation, a key process in the global nitrogen cycle, was thought to be mediated exclusively by a few bacterial groups. It has been shown now, that also Crenarchaeota are capable to perform this initial nitrification step. The abundance of ammonia oxidizing Bacteria and Archaea was determined using the bacterial and archaeal ammonia monooxygenase-alpha subunit (amoA) gene as functional markers in a quantitative PCR approach and related to the abundance of Bacteria and Archaea in the Eastern Mediterranean Sea. Archaeal amoA copy numbers decreased from 4000-5000 copies ml(-1) seawater from the 200-500 m depth layer to 20 copies ml(-1) at 1000 m depth. Beta-proteobacterial amoA genes were below the detection limit in all the samples. The archaeal amoA copy numbers were correlated with NO(2)(-) concentrations, suggesting that ammonia-oxidizing Archaea may play a significant role in the nitrification in the mesopelagic waters of the Eastern Mediterranean Sea. In the bathypelagic waters, however, archaeal amoA gene abundance was rather low although Crenarchaeota were abundant, indicating that Crenarchaeota might largely lack the amoA gene in these deep waters. Terminal restriction fragment length polymorphism analysis of the archaeal community revealed a distinct clustering with the mesopelagic community distinctly different from the archaeal communities of both, the surface waters and the 3000-4000 m layers. Hence, the archaeal community in the Eastern Mediterranean Sea appears to be highly stratified despite the absence of major temperature and density gradients between the meso- and bathypelagic waters of the Mediterranean Sea.},
}
@article {pmid18808198,
year = {2008},
author = {Mondal, UK and Das, B and Ghosh, TC and Sen, A and Bothra, AK},
title = {Nucleotide triplet based molecular phylogeny of class I and class II aminoacyl t-RNA synthetase in three domain of life process: bacteria, archaea, and eukarya.},
journal = {Journal of biomolecular structure &amp; dynamics},
volume = {26},
number = {3},
pages = {321-328},
doi = {10.1080/07391102.2008.10507247},
pmid = {18808198},
issn = {0739-1102},
mesh = {Amino Acyl-tRNA Synthetases/*genetics ; Archaea/*genetics ; Bacteria/*genetics ; Base Sequence ; *Eukaryotic Cells ; Evolution, Molecular ; Molecular Sequence Data ; Nucleotides/*genetics ; Phylogeny ; RNA, Transfer/*genetics ; Sequence Alignment ; },
abstract = {The aminoacyl-tRNA synthetases are one of the major protein components in the translation machinery. These essential proteins are found in all forms of life and are responsible for charging their cognate tRNAs with the correct amino acid. These important enzymes have been the subject of intense scientific inquiry for nearly half a century, but their complete evolutionary history has yet to emerge. Amino acids sequence based phylogeny has some limitation due to very low sequence similarity amongst the different tRNA synthetases and structure based phylogeny has also its limitation. In our study, tRNA nucleotide sequences of E. coli K12 (Bacteria), Saccharomyces cerevisiae (Eukarya), Thermococcus kodakaraensis KOD1, and Archaeoglobus fulgidus DSM 4304 (Archaea) were used for phylogenetic analysis. Our results complement the observation with the earlier studies based on multiple sequence alignment and structural alignment. We observed that relationship between archaeal tRNA synthetases are different that of bacteria and eucarya. Violation of Class rule of LysRS is observed here also. The uniqueness of this method is that it does not employ sequence alignment of complete nucleotide sequence of the corresponding gene.},
}
@article {pmid18798991,
year = {2008},
author = {Pride, DT and Schoenfeld, T},
title = {Genome signature analysis of thermal virus metagenomes reveals Archaea and thermophilic signatures.},
journal = {BMC genomics},
volume = {9},
number = {},
pages = {420},
pmid = {18798991},
issn = {1471-2164},
support = {R43 HG002714/HG/NHGRI NIH HHS/United States ; 1R43 HG002714-01/HG/NHGRI NIH HHS/United States ; },
mesh = {Archaea/*virology ; Archaeal Viruses/classification/*genetics ; Genomics/*methods ; Hot Springs/*virology ; Northwestern United States ; },
abstract = {BACKGROUND: Metagenomic analysis provides a rich source of biological information for otherwise intractable viral communities. However, study of viral metagenomes has been hampered by its nearly complete reliance on BLAST algorithms for identification of DNA sequences. We sought to develop algorithms for examination of viral metagenomes to identify the origin of sequences independent of BLAST algorithms. We chose viral metagenomes obtained from two hot springs, Bear Paw and Octopus, in Yellowstone National Park, as they represent simple microbial populations where comparatively large contigs were obtained. Thermal spring metagenomes have high proportions of sequences without significant Genbank homology, which has hampered identification of viruses and their linkage with hosts. To analyze each metagenome, we developed a method to classify DNA fragments using genome signature-based phylogenetic classification (GSPC), where metagenomic fragments are compared to a database of oligonucleotide signatures for all previously sequenced Bacteria, Archaea, and viruses.<br><br>RESULTS: From both Bear Paw and Octopus hot springs, each assembled contig had more similarity to other metagenome contigs than to any sequenced microbial genome based on GSPC analysis, suggesting a genome signature common to each of these extreme environments. While viral metagenomes from Bear Paw and Octopus share some similarity, the genome signatures from each locale are largely unique. GSPC using a microbial database predicts most of the Octopus metagenome has archaeal signatures, while bacterial signatures predominate in Bear Paw; a finding consistent with those of Genbank BLAST. When using a viral database, the majority of the Octopus metagenome is predicted to belong to archaeal virus Families Globuloviridae and Fuselloviridae, while none of the Bear Paw metagenome is predicted to belong to archaeal viruses. As expected, when microbial and viral databases are combined, each of the Octopus and Bear Paw metagenomic contigs are predicted to belong to viruses rather than to any Bacteria or Archaea, consistent with the apparent viral origin of both metagenomes.<br><br>CONCLUSION: That BLAST searches identify no significant homologs for most metagenome contigs, while GSPC suggests their origin as archaeal viruses or bacteriophages, indicates GSPC provides a complementary approach in viral metagenomic analysis.},
}
@article {pmid18768637,
year = {2008},
author = {Oren, A},
title = {Nomenclature and taxonomy of halophilic archaea--comments on the proposal by DasSarma and DasSarma for nomenclatural changes within the order Halobacteriales.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {58},
number = {Pt 9},
pages = {2245-2246},
doi = {10.1099/ijs.0.2008/005173-0},
pmid = {18768637},
issn = {1466-5026},
mesh = {Halobacteriales/*classification ; *Terminology as Topic ; },
abstract = {P. DasSarma &amp; S. DasSarma [Saline Systems 4 (2008), 5] have proposed far-reaching changes in the nomenclature and taxonomy of the halophilic archaea of the order Halobacteriales, family Halobacteriaceae. While re-evaluation of the taxonomic classification of strains within the group is to be encouraged, the nomenclatural changes proposed are in violation of the General Considerations, Principles and Rules of the International Code of Nomenclature of Bacteria.},
}
@article {pmid18761016,
year = {2008},
author = {Emptage, K and O'Neill, R and Solovyova, A and Connolly, BA},
title = {Interplay between DNA polymerase and proliferating cell nuclear antigen switches off base excision repair of uracil and hypoxanthine during replication in archaea.},
journal = {Journal of molecular biology},
volume = {383},
number = {4},
pages = {762-771},
doi = {10.1016/j.jmb.2008.08.018},
pmid = {18761016},
issn = {1089-8638},
support = {BBS/B/05060//Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Archaeal Proteins/genetics/*metabolism ; *DNA Repair ; *DNA Replication ; DNA, Archaeal/genetics/metabolism ; DNA-Directed DNA Polymerase/chemistry/genetics/*metabolism ; Deoxyribonuclease (Pyrimidine Dimer)/genetics/metabolism ; Hypoxanthine/*metabolism ; Macromolecular Substances/chemistry/metabolism ; Models, Molecular ; Proliferating Cell Nuclear Antigen/genetics/*metabolism ; *Pyrococcus furiosus/genetics/metabolism ; Templates, Genetic ; Uracil/*metabolism ; Uracil-DNA Glycosidase/genetics/metabolism ; },
abstract = {Archaeal family-B DNA polymerases bind tightly to uracil and hypoxanthine (the deamination products of cytosine and adenine), resulting in profound inhibition of DNA replication. Investigation of the mechanism of inhibition, using single-turnover kinetics with polymerase in excess of DNA, indicated that deoxy-NTPs were efficiently bound to the polymerase-DNA complex but very poorly incorporated into the extending chain. Addition of the processivity factor proliferating cell nuclear antigen (PCNA) resulted in increased affinity of the polymerase for all primer-templates, producing extremely tight complexes when uracil (K(d)=16 pM) or hypoxanthine (K(d)=65 pM) was present. Analytical ultracentrifugation confirmed the stability of these complexes and revealed a polymerase/PCNA/DNA stoichiometry of 1:1:1. However, PCNA had no influence on the ability of the polymerase to read through uracil and hypoxanthine, the same kinetic parameters being observed with or without the processivity factor. The specificity constants determined using single-turnover kinetics showed that uracil and hypoxanthine slowed the polymerase by factors of approximately 5000 and 3000, respectively. Uracil and hypoxanthine are removed from DNA by base excision repair, initiated by uracil-DNA glycosylase and endonuclease V, respectively. Both enzymes are profoundly inhibited by the simultaneous binding of both PCNA and polymerase to primer-templates, with polymerase alone being much less effective. Thus, when the PCNA-polymerase complex encounters uracil/hypoxanthine in DNA templates, base excision repair is switched off, protecting the complex from a repair pathway that is dangerous in the context of single-stranded DNA formed during replication.},
}
@article {pmid18760359,
year = {2008},
author = {Auernik, KS and Cooper, CR and Kelly, RM},
title = {Life in hot acid: pathway analyses in extremely thermoacidophilic archaea.},
journal = {Current opinion in biotechnology},
volume = {19},
number = {5},
pages = {445-453},
pmid = {18760359},
issn = {0958-1669},
support = {T32 GM008776/GM/NIGMS NIH HHS/United States ; },
mesh = {Acids/*metabolism ; Archaea/*physiology ; Archaeal Proteins/*metabolism ; Cell Survival ; *Ecosystem ; Hot Temperature ; Hydrogen-Ion Concentration ; *Models, Biological ; Signal Transduction/*physiology ; },
abstract = {The extremely thermoacidophilic archaea are a particularly intriguing group of microorganisms that must simultaneously cope with biologically extreme pHs (< or = 4) and temperatures (Topt > or = 60 degrees C) in their natural environments. Their expanding biotechnological significance relates to their role in biomining of base and precious metals and their unique mechanisms of survival in hot acid, at both the cellular and biomolecular levels. Recent developments, such as advances in understanding of heavy metal tolerance mechanisms, implementation of a genetic system, and discovery of a new carbon fixation pathway, have been facilitated by the availability of genome sequence data and molecular genetic systems. As a result, new insights into the metabolic pathways and physiological features that define extreme thermoacidophily have been obtained, in some cases suggesting prospects for biotechnological opportunities.},
}
@article {pmid18759006,
year = {2008},
author = {Ding, X and Lv, ZM and Zhao, Y and Min, H and Yang, WJ},
title = {MTH1745, a protein disulfide isomerase-like protein from thermophilic archaea, Methanothermobacter thermoautotrophicum involving in stress response.},
journal = {Cell stress &amp; chaperones},
volume = {13},
number = {2},
pages = {239-246},
pmid = {18759006},
issn = {1466-1268},
mesh = {Archaeal Proteins/chemistry/genetics/*physiology ; Citrate (si)-Synthase/chemistry ; Cold Temperature ; Escherichia coli ; Gene Expression Regulation, Archaeal ; *Genes, Archaeal ; Methanobacteriaceae/*enzymology/genetics/physiology ; Molecular Chaperones/chemistry/genetics/*physiology ; Protein Denaturation ; Protein Disulfide-Isomerases/genetics/*physiology ; Protein Folding ; Protein Structure, Tertiary ; Recombinant Fusion Proteins/physiology ; Stress, Physiological/genetics/physiology ; Thioredoxins/chemistry ; Up-Regulation ; },
abstract = {MTH1745 is a putative protein disulfide isomerase characterized with 151 amino acid residues and a CPAC active-site from the anaerobic archaea Methanothermobacter thermoautotrophicum. The potential functions of MTH1745 are not clear. In the present study, we show a crucial role of MTH1745 in protecting cells against stress which may be related to its functions as a disulfide isomerase and its chaperone properties. Using real-time polymerase chain reaction analyses, the level of MTH1745 messenger RNA (mRNA) in the thermophilic archaea M. thermoautotrophicum was found to be stress-induced in that it was significantly higher under low (50 degrees C) and high (70 degrees C) growth temperatures than under the optimal growth temperature for the organism (65 degrees C). Additionally, the expression of MTH1745 mRNA was up-regulated by cold shock (4 degrees C). Furthermore, the survival of MTH1745 expressing Escherichia coli cells was markedly higher than that of control cells in response to heat shock (51.0 degrees C). These results indicated that MTH1745 plays an important role in the resistance of stress. By assay of enzyme activities in vitro, MTH1745 also exhibited a chaperone function by promoting the functional folding of citrate synthase after thermodenaturation. On the other hand, MTH1745 was also shown to function as a disulfide isomerase on the refolding of denatured and reduced ribonuclease A. On the basis of its single thioredoxin domain, function as a disulfide isomerase, and its chaperone activity, we suggest that MTH1745 may be an ancient protein disulfide isomerase. These studies may provide clues to the understanding of the function of protein disulfide isomerase in archaea.},
}
@article {pmid18757236,
year = {2009},
author = {Conway de Macario, E and Macario, AJ},
title = {Methanogenic archaea in health and disease: a novel paradigm of microbial pathogenesis.},
journal = {International journal of medical microbiology : IJMM},
volume = {299},
number = {2},
pages = {99-108},
doi = {10.1016/j.ijmm.2008.06.011},
pmid = {18757236},
issn = {1618-0607},
mesh = {Animals ; Archaea/*isolation &amp; purification/metabolism/*physiology ; Colonic Neoplasms/microbiology ; Diverticulum/microbiology ; Female ; Humans ; Intestine, Large/microbiology ; Male ; Methane/*metabolism ; Mouth/microbiology ; Obesity/microbiology ; Periodontitis/microbiology ; Vagina/microbiology ; },
abstract = {Microbes that produce methane gas, methanogens, were identified as Archaea in the 1970s but their possible role in disease is only emerging now, after they were found in the large intestine, mouth, and vagina. Significant associations were observed, for instance, between levels of methanogens in periodontal pockets and severity of periodontitis, and between quantities of methanogens in the large intestine and diseases such as colon cancer and diverticulosis. Recently, a role for intestinal methanogens in obesity was proposed. The lesson learned is that for methanogens we have to look at their pathogenicity from a different angle in comparison to classic pathogens that invade tissues and release toxins. This type of pathogenicity has not yet been described for methanogens. Instead, methanogens seem to participate in pathogenicity indirectly, favoring the growth of other microbes, which are directly involved in pathogenesis. This indirect role should not be minimized. On the contrary, it has become clear that a fundamental change of approach to the understanding and control of microbial diseases must be implemented. A comprehensive strategy is needed to elucidate the syntrophic associations that are essential for a healthy relation among microbes (including methanogens) and between them and the host organism, and to unveil those associations that lead to disease.},
}
@article {pmid18721142,
year = {2008},
author = {Ettwig, KF and Shima, S and van de Pas-Schoonen, KT and Kahnt, J and Medema, MH and Op den Camp, HJ and Jetten, MS and Strous, M},
title = {Denitrifying bacteria anaerobically oxidize methane in the absence of Archaea.},
journal = {Environmental microbiology},
volume = {10},
number = {11},
pages = {3164-3173},
doi = {10.1111/j.1462-2920.2008.01724.x},
pmid = {18721142},
issn = {1462-2920},
mesh = {Archaea/enzymology/genetics ; Archaeal Proteins/genetics ; Methane/*metabolism ; Methanosarcinales/*metabolism ; Molecular Sequence Data ; Nitrites/metabolism ; Nitrogen/metabolism ; Oxidation-Reduction ; Sequence Analysis, DNA ; },
abstract = {Recently, a microbial consortium was shown to couple the anaerobic oxidation of methane to denitrification, predominantly in the form of nitrite reduction to dinitrogen gas. This consortium was dominated by bacteria of an as yet uncharacterized division and archaea of the order Methanosarcinales. The present manuscript reports on the upscaling of the enrichment culture, and addresses the role of the archaea in methane oxidation. The key gene of methanotrophic and methanogenic archaea, mcrA, was sequenced. The associated cofactor F(430) was shown to have a mass of 905 Da, the same as for methanogens and different from the heavier form (951 Da) found in methanotrophic archaea. After prolonged enrichment (> 1 year), no inhibition of anaerobic methane oxidation was observed in the presence of 20 mM bromoethane sulfonate, a specific inhibitor of MCR. Optimization of the cultivation conditions led to higher rates of methane oxidation and to the decline of the archaeal population, as shown by fluorescence in situ hybridization and quantitative MALDI-TOF analysis of F(430). Mass balancing showed that methane oxidation was still coupled to nitrite reduction in the total absence of oxygen. Together, our results show that bacteria can couple the anaerobic oxidation of methane to denitrification without the involvement of Archaea.},
}
@article {pmid18714086,
year = {2008},
author = {Römling, U},
title = {Great times for small molecules: c-di-AMP, a second messenger candidate in Bacteria and Archaea.},
journal = {Science signaling},
volume = {1},
number = {33},
pages = {pe39},
doi = {10.1126/scisignal.133pe39},
pmid = {18714086},
issn = {1937-9145},
mesh = {Adenylyl Cyclases/metabolism ; Archaea/*metabolism ; Archaeal Proteins/*metabolism ; Bacillus/*metabolism ; Bacterial Proteins/*metabolism ; Dinucleoside Phosphates/*chemistry ; Models, Biological ; Protein Binding ; Protein Structure, Tertiary ; *Second Messenger Systems ; Thermotoga maritima/metabolism ; },
abstract = {Successful cell division in pro- and eukaryotes is ensured by checkpoints that regulate cell cycle progression. Structural and biochemical analyses of the DNA integrity scanning protein (DisA) have recently shown that its domain of unknown function, DUF147 [renamed DAC (for diadenylate cyclase)], has diadenylate cyclase activity. This diadenylate cyclase activity is abolished when DisA binds to branched DNA substrates, which arise during DNA double-strand breaks that can spontaneously occur during DNA replication. This finding identifies cyclic di(3'-->5')-adenylic acid (c-di-AMP) as a second messenger candidate that signals DNA integrity in Bacillus subtilis during sporulation, a specialized cell division process that leads to formation of a dormant cell called a spore. The DAC domain is widespread in Bacteria and Archaea; moreover, it is found in proteins containing diverse domains, suggesting that c-di-AMP acts as a second messenger molecule in response to various signals besides branched DNA. To elucidate the biological importance and molecular mechanisms of action for c-di-AMP and the recently recognized second messenger c-di-GMP will require a multidisciplinary approach.},
}
@article {pmid18707623,
year = {2008},
author = {Yamabe, K and Maeda, H and Kokeguchi, S and Tanimoto, I and Sonoi, N and Asakawa, S and Takashiba, S},
title = {Distribution of Archaea in Japanese patients with periodontitis and humoral immune response to the components.},
journal = {FEMS microbiology letters},
volume = {287},
number = {1},
pages = {69-75},
doi = {10.1111/j.1574-6968.2008.01304.x},
pmid = {18707623},
issn = {0378-1097},
mesh = {Antibodies, Archaeal/*blood ; Antibody Formation ; Archaea/classification/genetics/*immunology/*isolation &amp; purification ; DNA, Archaeal/genetics ; Dental Plaque/microbiology ; Humans ; Immunoglobulin G/*blood ; Japan ; Methanobrevibacter/genetics/isolation &amp; purification ; Periodontitis/*immunology/*microbiology ; RNA, Ribosomal, 16S/genetics ; },
abstract = {There is controversy regarding the existence of archaeal pathogens. Periodontitis is one of the human diseases in which Archaea have been suggested to have roles as pathogens. This study was performed to investigate the distribution of Archaea in Japanese patients with periodontitis and to examine the serum IgG responses to archaeal components. Subgingival plaque samples were collected from 111 periodontal pockets of 49 patients (17 with aggressive periodontitis and 32 with chronic periodontitis), and 30 subgingival plaque samples were collected from 17 healthy subjects. By PCR targeting the 16S rRNA gene, Archaea were detected in 15 plaque samples (13.5% of total samples) from 11 patients (29.4% of patients with aggressive periodontitis and 18.8% of patients with chronic periodontitis). Archaea were detected mostly (14/15) in severe diseased sites (pocket depth > or =6 mm), while no amplicons were observed in any samples from healthy controls. Sequence analysis of the PCR products revealed that the majority of Archaea in periodontal pockets were a Methanobrevibacter oralis-like phylotype. Western immunoblotting detected IgG antibodies against M. oralis in eight of the 11 sera from patients. These results suggest the potential of Archaea (M. oralis) as an antigenic pathogen of periodontitis.},
}
@article {pmid18707612,
year = {2008},
author = {Siboni, N and Ben-Dov, E and Sivan, A and Kushmaro, A},
title = {Global distribution and diversity of coral-associated Archaea and their possible role in the coral holobiont nitrogen cycle.},
journal = {Environmental microbiology},
volume = {10},
number = {11},
pages = {2979-2990},
doi = {10.1111/j.1462-2920.2008.01718.x},
pmid = {18707612},
issn = {1462-2920},
mesh = {Animals ; Anthozoa/*microbiology ; Archaea/*classification/genetics/isolation &amp; purification/*metabolism ; Australia ; *Biodiversity ; DNA, Archaeal/chemistry/genetics ; DNA, Ribosomal/genetics ; Israel ; Molecular Sequence Data ; Nitrogen/*metabolism ; Phylogeny ; RNA, Archaeal/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; },
abstract = {Diversity, distribution and genetic comparison of Archaea associated with the surface mucus of corals from three genera, namely Acanthastrea sp., Favia sp. and Fungia sp., from the Gulf of Eilat, Israel and from Heron Island, Australia were studied. Sequencing of the 16S rRNA gene of the coral-associated Archaea revealed dominance of Crenarchaeota (79%, on average). In this phylum, 87% of the sequences were similar (>or= 97%) to the Thermoprotei, with 76% of these being similar (>or= 97%) to the ammonium oxidizer, Nitrosopumilus maritimus. Most of the coral-associated euryarchaeotal sequences (69%) were related to marine group II, while other euryarchaeotal clades were found to be related to anaerobic methanotrophs (8%), anaerobic nitrate reducers (i.e. denitrification, 15%) and marine group III (8%). Most of the crenarchaeotal and euryarchaeotal coral-associated 16S rRNA gene sequences from Heron Island (61%) and from the Gulf of Eilat (71%) were closely related (>or= 97%) to sequences previously derived from corals from the Virgin Islands. Analysis of archaeal amoA sequences obtained from the fungiid coral, Fungia granulosa, divided into three clades, all related to archaeal sequences previously obtained from the marine environment. These sequences were distantly related to amoA sequences previously found in association with other coral species. Preliminary experiments suggest that there is active oxidation of ammonia to nitrite in the mucus of F. granulosa. Thus, coral-associated Archaea may contribute to nitrogen recycling in the holobiont, presumably by acting as a nutritional sink for excess ammonium trapped in the mucus layer, through nitrification and denitrification processes.},
}
@article {pmid18707610,
year = {2008},
author = {Nicol, GW and Leininger, S and Schleper, C and Prosser, JI},
title = {The influence of soil pH on the diversity, abundance and transcriptional activity of ammonia oxidizing archaea and bacteria.},
journal = {Environmental microbiology},
volume = {10},
number = {11},
pages = {2966-2978},
doi = {10.1111/j.1462-2920.2008.01701.x},
pmid = {18707610},
issn = {1462-2920},
mesh = {Ammonia/*metabolism ; Archaeal Proteins/genetics ; Bacteria/*classification ; Bacterial Physiological Phenomena ; Bacterial Proteins/genetics ; *Biodiversity ; Cluster Analysis ; Crenarchaeota/*classification/physiology ; DNA Fingerprinting ; Electrophoresis, Polyacrylamide Gel ; Hydrogen-Ion Concentration ; Molecular Sequence Data ; Nitrites/metabolism ; Nucleic Acid Denaturation ; Oxidation-Reduction ; Oxidoreductases/genetics ; RNA, Archaeal/genetics ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; *Transcription, Genetic ; },
abstract = {Autotrophic ammonia oxidation occurs in acid soils, even though laboratory cultures of isolated ammonia oxidizing bacteria fail to grow below neutral pH. To investigate whether archaea possessing ammonia monooxygenase genes were responsible for autotrophic nitrification in acid soils, the community structure and phylogeny of ammonia oxidizing bacteria and archaea were determined across a soil pH gradient (4.9-7.5) by amplifying 16S rRNA and amoA genes followed by denaturing gradient gel electrophoresis (DGGE) and sequence analysis. The structure of both communities changed with soil pH, with distinct populations in acid and neutral soils. Phylogenetic reconstructions of crenarchaeal 16S rRNA and amoA genes confirmed selection of distinct lineages within the pH gradient and high similarity in phylogenies indicated a high level of congruence between 16S rRNA and amoA genes. The abundance of archaeal and bacterial amoA gene copies and mRNA transcripts contrasted across the pH gradient. Archaeal amoA gene and transcript abundance decreased with increasing soil pH, while bacterial amoA gene abundance was generally lower and transcripts increased with increasing pH. Short-term activity was investigated by DGGE analysis of gene transcripts in microcosms containing acidic or neutral soil or mixed soil with pH readjusted to that of native soils. Although mixed soil microcosms contained identical archaeal ammonia oxidizer communities, those adapted to acidic or neutral pH ranges showed greater relative activity at their native soil pH. Findings indicate that different bacterial and archaeal ammonia oxidizer phylotypes are selected in soils of different pH and that these differences in community structure and abundances are reflected in different contributions to ammonia oxidizer activity. They also suggest that both groups of ammonia oxidizers have distinct physiological characteristics and ecological niches, with consequences for nitrification in acid soils.},
}
@article {pmid18694827,
year = {2008},
author = {Abu-Qarn, M and Eichler, J and Sharon, N},
title = {Not just for Eukarya anymore: protein glycosylation in Bacteria and Archaea.},
journal = {Current opinion in structural biology},
volume = {18},
number = {5},
pages = {544-550},
doi = {10.1016/j.sbi.2008.06.010},
pmid = {18694827},
issn = {0959-440X},
mesh = {Archaea/chemistry/*metabolism ; Archaeal Proteins/*metabolism ; Bacteria/chemistry/*metabolism ; Bacterial Proteins/*metabolism ; Campylobacter jejuni/metabolism ; Carbohydrate Conformation ; Carbohydrate Sequence ; Glycosylation ; Haloferax volcanii/metabolism ; Models, Molecular ; Molecular Sequence Data ; Neisseria gonorrhoeae/metabolism ; Polysaccharides/*chemistry/*metabolism ; Protein Conformation ; },
abstract = {Of the many post-translational modifications proteins can undergo, glycosylation is the most prevalent and the most diverse. Today, it is clear that both N-glycosylation and O-glycosylation, once believed to be restricted to eukaryotes, also transpire in Bacteria and Archaea. Indeed, prokaryotic glycoproteins rely on a wider variety of monosaccharide constituents than do those of eukaryotes. In recent years, substantial progress in describing the enzymes involved in bacterial and archaeal glycosylation pathways has been made. It is becoming clear that enhanced knowledge of bacterial glycosylation enzymes may be of therapeutic value, while the demonstrated ability to introduce bacterial glycosylation genes into Escherichia coli represents a major step forward in glyco-engineering. A better understanding of archaeal protein glycosylation provides insight into this post-translational modification across evolution as well as protein processing under extreme conditions. Here, we discuss new structural and biosynthetic findings related to prokaryotic protein glycosylation, until recently a neglected topic.},
}
@article {pmid18685264,
year = {2008},
author = {Le Borgne, S and Paniagua, D and Vazquez-Duhalt, R},
title = {Biodegradation of organic pollutants by halophilic bacteria and archaea.},
journal = {Journal of molecular microbiology and biotechnology},
volume = {15},
number = {2-3},
pages = {74-92},
doi = {10.1159/000121323},
pmid = {18685264},
issn = {1660-2412},
mesh = {Archaea/*metabolism ; Bacteria/*metabolism ; *Biodegradation, Environmental ; Environmental Pollutants/*metabolism ; Environmental Pollution ; Organic Chemicals/metabolism ; Sodium Chloride/*metabolism ; Soil Microbiology ; },
abstract = {Hypersaline environments are important for both surface extension and ecological significance. As all other ecosystems, they are impacted by pollution. However, little information is available on the biodegradation of organic pollutants by halophilic microorganisms in such environments. In addition, it is estimated that 5% of industrial effluents are saline and hypersaline. Conventional nonextremophilic microorganisms are unable to efficiently perform the removal of organic pollutants at high salt concentrations. Halophilic microorganisms are metabolically different and are adapted to extreme salinity; these microorganisms are good candidates for the bioremediation of hypersaline environments and treatment of saline effluents. This literature survey indicates that both the moderately halophilic bacteria and the extremely halophilic archaea have a broader catabolic versatility and capability than previously thought. A diversity of contaminating compounds is susceptible to be degraded by halotolerant and halophile bacteria. Nevertheless, significant research efforts are still necessary in order to estimate the true potential of these microorganisms to be applied in environmental processes and in the remediation of contaminated hypersaline ecosystems. This effort should be also focused on basic research to understand the overall degradation mechanism, to identify the enzymes involved in the degradation process and the metabolism regulation.},
}
@article {pmid18676618,
year = {2008},
author = {Simon, DM and Clarke, NA and McNeil, BA and Johnson, I and Pantuso, D and Dai, L and Chai, D and Zimmerly, S},
title = {Group II introns in eubacteria and archaea: ORF-less introns and new varieties.},
journal = {RNA (New York, N.Y.)},
volume = {14},
number = {9},
pages = {1704-1713},
pmid = {18676618},
issn = {1469-9001},
mesh = {Archaea/enzymology/*genetics ; Bacteria/enzymology/*genetics ; *Introns/genetics ; Nucleic Acid Conformation ; Open Reading Frames ; Phylogeny ; RNA, Catalytic/*chemistry/*classification/genetics ; *Retroelements ; },
abstract = {Group II introns are a major class of ribozymes found in bacteria, mitochondria, and plastids. Many introns contain reverse transcriptase open reading frames (ORFs) that confer mobility to the introns and allow them to persist as selfish DNAs. Here, we report an updated compilation of group II introns in Eubacteria and Archaea comprising 234 introns. One new phylogenetic class is identified, as well as several specialized lineages. In addition, we undertake a detailed search for ORF-less group II introns in bacterial genomes in order to find undiscovered introns that either entirely lack an ORF or encode a novel ORF. Unlike organellar group II introns, we find only a handful of ORF-less introns in bacteria, suggesting that if a substantial number exist, they must be divergent from known introns. Together, these results highlight the retroelement character of bacterial group II introns, and suggest that their long-term survival is dependent upon retromobility.},
}
@article {pmid18671734,
year = {2008},
author = {Römisch-Margl, W and Eisenreich, W and Haase, I and Bacher, A and Fischer, M},
title = {2,5-diamino-6-ribitylamino-4(3H)-pyrimidinone 5'-phosphate synthases of fungi and archaea.},
journal = {The FEBS journal},
volume = {275},
number = {17},
pages = {4403-4414},
doi = {10.1111/j.1742-4658.2008.06586.x},
pmid = {18671734},
issn = {1742-464X},
mesh = {Amino Acid Sequence ; Archaea/*enzymology ; Cloning, Molecular ; Fungi/*enzymology ; Kinetics ; Magnetic Resonance Spectroscopy ; Molecular Sequence Data ; Nuclear Magnetic Resonance, Biomolecular ; Riboflavin Synthase/chemistry/genetics/*metabolism ; Sequence Homology, Amino Acid ; Stereoisomerism ; Ultracentrifugation ; },
abstract = {The pathway of riboflavin (vitamin B2) biosynthesis is significantly different in archaea, eubacteria, fungi and plants. Specifically, the first committed intermediate, 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate, can either undergo hydrolytic cleavage of the position 2 amino group by a deaminase (in plants and most eubacteria) or reduction of the ribose side chain by a reductase (in fungi and archaea). We compare 2,5-diamino-6-ribitylamino-4(3H)-pyrimidinone 5'-phosphate synthases from the yeast Candida glabrata, the archaeaon Methanocaldococcus jannaschii and the eubacterium Aquifex aeolicus. All three enzymes convert 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate into 2,5-diamino-6-ribitylamino-4(3H)-pyrimidinone 5'-phosphate, as shown by 13C-NMR spectroscopy using [2,1',2',3',4',5'-13C6]2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate as substrate. The beta anomer was found to be the authentic substrate, and the alpha anomer could serve as substrate subsequent to spontaneous anomerisation. The M. jannaschii and C. glabrata enzymes were shown to be A-type reductases catalysing the transfer of deuterium from the 4(R) position of NADPH to the 1' (S) position of the substrate. These results are in agreement with the known three-dimensional structure of the M. jannaschii enzyme.},
}
@article {pmid18644435,
year = {2008},
author = {Mihajlovski, A and Alric, M and Brugère, JF},
title = {A putative new order of methanogenic Archaea inhabiting the human gut, as revealed by molecular analyses of the mcrA gene.},
journal = {Research in microbiology},
volume = {159},
number = {7-8},
pages = {516-521},
doi = {10.1016/j.resmic.2008.06.007},
pmid = {18644435},
issn = {0923-2508},
mesh = {Adult ; Aged ; Archaea/*classification/enzymology/*genetics/isolation &amp; purification ; Archaeal Proteins/*genetics/metabolism ; DNA, Archaeal/genetics ; DNA, Ribosomal/genetics ; Feces/microbiology ; Female ; Gastrointestinal Tract/*microbiology ; Humans ; Male ; Methane/metabolism ; Middle Aged ; Molecular Sequence Data ; Oxidoreductases/*genetics/metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The diversity of methanogenic Archaea from the gut of 6 humans was investigated by targeting mcrA, a molecular metabolic marker of methanogenesis. Three operational taxonomic units (OTUs) were recovered from about 400 clones analyzed, two of which were attributed to the expected Methanobacteriales Methanobrevibacter smithii (4 volunteers) and Methanosphaera stadtmanae (1 volunteer). The third OTU (1 volunteer) corresponded to a distant phylotype that does not cluster with any of the five methanogenic orders. This result, also supported by 16S archaeal sequences retrieved from the same volunteer, strongly suggests there may be a sixth order and hence potential underestimation of the role of methanogens in gut physiology.},
}
@article {pmid18642902,
year = {2008},
author = {Mayr, S and Latkoczy, C and Krüger, M and Günther, D and Shima, S and Thauer, RK and Widdel, F and Jaun, B},
title = {Structure of an F430 variant from archaea associated with anaerobic oxidation of methane.},
journal = {Journal of the American Chemical Society},
volume = {130},
number = {32},
pages = {10758-10767},
doi = {10.1021/ja802929z},
pmid = {18642902},
issn = {1520-5126},
mesh = {Anaerobiosis ; Carbon Dioxide/metabolism ; Crystallography, X-Ray ; Magnetic Resonance Spectroscopy ; Metalloporphyrins/*chemistry/genetics ; Methane/*metabolism ; Methanobacteriaceae/*enzymology ; Molecular Structure ; Mutation ; Oxidation-Reduction ; Stereoisomerism ; },
abstract = {Microbial mats collected at cold methane seeps in the Black Sea carry out anaerobic oxidation of methane (AOM) to carbon dioxide using sulfate as the electron acceptor. These mats, which predominantly consist of sulfate-reducing bacteria and archaea of the ANME-1 and ANME-2 type, contain large amounts of proteins very similar to methyl-coenzyme M reductase from methanogenic archaea. Mass spectrometry of mat samples revealed the presence of two nickel-containing cofactors in comparable amounts, one with the same mass as coenzyme F430 from methanogens (m/z = 905) and one with a mass that is 46 Da higher (m/z = 951). The two cofactors were isolated and purified, and their constitution and absolute configuration were determined. The cofactor with m/z = 905 was proven to be identical to coenzyme F430 from methanogens. For the m/z = 951 species, high resolution ICP-MS pointed to F430 + CH2S as the molecular formula, and LA-ICP-SF MS finally confirmed the presence of one sulfur atom per nickel. Esterification gave two stereoisomeric pentamethyl esters with m/z = 1021, which could be purified by reverse phase HPLC and were subjected to comprehensive NMR analysis, allowing determination of their constitution and configuration as (17(2)S)-17(2)-methylthio-F430 pentamethyl ester and (17(2)R)-17(2)-methylthio-F430 pentamethyl ester. The corresponding diastereoisomeric pentaacids could also be separated by HPLC and were correlated to the esters via mild hydrolysis of the latter. Equilibration of the pentaacids under acid catalysis showed that the (17(2)S) isomer is the naturally occurring albeit thermodynamically less stable one. The more stable (17(2)R) isomer (80% at equilibrium) is an isolation artifact generated under the acidic conditions necessary for the isolation of the cofactors from the calcium carbonate-encrusted mats.},
}
@article {pmid18641970,
year = {2008},
author = {Huber, H and Soppa, J},
title = {Gene regulation and genome function in Archaea: a progress survey.},
journal = {Archives of microbiology},
volume = {190},
number = {3},
pages = {195-196},
doi = {10.1007/s00203-008-0412-4},
pmid = {18641970},
issn = {1432-072X},
mesh = {Archaea/*genetics ; *Gene Expression Regulation, Archaeal ; *Genome, Archaeal ; Genomics ; },
}
@article {pmid18641632,
year = {2008},
author = {Lipp, JS and Morono, Y and Inagaki, F and Hinrichs, KU},
title = {Significant contribution of Archaea to extant biomass in marine subsurface sediments.},
journal = {Nature},
volume = {454},
number = {7207},
pages = {991-994},
doi = {10.1038/nature07174},
pmid = {18641632},
issn = {1476-4687},
mesh = {Archaea/chemistry/genetics/*physiology ; Bacteria/genetics/isolation &amp; purification ; Bacterial Physiological Phenomena ; *Biomass ; Carbon/metabolism ; Colony Count, Microbial ; Genes, Archaeal/genetics ; Genes, Bacterial/genetics ; Geologic Sediments/*microbiology ; Membrane Lipids/metabolism ; Oceans and Seas ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Deep drilling into the marine sea floor has uncovered a vast sedimentary ecosystem of microbial cells. Extrapolation of direct counts of stained microbial cells to the total volume of habitable marine subsurface sediments suggests that between 56 Pg (ref. 1) and 303 Pg (ref. 3) of cellular carbon could be stored in this largely unexplored habitat. From recent studies using various culture-independent techniques, no clear picture has yet emerged as to whether Archaea or Bacteria are more abundant in this extensive ecosystem. Here we show that in subsurface sediments buried deeper than 1 m in a wide range of oceanographic settings at least 87% of intact polar membrane lipids, biomarkers for the presence of live cells, are attributable to archaeal membranes, suggesting that Archaea constitute a major fraction of the biomass. Results obtained from modified quantitative polymerase chain reaction and slot-blot hybridization protocols support the lipid-based evidence and indicate that these techniques have previously underestimated archaeal biomass. The lipid concentrations are proportional to those of total organic carbon. On the basis of this relationship, we derived an independent estimate of amounts of cellular carbon in the global marine subsurface biosphere. Our estimate of 90 Pg of cellular carbon is consistent, within an order of magnitude, with previous estimates, and underscores the importance of marine subsurface habitats for global biomass budgets.},
}
@article {pmid18635779,
year = {2008},
author = {Ettema, TJ and Andersson, SG},
title = {Comment on "A 3-hydroxypropionate/4-hydroxybutyrate autotrophic carbon dioxide assimilation pathway in Archaea".},
journal = {Science (New York, N.Y.)},
volume = {321},
number = {5887},
pages = {342; author reply 342},
doi = {10.1126/science.1158879},
pmid = {18635779},
issn = {1095-9203},
mesh = {Archaea/classification/genetics/*metabolism ; Autotrophic Processes ; Bacteria, Anaerobic/classification/genetics/metabolism ; Carbon Dioxide/*metabolism ; Hydro-Lyases/chemistry/*genetics/*metabolism ; Hydroxybutyrates/*metabolism ; Lactic Acid/*analogs &amp; derivatives/metabolism ; Metabolic Networks and Pathways ; Oceans and Seas ; Phylogeny ; Seawater/*microbiology ; },
abstract = {Berg et al. (Reports, 14 December 2007, p. 1782) reported the discovery of an autotrophic carbon dioxide-fixation pathway in Archaea and implicated a substantial role of this pathway in global carbon cycling based on sequence analysis of Global Ocean Sampling data. We question the validity of the latter claim.},
}
@article {pmid18634895,
year = {2008},
author = {Hirasawa, JS and Sarti, A and Del Aguila, NK and Varesche, MB},
title = {Application of molecular techniques to evaluate the methanogenic archaea and anaerobic bacteria in the presence of oxygen with different COD:sulfate ratios in a UASB reactor.},
journal = {Anaerobe},
volume = {14},
number = {4},
pages = {209-218},
doi = {10.1016/j.anaerobe.2008.06.003},
pmid = {18634895},
issn = {1095-8274},
mesh = {Archaea/classification/*drug effects/genetics/isolation &amp; purification ; Bacteria, Anaerobic/classification/*drug effects/genetics/isolation &amp; purification ; Bioreactors/*microbiology ; DNA Fingerprinting ; DNA, Archaeal/chemistry/genetics ; DNA, Bacterial/chemistry/genetics ; Electrophoresis, Polyacrylamide Gel ; Ethanol/*metabolism ; In Situ Hybridization, Fluorescence/methods ; Methane/metabolism ; Nucleic Acid Denaturation ; Oligonucleotide Probes/genetics ; Oxygen/*toxicity ; Sequence Analysis, DNA ; Sewage/microbiology ; Sulfates/*metabolism ; },
abstract = {In this paper, the microbial characteristics of the granular sludge in the presence of oxygen (3.0+/-0.7 mg O2 l(-1)) were analyzed using molecular biology techniques. The granules were provided by an upflow anaerobic sludge blanket (UASB) operated over 469 days and fed with synthetic substrate. Ethanol and sulfate were added to obtain different COD/SO4(2-) ratios (3.0, 2.0, and 1.6). The results of fluorescent in situ hybridization (FISH) analyses showed that archaeal cells, detected by the ARC915 probe, accounted for 77%, 84%, and 75% in the COD/SO(4)(2-) ratios (3.0, 2.0, and 1.6, respectively). Methanosaeta sp. was the predominant acetoclastic archaea observed by optical microscopy and FISH analyses, and confirmed by sequencing of the excised bands of the DGGE gel with a similarity of 96%. The sulfate-reducing bacterium Desulfovibrio vulgaris subsp. vulgaris (similarity of 99%) was verified by sequencing of the DGGE band. Others identified microorganism were similar to Shewanella sp. and Desulfitobacterium hafniense, with similarities of 95% and 99%, respectively. These results confirmed that the presence of oxygen did not severely affect the metabolism of microorganisms that are commonly considered strictly anaerobic. We obtained mean efficiencies of organic matter conversion and sulfate reducing higher than 74%.},
}
@article {pmid18625304,
year = {2008},
author = {Soler, N and Marguet, E and Verbavatz, JM and Forterre, P},
title = {Virus-like vesicles and extracellular DNA produced by hyperthermophilic archaea of the order Thermococcales.},
journal = {Research in microbiology},
volume = {159},
number = {5},
pages = {390-399},
doi = {10.1016/j.resmic.2008.04.015},
pmid = {18625304},
issn = {0923-2508},
mesh = {Cytoplasmic Vesicles/*chemistry/genetics/ultrastructure/virology ; DNA, Archaeal/*chemistry/genetics ; Temperature ; Thermococcales/*chemistry/*genetics/ultrastructure/virology ; },
abstract = {Cultures of hyperthermophilic archaea (order Thermococcales) have been analyzed by electron microscopy and epifluorescence staining for the presence of virus-like particles. We found that most strains of Thermococcus and Pyrococcus produce various types of spherical membrane vesicles and unusual filamentous structures. Cellular DNA can be strongly associated with vesicles and appears as fluorescent dots by epifluorescence microscopy, suggesting that some particles assumed to be viruses in ecological studies might instead be vesicles associated with extracellular DNA. DNA in vesicle preparations is remarkably resistant to DNase treatment and thermodenaturation, indicating that association with vesicles could be an important factor determining DNA stability in natural environments.},
}
@article {pmid18621894,
year = {2008},
author = {Ng, SY and Zolghadr, B and Driessen, AJ and Albers, SV and Jarrell, KF},
title = {Cell surface structures of archaea.},
journal = {Journal of bacteriology},
volume = {190},
number = {18},
pages = {6039-6047},
pmid = {18621894},
issn = {1098-5530},
mesh = {Archaea/*chemistry/genetics/metabolism/*ultrastructure ; Bacterial Proteins/genetics/metabolism ; Cell Surface Extensions/*chemistry/genetics/metabolism/*ultrastructure ; Models, Molecular ; },
}
@article {pmid18587410,
year = {2008},
author = {Thauer, RK and Kaster, AK and Seedorf, H and Buckel, W and Hedderich, R},
title = {Methanogenic archaea: ecologically relevant differences in energy conservation.},
journal = {Nature reviews. Microbiology},
volume = {6},
number = {8},
pages = {579-591},
doi = {10.1038/nrmicro1931},
pmid = {18587410},
issn = {1740-1534},
mesh = {Archaea/*classification/genetics/metabolism ; Archaeal Proteins/*genetics/metabolism ; Cytochromes/*metabolism ; DNA, Archaeal/genetics ; *Energy Metabolism ; Evolution, Molecular ; Genes, Archaeal/genetics ; Methane/*metabolism ; Phylogeny ; },
abstract = {Most methanogenic archaea can reduce CO(2) with H(2) to methane, and it is generally assumed that the reactions and mechanisms of energy conservation that are involved are largely the same in all methanogens. However, this does not take into account the fact that methanogens with cytochromes have considerably higher growth yields and threshold concentrations for H(2) than methanogens without cytochromes. These and other differences can be explained by the proposal outlined in this Review that in methanogens with cytochromes, the first and last steps in methanogenesis from CO(2) are coupled chemiosmotically, whereas in methanogens without cytochromes, these steps are energetically coupled by a cytoplasmic enzyme complex that mediates flavin-based electron bifurcation.},
}
@article {pmid18575848,
year = {2008},
author = {Oelgeschläger, E and Rother, M},
title = {Carbon monoxide-dependent energy metabolism in anaerobic bacteria and archaea.},
journal = {Archives of microbiology},
volume = {190},
number = {3},
pages = {257-269},
doi = {10.1007/s00203-008-0382-6},
pmid = {18575848},
issn = {1432-072X},
mesh = {Acetates/metabolism ; Aldehyde Oxidoreductases ; Anaerobiosis ; Bacteria, Anaerobic/*metabolism/physiology ; Carbon Monoxide/*metabolism ; *Energy Metabolism ; Hydrogen/metabolism ; Methane/metabolism ; Methanosarcina/*metabolism/physiology ; Multienzyme Complexes ; Sulfur/metabolism ; },
abstract = {Despite its toxicity for the majority of living matter on our planet, numerous microorganisms, both aerobic and anaerobic, can use carbon monoxide (CO) as a source of carbon and/or energy for growth. The capacity to employ carboxidotrophic energy metabolism anaerobically is found in phylogenetically diverse members of the Bacteria and the Archaea. The oxidation of CO is coupled to numerous respiratory processes, such as desulfurication, hydrogenogenesis, acetogenesis, and methanogenesis. Although as diverse as the organisms capable of it, any CO-dependent energy metabolism known depends on the presence of carbon monoxide dehydrogenase. This review summarizes recent insights into the CO-dependent physiology of anaerobic microorganisms with a focus on methanogenic archaea. Carboxidotrophic growth of Methanosarcina acetivorans, thought to strictly rely on the process of methanogenesis, also involves formation of methylated thiols, formate, and even acetogenesis, and, thus, exemplifies how the beneficial redox properties of CO can be exploited in unexpected ways by anaerobic microorganisms.},
}
@article {pmid18575118,
year = {2008},
author = {Sun, Y and Zuo, J and Chen, L and Wang, Y},
title = {Eubacteria and Archaea community of simultaneous methanogenesis and denitrification granular sludge.},
journal = {Journal of environmental sciences (China)},
volume = {20},
number = {5},
pages = {626-631},
doi = {10.1016/s1001-0742(08)62104-x},
pmid = {18575118},
issn = {1001-0742},
mesh = {Archaea/genetics/growth &amp; development/*metabolism ; Bacteria/genetics/growth &amp; development/*metabolism ; Bioreactors ; Methane/*metabolism ; Microscopy, Electron, Scanning ; Nitrates/*metabolism ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Sewage/*microbiology ; },
abstract = {Based on the successful performance of a lab-scale upflow anaerobic sludge blanket (UASB) reactor with the capacity of simultaneous methanogenesis and denitrification (SMD), the specific phylogenetic groups and community structure of microbes in the SMD granule in the UASB reactor were investigated by the construction of the Eubacteria and Archaea 16S rDNA clone libraries, fragment length polymorphism, and sequence blast. Real time quantitative-polymerase chain reaction (RTQ-PCR) technique was used to quantify the contents of Eubacteria and Archaea in the SMD granule. The contents of some special predominant methanogens were also investigated. The results indicated that the Methanosaeta and Methanobacteria were the predominant methanogens in all Archaea in the SMD granule, with contents of 71.59% and 22.73% in all 88 random Archaea clones, respectively. The diversity of Eubacteria was much more complex than that of Archaea. The low GC positive gram bacteria and epsilon-Protebacteria were the main predominant Eubacteria species in SMD granule, their contents were 49.62% and 12.03% in all 133 random Eubacteria clones respectively. The results of RTQ-PCR indicated that the content of Archaea was less than Eubacteria, the Archaea content in total microorganisms in SMD granule was about 27.6%.},
}
@article {pmid18535141,
year = {2008},
author = {Elkins, JG and Podar, M and Graham, DE and Makarova, KS and Wolf, Y and Randau, L and Hedlund, BP and Brochier-Armanet, C and Kunin, V and Anderson, I and Lapidus, A and Goltsman, E and Barry, K and Koonin, EV and Hugenholtz, P and Kyrpides, N and Wanner, G and Richardson, P and Keller, M and Stetter, KO},
title = {A korarchaeal genome reveals insights into the evolution of the Archaea.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {105},
number = {23},
pages = {8102-8107},
pmid = {18535141},
issn = {1091-6490},
mesh = {*Biological Evolution ; Cell Cycle ; DNA Replication ; Energy Metabolism ; Evolution, Molecular ; Genome, Archaeal/*genetics ; Korarchaeota/cytology/*genetics/ultrastructure ; Phylogeny ; Protein Biosynthesis ; Sequence Analysis, DNA ; Transcription, Genetic ; },
abstract = {The candidate division Korarchaeota comprises a group of uncultivated microorganisms that, by their small subunit rRNA phylogeny, may have diverged early from the major archaeal phyla Crenarchaeota and Euryarchaeota. Here, we report the initial characterization of a member of the Korarchaeota with the proposed name, "Candidatus Korarchaeum cryptofilum," which exhibits an ultrathin filamentous morphology. To investigate possible ancestral relationships between deep-branching Korarchaeota and other phyla, we used whole-genome shotgun sequencing to construct a complete composite korarchaeal genome from enriched cells. The genome was assembled into a single contig 1.59 Mb in length with a G + C content of 49%. Of the 1,617 predicted protein-coding genes, 1,382 (85%) could be assigned to a revised set of archaeal Clusters of Orthologous Groups (COGs). The predicted gene functions suggest that the organism relies on a simple mode of peptide fermentation for carbon and energy and lacks the ability to synthesize de novo purines, CoA, and several other cofactors. Phylogenetic analyses based on conserved single genes and concatenated protein sequences positioned the korarchaeote as a deep archaeal lineage with an apparent affinity to the Crenarchaeota. However, the predicted gene content revealed that several conserved cellular systems, such as cell division, DNA replication, and tRNA maturation, resemble the counterparts in the Euryarchaeota. In light of the known composition of archaeal genomes, the Korarchaeota might have retained a set of cellular features that represents the ancestral archaeal form.},
}
@article {pmid18515030,
year = {2008},
author = {Koga, Y and Nakano, M},
title = {A dendrogram of archaea based on lipid component parts composition and its relationship to rRNA phylogeny.},
journal = {Systematic and applied microbiology},
volume = {31},
number = {3},
pages = {169-182},
doi = {10.1016/j.syapm.2008.02.005},
pmid = {18515030},
issn = {0723-2020},
mesh = {Archaeal Proteins/*genetics ; Cluster Analysis ; Euryarchaeota/*chemistry/*classification/genetics/metabolism ; Evolution, Molecular ; Lipids/*analysis/biosynthesis/*chemistry/classification ; Membrane Lipids/analysis/biosynthesis/chemistry ; Mutation ; *Phylogeny ; RNA, Archaeal/genetics ; RNA, Ribosomal/*genetics ; },
abstract = {The results of two objective and quantitative, computer-assisted analyses of the lipid component parts distribution pattern among various archaeal organisms belonging to Euryarchaeota are reported. One was a cluster analysis and the other a selection of unique combinations of lipid component parts found exclusively in a given taxon. The cluster analysis revealed that the distribution of lipid component parts was correlated with phylogeny based on small subunit rRNA sequences, although there was some discrepancy with rRNA phylogeny. A hypothesis that may explain the reason for the correlation and the discrepancy is proposed. In our scenario, we assumed that random and independent mutations on the rRNA and lipid biosynthesis genes may result largely in coincided evolution. The fact that RNA and lipid are semantide and episemantic molecules, respectively, is the fundamental difference between the phylogeny of RNA and lipid. Moreover, different selective pressures on RNA and lipids exert different effects on their evolution. Unique lipid component parts were detected for eight out of nine orders, 14 families, and 22 genera of the Euryarchaeota analyzed. A unique lipid component parts combination pattern characterized the taxon. The results confirm and extend a previously reported conclusion based on a more statistical basis.},
}
@article {pmid18501543,
year = {2008},
author = {Klocke, M and Nettmann, E and Bergmann, I and Mundt, K and Souidi, K and Mumme, J and Linke, B},
title = {Characterization of the methanogenic Archaea within two-phase biogas reactor systems operated with plant biomass.},
journal = {Systematic and applied microbiology},
volume = {31},
number = {3},
pages = {190-205},
doi = {10.1016/j.syapm.2008.02.003},
pmid = {18501543},
issn = {0723-2020},
mesh = {Anaerobiosis ; *Biomass ; Bioreactors ; DNA, Archaeal/analysis/isolation &amp; purification ; DNA, Ribosomal/analysis ; Edible Grain/*metabolism/*microbiology ; Euryarchaeota/*classification/genetics/growth &amp; development/metabolism ; Gene Library ; Methane/*metabolism ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Restriction Mapping ; Sequence Analysis, DNA ; Silage/*microbiology ; },
abstract = {The two-phase leach-bed system is a biogas reactor system optimized for the utilization of energy crop silages at maximized loading rates under maintenance of an optimal microbial activity. In this study, a characterization of the methanogenic microbial community within this reactor system was conducted for the first time. Accordingly, effluent samples from the anaerobic filter and the silage digesting leach-bed reactors of both a laboratory-scale two-phase biogas reactor system and a scaled-up commercial on-farm pilot plant were investigated. In total, five Archaea-specific 16S rDNA libraries were constructed and analyzed by amplified rDNA restriction analysis (ARDRA), with subsequent phylogenetic analysis of nucleotide sequences for individual ARDRA patterns. A quantification of major methanogenic Archaea groups was conducted by real-time PCR. A total of 663 clones were analyzed and 45 operational taxonomic units (OTUs) related to methanogenic Archaea were detected. These OTUs were related to the orders Methanosarcinales, Methanomicrobiales and Methanobacteriales, as well as the hitherto uncultured CA-11 and ARC-I groups, and most of them occurred throughout all the compartments of both two-phase biogas reactors. The proportion of acetotrophic to hydrogenotrophic methanogens differed between the laboratory and the pilot scale system. A total of 56% of the clones from the 16S rDNA library derived from the laboratory biogas system were assigned to presumably acetotrophic members of Methanosarcinales. In contrast, these OTUs were less abundant in the 16S rDNA library derived from samples of the pilot plant. Therein, the most dominant OTUs were Methanoculleus-related OTUs, which presumably indicated the predominant presence of hydrogenotrophic methanogens. These findings were confirmed by group-specific quantitative real-time PCR assays. The results indicated that the fraction of acetotrophic and hydrogenotrophic methanogens within a biogas reactor caused certain variations, which may reflect varying substrate utilization during methanogenesis.},
}
@article {pmid18498366,
year = {2008},
author = {Jiang, H and Dong, H and Yu, B and Ye, Q and Shen, J and Rowe, H and Zhang, C},
title = {Dominance of putative marine benthic Archaea in Qinghai Lake, north-western China.},
journal = {Environmental microbiology},
volume = {10},
number = {9},
pages = {2355-2367},
doi = {10.1111/j.1462-2920.2008.01661.x},
pmid = {18498366},
issn = {1462-2920},
mesh = {Archaea/classification/*genetics ; *Biodiversity ; China ; DNA, Archaeal/genetics ; Fresh Water/chemistry/*microbiology ; Genes, Archaeal ; Genes, rRNA ; Geologic Sediments/chemistry/microbiology ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; *Water Microbiology ; },
abstract = {Recent studies have revealed important and versatile roles that Archaea play in a wide variety of environmental processes on Earth. In this study, we investigated the abundance and diversity of archaeal communities in lake water and a 5 m sediment core collected from Qinghai Lake on the Tibetan Plateau, north-western China. An integrated approach was employed including geochemistry, quantitative polymerase chain reaction (Q-PCR) and 16S rRNA gene analysis. Here, we show that Archaea dominated the prokaryotic community in the lake sediments. Members of putative marine benthic groups [Marine Benthic Group (MBG)-B, -C and -D] and Miscellaneous Crenarchaeotic Group (MCG) were dominant, many of which were previously reported to be predominantly present in deep-sea environments. These results demonstrate that these groups are not limited to marine sediments. Despite their ubiquitous presence in aquatic environments, metabolic functions of these important groups largely remain unknown. Whereas many of these groups (such as MBG-B and -D) have typically been found in methane-hydrate deposits in marine environments, our carbon isotopic and molecular results from Qinghai Lake sediments indicate a lacustrine origin.},
}
@article {pmid18485204,
year = {2008},
author = {DasSarma, P and DasSarma, S},
title = {On the origin of prokaryotic "species": the taxonomy of halophilic Archaea.},
journal = {Saline systems},
volume = {4},
number = {},
pages = {5},
pmid = {18485204},
issn = {1746-1448},
abstract = {The consistent use of the taxonomic system of binomial nomenclature (genus and species) was first popularized by Linnaeus nearly three-hundred years ago to classify mainly plants and animals. His main goal was to give labels that would ensure that biologists could agree on which organism was under investigation. One-hundred fifty years later, Darwin considered the term species as one of convenience and not essentially different from variety. In the modern era, exploration of the world's niches together with advances in genomics have expanded the number of named species to over 1.8 million, including many microorganisms. However, even this large number excludes over 90% of microorganisms that have yet to be cultured or classified. In naming new isolates in the microbial world, the challenge remains the lack of a universally held and evenly applied standard for a species. The definition of species based on the capacity to form fertile offspring is not applicable to microorganisms and 70% DNA-DNA hybridization appears rather crude in light of the many completed genome sequences. The popular phylogenetic marker, 16S rRNA, is tricky for classification since it does not provide multiple characteristics or phenotypes used classically for this purpose. Using most criteria, agreement may usually be found at the genus level, but species level distinctions are problematic. These observations lend credence to the proposal that the species concept is flawed when applied to prokaryotes. In order to address this topic, we have examined the taxonomy of extremely halophilic Archaea, where the order, family, and even a genus designation have become obsolete, and the naming and renaming of certain species has led to much confusion in the scientific community.},
}
@article {pmid18479447,
year = {2008},
author = {Aller, JY and Kemp, PF},
title = {Are Archaea inherently less diverse than Bacteria in the same environments?.},
journal = {FEMS microbiology ecology},
volume = {65},
number = {1},
pages = {74-87},
doi = {10.1111/j.1574-6941.2008.00498.x},
pmid = {18479447},
issn = {0168-6496},
mesh = {Archaea/*classification/genetics/growth &amp; development ; Bacteria/*classification/genetics/growth &amp; development ; Biodiversity ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; DNA, Ribosomal ; *Ecosystem ; Gene Library ; Genes, rRNA ; *Genetic Variation ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Like Bacteria, Archaea occur in a wide variety of environments, only some of which can be considered 'extreme'. We compare archaeal diversity, as represented by 173 16S rRNA gene libraries described in published reports, to bacterial diversity in 79 libraries from the same source environments. An objective assessment indicated that 114 archaeal libraries and 45 bacterial libraries were large enough to yield stable estimates of total phylotype richness. Archaeal libraries were seldom as large or diverse as bacterial libraries from the same environments. However, a relatively larger proportion of libraries were large enough to effectively capture rare as well as dominant phylotypes in archaeal communities. In contrast to bacterial libraries, the number of phylotypes did not correlate with library size; thus, 'larger' may not necessarily be 'better' for determining diversity in archaeal libraries. Differences in diversity suggest possible differences in ecological roles of Archaea and Bacteria; however, information is lacking on relative abundances and metabolic activities within the sampled communities, as well as the possible existence of microhabitats. The significance of phylogenetic diversity as opposed to functional diversity remains unclear, and should be a high priority for continuing research.},
}
@article {pmid18476920,
year = {2008},
author = {Yurist-Doutsch, S and Chaban, B and VanDyke, DJ and Jarrell, KF and Eichler, J},
title = {Sweet to the extreme: protein glycosylation in Archaea.},
journal = {Molecular microbiology},
volume = {68},
number = {5},
pages = {1079-1084},
doi = {10.1111/j.1365-2958.2008.06224.x},
pmid = {18476920},
issn = {1365-2958},
mesh = {Archaea/*chemistry/metabolism ; Archaeal Proteins/*chemistry/metabolism ; Glycoproteins/*chemistry/metabolism ; Glycosylation ; Protein Processing, Post-Translational/*physiology ; },
abstract = {Post-translational modifications account for much of the biological diversity generated at the proteome level. Of these, glycosylation is the most prevalent. Long thought to be unique to Eukarya, it is now clear that both Bacteria and Archaea are also capable of N-glycosylation, namely the covalent linkage of oligosaccharides to select target asparagine residues. However, while the eukaryal and bacterial N-glycosylation pathways are relatively well defined, little is known of the parallel process in Archaea. Of late, however, major advances have been made in describing the process of archaeal N-glycosylation. Such efforts have shown, as is often the case in archaeal biology, that protein N-glycosylation in Archaea combines particular aspects of the eukaryal and bacterial pathways along with traits unique to this life form. For instance, while the oligosaccharides of archaeal glycoproteins include nucleotide-activated sugars formed by bacterial pathways, the lipid carrier on which such oligosaccharides are assembled is the same as used in eukaryal N-glycosylation. By contrast, transfer of assembled oligosaccharides to their protein targets shows Archaea-specific properties. Finally, addressing N-glycosylation from an archaeal perspective is providing new general insight into this event, as exemplified by the solution of the first crystal structure of an oligosaccharide transferase from an archaeal source.},
}
@article {pmid18465082,
year = {2008},
author = {Park, SJ and Park, BJ and Rhee, SK},
title = {Comparative analysis of archaeal 16S rRNA and amoA genes to estimate the abundance and diversity of ammonia-oxidizing archaea in marine sediments.},
journal = {Extremophiles : life under extreme conditions},
volume = {12},
number = {4},
pages = {605-615},
pmid = {18465082},
issn = {1431-0651},
mesh = {Ammonia/*chemistry ; Archaea/*genetics ; Cloning, Molecular ; Gene Library ; Genetic Variation ; Geologic Sediments/*microbiology ; Models, Genetic ; Oxidoreductases/*genetics ; Oxygen/*chemistry ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Seawater/microbiology ; Sequence Analysis, DNA ; Software ; },
abstract = {Considering their abundance and broad distribution, non-extremophilic Crenarchaeota are likely to play important roles in global organic and inorganic matter cycles. The diversity and abundance of archaeal 16S rRNA and putative ammonia monooxygenase alpha-subunit (amoA) genes were comparatively analyzed to study genetic potential for nitrification of ammonia-oxidizing archaea (AOA) in the surface layers (0-1 cm) of four marine sediments of the East Sea, Korea. After analysis of a 16S rRNA gene clone library, we found various archaeal groups that include the crenarchaeotal group (CG) I.1a (54.8%) and CG I.1b (5.8%), both of which are known to harbor ammonia oxidizers. Notably, the 16S rRNA gene of CG I.1b has only previously been observed in terrestrial environments. The 16S rRNA gene sequence data revealed a distinct difference in archaeal community among sites of marine sediments. Most of the obtained amoA sequences were not closely related to those of the clones retrieved from estuarine sediments and marine water columns. Furthermore, clades of unique amoA sequences were likely to cluster according to sampling sites. Using real-time PCR, quantitative analysis of amoA copy numbers showed that the copy numbers of archaeal amoA ranged from 1.1x10(7) to 4.9x10(7) per gram of sediment and were more numerous than those of bacterial amoA, with ratios ranging from 11 to 28. In conclusion, diverse CG I.1a and CG I.1b AOA inhabit surface layers of marine sediments and AOA, and especially, CG I.1a are more numerous than other ammonia-oxidizing bacteria.},
}
@article {pmid18463691,
year = {2008},
author = {Martin-Cuadrado, AB and Rodriguez-Valera, F and Moreira, D and Alba, JC and Ivars-Martínez, E and Henn, MR and Talla, E and López-García, P},
title = {Hindsight in the relative abundance, metabolic potential and genome dynamics of uncultivated marine archaea from comparative metagenomic analyses of bathypelagic plankton of different oceanic regions.},
journal = {The ISME journal},
volume = {2},
number = {8},
pages = {865-886},
doi = {10.1038/ismej.2008.40},
pmid = {18463691},
issn = {1751-7370},
mesh = {Animals ; Archaea/*classification/genetics/*isolation &amp; purification ; Archaeal Proteins/genetics ; *Biodiversity ; Cloning, Molecular ; Conserved Sequence ; DNA, Archaeal/chemistry/genetics/*isolation &amp; purification ; DNA, Ribosomal/chemistry/genetics ; Gene Library ; Genome, Archaeal ; Molecular Sequence Data ; Phylogeny ; Plankton/*microbiology ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; Synteny ; },
abstract = {Marine planktonic archaea are widespread and abundant in deep oceanic waters but, despite their obvious ecological importance, little is known about them. Metagenomic analyses of large genome fragments allow access to both gene content and genome structure from single individuals of these cultivation-reluctant organisms. We present the comparative analysis of 22 archaeal genomic clones containing 16S rRNA genes that were selected from four metagenomic libraries constructed from meso- and bathypelagic plankton of different oceanic regions (South Atlantic, Antarctic Polar Front, Adriatic and Ionian Sea; depths from 500 to 3000 m). We sequenced clones of the divergent archaeal lineages Group 1A (Crenarchaeota) and Group III (Euryarchaeota) as well as clones from the more frequent Group I Crenarchaeota and Group II Euryarchaeota. Whenever possible, we analysed clones that had identical or nearly identical 16S rRNA genes and that were retrieved from distant geographical locations, that is, that defined pan-oceanic operational taxonomic units (OTUs). We detected genes involved in nitrogen fixation in Group 1A Crenarchaeota, and genes involved in carbon fixation pathways and oligopeptide importers in Group I Crenarchaeota, which could confirm the idea that these are mixotrophic. A two-component system resembling that found in ammonia-oxidizing bacteria was found in Group III Euryarchaeota, while genes for anaerobic respiratory chains were detected in Group II Euryarchaeota. Whereas gene sequence conservation was high, and recombination and gene shuffling extensive within and between OTUs in Group I Crenarchaeota, gene sequence conservation was low and global synteny maintained in Group II Euryarchaeota. This implies remarkable differences in genome dynamics in Group I Crenarchaeota and Group II Euryarchaeota with recombination and mutation being, respectively, the dominant genome-shaping forces. These observations, along with variations in GC content, led us to hypothesize that the two groups of organisms have fundamentally different lifestyles.},
}
@article {pmid18441051,
year = {2008},
author = {Targanski, I and Cherkasova, V},
title = {Analysis of genomic tRNA sets from Bacteria, Archaea, and Eukarya points to anticodon-codon hydrogen bonds as a major determinant of tRNA compositional variations.},
journal = {RNA (New York, N.Y.)},
volume = {14},
number = {6},
pages = {1095-1109},
pmid = {18441051},
issn = {1469-9001},
mesh = {Animals ; Anticodon/*chemistry ; Base Composition ; Base Pairing ; Base Sequence ; Codon/*chemistry ; *Genome ; *Genome, Archaeal ; *Genome, Bacterial ; Hydrogen Bonding ; Mice ; Molecular Sequence Data ; Nucleic Acid Conformation ; RNA, Transfer/*chemistry/genetics ; },
abstract = {Analysis of 100 complete sets of the cytoplasmic elongator tRNA genes from Bacteria, Archaea, and Eukarya pointed to correspondences between types of anticodon and composition of the rest of the tRNA body. The number of the hydrogen bonds formed between the complementary nucleotides in the anticodon-codon duplex appeared as a major quantitative parameter determining covariations in all three domains of life. Our analysis has supported and advanced the "extended anticodon" concept that is based on the argument that the decoding performance of the anticodon is enhanced by selection of a matching anticodon stem-loop sequence, as reported by Yarus in 1982. In addition to the anticodon stem-loop, we have found covariations between the anticodon nucleotides and the composition of the distant regions of their respective tRNAs that include dihydrouridine (D) and thymidyl (T) stem-loops. The majority of the covariable tRNA positions were found at the regions with the increased dynamic potential--such as stem-loop and stem-stem junctions. The consistent occurrences of the covariations on the multigenomic level suggest that the number and pattern of the hydrogen bonds in the anticodon-codon duplex constitute a major factor in the course of translation that is reflected in the fine-tuning of the tRNA composition and structure.},
}
@article {pmid18430011,
year = {2008},
author = {Chen, XP and Zhu, YG and Xia, Y and Shen, JP and He, JZ},
title = {Ammonia-oxidizing archaea: important players in paddy rhizosphere soil?.},
journal = {Environmental microbiology},
volume = {10},
number = {8},
pages = {1978-1987},
doi = {10.1111/j.1462-2920.2008.01613.x},
pmid = {18430011},
issn = {1462-2920},
mesh = {Ammonia/*metabolism ; *Archaea/genetics/metabolism ; DNA Fingerprinting ; Molecular Sequence Data ; Oryza/microbiology ; Oxidation-Reduction ; Oxidoreductases/*genetics/metabolism ; Phylogeny ; Plant Roots/microbiology ; *Soil Microbiology ; *Wetlands ; },
abstract = {The diversity (richness and community composition) of ammonia-oxidizing archaea (AOA) and bacteria (AOB) in paddy soil with different nitrogen (N) fertilizer amendments for 5 weeks were investigated using quantitative real-time polymerase chain reaction, denaturing gradient gel electrophoresis (DGGE) jand clone library analysis based on the ammonia monooxygenase alpha-subunit (amoA) gene. Ammonia-oxidizing archaea predominated among ammonia-oxidizing prokaryotes in the paddy soil, and the AOA:AOB DNA-targeted amoA gene ratios ranged from 1.2 to 69.3. Ammonia-oxidizing archaea were more abundant in the rhizosphere than in bulk soil. Rice cultivation led to greater abundance of AOA than AOB amoA gene copies and to differences in AOA and AOB community composition. These results show that AOA is dominant in the rhizosphere paddy soil in this study, and we assume that AOA were influenced more by exudation from rice root (e.g. oxygen, carbon dioxide) than AOB.},
}
@article {pmid18422645,
year = {2008},
author = {Ronconi, S and Jonczyk, R and Genschel, U},
title = {A novel isoform of pantothenate synthetase in the Archaea.},
journal = {The FEBS journal},
volume = {275},
number = {11},
pages = {2754-2764},
doi = {10.1111/j.1742-4658.2008.06416.x},
pmid = {18422645},
issn = {1742-464X},
mesh = {Adenosine Diphosphate/chemistry ; Adenosine Monophosphate/chemistry ; Archaea/*enzymology/metabolism ; Archaeal Proteins/*chemistry ; Conserved Sequence ; Escherichia coli/metabolism ; Genetic Complementation Test ; Genomics ; Kinetics ; Methanosarcina/*metabolism ; Models, Biological ; Peptide Synthases/*chemistry ; Protein Isoforms ; Recombinant Proteins/chemistry ; },
abstract = {The linear biosynthetic pathway leading from alpha-ketoisovalerate to pantothenate (vitamin B5) and on to CoA comprises eight steps in the Bacteria and Eukaryota. Genes for up to six steps of this pathway can be identified by sequence homology in individual archaeal genomes. However, there are no archaeal homologs to known isoforms of pantothenate synthetase (PS) or pantothenate kinase. Using comparative genomics, we previously identified two conserved archaeal protein families as the best candidates for the missing steps. Here we report the characterization of the predicted PS gene from Methanosarcina mazei, which encodes a hypothetical protein (MM2281) with no obvious homologs outside its own family. When expressed in Escherichia coli, MM2281 partially complemented an auxotrophic mutant without PS activity. Purified recombinant MM2281 showed no PS activity on its own, but the enzyme enabled substantial synthesis of [14C]4'-phosphopantothenate from [14C]beta-alanine, pantoate and ATP when coupled with E. coli pantothenate kinase. ADP, but not AMP, was detected as a coproduct of the coupled reaction. MM2281 also transferred the 14C-label from [14C]beta-alanine to pantothenate in the presence of pantoate and ADP, presumably through isotope exchange. No exchange took place when pantoate was removed or ADP replaced with AMP. Our results indicate that MM2281 represents a novel type of PS that forms ADP and is strongly inhibited by its product pantothenate. These properties differ substantially from those of bacterial PS, and may explain why PS genes, in contrast to other pantothenate biosynthetic genes, were not exchanged horizontally between the Bacteria and Archaea.},
}
@article {pmid18400081,
year = {2008},
author = {Berthon, J and Cortez, D and Forterre, P},
title = {Genomic context analysis in Archaea suggests previously unrecognized links between DNA replication and translation.},
journal = {Genome biology},
volume = {9},
number = {4},
pages = {R71},
pmid = {18400081},
issn = {1474-760X},
mesh = {Archaea/*genetics ; DNA Repair ; *DNA Replication ; Genome, Archaeal/*genetics ; Protein Binding ; *Protein Biosynthesis ; Systems Biology/*methods ; },
abstract = {BACKGROUND: Comparative analysis of genomes is valuable to explore evolution of genomes, deduce gene functions, or predict functional linking between proteins. Here, we have systematically analyzed the genomic environment of all known DNA replication genes in 27 archaeal genomes to infer new connections for DNA replication proteins from conserved genomic associations.<br><br>RESULTS: Two distinct sets of DNA replication genes frequently co-localize in archaeal genomes: the first includes the genes for PCNA, the small subunit of the DNA primase (PriS), and Gins15; the second comprises the genes for MCM and Gins23. Other genomic associations of genes encoding proteins involved in informational processes that may be functionally relevant at the cellular level have also been noted; in particular, the association between the genes for PCNA, transcription factor S, and NudF. Surprisingly, a conserved cluster of genes coding for proteins involved in translation or ribosome biogenesis (S27E, L44E, aIF-2 alpha, Nop10) is almost systematically contiguous to the group of genes coding for PCNA, PriS, and Gins15. The functional relevance of this cluster encoding proteins conserved in Archaea and Eukarya is strongly supported by statistical analysis. Interestingly, the gene encoding the S27E protein, also known as metallopanstimulin 1 (MPS-1) in human, is overexpressed in multiple cancer cell lines.<br><br>CONCLUSION: Our genome context analysis suggests specific functional interactions for proteins involved in DNA replication between each other or with proteins involved in DNA repair or transcription. Furthermore, it suggests a previously unrecognized regulatory network coupling DNA replication and translation in Archaea that may also exist in Eukarya.},
}
@article {pmid18393992,
year = {2008},
author = {Boyle-Yarwood, SA and Bottomley, PJ and Myrold, DD},
title = {Community composition of ammonia-oxidizing bacteria and archaea in soils under stands of red alder and Douglas fir in Oregon.},
journal = {Environmental microbiology},
volume = {10},
number = {11},
pages = {2956-2965},
doi = {10.1111/j.1462-2920.2008.01600.x},
pmid = {18393992},
issn = {1462-2920},
mesh = {Alnus/microbiology ; Ammonia/*metabolism ; Archaea/*classification/isolation &amp; purification/*metabolism ; Archaeal Proteins/genetics ; Bacteria/*classification/isolation &amp; purification/*metabolism ; Bacterial Proteins/genetics ; *Biodiversity ; Cluster Analysis ; DNA Fingerprinting ; Nitrites/metabolism ; Oregon ; Oxidation-Reduction ; Oxidoreductases/genetics ; Phylogeny ; Polymorphism, Restriction Fragment Length ; Pseudotsuga/microbiology ; Sequence Analysis, DNA ; *Soil Microbiology ; },
abstract = {This study determined nitrification activity and nitrifier community composition in soils under stands of red alder (Alnus rubra) and Douglas fir (Pseudotsuga menziesii) at two sites in Oregon. The H.J. Andrews Experimental Forest, located in the Cascade Mountains of Oregon, has low net N mineralization and gross nitrification rates. Cascade Head Experimental Forest, in the Coast Range, has higher net N mineralization and nitrification rates and soil pH is lower. Communities of putative bacterial [ammonia-oxidizing bacteria (AOB)] and archaeal [ammonia-oxidizing archaea (AOA)] ammonia oxidizers were examined by targeting the gene amoA, which codes for subunit A of ammonia monooxygenase. Nitrification potential was significantly higher in red alder compared with Douglas-fir soil and greater at Cascade Head than H.J. Andrews. Ammonia-oxidizing bacteria amoA genes were amplified from all soils, but AOA amoA genes could only be amplified at Cascade Head. Gene copy numbers of AOB and AOA amoA were similar at Cascade Head regardless of tree type (2.3-6.0 x 10(6)amoA gene copies g(-1) of soil). DNA sequences of amoA revealed that AOB were members of Nitrosospira clusters 1, 2 and 4. Ammonia-oxidizing bacteria community composition, determined by terminal restriction fragment length polymorphism (T-RFLP) profiles, varied among sites and between tree types. Many of the AOA amoA sequences clustered with environmental clones previously obtained from soil; however, several sequences were more similar to clones previously recovered from marine and estuarine sediments. As with AOB, the AOA community composition differed between red alder and Douglas-fir soils.},
}
@article {pmid18385982,
year = {2008},
author = {Scheuch, S and Marschaus, L and Sartorius-Neef, S and Pfeifer, F},
title = {Regulation of gvp genes encoding gas vesicle proteins in halophilic Archaea.},
journal = {Archives of microbiology},
volume = {190},
number = {3},
pages = {333-339},
doi = {10.1007/s00203-008-0362-x},
pmid = {18385982},
issn = {1432-072X},
mesh = {Archaeal Proteins/*genetics ; Base Sequence ; *Gene Expression Regulation, Archaeal ; Genes, Archaeal ; Genes, Regulator ; Halobacterium salinarum/*genetics ; Haloferax mediterranei/*genetics ; Molecular Sequence Data ; Multigene Family ; Promoter Regions, Genetic ; Proteins/*genetics ; Transcription, Genetic ; },
abstract = {Three gas vesicle gene clusters derived from Halobacterium salinarum (p-vac and c-vac) and Haloferax mediterranei (mc-vac) are used as model systems to study gene regulation in Archaea. An unusual pair of regulatory proteins is involved here, with GvpE acting as transcription activator and GvpD exhibiting a repressing function. Both regulators are able to interact leading to the loss of GvpE and the repression (or turnoff) of the gas vesicle formation. The latter function of GvpD requires a p-loop motif and an arginine-rich region, bR1. Both regulator proteins are differentially expressed from the same gvp transcript in Hfx. mediterranei and Hbt. salinarum PHH4. GvpE appears to recognize a 20-nucleotide activator sequence (UAS) located upstream and adjacent to the TFB-recognition element BRE of the two promoters driving the transcription of the divergently oriented gvpACNO and gvpDEFGHIJKLM gene clusters. The BRE elements of these two promoters are separated by 35 nucleotides only, and the distal portions of the two GvpE-UAS overlap considerably in the center of this region. Mutations here negatively affect the GvpE-induced activities of both gvp promoters, whereas alterations in the proximal UAS portions only affect the activity of the promoter located close by.},
}
@article {pmid18378594,
year = {2008},
author = {Liu, Y and Whitman, WB},
title = {Metabolic, phylogenetic, and ecological diversity of the methanogenic archaea.},
journal = {Annals of the New York Academy of Sciences},
volume = {1125},
number = {},
pages = {171-189},
doi = {10.1196/annals.1419.019},
pmid = {18378594},
issn = {0077-8923},
mesh = {Animals ; Archaea/classification/genetics/isolation &amp; purification/*metabolism ; Biomass ; Ecosystem ; Gastrointestinal Diseases/microbiology ; *Genetic Variation ; Humans ; Isoptera/microbiology ; Methane/metabolism ; Methanomicrobiaceae/classification/genetics/*metabolism ; Oryza/microbiology ; *Phylogeny ; Ruminants/microbiology ; Seawater/microbiology ; Thermodynamics ; },
abstract = {Although of limited metabolic diversity, methanogenic archaea or methanogens possess great phylogenetic and ecological diversity. Only three types of methanogenic pathways are known: CO(2)-reduction, methyl-group reduction, and the aceticlastic reaction. Cultured methanogens are grouped into five orders based upon their phylogeny and phenotypic properties. In addition, uncultured methanogens that may represent new orders are present in many environments. The ecology of methanogens highlights their complex interactions with other anaerobes and the physical and chemical factors controlling their function.},
}
@article {pmid18369418,
year = {2008},
author = {Sun, FJ and Caetano-Anollés, G},
title = {Evolutionary patterns in the sequence and structure of transfer RNA: early origins of archaea and viruses.},
journal = {PLoS computational biology},
volume = {4},
number = {3},
pages = {e1000018},
pmid = {18369418},
issn = {1553-7358},
mesh = {Base Sequence ; *Biological Evolution ; *Evolution, Molecular ; Genetic Variation/genetics ; *Models, Genetic ; Molecular Sequence Data ; Pattern Recognition, Automated/methods ; RNA, Archaeal/*chemistry ; RNA, Transfer/*genetics ; RNA, Viral/*genetics ; Sequence Alignment/methods ; Sequence Analysis, RNA/*methods ; },
abstract = {Transfer RNAs (tRNAs) are ancient molecules that are central to translation. Since they probably carry evolutionary signatures that were left behind when the living world diversified, we reconstructed phylogenies directly from the sequence and structure of tRNA using well-established phylogenetic methods. The trees placed tRNAs with long variable arms charging Sec, Tyr, Ser, and Leu consistently at the base of the rooted phylogenies, but failed to reveal groupings that would indicate clear evolutionary links to organismal origin or molecular functions. In order to uncover evolutionary patterns in the trees, we forced tRNAs into monophyletic groups using constraint analyses to generate timelines of organismal diversification and test competing evolutionary hypotheses. Remarkably, organismal timelines showed Archaea was the most ancestral superkingdom, followed by viruses, then superkingdoms Eukarya and Bacteria, in that order, supporting conclusions from recent phylogenomic studies of protein architecture. Strikingly, constraint analyses showed that the origin of viruses was not only ancient, but was linked to Archaea. Our findings have important implications. They support the notion that the archaeal lineage was very ancient, resulted in the first organismal divide, and predated diversification of tRNA function and specificity. Results are also consistent with the concept that viruses contributed to the development of the DNA replication machinery during the early diversification of the living world.},
}
@article {pmid18355287,
year = {2008},
author = {Einen, J and Thorseth, IH and Ovreås, L},
title = {Enumeration of Archaea and Bacteria in seafloor basalt using real-time quantitative PCR and fluorescence microscopy.},
journal = {FEMS microbiology letters},
volume = {282},
number = {2},
pages = {182-187},
doi = {10.1111/j.1574-6968.2008.01119.x},
pmid = {18355287},
issn = {0378-1097},
mesh = {Archaea/enzymology/genetics/*isolation &amp; purification ; Bacteria/enzymology/genetics/*isolation &amp; purification ; Bacterial Typing Techniques ; DNA, Bacterial/analysis ; Fluorescent Dyes ; Microscopy, Fluorescence/*methods ; Organic Chemicals/metabolism ; Polymerase Chain Reaction/*methods ; Seawater/*microbiology ; Silicates ; },
abstract = {A SYBR Green real-time quantitative PCR (Q-PCR) assay for the detection and quantification of Bacteria and Archaea present in the glassy rind of seafloor basalts of different ages and water depths is presented. Two sets of domain-specific primers were designed and validated for specific detection and quantification of bacterial and archaeal 16S rRNA genes in DNA extracted from basaltic glass. Total cell numbers were also estimated by fluorescence microscopy analysis of SYBR Gold-stained samples. The results from the two different approaches were concurrent, and Q-PCR results showed that the total number of cells present in basalts was in the range from 6 x 10(5) to 4 x 10(6) cells g(-1) basaltic glass. Further, it was demonstrated that these cells were almost exclusively from the domain Bacteria. When applying the same methods on samples of different ages (22 years-0.1 Ma) and water depths (139-3390 mbsl), no significant differences in cell concentrations or in the relative abundance of Archaea and Bacteria were detected.},
}
@article {pmid18344332,
year = {2008},
author = {Herrmann, M and Saunders, AM and Schramm, A},
title = {Archaea dominate the ammonia-oxidizing community in the rhizosphere of the freshwater macrophyte Littorella uniflora.},
journal = {Applied and environmental microbiology},
volume = {74},
number = {10},
pages = {3279-3283},
pmid = {18344332},
issn = {1098-5336},
mesh = {Ammonia/*metabolism ; Archaea/classification/*isolation &amp; purification/metabolism ; Archaeal Proteins/genetics/metabolism ; Bacteria/classification/*isolation &amp; purification/metabolism ; Bacterial Proteins/genetics/metabolism ; *Biodiversity ; DNA, Archaeal/chemistry/genetics ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Genes, rRNA ; Molecular Sequence Data ; Oxidation-Reduction ; Oxidoreductases/genetics/metabolism ; Phylogeny ; Plant Roots/*microbiology ; Plantago/*microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; },
abstract = {Archaeal and bacterial ammonia monooxygenase genes (amoA) had similar low relative abundances in freshwater sediment. In the rhizosphere of the submersed macrophyte Littorella uniflora, archaeal amoA was 500- to >8,000-fold enriched compared to bacterial amoA, suggesting that the enhanced nitrification activity observed in the rhizosphere was due to ammonia-oxidizing Archaea.},
}
@article {pmid18338569,
year = {2008},
author = {Pei, C and Mao, S and Zhu, W},
title = {[Molecular diversity of rumen Archaea from Jinnan cattle].},
journal = {Wei sheng wu xue bao = Acta microbiologica Sinica},
volume = {48},
number = {1},
pages = {8-14},
pmid = {18338569},
issn = {0001-6209},
mesh = {Animals ; Archaea/classification/*genetics/*isolation &amp; purification ; Cattle ; China ; DNA Primers/genetics ; DNA, Archaeal/genetics ; DNA, Ribosomal/genetics ; *Genetic Variation ; Molecular Sequence Data ; Phylogeny ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Rumen/*microbiology ; },
abstract = {Molecular diversities of rumen archaea of Jinnan (South Shanxi Province, China) cattle was analyzed and compared by 16S rRNA gene sequencing from three clone libraries generated using three different archaea-specific primer sets, respectively. DNA from rumen of 4 Jinnan cattle was extracted, and methanogen 16S rRNA gene was amplified using archaea-specific primer sets. Three clone libraries were generated by using vector pGEM-T and cloning into E.coli JM109. One hundred clones were randomly picked up for each library and RFLP was analyzed for each clone to obtain OTUs. Sequences from each OTU were analyzed and compared with available sequences in GenBank. The first library, generated with primers Arch f364/1386, produced four groups of sequences, affiliated with 4 Methanobrevibacter strains, 1Y (61% of clones), SM9 (23% of clones), NT7 (14% of clones), and AK-87(2% of clones). The second library, generated with primers 1 Af/1100Ar, two groups of sequences, one affiliated with Methanobacterium aarhusense (72% of clones) and the other with Methanosphaera stadtmanae DSM 3091 (28% of clones). The third library, generated with primers Met86F/Met1340R, produced a high degree of diversity. It included the sequence groups found in the first and the second libraries, as well as sequences affiliated with the Methanomicrobium mobile (2% of clones) and uncultured euryarchaeote sequences (7% of clones). The phylogenetic analysis indicated that archaea found in the three libraries were clustered in Methanobrevibacter, Methanobacterium, Methanosphaera, Methanomicrobium, and unidentified euryarchaeote of the Euryarcharota. There were 25 unidentified sequences belonged to Euryarchaeota. This suggests the existence of novel methanogens in the rumen of Jinnan cattle.},
}
@article {pmid18336563,
year = {2008},
author = {Shen, JP and Zhang, LM and Zhu, YG and Zhang, JB and He, JZ},
title = {Abundance and composition of ammonia-oxidizing bacteria and ammonia-oxidizing archaea communities of an alkaline sandy loam.},
journal = {Environmental microbiology},
volume = {10},
number = {6},
pages = {1601-1611},
doi = {10.1111/j.1462-2920.2008.01578.x},
pmid = {18336563},
issn = {1462-2920},
mesh = {Ammonia/*metabolism ; Archaea/*classification/*isolation &amp; purification/metabolism ; Bacteria/*classification/*isolation &amp; purification/metabolism ; Cell Count/methods ; Colony Count, Microbial/methods ; DNA Fingerprinting ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; Electrophoresis, Polyacrylamide Gel ; Genes, Archaeal ; Genes, Bacterial ; Hydrogen-Ion Concentration ; Molecular Sequence Data ; Nucleic Acid Denaturation ; Oxidation-Reduction ; Phylogeny ; Sequence Analysis, DNA ; Sequence Homology ; Soil Microbiology ; },
abstract = {The abundance and composition of soil ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) communities under different long-term (17 years) fertilization practices were investigated using real-time polymerase chain reaction and denaturing gradient gel electrophoresis (DGGE). A sandy loam with pH (H(2)O) ranging from 8.3 to 8.7 was sampled in years 2006 and 2007, including seven fertilization treatments of control without fertilizers (CK), those with combinations of fertilizer nitrogen (N), phosphorus (P) and potassium (K): NP, NK, PK and NPK, half chemical fertilizers NPK plus half organic manure (1/2OMN) and organic manure (OM). The highest bacterial amoA gene copy numbers were found in those treatments receiving N fertilizer. The archaeal amoA gene copy numbers ranging from 1.54 x 10(7) to 4.25 x 10(7) per gram of dry soil were significantly higher than those of bacterial amoA genes, ranging from 1.24 x 10(5) to 2.79 x 10(6) per gram of dry soil, which indicated a potential role of AOA in nitrification. Ammonia-oxidizing bacteria abundance had significant correlations with soil pH and potential nitrification rates. Denaturing gradient gel electrophoresis patterns revealed that the fertilization resulted in an obvious change of the AOB community, while no significant change of the AOA community was observed among different treatments. Phylogenetic analysis showed a dominance of Nitrosospira-like sequences, while three bands were affiliated with the Nitrosomonas genus. All AOA sequences fell within cluster S (soil origin) and cluster M (marine and sediment origin). These results suggest that long-term fertilization had a significant impact on AOB abundance and composition, while minimal on AOA in the alkaline soil.},
}
@article {pmid18336555,
year = {2008},
author = {Sahan, E and Muyzer, G},
title = {Diversity and spatio-temporal distribution of ammonia-oxidizing Archaea and Bacteria in sediments of the Westerschelde estuary.},
journal = {FEMS microbiology ecology},
volume = {64},
number = {2},
pages = {175-186},
doi = {10.1111/j.1574-6941.2008.00462.x},
pmid = {18336555},
issn = {0168-6496},
mesh = {Ammonia/*metabolism ; Archaea/*classification/*genetics/isolation &amp; purification/metabolism ; Archaeal Proteins/genetics ; Bacteria/*classification/*genetics/isolation &amp; purification/metabolism ; Bacterial Proteins/genetics ; Biodiversity ; DNA Fingerprinting ; DNA, Archaeal/chemistry/genetics ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Electrophoresis, Polyacrylamide Gel ; Geologic Sediments/*microbiology ; Molecular Sequence Data ; Netherlands ; Nucleic Acid Denaturation ; Oxidation-Reduction ; Oxidoreductases/genetics ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sequence Homology ; Time Factors ; },
abstract = {The diversity and spatio-temporal distribution of ammonia-oxidizing Archaea (AOA) and Bacteria (AOB) were investigated along a salinity gradient in sediments of the Westerschelde estuary. Sediment samples were collected from three sites with different salinities, and at six time points over the year. Denaturing gradient gel electrophoresis of PCR-amplified 16S rRNA and amoA gene fragments was used to identify the AOA and AOB present. Members of the AOA were mainly belonging to the Crenarchaeota Group 1, which were found at all sites, while members of the genus Nitrosomonas, which were abundant at the brackish sites, and of the genus Nitrosospira, which were present in early spring at the marine sites, were found to be the dominant AOB. Statistical analysis indicated that salinity and temperature were the main factors controlling the diversity and distribution of both AOA and AOB. Variability in net primary production rates was also correlated with species composition of both groups, but changes in the nitrite concentration only to the distribution of the AOA.},
}
@article {pmid18331336,
year = {2008},
author = {Ellis, DG and Bizzoco, RW and Kelley, ST},
title = {Halophilic Archaea determined from geothermal steam vent aerosols.},
journal = {Environmental microbiology},
volume = {10},
number = {6},
pages = {1582-1590},
doi = {10.1111/j.1462-2920.2008.01574.x},
pmid = {18331336},
issn = {1462-2920},
mesh = {*Aerosols ; Archaea/*classification/cytology/*isolation &amp; purification ; California ; Cell Count ; DNA, Archaeal/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Genes, rRNA ; Hawaii ; Hot Springs/*microbiology ; Molecular Sequence Data ; New Mexico ; Phylogeny ; RNA, Archaeal/genetics ; RNA, Ribosomal, 16S/genetics ; Russia ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; Sodium Chloride/metabolism ; *Steam ; Wyoming ; },
abstract = {Hydrothermal vents, known as 'fumaroles', are ubiquitous features of geothermal areas. Although their geology has been extensively characterized, little is known about the subsurface microbial ecology of fumaroles largely because of the difficulty in collecting sufficient numbers of cells from boiling steam water for DNA extraction and culture isolation. Here we describe the first collection, molecular analysis and isolation of microbes from fumarole steam waters in Russia (Kamchatka) and the USA (Hawaii, New Mexico, California and Wyoming). Surprisingly, the steam vent waters from all the fumaroles contained halophilic Archaea closely related to the Haloarcula spp. found in non-geothermal salt mats, saline soils, brine pools and salt lakes around the world. Microscopic cell counting estimated the cell dispersal rate at approximately 1.6 x 10(9) cells year(-1) from a single fumarole. We also managed to enrich microbes in high-salt media from every vent sample, and to isolate Haloarcula from a Yellowstone vent in a 20% salt medium after a month-long incubation, demonstrating both salt tolerance and viability of cells collected from high-temperature steam. Laboratory tests determined that microbes enriched in salt media survived temperatures greater than 75 degrees C for between 5 and 30 min during the collection process. Hawaiian fumaroles proved to contain the greatest diversity of halophilic Archaea with four new lineages that may belong to uncultured haloarchaeal genera. This high diversity may have resulted from the leaching of salts and minerals through the highly porous volcanic rock, creating a chemically complex saline subsurface.},
}
@article {pmid18326571,
year = {2008},
author = {Vianna, ME and Holtgraewe, S and Seyfarth, I and Conrads, G and Horz, HP},
title = {Quantitative analysis of three hydrogenotrophic microbial groups, methanogenic archaea, sulfate-reducing bacteria, and acetogenic bacteria, within plaque biofilms associated with human periodontal disease.},
journal = {Journal of bacteriology},
volume = {190},
number = {10},
pages = {3779-3785},
pmid = {18326571},
issn = {1098-5530},
mesh = {Acetates/metabolism ; Acetobacter/genetics/*physiology ; Biofilms/*growth &amp; development ; DNA, Bacterial/analysis ; Dental Plaque/*microbiology ; Euryarchaeota/genetics/*physiology ; Humans ; Hydrogen/metabolism ; Molecular Sequence Data ; Periodontal Diseases/*microbiology ; Periodontal Pocket/microbiology ; Phylogeny ; Sulfates/metabolism ; Sulfur-Reducing Bacteria/genetics/*physiology ; },
abstract = {Human subgingival plaque biofilms are highly complex microbial ecosystems that may depend on H(2)-metabolizing processes. Here we investigated the ubiquity and proportions of methanogenic archaea, sulfate reducers, and acetogens in plaque samples from 102 periodontitis patients. In contrast to the case for 65 healthy control subjects, hydrogenotrophic groups were almost consistently detected in periodontal pockets, with the proportions of methanogens and sulfate reducers being significantly elevated in severe cases. In addition, antagonistic interactions among the three microbial groups indicated that they may function as alternative syntrophic partners of secondary fermenting periodontal pathogens.},
}
@article {pmid18325029,
year = {2008},
author = {Tourna, M and Freitag, TE and Nicol, GW and Prosser, JI},
title = {Growth, activity and temperature responses of ammonia-oxidizing archaea and bacteria in soil microcosms.},
journal = {Environmental microbiology},
volume = {10},
number = {5},
pages = {1357-1364},
doi = {10.1111/j.1462-2920.2007.01563.x},
pmid = {18325029},
issn = {1462-2920},
mesh = {Ammonia/*metabolism ; *Bacteria/genetics/growth &amp; development/metabolism ; *Crenarchaeota/genetics/growth &amp; development/metabolism ; DNA, Archaeal/analysis ; DNA, Bacterial/analysis ; *Ecosystem ; Molecular Sequence Data ; Oxidation-Reduction ; Oxidoreductases/genetics/metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; *Temperature ; },
abstract = {Ammonia oxidation, as the first step in the nitrification process, plays a central role in the global cycling of nitrogen. Although bacteria are traditionally considered to be responsible for ammonia oxidation, a role for archaea has been suggested by data from metagenomic studies and by the isolation of a marine, autotrophic, ammonia-oxidizing, non-thermophilic crenarchaeon. Evidence for ammonia oxidation by non-thermophilic crenarchaea in marine and terrestrial environments is largely based on abundance of bacterial and archaeal ammonia monooxygenase (amo) genes, rather than activity. In this study, we have determined the influence of temperature on the response of ammonia-oxidizing bacteria and archaea in nitrifying soil microcosms using two approaches, involving analysis of transcriptional activity of 16S rRNA genes and of a key functional gene, amoA, which encodes ammonia monooxygenase subunit A. There was little evidence of changes in relative abundance or transcriptional activity of ammonia-oxidizing bacteria during nitrification. In contrast, denaturing gradient gel electrophoresis analysis of crenarchaeal 16S rRNA and crenarchaeal amoA genes provided strong evidence of changes in community structure of active archaeal ammonia oxidizers. Community structure changes were similar during incubation at different temperatures and much of the activity was due to a group of non-thermophilic crenarchaea associated with subsurface and marine environments, rather than soil. The findings suggest a role for crenarchaea in soil nitrification and that further information is required on their biogeography.},
}
@article {pmid18302972,
year = {2008},
author = {Cleland, D and Krader, P and Emerson, D},
title = {Use of the DiversiLab repetitive sequence-based PCR system for genotyping and identification of Archaea.},
journal = {Journal of microbiological methods},
volume = {73},
number = {2},
pages = {172-178},
doi = {10.1016/j.mimet.2007.12.008},
pmid = {18302972},
issn = {0167-7012},
mesh = {Cluster Analysis ; Crenarchaeota/*classification/*genetics ; DNA Fingerprinting ; DNA Primers/genetics ; DNA, Archaeal/*genetics ; Euryarchaeota/*classification/*genetics ; Genotype ; Polymerase Chain Reaction/*methods ; *Repetitive Sequences, Nucleic Acid ; Reproducibility of Results ; Sensitivity and Specificity ; },
abstract = {Repetitive elements are short stretches of DNA that are randomly distributed throughout the chromosomes of prokaryotes. The use of PCR primers to amplify intervening sequences of DNA between specific repetitive elements in Bacteria has become a standard method for rapidly genotyping bacterial strains and providing good resolution between multiple strains within a single species. Rapid, standardized methods for high resolution genotyping of Archaea are not widely available. We evaluated the DiversiLab system from Bacterial Barcodes that utilizes a kit-based repetitive sequence-based (rep-PCR) method that has been optimized for genotyping DNA was extracted from the source organisms using either a standard chemical DNA extraction kit or Whatman FTA paper. Rep-PCR was performed using an archaeal primer set and, the products were run on an Agilent, Lab-on-a-Chip DNA analyzer. Results were analyzed and compared using DiversiLab web-based software from Bacterial Barcodes. Seventy-nine strains representing 27 genera of Crenarchaeota and Euryarchaeota were analyzed. All the organisms could be successfully genotyped and the results were reproducible. We could not detect differences in rep-PCR profiles between DNA extracted using the chemical extraction kit and FTA paper. Thus far, 14 genera and 32 species of methanogens have been analyzed, and all yielded unique genotypes. For halophiles, 11 genera and 28 different species were analyzed, and all yielded unique genotypes. A comparison of 7 different strains of Halobacterium salinarium demonstrated that 6 of the 7 strains had a unique genotype. A comparison of 4 strains of Methanosarcina mazei indicated that each strain produced a unique genotype. There was little systematic inference that could be made from dendrograms comparing different strains, species, and genera of Archaea based on UPGMA cluster analysis. Based on these results, rep-PCR was a useful tool for the genotyping and strain identification of Archaea.},
}
@article {pmid18278431,
year = {2008},
author = {Falb, M and Müller, K and Königsmaier, L and Oberwinkler, T and Horn, P and von Gronau, S and Gonzalez, O and Pfeiffer, F and Bornberg-Bauer, E and Oesterhelt, D},
title = {Metabolism of halophilic archaea.},
journal = {Extremophiles : life under extreme conditions},
volume = {12},
number = {2},
pages = {177-196},
pmid = {18278431},
issn = {1431-0651},
mesh = {Euryarchaeota/*physiology ; Folic Acid/*biosynthesis ; Genome, Archaeal/*physiology ; Glycerol/*metabolism ; Pentoses/*metabolism ; },
abstract = {In spite of their common hypersaline environment, halophilic archaea are surprisingly different in their nutritional demands and metabolic pathways. The metabolic diversity of halophilic archaea was investigated at the genomic level through systematic metabolic reconstruction and comparative analysis of four completely sequenced species: Halobacterium salinarum, Haloarcula marismortui, Haloquadratum walsbyi, and the haloalkaliphile Natronomonas pharaonis. The comparative study reveals different sets of enzyme genes amongst halophilic archaea, e.g. in glycerol degradation, pentose metabolism, and folate synthesis. The carefully assessed metabolic data represent a reliable resource for future system biology approaches as it also links to current experimental data on (halo)archaea from the literature.},
}
@article {pmid18266758,
year = {2008},
author = {Santoro, AE and Francis, CA and de Sieyes, NR and Boehm, AB},
title = {Shifts in the relative abundance of ammonia-oxidizing bacteria and archaea across physicochemical gradients in a subterranean estuary.},
journal = {Environmental microbiology},
volume = {10},
number = {4},
pages = {1068-1079},
doi = {10.1111/j.1462-2920.2007.01547.x},
pmid = {18266758},
issn = {1462-2920},
mesh = {Ammonia/*metabolism ; Archaea/genetics/*isolation &amp; purification/metabolism ; Betaproteobacteria/genetics/*isolation &amp; purification/metabolism ; California ; *Ecosystem ; Fresh Water/analysis/*microbiology ; Genes, Archaeal ; Genes, Bacterial ; Geologic Sediments/analysis/*microbiology ; Inorganic Chemicals/metabolism ; Molecular Sequence Data ; Nitrogen/metabolism ; Oxidoreductases/genetics ; Oxygen/metabolism ; Salinity ; Seawater/analysis/*microbiology ; *Soil Microbiology ; *Water Microbiology ; },
abstract = {Submarine groundwater discharge to coastal waters can be a significant source of both contaminants and biologically limiting nutrients. Nitrogen cycling across steep gradients in salinity, oxygen and dissolved inorganic nitrogen in sandy 'subterranean estuaries' controls both the amount and form of nitrogen discharged to the coastal ocean. We determined the effect of these gradients on betaproteobacterial ammonia-oxidizing bacteria (beta-AOB) and ammonia-oxidizing archaea (AOA) in a subterranean estuary using the functional gene encoding ammonia monooxygenase subunit A (amoA). The abundance of beta-AOB was dramatically lower in the freshwater stations compared with saline stations, while AOA abundance remained nearly constant across the study site. This differing response to salinity altered the ratio of beta-AOB to AOA such that bacterial amoA was 30 times more abundant than crenarchaeal amoA at the oxic marine station, but nearly 10 times less abundant at the low-oxygen fresh and brackish stations. As the location of the brackish mixing zone within the aquifer shifted from landward in winter to oceanward in summer, the location of the transition from a beta-AOB-dominated to an AOA-dominated community also shifted, demonstrating the intimate link between microbial communities and coastal hydrology. Analysis of ammonia-oxidizing enrichment cultures at a range of salinities revealed that AOA persisted solely in the freshwater enrichments where they actively express amoA. Diversity (as measured by total richness) of crenarchaeal amoA was high at all stations and time points, in sharp contrast to betaproteobacterial amoA for which only two sequence types were found. These results offer new insights into the ecology of AOA and beta-AOB by elucidating conditions that may favour the numerical dominance of beta-AOB over AOA in coastal sediments.},
}
@article {pmid18264658,
year = {2008},
author = {Manerkar, MA and Seena, S and Bärlocher, F},
title = {Q-RT-PCR for assessing archaea, bacteria, and fungi during leaf decomposition in a stream.},
journal = {Microbial ecology},
volume = {56},
number = {3},
pages = {467-473},
pmid = {18264658},
issn = {0095-3628},
mesh = {Archaea/genetics/*growth &amp; development ; Bacteria/genetics/*growth &amp; development ; Biomass ; DNA, Archaeal/chemistry/genetics ; DNA, Bacterial/chemistry/genetics ; DNA, Fungal/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; Ecosystem ; Ergosterol/metabolism ; Fungi/genetics/*growth &amp; development ; Plant Leaves/metabolism/*microbiology ; Polymerase Chain Reaction/methods ; RNA, Ribosomal, 16S/chemistry/genetics ; RNA, Ribosomal, 5.8S/chemistry/genetics ; Rivers ; },
abstract = {Leaf disks of Tilia cordata were exposed for up to 5 weeks in a first-order stream in Nova Scotia, Canada. The exponential decay rate k was 0.008 day(-1). Ergosterol levels increased linearly to a maximum of 134 microg g(-1) dry leaf mass. Release of conidia peaked at 700 day(-1) mg(-1) on leaves that had been exposed for 3 weeks; after 5 weeks, it declined to 15 mg(-1). In total, 23 taxa of aquatic hyphomycetes were distinguished. Anguillospora filiformis contributed over 76% of the conidia during weeks 1, 2, and 3, and 16.5% in week 5. Three sets of primers specific for Bacteria, Archaea, and Fungi were applied in quantitative real-time polymerase chain reaction (Q-RT-PCR) to estimate relative DNA amounts. Archaeal DNA was consistently present at low levels. Bacterial and fungal DNA peaked between weeks 2 and 3, and declined in week 5. With the exception of week 1, fungal DNA exceeded bacterial DNA by between 12 and 110%.},
}
@article {pmid18239270,
year = {2008},
author = {Kawashima, T and Aramaki, H and Oyamada, T and Makino, K and Yamada, M and Okamura, H and Yokoyama, K and Ishijima, SA and Suzuki, M},
title = {Transcription regulation by feast/famine regulatory proteins, FFRPs, in archaea and eubacteria.},
journal = {Biological &amp; pharmaceutical bulletin},
volume = {31},
number = {2},
pages = {173-186},
doi = {10.1248/bpb.31.173},
pmid = {18239270},
issn = {0918-6158},
mesh = {Amino Acid Sequence ; Amino Acids/chemistry/metabolism ; Archaea/*metabolism ; Archaeal Proteins/biosynthesis/genetics ; Bacteria/*metabolism ; Bacterial Proteins/biosynthesis/genetics ; Crystallography, X-Ray ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Transcription Factors/*biosynthesis/genetics ; },
abstract = {Feast/famine regulatory proteins (FFRPs) comprise a single group of transcription factors systematically distributed throughout archaea and eubacteria. In the eubacterial domain in Escherichia coli, autotrophic pathways are activated and heterotrophic pathways are repressed by an FFRP, the leucine-responsive regulatory protein (Lrp), in some cases in interaction with other transcription factors. By sensing the concentration of leucine, Lrp changes its association state between hexadecamers and octamers to adapt the autotrophic or heterotrophic mode. The lrp gene is regulated so that the concentration of Lrp decreases in the presence of rich nutrition. In the archaeal domain a large part of the metabolism of Pyrococcus OT3 is regulated by another FFRP, FL11. In the presence of rich nutrition, the metabolism is released from repression by FL11; transcription of fl11 is terminated by FL11 forming octamers in interaction with lysine. When the nutrient is depleted, the metabolism is arrested by a high concentration of FL11; FL11 disassembles to dimers in the absence of lysine, and repression of transcription of fl11 is relaxed. Common characteristics of the master regulations by FL11 and Lrp hint at the prototype regulation once achieved in the common ancestor of all extant organisms. Mechanisms of discrimination by FFRPs between DNA sequences and also between co-regulatory molecules, mostly amino acids, and variations of transcription regulations observed with archaea and eubacteria are reviewed.},
}
@article {pmid18235446,
year = {2008},
author = {Hirata, A and Klein, BJ and Murakami, KS},
title = {The X-ray crystal structure of RNA polymerase from Archaea.},
journal = {Nature},
volume = {451},
number = {7180},
pages = {851-854},
pmid = {18235446},
issn = {1476-4687},
support = {R01 GM071897/GM/NIGMS NIH HHS/United States ; R01 GM071897-04/GM/NIGMS NIH HHS/United States ; },
mesh = {Crystallography, X-Ray ; DNA-Directed RNA Polymerases/*chemistry/metabolism ; Iron-Sulfur Proteins/chemistry/metabolism ; Models, Molecular ; Protein Folding ; Protein Structure, Tertiary ; Protein Subunits/chemistry/metabolism ; Saccharomyces cerevisiae/enzymology ; Sulfolobus solfataricus/*enzymology ; Taq Polymerase/chemistry ; },
abstract = {The transcription apparatus in Archaea can be described as a simplified version of its eukaryotic RNA polymerase (RNAP) II counterpart, comprising an RNAPII-like enzyme as well as two general transcription factors, the TATA-binding protein (TBP) and the eukaryotic TFIIB orthologue TFB. It has been widely understood that precise comparisons of cellular RNAP crystal structures could reveal structural elements common to all enzymes and that these insights would be useful in analysing components of each enzyme that enable it to perform domain-specific gene expression. However, the structure of archaeal RNAP has been limited to individual subunits. Here we report the first crystal structure of the archaeal RNAP from Sulfolobus solfataricus at 3.4 A resolution, completing the suite of multi-subunit RNAP structures from all three domains of life. We also report the high-resolution (at 1.76 A) crystal structure of the D/L subcomplex of archaeal RNAP and provide the first experimental evidence of any RNAP possessing an iron-sulphur (Fe-S) cluster, which may play a structural role in a key subunit of RNAP assembly. The striking structural similarity between archaeal RNAP and eukaryotic RNAPII highlights the simpler archaeal RNAP as an ideal model system for dissecting the molecular basis of eukaryotic transcription.},
}
@article {pmid18219285,
year = {2008},
author = {Goffredi, SK and Wilpiszeski, R and Lee, R and Orphan, VJ},
title = {Temporal evolution of methane cycling and phylogenetic diversity of archaea in sediments from a deep-sea whale-fall in Monterey Canyon, California.},
journal = {The ISME journal},
volume = {2},
number = {2},
pages = {204-220},
doi = {10.1038/ismej.2007.103},
pmid = {18219285},
issn = {1751-7362},
mesh = {Archaea/classification/*genetics/metabolism ; California ; DNA, Archaeal/analysis ; Ecosystem ; *Evolution, Molecular ; Genetic Variation ; Geologic Sediments/chemistry/*microbiology ; Methane/*metabolism ; Methanomicrobiaceae/enzymology/genetics/metabolism ; Methanosarcinaceae/enzymology/genetics ; Molecular Sequence Data ; Oxidoreductases/genetics/metabolism ; *Phylogeny ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Seawater/chemistry/*microbiology ; Sequence Analysis, DNA ; },
abstract = {Whale-falls represent localized areas of extreme organic enrichment in an otherwise oligotrophic deep-sea environment. Anaerobic remineralization within these habitats is typically portrayed as sulfidogenic; however, we demonstrate that these systems are also favorable for diverse methane-producing archaeal assemblages, representing up to 40% of total cell counts. Chemical analyses revealed elevated methane and depleted sulfate concentrations in sediments under the whale-fall, as compared to surrounding sediments. Carbon was enriched (up to 3.5%) in whale-fall sediments, as well as the surrounding sea floor to at least 10 m, forming a 'bulls eye' of elevated carbon. The diversity of sedimentary archaea associated with the 2893 m whale-fall in Monterey Canyon (California) varied both spatially and temporally. 16S rRNA diversity, determined by both sequencing and terminal restriction fragment length polymorphism analysis, as well as quantitative PCR of the methyl-coenzyme M reductase gene, revealed that methanogens, including members of the Methanomicrobiales and Methanosarcinales, were the dominant archaea (up to 98%) in sediments immediately beneath the whale-fall. Temporal changes in this archaeal community included the early establishment of methylotrophic methanogens followed by development of methanogens thought to be hydrogenotrophic, as well as members related to the newly described methanotrophic lineage, ANME-3. In comparison, archaeal assemblages in 'reference' sediments collected 10 m from the whale-fall primarily consisted of Crenarchaeota affiliated with marine group I and marine benthic group B. Overall, these results indicate that whale-falls can favor the establishment of metabolically and phylogenetically diverse methanogen assemblages, resulting in an active near-seafloor methane cycle in the deep sea.},
}
@article {pmid18218090,
year = {2008},
author = {Zhou, F and Olman, V and Xu, Y},
title = {Insertion Sequences show diverse recent activities in Cyanobacteria and Archaea.},
journal = {BMC genomics},
volume = {9},
number = {},
pages = {36},
pmid = {18218090},
issn = {1471-2164},
mesh = {Archaea/*genetics/*metabolism ; Base Sequence ; Chromosome Mapping ; Chromosomes, Bacterial ; Cyanobacteria/*genetics/*metabolism ; *DNA Transposable Elements ; Genome, Archaeal ; Genome, Bacterial ; Models, Genetic ; *Mutagenesis, Insertional ; Nucleic Acid Conformation ; Open Reading Frames ; Phylogeny ; Repetitive Sequences, Nucleic Acid ; Templates, Genetic ; Terminal Repeat Sequences ; },
abstract = {BACKGROUND: Mobile genetic elements (MGEs) play an essential role in genome rearrangement and evolution, and are widely used as an important genetic tool.<br><br>RESULTS: In this article, we present genetic maps of recently active Insertion Sequence (IS) elements, the simplest form of MGEs, for all sequenced cyanobacteria and archaea, predicted based on the previously identified ~1,500 IS elements. Our predicted IS maps are consistent with the NCBI annotations of the IS elements. By linking the predicted IS elements to various characteristics of the organisms under study and the organism's living conditions, we found that (a) the activities of IS elements heavily depend on the environments where the host organisms live; (b) the number of recently active IS elements in a genome tends to increase with the genome size; (c) the flanking regions of the recently active IS elements are significantly enriched with genes encoding DNA binding factors, transporters and enzymes; and (d) IS movements show no tendency to disrupt operonic structures.<br><br>CONCLUSION: This is the first genome-scale maps of IS elements with detailed structural information on the sequence level. These genetic maps of recently active IS elements and the several interesting observations would help to improve our understanding of how IS elements proliferate and how they are involved in the evolution of the host genomes.},
}
@article {pmid18205815,
year = {2008},
author = {Elevi Bardavid, R and Oren, A},
title = {Sensitivity of Haloquadratum and Salinibacter to antibiotics and other inhibitors: implications for the assessment of the contribution of Archaea and Bacteria to heterotrophic activities in hypersaline environments.},
journal = {FEMS microbiology ecology},
volume = {63},
number = {3},
pages = {309-315},
doi = {10.1111/j.1574-6941.2007.00433.x},
pmid = {18205815},
issn = {0168-6496},
mesh = {Amino Acids/metabolism ; Anti-Bacterial Agents/*pharmacology ; Bacteroidetes/*drug effects/growth &amp; development/metabolism ; Bile Acids and Salts/*pharmacology ; Chloramphenicol/pharmacology ; Ecosystem ; Erythromycin/pharmacology ; Fresh Water/*microbiology ; Halobacteriaceae/*drug effects/growth &amp; development/metabolism ; *Sodium Chloride ; Taurocholic Acid/pharmacology ; },
abstract = {Antibiotics and bile salts have been used to differentiate between heterotrophic activity of halophilic Archaea and Bacteria in saltern ponds. In NaCl-saturated brines of crystallizer ponds, most activity was attributed to Archaea. Following the recent isolation of Haloquadratum, the dominant archaeon in the salterns (reported to be sensitive to chloramphenicol and erythromycin), and the discovery of Salinibacter, a representative of the Bacteria, in the same ecosystem, reevaluation of the earlier data is required. The authors measured amino acid incorporation by Haloquadratum and Salinibacter suspended in crystallizer brine to investigate the suitability of antibiotics and bile salts to distinguish between archaeal and bacterial activities. The amino acid uptake rate per cell in Salinibacter was two orders of magnitude lower than that of Haloquadratum under the same conditions. Salinibacter was inhibited by chloramphenicol, erythromycin, and deoxycholate, but not by taurocholate. Erythromycin did not inhibit incorporation by Haloquadratum, but moderate inhibition was found by chloramphenicol at 10-50 microg mL(-1). Deoxycholate was highly inhibitory, but only partial inhibition was obtained in the presence of 25 microg mL(-1) taurocholate. Inhibition by chloramphenicol and taurocholate increased with increasing salt concentration. Erythromycin and taurocholate proved most valuable to differentiate between archaeal and bacterial activities in saltern brines.},
}
@article {pmid18204798,
year = {2008},
author = {Adair, KL and Schwartz, E},
title = {Evidence that ammonia-oxidizing archaea are more abundant than ammonia-oxidizing bacteria in semiarid soils of northern Arizona, USA.},
journal = {Microbial ecology},
volume = {56},
number = {3},
pages = {420-426},
pmid = {18204798},
issn = {0095-3628},
mesh = {Ammonia/*metabolism ; Archaea/enzymology/genetics/*metabolism ; Arizona ; Bacteria/enzymology/genetics/*metabolism ; DNA, Archaeal/chemistry/genetics ; DNA, Bacterial/chemistry/genetics ; Desert Climate ; Ecosystem ; Gene Dosage ; Linear Models ; Multivariate Analysis ; Oxidation-Reduction ; Oxidoreductases/genetics/*isolation &amp; purification/metabolism ; Polymerase Chain Reaction ; *Soil Microbiology ; },
abstract = {Autotrophic ammonia-oxidizing communities, which are responsible for the rate-limiting step of nitrification in most soils, have not been studied extensively in semiarid ecosystems. Abundances of soil archaeal and bacterial amoA were measured with real-time polymerase chain reaction along an elevation gradient in northern Arizona. Archaeal amoA was the predominant form of amoA at all sites; however, ratios of archaeal to bacterial amoA ranged from 17 to more than 1,600. Although size of ammonia-oxidizing bacteria populations was correlated with precipitation, temperature, percent sand, and soil C/N, there were no significant relationships between ammonia-oxidizing archaea populations and any of the environmental parameters evaluated in this study. Our results suggest that in these soils, archaea may be the primary ammonia oxidizers, and that ammonia-oxidizing archaea and ammonia-oxidizing bacteria occupy different niches.},
}
@article {pmid18192060,
year = {2008},
author = {Klipcan, L and Frenkel-Morgenstern, M and Safro, MG},
title = {Presence of tRNA-dependent pathways correlates with high cysteine content in methanogenic Archaea.},
journal = {Trends in genetics : TIG},
volume = {24},
number = {2},
pages = {59-63},
doi = {10.1016/j.tig.2007.11.007},
pmid = {18192060},
issn = {0168-9525},
mesh = {Amino Acids/biosynthesis ; Amino Acyl-tRNA Synthetases/genetics/metabolism ; Archaeal Proteins/chemistry/*genetics/*metabolism ; Cysteine/analysis ; Euryarchaeota/classification/*genetics/*metabolism ; Genome, Archaeal ; Methane/metabolism ; Phylogeny ; Proteome ; RNA, Archaeal/*genetics/*metabolism ; RNA, Transfer/*genetics/*metabolism ; },
abstract = {Archeal proteomes can be clustered into two groups based on their cysteine content. One group of proteomes displays a low cysteine content (approximately 0.7% of the entire proteome), whereas the second group contains twice as many cysteines as the first (approximately 1.3%). All cysteine-rich organisms belong to the methanogenic Archaea, which generates special cysteine clusters associated with primitive metabolic reactions. Our findings suggest that cysteine plays an important role in early forms of life.},
}
@article {pmid18183358,
year = {2008},
author = {Hemp, J and Gennis, RB},
title = {Diversity of the heme-copper superfamily in archaea: insights from genomics and structural modeling.},
journal = {Results and problems in cell differentiation},
volume = {45},
number = {},
pages = {1-31},
doi = {10.1007/400_2007_046},
pmid = {18183358},
issn = {0080-1844},
support = {R01 HL016101/HL/NHLBI NIH HHS/United States ; },
mesh = {Amino Acid Sequence ; Archaea/*genetics/*physiology ; Archaeal Proteins/*metabolism ; Copper/*chemistry ; Genome, Archaeal ; Genomics ; Heme/*chemistry ; Models, Chemical ; Molecular Conformation ; Molecular Sequence Data ; Oxidoreductases/chemistry ; Oxygen/chemistry ; Oxygenases/chemistry ; Phylogeny ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; },
abstract = {Recent advances in DNA sequencing technologies have provided unprecedented access into the diversity of the microbial world. Herein we use the comparative genomic analysis of microbial genomes and environmental metagenomes coupled with structural modelling to explore the diversity of aerobic respiration in Archaea. We focus on the heme-copper oxidoreductase superfamily which is responsible for catalyzing the terminal reaction in aerobic respiration-the reduction of molecular oxygen to water. Sequence analyses demonstrate that there are at least eight heme-copper oxygen reductase families: A-, B-, C-, D-, E-, F-, G-, and H-families. Interestingly, five of these oxygen reductase families (D-, E-, F-, G-, and H-families) are currently found exclusively in Archaea. We review the structural properties of all eight families focusing on the members found within Archaea. Structural modelling coupled with sequence analysis suggests that many of the oxygen reductases identified from thermophilic Archaea have modified proton channel properties compared to the currently studied mesophilic bacterial oxygen reductases. These structural differences may be due to adaptation to the specific environments in which these enzymes function. We conclude with a brief analysis of the phylogenetic distribution and evolution of Archaeal heme-copper oxygen reductases.},
}
@article {pmid18182021,
year = {2008},
author = {Spitalny, P and Thomm, M},
title = {A polymerase III-like reinitiation mechanism is operating in regulation of histone expression in archaea.},
journal = {Molecular microbiology},
volume = {67},
number = {5},
pages = {958-970},
pmid = {18182021},
issn = {1365-2958},
mesh = {Archaea/*enzymology/metabolism ; Archaeal Proteins/*metabolism ; Base Sequence ; DNA-Directed RNA Polymerases/*metabolism ; Gene Expression Regulation, Archaeal ; Histones/chemistry/*genetics ; Molecular Sequence Data ; Nucleic Acid Conformation ; Promoter Regions, Genetic ; Pyrococcus furiosus/*genetics ; RNA Polymerase III/metabolism ; RNA, Archaeal/chemistry/genetics ; Sequence Alignment ; Temperature ; Terminator Regions, Genetic ; Transcription Initiation Site ; Transcription, Genetic ; },
abstract = {An archaeal histone gene from the hyperthermophile Pyrococcus furiosus containing four consecutive putative oligo-dT terminator sequences was used as a model system to investigate termination signals and the mechanism of termination in vitro. The archaeal RNA polymerase terminated with high efficiency at the first terminator at 90 degrees C when it contained five to six T residues, at 80 degrees C readthrough was significantly increased. A putative hairpin structure upstream of the first terminator had no effect on termination efficiency. Template competition experiments starting with RNA polymerase molecules engaged in ternary complexes revealed recycling of RNA polymerase from the terminator to the promoter of the same template. This facilitated reinitiation was dependent upon the presence of a terminator sequence suggesting that pausing at the terminator is required for recycling as in the RNA polymerase III system. Replacement of the sequences immediately downstream of the oligo-dT terminator by an AT-rich segment improved termination efficiency. Both AT-rich and GC-rich downstream sequences seemed to impair the facilitated reinitiation pathway. Our data suggest that recycling is dependent on a subtle interplay of pausing of RNA polymerase at the terminator and RNA polymerase translocation beyond the oligo-dT termination signal that is dramatically affected by downstream sequences.},
}
@article {pmid18180745,
year = {2008},
author = {Høj, L and Olsen, RA and Torsvik, VL},
title = {Effects of temperature on the diversity and community structure of known methanogenic groups and other archaea in high Arctic peat.},
journal = {The ISME journal},
volume = {2},
number = {1},
pages = {37-48},
doi = {10.1038/ismej.2007.84},
pmid = {18180745},
issn = {1751-7362},
mesh = {Archaea/*classification/*genetics/isolation &amp; purification ; Arctic Regions ; DNA, Archaeal/genetics ; Gene Library ; In Situ Hybridization, Fluorescence ; *Methane/metabolism ; Methanobacterium/classification/genetics/isolation &amp; purification ; Methanomicrobiales/classification/genetics/isolation &amp; purification ; Methanosarcinaceae/classification/genetics/isolation &amp; purification ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/classification/genetics ; *Soil Microbiology ; Svalbard ; Temperature ; },
abstract = {Archaeal populations are abundant in cold and temperate environments, but little is known about their potential response to climate change-induced temperature changes. The effects of temperature on archaeal communities in unamended slurries of weakly acidic peat from Spitsbergen were studied using a combination of fluorescent in situ hybridization (FISH), 16S rRNA gene clone libraries and denaturing gradient gel electrophoresis (DGGE). A high relative abundance of active archaeal cells (11-12% of total count) was seen at low temperatures (1 and 5 degrees C), and this community was dominated by Group 1.3b Crenarchaeota and the euryarchaeal clusters rice cluster V (RC-V), and Lake Dagow sediment (LDS). Increasing temperature reduced the diversity and relative abundance of these clusters. The methanogenic community in the slurries was diverse and included representatives of Methanomicrobiales, Methanobacterium, Methanosarcina and Methanosaeta. The overall relative abundance and diversity of the methanogenic archaea increased with increasing temperature, in accordance with a strong stimulation of methane production rates. However, DGGE profiling showed that the structure of this community changed with temperature and time. While the relative abundance of some populations was affected directly by temperature, the relative abundance of other populations was controlled by indirect effects or did not respond to temperature.},
}
@article {pmid18180743,
year = {2008},
author = {Teske, A and Sørensen, KB},
title = {Uncultured archaea in deep marine subsurface sediments: have we caught them all?.},
journal = {The ISME journal},
volume = {2},
number = {1},
pages = {3-18},
doi = {10.1038/ismej.2007.90},
pmid = {18180743},
issn = {1751-7362},
mesh = {Archaea/*classification/*genetics/isolation &amp; purification ; DNA Primers ; DNA, Archaeal/genetics ; DNA, Ribosomal/genetics ; Geologic Sediments/*microbiology ; Phylogeny ; Polymerase Chain Reaction/methods ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Deep marine subsurface sediments represent a novel archaeal biosphere with unknown physiology; the sedimentary subsurface harbors numerous novel phylogenetic lineages of archaea that are at present uncultured. Archaeal 16S rRNA analyses of deep subsurface sediments demonstrate their global occurrence and wide habitat range, including deep subsurface sediments, methane seeps and organic-rich coastal sediments. These subsurface archaeal lineages were discovered by PCR of extracted environmental DNA; their detection ultimately depends on the specificity of the archaeal PCR 16S rRNA primers. Surprisingly high mismatch frequencies for some archaeal PCR primers result in amplification bias against the corresponding archaeal lineages; this review presents some examples. Obviously, most archaeal 16S rRNA PCR primers were developed either before the discovery of these deep subsurface archaeal lineages, or without taking their sequence variants into account. PCR surveys with multiple primer combinations, revision and updates of primers whenever possible, and increasing use of PCR-independent methods in molecular microbial ecology will contribute to a more comprehensive view of subsurface archaeal communities.},
}
@article {pmid18177367,
year = {2008},
author = {Steger, D and Ettinger-Epstein, P and Whalan, S and Hentschel, U and de Nys, R and Wagner, M and Taylor, MW},
title = {Diversity and mode of transmission of ammonia-oxidizing archaea in marine sponges.},
journal = {Environmental microbiology},
volume = {10},
number = {4},
pages = {1087-1094},
doi = {10.1111/j.1462-2920.2007.01515.x},
pmid = {18177367},
issn = {1462-2920},
mesh = {Ammonia/metabolism ; Animals ; Archaeal Proteins/genetics ; Biodiversity ; Caribbean Region ; Crenarchaeota/*classification/genetics/metabolism ; Genes, Archaeal ; Larva/microbiology ; *Marine Biology ; Mediterranean Sea ; Molecular Sequence Data ; Oxidation-Reduction ; Oxidoreductases/genetics ; Pacific Ocean ; Phylogeny ; Porifera/growth &amp; development/metabolism/*microbiology ; Protein Subunits/genetics ; RNA, Archaeal/genetics ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The model marine crenarchaeote 'Cenarchaeum symbiosum' is until now the only ammonia-oxidizing archaeon known from a marine sponge. Here, phylogenetic analyses based on the 16S rRNA and ammonia monooxygenase subunit A (amoA) genes revealed the presence of putative ammonia-oxidizing archaea (AOA) in a diverse range of sponges from the western Pacific, Caribbean and Mediterranean. amoA diversity was limited even between different oceans, with many of the obtained sequences (75.9%; n(total) = 83) forming a monophyletic, apparently sponge- (and coral-) specific lineage, analogous to those previously inferred from comparative 16S rRNA gene studies of sponge-associated microbes. The presence of AOA in sponge larvae, as detected by 16S rRNA and amoA PCR assays as well as by fluorescence in situ hybridization, suggests they are vertically transmitted and thus might be of importance for ammonia detoxification within the sponge.},
}
@article {pmid18165302,
year = {2008},
author = {Jahn, U and Gallenberger, M and Paper, W and Junglas, B and Eisenreich, W and Stetter, KO and Rachel, R and Huber, H},
title = {Nanoarchaeum equitans and Ignicoccus hospitalis: new insights into a unique, intimate association of two archaea.},
journal = {Journal of bacteriology},
volume = {190},
number = {5},
pages = {1743-1750},
pmid = {18165302},
issn = {1098-5530},
mesh = {Amino Acids/metabolism/pharmacology ; Cell Division/drug effects/physiology ; DNA, Archaeal/genetics ; Desulfurococcaceae/genetics/*growth &amp; development/ultrastructure ; Fermentation/drug effects ; Hydrogen-Ion Concentration ; Magnetic Resonance Spectroscopy ; Microscopy, Electron ; Nanoarchaeota/genetics/*growth &amp; development/ultrastructure ; RNA, Ribosomal, 16S/genetics ; Sodium Chloride/pharmacology ; Sulfites/metabolism/pharmacology ; Temperature ; },
abstract = {Nanoarchaeum equitans and Ignicoccus hospitalis represent a unique, intimate association of two archaea. Both form a stable coculture which is mandatory for N. equitans but not for the host I. hospitalis. Here, we investigated interactions and mutual influence between these microorganisms. Fermentation studies revealed that during exponential growth only about 25% of I. hospitalis cells are occupied by N. equitans cells (one to three cells). The latter strongly proliferate in the stationary phase of I. hospitalis, until 80 to 90% of the I. hospitalis cells carry around 10 N. equitans cells. Furthermore, the expulsion of H2S, the major metabolic end product of I. hospitalis, by strong gas stripping yields huge amounts of free N. equitans cells. N. equitans had no influence on the doubling times, final cell concentrations, and growth temperature, pH, or salt concentration ranges or optima of I. hospitalis. However, isolation studies using optical tweezers revealed that infection with N. equitans inhibited the proliferation of individual I. hospitalis cells. This inhibition might be caused by deprivation of the host of cell components like amino acids, as demonstrated by 13C-labeling studies. The strong dependence of N. equitans on I. hospitalis was affirmed by live-dead staining and electron microscopic analyses, which indicated a tight physiological and structural connection between the two microorganisms. No alternative hosts, including other Ignicoccus species, were accepted by N. equitans. In summary, the data show a highly specialized association of N. equitans and I. hospitalis which so far cannot be assigned to a classical symbiosis, commensalism, or parasitism.},
}
@article {pmid18159946,
year = {2007},
author = {Brenneis, M and Hering, O and Lange, C and Soppa, J},
title = {Experimental characterization of Cis-acting elements important for translation and transcription in halophilic archaea.},
journal = {PLoS genetics},
volume = {3},
number = {12},
pages = {e229},
pmid = {18159946},
issn = {1553-7404},
mesh = {3' Untranslated Regions ; 5' Untranslated Regions ; Base Sequence ; Computational Biology ; DNA, Archaeal/genetics ; Gene Fusion ; Genes, Archaeal ; Genes, Reporter ; Genetic Complementation Test ; Halobacterium salinarum/*genetics ; Haloferax volcanii/*genetics ; Molecular Sequence Data ; Promoter Regions, Genetic ; Protein Biosynthesis ; RNA, Archaeal/genetics ; Transcription, Genetic ; },
abstract = {The basal transcription apparatus of archaea is well characterized. However, much less is known about the mechanisms of transcription termination and translation initation. Recently, experimental determination of the 5'-ends of ten transcripts from Pyrobaculum aerophilum revealed that these are devoid of a 5'-UTR. Bioinformatic analysis indicated that many transcripts of other archaeal species might also be leaderless. The 5'-ends and 3'-ends of 40 transcripts of two haloarchaeal species, Halobacterium salinarum and Haloferax volcanii, have been determined. They were used to characterize the lengths of 5'-UTRs and 3'-UTRs and to deduce consensus sequence-elements for transcription and translation. The experimental approach was complemented with a bioinformatics analysis of the H. salinarum genome sequence. Furthermore, the influence of selected 5'-UTRs and 3'-UTRs on transcript stability and translational efficiency in vivo was characterized using a newly established reporter gene system, gene fusions, and real-time PCR. Consensus sequences for basal promoter elements could be refined and a novel element was discovered. A consensus motif probably important for transcriptional termination was established. All 40 haloarchaeal transcripts analyzed had a 3'-UTR (average size 57 nt), and their 3'-ends were not posttranscriptionally modified. Experimental data and genome analyses revealed that the majority of haloarchaeal transcripts are leaderless, indicating that this is the predominant mode for translation initiation in haloarchaea. Surprisingly, the 5'-UTRs of most leadered transcripts did not contain a Shine-Dalgarno (SD) sequence. A genome analysis indicated that less than 10% of all genes are preceded by a SD sequence and even most proximal genes in operons lack a SD sequence. Seven different leadered transcripts devoid of a SD sequence were efficiently translated in vivo, including artificial 5'-UTRs of random sequences. Thus, an interaction of the 5'-UTRs of these leadered transcripts with the 16S rRNA could be excluded. Taken together, either a scanning mechanism similar to the mechanism of translation initiation operating in eukaryotes or a novel mechanism must operate on most leadered haloarchaeal transcripts.},
}
@article {pmid18157154,
year = {2008},
author = {Sorek, R and Kunin, V and Hugenholtz, P},
title = {CRISPR--a widespread system that provides acquired resistance against phages in bacteria and archaea.},
journal = {Nature reviews. Microbiology},
volume = {6},
number = {3},
pages = {181-186},
doi = {10.1038/nrmicro1793},
pmid = {18157154},
issn = {1740-1534},
mesh = {Archaea/*genetics/virology ; Bacteria/*genetics/virology ; Bacterial Proteins/genetics ; Bacteriophages/physiology ; DNA, Intergenic ; Gene Silencing ; Genome, Archaeal ; Genome, Bacterial ; Interspersed Repetitive Sequences/*physiology ; Multigene Family/genetics ; Viral Interference ; },
abstract = {Arrays of clustered, regularly interspaced short palindromic repeats (CRISPRs) are widespread in the genomes of many bacteria and almost all archaea. These arrays are composed of direct repeats that are separated by similarly sized non-repetitive spacers. CRISPR arrays, together with a group of associated proteins, confer resistance to phages, possibly by an RNA-interference-like mechanism. This Progress discusses the structure and function of this newly recognized antiviral mechanism.},
}
@article {pmid18096851,
year = {2008},
author = {Grochowski, LL and White, RH},
title = {Promiscuous anaerobes: new and unconventional metabolism in methanogenic archaea.},
journal = {Annals of the New York Academy of Sciences},
volume = {1125},
number = {},
pages = {190-214},
doi = {10.1196/annals.1419.001},
pmid = {18096851},
issn = {0077-8923},
mesh = {Aerobiosis ; Amino Acids/metabolism ; Anaerobiosis ; Methanococcaceae/*metabolism ; Nucleosides/biosynthesis ; Nucleotides/biosynthesis ; Polyamines/metabolism ; Pyrimidines/biosynthesis ; },
abstract = {The development of an oxygenated atmosphere on earth resulted in the polarization of life into two major groups, those that could live in the presence of oxygen and those that could not-the aerobes and the anaerobes. The evolution of aerobes from the earliest anaerobic prokaryotes resulted in a variety of metabolic adaptations. Many of these adaptations center on the need to sustain oxygen-sensitive reactions and cofactors to function in the new oxygen-containing atmosphere. Still other metabolic pathways that were not sensitive to oxygen also diverged. This is likely due to the physical separation of the organisms, based on their ability to live in the presence of oxygen, which allowed for the independent evolution of the pathways. Through the study of metabolic pathways in anaerobes and comparison to the more established pathways from aerobes, insight into metabolic evolution can be gained. This, in turn, can allow for extra- polation to those metabolic pathways occurring in the Last Universal Common Ancestor (LUCA). Some of the unique and uncanonical metabolic pathways that have been identified in the archaea with emphasis on the biochemistry of an obligate anaerobic methanogen, Methanocaldococcus jannaschii are reviewed.},
}
@article {pmid18083874,
year = {2008},
author = {Yu, Z and García-González, R and Schanbacher, FL and Morrison, M},
title = {Evaluations of different hypervariable regions of archaeal 16S rRNA genes in profiling of methanogens by Archaea-specific PCR and denaturing gradient gel electrophoresis.},
journal = {Applied and environmental microbiology},
volume = {74},
number = {3},
pages = {889-893},
pmid = {18083874},
issn = {1098-5336},
mesh = {Animal Feed ; Animals ; Complementarity Determining Regions/*genetics ; DNA Primers ; Dietary Fats ; Electrophoresis, Agar Gel/*methods ; Genes, Archaeal ; Methane/metabolism ; Methanobacteriaceae/*classification/genetics ; Methanobrevibacter/classification/genetics ; Molecular Sequence Data ; Polymerase Chain Reaction/*methods ; RNA, Ribosomal, 16S/*genetics ; Rumen/microbiology ; Sequence Analysis, DNA ; Sheep ; Species Specificity ; },
abstract = {Different hypervariable (V) regions of the archaeal 16S rRNA gene (rrs) were compared systematically to establish a preferred V region(s) for use in Archaea-specific PCR-denaturing gradient gel electrophoresis (DGGE). The PCR products of the V3 region produced the most informative DGGE profiles and permitted identification of common methanogens from rumen samples from sheep. This study also showed that different methanogens might be detected when different V regions are targeted by PCR-DGGE. Dietary fat appeared to transiently stimulate Methanosphaera stadtmanae but inhibit Methanobrevibacter sp. strain AbM4 in rumen samples.},
}
@article {pmid18080156,
year = {2008},
author = {Wilson, MS and Siering, PL and White, CL and Hauser, ME and Bartles, AN},
title = {Novel archaea and bacteria dominate stable microbial communities in North America's Largest Hot Spring.},
journal = {Microbial ecology},
volume = {56},
number = {2},
pages = {292-305},
pmid = {18080156},
issn = {0095-3628},
support = {//Howard Hughes Medical Institute/United States ; },
mesh = {*Archaea/classification/genetics/growth &amp; development/isolation &amp; purification ; *Bacteria/classification/genetics/growth &amp; development/isolation &amp; purification ; California ; Cloning, Molecular ; DNA, Ribosomal/analysis ; *Ecosystem ; Fungi/classification/genetics/growth &amp; development/isolation &amp; purification ; Gene Library ; Genes, rRNA ; Hot Springs/*microbiology ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 18S/genetics ; Sequence Analysis, DNA ; },
abstract = {Boiling Springs Lake is an approximately 12,000 m(2), 55 degrees C, pH 2 thermal feature located in Lassen Volcanic National Park in northern California, USA. We assessed the microbial diversity in the lake by analyzing approximately 500 sequences from clone libraries constructed using three different primer sets targeted at 16S rRNA genes and one targeted at 18S rRNA genes. We assessed the stability of the microbial community by constructing terminal restriction fragment length polymorphism (T-RFLP) profiles using DNA extracts collected in four separate years over a 7-year period. The four most prevalent phylotypes in the clone libraries shared an average approximately 85% sequence identity with their closest cultured relatives, and three fourths of the prokaryotic sequences shared less than 91% identity. Phylogenetic analyses revealed novel lineages devoid of cultivated representatives in the Bacterial and Archaeal domains. Many detected phylotypes were related to taxonomically diverse genera previously associated with high-temperature environments, while others were related to diverse Proteobacteria and Firmicutes that would not be expected to grow within BSL conditions. All of the 18S rRNA sequences most closely matched fungi in the phyla Ascomycota and Basidiomycota (91-99% identity). T-RFLP detected fragments corresponding to the most prevalent phylotypes detected in 16S rRNA gene libraries. The T-RFLPs from separate years were similar, and the water-derived T-RFLPs were similar to the sediment-derived (average pairwise Sorenson's similarity index of 0.74, and 0.78, respectively). Collectively, these results indicate that a stable community of diverse novel microorganisms exists in Boiling Springs Lake.},
}
@article {pmid18079405,
year = {2007},
author = {Berg, IA and Kockelkorn, D and Buckel, W and Fuchs, G},
title = {A 3-hydroxypropionate/4-hydroxybutyrate autotrophic carbon dioxide assimilation pathway in Archaea.},
journal = {Science (New York, N.Y.)},
volume = {318},
number = {5857},
pages = {1782-1786},
doi = {10.1126/science.1149976},
pmid = {18079405},
issn = {1095-9203},
mesh = {Acetyl Coenzyme A/metabolism ; Acetyl-CoA Carboxylase/metabolism ; Acyl Coenzyme A/metabolism ; Amino Acid Sequence ; Anaerobiosis ; Archaea/genetics/metabolism ; Autotrophic Processes ; Bicarbonates/metabolism ; Carbon Dioxide/*metabolism ; Genes, Archaeal ; Hydro-Lyases/genetics/metabolism ; Hydroxybutyrates/*metabolism ; Kinetics ; Lactic Acid/*analogs &amp; derivatives/metabolism ; Metabolic Networks and Pathways ; Molecular Sequence Data ; Oxidation-Reduction ; Photosynthesis ; Phylogeny ; Sulfolobaceae/genetics/*metabolism ; },
abstract = {The assimilation of carbon dioxide (CO2) into organic material is quantitatively the most important biosynthetic process. We discovered that an autotrophic member of the archaeal order Sulfolobales, Metallosphaera sedula, fixed CO2 with acetyl-coenzyme A (acetyl-CoA)/propionyl-CoA carboxylase as the key carboxylating enzyme. In this system, one acetyl-CoA and two bicarbonate molecules were reductively converted via 3-hydroxypropionate to succinyl-CoA. This intermediate was reduced to 4-hydroxybutyrate and converted into two acetyl-CoA molecules via 4-hydroxybutyryl-CoA dehydratase. The key genes of this pathway were found not only in Metallosphaera but also in Sulfolobus, Archaeoglobus, and Cenarchaeum species. Moreover, the Global Ocean Sampling database contains half as many 4-hydroxybutyryl-CoA dehydratase sequences as compared with those found for another key photosynthetic CO2-fixing enzyme, ribulose-1,5-bisphosphate carboxylase-oxygenase. This indicates the importance of this enzyme in global carbon cycling.},
}
@article {pmid18075710,
year = {2008},
author = {Ohene-Adjei, S and Chaves, AV and McAllister, TA and Benchaar, C and Teather, RM and Forster, RJ},
title = {Evidence of increased diversity of methanogenic archaea with plant extract supplementation.},
journal = {Microbial ecology},
volume = {56},
number = {2},
pages = {234-242},
pmid = {18075710},
issn = {0095-3628},
mesh = {Animals ; Cinnamomum zeylanicum/chemistry ; DNA, Archaeal/analysis ; DNA, Ribosomal/analysis ; Ecosystem ; Female ; Garlic/chemistry ; Genes, rRNA ; *Genetic Variation ; Methane/*metabolism ; *Methanobacteriaceae/classification/drug effects/genetics/growth &amp; development ; Molecular Sequence Data ; Phylogeny ; Plant Oils/administration &amp; dosage/*pharmacology ; RNA, Ribosomal, 16S/genetics ; Rumen/*microbiology ; Sequence Analysis, DNA ; Sheep ; },
abstract = {This study evaluated the effects of selected essential oils on archaeal communities using the ovine rumen model. Forty weaned Canadian Arcott ewes, fed with barley-based diet, were allotted to one of three essential oil supplementation treatments or a control (10 ewes per treatment) for 13 weeks. The treatments were cinnamaldehyde, garlic oil, juniper berry oil, and a control with no additive. Rumen content was sampled after slaughter and grouped by treatment by combining subsamples from each animal. DNA was extracted from the pooled samples and analyzed for methanogenic archaea using quantitative polymerase chain reaction, denaturing gradient gel electrophoresis, cloning, and sequencing. Our results suggest that the total copy number of archaeal 16S rRNA was not significantly affected by the treatments. The phylogenetic analysis indicated a trend toward an increased diversity of methanogenic archaea related to Methanosphaera stadtmanae, Methanobrevibacter smithii, and some uncultured groups with cinnamaldehyde, garlic, and juniper berry oil supplementation. The trends in the diversity of methanogenic archaea observed with the essential oil supplementation may have resulted from changes in associated protozoal species. Supplementation of ruminant diets with essential oils may alter the diversity of rumen methanogens without affecting the methanogenic capacity of the rumen.},
}
@article {pmid18069966,
year = {2008},
author = {Urbonavicius, J and Auxilien, S and Walbott, H and Trachana, K and Golinelli-Pimpaneau, B and Brochier-Armanet, C and Grosjean, H},
title = {Acquisition of a bacterial RumA-type tRNA(uracil-54, C5)-methyltransferase by Archaea through an ancient horizontal gene transfer.},
journal = {Molecular microbiology},
volume = {67},
number = {2},
pages = {323-335},
doi = {10.1111/j.1365-2958.2007.06047.x},
pmid = {18069966},
issn = {0950-382X},
mesh = {Archaea/classification/*enzymology/*genetics ; Bacteria/genetics ; Bacterial Proteins/*genetics ; Base Sequence ; Computational Biology ; Conserved Sequence ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Genome, Archaeal ; Iron/metabolism ; Magnesium/metabolism ; Methylation ; Molecular Sequence Data ; Nanoarchaeota/genetics ; Phylogeny ; Pyrococcus abyssi/genetics ; RNA, Transfer/metabolism ; Recombinant Fusion Proteins/isolation &amp; purification/metabolism ; Sulfur/metabolism ; Thermococcales/genetics ; Uracil/metabolism ; Uridine/metabolism ; tRNA Methyltransferases/*genetics/metabolism ; },
abstract = {The Pyrococcus abyssi genome displays two genes possibly coding for S-adenosyl-l-methionine-dependent RNA(uracil, C5)-methyltransferases (PAB0719 and PAB0760). Their amino acid sequences are more closely related to Escherichia coli RumA catalysing the formation of 5-methyluridine (m(5)U)-1939 in 23S rRNA than to E. coli TrmA (tRNA methyltransferase A) methylating uridine-54 in tRNA. Comparative genomic and phylogenetic analyses show that homologues of PAB0719 and PAB0760 occur only in a few Archaea, these genes having been acquired via a single horizontal gene transfer from a bacterial donor to the common ancestor of Thermococcales and Nanoarchaea. This transfer event was followed by a duplication event in Thermococcales leading to two closely related genes. None of the gene products of the two P. abyssi paralogues catalyses in vitro the formation of m(5)U in a P. abyssi rRNA fragment homologous to the bacterial RumA substrate. Instead, PAB0719 enzyme (renamed (Pab)TrmU54) displays an identical specificity to TrmA, as it catalyses the in vitro formation of m(5)U-54 in tRNA. Thus, during evolution, at least one of the two P. abyssi RumA-type enzymes has changed of target specificity. This functional shift probably occurred in an ancestor of all Thermococcales. This study also provides new evidence in favour of a close relationship between Thermococcales and Nanoarchaea.},
}
@article {pmid18065610,
year = {2008},
author = {Urakawa, H and Tajima, Y and Numata, Y and Tsuneda, S},
title = {Low temperature decreases the phylogenetic diversity of ammonia-oxidizing archaea and bacteria in aquarium biofiltration systems.},
journal = {Applied and environmental microbiology},
volume = {74},
number = {3},
pages = {894-900},
pmid = {18065610},
issn = {1098-5336},
mesh = {Ammonia/*metabolism ; Animals ; Aquaculture/instrumentation/*methods ; Archaea/*classification/genetics/growth &amp; development ; Bacteria/*classification/genetics/growth &amp; development ; *Cold Temperature ; Fishes/classification/growth &amp; development ; Genetic Variation ; Molecular Sequence Data ; Oxidation-Reduction ; Oxidoreductases/genetics ; *Phylogeny ; Seawater/*microbiology ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {The phylogenetic diversity and species richness of ammonia-oxidizing archaea (AOA) and bacteria (AOB) were examined with aquarium biofiltration systems. Species richness, deduced from rarefaction analysis, and diversity indices indicated that the phylogenetic diversity and species richness of AOA are greater than those of AOB; the diversity of AOA and of AOB is minimized in cold-water aquaria. This finding implies that temperature is a key factor influencing the population structure and diversity of AOA and AOB in aquarium biofiltration systems.},
}
@article {pmid18056077,
year = {2008},
author = {Bauer, M and Marschaus, L and Reuff, M and Besche, V and Sartorius-Neef, S and Pfeifer, F},
title = {Overlapping activator sequences determined for two oppositely oriented promoters in halophilic Archaea.},
journal = {Nucleic acids research},
volume = {36},
number = {2},
pages = {598-606},
pmid = {18056077},
issn = {1362-4962},
mesh = {Archaeal Proteins/*genetics/metabolism ; Base Sequence ; Conserved Sequence ; *Gene Expression Regulation, Archaeal ; Halobacterium salinarum/*genetics ; Haloferax mediterranei/genetics ; Haloferax volcanii/genetics ; Molecular Sequence Data ; Mutagenesis ; *Promoter Regions, Genetic ; Proteins/*genetics/metabolism ; Trans-Activators/metabolism ; *Transcriptional Activation ; },
abstract = {Transcription of the genomic region involved in gas vesicle formation in Halobacterium salinarum (p-vac) and Haloferax mediterranei (mc-vac) is driven by two divergent promoters, P(A) and P(D), separated by only 35 nt. Both promoters are activated by the transcription activator GvpE which in the case of P(mcA) requires a 20-nt sequence (UAS) consisting of two conserved 8-nt sequence portions located upstream of BRE. Here, we determined the two UAS elements in the promoter region of p-vac by scanning mutageneses using constructs containing P(pD) (without P(pA)) fused to the bgaH reporter gene encoding an enzyme with beta-galactosidase activity, or the dual reporter construct pApD with P(pD) fused to bgaH and P(pA) to an altered version of gvpA. The two UAS elements found exhibited a similar extension and distance to BRE as previously determined for the UAS in P(mcA). Their distal 8-nt portions almost completely overlapped in the centre of P(pD)-P(pA), and mutations in this region negatively affected the GvpE-mediated activation of both promoters. Any alteration of the distance between BRE and UAS resulted in the loss of the GvpE activation, as did a complete substitution of the proximal 8-nt portion, underlining that a close location of UAS and BRE was very important.},
}
@article {pmid18050949,
year = {2007},
author = {Park, NY and Cha, J and Kim, DO and Park, CS},
title = {Enzymatic characterization and substrate specificity of thermostable beta-glycosidase from hyperthermophilic archaea, Sulfolobus shibatae, expressed in E. coli.},
journal = {Journal of microbiology and biotechnology},
volume = {17},
number = {3},
pages = {454-460},
pmid = {18050949},
issn = {1017-7825},
mesh = {Biotechnology ; Carbohydrate Sequence ; Dimerization ; Enzyme Stability ; Escherichia coli/enzymology/genetics ; Glucosidases/genetics/*metabolism ; Glycosylation ; *Hot Temperature ; Hydrogen-Ion Concentration ; Molecular Sequence Data ; Oligosaccharides/chemistry/metabolism ; Substrate Specificity ; Sulfolobus/*enzymology/genetics ; Temperature ; },
abstract = {Enzymatic properties and substrate specificity of recombinant beta-glycosidases from a hyperthermophilic archaeon, Sulfolobus shibatae (rSSG), were analyzed. rSSG showed its optimum temperature and pH at 95 degrees C and pH 5.0, respectively. Thermal inactivation of rSSG showed that its half-life of enzymatic activity at 75 degrees C was 15 h whereas it drastically decreased to 3.9 min at 95 degrees C. The addition of 10 mM of MnCl2 enhanced the hydrolysis activity of rSSG up to 23% whereas most metal ions did not show any considerable effect. Dithiothreitol (DTT) and 2-mercaptoethanol exhibited significant influence on the increase of the hydrolysis activity of rSSG. rSSG apparently preferred laminaribiose (beta1-->3Glc), followed by sophorose (beta1-->2Glc), gentiobiose (beta1-->6Glc), and cellobiose (beta1--4Glc). Various intermolecular transfer products were formed by rSSG in the lactose reaction, indicating that rSSG prefers lactose as a good acceptor as well as a donor. The strong intermolecular transglycosylation activity of rSSG can be applied in making functional oligosaccharides.},
}
@article {pmid18050917,
year = {2007},
author = {Ozcan, B and Ozcengiz, G and Coleri, A and Cokmus, C},
title = {Diversity of halophilic archaea from six hypersaline environments in Turkey.},
journal = {Journal of microbiology and biotechnology},
volume = {17},
number = {6},
pages = {985-992},
pmid = {18050917},
issn = {1017-7825},
mesh = {Halobacteriaceae/*classification/drug effects/genetics ; Lipids/analysis ; Phylogeny ; Plasmids ; RNA, Ribosomal, 16S/genetics ; Sodium Chloride ; *Water Microbiology ; },
abstract = {The diversity of archaeal strains from six hypersaline environments in Turkey was analyzed by comparing their phenotypic characteristics and 16S rDNA sequences. Thirty-three isolates were characterized in terms of their phenotypic properties including morphological and biochemical characteristics, susceptibility to different antibiotics, and total lipid and plasmid contents, and finally compared by 16S rDNA gene sequences. The results showed that all isolates belong to the family Halobacteriaceae. Phylogenetic analyses using approximately 1,388 bp comparisions of 16S rDNA sequences demonstrated that all isolates clustered closely to species belonging to 9 genera, namely Halorubrum (8 isolates), Natrinema (5 isolates), Haloarcula (4 isolates), Natronococcus (4 isolates), Natrialba (4 isolates), Haloferax (3 isolates), Haloterrigena (3 isolates), Halalkalicoccus (1 isolate), and Halomicrobium (1 isolate). The results revealed a high diversity among the isolated halophilic strains and indicated that some of these strains constitute new taxa of extremely halophilic archaea.},
}
@article {pmid18043673,
year = {2007},
author = {Caffrey, JM and Bano, N and Kalanetra, K and Hollibaugh, JT},
title = {Ammonia oxidation and ammonia-oxidizing bacteria and archaea from estuaries with differing histories of hypoxia.},
journal = {The ISME journal},
volume = {1},
number = {7},
pages = {660-662},
doi = {10.1038/ismej.2007.79},
pmid = {18043673},
issn = {1751-7362},
mesh = {Ammonia/*metabolism ; Archaea/classification/genetics/*metabolism ; Bacteria/classification/genetics/*metabolism ; Geologic Sediments/microbiology ; Nitrogen/metabolism ; Oxidation-Reduction ; Oxidoreductases/genetics/metabolism ; Oxygen/metabolism ; RNA, Ribosomal, 16S/genetics ; Salinity ; Sulfides/metabolism ; *Water Microbiology ; },
abstract = {Nitrification, the oxidation of NH(4)(+) to NO(2)(-) and subsequently to NO(3)(-), plays a central role in the nitrogen cycle and is often a critical first step in nitrogen removal from estuarine and coastal environments. The first and rate-limiting step in nitrification is catalyzed by the enzyme ammonia monooxygenase (AmoA). We evaluate the relationships between the abundance of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) amoA genes; potential nitrification rates and environmental variables to identify factors influencing AOA abundance and nitrifier activity in estuarine sediments. Our results showed that potential nitrification rates increased as abundance of AOA amoA increased. In contrast, there was no relationship between potential nitrification rates and AOB amoA abundance. This suggests that AOA are significant in estuarine nitrogen cycling. Surprisingly, more of the variability in potential nitrification rates was predicted by salinity and pore water sulfide than by dissolved oxygen history.},
}
@article {pmid18043663,
year = {2007},
author = {Radl, V and Gattinger, A and Chronáková, A and Nemcová, A and Cuhel, J and Simek, M and Munch, JC and Schloter, M and Elhottová, D},
title = {Effects of cattle husbandry on abundance and activity of methanogenic archaea in upland soils.},
journal = {The ISME journal},
volume = {1},
number = {5},
pages = {443-452},
doi = {10.1038/ismej.2007.60},
pmid = {18043663},
issn = {1751-7362},
mesh = {*Animal Husbandry ; Animals ; Biomass ; Cattle/*physiology ; Czech Republic ; Euryarchaeota/*genetics/*metabolism ; Genes, Archaeal ; Genetic Variation ; Methane/metabolism ; Phylogeny ; Seasons ; *Soil Microbiology ; },
abstract = {In the present study, we tested the hypothesis that animal treading associated with a high input of organic matter would favour methanogenesis in soils used as overwintering pasture. Hence, methane emissions and methanogen populations were examined at sections with different degree of cattle impact in a Farm in South Bohemia, Czech Republic. In spring, methane emission positively corresponded to the gradient of animal impact. Applying phospholipid etherlipid analysis, the highest archaeal biomass was found in section severe impact (SI), followed by moderate impact (MI) and no impact. The same trend was observed for the methanogens as showed by real-time quantitative PCR analyses of methyl coenzyme M reductase (mcrA) genes. The detection of monounsaturated isoprenoid side chain hydrocarbons (i20:1) indicated the presence of acetoclastic methanogens in the cattle-impacted sites. This result was corroborated by the phylogenetic analysis of mcrA gene sequences obtained from section SI, which showed that 33% of the analysed clones belonged to the genus Methanosarcina. The majority of the sequenced clones (41%) showed close affiliations with uncultured rumen archaeons. This leads to the assumption that a substantial part of the methanogenic community in plot SI derived from the grazing cattle itself. Compared to the spring sampling, in autumn, a significant reduction in archaeal biomass and number of copies of mcrA genes was observed mainly for section MI. It can be concluded that after 5 months without cattle impact, the severely impact section maintained its methane production potential, whereas the methane production potential under moderate impact returned to background values.},
}
@article {pmid18042280,
year = {2007},
author = {Makarova, KS and Sorokin, AV and Novichkov, PS and Wolf, YI and Koonin, EV},
title = {Clusters of orthologous genes for 41 archaeal genomes and implications for evolutionary genomics of archaea.},
journal = {Biology direct},
volume = {2},
number = {},
pages = {33},
pmid = {18042280},
issn = {1745-6150},
support = {//Intramural NIH HHS/United States ; },
mesh = {Archaea/*genetics ; Archaeal Proteins/genetics ; Cluster Analysis ; Crenarchaeota/genetics ; Databases, Factual ; Databases, Protein ; *Evolution, Molecular ; *Genes, Archaeal ; *Genome, Archaeal ; Genomics/*methods ; Phylogeny ; Sequence Alignment ; },
abstract = {BACKGROUND: An evolutionary classification of genes from sequenced genomes that distinguishes between orthologs and paralogs is indispensable for genome annotation and evolutionary reconstruction. Shortly after multiple genome sequences of bacteria, archaea, and unicellular eukaryotes became available, an attempt on such a classification was implemented in Clusters of Orthologous Groups of proteins (COGs). Rapid accumulation of genome sequences creates opportunities for refining COGs but also represents a challenge because of error amplification. One of the practical strategies involves construction of refined COGs for phylogenetically compact subsets of genomes.<br><br>RESULTS: New Archaeal Clusters of Orthologous Genes (arCOGs) were constructed for 41 archaeal genomes (13 Crenarchaeota, 27 Euryarchaeota and one Nanoarchaeon) using an improved procedure that employs a similarity tree between smaller, group-specific clusters, semi-automatically partitions orthology domains in multidomain proteins, and uses profile searches for identification of remote orthologs. The annotation of arCOGs is a consensus between three assignments based on the COGs, the CDD database, and the annotations of homologs in the NR database. The 7538 arCOGs, on average, cover approximately 88% of the genes in a genome compared to a approximately 76% coverage in COGs. The finer granularity of ortholog identification in the arCOGs is apparent from the fact that 4538 arCOGs correspond to 2362 COGs; approximately 40% of the arCOGs are new. The archaeal gene core (protein-coding genes found in all 41 genome) consists of 166 arCOGs. The arCOGs were used to reconstruct gene loss and gene gain events during archaeal evolution and gene sets of ancestral forms. The Last Archaeal Common Ancestor (LACA) is conservatively estimated to possess 996 genes compared to 1245 and 1335 genes for the last common ancestors of Crenarchaeota and Euryarchaeota, respectively. It is inferred that LACA was a chemoautotrophic hyperthermophile that, in addition to the core archaeal functions, encoded more idiosyncratic systems, e.g., the CASS systems of antivirus defense and some toxin-antitoxin systems.<br><br>CONCLUSION: The arCOGs provide a convenient, flexible framework for functional annotation of archaeal genomes, comparative genomics and evolutionary reconstructions. Genomic reconstructions suggest that the last common ancestor of archaea might have been (nearly) as advanced as the modern archaeal hyperthermophiles. ArCOGs and related information are available at: ftp://ftp.ncbi.nih.gov/pub/koonin/arCOGs/.},
}
@article {pmid18039820,
year = {2008},
author = {Feinberg, LF and Srikanth, R and Vachet, RW and Holden, JF},
title = {Constraints on anaerobic respiration in the hyperthermophilic Archaea Pyrobaculum islandicum and Pyrobaculum aerophilum.},
journal = {Applied and environmental microbiology},
volume = {74},
number = {2},
pages = {396-402},
pmid = {18039820},
issn = {1098-5336},
mesh = {Anaerobiosis ; FMN Reductase/metabolism ; Hydrogen-Ion Concentration ; Iron/metabolism ; Nitrates/metabolism ; Oxidation-Reduction ; Pyrobaculum/*growth &amp; development/*metabolism ; Species Specificity ; Sulfur/metabolism ; Sulfurtransferases/metabolism ; Thiosulfates/metabolism ; },
abstract = {Pyrobaculum islandicum uses iron, thiosulfate, and elemental sulfur for anaerobic respiration, while Pyrobaculum aerophilum uses iron and nitrate; however, the constraints on these processes and their physiological mechanisms for iron and sulfur reduction are not well understood. Growth rates on sulfur compounds are highest at pH 5 to 6 and highly reduced (<-420-mV) conditions, while growth rates on nitrate and iron are highest at pH 7 to 9 and more-oxidized (>-210-mV) conditions. Growth on iron expands the known pH range of growth for both organisms. P. islandicum differs from P. aerophilum in that it requires direct contact with insoluble iron oxide for growth, it did not produce any extracellular compounds when grown on insoluble iron, and it lacked 2,6-anthrahydroquinone disulfonate oxidase activity. Furthermore, iron reduction in P. islandicum appears to be completely independent of c-type cytochromes. Like that in P. aerophilum, NADH-dependent ferric reductase activity in P. islandicum increased significantly in iron-grown cultures relative to that in non-iron-grown cultures. Proteomic analyses showed that there were significant increases in the amounts of a putative membrane-bound thiosulfate reductase in P. islandicum cultures grown on thiosulfate relative to those in cultures grown on iron and elemental sulfur. This is the first evidence of this enzyme being used in either a hyperthermophile or an archaeon. Pyrobaculum arsenaticum and Pyrobaculum calidifontis also grew on Fe(III) citrate and insoluble iron oxide, but only P. arsenaticum could grow on insoluble iron without direct contact.},
}
@article {pmid18035520,
year = {2008},
author = {Wu, J and Wang, S and Bai, J and Shi, L and Li, D and Xu, Z and Niu, Y and Lu, J and Bao, Q},
title = {ArchaeaTF: an integrated database of putative transcription factors in Archaea.},
journal = {Genomics},
volume = {91},
number = {1},
pages = {102-107},
doi = {10.1016/j.ygeno.2007.09.007},
pmid = {18035520},
issn = {1089-8646},
mesh = {Archaea/*genetics ; Archaeal Proteins/*genetics ; DNA-Binding Proteins/*genetics ; *Databases, Protein ; Internet ; *Phylogeny ; Protein Structure, Tertiary/genetics ; Transcription Factors/*genetics ; },
abstract = {Identification of all the transcription factors (TFs) encoded in a given genome is a prerequisite for understanding transcriptional regulatory networks. Archaea are prokaryotes that constitute one of the three main branches of organisms with an astounding diversity of habitats. In this report, we establish the ArchaeaTF database to provide an integrated information resource about TFs in Archaea, such as basic characteristics, domain architectures, and sequence similarities against the linked databases. Through its Web interface, ArchaeaTF provides three different ways for users to retrieve the data: simple browse, keyword search, and BLAST search. Moreover, ArchaeaTF can serve as a useful platform for comparative genomics analysis of archaeal TFs since it implements a series of tools, including MUSCLE for multiple sequence alignments of the DNA-binding domains, QuickTree for phylogenetic tree construction, and OrthoMCL for ortholog identification. The released ArchaeaTF 1.0 contains 2135 putative TFs from 37 completed archaeal genomes. In conclusion, we believe that ArchaeaTF will be a useful resource and convenient platform for researchers working on TFs and transcriptional regulatory networks to retrieve information from TFs in Archaea rapidly. ArchaeaTF is accessible at http://bioinformatics.zj.cn/archaeatf.},
}
@article {pmid18032433,
year = {2008},
author = {Wardle, J and Burgers, PM and Cann, IK and Darley, K and Heslop, P and Johansson, E and Lin, LJ and McGlynn, P and Sanvoisin, J and Stith, CM and Connolly, BA},
title = {Uracil recognition by replicative DNA polymerases is limited to the archaea, not occurring with bacteria and eukarya.},
journal = {Nucleic acids research},
volume = {36},
number = {3},
pages = {705-711},
pmid = {18032433},
issn = {1362-4962},
support = {G0000076/MRC_/Medical Research Council/United Kingdom ; R01 GM032431/GM/NIGMS NIH HHS/United States ; GM 32431/GM/NIGMS NIH HHS/United States ; },
mesh = {Amino Acid Sequence ; Archaea/*enzymology ; Archaeal Proteins/chemistry/*metabolism ; DNA/chemistry ; DNA Polymerase III/metabolism ; DNA Replication ; DNA-Directed DNA Polymerase/chemistry/*metabolism ; Escherichia coli/enzymology ; Humans ; Methanosarcina/enzymology ; Pyrococcus furiosus/enzymology ; Saccharomyces cerevisiae/enzymology ; Sequence Alignment ; Templates, Genetic ; Uracil/*metabolism ; },
abstract = {Family B DNA polymerases from archaea such as Pyrococcus furiosus, which live at temperatures approximately 100 degrees C, specifically recognize uracil in DNA templates and stall replication in response to this base. Here it is demonstrated that interaction with uracil is not restricted to hyperthermophilic archaea and that the polymerase from mesophilic Methanosarcina acetivorans shows identical behaviour. The family B DNA polymerases replicate the genomes of archaea, one of the three fundamental domains of life. This publication further shows that the DNA replicating polymerases from the other two domains, bacteria (polymerase III) and eukaryotes (polymerases delta and epsilon for nuclear DNA and polymerase gamma for mitochondrial) are also unable to recognize uracil. Uracil occurs in DNA as a result of deamination of cytosine, either in G:C base-pairs or, more rapidly, in single stranded regions produced, for example, during replication. The resulting G:U mis-pairs/single stranded uracils are promutagenic and, unless repaired, give rise to G:C to A:T transitions in 50% of the progeny. The confinement of uracil recognition to polymerases of the archaeal domain is discussed in terms of the DNA repair pathways necessary for the elimination of uracil.},
}
@article {pmid18004773,
year = {2008},
author = {Vasile, F and Pechkova, E and Nicolini, C},
title = {Solution structure of the beta-subunit of the translation initiation factor aIF2 from archaebacteria Sulfolobus solfataricus.},
journal = {Proteins},
volume = {70},
number = {3},
pages = {1112-1115},
doi = {10.1002/prot.21797},
pmid = {18004773},
issn = {1097-0134},
mesh = {Amino Acid Sequence ; Archaeal Proteins/*chemistry/metabolism ; Crystallography, X-Ray ; Models, Molecular ; Molecular Sequence Data ; Peptide Initiation Factors/*chemistry/metabolism ; Protein Structure, Secondary ; Protein Subunits/*chemistry/metabolism ; Solutions/metabolism ; Sulfolobus solfataricus/chemistry/*metabolism ; },
}
@article {pmid17997854,
year = {2007},
author = {Lange, C and Zaigler, A and Hammelmann, M and Twellmeyer, J and Raddatz, G and Schuster, SC and Oesterhelt, D and Soppa, J},
title = {Genome-wide analysis of growth phase-dependent translational and transcriptional regulation in halophilic archaea.},
journal = {BMC genomics},
volume = {8},
number = {},
pages = {415},
pmid = {17997854},
issn = {1471-2164},
mesh = {Evolution, Molecular ; *Gene Expression Regulation, Archaeal ; Genes, Archaeal ; Genome, Archaeal/*genetics ; Halobacterium salinarum/*genetics/*growth &amp; development ; Haloferax/*genetics/*growth &amp; development ; Models, Genetic ; Oligonucleotide Array Sequence Analysis ; *Protein Biosynthesis ; RNA, Messenger/genetics/metabolism ; Repressor Proteins/genetics ; Reproducibility of Results ; Reverse Transcriptase Polymerase Chain Reaction ; Species Specificity ; Transcription, Genetic ; },
abstract = {BACKGROUND: Differential expression of genes can be regulated on many different levels. Most global studies of gene regulation concentrate on transcript level regulation, and very few global analyses of differential translational efficiencies exist. The studies have revealed that in Saccharomyces cerevisiae, Arabidopsis thaliana, and human cell lines translational regulation plays a significant role. Additional species have not been investigated yet. Particularly, until now no global study of translational control with any prokaryotic species was available.<br><br>RESULTS: A global analysis of translational control was performed with two haloarchaeal model species, Halobacterium salinarum and Haloferax volcanii. To identify differentially regulated genes, exponentially growing and stationary phase cells were compared. More than 20% of H. salinarum transcripts are translated with non-average efficiencies. By far the largest group is comprised of genes that are translated with above-average efficiency specifically in exponential phase, including genes for many ribosomal proteins, RNA polymerase subunits, enzymes, and chemotaxis proteins. Translation of 1% of all genes is specifically repressed in either of the two growth phases. For comparison, DNA microarrays were also used to identify differential transcriptional regulation in H. salinarum, and 17% of all genes were found to have non-average transcript levels in exponential versus stationary phase. In H. volcanii, 12% of all genes are translated with non-average efficiencies. The overlap with H. salinarum is negligible. In contrast to H. salinarum, 4.6% of genes have non-average translational efficiency in both growth phases, and thus they might be regulated by other stimuli than growth phase.<br><br>CONCLUSION: For the first time in any prokaryotic species it was shown that a significant fraction of genes is under differential translational control. Groups of genes with different regulatory patterns were discovered. However, neither the fractions nor the identity of regulated genes are conserved between H. salinarum and H. volcanii, indicating that prokaryotes as well as eukaryotes use differential translational control for the regulation of gene expression, but that the identity of regulated genes is not conserved. For 70 H. salinarum genes potentiation of regulation was observed, but for the majority of regulated genes either transcriptional or translational regulation is employed.},
}
@article {pmid17991018,
year = {2007},
author = {Herfort, L and Schouten, S and Abbas, B and Veldhuis, MJ and Coolen, MJ and Wuchter, C and Boon, JP and Herndl, GJ and Sinninghe Damsté, JS},
title = {Variations in spatial and temporal distribution of Archaea in the North Sea in relation to environmental variables.},
journal = {FEMS microbiology ecology},
volume = {62},
number = {3},
pages = {242-257},
doi = {10.1111/j.1574-6941.2007.00397.x},
pmid = {17991018},
issn = {0168-6496},
mesh = {Crenarchaeota/chemistry/classification/genetics/*isolation &amp; purification ; DNA, Archaeal/analysis ; *Ecosystem ; Euryarchaeota/chemistry/classification/genetics/*isolation &amp; purification ; Genes, rRNA ; Membrane Lipids/analysis ; Molecular Sequence Data ; Nitrites/metabolism ; North Sea ; Nucleic Acid Hybridization ; Oxidoreductases/genetics/metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seasons ; Seawater/*chemistry/*microbiology ; Sequence Analysis, DNA ; },
abstract = {The spatial and temporal distribution of pelagic Archaea was studied in the southern North Sea by rRNA hybridization, sequencing and quantification of 16S rRNA gene and membrane lipid analyses and related to physical, chemical and biological parameters to determine the factors influencing archaeal biogeography. A clear temporal variability was observed, with marine Crenarchaeota (Group I.1a) being relatively more abundant in winter and Euryarchaeota dominating the archaeal assemblage in spring and summer. Spatial differences in the lateral distribution of Crenarchaeota were also evident. In fact, their abundance was positively correlated with the copy number of the gene encoding the alpha subunit of crenarchaeotal ammonia monooxygenase (amoA) and with concentrations of ammonia, nitrate, nitrite and phosphorus. This suggests that most Crenarchaeota in the North Sea are nitrifiers and that their distribution is determined by nutrient concentrations. However, Crenarchaeota were not abundant when larger phytoplankton (>3 microm) dominated the algal population. It is hypothesized that together with nutrient concentration, phytoplankton biomass and community structure can predict crenarchaeotal abundance in the southern North Sea. Euryarchaeotal abundance was positively correlated with chlorophyll a concentrations, but not with phytoplankton community structure. Whether this is related to the potential of Euryarchaeota to perform aerobic anoxygenic phototrophy remains to be shown, but the conspicuous seasonal distribution pattern of Crenarchaeota and Euryarchaeota suggests that they occupy a different ecological niche.},
}
@article {pmid17988815,
year = {2007},
author = {Thummes, K and Schäfer, J and Kämpfer, P and Jäckel, U},
title = {Thermophilic methanogenic Archaea in compost material: occurrence, persistence and possible mechanisms for their distribution to other environments.},
journal = {Systematic and applied microbiology},
volume = {30},
number = {8},
pages = {634-643},
doi = {10.1016/j.syapm.2007.08.001},
pmid = {17988815},
issn = {0723-2020},
mesh = {DNA, Bacterial/genetics ; Desiccation ; Hot Temperature ; Methane/*biosynthesis ; Methanobacterium/classification/genetics/*isolation &amp; purification ; Methanomicrobiaceae/classification/genetics/*isolation &amp; purification ; Methanosarcina/classification/genetics/*isolation &amp; purification ; Molecular Sequence Data ; Polymorphism, Single-Stranded Conformational ; Sequence Analysis, DNA ; *Soil Microbiology ; Ultraviolet Rays ; },
abstract = {Since compost is widely used as soil amendment and the fact that during the processing of compost material high amounts of microorganisms are released into the air, we investigated whether compost may act as a carrier for thermophilic methanogens to temperate soils. All eight investigated compost materials showed a clear methane production potential between 0.01 and 0.98 micromol CH(4) g dw(-1)h(-1) at 50 degrees C. Single strand conformation polymorphism (SSCP) and cloning analysis indicated the presence of Methanosarcina thermophila, Methanoculleus thermophilus, and Methanobacterium formicicum. Bioaerosols collected during the turning of a compost pile showed both a highly similar SSCP profile compared to the corresponding compost material and clear methane production during anoxic incubation in selective medium at 50 degrees C. Both observations indicated a considerable release of thermophilic methanogens into the air. To analyse the persistence of compost-borne thermophilic methanogens in temperate oxic soils, we therefore studied their potential activity in compost and compost/soil mixtures, which was brought to a meadow soil, as well as in an agricultural soil fertilised with compost. After 24h anoxic incubation at 50 degrees C, all samples containing compost showed a clear methanogenic activity, even 1 year after application. In combination with the in vitro observed resilience of the compost-borne methanogens against desiccation and UV radiation we assume that compost material acts as an effective carrier for the distribution of thermophilic methanogens by fertilisation and wind.},
}
@article {pmid17959927,
year = {2007},
author = {Nielsen, JS and Bøggild, A and Andersen, CB and Nielsen, G and Boysen, A and Brodersen, DE and Valentin-Hansen, P},
title = {An Hfq-like protein in archaea: crystal structure and functional characterization of the Sm protein from Methanococcus jannaschii.},
journal = {RNA (New York, N.Y.)},
volume = {13},
number = {12},
pages = {2213-2223},
pmid = {17959927},
issn = {1469-9001},
mesh = {Amino Acid Sequence ; Archaeal Proteins/*chemistry ; Conserved Sequence ; Crystallography, X-Ray ; Host Factor 1 Protein/*chemistry ; Methanococcus/*chemistry ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; RNA, Archaeal/*chemistry ; RNA-Binding Proteins/*chemistry ; Ribonucleoproteins, Small Nuclear/*chemistry ; },
abstract = {The Sm and Sm-like proteins are conserved in all three domains of life and have emerged as important players in many different RNA-processing reactions. Their proposed role is to mediate RNA-RNA and/or RNA-protein interactions. In marked contrast to eukaryotes, bacteria appear to contain only one distinct Sm-like protein belonging to the Hfq family of proteins. Similarly, there are generally only one or two subtypes of Sm-related proteins in archaea, but at least one archaeon, Methanococcus jannaschii, encodes a protein that is related to Hfq. This archaeon does not contain any gene encoding a conventional archaeal Sm-type protein, suggesting that Hfq proteins and archaeal Sm-homologs can complement each other functionally. Here, we report the functional characterization of M. jannaschii Hfq and its crystal structure at 2.5 A resolution. The protein forms a hexameric ring. The monomer fold, as well as the overall structure of the complex is similar to that found for the bacterial Hfq proteins. However, clear differences are seen in the charge distribution on the distal face of the ring, which is unusually negative in M. jannaschii Hfq. Moreover, owing to a very short N-terminal alpha-helix, the overall diameter of the archaeal Hfq hexamer is significantly smaller than its bacterial counterparts. Functional analysis reveals that Escherichia coli and M. jannaschii Hfqs display very similar biochemical and biological properties. It thus appears that the archaeal and bacterial Hfq proteins are largely functionally interchangeable.},
}
@article {pmid17956224,
year = {2008},
author = {Majerník, AI and Chong, JP},
title = {A conserved mechanism for replication origin recognition and binding in archaea.},
journal = {The Biochemical journal},
volume = {409},
number = {2},
pages = {511-518},
doi = {10.1042/BJ20070213},
pmid = {17956224},
issn = {1470-8728},
support = {BB/D525056/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Amino Acid Sequence ; Archaea/*genetics/metabolism ; Archaeal Proteins/genetics/metabolism ; Base Sequence ; Binding Sites ; Conserved Sequence ; Kinetics ; Molecular Sequence Data ; Origin Recognition Complex/*metabolism ; },
abstract = {To date, methanogens are the only group within the archaea where firing DNA replication origins have not been demonstrated in vivo. In the present study we show that a previously identified cluster of ORB (origin recognition box) sequences do indeed function as an origin of replication in vivo in the archaeon Methanothermobacter thermautotrophicus. Although the consensus sequence of ORBs in M. thermautotrophicus is somewhat conserved when compared with ORB sequences in other archaea, the Cdc6-1 protein from M. thermautotrophicus (termed MthCdc6-1) displays sequence-specific binding that is selective for the MthORB sequence and does not recognize ORBs from other archaeal species. Stabilization of in vitro MthORB DNA binding by MthCdc6-1 requires additional conserved sequences 3' to those originally described for M. thermautotrophicus. By testing synthetic sequences bearing mutations in the MthORB consensus sequence, we show that Cdc6/ORB binding is critically dependent on the presence of an invariant guanine found in all archaeal ORB sequences. Mutation of a universally conserved arginine residue in the recognition helix of the winged helix domain of archaeal Cdc6-1 shows that specific origin sequence recognition is dependent on the interaction of this arginine residue with the invariant guanine. Recognition of a mutated origin sequence can be achieved by mutation of the conserved arginine residue to a lysine or glutamine residue. Thus despite a number of differences in protein and DNA sequences between species, the mechanism of origin recognition and binding appears to be conserved throughout the archaea.},
}
@article {pmid17929831,
year = {2007},
author = {Mehrotra, S and Balaram, H},
title = {Kinetic characterization of adenylosuccinate synthetase from the thermophilic archaea Methanocaldococcus jannaschii.},
journal = {Biochemistry},
volume = {46},
number = {44},
pages = {12821-12832},
doi = {10.1021/bi701009y},
pmid = {17929831},
issn = {0006-2960},
mesh = {Adenylosuccinate Synthase/*chemistry/isolation &amp; purification/*metabolism ; Cloning, Molecular ; Kinetics ; Methanococcus/*enzymology ; Models, Biological ; Protein Structure, Quaternary ; },
abstract = {Adenylosuccinate synthetase (AdSS) catalyzes the Mg2+ dependent condensation of a molecule of IMP with aspartate to form adenylosuccinate, in a reaction driven by the hydrolysis of GTP to GDP. AdSS from the thermophilic archaea, Methanocaldococcus jannaschii (MjAdSS) is 345 amino acids long against an average length of 430-457 amino acids for most mesophilic AdSS. This short AdSS has two large deletions that map to the middle and C-terminus of the protein. This article discusses the detailed kinetic characterization of MjAdSS. Initial velocity and product inhibition studies, carried out at 70 degrees C, suggest a rapid equilibrium random AB steady-state ordered C kinetic mechanism for the MjAdSS catalyzed reaction. AdSS are known to exhibit monomer-dimer equilibrium with the dimer being implicated in catalysis. In contrast, our studies show that MjAdSS is an equilibrium mixture of dimers and tetramers with the tetramer being the catalytically active form. The tetramer dissociates into dimers with a minor increase in ionic strength of the buffer, while the dimer is extremely stable and does not dissociate even at 1.2 M NaCl. Phosphate, a product of the reaction, was found to be a potent inhibitor of MjAdSS showing biphasic inhibition of enzyme activity. The inhibition was competitive with IMP and noncompetitive with GTP. MjAdSS, like the mouse acidic isozyme, exhibits substrate inhibition, with IMP inhibiting enzyme activity at subsaturating GTP concentrations. Regulation of enzyme activity by the glycolytic intermediate, fructose 1,6 bisphosphate, was also observed with the inhibition being competitive with IMP and noncompetitive against GTP.},
}
@article {pmid17924153,
year = {2008},
author = {Vogt, S and Lyon, EJ and Shima, S and Thauer, RK},
title = {The exchange activities of [Fe] hydrogenase (iron-sulfur-cluster-free hydrogenase) from methanogenic archaea in comparison with the exchange activities of [FeFe] and [NiFe] hydrogenases.},
journal = {Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry},
volume = {13},
number = {1},
pages = {97-106},
pmid = {17924153},
issn = {0949-8257},
mesh = {Archaea/*enzymology ; Catalysis ; Hydrogenase/isolation &amp; purification/*metabolism ; Iron-Sulfur Proteins/isolation &amp; purification/*metabolism ; Mass Spectrometry ; Sensitivity and Specificity ; },
abstract = {[Fe] hydrogenase (iron-sulfur-cluster-free hydrogenase) catalyzes the reversible reduction of methenyltetrahydromethanopterin (methenyl-H4MPT+) with H2 to methylene-H4MPT, a reaction involved in methanogenesis from H2 and CO2 in many methanogenic archaea. The enzyme harbors an iron-containing cofactor, in which a low-spin iron is complexed by a pyridone, two CO and a cysteine sulfur. [Fe] hydrogenase is thus similar to [NiFe] and [FeFe] hydrogenases, in which a low-spin iron carbonyl complex, albeit in a dinuclear metal center, is also involved in H2 activation. Like the [NiFe] and [FeFe] hydrogenases, [Fe] hydrogenase catalyzes an active exchange of H2 with protons of water; however, this activity is dependent on the presence of the hydride-accepting methenyl-H4MPT+. In its absence the exchange activity is only 0.01% of that in its presence. The residual activity has been attributed to the presence of traces of methenyl-H4MPT+ in the enzyme preparations, but it could also reflect a weak binding of H2 to the iron in the absence of methenyl-H4MPT+. To test this we reinvestigated the exchange activity with [Fe] hydrogenase reconstituted from apoprotein heterologously produced in Escherichia coli and highly purified iron-containing cofactor and found that in the absence of added methenyl-H4MPT+ the exchange activity was below the detection limit of the tritium method employed (0.1 nmol min(-1) mg(-1)). The finding reiterates that for H2 activation by [Fe] hydrogenase the presence of the hydride-accepting methenyl-H4MPT+ is essentially required. This differentiates [Fe] hydrogenase from [FeFe] and [NiFe] hydrogenases, which actively catalyze H2/H2O exchange in the absence of exogenous electron acceptors.},
}
@article {pmid17922818,
year = {2007},
author = {Saengkerdsub, S and Herrera, P and Woodward, CL and Anderson, RC and Nisbet, DJ and Ricke, SC},
title = {Detection of methane and quantification of methanogenic archaea in faeces from young broiler chickens using real-time PCR.},
journal = {Letters in applied microbiology},
volume = {45},
number = {6},
pages = {629-634},
doi = {10.1111/j.1472-765X.2007.02243.x},
pmid = {17922818},
issn = {0266-8254},
mesh = {Animals ; Archaea/genetics/*isolation &amp; purification/metabolism ; Chickens/*microbiology ; DNA, Archaeal/*genetics ; DNA, Ribosomal/genetics ; Diptera/microbiology ; Feces/*microbiology ; Methane/*metabolism ; Polymerase Chain Reaction/*methods ; RNA, Ribosomal, 16S/genetics ; Soil Microbiology ; },
abstract = {AIMS: To detect the presence of methanogens in the faeces of broiler chicks during the first 2 weeks of age.<br><br>METHODS AND RESULTS: Chicken faecal samples from 120 broiler chicks were incubated for methane gas formation and methanogenic archaea were analysed using real-time PCR. The copy number of the order Methanobacteriales 16S rDNA gene in chicken faeces when the broilers were 3-12 days of age, litter and house flies collected in the bird house ranged from 4.19 to 5.51 log(10) g(-1) wet weight. The number of positive methane culture tubes increased from 25% to 100% as the birds aged.<br><br>CONCLUSIONS: Methanogens were successfully detected in faecal samples from 3- to 12-day-old broilers, as well as litter and house flies using real-time PCR. The copy number of methanogenic 16S rDNA gene in these samples was also similar to the number observed in litter and house flies.<br><br>The same methanogens consistently appeared in chicken faeces a few days after birth. Detection of the methanogenic bacteria in litter and house flies implicated them as potential environmental sources for methanogen colonization in broiler chicks.},
}
@article {pmid17916946,
year = {2007},
author = {Xu, XM and Carlson, BA and Zhang, Y and Mix, H and Kryukov, GV and Glass, RS and Berry, MJ and Gladyshev, VN and Hatfield, DL},
title = {New developments in selenium biochemistry: selenocysteine biosynthesis in eukaryotes and archaea.},
journal = {Biological trace element research},
volume = {119},
number = {3},
pages = {234-241},
doi = {10.1007/s12011-007-8003-9},
pmid = {17916946},
issn = {0163-4984},
support = {CA-41108/CA/NCI NIH HHS/United States ; CA080946/CA/NCI NIH HHS/United States ; DK47320/DK/NIDDK NIH HHS/United States ; DK52963/DK/NIDDK NIH HHS/United States ; GM061603/GM/NIGMS NIH HHS/United States ; GM065204/GM/NIGMS NIH HHS/United States ; //Intramural NIH HHS/United States ; },
mesh = {Animals ; Archaea/*metabolism ; Humans ; Mammals/metabolism ; Models, Biological ; Phosphotransferases/metabolism ; RNA, Transfer, Amino Acyl/metabolism ; Selenium/*metabolism ; Selenocysteine/*biosynthesis ; Selenoproteins/metabolism ; },
abstract = {We used comparative genomics and experimental analyses to show that (1) eukaryotes and archaea, which possess the selenocysteine (Sec) protein insertion machinery contain an enzyme, O-phosphoseryl-transfer RNA (tRNA) [Ser]Sec kinase (designated PSTK), which phosphorylates seryl-tRNA [Ser]Sec to form O-phosphoseryl-tRNA [Ser]Sec and (2) the Sec synthase (SecS) in mammals is a pyridoxal phosphate-containing protein previously described as the soluble liver antigen (SLA). SecS uses the product of PSTK, O-phosphoseryl-tRNA[Ser]Sec, and selenophosphate as substrates to generate selenocysteyl-tRNA [Ser]Sec. Sec could be synthesized on tRNA [Ser]Sec from selenide, adenosine triphosphate (ATP), and serine using tRNA[Ser]Sec, seryl-tRNA synthetase, PSTK, selenophosphate synthetase, and SecS. The enzyme that synthesizes monoselenophosphate is a previously identified selenoprotein, selenophosphate synthetase 2 (SPS2), whereas the previously identified mammalian selenophosphate synthetase 1 did not serve this function. Monoselenophosphate also served directly in the reaction replacing ATP, selenide, and SPS2, demonstrating that this compound was the active selenium donor. Conservation of the overall pathway of Sec biosynthesis suggests that this pathway is also active in other eukaryotes and archaea that contain selenoproteins.},
}
@article {pmid17886855,
year = {2007},
author = {Sawai, H and Nagashima, J and Kuwahara, M and Kitagata, R and Tamura, T and Matsui, I},
title = {Differences in substrate specificity of C(5)-substituted or C(5)-unsubstituted pyrimidine nucleotides by DNA polymerases from thermophilic bacteria, archaea, and phages.},
journal = {Chemistry &amp; biodiversity},
volume = {4},
number = {9},
pages = {1979-1995},
doi = {10.1002/cbdv.200790165},
pmid = {17886855},
issn = {1612-1880},
mesh = {Archaea/enzymology ; Archaeal Proteins/*chemistry ; Bacteria/enzymology ; Bacterial Proteins/*chemistry ; Bacteriophages/enzymology ; DNA/chemistry ; DNA Replication ; DNA-Directed DNA Polymerase/*chemistry ; *Evolution, Molecular ; *Hot Temperature ; Pyrimidine Nucleotides/*chemistry ; RNA/chemistry ; Substrate Specificity ; Viral Nonstructural Proteins/*chemistry ; },
abstract = {The pyrimidine bases of RNA are uracil (U) and cytosine (C), while thymine (T) and C are used for DNA. The C(5) position of C and U is unsubstituted, whereas the C(5) of T is substituted with a Me group. Miller et al. hypothesized that various C(5)-substituted uracil derivatives were formed during chemical evolution, and that C(5)-substituted U derivatives may have played important roles in the transition from an 'RNA world' to a 'DNA-RNA-protein world'. Hyperthermophilic bacteria and archaea are considered to be primitive organisms that are evolutionarily close to the universal ancestor of all life on earth. Thus, we examined the substrate specificity of several C(5)-substituted or C(5)-unsubstituted dUTP and dCTP analogs for several DNA polymerases from hyperthermophilic bacteria, hyperthermophilic archaea, and viruses during PCR or primer extension reaction. The substrate specificity of the C(5)-substituted or C(5)-unsubstituted pyrimidine nucleotides varied greatly depending on the type of DNA polymerase. The significance of this difference in substrate specificity in terms of the origin and evolution of the DNA replication system is discussed briefly.},
}
@article {pmid17827313,
year = {2007},
author = {Fierer, N and Breitbart, M and Nulton, J and Salamon, P and Lozupone, C and Jones, R and Robeson, M and Edwards, RA and Felts, B and Rayhawk, S and Knight, R and Rohwer, F and Jackson, RB},
title = {Metagenomic and small-subunit rRNA analyses reveal the genetic diversity of bacteria, archaea, fungi, and viruses in soil.},
journal = {Applied and environmental microbiology},
volume = {73},
number = {21},
pages = {7059-7066},
pmid = {17827313},
issn = {0099-2240},
support = {T32 GM008759/GM/NIGMS NIH HHS/United States ; T32 GM142607/GM/NIGMS NIH HHS/United States ; },
mesh = {Archaea/*classification/genetics ; Bacteria/*classification/genetics/growth &amp; development ; DNA/isolation &amp; purification ; DNA, Ribosomal/analysis/genetics ; *Genetic Variation ; *Genome ; RNA, Bacterial/genetics ; RNA, Ribosomal/*analysis/genetics ; *Soil Microbiology ; Viruses/*classification/genetics ; },
abstract = {Recent studies have highlighted the surprising richness of soil bacterial communities; however, bacteria are not the only microorganisms found in soil. To our knowledge, no study has compared the diversities of the four major microbial taxa, i.e., bacteria, archaea, fungi, and viruses, from an individual soil sample. We used metagenomic and small-subunit RNA-based sequence analysis techniques to compare the estimated richness and evenness of these groups in prairie, desert, and rainforest soils. By grouping sequences at the 97% sequence similarity level (an operational taxonomic unit [OTU]), we found that the archaeal and fungal communities were consistently less even than the bacterial communities. Although total richness levels are difficult to estimate with a high degree of certainty, the estimated number of unique archaeal or fungal OTUs appears to rival or exceed the number of unique bacterial OTUs in each of the collected soils. In this first study to comprehensively survey viral communities using a metagenomic approach, we found that soil viruses are taxonomically diverse and distinct from the communities of viruses found in other environments that have been surveyed using a similar approach. Within each of the four microbial groups, we observed minimal taxonomic overlap between sites, suggesting that soil archaea, bacteria, fungi, and viruses are globally as well as locally diverse.},
}
@article {pmid17825838,
year = {2007},
author = {Nikonov, O and Stolboushkina, E and Nikulin, A and Hasenöhrl, D and Bläsi, U and Manstein, DJ and Fedorov, R and Garber, M and Nikonov, S},
title = {New insights into the interactions of the translation initiation factor 2 from archaea with guanine nucleotides and initiator tRNA.},
journal = {Journal of molecular biology},
volume = {373},
number = {2},
pages = {328-336},
doi = {10.1016/j.jmb.2007.07.048},
pmid = {17825838},
issn = {0022-2836},
mesh = {Amino Acid Sequence ; Archaeal Proteins/*chemistry/metabolism ; Binding Sites ; Guanosine Diphosphate/*chemistry/metabolism ; Guanosine Triphosphate/*chemistry/metabolism ; Molecular Sequence Data ; Prokaryotic Initiation Factor-2/*chemistry/metabolism ; Protein Conformation ; RNA, Transfer/chemistry/metabolism ; RNA, Transfer, Met/*chemistry/metabolism ; Sulfolobus solfataricus/metabolism ; },
abstract = {Heterotrimeric a/eIF2alphabetagamma (archaeal homologue of the eukaryotic translation initiation factor 2 with alpha, beta and gamma subunits) delivers charged initiator tRNA (tRNAi) to the small ribosomal subunit. In this work, we determined the structures of aIF2gamma from the archaeon Sulfolobus solfataricus in the nucleotide-free and GDP-bound forms. Comparison of the free, GDP and Gpp(NH)p-Mg2+ forms of aIF2gamma revealed a sequence of conformational changes upon GDP and GTP binding. Our results show that the affinity of GDP to the G domain of the gamma subunit is higher than that of Gpp(NH)p. In analyzing a pyrophosphate molecule binding to domain II of the gamma subunit, we found a cleft that is very suitable for the acceptor stem of tRNA accommodation. It allows the suggestion of an alternative position for Met-tRNA i Met on the alphagamma intersubunit dimer, at variance with a recently published one. In the model reported here, the acceptor stem of the tRNAi is approximately perpendicular to that of tRNA in the ternary complex elongation factor Tu-Gpp(NH)p-tRNA. According to our analysis, the elbow and T stem of Met-tRNA i Met in this position should make extensive contact with the alpha subunit of aIF2. Thus, this model is in good agreement with experimental data showing that the alpha subunit of aIF2 is necessary for the stable interaction of aIF2gamma with Met-tRNA i Met.},
}
@article {pmid17764951,
year = {2007},
author = {Lee, SJ and Böhm, A and Krug, M and Boos, W},
title = {The ABC of binding-protein-dependent transport in Archaea.},
journal = {Trends in microbiology},
volume = {15},
number = {9},
pages = {389-397},
doi = {10.1016/j.tim.2007.08.002},
pmid = {17764951},
issn = {0966-842X},
mesh = {ATP-Binding Cassette Transporters/chemistry/genetics/*physiology ; Adenosine Triphosphate/metabolism ; Amino Acid Sequence ; Archaea/*metabolism ; Biological Transport ; Gene Expression Regulation, Archaeal ; Molecular Sequence Data ; Protein Structure, Tertiary ; Protein Subunits ; },
abstract = {The recent solution of the crystal structure of an entire binding-protein-dependent ABC transporter complex from the archaeon Archaeoglobus fulgidus by Locher and his colleagues marks a milestone in the understanding of the ABC transport mechanism. The structure elegantly demonstrates how the motor ATPase alternately opens and closes the inside and outside pores of the transporter and how the substrate-binding protein delivers its substrate. Binding-protein-dependent sugar ABC transporters in the archaea and in bacteria have an additional feature that could connect ABC transporters to gene regulation and to the control of transport activity by cellular processes.},
}
@article {pmid17726114,
year = {2007},
author = {Ventura, GT and Kenig, F and Reddy, CM and Schieber, J and Frysinger, GS and Nelson, RK and Dinel, E and Gaines, RB and Schaeffer, P},
title = {Molecular evidence of Late Archean archaea and the presence of a subsurface hydrothermal biosphere.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {104},
number = {36},
pages = {14260-14265},
pmid = {17726114},
issn = {0027-8424},
mesh = {Archaea/chemistry/*genetics/metabolism/ultrastructure ; Carbon/chemistry/metabolism ; Catalysis ; Chromatography, Gas ; *Evolution, Molecular ; Fossils ; Graphite/chemistry/metabolism ; Hydrocarbons/metabolism ; Hydrogen/metabolism ; Lipid Metabolism ; Microscopy, Electron, Scanning ; Molecular Structure ; Organic Chemicals/chemistry/metabolism ; *Temperature ; Time Factors ; Water/*metabolism ; },
abstract = {Highly cracked and isomerized archaeal lipids and bacterial lipids, structurally changed by thermal stress, are present in solvent extracts of 2,707- to 2,685-million-year-old (Ma) metasedimentary rocks from Timmins, ON, Canada. These lipids appear in conventional gas chromatograms as unresolved complex mixtures and include cyclic and acyclic biphytanes, C36-C39 derivatives of the biphytanes, and C31-C35 extended hopanes. Biphytane and extended hopanes are also found in high-pressure catalytic hydrogenation products released from solvent-extracted sediments, indicating that archaea and bacteria were present in Late Archean sedimentary environments. Postdepositional, hydrothermal gold mineralization and graphite precipitation occurred before metamorphism (approximately 2,665 Ma). Late Archean metamorphism significantly reduced the kerogen's adsorptive capacity and severely restricted sediment porosity, limiting the potential for post-Archean additions of organic matter to the samples. Argillites exposed to hydrothermal gold mineralization have disproportionately high concentrations of extractable archaeal and bacterial lipids relative to what is releasable from their respective high-pressure catalytic hydrogenation product and what is observed for argillites deposited away from these hydrothermal settings. The addition of these lipids to the sediments likely results from a Late Archean subsurface hydrothermal biosphere of archaea and bacteria.},
}
@article {pmid17725644,
year = {2007},
author = {Kahnt, J and Buchenau, B and Mahlert, F and Krüger, M and Shima, S and Thauer, RK},
title = {Post-translational modifications in the active site region of methyl-coenzyme M reductase from methanogenic and methanotrophic archaea.},
journal = {The FEBS journal},
volume = {274},
number = {18},
pages = {4913-4921},
doi = {10.1111/j.1742-4658.2007.06016.x},
pmid = {17725644},
issn = {1742-464X},
mesh = {Amino Acid Sequence ; Archaea/*enzymology/*metabolism ; Arginine/analogs &amp; derivatives/metabolism ; Binding Sites ; Cysteine/analogs &amp; derivatives/metabolism ; Glutamine/analogs &amp; derivatives/metabolism ; Glycine/analogs &amp; derivatives/metabolism ; Histidine/analogs &amp; derivatives/metabolism ; Methane/*metabolism ; Molecular Sequence Data ; Oxidoreductases/*chemistry/*metabolism ; *Protein Processing, Post-Translational ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; Trypsin/metabolism ; },
abstract = {Methyl-coenzyme M reductase (MCR) catalyzes the methane-forming step in methanogenic archaea. Isoenzyme I from Methanothermobacter marburgensiswas shown to contain a thioxo peptide bond and four methylated amino acids in the active site region. We report here that MCRs from all methanogens investigated contain the thioxo peptide bond, but that the enzymes differ in their post-translational methylations. The MS analysis included MCR I and MCR II from Methanothermobacter marburgensis, MCR I from Methanocaldococcus jannaschii and Methanoculleus thermophilus, and MCR from Methanococcus voltae, Methanopyrus kandleri and Methanosarcina barkeri. Two MCRs isolated from Black Sea mats containing mainly methanotrophic archaea of the ANME-1 cluster were also analyzed.},
}
@article {pmid17723094,
year = {2007},
author = {Marshall, CP and Leuko, S and Coyle, CM and Walter, MR and Burns, BP and Neilan, BA},
title = {Carotenoid analysis of halophilic archaea by resonance Raman spectroscopy.},
journal = {Astrobiology},
volume = {7},
number = {4},
pages = {631-643},
doi = {10.1089/ast.2006.0097},
pmid = {17723094},
issn = {1531-1074},
mesh = {Carotenoids/analysis ; Chromatography, High Pressure Liquid ; *Exobiology ; Halobacteriales/chemistry/growth &amp; development/*isolation &amp; purification ; Halobacterium salinarum/chemistry/growth &amp; development/*isolation &amp; purification ; Mars ; Mass Spectrometry ; Spectrum Analysis, Raman/methods ; United States ; United States National Aeronautics and Space Administration ; beta Carotene/analysis ; },
abstract = {Recently, halite and sulfate evaporate rocks have been discovered on Mars by the NASA rovers, Spirit and Opportunity. It is reasonable to propose that halophilic microorganisms could have potentially flourished in these settings. If so, biomolecules found in microorganisms adapted to high salinity and basic pH environments on Earth may be reliable biomarkers for detecting life on Mars. Therefore, we investigated the potential of Resonance Raman (RR) spectroscopy to detect biomarkers derived from microorganisms adapted to hypersaline environments. RR spectra were acquired using 488.0 and 514.5 nm excitation from a variety of halophilic archaea, including Halobacterium salinarum NRC-1, Halococcus morrhuae, and Natrinema pallidum. It was clearly demonstrated that RR spectra enhance the chromophore carotenoid molecules in the cell membrane with respect to the various protein and lipid cellular components. RR spectra acquired from all halophilic archaea investigated contained major features at approximately 1000, 1152, and 1505 cm(-1). The bands at 1505 cm(-1) and 1152 cm(-1) are due to in-phase C=C (nu(1)) and C-C stretching (nu(2)) vibrations of the polyene chain in carotenoids. Additionally, in-plane rocking modes of CH(3) groups attached to the polyene chain coupled with C-C bonds occur in the 1000 cm(-1) region. We also investigated the RR spectral differences between bacterioruberin and bacteriorhodopsin as another potential biomarker for hypersaline environments. By comparison, the RR spectrum acquired from bacteriorhodopsin is much more complex and contains modes that can be divided into four groups: the C=C stretches (1600-1500 cm(-1)), the CCH in-plane rocks (1400-1250 cm(-1)), the C-C stretches (1250-1100 cm(-1)), and the hydrogen out-of-plane wags (1000-700 cm(-1)). RR spectroscopy was shown to be a useful tool for the analysis and remote in situ detection of carotenoids from halophilic archaea without the need for large sample sizes and complicated extractions, which are required by analytical techniques such as high performance liquid chromatography and mass spectrometry.},
}
@article {pmid17713742,
year = {2008},
author = {Deppenmeier, U and Müller, V},
title = {Life close to the thermodynamic limit: how methanogenic archaea conserve energy.},
journal = {Results and problems in cell differentiation},
volume = {45},
number = {},
pages = {123-152},
doi = {10.1007/400_2006_026},
pmid = {17713742},
issn = {0080-1844},
mesh = {Acetates/chemistry ; Adenosine Triphosphate/chemistry ; Archaea/*metabolism ; Biological Transport ; Electron Transport ; Euryarchaeota/metabolism ; Evolution, Molecular ; Ions ; Methane/chemistry ; Models, Biological ; Models, Chemical ; Phenazines/chemistry ; Protons ; Sodium/chemistry ; Thermodynamics ; },
abstract = {Methane-forming archaea are strictly anaerobic, ancient microbes that are widespread in nature. These organisms are commonly found in anaerobic environments such as rumen, anaerobic sediments of rivers and lakes, hyperthermal deep sea vents and even hypersaline environments. From an evolutionary standpoint they are close to the origin of life. Common to all methanogens is the biological production of methane by a unique pathway currently only found in archaea. Methanogens can grow on only a limited number of substrates such as H(2) + CO(2), formate, methanol and other methyl group-containing substrates and some on acetate. The free energy change associated with methanogenesis from these compounds allows for the synthesis of 1 (acetate) to a maximum of only 2 mol of ATP under standard conditions while under environmental conditions less than one ATP can be synthesized. Therefore, methanogens live close to the thermodynamic limit. To cope with this problem, they have evolved elaborate mechanisms of energy conservation using both protons and sodium ions as the coupling ion in one pathway. These energy conserving mechanisms are comprised of unique enzymes, cofactors and electron carriers present only in methanogens. This review will summarize the current knowledge of energy conservation of methanogens and focus on recent insights into structure and function of ion translocating enzymes found in these organisms.},
}
@article {pmid17686032,
year = {2007},
author = {He, JZ and Shen, JP and Zhang, LM and Zhu, YG and Zheng, YM and Xu, MG and Di, H},
title = {Quantitative analyses of the abundance and composition of ammonia-oxidizing bacteria and ammonia-oxidizing archaea of a Chinese upland red soil under long-term fertilization practices.},
journal = {Environmental microbiology},
volume = {9},
number = {9},
pages = {2364-2374},
doi = {10.1111/j.1462-2920.2007.01358.x},
pmid = {17686032},
issn = {1462-2912},
mesh = {Ammonia/*metabolism ; *Archaea/classification/genetics/growth &amp; development/metabolism ; *Bacteria/classification/genetics/growth &amp; development/metabolism ; China ; Ecosystem ; Fertilizers/*microbiology ; Molecular Sequence Data ; Oxidation-Reduction ; Phylogeny ; Population Dynamics ; RNA, Ribosomal, 16S/*classification ; *Soil Microbiology ; },
abstract = {The abundance and composition of soil ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) were investigated by using quantitative real-time polymerase chain reaction, cloning and sequencing approaches based on amoA genes. The soil, classified as agri-udic ferrosols with pH (H(2)O) ranging from 3.7 to 6.0, was sampled in summer and winter from long-term field experimental plots which had received 16 years continuous fertilization treatments, including fallow (CK0), control without fertilizers (CK) and those with combinations of fertilizer nitrogen (N), phosphorus (P) and potassium (K): N, NP, NK, PK, NPK and NPK plus organic manure (OM). Population sizes of AOB and AOA changed greatly in response to the different fertilization treatments. The NPK + OM treatment had the highest copy numbers of AOB and AOA amoA genes among the treatments that received mineral fertilizers, whereas the lowest copy numbers were recorded in the N treatment. Ammonia-oxidizing archaea were more abundant than AOB in all the corresponding treatments, with AOA to AOB ratios ranging from 1.02 to 12.36. Significant positive correlations were observed among the population sizes of AOB and AOA, soil pH and potential nitrification rates, indicating that both AOB and AOA played an important role in ammonia oxidation in the soil. Phylogenetic analyses of the amoA gene fragments showed that all AOB sequences from different treatments were affiliated with Nitrosospira or Nitrosospira-like species and grouped into cluster 3, and little difference in AOB community composition was recorded among different treatments. All AOA sequences fell within cluster S (soil origin) and cluster M (marine and sediment origin). Cluster M dominated exclusively in the N, NP, NK and PK treatments, indicating a pronounced difference in the community composition of AOA in response to the long-term fertilization treatments. These findings could be fundamental to improve our understanding of the importance of both AOB and AOA in the cycling of nitrogen and other nutrients in terrestrial ecosystems.},
}
@article {pmid17644217,
year = {2007},
author = {da P Lima, G and Sleep, BE},
title = {The spatial distribution of eubacteria and archaea in sand-clay columns degrading carbon tetrachloride and methanol.},
journal = {Journal of contaminant hydrology},
volume = {94},
number = {1-2},
pages = {34-48},
doi = {10.1016/j.jconhyd.2007.05.001},
pmid = {17644217},
issn = {0169-7722},
mesh = {*Aluminum Silicates ; Anaerobiosis ; Archaea/*metabolism ; Bacteria/*metabolism ; Base Sequence ; Biodegradation, Environmental ; Carbon Tetrachloride/*metabolism ; Clay ; Electrophoresis ; Methanol/*metabolism ; Polymerase Chain Reaction ; *Silicon Dioxide ; Soil Microbiology ; Soil Pollutants/*metabolism ; Time Factors ; },
abstract = {The spatial distribution of microbial communities was investigated in anaerobic sand-clay columns fed methanol and carbon tetrachloride (CT). Microbial communities were characterized through analysis of soil samples with denaturing gradient gel electrophoresis (DGGE) and quantitative polymerase chain reaction (qPCR) for archaea and eubacteria. Increasing CT inlet concentrations to 29 microM lead to complete inhibition of methanol consumption in both columns. Although low levels of eubacteria and archaea were initially present in the clay soils in both columns, there was no significant microbial growth over 400 days in the clays beyond the interface with the sand zone. Thus, the potential for increased contaminant attenuation in heterogeneous sand-clay systems through biodegradation in the clay matrix zones may be limited in many systems.},
}
@article {pmid17621634,
year = {2007},
author = {Mueller-Cajar, O and Badger, MR},
title = {New roads lead to Rubisco in archaebacteria.},
journal = {BioEssays : news and reviews in molecular, cellular and developmental biology},
volume = {29},
number = {8},
pages = {722-724},
doi = {10.1002/bies.20616},
pmid = {17621634},
issn = {0265-9247},
mesh = {Archaea/*enzymology/genetics ; Evolution, Molecular ; Models, Biological ; Photosynthesis/genetics ; Ribulose-Bisphosphate Carboxylase/genetics/*physiology ; Sequence Homology, Nucleic Acid ; },
abstract = {The discovery of the CO(2)-fixing enzyme Rubisco in the Archaebacteria has presented a conundrum in that they apparently lack the gene for phosphoribulokinase, which is required to generate Rubisco's substrate ribulose 1,5-bisphosphate (RuBP). However, two groups have now demonstrated novel RuBP synthesis pathways, demystifying Rubisco's non-autotrophic and perhaps ancient role. A new CO(2) fixing role for Rubisco, which is distinct from the globally dominant Calvin cycle, is providing important clues furthering our understanding of the evolution of autotrophy. This perspective is strengthened by the additional recognition in this commentary that some Rubisco-containing Archaea do also contain PRK and may represent an interesting autotrophic evolutionary transition. Supplementary material for this article can be found on the BioEssays website (http://www.interscience.wiley.com/jpages/0265-9247/suppmat/index.html).},
}
@article {pmid17619187,
year = {2007},
author = {Chernyh, NA and Gavrilov, SN and Sorokin, VV and German, KE and Sergeant, C and Simonoff, M and Robb, F and Slobodkin, AI},
title = {Characterization of technetium(vII) reduction by cell suspensions of thermophilic bacteria and archaea.},
journal = {Applied microbiology and biotechnology},
volume = {76},
number = {2},
pages = {467-472},
doi = {10.1007/s00253-007-1034-5},
pmid = {17619187},
issn = {0175-7598},
mesh = {Archaea/*metabolism ; Bacteria/*metabolism ; *Oxidation-Reduction ; Technetium/*metabolism ; },
abstract = {Washed cell suspensions of the anaerobic hyperthermophilic archaea Thermococcus pacificus and Thermoproteus uzoniensis and the anaerobic thermophilic gram-positive bacteria Thermoterrabacterium ferrireducens and Tepidibacter thalassicus reduced technetium [(99)Tc(VII)], supplied as soluble pertechnetate with molecular hydrogen as an electron donor, forming highly insoluble Tc(IV)-containing grayish-black precipitate. Apart from molecular hydrogen, T. ferrireducens reduced Tc(VII) with lactate, glycerol, and yeast extract as electron donors, and T. thalassicus reduced it with peptone. Scanning electron microscopy and X-ray microanalysis of cell suspensions of T. ferrireducens showed the presence of Tc-containing particles attached to the surfaces of non-lysed cells. This is the first report on the reduction in Tc(VII) by thermophilic microorganisms of the domain Bacteria and by archaea of the phylum Euryarchaeota.},
}
@article {pmid17576673,
year = {2007},
author = {Berkner, S and Grogan, D and Albers, SV and Lipps, G},
title = {Small multicopy, non-integrative shuttle vectors based on the plasmid pRN1 for Sulfolobus acidocaldarius and Sulfolobus solfataricus, model organisms of the (cren-)archaea.},
journal = {Nucleic acids research},
volume = {35},
number = {12},
pages = {e88},
pmid = {17576673},
issn = {1362-4962},
mesh = {DNA Replication ; DNA Transposable Elements ; Escherichia coli/genetics ; Gene Dosage ; Genes, Reporter ; Genetic Vectors/*chemistry ; Glucosidases/biosynthesis/genetics ; Models, Genetic ; Plasmids/biosynthesis/*genetics ; Sulfolobus acidocaldarius/*genetics/growth &amp; development ; Sulfolobus solfataricus/*genetics ; Transformation, Genetic ; },
abstract = {The extreme thermoacidophiles of the genus Sulfolobus are among the best-studied archaea but have lacked small, reliable plasmid vectors, which have proven extremely useful for manipulating and analyzing genes in other microorganisms. Here we report the successful construction of a series of Sulfolobus-Escherichia coli shuttle vectors based on the small multicopy plasmid pRN1 from Sulfolobus islandicus. Selection in suitable uracil auxotrophs is provided through inclusion of pyrEF genes in the plasmid. The shuttle vectors do not integrate into the genome and do not rearrange. The plasmids allow functional overexpression of genes, as could be demonstrated for the beta-glycosidase (lacS) gene of S. solfataricus. In addition, we demonstrate that this beta-glycosidase gene could function as selectable marker in S. solfataricus. The shuttle plasmids differ in their interruption sites within pRN1 and allowed us to delineate functionally important regions of pRN1. The orf56/orf904 operon appears to be essential for pRN1 replication, in contrast interruption of the highly conserved orf80/plrA gene is tolerated. The new vector system promises to facilitate genetic studies of Sulfolobus and to have biotechnological uses, such as the overexpression or optimization of thermophilic enzymes that are not readily performed in mesophilic hosts.},
}
@article {pmid17576516,
year = {2007},
author = {Johnsen, U and Schönheit, P},
title = {Characterization of cofactor-dependent and cofactor-independent phosphoglycerate mutases from Archaea.},
journal = {Extremophiles : life under extreme conditions},
volume = {11},
number = {5},
pages = {647-657},
pmid = {17576516},
issn = {1431-0651},
mesh = {2,3-Diphosphoglycerate/*metabolism ; Amino Acid Sequence ; Archaeal Proteins/antagonists &amp; inhibitors/chemistry/genetics/*metabolism ; Archaeoglobus fulgidus/*enzymology/genetics ; Catalytic Domain ; Cloning, Molecular ; Coenzymes/*metabolism ; Databases, Genetic ; Dimerization ; Edetic Acid/pharmacology ; Enzyme Inhibitors/pharmacology ; Enzyme Stability ; Histidine/chemistry ; Manganese/metabolism ; Molecular Sequence Data ; Molecular Weight ; Mutagenesis, Site-Directed ; Open Reading Frames ; Phosphoglycerate Mutase/antagonists &amp; inhibitors/chemistry/genetics/*metabolism ; Phylogeny ; Recombinant Proteins/metabolism ; Sequence Alignment ; Temperature ; Thermoplasma/*enzymology/genetics ; Vanadates/pharmacology ; },
abstract = {Phosphoglycerate mutases (PGM) catalyze the reversible conversion of 3-phosphoglycerate and 2-phosphoglycerate as part of glycolysis and gluconeogenesis. Two structural and mechanistically unrelated types of PGMs are known, a cofactor (2,3-bisphosphoglycerate)-dependent (dPGM) and a cofactor-independent enzyme (iPGM). Here, we report the characterization of the first archaeal cofactor-dependent PGM from Thermoplasma acidophilum, which is encoded by ORF TA1347. This ORF was cloned and expressed in Escherichia coli and the recombinant protein was characterized as functional dPGM. The enzyme constitutes a 46 kDa homodimeric protein. Enzyme activity required 2,3-bisphosphoglycerate as cofactor and was inhibited by vanadate, a specific inhibitor of dPGMs in bacteria and eukarya; inhibition could be partially relieved by EDTA. Histidine 23 of the archaeal dPGM of T. acidophilum, which corresponds to active site histidine in dPGMs from bacteria and eukarya, was exchanged for alanine by site directed mutagenesis. The H23A mutant was catalytically inactive supporting the essential role of H23 in catalysis of the archaeal dPGM. Further, an archaeal cofactor-independent PGM encoded by ORF AF1751 from the hyperthermophilic sulfate reducer Archaeoglobus fulgidus was characterized after expression in E. coli. The monomeric 46 kDa protein showed cofactor-independent PGM activity and was stimulated by Mn(2+) and exhibited high thermostability up to 70 degrees C. A comprehensive phylogenetic analysis of both types of archaeal phosphoglycerate mutases is also presented.},
}
@article {pmid17565388,
year = {2007},
author = {Zmijewski, MA and Skórko-Glonek, J and Tanfani, F and Banecki, B and Kotlarz, A and Macario, AJ and Lipińska, B},
title = {Structural basis of the interspecies interaction between the chaperone DnaK(Hsp70) and the co-chaperone GrpE of archaea and bacteria.},
journal = {Acta biochimica Polonica},
volume = {54},
number = {2},
pages = {245-252},
pmid = {17565388},
issn = {0001-527X},
mesh = {Archaeal Proteins/*chemistry/*metabolism ; Escherichia coli/chemistry/metabolism ; Escherichia coli Proteins/*chemistry/*metabolism ; HSP70 Heat-Shock Proteins/*chemistry/*metabolism ; Heat-Shock Proteins/*chemistry/*metabolism ; Methanosarcina/chemistry/metabolism ; Models, Molecular ; Multiprotein Complexes ; Protein Binding ; Protein Structure, Secondary ; Species Specificity ; Spectroscopy, Fourier Transform Infrared ; },
abstract = {Hsp70s are chaperone proteins that are conserved in evolution and present in all prokaryotic and eukaryotic organisms. In the archaea, which form a distinct kingdom, the Hsp70 chaperones have been found in some species only, including Methanosarcina mazei. Both the bacterial and archaeal Hsp70(DnaK) chaperones cooperate with a GrpE co-chaperone which stimulates the ATPase activity of the DnaK protein. It is currently believed that the archaeal Hsp70 system was obtained by the lateral transfer of chaperone genes from bacteria. Our previous finding that the DnaK and GrpE proteins of M. mazei can functionally cooperate with the Escherichia coli GrpE and DnaK supported this hypothesis. However, the cooperation was surprising, considering the very low identity of the GrpE proteins (26%) and the relatively low identity of the DnaK proteins (56%). The aim of this work was to investigate the molecular basis of the observed interspecies chaperone interaction. Infrared resolution-enhanced spectra of the M. mazei and E. coli DnaK proteins were almost identical, indicating high similarity of their secondary structures, however, some small differences in band position and in the intensity of amide I' band components were observed and discussed. Profiles of thermal denaturation of both proteins were similar, although they indicated a higher thermostability of the M. mazei DnaK compared to the E. coli DnaK. Electrophoresis under non-denaturing conditions demonstrated that purified DnaK and GrpE of E. coli and M. mazei formed mixed complexes. Protein modeling revealed high similarity of the 3-dimensional structures of the archaeal and bacterial DnaK and GrpE proteins.},
}
@article {pmid17557330,
year = {2007},
author = {Ming, H and Kato, Y and Miyazono, K and Ito, K and Kamo, M and Nagata, K and Tanokura, M},
title = {Crystal structure of thioredoxin domain of ST2123 from thermophilic archaea Sulfolobus tokodaii strain7.},
journal = {Proteins},
volume = {69},
number = {1},
pages = {204-208},
doi = {10.1002/prot.21467},
pmid = {17557330},
issn = {1097-0134},
mesh = {Archaeal Proteins/*chemistry ; Binding Sites ; Crystallography, X-Ray/methods ; Genetic Vectors ; Hot Temperature ; Image Processing, Computer-Assisted/methods ; Protein Conformation ; Protein Structure, Tertiary ; Recombinant Proteins/chemistry ; Sulfolobus/*chemistry ; Thioredoxins/*chemistry/isolation &amp; purification ; },
}
@article {pmid17553803,
year = {2007},
author = {Horwitz, AA and Navon, A and Groll, M and Smith, DM and Reis, C and Goldberg, AL},
title = {ATP-induced structural transitions in PAN, the proteasome-regulatory ATPase complex in Archaea.},
journal = {The Journal of biological chemistry},
volume = {282},
number = {31},
pages = {22921-22929},
doi = {10.1074/jbc.M702846200},
pmid = {17553803},
issn = {0021-9258},
support = {R01 GM051923/GM/NIGMS NIH HHS/United States ; R01 GM051923-12/GM/NIGMS NIH HHS/United States ; },
mesh = {Adenosine Triphosphatases/*chemistry ; Adenosine Triphosphate/*chemistry ; Amino Acid Motifs ; Animals ; Archaea/*metabolism ; Archaeal Proteins/*chemistry ; Dose-Response Relationship, Drug ; Endopeptidase K/chemistry ; Humans ; Hydrolysis ; Kinetics ; Methanococcus/metabolism ; Molecular Conformation ; Proteasome Endopeptidase Complex/metabolism ; Trypsin/chemistry ; },
abstract = {ATP binding to the PAN-ATPase complex in Archaea or the homologous 19 S protease-regulatory complex in eukaryotes induces association with the 20 S proteasome and opening of its substrate entry channel, whereas ATP hydrolysis allows unfolding of globular substrates. To clarify the conformational changes associated with ATP binding and hydrolysis, we used protease sensitivity to monitor the conformations of the PAN ATPase from Methanococcus jannischii. Exhaustive trypsin treatment of PAN generated five distinct fragments, two of which differed when a nucleotide (either ATP, ATP gamma S, or ADP) was bound. Surprisingly, the nucleotide concentrations altering protease sensitivity were much lower (K(a) 20-40 microm) than are required for ATP-dependent protein breakdown by the PAN-20S proteasome complex (K(m) approximately 300-500 microm). Unlike trypsin, proteinase K yielded several fragments that differed in the ATP gamma S and ADP-bound forms, and thus revealed conformational transitions associated with ATP hydrolysis. Mapping the fragments generated by each revealed that nucleotide binding and hydrolysis induce local conformational changes, affecting the Walker A and B nucleotide-binding motif, as well as global changes extending to its carboxyl terminus. The location and overlap of the fragments also suggest that the conformation of the six subunits is not identical, probably because they do not all bind ATP simultaneously. Partial nucleotide occupancy was supported by direct assays, which demonstrated that, at saturating conditions, only four nucleotides are bound to hexameric PAN. Using the protease protection maps, we modeled the conformational changes associated with ATP binding and hydrolysis in PAN based on the x-ray structures of the homologous AAA ATPase, HslU.},
}
@article {pmid17545280,
year = {2007},
author = {Giaquinto, L and Curmi, PM and Siddiqui, KS and Poljak, A and DeLong, E and DasSarma, S and Cavicchioli, R},
title = {Structure and function of cold shock proteins in archaea.},
journal = {Journal of bacteriology},
volume = {189},
number = {15},
pages = {5738-5748},
pmid = {17545280},
issn = {0021-9193},
mesh = {Amino Acid Sequence ; Archaeal Proteins/chemistry/genetics/isolation &amp; purification/*physiology ; *Cold Temperature ; Crenarchaeota/chemistry/genetics/*physiology ; Escherichia coli/genetics/growth &amp; development ; Euryarchaeota/chemistry/genetics/*physiology ; Genetic Complementation Test ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Phylogeny ; Protein Binding ; Protein Conformation ; RNA/metabolism ; RNA-Binding Proteins/chemistry/genetics/isolation &amp; purification/*physiology ; Sequence Homology, Amino Acid ; },
abstract = {Archaea are abundant and drive critical microbial processes in the Earth's cold biosphere. Despite this, not enough is known about the molecular mechanisms of cold adaptation and no biochemical studies have been performed on stenopsychrophilic archaea (e.g., Methanogenium frigidum). This study examined the structural and functional properties of cold shock proteins (Csps) from archaea, including biochemical analysis of the Csp from M. frigidum. csp genes are present in most bacteria and some eucarya but absent from most archaeal genome sequences, most notably, those of all archaeal thermophiles and hyperthermophiles. In bacteria, Csps are small, nucleic acid binding proteins involved in a variety of cellular processes, such as transcription. In this study, archaeal Csp function was assessed by examining the ability of csp genes from psychrophilic and mesophilic Euryarchaeota and Crenarchaeota to complement a cold-sensitive growth defect in Escherichia coli. In addition, an archaeal gene with a cold shock domain (CSD) fold but little sequence identity to Csps was also examined. Genes encoding Csps or a CSD structural analog from three psychrophilic archaea rescued the E. coli growth defect. The three proteins were predicted to have a higher content of solvent-exposed basic residues than the noncomplementing proteins, and the basic residues were located on the nucleic acid binding surface, similar to their arrangement in E. coli CspA. The M. frigidum Csp was purified and found to be a single-domain protein that folds by a reversible two-state mechanism and to exhibit a low conformational stability typical of cold-adapted proteins. Moreover, M. frigidum Csp was characterized as binding E. coli single-stranded RNA, consistent with its ability to complement function in E. coli. The studies show that some Csp and CSD fold proteins have retained sufficient similarity throughout evolution in the Archaea to be able to function effectively in the Bacteria and that the function of the archaeal proteins relates to cold adaptation. The initial biochemical analysis of M. frigidum Csp has developed a platform for further characterization and demonstrates the potential for expanding molecular studies of proteins from this important archaeal stenopsychrophile.},
}
@article {pmid17513586,
year = {2007},
author = {Ohene-Adjei, S and Teather, RM and Ivan, M and Forster, RJ},
title = {Postinoculation protozoan establishment and association patterns of methanogenic archaea in the ovine rumen.},
journal = {Applied and environmental microbiology},
volume = {73},
number = {14},
pages = {4609-4618},
pmid = {17513586},
issn = {0099-2240},
mesh = {Animals ; Archaea/*classification/genetics/*isolation &amp; purification ; Biodiversity ; DNA Fingerprinting ; DNA, Archaeal/chemistry/genetics ; DNA, Protozoan/genetics ; DNA, Ribosomal/chemistry/genetics ; Electrophoresis, Polyacrylamide Gel ; Eukaryota/*growth &amp; development ; Molecular Sequence Data ; Nucleic Acid Denaturation ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 18S/genetics ; Rumen/*microbiology/*parasitology ; Sequence Analysis, DNA ; Sequence Homology ; Sheep ; },
abstract = {Association patterns between archaea and rumen protozoa were evaluated by analyzing archaeal 16S rRNA gene clone libraries from ovine rumen inoculated with different protozoa. Five protozoan inoculation treatments, fauna free (negative control), holotrich and cellulolytic protozoa, Isotricha and Dasytricha spp., Entodinium spp., and total fauna (type A) were tested. We used denaturing gradient gel electrophoresis, quantitative PCR, and phylogenetic analysis to evaluate the impact of the protozoan inoculants on the respective archaeal communities. Protozoan 18S ribosomal DNA clone libraries were also evaluated to monitor the protozoal population that was established by the inoculation. Phylogenetic analysis suggested that archaeal clones associated with the fauna-free, the Entodinium, and the type A inoculations clustered primarily with uncultured phylotypes. Polyplastron multivesiculatum was the predominant protozoan strain established by the holotrich and cellulolytic protozoan treatment, and this resulted predominantly in archaeal clones affiliated with uncultured and cultured methanogenic phylotypes (Methanosphaera stadtmanae, Methanobrevibacter ruminantium, and Methanobacterium bryantii). Furthermore, the Isotricha and Dasytricha inoculation treatment resulted primarily in archaeal clones affiliated with Methanobrevibacter smithii. This report provides the first assessment of the influence of protozoa on archaea within the rumen microbial community and provides evidence to suggest that different archaeal phylotypes associate with specific groups of protozoa. The observed patterns may be linked to the evolution of commensal and symbiotic relationships between archaea and protozoa in the ovine rumen environment. This report further underscores the prevalence and potential importance of a rather large group of uncultivated archaea in the ovine rumen, probably unrelated to known methanogens and undocumented in the bovine rumen.},
}
@article {pmid17512006,
year = {2007},
author = {Fukunaga, R and Yokoyama, S},
title = {Structural insights into the second step of RNA-dependent cysteine biosynthesis in archaea: crystal structure of Sep-tRNA:Cys-tRNA synthase from Archaeoglobus fulgidus.},
journal = {Journal of molecular biology},
volume = {370},
number = {1},
pages = {128-141},
doi = {10.1016/j.jmb.2007.04.050},
pmid = {17512006},
issn = {0022-2836},
mesh = {Amino Acid Sequence ; Amino Acyl-tRNA Synthetases/*chemistry/genetics/*metabolism ; Archaeal Proteins/*chemistry/genetics/*metabolism ; Archaeoglobus fulgidus/*enzymology ; Binding Sites ; Crystallography, X-Ray ; Cysteine/*biosynthesis ; Dimerization ; Models, Molecular ; Molecular Sequence Data ; Molecular Structure ; *Protein Structure, Quaternary ; Protein Subunits/chemistry/genetics/metabolism ; RNA/metabolism ; RNA, Transfer, Amino Acyl/chemistry/metabolism ; Sequence Alignment ; Static Electricity ; Sulfates/metabolism ; },
abstract = {In the ancient organisms, methanogenic archaea, lacking the canonical cysteinyl-tRNA synthetase, Cys-tRNA(Cys) is produced by an indirect pathway, in which O-phosphoseryl-tRNA synthetase ligates O-phosphoserine (Sep) to tRNA(Cys) and Sep-tRNA:Cys-tRNA synthase (SepCysS) converts Sep-tRNA(Cys) to Cys-tRNA(Cys). In this study, the crystal structure of SepCysS from Archaeoglobus fulgidus has been determined at 2.4 A resolution. SepCysS forms a dimer, composed of monomers bearing large and small domains. The large domain harbors the seven-stranded beta-sheet, which is typical of the pyridoxal 5'-phosphate (PLP)-dependent enzymes. In the active site, which is located near the dimer interface, PLP is covalently bound to the side-chain of the conserved Lys209. In the proximity of PLP, a sulfate ion is bound by the side-chains of the conserved Arg79, His103, and Tyr104 residues. The active site is located deep within the large, basic cleft to accommodate Sep-tRNA(Cys). On the basis of the surface electrostatic potential, the amino acid residue conservation mapping, the position of the bound sulfate ion, and the substrate amino acid binding manner in other PLP-dependent enzymes, a binding model of Sep-tRNA(Cys) to SepCysS was constructed. One of the three strictly conserved Cys residues (Cys39, Cys42, or Cys247), of one subunit may play a crucial role in the catalysis in the active site of the other subunit.},
}
@article {pmid17508126,
year = {2008},
author = {Ladenstein, R and Ren, B},
title = {Reconsideration of an early dogma, saying "there is no evidence for disulfide bonds in proteins from archaea".},
journal = {Extremophiles : life under extreme conditions},
volume = {12},
number = {1},
pages = {29-38},
pmid = {17508126},
issn = {1431-0651},
mesh = {Amino Acid Motifs/physiology ; Archaea/*enzymology/genetics ; Archaeal Proteins/genetics/*metabolism ; Bacteria/enzymology/genetics ; Bacterial Proteins/genetics/metabolism ; Disulfides/*metabolism ; Oxidation-Reduction ; Protein Disulfide-Isomerases/genetics/*metabolism ; Protein Structure, Tertiary/physiology ; Thioredoxins/genetics/metabolism ; },
abstract = {Stability and function of a large number of proteins are crucially dependent on the presence of disulfide bonds. Recent genome analysis has pointed out an important role of disulfide bonds for the structural stabilization of intracellular proteins from hyperthermophilic archaea and bacteria. These findings contradict the conventional view that disulfide bonds are rare in those proteins. A specific protein, known as protein disulfide oxidoreductase (PDO) is recognized as a potential key enzyme in intracellular disulfide-shuffling in hyperthermophiles. The structure of this protein consists of two combined thioredoxin-related units which together, in tandem-like manner, form a closed protein domain. Each of these units contains a distinct CXXC active site motif. Both sites seem to have different redox properties. A relation to eukaryotic protein disulfide isomerase is suggested by the observed structural and functional characteristics of the protein. Enzymological studies have revealed that both, the archaeal and bacterial forms of this protein show oxidative and reductive activity and are able to isomerize protein disulfides. The variety of active site disulfides found in PDO's from hyperthermophiles is puzzling. It is assumed, that PDO enzymes in hyperthermophilic archaea and bacteria may be part of a complex system involved in the maintenance of protein disulfide bonds.},
}
@article {pmid17506680,
year = {2007},
author = {Leigh, JA and Dodsworth, JA},
title = {Nitrogen regulation in bacteria and archaea.},
journal = {Annual review of microbiology},
volume = {61},
number = {},
pages = {349-377},
doi = {10.1146/annurev.micro.61.080706.093409},
pmid = {17506680},
issn = {0066-4227},
support = {GM55255/GM/NIGMS NIH HHS/United States ; },
mesh = {Alphaproteobacteria/metabolism ; Archaea/*metabolism ; Bacteria/*metabolism ; Bacterial Proteins/chemistry/physiology ; Cyanobacteria/metabolism ; Escherichia coli/metabolism ; Escherichia coli Proteins/chemistry/physiology ; Glutamate-Ammonia Ligase/genetics ; Nitrogen/*metabolism ; Nucleotidyltransferases/chemistry/physiology ; PII Nitrogen Regulatory Proteins/chemistry/physiology ; Phylogeny ; Signal Transduction ; },
abstract = {A wide range of Bacteria and Archaea sense cellular 2-oxoglutarate (2OG) as an indicator of nitrogen limitation. 2OG sensor proteins are varied, but most of those studied belong to the PII superfamily. Within the PII superfamily, GlnB and GlnK represent a widespread family of homotrimeric proteins (GlnB-K) that bind and respond to 2OG and ATP. In some bacterial phyla, GlnB-K proteins are covalently modified, depending on enzymes that sense cellular glutamine as an indicator of nitrogen sufficiency. GlnB-K proteins are central clearing houses of nitrogen information and bind and modulate a variety of nitrogen assimilation regulators and enzymes. NifI(1) and NifI(2) comprise a second widespread family of PII proteins (NifI) that are heteromultimeric, respond to 2OG and ATP, and bind and regulate dinitrogenase in Euryarchaeota and many Bacteria.},
}
@article {pmid17502615,
year = {2007},
author = {Hendrickson, EL and Haydock, AK and Moore, BC and Whitman, WB and Leigh, JA},
title = {Functionally distinct genes regulated by hydrogen limitation and growth rate in methanogenic Archaea.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {104},
number = {21},
pages = {8930-8934},
pmid = {17502615},
issn = {0027-8424},
support = {R01 GM060403/GM/NIGMS NIH HHS/United States ; R24 GM074783/GM/NIGMS NIH HHS/United States ; GM60403/GM/NIGMS NIH HHS/United States ; GM74783/GM/NIGMS NIH HHS/United States ; },
mesh = {Archaeal Proteins/genetics/metabolism ; Cell Proliferation ; Gene Expression Regulation, Archaeal/*genetics ; Hydrogen/*pharmacology ; Methane/*metabolism ; Methanococcus/cytology/drug effects/*genetics/*metabolism ; Oxidoreductases/metabolism ; RNA, Messenger/genetics ; },
abstract = {The use of molecular hydrogen as electron donor for energy generation is a defining characteristic of the hydrogenotrophic methanogens, an ancient group that dominates the phylum Euryarchaeota. We present here a global study of changes in mRNA abundance in response to hydrogen availability for a hydrogenotrophic methanogen. Cells of Methanococcus maripaludis were grown by using continuous culture to deconvolute the effects of hydrogen limitation and growth rate, and microarray analyses were conducted. Hydrogen limitation markedly increased mRNA levels for genes encoding enzymes of the methanogenic pathway that reduce or oxidize the electron-carrying deazaflavin, coenzyme F(420). F(420)-dependent redox functions in energy-generating metabolism are characteristic of the methanogenic Archaea, and the results show that their regulation is distinct from other redox processes in the cell. Rapid growth increased mRNA levels of the gene for an unusual hydrogenase, the hydrogen-dependent methylenetetrahydromethanopterin dehydrogenase.},
}
@article {pmid17496958,
year = {2007},
author = {Midgley, DJ and Saleeba, JA and Stewart, MI and McGee, PA},
title = {Novel soil lineages of Archaea are present in semi-arid soils of eastern Australia.},
journal = {Canadian journal of microbiology},
volume = {53},
number = {1},
pages = {129-138},
doi = {10.1139/w06-104},
pmid = {17496958},
issn = {0008-4166},
mesh = {Agriculture ; Australia ; Biodiversity ; Classification ; Crenarchaeota/*classification ; DNA Fingerprinting/methods ; DNA, Ribosomal/classification ; Environmental Monitoring ; Euryarchaeota/*classification ; Molecular Sequence Data ; *Phylogeny ; *Soil Microbiology ; Trees ; },
abstract = {The diversity of Archaea was studied in vertisolic and loam soils of a semi-arid region in Australia. Sampling was undertaken at an agricultural site, two grassland environments, and a brigalow (Acacia harpophylla) woodland. Archaeal community structure was profiled using amplified ribosomal DNA restriction analysis (ARDRA) combined with rDNA sequencing of an example of each restriction fragment length polymorphism type. Sequence comparison and phylogenetic analysis demonstrated that both crenarchaeotal and euryarchaeotal Archaea were present at oxic depths in the soil at all field sites. Along with previously described soil archaeal lineages, novel soil lineages and the deeply divergent Pendant-33 group of Euryarchaeota were also detected. A novel statistical method for comparing ARDRA derived data was demonstrated and implemented using the archaeal communities from the four field sites. Archaeal diversity, as measured by this method, was significantly higher in the agricultural site than at either of the grassland sites or the brigalow woodland.},
}
@article {pmid17483216,
year = {2007},
author = {Escalante-Semerena, JC},
title = {Conversion of cobinamide into adenosylcobamide in bacteria and archaea.},
journal = {Journal of bacteriology},
volume = {189},
number = {13},
pages = {4555-4560},
pmid = {17483216},
issn = {0021-9193},
support = {R01 GM040313/GM/NIGMS NIH HHS/United States ; R01 GM 40313/GM/NIGMS NIH HHS/United States ; },
mesh = {Archaea/*metabolism ; Bacteria/*metabolism ; Cobamides/chemistry/*metabolism ; Molecular Structure ; },
}
@article {pmid17480207,
year = {2007},
author = {Seedorf, H and Hagemeier, CH and Shima, S and Thauer, RK and Warkentin, E and Ermler, U},
title = {Structure of coenzyme F420H2 oxidase (FprA), a di-iron flavoprotein from methanogenic Archaea catalyzing the reduction of O2 to H2O.},
journal = {The FEBS journal},
volume = {274},
number = {6},
pages = {1588-1599},
doi = {10.1111/j.1742-4658.2007.05706.x},
pmid = {17480207},
issn = {1742-464X},
mesh = {Archaea/enzymology/*metabolism ; Catalysis ; Flavin Mononucleotide/metabolism ; Flavoproteins/*chemistry/metabolism ; Models, Molecular ; Oxidation-Reduction ; Oxidoreductases/*chemistry/metabolism ; Oxygen/*metabolism ; Protein Binding ; Protein Conformation ; Water/*metabolism ; },
abstract = {The di-iron flavoprotein F(420)H(2) oxidase found in methanogenic Archaea catalyzes the four-electron reduction of O(2) to 2H(2)O with 2 mol of reduced coenzyme F(420)(7,8-dimethyl-8-hydroxy-5-deazariboflavin). We report here on crystal structures of the homotetrameric F(420)H(2) oxidase from Methanothermobacter marburgensis at resolutions of 2.25 A, 2.25 A and 1.7 A, respectively, from which an active reduced state, an inactive oxidized state and an active oxidized state could be extracted. As found in structurally related A-type flavoproteins, the active site is formed at the dimer interface, where the di-iron center of one monomer is juxtaposed to FMN of the other. In the active reduced state [Fe(II)Fe(II)FMNH(2)], the two irons are surrounded by four histidines, one aspartate, one glutamate and one bridging aspartate. The so-called switch loop is in a closed conformation, thus preventing F(420) binding. In the inactive oxidized state [Fe(III)FMN], the iron nearest to FMN has moved to two remote binding sites, and the switch loop is changed to an open conformation. In the active oxidized state [Fe(III)Fe(III)FMN], both irons are positioned as in the reduced state but the switch loop is found in the open conformation as in the inactive oxidized state. It is proposed that the redox-dependent conformational change of the switch loop ensures alternate complete four-electron O(2) reduction and redox center re-reduction. On the basis of the known Si-Si stereospecific hydride transfer, F(420)H(2) was modeled into the solvent-accessible pocket in front of FMN. The inactive oxidized state might provide the molecular basis for enzyme inactivation by long-term O(2) exposure observed in some members of the FprA family.},
}
@article {pmid17444671,
year = {2007},
author = {Aivaliotis, M and Gevaert, K and Falb, M and Tebbe, A and Konstantinidis, K and Bisle, B and Klein, C and Martens, L and Staes, A and Timmerman, E and Van Damme, J and Siedler, F and Pfeiffer, F and Vandekerckhove, J and Oesterhelt, D},
title = {Large-scale identification of N-terminal peptides in the halophilic archaea Halobacterium salinarum and Natronomonas pharaonis.},
journal = {Journal of proteome research},
volume = {6},
number = {6},
pages = {2195-2204},
doi = {10.1021/pr0700347},
pmid = {17444671},
issn = {1535-3893},
mesh = {Archaeal Proteins/*analysis/genetics ; Chromatography/methods ; Chromatography, Ion Exchange/methods ; Genes, Archaeal ; Halobacteriaceae/*chemistry/genetics ; Halobacterium salinarum/*chemistry/genetics ; Peptides/analysis ; *Proteomics ; Sequence Analysis, Protein ; },
abstract = {Characterization of protein N-terminal peptides supports the quality assessment of data derived from genomic sequences (e.g., the correct assignment of start codons) and hints to in vivo N-terminal modifications such as N-terminal acetylation and removal of the initiator methionine. The current work represents the first large-scale identification of N-terminal peptides from prokaryotes, of the two halophilic euryarchaeota Halobacterium salinarum and Natronomonas pharaonis. Two methods were used that specifically allow the characterization of protein N-terminal peptides: combined fractional diagonal chromatography (COFRADIC) and strong cation exchange chromatography (SCX), both known to enrich for N-terminally blocked peptides. In addition to these specific methods, N-terminal peptide identifications were extracted from our previous genome-wide proteomic data. Combining all data, 606 N-terminal peptides from Hbt. salinarum and 328 from Nmn. pharaonis were reliably identified. These results constitute the largest available dataset holding identified and characterized protein N-termini for prokaryotes (archaea and bacteria). They allowed the validation/improvement of start codon assignments as automatic gene finders tend to misassign start codons for GC-rich genomes. In addition, the dataset allowed unravelling N-terminal protein maturation in archaea, showing that 60% of the proteins undergo methionine cleavage and that-in contrast to current knowledge-Nalpha-acetylation is common in the archaeal domain of life with 13-18% of the proteins being Nalpha-acetylated. The protein sets described in this paper are available by FTP and might be used as reference sets to test the performance of new gene finders.},
}
@article {pmid17433860,
year = {2007},
author = {Burbano, HA and Andrade, E},
title = {Analysis of tRNA abstract shapes of precursor/derivative amino acids in Archaea.},
journal = {Gene},
volume = {396},
number = {1},
pages = {75-83},
doi = {10.1016/j.gene.2007.02.024},
pmid = {17433860},
issn = {0378-1119},
mesh = {Amino Acids/*genetics ; Archaea/*genetics ; Base Composition/genetics ; Base Pairing ; Base Sequence ; Evolution, Molecular ; Genetic Code ; Molecular Sequence Data ; RNA, Transfer/*chemistry/genetics ; Thermodynamics ; },
abstract = {Wong's theory of the genetic code's origin states that because of historical constraints, codon assignment depends on the relation between precursor and derivative amino acids, a result of the coevolutionary process between amino acids' biosynthetic pathways and tRNAs. Based on arguments supporting the assumption that natural selection favors more stable and thus functionally constrained structures, we tested whether precursor and derivative tRNAs are equally evolved by measuring their structural parameters, thermostability and molecular plasticity. We also estimated the extent to which precursor and derivative tRNAs differ within Archaea. We used Archaea sequences of both precursor and derivative tRNAs in order to examine the plastic repertoires or sets of suboptimal structures at a defined free energy interval. We grouped secondary structures according to their helix nesting and adjacency using abstract shapes analysis. This clustering enabled us to infer a consensus sequence for all shapes that fit the clover leaf secondary structure [Giegerich, R., et al., Nucleic Acids Res 2004; 32 (16): 4843-51.]. This consensus sequence was then folded in order to retrieve a set of suboptimal structures. For each pair of precursor and derivative tRNAs, we compared these plastic repertoires based on the number of secondary structures, the thermostability of the minimum free energy structure and two structural parameters (base pair propensity (P) and mean length of helical stem structures (S)), which were measured for every representative secondary structure [Schultes, E.A., et al., J Mol Evol 1999; 49 (1): 76-83.]. We found that derivative tRNAs have fewer numbers of shapes, higher thermostability and more stable parameters than precursor tRNAs, a fact in full agreement with Wong's coevolution theory of the genetic code.},
}
@article {pmid17428303,
year = {2007},
author = {Morozova, D and Wagner, D},
title = {Stress response of methanogenic archaea from Siberian permafrost compared with methanogens from nonpermafrost habitats.},
journal = {FEMS microbiology ecology},
volume = {61},
number = {1},
pages = {16-25},
doi = {10.1111/j.1574-6941.2007.00316.x},
pmid = {17428303},
issn = {0168-6496},
mesh = {*Adaptation, Physiological ; Arctic Regions ; Euryarchaeota/metabolism/*physiology ; Extraterrestrial Environment ; Freezing ; Methanobacterium/metabolism/physiology ; Oxygen/physiology ; Sodium Chloride ; Water/physiology ; },
abstract = {We examined the survival potential of methanogenic archaea exposed to different environmental stress conditions such as low temperature (down to -78.5 degrees C), high salinity (up to 6 M NaCl), starvation (up to 3 months), long-term freezing (up to 2 years), desiccation (up to 25 days) and oxygen exposure (up to 72 h). The experiments were conducted with methanogenic archaea from Siberian permafrost and were complemented by experiments on well-studied methanogens from nonpermafrost habitats. Our results indicate a high survival potential of a methanogenic archaeon from Siberian permafrost when exposed to the extreme conditions tested. In contrast, these stress conditions were lethal for methanogenic archaea isolated from nonpermafrost habitats. A better adaptation to stress was observed at a low temperature (4 degrees C) compared with a higher one (28 degrees C). Given the unique metabolism of methanogenic archaea in general and the long-term survival and high tolerance to extreme conditions of the methanogens investigated in this study, methanogenic archaea from permafrost should be considered as primary candidates for possible subsurface Martian life.},
}
@article {pmid17428301,
year = {2007},
author = {Rivkina, E and Shcherbakova, V and Laurinavichius, K and Petrovskaya, L and Krivushin, K and Kraev, G and Pecheritsina, S and Gilichinsky, D},
title = {Biogeochemistry of methane and methanogenic archaea in permafrost.},
journal = {FEMS microbiology ecology},
volume = {61},
number = {1},
pages = {1-15},
doi = {10.1111/j.1574-6941.2007.00315.x},
pmid = {17428301},
issn = {0168-6496},
mesh = {Arctic Regions ; Carbon Isotopes/analysis ; Conservation of Natural Resources ; Euryarchaeota/*isolation &amp; purification/metabolism ; Geologic Sediments/*chemistry/microbiology ; Methane/*analysis/metabolism ; Methanobacterium/*isolation &amp; purification/metabolism ; },
abstract = {This study summarizes the findings of our research on the genesis of methane, its content and distribution in permafrost horizons of different age and origin. Supported by reliable data from a broad geographical sweep, these findings confirm the presence of methane in permanently frozen fine-grained sediments. In contrast to the omnipresence of carbon dioxide in permafrost, methane-containing horizons (up to 40.0 mL kg(-1)) alternate with strata free of methane. Discrete methane-containing horizons representing over tens of thousands of years are indicative of the absence of methane diffusion through the frozen layers. Along with the isotopic composition of CH(4) carbon (delta(13)C -64 per thousand to -99 per thousand), this confirms its biological origin and points to in situ formation of this biogenic gas. Using (14)C-labeled substrates, the possibility of methane formation within permafrost was experimentally shown, as confirmed by delta(13)C values. Extremely low values (near -99 per thousand) indicate that the process of CH(4) formation is accompanied by the substantial fractionation of carbon isotopes. For the first time, cultures of methane-forming archaea, Methanosarcina mazei strain JL01 VKM B-2370, Methanobacterium sp. strain M2 VKM B-2371 and Methanobacterium sp. strain MK4 VKM B-2440 from permafrost, were isolated and described.},
}
@article {pmid17395404,
year = {2007},
author = {Di Giulio, M},
title = {The evidence that the tree of life is not rooted within the Archaea is unreliable: a reply to Skophammer et al.},
journal = {Gene},
volume = {394},
number = {1-2},
pages = {105-106},
doi = {10.1016/j.gene.2007.01.024},
pmid = {17395404},
issn = {0378-1119},
mesh = {Amino Acid Sequence ; Archaea/classification/*genetics ; Archaeal Proteins/genetics ; *Evolution, Molecular ; Molecular Sequence Data ; Peptide Elongation Factor G/genetics ; Peptide Elongation Factor Tu/genetics ; Sequence Alignment ; },
abstract = {Skophammer et al. [Skophammer, RG, Herbold, CW, Rivera, MC, Servin, JA, Lake, JA. 2006. Evidence that the root of the tree of life is not within the Archaea. Mol Biol Evol, 23, 1648-1651] report evidence suggesting that the tree of life cannot be rooted within the Archaea domain. I have observed that an alignment used in their analysis is not reliable and that, therefore, their conclusions are unjustified.},
}
@article {pmid17394648,
year = {2007},
author = {Gao, B and Gupta, RS},
title = {Phylogenomic analysis of proteins that are distinctive of Archaea and its main subgroups and the origin of methanogenesis.},
journal = {BMC genomics},
volume = {8},
number = {},
pages = {86},
pmid = {17394648},
issn = {1471-2164},
mesh = {Archaea/classification/*genetics/*metabolism ; Archaeal Proteins/*genetics/*metabolism ; Crenarchaeota/genetics/metabolism ; Euryarchaeota/genetics/metabolism ; *Genome, Archaeal ; Methane/*biosynthesis ; Open Reading Frames ; Phylogeny ; Species Specificity ; },
abstract = {BACKGROUND: The Archaea are highly diverse in terms of their physiology, metabolism and ecology. Presently, very few molecular characteristics are known that are uniquely shared by either all archaea or the different main groups within archaea. The evolutionary relationships among different groups within the Euryarchaeota branch are also not clearly understood.<br><br>RESULTS: We have carried out comprehensive analyses on each open reading frame (ORFs) in the genomes of 11 archaea (3 Crenarchaeota--Aeropyrum pernix, Pyrobaculum aerophilum and Sulfolobus acidocaldarius; 8 Euryarchaeota--Pyrococcus abyssi, Methanococcus maripaludis, Methanopyrus kandleri, Methanococcoides burtonii, Halobacterium sp. NCR-1, Haloquadratum walsbyi, Thermoplasma acidophilum and Picrophilus torridus) to search for proteins that are unique to either all Archaea or for its main subgroups. These studies have identified 1448 proteins or ORFs that are distinctive characteristics of Archaea and its various subgroups and whose homologues are not found in other organisms. Six of these proteins are unique to all Archaea, 10 others are only missing in Nanoarchaeum equitans and a large number of other proteins are specific for various main groups within the Archaea (e.g. Crenarchaeota, Euryarchaeota, Sulfolobales and Desulfurococcales, Halobacteriales, Thermococci, Thermoplasmata, all methanogenic archaea or particular groups of methanogens). Of particular importance is the observation that 31 proteins are uniquely present in virtually all methanogens (including M. kandleri) and 10 additional proteins are only found in different methanogens as well as A. fulgidus. In contrast, no protein was exclusively shared by various methanogen and any of the Halobacteriales or Thermoplasmatales. These results strongly indicate that all methanogenic archaea form a monophyletic group exclusive of other archaea and that this lineage likely evolved from Archaeoglobus. In addition, 15 proteins that are uniquely shared by M. kandleri and Methanobacteriales suggest a close evolutionary relationship between them. In contrast to the phylogenomics studies, a monophyletic grouping of archaea is not supported by phylogenetic analyses based on protein sequences.<br><br>CONCLUSION: The identified archaea-specific proteins provide novel molecular markers or signature proteins that are distinctive characteristics of Archaea and all of its major subgroups. The species distributions of these proteins provide novel insights into the evolutionary relationships among different groups within Archaea, particularly regarding the origin of methanogenesis. Most of these proteins are of unknown function and further studies should lead to discovery of novel biochemical and physiological characteristics that are unique to either all archaea or its different subgroups.},
}
@article {pmid17379705,
year = {2007},
author = {Scheuch, S and Pfeifer, F},
title = {GvpD-induced breakdown of the transcriptional activator GvpE of halophilic archaea requires a functional p-loop and an arginine-rich region of GvpD.},
journal = {Microbiology (Reading, England)},
volume = {153},
number = {Pt 4},
pages = {947-958},
doi = {10.1099/mic.0.2006/004499-0},
pmid = {17379705},
issn = {1350-0872},
mesh = {Amino Acid Motifs ; Archaeal Proteins/chemistry/genetics/*metabolism ; Gene Deletion ; Gene Expression Regulation, Archaeal ; Halobacterium salinarum/*chemistry/genetics/*metabolism ; Haloferax mediterranei/*chemistry/genetics/*metabolism ; Molecular Sequence Data ; Trans-Activators/chemistry/genetics/*metabolism ; Transformation, Genetic ; },
abstract = {The two proteins involved in the regulation of gas vesicle formation in Haloferax mediterranei, mcGvpE (activator) and mcGvpD (repressive function), are able to interact in vitro. It was also found that the respective proteins cGvpE and cGvpD of Halobacterium salinarum and the heterologous pairs mcGvpD-cGvpE and cGvpD-mcGvpE were able to interact. Previously constructed mcGvpD mutants with alterations in regions affecting the repressive function of GvpD (p-loop motif or the two arginine-rich regions bR1 and bR2) were tested for their ability to interact with GvpE, and all still bound GvpE. Even a deletion of or near the p-loop motif in GvpD did not affect this ability to interact. Further deletion variants lacking larger N- or C-terminal portions of mcGvpD yielded that neither the N-terminal region with the p-loop motif nor the C-terminal portion were important for the binding of GvpE, and suggested that the central portion is involved in GvpE binding. The GvpD protein also induces a reduction in the amount of GvpE in Haloferax volcanii transformants expressing both genes under fdx promoter control on a single plasmid. Such DE(ex) transformants contain GvpD, but no detectable GvpE, whereas large amounts of GvpE are found in DeltaDE(ex) transformants that have incurred a deletion within the gvpD gene. A similar reduction was observed in D(ex)+E(ex) transformants harbouring both reading frames under fdx promoter control on two different plasmids. GvpD wild-type and also GvpD mutants were tested, and a significant reduction in the amount of GvpE was obtained in the case of GvpD wild-type and the super-repressor mutant GvpD(3-AAA). In contrast, transformants harbouring GvpD mutants with alterations in the p-loop motif or the bR1 region still contained GvpE. Since the amount of gvpE transcript was not reduced, the reduction occurred at the protein level. These results underlined that a functional p-loop and the arginine-rich region bR1 of GvpD were required for the GvpD-mediated reduction in the amount of GvpE.},
}
@article {pmid17369163,
year = {2007},
author = {Xu, XH and Wu, M and Zhang, HB and Liu, ZH},
title = {[Genetic analysis of the br gene in halophilic archaea isolated from Xingjiang region].},
journal = {Yi chuan = Hereditas},
volume = {29},
number = {3},
pages = {376-380},
doi = {10.1360/yc-007-0376},
pmid = {17369163},
issn = {0253-9772},
mesh = {Bacteriorhodopsins/*genetics ; China ; DNA, Archaeal/*analysis/genetics ; DNA, Ribosomal/analysis ; Gammaproteobacteria/*classification/genetics ; Halobacteriaceae/classification/genetics ; Halobacteriales/*classification/genetics ; Molecular Sequence Data ; *Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/*analysis/genetics ; },
abstract = {Some novel members of extremely halophilic Archaea, strain AJ11, AJ12 and AJ13, were isolated from Aularz Lake located in Altun Mountain National Nature Reserve of Xinjiang Uygur Autonomous Region in China. Partial DNA fragments encoding a bacteriorhodopsin (BR) as well as for 16S rRNA of isolated strains were amplified by PCR and their DNA sequences were determined subsequently. On the basis of homology and phylogenetic analysis about 16S rDNA, it was considered that the isolated strains formed a microbiological population are the members of genus Natrinema. The results of genetic analysis, such as GC content, transition/transversion (Ti/Tv) rate ratios, synonymous substitution rates (Ks), indicated that the br fragments with high level of genetic divergence are faced with both purifying selection and bias mutation pressure. The study provides the base for using of species and BR proteins resources.},
}
@article {pmid17366887,
year = {2007},
author = {Xugela, H and Dilbar, T and Wu, M and Zhou, PJ},
title = {[Studies on bacteriorhodopsin gene and sequence of 16S rRNA encoding genes of halophilic archaea of Xingjiang Aibi Lake].},
journal = {Sheng wu gong cheng xue bao = Chinese journal of biotechnology},
volume = {23},
number = {1},
pages = {46-50},
doi = {10.1016/s1872-2075(07)60004-1},
pmid = {17366887},
issn = {1000-3061},
mesh = {Amino Acid Sequence ; Bacteriorhodopsins/*genetics ; China ; DNA, Archaeal/chemistry/genetics ; Fresh Water/*microbiology ; Halobacteriaceae/classification/*genetics/isolation &amp; purification ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; },
abstract = {One hundred and forty-eight strains of halophilic archaea were isolated from 40 samples of soil, lake water, and silt. To study and analyze the species and bacteriorhodopsin(BR) protein resource, partial DNA fragments encoding BR protein from helix C to helix G andl6S rRNA encoding genes from 6 strains of halophilic archaea were amplified by polymerase chain(PCR) , and their DNA sequences were determined. The results indicate that the reduced amino acid sequences of BR protein from helix C to helix G of ABDH11 is obviously different from those of other existing proteins. The results of homology analysis on BR gene andl6S rRNA and phylogenetic analysis on 16S rRNA show that strains ABDH10 and ABDH40 are novel members of genus Natronorubrum and Natrinema, respectively; the sequence of ABDH40 was obtained from GenBank and the number of sequence is AY989910. The protein from helix C to helix G of ABDH11 is significantly different from that of other strains.},
}
@article {pmid17360575,
year = {2007},
author = {Facciotti, MT and Reiss, DJ and Pan, M and Kaur, A and Vuthoori, M and Bonneau, R and Shannon, P and Srivastava, A and Donohoe, SM and Hood, LE and Baliga, NS},
title = {General transcription factor specified global gene regulation in archaea.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {104},
number = {11},
pages = {4630-4635},
pmid = {17360575},
issn = {0027-8424},
support = {P50 GM076547/GM/NIGMS NIH HHS/United States ; P050 GM 076547/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; Archaea ; Chromatin Immunoprecipitation ; Evolution, Molecular ; *Gene Expression Regulation ; Gene Regulatory Networks ; Genetic Techniques ; Models, Biological ; Phylogeny ; Plasmids/metabolism ; Promoter Regions, Genetic ; Protein Interaction Mapping ; RNA, Messenger/metabolism ; Transcription Factors, General/*biosynthesis ; Transcription, Genetic ; },
abstract = {Cells responding to dramatic environmental changes or undergoing a developmental switch typically change the expression of numerous genes. In bacteria, sigma factors regulate much of this process, whereas in eukaryotes, four RNA polymerases and a multiplicity of generalized transcription factors (GTFs) are required. Here, by using a systems approach, we provide experimental evidence (including protein-coimmunoprecipitation, ChIP-Chip, GTF perturbation and knockout, and measurement of transcriptional changes in these genetically perturbed strains) for how archaea likely accomplish similar large-scale transcriptional segregation and modulation of physiological functions. We are able to associate GTFs to nearly half of all putative promoters and show evidence for at least 7 of the possible 42 functional GTF pairs. This report represents a significant contribution toward closing the gap in our understanding of gene regulation by GTFs for all three domains of life and provides an example for how to use various experimental techniques to rapidly learn significant portions of a global gene regulatory network of organisms for which little has been previously known.},
}
@article {pmid17359262,
year = {2007},
author = {Ehrhardt, CJ and Haymon, RM and Lamontagne, MG and Holden, PA},
title = {Evidence for hydrothermal Archaea within the basaltic flanks of the East Pacific Rise.},
journal = {Environmental microbiology},
volume = {9},
number = {4},
pages = {900-912},
doi = {10.1111/j.1462-2920.2006.01211.x},
pmid = {17359262},
issn = {1462-2912},
mesh = {Archaea/classification/*genetics ; Biodiversity ; Copper ; DNA, Bacterial/analysis ; Ecosystem ; Ferric Compounds/metabolism ; Geologic Sediments/analysis/*microbiology ; Hot Temperature ; Molecular Sequence Data ; Pacific Ocean ; *Phylogeny ; RNA, Ribosomal, 16S/classification ; Seawater/*microbiology ; Sulfides/metabolism ; Water Movements ; },
abstract = {Little is known about the fluids or the microbial communities present within potentially vast hydrothermal reservoirs contained in still-hot volcanic ocean crust beneath the flanks of the mid-ocean ridge. During Alvin dives in 2002, organic material attached to basalt was collected at low, near-ambient temperatures from an abyssal hill fault scarp in 0.5 Ma lithosphere on the western ridge flank of the East Pacific Rise. Mineral analysis by X-ray diffractometry and scanning electron microscopy revealed high-temperature (> 110 degrees C) phases chalcopyrite (Cu(5)FeS(4)) and 1C pyrrhotite (Fe(1-x)S) within the fault scarp materials. A molecular survey of archaeal genes encoding 16S rRNA identified a diverse hyperthermophilic community, including groups within Crenarchaeota, Euryarchaeota, and Korarchaeota. We propose that the sulfide, metals and archaeal communities originated within a basalt-hosted subseafloor hydrothermal habitat beneath the East Pacific Rise ridge flank and were transported to the seafloor during a recent episode of hydrothermal venting from the abyssal hill fault. Additionally, inferred metabolisms from the fault scarp community suggest that an ecologically unique high-temperature archaeal biosphere may thrive beneath the young East Pacific Rise ridge flank and that abyssal hill fault scarps may present new opportunities for sampling for this largely unexplored microbial habitat.},
}
@article {pmid17357157,
year = {2007},
author = {Ausili, A and Cobucci-Ponzano, B and Di Lauro, B and D'Avino, R and Perugino, G and Bertoli, E and Scirè, A and Rossi, M and Tanfani, F and Moracci, M},
title = {A comparative infrared spectroscopic study of glycoside hydrolases from extremophilic archaea revealed different molecular mechanisms of adaptation to high temperatures.},
journal = {Proteins},
volume = {67},
number = {4},
pages = {991-1001},
doi = {10.1002/prot.21368},
pmid = {17357157},
issn = {1097-0134},
mesh = {*Adaptation, Biological ; Computational Biology ; Desulfurococcaceae/*enzymology ; Glycoside Hydrolases/*chemistry/*metabolism ; Models, Molecular ; Protein Denaturation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Pyrococcus furiosus/*enzymology ; Spectrophotometry, Infrared ; Sulfolobus solfataricus/*enzymology ; Temperature ; },
abstract = {The identification of the determinants of protein thermal stabilization is often pursued by comparing enzymes from hyperthermophiles with their mesophilic counterparts while direct structural comparisons among proteins and enzymes from hyperthermophiles are rather uncommon. Here, oligomeric beta-glycosidases from the hyperthermophilic archaea Sulfolobus solfataricus (Ss beta-gly), Thermosphaera aggregans (Ta beta-gly), and Pyrococcus furiosus (Pf beta-gly), have been compared. Studies of FTIR spectroscopy and kinetics of thermal inactivation showed that the three enzymes had similar secondary structure composition, but Ss beta-gly and Ta beta-gly (temperatures of melting 98.1 and 98.4 degrees C, respectively) were less stable than Pf beta-gly, which maintained its secondary structure even at 99.5 degrees C. The thermal denaturation of Pf beta-gly, followed in the presence of SDS, suggested that this enzyme is stabilized by hydrophobic interactions. A detailed inspection of the 3D-structures of these enzymes supported the experimental results: Ss beta-gly and Ta beta-gly are stabilized by a combination of ion-pairs networks and intrasubunit S-S bridges while the increased stability of Pf beta-gly resides in a more compact protein core. The different strategies of protein stabilization give experimental support to recent theories on thermophilic adaptation and suggest that different stabilization strategies could have been adopted among archaea.},
}
@article {pmid17357153,
year = {2007},
author = {Miyazono, K and Tsujimura, M and Kawarabayasi, Y and Tanokura, M},
title = {Crystal structure of an archaeal homologue of multidrug resistance repressor protein, EmrR, from hyperthermophilic archaea Sulfolobus tokodaii strain 7.},
journal = {Proteins},
volume = {67},
number = {4},
pages = {1138-1146},
doi = {10.1002/prot.21327},
pmid = {17357153},
issn = {1097-0134},
mesh = {Amino Acid Sequence ; Archaeal Proteins/*chemistry/genetics/*metabolism ; Crystallography, X-Ray ; *Drug Resistance, Multiple ; Models, Molecular ; Molecular Sequence Data ; Protein Structure, Tertiary ; Repressor Proteins/*chemistry/genetics/*metabolism ; Sequence Alignment ; Sequence Homology, Amino Acid ; Sulfolobus/*enzymology ; Temperature ; },
abstract = {MarR family proteins, MarR, MexR, and EmrR, are known as bacterial regulators for a phenotype resistant to multiple antibiotic drugs. Genomic data have indicated the presence of bacterial-type transcriptional regulators, including MarR family proteins in archaea, though the archaeal transcription system is close to that of eukaryote. To elucidate the structural basis of the transcriptional regulation mechanism of archaeal MarR family proteins, the crystal structure of the ST1710 protein, which was identified as an archaeal EmrR homologue, StEmrR, from hyperthermophilic archaeon Sulfolobus tokodaii strain 7 was determined at 1.45-A resolution. The protein was composed of two N- and C-terminal dimerization domains, and the DNA-binding domain consisted of a winged helix motif, as in the case of bacterial MarR family proteins. Despite the relatively low overall structural similarity between StEmrR and bacterial MarR family proteins, the structure of the DNA-binding domain displayed high structural similarity. A comparison with the crystal structures of bacterial MarR family proteins revealed that structural variation was mainly due to the different orientation of the two helices at the N- and C-termini. Our results indicated that the distance between the two DNA-binding domains of MarR family proteins would be changed by the rotation of the two terminal helices to interact with the target DNA.},
}
@article {pmid17351629,
year = {2007},
author = {Fukunaga, R and Yokoyama, S},
title = {Structural insights into the first step of RNA-dependent cysteine biosynthesis in archaea.},
journal = {Nature structural &amp; molecular biology},
volume = {14},
number = {4},
pages = {272-279},
doi = {10.1038/nsmb1219},
pmid = {17351629},
issn = {1545-9993},
mesh = {Amino Acid Sequence ; Anticodon/genetics ; Archaeal Proteins/*chemistry/*metabolism ; Archaeoglobus fulgidus/*enzymology ; Biological Evolution ; Crystallography, X-Ray ; Cysteine/*biosynthesis ; Models, Molecular ; Molecular Sequence Data ; Mutant Proteins/chemistry/metabolism ; Phosphoserine/metabolism ; Protein Engineering ; Protein Structure, Secondary ; RNA, Archaeal/*metabolism ; RNA, Transfer, Cys/metabolism ; },
abstract = {Cysteine is ligated to tRNA(Cys) by cysteinyl-tRNA synthetase in most organisms. However, in methanogenic archaea lacking cysteinyl-tRNA synthetase, O-phosphoserine is ligated to tRNA(Cys) by O-phosphoseryl-tRNA synthetase (SepRS), and the phosphoseryl-tRNA(Cys) is converted to cysteinyl-tRNA(Cys). In this study, we determined the crystal structure of the SepRS tetramer in complex with tRNA(Cys) and O-phosphoserine at 2.6-A resolution. The catalytic domain of SepRS recognizes the negatively charged side chain of O-phosphoserine at a noncanonical site, using the dipole moment of a conserved alpha-helix. The unique C-terminal domain specifically recognizes the anticodon GCA of tRNA(Cys). On the basis of the structure, we engineered SepRS to recognize tRNA(Cys) mutants with the anticodons UCA and CUA and clarified the anticodon recognition mechanism by crystallography. The mutant SepRS-tRNA pairs may be useful for translational incorporation of O-phosphoserine into proteins in response to the stop codons UGA and UAG.},
}
@article {pmid17350934,
year = {2007},
author = {van Passel, MW and Smillie, CS and Ochman, H},
title = {Gene decay in archaea.},
journal = {Archaea (Vancouver, B.C.)},
volume = {2},
number = {2},
pages = {137-143},
pmid = {17350934},
issn = {1472-3646},
support = {R01 GM056120/GM/NIGMS NIH HHS/United States ; GM56120/GM/NIGMS NIH HHS/United States ; },
mesh = {Archaea/classification/*genetics ; Bacteria/genetics ; Base Composition ; Gene Silencing ; *Genes, Archaeal ; Genome, Archaeal ; Phylogeny ; *Pseudogenes ; },
abstract = {The gene-dense chromosomes of archaea and bacteria were long thought to be devoid of pseudogenes, but with the massive increase in available genome sequences, whole genome comparisons between closely related species have identified mutations that have rendered numerous genes inactive. Comparative analyses of sequenced archaeal genomes revealed numerous pseudogenes, which can constitute up to 8.6% of the annotated coding sequences in some genomes. The largest proportion of pseudogenes is created by gene truncations, followed by frameshift mutations. Within archaeal genomes, large numbers of pseudogenes contain more than one inactivating mutation, suggesting that pseudogenes are deleted from the genome more slowly in archaea than in bacteria. Although archaea seem to retain pseudogenes longer than do bacteria, most archaeal genomes have unique repertoires of pseudogenes.},
}
@article {pmid17350930,
year = {2007},
author = {Ingram-Smith, C and Smith, KS},
title = {AMP-forming acetyl-CoA synthetases in Archaea show unexpected diversity in substrate utilization.},
journal = {Archaea (Vancouver, B.C.)},
volume = {2},
number = {2},
pages = {95-107},
pmid = {17350930},
issn = {1472-3646},
support = {R15 GM069374/GM/NIGMS NIH HHS/United States ; GM69374-01A1/GM/NIGMS NIH HHS/United States ; },
mesh = {Acetate-CoA Ligase/*chemistry/genetics/*metabolism ; Adenosine Monophosphate/metabolism ; Amino Acid Sequence ; Archaea/classification/*enzymology/metabolism ; Methanobacteriaceae/enzymology/genetics ; Models, Molecular ; Molecular Sequence Data ; Open Reading Frames ; Phylogeny ; Sequence Alignment ; Substrate Specificity ; },
abstract = {Adenosine monophosphate (AMP)-forming acetyl-CoA synthetase (ACS; acetate:CoA ligase (AMP-forming), EC 6.2.1.1) is a key enzyme for conversion of acetate to acetyl-CoA, an essential intermediate at the junction of anabolic and catabolic pathways. Phylogenetic analysis of putative short and medium chain acyl-CoA synthetase sequences indicates that the ACSs form a distinct clade from other acyl-CoA synthetases. Within this clade, the archaeal ACSs are not monophyletic and fall into three groups composed of both bacterial and archaeal sequences. Kinetic analysis of two archaeal enzymes, an ACS from Methanothermobacter thermautotrophicus (designated as MT-ACS1) and an ACS from Archaeoglobus fulgidus (designated as AF-ACS2), revealed that these enzymes have very different properties. MT-ACS1 has nearly 11-fold higher affinity and 14-fold higher catalytic efficiency with acetate than with propionate, a property shared by most ACSs. However, AF-ACS2 has only 2.3-fold higher affinity and catalytic efficiency with acetate than with propionate. This enzyme has an affinity for propionate that is almost identical to that of MT-ACS1 for acetate and nearly tenfold higher than the affinity of MT-ACS1 for propionate. Furthermore, MT-ACS1 is limited to acetate and propionate as acyl substrates, whereas AF-ACS2 can also utilize longer straight and branched chain acyl substrates. Phylogenetic analysis, sequence alignment and structural modeling suggest a molecular basis for the altered substrate preference and expanded substrate range of AF-ACS2 versus MT-ACS1.},
}
@article {pmid17347521,
year = {2007},
author = {Filée, J and Siguier, P and Chandler, M},
title = {Insertion sequence diversity in archaea.},
journal = {Microbiology and molecular biology reviews : MMBR},
volume = {71},
number = {1},
pages = {121-157},
pmid = {17347521},
issn = {1092-2172},
mesh = {Archaea/classification/*genetics ; Base Sequence ; DNA Transposable Elements/*genetics ; *Genetic Variation ; Genome, Archaeal ; *Mutagenesis, Insertional ; Phylogeny ; },
abstract = {Insertion sequences (ISs) can constitute an important component of prokaryotic (bacterial and archaeal) genomes. Over 1,500 individual ISs are included at present in the ISfinder database (www-is.biotoul.fr), and these represent only a small portion of those in the available prokaryotic genome sequences and those that are being discovered in ongoing sequencing projects. In spite of this diversity, the transposition mechanisms of only a few of these ubiquitous mobile genetic elements are known, and these are all restricted to those present in bacteria. This review presents an overview of ISs within the archaeal kingdom. We first provide a general historical summary of the known properties and behaviors of archaeal ISs. We then consider how transposition might be regulated in some cases by small antisense RNAs and by termination codon readthrough. This is followed by an extensive analysis of the IS content in the sequenced archaeal genomes present in the public databases as of June 2006, which provides an overview of their distribution among the major archaeal classes and species. We show that the diversity of archaeal ISs is very great and comparable to that of bacteria. We compare archaeal ISs to known bacterial ISs and find that most are clearly members of families first described for bacteria. Several cases of lateral gene transfer between bacteria and archaea are clearly documented, notably for methanogenic archaea. However, several archaeal ISs do not have bacterial equivalents but can be grouped into Archaea-specific groups or families. In addition to ISs, we identify and list nonautonomous IS-derived elements, such as miniature inverted-repeat transposable elements. Finally, we present a possible scenario for the evolutionary history of ISs in the Archaea.},
}
@article {pmid17347520,
year = {2007},
author = {Koga, Y and Morii, H},
title = {Biosynthesis of ether-type polar lipids in archaea and evolutionary considerations.},
journal = {Microbiology and molecular biology reviews : MMBR},
volume = {71},
number = {1},
pages = {97-120},
pmid = {17347520},
issn = {1092-2172},
mesh = {Archaea/classification/genetics/*metabolism ; Archaeal Proteins/genetics/metabolism ; CDPdiacylglycerol-Serine O-Phosphatidyltransferase/genetics/metabolism ; *Evolution, Molecular ; Glycerolphosphate Dehydrogenase/genetics/metabolism ; Lipids/*biosynthesis/chemistry ; Molecular Structure ; Phylogeny ; },
abstract = {This review deals with the in vitro biosynthesis of the characteristics of polar lipids in archaea along with preceding in vivo studies. Isoprenoid chains are synthesized through the classical mevalonate pathway, as in eucarya, with minor modifications in some archaeal species. Most enzymes involved in the pathway have been identified enzymatically and/or genomically. Three of the relevant enzymes are found in enzyme families different from the known enzymes. The order of reactions in the phospholipid synthesis pathway (glycerophosphate backbone formation, linking of glycerophosphate with two radyl chains, activation by CDP, and attachment of common polar head groups) is analogous to that of bacteria. sn-Glycerol-1-phosphate dehydrogenase is responsible for the formation of the sn-glycerol-1-phosphate backbone of phospholipids in all archaea. After the formation of two ether bonds, CDP-archaeol acts as a common precursor of various archaeal phospholipid syntheses. Various phospholipid-synthesizing enzymes from archaea and bacteria belong to the same large CDP-alcohol phosphatidyltransferase family. In short, the first halves of the phospholipid synthesis pathways play a role in synthesis of the characteristic structures of archaeal and bacterial phospholipids, respectively. In the second halves of the pathways, the polar head group-attaching reactions and enzymes are homologous in both domains. These are regarded as revealing the hybrid nature of phospholipid biosynthesis. Precells proposed by Wächtershäuser are differentiated into archaea and bacteria by spontaneous segregation of enantiomeric phospholipid membranes (with sn-glycerol-1-phosphate and sn-glycerol-3-phosphate backbones) and the fusion and fission of precells. Considering the nature of the phospholipid synthesis pathways, we here propose that common phospholipid polar head groups were present in precells before the differentiation into archaea and bacteria.},
}
@article {pmid17334387,
year = {2007},
author = {Valentine, DL},
title = {Adaptations to energy stress dictate the ecology and evolution of the Archaea.},
journal = {Nature reviews. Microbiology},
volume = {5},
number = {4},
pages = {316-323},
doi = {10.1038/nrmicro1619},
pmid = {17334387},
issn = {1740-1534},
mesh = {*Adaptation, Biological ; Archaea/*genetics/*metabolism ; *Biological Evolution ; Ecology ; *Energy Metabolism/genetics ; },
abstract = {The three domains of life on Earth include the two prokaryotic groups, Archaea and Bacteria. The Archaea are distinguished from Bacteriabased on phylogenetic and biochemical differences, but currently there is no unifying ecological principle to differentiate these groups. The ecology of the Archaea is reviewed here in terms of cellular bioenergetics. Adaptation to chronic energy stress is hypothesized to be the crucial factor that distinguishes the Archaea from Bacteria. The biochemical mechanisms that enable archaea to cope with chronic energy stress include low-permeability membranes and specific catabolic pathways. Based on the ecological unity and biochemical adaptations among archaea, I propose the hypothesis that chronic energy stress is the primary selective pressure governing the evolution of the Archaea.},
}
@article {pmid17327157,
year = {2007},
author = {Robertson, CE},
title = {Electron microscopy of Archaea.},
journal = {Methods in cell biology},
volume = {79},
number = {},
pages = {169-191},
doi = {10.1016/S0091-679X(06)79007-0},
pmid = {17327157},
issn = {0091-679X},
mesh = {Cryoelectron Microscopy/*methods ; Cryopreservation ; Cryoprotective Agents/pharmacology ; Freezing ; Imaging, Three-Dimensional/*methods ; Sulfolobus solfataricus/drug effects/*ultrastructure ; },
}
@article {pmid17321663,
year = {2007},
author = {Ogata, N},
title = {Elongation of palindromic repetitive DNA by DNA polymerase from hyperthermophilic archaea: a mechanism of DNA elongation and diversification.},
journal = {Biochimie},
volume = {89},
number = {5},
pages = {702-712},
doi = {10.1016/j.biochi.2006.12.011},
pmid = {17321663},
issn = {0300-9084},
mesh = {Archaeal Proteins ; Base Sequence ; DNA Replication ; DNA, Archaeal/*genetics ; DNA-Directed DNA Polymerase/*metabolism ; *Repetitive Sequences, Nucleic Acid ; Thermococcus/*genetics ; },
abstract = {DNA polymerase from hyperthermophilic bacteria can elongate tandem repetitive oligoDNA with a complete or incomplete palindromic sequence under isothermal conditions by "hairpin elongation". However, the product of the reaction has not yet been sufficiently characterized. Here, I demonstrate that when palindromic repetitive oligoDNA, e.g., (5'AGATATCT3')(6), was added as a "seed" to the DNA synthesis reaction catalyzed by DNA polymerase from the archaea Thermococcus litoralis (Vent polymerase) at 74 degrees C, the product was (5'AGATATCT3')(n). The product itself was palindromic and repetitive, and its motif (unit) sequence was exactly the same as that of the seed oligoDNA. On the other hand, when a pseudopalindrome, which contains a palindrome-breaking nucleotide (underlined), was present in seed oligoDNA, e.g., (5'GATTC3')(6), the product was (5'GATATC3')(n), which had a different motif sequence from that of the seed oligoDNA. When a pseudopalindrome (5'AGATATCA3')(6) was added to the reaction, the products were 5'TATCA . (AGATATCA)(3) . AGATATCT . (TGATATCT)(5) . TGATA3', etc. When 5'AGATATCA . (AGATATCT3')(5) was added, products were 5'TATCT . (AGATATCT)(2).TGATATCT . AGATATCT . AGATATCA . AGATATCT . AGA3', etc., demonstrating the generation of many "mutations" in the product DNA. I conclude that a tandem repetitive sequence is faithfully elongated (amplified) by hyperthermophilic DNA polymerase if it is completely palindromic, but is elongated with many errors if it is incompletely palindromic (pseudopalindromic) or mixed with a pseudopalindrome. The results suggest a protein-catalyzed elongation/diversification mechanism of short repetitive DNAs on the early earth.},
}
@article {pmid17305820,
year = {2007},
author = {Di Giulio, M},
title = {The universal ancestor and the ancestors of Archaea and Bacteria were anaerobes whereas the ancestor of the Eukarya domain was an aerobe.},
journal = {Journal of evolutionary biology},
volume = {20},
number = {2},
pages = {543-548},
doi = {10.1111/j.1420-9101.2006.01259.x},
pmid = {17305820},
issn = {1010-061X},
mesh = {Archaea/*classification/genetics/metabolism ; Bacteria/*classification/genetics/metabolism ; Environment ; Eukaryotic Cells/*classification/metabolism ; Likelihood Functions ; Oxygen/*metabolism ; *Phylogeny ; Proteins/chemistry/genetics ; },
abstract = {The use of an oxyphobic index (OI) based on the propensity of amino acids to enter more frequently the proteins of anaerobes makes it possible to make inferences on the environment in which the last universal common ancestor (LUCA) lived. The reconstruction of the ancestral sequences of proteins using a method based on maximum likelihood and their attribution by means of the OI to the set of aerobe or anaerobe sequences has led to the following conclusions: the LUCA was an anaerobic 'organism', as were the ancestors of Archaea and Bacteria, whereas the ancestor of Eukarya was an aerobe. These observations seem to falsify the hypothesis that the LUCA was an aerobe and help to identify better the environment in which the first organisms lived.},
}
@article {pmid17298362,
year = {2007},
author = {Gattinger, A and Höfle, MG and Schloter, M and Embacher, A and Böhme, F and Munch, JC and Labrenz, M},
title = {Traditional cattle manure application determines abundance, diversity and activity of methanogenic Archaea in arable European soil.},
journal = {Environmental microbiology},
volume = {9},
number = {3},
pages = {612-624},
doi = {10.1111/j.1462-2920.2006.01181.x},
pmid = {17298362},
issn = {1462-2912},
mesh = {Agriculture ; Animals ; *Archaea/classification/genetics/growth &amp; development/metabolism ; Cattle ; DNA, Archaeal/analysis ; DNA, Ribosomal/analysis ; Fertilizers ; Genes, rRNA ; Germany ; *Manure ; Methane/*metabolism ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Soil/analysis ; *Soil Microbiology ; },
abstract = {Based on lipid analyses, 16S rRNA/rRNA gene single-strand conformation polymorphism fingerprints and methane flux measurements, influences of the fertilization regime on abundance and diversity of archaeal communities were investigated in soil samples from the long-term (103 years) field trial in Bad Lauchstädt, Germany. The investigated plots followed a gradient of increasing fertilization beginning at no fertilization and ending at the 'cattle manure' itself. The archaeal phospholipid etherlipid (PLEL) concentration was used as an indicator for archaeal biomass and increased with the gradient of increasing fertilization, whereby the concentrations determined for organically fertilized soils were well above previously reported values. Methane emission, although at a low level, were occasionally only observed in organically fertilized soils, whereas the other treatments showed significant methane uptake. Euryarchaeotal organisms were abundant in all investigated samples but 16S rRNA analysis also demonstrated the presence of Crenarchaeota in fertilized soils. Lowest molecular archaeal diversity was found in highest fertilized treatments. Archaea phylogenetically most closely related to cultured methanogens were abundant in these fertilized soils, whereas Archaea with low relatedness to cultured microorganisms dominated in non-fertilized soils. Relatives of Methanoculleus spp. were found almost exclusively in organically fertilized soils or cattle manure. Methanosarcina-related microorganisms were detected in all soils as well as in the cattle manure, but soils with highest organic application rate were specifically dominated by a close phylogenetic relative of Methanosarcina thermophila. Our findings suggest that regular application of cattle manure increased archaeal biomass, but reduced archaeal diversity and selected for methanogenic Methanoculleus and Methanosarcina strains, leading to the circumstance that high organic fertilized soils did not function as a methane sink at the investigated site anymore.},
}
@article {pmid17286573,
year = {2007},
author = {Ring, G and Londei, P and Eichler, J},
title = {Protein biogenesis in Archaea: addressing translation initiation using an in vitro protein synthesis system for Haloferax volcanii.},
journal = {FEMS microbiology letters},
volume = {270},
number = {1},
pages = {34-41},
doi = {10.1111/j.1574-6968.2007.00649.x},
pmid = {17286573},
issn = {0378-1097},
mesh = {Amino Acid Motifs/genetics ; Archaea/*genetics/metabolism ; Archaeal Proteins/genetics/metabolism ; Electrophoresis, Polyacrylamide Gel ; Haloferax volcanii/*genetics/metabolism ; Immunoblotting ; Peptide Chain Initiation, Translational ; Protein Biosynthesis/*genetics ; RNA, Archaeal/genetics/metabolism ; RNA, Messenger/genetics/metabolism ; Ribosomes/metabolism ; Transcription, Genetic ; },
abstract = {Translation initiation in Archaea combines aspects of the parallel process in Eukarya and Bacteria alongside traits unique to this domain. To better understand translation initiation in Archaea, an in vitro translation system from the haloarchaeon Haloferax volcanii has been developed. The ability to translate individual mRNAs both under the conditions used in previously developed poly(U)-dependent poly(Phe) synthesis systems as well as under physiological conditions was shown. Using the H. volcanii system, mRNAs proceeded by either 'strong' or 'weak' Shine-Dalgarno (SD) motifs, or completely lacking leader sequences were effectively translated. The in vitro haloarchaeal system also successfully translated mRNA from Bacteria, again either presenting a SD initiation motif or completely lacking a leader sequence. Thus, the ability to translate individual mRNAs in vitro offers a system to address translation initiation as well as other aspects of protein biogenesis in Archaea.},
}
@article {pmid17277228,
year = {2007},
author = {Kimura, H and Ishibashi, J and Masuda, H and Kato, K and Hanada, S},
title = {Selective phylogenetic analysis targeting 16S rRNA genes of hyperthermophilic archaea in the deep-subsurface hot biosphere.},
journal = {Applied and environmental microbiology},
volume = {73},
number = {7},
pages = {2110-2117},
pmid = {17277228},
issn = {0099-2240},
mesh = {Archaea/*classification/genetics ; Base Composition ; Cloning, Molecular ; Hot Springs/*microbiology ; Hot Temperature ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/*genetics ; },
abstract = {International drilling projects for the study of microbial communities in the deep-subsurface hot biosphere have been expanded. Core samples obtained by deep drilling are commonly contaminated with mesophilic microorganisms in the drilling fluid, making it difficult to examine the microbial community by 16S rRNA gene clone library analysis. To eliminate mesophilic organism contamination, we previously developed a new method (selective phylogenetic analysis [SePA]) based on the strong correlation between the guanine-plus-cytosine (G+C) contents of the 16S rRNA genes and the optimal growth temperatures of prokaryotes, and we verified the method's effectiveness (H. Kimura, M. Sugihara, K. Kato, and S. Hanada, Appl. Environ. Microbiol. 72:21-27, 2006). In the present study we ascertained SePA's ability to eliminate contamination by archaeal rRNA genes, using deep-sea hydrothermal fluid (117 degrees C) and surface seawater (29.9 degrees C) as substitutes for deep-subsurface geothermal samples and drilling fluid, respectively. Archaeal 16S rRNA gene fragments, PCR amplified from the surface seawater, were denatured at 82 degrees C and completely digested with exonuclease I (Exo I), while gene fragments from the deep-sea hydrothermal fluid remained intact after denaturation at 84 degrees C because of their high G+C contents. An examination using mixtures of DNAs from the two environmental samples showed that denaturation at 84 degrees C and digestion with Exo I completely eliminated archaeal 16S rRNA genes from the surface seawater. Our method was quite useful for culture-independent community analysis of hyperthermophilic archaea in core samples recovered from deep-subsurface geothermal environments.},
}
@article {pmid17261512,
year = {2007},
author = {Lehours, AC and Evans, P and Bardot, C and Joblin, K and Gérard, F},
title = {Phylogenetic diversity of archaea and bacteria in the anoxic zone of a meromictic lake (Lake Pavin, France).},
journal = {Applied and environmental microbiology},
volume = {73},
number = {6},
pages = {2016-2019},
pmid = {17261512},
issn = {0099-2240},
mesh = {Archaea/*classification/*isolation &amp; purification ; Bacteria/*classification/*isolation &amp; purification ; Base Sequence ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; France ; Fresh Water/*microbiology ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Water Microbiology ; },
abstract = {The compositions of archaeal and bacterial populations at different depths (60 m [mixolimnion-chemocline interface], 70 m [chemocline-subchemocline interface], 90 m, and 92 m [the water-sediment interface]) in the anoxic zone of the water column in Lake Pavin, a freshwater permanently stratified mountain lake in France, were determined. Phylogenetic trees were constructed from sequences to assess archaeal and bacterial diversity at the four sites.},
}
@article {pmid17253090,
year = {2007},
author = {Payandeh, J and Pai, EF},
title = {Enzyme-driven speciation: crystallizing Archaea via lipid capture.},
journal = {Journal of molecular evolution},
volume = {64},
number = {3},
pages = {364-374},
pmid = {17253090},
issn = {0022-2844},
mesh = {Alkyl and Aryl Transferases/*genetics ; Amino Acid Sequence ; Archaea/enzymology/*genetics ; Archaeal Proteins/*genetics ; Archaeoglobus/enzymology/genetics ; *Evolution, Molecular ; Genome, Archaeal ; Membrane Lipids/*biosynthesis/chemistry ; Models, Molecular ; },
abstract = {As the origin(s) of life on Earth remains an open question, detailed characteristics about the "last universal ancestor" (LUA) continue to be obscured. Here we provide arguments that strengthen the bacterial-like nature of the LUA. Our view attempts to recreate the evolution of archaeal lipids, the major components of the distinctive membrane that encapsulates these ancient prokaryotes. We show that (S)- 3-O-geranylgeranylglyceryl phosphate synthase (GGGPS), a TIM-barrel protein that performs the committed step in archaeal lipid synthesis, likely evolved from the duplication and fusion of a (betaalpha)4 half-barrel ancestor. By comparison to the well-characterized HisA and HisF TIM-barrel proteins, we propose a time line for the invention of this diagnostic archaeal biosynthetic pathway. After excluding the possibility of horizontal gene transfer, we conclude that the evolutionary history of GGGPS mirrors the emergence of Archaea from the LUA. We illustrate aspects of this "lipid capture" model that support its likelihood in recreating key evolutionary events and, as our hypothesis is built on a single initiating event, we suggest that the appearance of GGGPS represents an example of enzyme-driven speciation.},
}
@article {pmid17237472,
year = {2007},
author = {French, SL and Santangelo, TJ and Beyer, AL and Reeve, JN},
title = {Transcription and translation are coupled in Archaea.},
journal = {Molecular biology and evolution},
volume = {24},
number = {4},
pages = {893-895},
doi = {10.1093/molbev/msm007},
pmid = {17237472},
issn = {0737-4038},
support = {1F32-GM073336-01/GM/NIGMS NIH HHS/United States ; GM53185/GM/NIGMS NIH HHS/United States ; GM63952/GM/NIGMS NIH HHS/United States ; },
mesh = {Archaea/*genetics/ultrastructure ; Microscopy, Electron ; Protein Biosynthesis/*genetics ; Thermococcus/genetics/ultrastructure ; Transcription, Genetic/*genetics ; },
abstract = {Polysomes have been visualized by electron microscopy attached directly to dispersed strands of genomic DNA extruded from lysed cells of the hyperthermophilic archaeon Thermococcus kodakaraensis. These complexes are consistent with transcription and translation being coupled in this Archaeon, with translation of transcripts being initiated before the transcript is complete.},
}
@article {pmid17227427,
year = {2007},
author = {Schwarz, JI and Lueders, T and Eckert, W and Conrad, R},
title = {Identification of acetate-utilizing Bacteria and Archaea in methanogenic profundal sediments of Lake Kinneret (Israel) by stable isotope probing of rRNA.},
journal = {Environmental microbiology},
volume = {9},
number = {1},
pages = {223-237},
doi = {10.1111/j.1462-2920.2006.01133.x},
pmid = {17227427},
issn = {1462-2912},
mesh = {Acetates/*metabolism ; Archaea/*classification/genetics/metabolism ; Bacteria/*classification/genetics/metabolism ; DNA, Ribosomal/genetics ; Fresh Water/*microbiology ; Geologic Sediments/*microbiology ; Israel ; Methane/metabolism ; Phylogeny ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; RNA, Archaeal/genetics ; RNA, Bacterial/genetics ; RNA, Ribosomal/genetics ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Acetate is an important intermediate in the decomposition of organic matter in anoxic freshwater sediments. Here, we identified distinct microorganisms active in its oxidation and transformation to methane in the anoxic methanogenic layers of Lake Kinneret (Israel) profundal sediment by rRNA-based stable isotope probing (RNA-SIP). After 18 days of incubation with amended [U-(13)C]acetate we found that archaeal 16S rRNA was (13)C-labelled to a far greater extent than bacterial rRNA. We identified acetoclastic methanogens related to Methanosaeta concilii as being most active in the degradation and assimilation of acetate. Oxidation of the acetate-methyl group played only a minor role, but nevertheless 'heavy'(13)C-labelled bacterial rRNA templates were identified. 'Heavy' bacteria were mainly affiliated with the Betaproteobacteria (mostly Rhodocyclales and Nitrosomonadales), the Nitrospira phylum (related to 'Magnetobacterium bavaricum' and Thermodesulfovibrio yellowstonii), and also with the candidate phylum 'Endomicrobia'. However, the mode of energy gain that allowed for the assimilation of (13)C-acetate by these bacterial groups remains unknown. It may have involved syntrophic oxidation of acetate, reduction of chlorinated compounds, reduction of humic substances, fermentation of organic compounds, or even predation of (13)C-labelled Methanosaeta spp. In summary, this SIP experiment shows that acetate carbon was predominantly consumed by acetoclastic methanogens in profundal Lake Kinneret sediment, while it was also utilized by a small and heterogeneous community of bacteria.},
}
@article {pmid17205811,
year = {2006},
author = {Ozcan, B and Cokmus, C and Coleri, A and Caliskan, M},
title = {[Characterization of extremely halophilic archaea isolated from saline environment in different parts of Turkey].},
journal = {Mikrobiologiia},
volume = {75},
number = {6},
pages = {849-856},
pmid = {17205811},
issn = {0026-3656},
mesh = {Anti-Bacterial Agents/pharmacology ; Archaeal Proteins/analysis ; Culture Media ; Electrophoresis, Agar Gel ; Electrophoresis, Polyacrylamide Gel ; Fresh Water/*microbiology ; *Halobacteriaceae/chemistry/drug effects/isolation &amp; purification/physiology ; Molecular Weight ; Plasmids/analysis/chemistry ; Sodium Chloride ; *Soil Microbiology ; Turkey ; },
abstract = {Ninety-five extremely halophilic strains were isolated from six distinct saline regions of Turkey by using complex medium containing 25% NaCl. The selected regions are Tuz Golu (salt lake), Ankara; Aci Lake, Denizli; Salda Lake, Denizli; Seyfe Lake, Kirsehir; Tuzla Lake, Kayseri; and Bolluk Lake, Konya. The isolated strains were tested for motility, Gram reaction, cell and colony morphologies, pigmentation, biochemical characteristics, and antibiotic sensitivities. According to membrane glycerol diether moieties and antibiotic susceptibilities, all isolated strains were found to belong to the domain Archaea. All isolates were examined for the presence of plasmids by agarose gel electrophoresis and it was established that most isolates contained plasmids that varied in number and whose molecular sizes ranged from 1 to 36.9 kbp. Whole-cell protein profiles from isolates were analyzed by SDS-PAGE and a similarity dendogram was constructed using the UPGMA method. Significant similarities and differences were observed among the isolates. The strains were clustered in eight groups and ten of our isolates were placed in the same group with the standard strains. The current study represents the first isolation and characterization of such a large collection of archeal strains from Turkey.},
}
@article {pmid17187352,
year = {2007},
author = {Cavicchioli, R and Demaere, MZ and Thomas, T},
title = {Metagenomic studies reveal the critical and wide-ranging ecological importance of uncultivated Archaea: the role of ammonia oxidizers.},
journal = {BioEssays : news and reviews in molecular, cellular and developmental biology},
volume = {29},
number = {1},
pages = {11-14},
doi = {10.1002/bies.20519},
pmid = {17187352},
issn = {0265-9247},
mesh = {Ammonia/*metabolism ; Archaea/*genetics/*metabolism ; Crenarchaeota/genetics/metabolism ; Ecosystem ; Genomics ; Oxidation-Reduction ; Soil Microbiology ; },
abstract = {Microbial genome sequencing has entered a new phase, where DNA sequence information is gathered from entire microbial communities (metagenomics or environmental genomics) rather than from individual microorganisms. By providing access to the genetic material of vast numbers of organisms, most of which are organisms that have never been isolated or cultivated, a new level of insight is being gained into the diversity and extent of the microbial processes that are presently occuring in environmental communities. By extending metagenomic-based approaches to the study of very complex and methodologically recalcitrant soil environments, a recent study has found that ammonia-oxidizing archaea are more abundant in many soils than bacteria.1 These findings not only highlight the undoubtedly critical yet unknown roles that archaea play in global nutrient cycles but illustrate the importance of genomic studies for informing us about the functional capacity of life on Earth.},
}
@article {pmid17185602,
year = {2006},
author = {Baker, BJ and Tyson, GW and Webb, RI and Flanagan, J and Hugenholtz, P and Allen, EE and Banfield, JF},
title = {Lineages of acidophilic archaea revealed by community genomic analysis.},
journal = {Science (New York, N.Y.)},
volume = {314},
number = {5807},
pages = {1933-1935},
doi = {10.1126/science.1132690},
pmid = {17185602},
issn = {1095-9203},
mesh = {Amino Acid Sequence ; Base Sequence ; *Biofilms ; California ; Cell Membrane/ultrastructure ; DNA Transposable Elements ; DNA, Archaeal ; Databases, Genetic ; *Ecosystem ; *Euryarchaeota/genetics/physiology/ultrastructure ; Genes, Archaeal ; Genes, rRNA ; *Genome, Archaeal ; Hydrogen-Ion Concentration ; Microscopy, Electron, Transmission ; Mining ; Molecular Sequence Data ; Oligonucleotide Probes ; Phylogeny ; Pyrophosphatases/genetics/metabolism ; RNA, Ribosomal, 16S/genetics ; Temperature ; },
abstract = {Novel, low-abundance microbial species can be easily overlooked in standard polymerase chain reaction (PCR)-based surveys. We used community genomic data obtained without PCR or cultivation to reconstruct DNA fragments bearing unusual 16S ribosomal RNA (rRNA) and protein-coding genes from organisms belonging to novel archaeal lineages. The organisms are minor components of all biofilms growing in pH 0.5 to 1.5 solutions within the Richmond Mine, California. Probes specific for 16S rRNA showed that the fraction less than 0.45 micrometers in diameter is dominated by these organisms. Transmission electron microscope images revealed that the cells are pleomorphic with unusual folded membrane protrusions and have apparent volumes of <0.006 cubic micrometer.},
}
@article {pmid17183724,
year = {2006},
author = {Breuert, S and Allers, T and Spohn, G and Soppa, J},
title = {Regulated polyploidy in halophilic archaea.},
journal = {PloS one},
volume = {1},
number = {1},
pages = {e92},
pmid = {17183724},
issn = {1932-6203},
mesh = {Archaea/*genetics/growth &amp; development ; Base Sequence ; Chromosomes, Archaeal ; DNA Primers/genetics ; DNA, Archaeal/analysis/genetics ; Escherichia coli/genetics/growth &amp; development ; Gene Dosage ; Gene Expression Regulation, Archaeal ; Gene Expression Regulation, Developmental ; Genetic Techniques ; Genome, Archaeal ; Genome, Bacterial ; Halobacterium salinarum/genetics/growth &amp; development ; Haloferax volcanii/genetics/growth &amp; development ; Polymerase Chain Reaction ; *Polyploidy ; Replicon ; },
abstract = {Polyploidy is common in higher eukaryotes, especially in plants, but it is generally assumed that most prokaryotes contain a single copy of a circular chromosome and are therefore monoploid. We have used two independent methods to determine the genome copy number in halophilic archaea, 1) cell lysis in agarose blocks and Southern blot analysis, and 2) Real-Time quantitative PCR. Fast growing H. salinarum cells contain on average about 25 copies of the chromosome in exponential phase, and their ploidy is downregulated to 15 copies in early stationary phase. The chromosome copy number is identical in cultures with a twofold lower growth rate, in contrast to the results reported for several other prokaryotic species. Of three additional replicons of H. salinarum, two have a low copy number that is not growth-phase regulated, while one replicon even shows a higher degree of growth phase-dependent regulation than the main replicon. The genome copy number of H. volcanii is similarly high during exponential phase (on average 18 copies/cell), and it is also downregulated (to 10 copies) as the cells enter stationary phase. The variation of genome copy numbers in the population was addressed by fluorescence microscopy and by FACS analysis. These methods allowed us to verify the growth phase-dependent regulation of ploidy in H. salinarum, and they revealed that there is a wide variation in genome copy numbers in individual cells that is much larger in exponential than in stationary phase. Our results indicate that polyploidy might be more widespread in archaea (or even prokaryotes in general) than previously assumed. Moreover, the presence of so many genome copies in a prokaryote raises questions about the evolutionary significance of this strategy.},
}
@article {pmid17183489,
year = {2006},
author = {Trivedi, S and Gehlot, HS and Rao, SR},
title = {Protein thermostability in Archaea and Eubacteria.},
journal = {Genetics and molecular research : GMR},
volume = {5},
number = {4},
pages = {816-827},
pmid = {17183489},
issn = {1676-5680},
mesh = {Adaptation, Biological ; Amino Acids/metabolism ; Archaea/genetics/*metabolism ; Archaeal Proteins/*metabolism ; Bacteria/genetics/*metabolism ; Bacterial Proteins/*metabolism ; *Hot Temperature ; Structure-Activity Relationship ; *Thermodynamics ; },
abstract = {In order to survive at high temperatures, thermophilic prokaryotes (Archaea and Eubacteria) adopt different strategies. Among several important contributing factors for stability of proteins are CG-rich codons, the ratio of charged amino acids compared to uncharged amino acids, ionic interactions, amino acid preferences and their distribution, post-translational modifications, and solute accumulation. However, these factors may differ from taxon to taxon, both within and between species depending upon the composition of proteins found in these organisms. This is exemplified in the case of differences in strategies adopted by soluble proteins and membrane proteins. Therefore, it appears that no single factor or combination of factors together can be universally attributed to the provision of thermal stability in proteins.},
}
@article {pmid17183484,
year = {2006},
author = {Trivedi, S},
title = {Comparison of simple sequence repeats in 19 Archaea.},
journal = {Genetics and molecular research : GMR},
volume = {5},
number = {4},
pages = {741-772},
pmid = {17183484},
issn = {1676-5680},
mesh = {Archaea/*genetics ; Base Sequence ; *Chromosome Mapping ; Genome, Archaeal/*genetics ; Microsatellite Repeats/*genetics ; Molecular Sequence Data ; },
abstract = {All organisms that have been studied until now have been found to have differential distribution of simple sequence repeats (SSRs), with more SSRs in intergenic than in coding sequences. SSR distribution was investigated in Archaea genomes where complete chromosome sequences of 19 Archaea were analyzed with the program SPUTNIK to find di- to penta-nucleotide repeats. The number of repeats was determined for the complete chromosome sequences and for the coding and non-coding sequences. Different from what has been found for other groups of organisms, there is an abundance of SSRs in coding regions of the genome of some Archaea. Dinucleotide repeats were rare and CG repeats were found in only two Archaea. In general, trinucleotide repeats are the most abundant SSR motifs; however, pentanucleotide repeats are abundant in some Archaea. Some of the tetranucleotide and pentanucleotide repeat motifs are organism specific. In general, repeats are short and CG-rich repeats are present in Archaea having a CG-rich genome. Among the 19 Archaea, SSR density was not correlated with genome size or with optimum growth temperature. Pentanucleotide density had an inverse correlation with the CG content of the genome.},
}
@article {pmid17160628,
year = {2007},
author = {Morozova, D and Möhlmann, D and Wagner, D},
title = {Survival of methanogenic archaea from Siberian permafrost under simulated Martian thermal conditions.},
journal = {Origins of life and evolution of the biosphere : the journal of the International Society for the Study of the Origin of Life},
volume = {37},
number = {2},
pages = {189-200},
pmid = {17160628},
issn = {0169-6149},
mesh = {Archaea/metabolism/*physiology ; Cell Count ; Computer Simulation ; Ecosystem ; Environment ; Exobiology/*methods ; Extraterrestrial Environment ; Ice ; In Situ Hybridization, Fluorescence ; Mars ; Methane ; Soil Microbiology ; Temperature ; Time Factors ; Water/chemistry ; },
abstract = {Methanogenic archaea from Siberian permafrost complementary to the already well-studied methanogens from non-permafrost habitats were exposed to simulated Martian conditions. After 22 days of exposure to thermo-physical conditions at Martian low- and mid-latitudes up to 90% of methanogenic archaea from Siberian permafrost survived in pure cultures as well as in environmental samples. In contrast, only 0.3%-5.8% of reference organisms from non-permafrost habitats survived at these conditions. This suggests that methanogens from terrestrial permafrost seem to be remarkably resistant to Martian conditions. Our data also suggest that in scenario of subsurface lithoautotrophic life on Mars, methanogenic archaea from Siberian permafrost could be used as appropriate candidates for the microbial life on Mars.},
}
@article {pmid17158702,
year = {2006},
author = {Barry, ER and Bell, SD},
title = {DNA replication in the archaea.},
journal = {Microbiology and molecular biology reviews : MMBR},
volume = {70},
number = {4},
pages = {876-887},
pmid = {17158702},
issn = {1092-2172},
mesh = {Archaea/enzymology/*genetics ; Carrier Proteins/metabolism ; *DNA Replication ; DNA, Archaeal/biosynthesis ; DNA-Directed DNA Polymerase/metabolism ; Gene Expression Regulation, Archaeal/physiology ; *Genome, Archaeal ; },
abstract = {The archaeal DNA replication machinery bears striking similarity to that of eukaryotes and is clearly distinct from the bacterial apparatus. In recent years, considerable advances have been made in understanding the biochemistry of the archaeal replication proteins. Furthermore, a number of structures have now been obtained for individual components and higher-order assemblies of archaeal replication factors, yielding important insights into the mechanisms of DNA replication in both archaea and eukaryotes.},
}
@article {pmid17142313,
year = {2006},
author = {Yuan, J and Palioura, S and Salazar, JC and Su, D and O'Donoghue, P and Hohn, MJ and Cardoso, AM and Whitman, WB and Söll, D},
title = {RNA-dependent conversion of phosphoserine forms selenocysteine in eukaryotes and archaea.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {103},
number = {50},
pages = {18923-18927},
pmid = {17142313},
issn = {0027-8424},
support = {R01 GM022854/GM/NIGMS NIH HHS/United States ; R37 GM022854/GM/NIGMS NIH HHS/United States ; GM 22854/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; Escherichia coli/genetics/*metabolism ; Escherichia coli Proteins/genetics/metabolism ; Evolution, Molecular ; Gene Deletion ; Humans ; Methanococcus/genetics/*metabolism ; Phosphoserine/*metabolism ; Phylogeny ; RNA, Archaeal/*genetics ; RNA, Bacterial/*genetics ; RNA, Transfer, Amino Acyl/*genetics ; Selenocysteine/*biosynthesis ; },
abstract = {The trace element selenium is found in proteins as selenocysteine (Sec), the 21st amino acid to participate in ribosome-mediated translation. The substrate for ribosomal protein synthesis is selenocysteinyl-tRNA(Sec). Its biosynthesis from seryl-tRNA(Sec) has been established for bacteria, but the mechanism of conversion from Ser-tRNA(Sec) remained unresolved for archaea and eukarya. Here, we provide evidence for a different route present in these domains of life that requires the tRNA(Sec)-dependent conversion of O-phosphoserine (Sep) to Sec. In this two-step pathway, O-phosphoseryl-tRNA(Sec) kinase (PSTK) converts Ser-tRNA(Sec) to Sep-tRNA(Sec). This misacylated tRNA is the obligatory precursor for a Sep-tRNA:Sec-tRNA synthase (SepSecS); this protein was previously annotated as SLA/LP. The human and archaeal SepSecS genes complement in vivo an Escherichia coli Sec synthase (SelA) deletion strain. Furthermore, purified recombinant SepSecS converts Sep-tRNA(Sec) into Sec-tRNA(Sec) in vitro in the presence of sodium selenite and purified recombinant E. coli selenophosphate synthetase (SelD). Phylogenetic arguments suggest that Sec decoding was present in the last universal common ancestor. SepSecS and PSTK coevolved with the archaeal and eukaryotic lineages, but the history of PSTK is marked by several horizontal gene transfer events, including transfer to non-Sec-decoding Cyanobacteria and fungi.},
}
@article {pmid17126041,
year = {2007},
author = {Yudina, TG and Brioukhanov, AL and Zalunin, IA and Revina, LP and Shestakov, AI and Voyushina, NE and Chestukhina, GG and Netrusov, AI},
title = {Antimicrobial activity of different proteins and their fragments from Bacillus thuringiensis parasporal crystals against clostridia and archaea.},
journal = {Anaerobe},
volume = {13},
number = {1},
pages = {6-13},
doi = {10.1016/j.anaerobe.2006.09.006},
pmid = {17126041},
issn = {1075-9964},
mesh = {Archaea/*drug effects ; Bacillus thuringiensis/*chemistry/metabolism ; Bacillus thuringiensis Toxins ; Bacterial Proteins/chemistry/isolation &amp; purification/*pharmacology ; Bacterial Toxins/chemistry/isolation &amp; purification/*pharmacology ; Clostridium/*drug effects ; Electrophoresis, Polyacrylamide Gel/methods ; Endotoxins/chemistry/isolation &amp; purification/*pharmacology ; Hemolysin Proteins/chemistry/isolation &amp; purification/*pharmacology ; Microbial Sensitivity Tests ; Peptide Fragments/chemistry/*pharmacology ; },
abstract = {Proteins of parasporal crystals (Cry proteins) from entomopathogenic bacterium Bacillus thuringiensis (subspecies kurstaki, galleriae, tenebrionis) as well as some fragments of these proteins, obtained by limited proteolysis, are capable of antimicrobial action against anaerobic bacteria and archaea-Clostridium butyricum, Clostridium acetobutylicum and Methanosarcina barkeri. The MICs are 45-150 microg/mL. Electron microscopy showed that lysis of M. barkeri cells in the presence of 49kDa fragment of Cry3Aa toxin is generally similar to the bacterial cell lysis, which has been previously detected in the presence of Cry11A, Cry1Ab and other Cry proteins. The Cry1D-like toxin from crystals of B. thuringiensis subsp. galleriae has been put forward as an example of the supposition that cell wall and some of its components like teichoic acid and N-acetylgalactosamine have possible influence on Cry toxins, enhancing their antimicrobial activity. The possible ecological role of the antimicrobial activity of Cry proteins is also discussed.},
}
@article {pmid17123129,
year = {2007},
author = {Iro, M and Klein, R and Gálos, B and Baranyi, U and Rössler, N and Witte, A},
title = {The lysogenic region of virus phiCh1: identification of a repressor-operator system and determination of its activity in halophilic Archaea.},
journal = {Extremophiles : life under extreme conditions},
volume = {11},
number = {2},
pages = {383-396},
pmid = {17123129},
issn = {1431-0651},
mesh = {Archaeal Viruses/*genetics/metabolism ; Gene Expression Regulation, Viral/physiology ; Halobacteriales/genetics/*virology ; Lysogeny/*genetics ; Mutation ; Open Reading Frames ; *Operator Regions, Genetic ; Promoter Regions, Genetic ; Repressor Proteins/*genetics ; Transcription, Genetic/physiology ; Viral Proteins/*genetics/metabolism ; },
abstract = {phiCh1 is a temperate virus infecting the haloalkaliphilic archaeon Natrialba magadii. As for all temperate viruses, a control of the lysogenic state versus the lytic life cycle is essential. Two open reading frames (ORFs) have been identified as putative repressor encoding genes: ORF48 and ORF49. The protein of ORF48 showed sequence similarities to putative repressor molecules. ORF49 was identified by the analysis of a mutant of phiCh1: the lysogenic strain carrying mutant phiCh1-1 showed a different lysis behavior than wild type virus phiCh1, indicating a dysfunction in the regulation of gene expression. Here, we show that the intergenic region between ORF48 and ORF49 comprises a promoter/operator sequence that is a transcriptionally active region in the model system Haloferax volcanii. Transcription from this region can be repressed by the activity of the ORF48 gene product. Gp43/gp44 has an enhancing effect on this regulatory sequence. Evidence is given for a possible binding site of Rep and gp43/gp44 within the coding region of the rep gene.},
}
@article {pmid17122405,
year = {2007},
author = {Kendall, MM and Wardlaw, GD and Tang, CF and Bonin, AS and Liu, Y and Valentine, DL},
title = {Diversity of Archaea in marine sediments from Skan Bay, Alaska, including cultivated methanogens, and description of Methanogenium boonei sp. nov.},
journal = {Applied and environmental microbiology},
volume = {73},
number = {2},
pages = {407-414},
pmid = {17122405},
issn = {0099-2240},
mesh = {Acetates/metabolism ; Alaska ; Carbon Dioxide/metabolism ; Crenarchaeota/*classification/genetics/growth &amp; development/isolation &amp; purification ; Culture Media ; DNA, Archaeal/analysis ; Euryarchaeota/*classification/genetics/growth &amp; development/isolation &amp; purification ; Geologic Sediments/*microbiology ; Methane/*metabolism ; Methanomicrobiaceae/*classification/genetics/growth &amp; development/isolation &amp; purification ; Methanosarcinales/classification/genetics/growth &amp; development/isolation &amp; purification ; Molecular Sequence Data ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; Sequence Analysis, DNA ; },
abstract = {Methanogenesis in cold marine sediments is a globally important process leading to methane hydrate deposits, cold seeps, physical instability of sediment, and atmospheric methane emissions. We employed a multidisciplinary approach that combined culture-dependent and -independent analyses with geochemical measurements in the sediments of Skan Bay, Alaska (53 degrees N, 167 degrees W), to investigate methanogenesis there. Cultivation-independent analyses of the archaeal community revealed that uncultivated microbes of the kingdoms Euryarchaeota and Crenarchaeota are present at Skan Bay and that methanogens constituted a small proportion of the archaeal community. Methanogens were cultivated from depths of 0 to 60 cm in the sediments, and several strains related to the orders Methanomicrobiales and Methanosarcinales were isolated. Isolates were psychrotolerant marine-adapted strains and included an aceticlastic methanogen, strain AK-6, as well as three strains of CO(2)-reducing methanogens: AK-3, AK7, and AK-8. The phylogenetic positions and physiological characteristics of these strains are described. We propose a new species, Methanogenium boonei, with strain AK-7 as the type strain.},
}
@article {pmid17121273,
year = {2006},
author = {Roberts, MF},
title = {Inositol in bacteria and archaea.},
journal = {Sub-cellular biochemistry},
volume = {39},
number = {},
pages = {103-133},
doi = {10.1007/0-387-27600-9_5},
pmid = {17121273},
issn = {0306-0225},
support = {GM60418/GM/NIGMS NIH HHS/United States ; },
mesh = {Amino Acid Sequence ; Archaea/*metabolism ; Bacteria/*metabolism ; Inositol/*chemistry/*metabolism ; Molecular Sequence Data ; },
}
@article {pmid17120127,
year = {2006},
author = {Cobucci-Ponzano, B and Rossi, M and Moracci, M},
title = {Interrupted genes in extremophilic archaea: mechanisms of gene expression in early organisms.},
journal = {Origins of life and evolution of the biosphere : the journal of the International Society for the Study of the Origin of Life},
volume = {36},
number = {5-6},
pages = {487-492},
pmid = {17120127},
issn = {0169-6149},
mesh = {Amino Acid Sequence ; Archaea/*genetics/growth &amp; development ; Archaeal Proteins/*genetics ; Base Sequence ; Evolution, Molecular ; Gene Expression Regulation, Archaeal ; *Genes, Archaeal ; Molecular Sequence Data ; Sequence Alignment ; Time Factors ; },
abstract = {Extremophilic Archaea populate biotopes previously considered inaccessible for life. This feature, and the possibility that they are the extant forms of life closest to the last common ancestor, make these organisms excellent candidates for the study of evolution on Earth and stimulate the exobiological research in planets previously considered totally inhospitable. Among the other aspects of the physiology of these organisms, the study of the molecular genetics of extremophilic Archaea can give hints on how the genetic information is transmitted and propagated in ancient forms of life. We review here the expression of interrupted genes in a recently discovered nanoarchaeon and the mechanisms of reprogrammed genetic decoding in Archaea.},
}
@article {pmid17111090,
year = {2007},
author = {Edgcomb, VP and Molyneaux, SJ and Böer, S and Wirsen, CO and Saito, M and Atkins, MS and Lloyd, K and Teske, A},
title = {Survival and growth of two heterotrophic hydrothermal vent archaea, Pyrococcus strain GB-D and Thermococcus fumicolans, under low pH and high sulfide concentrations in combination with high temperature and pressure regimes.},
journal = {Extremophiles : life under extreme conditions},
volume = {11},
number = {2},
pages = {329-342},
pmid = {17111090},
issn = {1431-0651},
mesh = {Hot Temperature ; Hydrogen-Ion Concentration ; Oxidation-Reduction ; Pressure ; Pyrococcus/*growth &amp; development ; Sulfides/*metabolism ; Thermococcus/*growth &amp; development ; },
abstract = {Growth and survival of hyperthermophilic archaea in their extreme hydrothermal vent and subsurface environments are controlled by chemical and physical key parameters. This study examined the effects of elevated sulfide concentrations, temperature, and acidic pH on growth and survival of two hydrothermal vent archaea (Pyrococcus strain GB-D and Thermococcus fumicolans) under high temperature and pressure regimes. These two strains are members of the Thermococcales, a family of hyperthermophilic, heterotrophic, sulfur-reducing archaea that occur in high densities at vent sites. As actively growing cells, these two strains tolerated regimes of pH, pressure, and temperature that were in most cases not tolerated under severe substrate limitation. A moderate pH of 5.5-7 extends their survival and growth range over a wider range of sulfide concentrations, temperature and pressure, relative to lower pH conditions. T. fumicolans and Pyrococcus strain GB-D grew under very high pressures that exceeded in-situ pressures typical of hydrothermal vent depths, and included deep subsurface pressures. However, under the same conditions, but in the absence of carbon substrates and electron acceptors, survival was generally lower, and decreased rapidly when low pH stress was combined with high pressure and high temperature.},
}
@article {pmid17085711,
year = {2007},
author = {Weidler, GW and Dornmayr-Pfaffenhuemer, M and Gerbl, FW and Heinen, W and Stan-Lotter, H},
title = {Communities of archaea and bacteria in a subsurface radioactive thermal spring in the Austrian Central Alps, and evidence of ammonia-oxidizing Crenarchaeota.},
journal = {Applied and environmental microbiology},
volume = {73},
number = {1},
pages = {259-270},
pmid = {17085711},
issn = {0099-2240},
support = {P 19250/FWF_/Austrian Science Fund FWF/Austria ; },
mesh = {Ammonia/*metabolism ; Archaea/*classification/genetics/growth &amp; development ; Austria ; Bacteria/*classification/genetics/growth &amp; development ; Biofilms/growth &amp; development ; Crenarchaeota/classification/isolation &amp; purification ; DNA, Archaeal/analysis ; DNA, Bacterial/analysis ; Ecosystem ; Hot Springs/chemistry/*microbiology ; Molecular Sequence Data ; Oxidation-Reduction ; Oxidoreductases/genetics ; Proteobacteria/classification/genetics/growth &amp; development ; RNA, Ribosomal, 16S/genetics ; *Radium ; *Radon ; Sequence Analysis, DNA ; },
abstract = {Scanning electron microscopy revealed great morphological diversity in biofilms from several largely unexplored subterranean thermal Alpine springs, which contain radium 226 and radon 222. A culture-independent molecular analysis of microbial communities on rocks and in the water of one spring, the "Franz-Josef-Quelle" in Bad Gastein, Austria, was performed. Four hundred fifteen clones were analyzed. One hundred thirty-two sequences were affiliated with 14 bacterial operational taxonomic units (OTUs) and 283 with four archaeal OTUs. Rarefaction analysis indicated a high diversity of bacterial sequences, while archaeal sequences were less diverse. The majority of the cloned archaeal 16S rRNA gene sequences belonged to the soil-freshwater-subsurface (1.1b) crenarchaeotic group; other representatives belonged to the freshwater-wastewater-soil (1.3b) group, except one clone, which was related to a group of uncultivated Euryarchaeota. These findings support recent reports that Crenarchaeota are not restricted to high-temperature environments. Most of the bacterial sequences were related to the Proteobacteria (alpha, beta, gamma, and delta), Bacteroidetes, and Planctomycetes. One OTU was allied with Nitrospina sp. (delta-Proteobacteria) and three others grouped with Nitrospira. Statistical analyses suggested high diversity based on 16S rRNA gene analyses; the rarefaction plot of archaeal clones showed a plateau. Since Crenarchaeota have been implicated recently in the nitrogen cycle, the spring environment was probed for the presence of the ammonia monooxygenase subunit A (amoA) gene. Sequences were obtained which were related to crenarchaeotic amoA genes from marine and soil habitats. The data suggested that nitrification processes are occurring in the subterranean environment and that ammonia may possibly be an energy source for the resident communities.},
}
@article {pmid17085694,
year = {2007},
author = {Saengkerdsub, S and Anderson, RC and Wilkinson, HH and Kim, WK and Nisbet, DJ and Ricke, SC},
title = {Identification and quantification of methanogenic Archaea in adult chicken ceca.},
journal = {Applied and environmental microbiology},
volume = {73},
number = {1},
pages = {353-356},
pmid = {17085694},
issn = {0099-2240},
mesh = {Animals ; Archaea/*classification/genetics/*isolation &amp; purification/metabolism ; Cecum/*microbiology ; Chickens/*microbiology ; DNA, Archaeal/analysis ; Female ; Methane/*metabolism ; Methanobrevibacter/classification/genetics/isolation &amp; purification/metabolism ; Molecular Sequence Data ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; },
abstract = {By using molecular methods for the identification and quantification of methanogenic archaea in adult chicken ceca, 16S rRNA genes of 11 different phylotypes, 10 of which were 99% similar to Methanobrevibacter woesei, were found. Methanogen populations, as assessed by cultivation, and the 16S rRNA copy number were between 6.38 and 8.23 cells/g (wet weight) and 5.50 and 7.19 log(10)/g (wet weight), respectively.},
}
@article {pmid17071750,
year = {2007},
author = {Yurist, S and Dahan, I and Eichler, J},
title = {SRP19 is a dispensable component of the signal recognition particle in Archaea.},
journal = {Journal of bacteriology},
volume = {189},
number = {1},
pages = {276-279},
pmid = {17071750},
issn = {0021-9193},
mesh = {Archaea/*metabolism ; Archaeal Proteins/*metabolism ; RNA, Archaeal/metabolism ; Signal Recognition Particle/*metabolism/physiology ; },
abstract = {In vitro, archaeal SRP54 binds SRP RNA in the absence of SRP19, suggesting the latter to be expendable in Archaea. Accordingly, the Haloferax volcanii SRP19 gene was deleted. Although normally transcribed at a level comparable to that of the essential SRP54 gene, SRP19 deletion had no effect on cell growth, membrane protein insertion, protein secretion, or ribosome levels. The absence of SRP19 did, however, increase membrane bacterioruberin levels.},
}
@article {pmid17070673,
year = {2006},
author = {Juottonen, H and Galand, PE and Yrjälä, K},
title = {Detection of methanogenic Archaea in peat: comparison of PCR primers targeting the mcrA gene.},
journal = {Research in microbiology},
volume = {157},
number = {10},
pages = {914-921},
doi = {10.1016/j.resmic.2006.08.006},
pmid = {17070673},
issn = {0923-2508},
mesh = {Amino Acid Sequence ; Archaea/genetics/*isolation &amp; purification ; Biodiversity ; *DNA Primers ; Molecular Sequence Data ; Oxidoreductases/*genetics ; Phylogeny ; Polymerase Chain Reaction/methods ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; },
abstract = {Methanogens (domain Archaea) have a unique role in the carbon cycle as producers of the greenhouse gas methane (CH(4)). Methyl-coenzyme M reductase (MCR) is a vital enzyme in CH(4) production, and the mcrA gene coding for a subunit of MCR has been employed as a specific marker for the detection and differentiation of methanogen communities. A critical step in assessing environmental mcrA diversity is the selection of PCR primers. The objective of this study was to compare the diversity coverage of three published mcrA primer sets MCR, ME and ML (also known as MCR and Luton-mcrA) and their ability to discern methanogen communities in a drained peatland. The primers were applied to DNA extracts from unfertilised and ash-fertilised peat from two different depths. Amplified mcrA communities were cloned and sequenced, and the sequences were divided into operational taxonomic units (OTUs) by restriction fragment length polymorphism (RFLP) and sequence analysis. All primers recovered characteristic OTUs associated with the peat depths and treatments and confirmed a previous observation of low methanogen diversity. The minor differences in OTU ranges of the primers did not greatly affect the observed community composition. However, as the proportions of several OTUs varied strongly, the primers provided different quantitative representations of mcrA communities. We concluded that the ML and MCR primers had better amplification ranges than the ME set, but the use of MCR with peat samples was problematic due to poor amplification. Consequently, the ML primers were best suited for mcrA analysis of peatland methanogen communities.},
}
@article {pmid17065466,
year = {2006},
author = {Portnoy, V and Schuster, G},
title = {RNA polyadenylation and degradation in different Archaea; roles of the exosome and RNase R.},
journal = {Nucleic acids research},
volume = {34},
number = {20},
pages = {5923-5931},
pmid = {17065466},
issn = {1362-4962},
mesh = {Archaea/*enzymology/genetics ; Euryarchaeota/enzymology/genetics ; Exoribonucleases/*metabolism ; *Gene Expression Regulation, Archaeal ; Genes, Archaeal ; Haloferax volcanii/enzymology/genetics ; Nucleic Acid Conformation ; *Polyadenylation ; RNA, Archaeal/chemistry/*metabolism ; },
abstract = {Polyadenylation is a process common to almost all organisms. In eukaryotes, stable poly(A)-tails, important for mRNA stability and translation initiation, are added to the 3' ends of most mRNAs. Contrarily, polyadenylation can stimulate RNA degradation, a phenomenon witnessed in prokaryotes, organelles and recently, for nucleus-encoded RNA as well. Polyadenylation takes place in hyperthermophilic archaea and is mediated by the archaeal exosome, but no RNA polyadenylation was detected in halophiles. Here, we analyzed polyadenylation in the third archaea group, the methanogens, in which some members contain genes encoding the exosome but others lack these genes. Polyadenylation was found in the methanogen, Methanopyrus kandleri, containing the exosome genes, but not in members which lack these genes. To explore how RNA is degraded in the absence of the exosome and without polyadenylation, we searched for the exoribonuclease that is involved in this process. No homologous proteins for any other known exoribonuclease were detected in this group. However, the halophilic archaea contain a gene homologous to the exoribonuclease RNase R. This ribonuclease is not able to degrade structured RNA better than PNPase. RNase R, which appears to be the only exoribonucleases in Haloferax volcanii, was found to be essential for viability.},
}
@article {pmid17065082,
year = {2006},
author = {Clausen, AR and Matakos, A and Sandrini, MP and Piskur, J},
title = {Thymidine kinases in archaea.},
journal = {Nucleosides, nucleotides &amp; nucleic acids},
volume = {25},
number = {9-11},
pages = {1159-1163},
doi = {10.1080/15257770600894485},
pmid = {17065082},
issn = {1525-7770},
mesh = {Amino Acid Sequence ; Animals ; Archaea/*enzymology ; Archaeal Proteins/*chemistry ; Bacterial Proteins/chemistry ; Databases, Genetic ; Evolution, Molecular ; *Gene Expression Regulation ; Humans ; Molecular Sequence Data ; Phosphotransferases (Alcohol Group Acceptor)/chemistry ; Phylogeny ; Species Specificity ; Thymidine Kinase/*biosynthesis ; },
abstract = {Twenty-six fully sequenced archaeal genomes were searched for genes coding for putative deoxyribonucleoside kinases (dNKs). We identified only 5 human-like thymidine kinase 1 genes (TK1s) and none for non-TK1 kinases. Four TK1s were identified in the Euryarchaea and one was found in the Crenarchaea, while none was found in Nanoarchaeum. The identified TK1s have high identity to Gram-positive bacteria TK1s. The TK1s from archaea, Gram-positive bacteria and eukaryotes share the same common ancestor, while the TK1s from Gram-negative bacteria belong to a less-related subgroup. It seems that a functional deoxyribonucleoside salvage pathway is not crucial for the archaeal cell.},
}
@article {pmid17059478,
year = {2007},
author = {Wilms, R and Sass, H and Köpke, B and Cypionka, H and Engelen, B},
title = {Methane and sulfate profiles within the subsurface of a tidal flat are reflected by the distribution of sulfate-reducing bacteria and methanogenic archaea.},
journal = {FEMS microbiology ecology},
volume = {59},
number = {3},
pages = {611-621},
doi = {10.1111/j.1574-6941.2006.00225.x},
pmid = {17059478},
issn = {0168-6496},
mesh = {Anaerobiosis ; Archaea/classification/genetics/*isolation &amp; purification/metabolism ; Bacteria/classification/genetics/*isolation &amp; purification/metabolism ; Colony Count, Microbial ; *Ecosystem ; Electrophoresis, Gel, Two-Dimensional ; Genes, Archaeal/genetics ; Genes, Bacterial/genetics ; Germany ; *Marine Biology ; Methane/analysis/metabolism ; Oxidation-Reduction ; Polymerase Chain Reaction ; Species Specificity ; Sulfates/analysis/metabolism ; Water/*analysis ; *Water Microbiology ; },
abstract = {The anoxic layers of marine sediments are dominated by sulfate reduction and methanogenesis as the main terminal oxidation processes. The aim of this study was to analyze the vertical succession of microbial populations involved in these processes along the first 4.5 m of a tidal-flat sediment. Therefore, a quantitative PCR approach was applied using primers targeting the domains of Bacteria and Archaea, and key functional genes for sulfate reduction (dsrA) and methanogenesis (mcrA). The sampling site was characterized by an unusual sulfate peak at 250 cm depth resulting in separate sulfate-methane transition zones. Methane and sulfate profiles were diametrically opposed, with a methane maximum in the sulfate-depleted zone showing high numbers of archaea and methanogens. The methane-sulfate interfaces harbored elevated numbers of sulfate reducers, and revealed a slight increase in mcrA and archaeal 16S rRNA genes, suggesting sulfate-dependent anaerobic oxidation of methane. A diversity analysis of both functional genes by PCR-denaturing gradient gel electrophoresis revealed a vertical succession of subpopulations that were governed by geochemical and sedimentologic conditions. Along the upper 200 cm, sulfate-reducing populations appeared quite uniform and were dominated by the Deltaproteobacteria. In the layers beneath, an apparent increase in diversity and a shift to the Firmicutes as the predominant group was observed.},
}
@article {pmid17053098,
year = {2006},
author = {Shcherbakov, D and Dontsova, M and Tribus, M and Garber, M and Piendl, W},
title = {Stability of the 'L12 stalk' in ribosomes from mesophilic and (hyper)thermophilic Archaea and Bacteria.},
journal = {Nucleic acids research},
volume = {34},
number = {20},
pages = {5800-5814},
pmid = {17053098},
issn = {1362-4962},
mesh = {Archaea/*genetics ; Archaeal Proteins/metabolism ; Bacteria/*genetics ; Bacterial Proteins/metabolism ; Base Sequence ; Binding Sites ; Molecular Sequence Data ; Protein Binding ; RNA, Archaeal/chemistry/metabolism ; RNA, Ribosomal, 23S/*chemistry/metabolism ; Ribosomal Protein L10 ; Ribosomal Proteins/*metabolism ; Temperature ; },
abstract = {The ribosomal stalk complex, consisting of one molecule of L10 and four or six molecules of L12, is attached to 23S rRNA via protein L10. This complex forms the so-called 'L12 stalk' on the 50S ribosomal subunit. Ribosomal protein L11 binds to the same region of 23S rRNA and is located at the base of the 'L12 stalk'. The 'L12 stalk' plays a key role in the interaction of the ribosome with translation factors. In this study stalk complexes from mesophilic and (hyper)thermophilic species of the archaeal genus Methanococcus and from the Archaeon Sulfolobus solfataricus, as well as from the Bacteria Escherichia coli, Geobacillus stearothermophilus and Thermus thermophilus, were overproduced in E.coli and purified under non-denaturing conditions. Using filter-binding assays the affinities of the archaeal and bacterial complexes to their specific 23S rRNA target site were analyzed at different pH, ionic strength and temperature. Affinities of both archaeal and bacterial complexes for 23S rRNA vary by more than two orders of magnitude, correlating very well with the growth temperatures of the organisms. A cooperative effect of binding to 23S rRNA of protein L11 and the L10/L12(4) complex from mesophilic and thermophilic Archaea was shown to be temperature-dependent.},
}
@article {pmid17041631,
year = {2006},
author = {Prangishvili, D and Forterre, P and Garrett, RA},
title = {Viruses of the Archaea: a unifying view.},
journal = {Nature reviews. Microbiology},
volume = {4},
number = {11},
pages = {837-848},
doi = {10.1038/nrmicro1527},
pmid = {17041631},
issn = {1740-1534},
mesh = {Archaea/*virology ; Archaeal Viruses/*classification/*genetics/ultrastructure ; Biological Evolution ; Genome, Viral ; },
abstract = {DNA viruses of the Archaea have highly diverse and often exceptionally complex morphotypes. Many have been isolated from geothermally heated hot environments, raising intriguing questions about their origins, and contradicting the widespread notion of limited biodiversity in extreme environments. Here, we provide a unifying view on archaeal viruses, and present them as a particular assemblage that is fundamentally different in morphotype and genome from the DNA viruses of the other two domains of life, the Bacteria and Eukarya.},
}
@article {pmid17027372,
year = {2007},
author = {Zumft, WG and Kroneck, PM},
title = {Respiratory transformation of nitrous oxide (N2O) to dinitrogen by Bacteria and Archaea.},
journal = {Advances in microbial physiology},
volume = {52},
number = {},
pages = {107-227},
doi = {10.1016/S0065-2911(06)52003-X},
pmid = {17027372},
issn = {0065-2911},
mesh = {Amino Acid Sequence ; Archaea/enzymology/genetics/*metabolism ; Bacteria/enzymology/genetics/*metabolism ; Models, Molecular ; Molecular Sequence Data ; Nitrogen/*metabolism ; Nitrous Oxide/*metabolism ; Oxidoreductases/chemistry/genetics/metabolism ; Phylogeny ; Sequence Alignment ; },
abstract = {N2O is a potent greenhouse gas and stratospheric reactant that has been steadily on the rise since the beginning of industrialization. It is an obligatory inorganic metabolite of denitrifying bacteria, and some production of N2O is also found in nitrifying and methanotrophic bacteria. We focus this review on the respiratory aspect of N2O transformation catalysed by the multicopper enzyme nitrous oxide reductase (N2OR) that provides the bacterial cell with an electron sink for anaerobic growth. Two types of Cu centres discovered in N2OR were both novel structures among the Cu proteins: the mixed-valent dinuclear Cu(A) species at the electron entry site of the enzyme, and the tetranuclear Cu(Z) centre as the first catalytically active Cu-sulfur complex known. Several accessory proteins function as Cu chaperone and ABC transporter systems for the biogenesis of the catalytic centre. We describe here the paradigm of Z-type N2OR, whose characteristics have been studied in most detail in the genera Pseudomonas and Paracoccus. Sequenced bacterial genomes now provide an invaluable additional source of information. New strains harbouring nos genes and capability of N2O utilization are being uncovered. This reveals previously unknown relationships and allows pattern recognition and predictions. The core nos genes, nosZDFYL, share a common phylogeny. Most principal taxonomic lineages follow the same biochemical and genetic pattern and share the Z-type enzyme. A modified N2OR is found in Wolinella succinogenes, and circumstantial evidence also indicates for certain Archaea another type of N2OR. The current picture supports the view of evolution of N2O respiration prior to the separation of the domains Bacteria and Archaea. Lateral nos gene transfer from an epsilon-proteobacterium as donor is suggested for Magnetospirillum magnetotacticum and Dechloromonas aromatica. In a few cases, nos gene clusters are plasmid borne. Inorganic N2O metabolism is associated with a diversity of physiological traits and biochemically challenging metabolic modes or habitats, including halorespiration, diazotrophy, symbiosis, pathogenicity, psychrophily, thermophily, extreme halophily and the marine habitat down to the greatest depth. Components for N2O respiration cover topologically the periplasm and the inner and outer membranes. The Sec and Tat translocons share the task of exporting Nos components to their functional sites. Electron donation to N2OR follows pathways with modifications depending on the host organism. A short chronology of the field is also presented.},
}
@article {pmid17021241,
year = {2006},
author = {Fuchsman, CA and Rocap, G},
title = {Whole-genome reciprocal BLAST analysis reveals that planctomycetes do not share an unusually large number of genes with Eukarya and Archaea.},
journal = {Applied and environmental microbiology},
volume = {72},
number = {10},
pages = {6841-6844},
pmid = {17021241},
issn = {0099-2240},
mesh = {Archaea/*genetics ; Bacteria/classification/*genetics ; Base Sequence ; Genes, Archaeal/*genetics ; Genes, Bacterial/*genetics ; Molecular Sequence Data ; Sequence Alignment ; Sequence Homology, Nucleic Acid ; Software ; },
abstract = {The genome sequences of Rhodopirellula baltica, formerly Pirellula sp. strain 1, Blastopirellula marina, Gemmata obscuriglobus, and Kuenenia stuttgartiensis were used in a series of pairwise reciprocal best-hit analyses to evaluate the contested evolutionary position of Planctomycetes. Contrary to previous reports which suggested that R. baltica had a high percentage of genes with closest matches to Archaea and Eukarya, we show here that these Planctomycetes do not share an unusually large number of genes with the Archaea or Eukarya, compared with other Bacteria. Thus, best-hit analyses may assign phylogenetic affinities incorrectly if close relatives are absent from the sequence database.},
}
@article {pmid17012598,
year = {2006},
author = {Beman, JM and Francis, CA},
title = {Diversity of ammonia-oxidizing archaea and bacteria in the sediments of a hypernutrified subtropical estuary: Bahía del Tóbari, Mexico.},
journal = {Applied and environmental microbiology},
volume = {72},
number = {12},
pages = {7767-7777},
pmid = {17012598},
issn = {0099-2240},
mesh = {Ammonia/*metabolism ; *Crenarchaeota/classification/genetics/isolation &amp; purification ; *Ecosystem ; Geologic Sediments/*microbiology ; Mexico ; Molecular Sequence Data ; *Nitrosomonas/classification/genetics/isolation &amp; purification ; Oxidation-Reduction ; Oxidoreductases/genetics/metabolism ; Phylogeny ; Seawater/*microbiology ; Sequence Analysis, DNA ; },
abstract = {Nitrification within estuarine sediments plays an important role in the nitrogen cycle, both at the global scale and in individual estuaries. Although bacteria were once thought to be solely responsible for catalyzing the first and rate-limiting step of this process, several recent studies have suggested that mesophilic Crenarchaeota are capable of performing ammonia oxidation. Here we examine the diversity (richness and community composition) of ammonia-oxidizing archaea (AOA) and bacteria (AOB) within sediments of Bahía del Tóbari, a hypernutrified estuary receiving substantial amounts of ammonium in agricultural runoff. Using PCR primers designed to specifically target the archaeal ammonia monooxygenase alpha-subunit (amoA) gene, we found AOA to be present at five sampling sites within this estuary and at two sampling time points (January and October 2004). In contrast, the bacterial amoA gene was PCR amplifiable from only 40% of samples. Bacterial amoA libraries were dominated by a few widely distributed Nitrosomonas-like sequence types, whereas AOA diversity showed significant variation in both richness and community composition. AOA communities nevertheless exhibited consistent spatial structuring, with two distinct end member assemblages recovered from the interior and the mouths of the estuary and a mixed assemblage from an intermediate site. These findings represent the first detailed examination of archaeal amoA diversity in estuarine sediments and demonstrate that diverse communities of Crenarchaeota capable of ammonia oxidation are present within estuaries, where they may be actively involved in nitrification.},
}
@article {pmid17012592,
year = {2006},
author = {de Bok, FA and van Leerdam, RC and Lomans, BP and Smidt, H and Lens, PN and Janssen, AJ and Stams, AJ},
title = {Degradation of methanethiol by methylotrophic methanogenic archaea in a lab-scale upflow anaerobic sludge blanket reactor.},
journal = {Applied and environmental microbiology},
volume = {72},
number = {12},
pages = {7540-7547},
pmid = {17012592},
issn = {0099-2240},
mesh = {Anaerobiosis ; Biodegradation, Environmental ; *Bioreactors ; Industrial Waste ; Laboratories ; Methanobacterium/genetics/growth &amp; development/metabolism ; Methanosarcinaceae/classification/genetics/growth &amp; development/*metabolism ; Molecular Sequence Data ; *Paper ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sewage/*microbiology ; Sulfhydryl Compounds/*metabolism ; Waste Disposal, Fluid/*methods ; },
abstract = {In a lab-scale upflow anaerobic sludge blanket reactor inoculated with granular sludge from a full-scale wastewater treatment plant treating paper mill wastewater, methanethiol (MT) was degraded at 30 degrees C to H2S, CO2, and CH4. At a hydraulic retention time of 9 h, a maximum influent concentration of 6 mM MT was applied, corresponding to a volumetric loading rate of 16.5 mmol liter-1 day-1. The archaeal community within the reactor was characterized by anaerobic culturing and denaturing gradient gel electrophoresis analysis, cloning, and sequencing of 16S rRNA genes and quantitative PCR. Initially, MT-fermenting methanogenic archaea related to members of the genus Methanolobus were enriched in the reactor. Later, they were outcompeted by Methanomethylovorans hollandica, which was detected in aggregates but not inside the granules that originated from the inoculum, the microbial composition of which remained fairly unchanged. Possibly other species within the Methanosarcinacaea also contributed to the fermentation of MT, but they were not enriched by serial dilution in liquid media. The archaeal community within the granules, which was dominated by Methanobacterium beijingense, did not change substantially during the reactor operation. Some of the species related to Methanomethylovorans hollandica were enriched by serial dilutions, but their growth rates were very low. Interestingly, the enrichments could be sustained only in the presence of MT and did not utilize any of the other typical substrates for methylotrophic methanogens, such as methanol, methyl amine, or dimethylsulfide.},
}
@article {pmid17008219,
year = {2006},
author = {Wächtershäuser, G},
title = {From volcanic origins of chemoautotrophic life to Bacteria, Archaea and Eukarya.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {361},
number = {1474},
pages = {1787-806; discussion 1806-8},
pmid = {17008219},
issn = {0962-8436},
mesh = {Archaea/genetics/*metabolism ; Bacteria/genetics/*metabolism ; *Biological Evolution ; *Chemoautotrophic Growth ; Eukaryotic Cells/*metabolism ; Evolution, Chemical ; Origin of Life ; *Volcanic Eruptions ; },
abstract = {The theory of a chemoautotrophic origin of life in a volcanic iron-sulphur world postulates a pioneer organism at sites of reducing volcanic exhalations. The pioneer organism is characterized by a composite structure with an inorganic substructure and an organic superstructure. Within the surfaces of the inorganic substructure iron, cobalt, nickel and other transition metal centres with sulphido, carbonyl and other ligands were catalytically active and promoted the growth of the organic superstructure through carbon fixation, driven by the reducing potential of the volcanic exhalations. This pioneer metabolism was reproductive by an autocatalytic feedback mechanism. Some organic products served as ligands for activating catalytic metal centres whence they arose. The unitary structure-function relationship of the pioneer organism later gave rise to two major strands of evolution: cellularization and emergence of the genetic machinery. This early phase of evolution ended with segregation of the domains Bacteria, Archaea and Eukarya from a rapidly evolving population of pre-cells. Thus, life started with an initial, direct, deterministic chemical mechanism of evolution giving rise to a later, indirect, stochastic, genetic mechanism of evolution and the upward evolution of life by increase of complexity is grounded ultimately in the synthetic redox chemistry of the pioneer organism.},
}
@article {pmid16997958,
year = {2006},
author = {Sun, C and Zhou, M and Li, Y and Xiang, H},
title = {Molecular characterization of the minimal replicon and the unidirectional theta replication of pSCM201 in extremely halophilic archaea.},
journal = {Journal of bacteriology},
volume = {188},
number = {23},
pages = {8136-8144},
pmid = {16997958},
issn = {0021-9193},
mesh = {Base Sequence ; *DNA Replication ; DNA, Archaeal/*genetics/ultrastructure ; Haloarcula/*genetics ; Microscopy, Electron ; Molecular Sequence Data ; *Plasmids/ultrastructure ; RNA, Archaeal/genetics ; RNA, Ribosomal, 16S/genetics ; Replication Origin/genetics ; Replicon/*genetics ; },
abstract = {A 3,463-bp plasmid, pSCM201, was isolated from a halophilic archaeon, Haloarcula sp. strain AS7094. The minimal replicon that is essential and sufficient for autonomous replication and stable maintenance in Haloarcula hispanica was determined by deletion analysis of the plasmid. This minimal replicon (approximately 1.8 kb) consisted of only two functionally related segments: (i) a putative origin (ori201) containing an AT-rich region and sets of repeats and (ii) an adjacent gene encoding a putative replication initiation protein (Rep201). Electron microscopic observation and Southern blotting analysis demonstrated that pSCM201 replicates via a theta mechanism. Precise mapping of the putative origin suggested that the replication initiated from a fixed site close to the AT-rich region and proceeded unidirectionally toward the downstream rep201 gene, which was further confirmed by electron microscopic analysis of the ClaI-digested replication intermediates. To our knowledge, this is the first unidirectional theta replication plasmid experimentally identified in the domain of archaea. It provides a novel plasmid system to conduct research on archaeal DNA replication.},
}
@article {pmid16984812,
year = {2006},
author = {Maupin-Furlow, JA and Humbard, MA and Kirkland, PA and Li, W and Reuter, CJ and Wright, AJ and Zhou, G},
title = {Proteasomes from structure to function: perspectives from Archaea.},
journal = {Current topics in developmental biology},
volume = {75},
number = {},
pages = {125-169},
doi = {10.1016/S0070-2153(06)75005-0},
pmid = {16984812},
issn = {0070-2153},
support = {R01 GM057498/GM/NIGMS NIH HHS/United States ; },
mesh = {Archaea/*chemistry/*enzymology ; Archaeal Proteins/*chemistry/*physiology ; Proteasome Endopeptidase Complex/*chemistry/*physiology ; Structure-Activity Relationship ; },
abstract = {Insight into the world of proteolysis has expanded considerably over the past decade. Energy-dependent proteases, such as the proteasome, are no longer viewed as nonspecific degradative enzymes associated solely with protein catabolism but are intimately involved in controlling biological processes that span life to death. The proteasome maintains this exquisite control by catalyzing the precisely timed and rapid turnover of key regulatory proteins. Proteasomes also interplay with chaperones to ensure protein quality and to readjust the composition of the proteome following stress. Archaea encode proteasomes that are highly related to those of eukaryotes in basic structure and function. Investigations of archaeal proteasomes coupled with those of eukaryotes has greatly facilitated our understanding of the molecular mechanisms that govern regulated protein degradation by this elaborate nanocompartmentalized machine.},
}
@article {pmid16980428,
year = {2006},
author = {Lloyd, KG and Lapham, L and Teske, A},
title = {An anaerobic methane-oxidizing community of ANME-1b archaea in hypersaline Gulf of Mexico sediments.},
journal = {Applied and environmental microbiology},
volume = {72},
number = {11},
pages = {7218-7230},
pmid = {16980428},
issn = {0099-2240},
mesh = {Anaerobiosis ; Bacteria/genetics/growth &amp; development/metabolism ; DNA, Archaeal/analysis ; DNA, Bacterial/analysis ; DNA, Ribosomal/analysis ; Ecosystem ; Euryarchaeota/genetics/*growth &amp; development/*isolation &amp; purification/metabolism ; Geologic Sediments/chemistry/*microbiology ; Methane/*metabolism ; Mexico ; Molecular Sequence Data ; Oxidation-Reduction ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; Sequence Analysis, DNA ; Sodium Chloride ; Sulfates/metabolism ; },
abstract = {Sediments overlying a brine pool methane seep in the Gulf of Mexico (Green Canyon 205) were analyzed using molecular and geochemical approaches to identify geochemical controls on microbial community composition and stratification. 16S rRNA gene and rRNA clone libraries, as well as mcrA gene clone libraries, showed that the archaeal community consists predominantly of ANME-1b methane oxidizers; no archaea of other ANME subgroups were found with general and group-specific PCR primers. The ANME-1b community was found in the sulfate-methane interface, where undersaturated methane concentrations of ca. 100 to 250 microM coexist with sulfate concentrations around 10 mM. Clone libraries of dsrAB genes and bacterial 16S rRNA genes show diversified sulfate-reducing communities within and above the sulfate-methane interface. Their phylogenetic profiles and occurrence patterns are not linked to ANME-1b populations, indicating that electron donors other than methane, perhaps petroleum-derived hydrocarbons, drive sulfate reduction. The archaeal component of anaerobic oxidation of methane is comprised of an active population of mainly ANME-1b in this hypersaline sediment.},
}
@article {pmid16973267,
year = {2007},
author = {Mertoglu, B and Calli, B and Guler, N and Inanc, B and Inoue, Y},
title = {Effects of insufficient air injection on methanogenic Archaea in landfill bioreactor.},
journal = {Journal of hazardous materials},
volume = {142},
number = {1-2},
pages = {258-265},
doi = {10.1016/j.jhazmat.2006.08.008},
pmid = {16973267},
issn = {0304-3894},
mesh = {*Air ; Archaea/classification/genetics/*physiology ; Base Sequence ; *Bioreactors ; Colony Count, Microbial ; DNA Primers ; Methane/*biosynthesis ; Nucleic Acid Hybridization ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; *Refuse Disposal ; },
abstract = {In this study, methanogenic Archaea diversity in an aerated landfill bioreactor filled with co-disposed incineration bottom ashes and shredded incombustible wastes was monitored and analyzed as a function of time using molecular techniques. Besides, the effects of insufficient air injection on the bioreactor performance and methanogenic diversity were evaluated thoroughly. Results indicated that rapid bio-stabilization of solid waste are possible with aerated landfill bioreactor at various oxygen and oxidation reduction potential levels. Slot-blot hybridization results of leachate samples collected from aerated landfill bioreactor showed that archaeal and bacterial activities increased as stabilization accelerated and bacterial populations constituted almost 95% of all microorganisms. The results of slot-blot hybridization and phylogenetic analysis based on 16S rRNA gene revealed that Methanobacteriales and Methanomicrobiales were dominant species at the beginning while substituted by Methanosarcina-related methanogens close to the end of the operation of bioreactor.},
}
@article {pmid16968113,
year = {2007},
author = {Jung, KH},
title = {The distinct signaling mechanisms of microbial sensory rhodopsins in Archaea, Eubacteria and Eukarya.},
journal = {Photochemistry and photobiology},
volume = {83},
number = {1},
pages = {63-69},
doi = {10.1562/2006-03-20-IR-853},
pmid = {16968113},
issn = {0031-8655},
mesh = {Amino Acid Sequence ; Archaea/*metabolism ; Bacteria/*metabolism ; Eukaryotic Cells/*metabolism ; Models, Biological ; Models, Chemical ; Molecular Sequence Data ; *Photochemistry ; Rhodopsins, Microbial/chemistry/*metabolism ; Sensory Rhodopsins/chemistry/*metabolism ; },
abstract = {Most of the known archaeal-type microbial rhodopsins are retinal-binding ion transporters, such as bacteriorhodopsin (BR) and proteorhodopsin (PR). Their identification is the result of extensive studies of their photochemical and biophysical properties. The cells containing these pigments, however, use other microbial rhodopsins as photosensors to monitor environmental light signals. From the early studies of sensory rhodopsin I (HsSRI) in Halobacterium salinarum and sensory rhodopsin II (NpSRII) in Natronomonas pharaonis, we now know that several microbial sensory rhodopsins in the other major domain of life relay information on light intensity and quality to the cell. Three of the most studied photosensory transduction mechanisms of these microbial rhodopsins are dealt with in this review. We discuss recent progress in the understanding of genomic organization, photochemical properties and photosignaling mechanisms with respect to biological function.},
}
@article {pmid16929673,
year = {2006},
author = {Cavicchioli, R and Goodchild, A and Raftery, M},
title = {Proteomics of Archaea.},
journal = {Methods of biochemical analysis},
volume = {49},
number = {},
pages = {57-72},
doi = {10.1002/0471973165.ch5},
pmid = {16929673},
issn = {0076-6941},
mesh = {Archaeal Proteins/*chemistry ; Chromatography, Liquid ; Electrophoresis, Gel, Two-Dimensional ; Mass Spectrometry ; Membrane Proteins/chemistry ; Phylogeny ; Protein Processing, Post-Translational ; Proteome ; Proteomics/*methods ; Temperature ; },
}
@article {pmid16920107,
year = {2006},
author = {Allen, JW and Harvat, EM and Stevens, JM and Ferguson, SJ},
title = {A variant System I for cytochrome c biogenesis in archaea and some bacteria has a novel CcmE and no CcmH.},
journal = {FEBS letters},
volume = {580},
number = {20},
pages = {4827-4834},
doi = {10.1016/j.febslet.2006.07.073},
pmid = {16920107},
issn = {0014-5793},
support = {BB/C508118/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; C20071/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Amino Acid Sequence ; Archaea/genetics/*metabolism ; Archaeal Proteins/classification/genetics/*metabolism ; Bacterial Outer Membrane Proteins/classification/genetics/*metabolism ; Cytochromes c/*biosynthesis ; Escherichia coli Proteins/classification/genetics/*metabolism ; Genome, Archaeal ; Hemeproteins/classification/genetics/*metabolism ; Molecular Sequence Data ; Phylogeny ; Sequence Homology, Amino Acid ; },
abstract = {C-type cytochromes are characterized by post-translational covalent attachment of heme to thiols that occur in a Cys-Xxx-Xxx-Cys-His motif. Three distinct biogenesis systems are known for this heme attachment. Archaea are now shown to contain a significantly modified form of cytochrome c maturation System I (the Ccm system). The most notable adaptation relative to the well-studied apparatus from proteobacteria and plants is a novel form of the heme chaperone CcmE, lacking the highly conserved histidine that covalently binds heme and is essential for function in Escherichia coli. In most archaeal CcmEs this histidine, normally found in a His-Xxx-Xxx-Xxx-Tyr motif, is replaced by a cysteine residue that occurs in a Cys-Xxx-Xxx-Xxx-Tyr motif. The CcmEs from two halobacteria contain yet another form of CcmE, having HxxxHxxxH approximately corresponding in alignment to the H/CxxxY motif. The CxxxY-type of CcmE is, surprisingly, also found in some bacterial genomes (including Desulfovibrio species). All of the modified CcmEs cluster together in a phylogenetic tree, as do other Ccm proteins from the same organisms. Significantly, CcmH is absent from all of the complete archaeal genomes we have studied, and also from most of the bacterial genomes that have CxxxY-type CcmE.},
}
@article {pmid16915287,
year = {2006},
author = {Leininger, S and Urich, T and Schloter, M and Schwark, L and Qi, J and Nicol, GW and Prosser, JI and Schuster, SC and Schleper, C},
title = {Archaea predominate among ammonia-oxidizing prokaryotes in soils.},
journal = {Nature},
volume = {442},
number = {7104},
pages = {806-809},
doi = {10.1038/nature04983},
pmid = {16915287},
issn = {1476-4687},
mesh = {Ammonia/*metabolism ; Archaea/enzymology/genetics/*metabolism ; Bacteria/enzymology/genetics/metabolism ; DNA, Complementary/analysis/genetics ; Ecosystem ; Gene Dosage/genetics ; Gene Library ; Genes, Archaeal/genetics ; Genes, Bacterial/genetics ; Genes, rRNA/genetics ; Lipids/analysis ; Molecular Sequence Data ; Oxidation-Reduction ; Oxidoreductases/genetics/metabolism ; Prokaryotic Cells/*metabolism ; RNA, Archaeal/analysis/genetics ; *Soil Microbiology ; },
abstract = {Ammonia oxidation is the first step in nitrification, a key process in the global nitrogen cycle that results in the formation of nitrate through microbial activity. The increase in nitrate availability in soils is important for plant nutrition, but it also has considerable impact on groundwater pollution owing to leaching. Here we show that archaeal ammonia oxidizers are more abundant in soils than their well-known bacterial counterparts. We investigated the abundance of the gene encoding a subunit of the key enzyme ammonia monooxygenase (amoA) in 12 pristine and agricultural soils of three climatic zones. amoA gene copies of Crenarchaeota (Archaea) were up to 3,000-fold more abundant than bacterial amoA genes. High amounts of crenarchaeota-specific lipids, including crenarchaeol, correlated with the abundance of archaeal amoA gene copies. Furthermore, reverse transcription quantitative PCR studies and complementary DNA analysis using novel cloning-independent pyrosequencing technology demonstrated the activity of the archaea in situ and supported the numerical dominance of archaeal over bacterial ammonia oxidizers. Our results indicate that crenarchaeota may be the most abundant ammonia-oxidizing organisms in soil ecosystems on Earth.},
}
@article {pmid16914298,
year = {2007},
author = {Zeng, Y and Li, H and Jiao, N},
title = {Phylogenetic diversity of planktonic archaea in the estuarine region of East China Sea.},
journal = {Microbiological research},
volume = {162},
number = {1},
pages = {26-36},
doi = {10.1016/j.micres.2006.03.007},
pmid = {16914298},
issn = {0944-5013},
mesh = {Biodiversity ; China ; Crenarchaeota/*classification/genetics/*isolation &amp; purification ; DNA Fingerprinting ; DNA, Archaeal/chemistry/isolation &amp; purification ; DNA, Ribosomal/chemistry/isolation &amp; purification ; Euryarchaeota/*classification/genetics/*isolation &amp; purification ; Genes, rRNA ; Molecular Sequence Data ; Phylogeny ; Polymorphism, Restriction Fragment Length ; RNA, Archaeal/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; *Water Microbiology ; },
abstract = {To examine the diversity and structure of archaeal communities in the Yangtze River estuarine region of East China Sea (ECS), the 16S rRNA gene clone libraries of two typical sites were constructed with the archaea-specific primers. In total, 71 clones randomly selected were screened by PCR-restriction fragment length polymorphism (PCR-RFLP) analysis and 21 clones with unique RFLP pattern were sequenced. All the sequences are clustered into the two groups of Marine Group I (MGI) and Marine Group II (MGII) which are affiliated with the phyla Crenarchaeota and Euryarchaeota, respectively. MGI clones dominate both libraries with 20 MGI sequences obtained. The majority of sequences are closely related to uncultured marine archaea except for two sequences of which the nearest neighbor is a newly identified isolate of nitrifying marine archaeon Nitrosopumilus maritimus (98% identity). The results indicate that ECS coastal waters are inhabited by archaeal community with low dominance and high diversity corresponding to the complex estuarine environments, suggesting that archaea may perform an important role in the estuarine ecosystem.},
}
@article {pmid16907759,
year = {2006},
author = {Moussard, H and Moreira, D and Cambon-Bonavita, MA and López-García, P and Jeanthon, C},
title = {Uncultured Archaea in a hydrothermal microbial assemblage: phylogenetic diversity and characterization of a genome fragment from a euryarchaeote.},
journal = {FEMS microbiology ecology},
volume = {57},
number = {3},
pages = {452-469},
doi = {10.1111/j.1574-6941.2006.00128.x},
pmid = {16907759},
issn = {0168-6496},
mesh = {Archaea/*genetics/growth &amp; development ; Biodiversity ; Euryarchaeota/*genetics/growth &amp; development ; Genome Components ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The polychaete Alvinella pompejana lives in organic tubes on the walls of active hydrothermal chimneys along the East Pacific Rise. To examine the diversity of the archaeal community associated with the polychaete tubes, we constructed libraries by direct PCR amplification and cloning of 16S rRNA genes. Almost half of the sequences of the 16S rRNA gene libraries clustered with uncultured archaeal groups. In an effort to access genomic information from uncultured archaeal members we further constructed a fosmid library from the same DNA source. One of the clones, Alv-FOS5, was sequenced completely. Its sequence analysis revealed an incomplete rRNA operon and 32 predicted ORFs. Seventeen of these ORFs have been assigned putative functions, including transcription and translation, cellular processes and signalling, transport systems and metabolic pathways. Phylogenetic analyses of the 16S rRNA gene suggested that Alv-FOS5 formed a new lineage related to members of Deep-Sea Hydrothermal Vent Euryarchaeota group II. Phylogenetic analyses of predicted proteins revealed the existence of likely cases of horizontal gene transfer, both between Crenarchaeota and Euryarchaeota and between Archaea and Bacteria. This study is the first step in using genomics to reveal the physiology of an as yet uncultured group of archaea from deep-sea hydrothermal vents.},
}
@article {pmid16902403,
year = {2006},
author = {Hussain, T and Kruparani, SP and Pal, B and Dock-Bregeon, AC and Dwivedi, S and Shekar, MR and Sureshbabu, K and Sankaranarayanan, R},
title = {Post-transfer editing mechanism of a D-aminoacyl-tRNA deacylase-like domain in threonyl-tRNA synthetase from archaea.},
journal = {The EMBO journal},
volume = {25},
number = {17},
pages = {4152-4162},
pmid = {16902403},
issn = {0261-4189},
support = {//Wellcome Trust/United Kingdom ; },
mesh = {Amino Acid Sequence ; Archaeal Proteins/*chemistry/genetics ; Binding Sites ; Lysine/chemistry ; *Models, Molecular ; Molecular Sequence Data ; Protein Structure, Tertiary ; Pyrococcus abyssi/*enzymology/genetics ; *RNA Editing ; RNA, Transfer, Amino Acyl/*chemistry/genetics ; Stereoisomerism ; Threonine-tRNA Ligase/*chemistry/genetics ; Transfer RNA Aminoacylation ; },
abstract = {To ensure a high fidelity during translation, threonyl-tRNA synthetases (ThrRSs) harbor an editing domain that removes noncognate L-serine attached to tRNAThr. Most archaeal ThrRSs possess a unique editing domain structurally similar to D-aminoacyl-tRNA deacylases (DTDs) found in eubacteria and eukaryotes that specifically removes D-amino acids attached to tRNA. Here, we provide mechanistic insights into the removal of noncognate L-serine from tRNAThr by a DTD-like editing module from Pyrococcus abyssi ThrRS (Pab-NTD). High-resolution crystal structures of Pab-NTD with pre- and post-transfer substrate analogs and with L-serine show mutually nonoverlapping binding sites for the seryl moiety. Although the pre-transfer editing is excluded, the analysis reveals the importance of main chain atoms in proper positioning of the post-transfer substrate for its hydrolysis. A single residue has been shown to play a pivotal role in the inversion of enantioselectivity both in Pab-NTD and DTD. The study identifies an enantioselectivity checkpoint that filters opposite chiral molecules and thus provides a fascinating example of how nature has subtly engineered this domain for the selection of chiral molecules during translation.},
}
@article {pmid16902017,
year = {2006},
author = {Cui, HL and Tohty, D and Zhou, PJ and Liu, SJ},
title = {Haloterrigena longa sp. nov. and Haloterrigena limicola sp. nov., extremely halophilic archaea isolated from a salt lake.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {56},
number = {Pt 8},
pages = {1837-1840},
doi = {10.1099/ijs.0.64372-0},
pmid = {16902017},
issn = {1466-5026},
mesh = {Archaea/chemistry/*classification/genetics/growth &amp; development/isolation &amp; purification ; China ; Culture Media ; DNA, Archaeal/genetics ; Fresh Water/*microbiology ; Lipids/analysis ; Magnesium/analysis ; Molecular Sequence Data ; Oligosaccharides/analysis ; Phylogeny ; Sequence Homology, Nucleic Acid ; Species Specificity ; *Water Microbiology ; },
abstract = {Halophilic archaeal strains ABH32(T) and AX-7(T) were isolated from Aibi salt lake in Xin-Jiang, China, and were subjected to taxonomic studies. The cells of both strains were rod-shaped, and growth required at least 10 % (w/v) NaCl. The cellular polar lipids were identified as phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester and mannose-2,6-disulfate (1-->2)-glucose glycerol diether (S(2)-DGD). The isolates were different in that strain ABH32(T) did not require magnesium and had strong ability to assimilate sugars for growth, whereas strain AX-7(T) required magnesium and did not assimilate glucose, sucrose or maltose for growth. Both strain ABH32(T) and strain AX-7(T) were most closely related to members of the genera Haloterrigena and Natrinema. On the basis of phenotypic and genotypic characteristics, especially their cellular polar lipids, the two isolates were assigned to the genus Haloterrigena. Moreover, the DNA relatedness values for strains ABH32(T) and AX-7(T) with respect to members of the genus Haloterrigena were found to be well below 70 %. Thus, strains ABH32(T) and AX-7(T) represent two novel species within the genus Haloterrigena, for which the names Haloterrigena longa sp. nov. (type strain ABH32(T)=CGMCC 1.5334(T)=JCM 13562(T)) and Haloterrigena limicola sp. nov. (type strain AX-7(T)=CGMCC 1.5333(T)=JCM 13563(T)) are proposed.},
}
@article {pmid16895922,
year = {2006},
author = {Makarova, KS and Grishin, NV and Koonin, EV},
title = {The HicAB cassette, a putative novel, RNA-targeting toxin-antitoxin system in archaea and bacteria.},
journal = {Bioinformatics (Oxford, England)},
volume = {22},
number = {21},
pages = {2581-2584},
doi = {10.1093/bioinformatics/btl418},
pmid = {16895922},
issn = {1367-4811},
support = {//Intramural NIH HHS/United States ; },
mesh = {Antitoxins ; Archaea/genetics/*metabolism ; Bacteria/genetics/*pathogenicity ; Bacterial Toxins/*chemistry/genetics/metabolism ; Binding Sites ; Gene Targeting ; Integrons/genetics ; Protein Binding ; RNA, Archaeal/*chemistry/metabolism ; RNA, Bacterial/*chemistry/metabolism ; RNA-Binding Proteins/*chemistry/genetics/metabolism ; Sequence Analysis, Protein ; },
abstract = {Toxin-antitoxin systems (TAS) are abundant, diverse, horizontally mobile gene modules that encode powerful resistance mechanisms in prokaryotes. We use the comparative-genomic approach to predict a new TAS that consists of a two-gene cassette encoding uncharacterized HicA and HicB proteins. Numerous bacterial and archaeal genomes encode from one to eight HicAB modules which appear to be highly prone to horizontal gene transfer. The HicB protein (COG1598/COG4226) has a partially degraded RNAse H fold, whereas HicA (COG1724) contains a double-stranded RNA-binding domain. The stable combination of these two domains suggests a link to RNA metabolism, possibly, via an RNA interference-type mechanism. In most HicB proteins, the RNAse H-like domain is fused to a DNA-binding domain, either of the ribbon-helix-helix or of the helix-turn-helix class; in other TAS, proteins containing these DNA-binding domains function as antitoxins. Thus, the HicAB module is predicted to be a novel TAS whose mechanism involves RNA-binding and, possibly, cleavage.},
}
@article {pmid16887666,
year = {2000},
author = {Garcia, JL and Patel, BK and Ollivier, B},
title = {Taxonomic, phylogenetic, and ecological diversity of methanogenic Archaea.},
journal = {Anaerobe},
volume = {6},
number = {4},
pages = {205-226},
doi = {10.1006/anae.2000.0345},
pmid = {16887666},
issn = {1075-9964},
}
@article {pmid16885322,
year = {2006},
author = {Park, HD and Wells, GF and Bae, H and Criddle, CS and Francis, CA},
title = {Occurrence of ammonia-oxidizing archaea in wastewater treatment plant bioreactors.},
journal = {Applied and environmental microbiology},
volume = {72},
number = {8},
pages = {5643-5647},
pmid = {16885322},
issn = {0099-2240},
mesh = {Ammonia/*metabolism ; Archaea/enzymology/genetics/*metabolism ; *Bioreactors ; DNA, Archaeal/analysis ; Molecular Sequence Data ; Oxidation-Reduction ; Oxidoreductases/genetics ; Phylogeny ; Polymerase Chain Reaction/methods ; Sequence Analysis, DNA ; Sewage/*microbiology ; Waste Disposal, Fluid/*methods ; },
abstract = {We report molecular evidence that ammonia-oxidizing archaea (AOA) occur in activated sludge bioreactors used to remove ammonia from wastewater. Using PCR primers targeting archaeal ammonia monooxygenase subunit A (amoA) genes, we retrieved and compared 75 sequences from five wastewater treatment plants operating with low dissolved oxygen levels and long retention times. All of these sequences showed similarity to sequences previously found in soil and sediments, and they were distributed primarily in four major phylogenetic clusters. One of these clusters contained virtually identical amoA sequences obtained from all five activated sludge samples (from Oregon, Wisconsin, Pennsylvania, and New Jersey) and accounted for 67% of all the sequences, suggesting that this AOA phylotype may be widespread in nitrifying bioreactors.},
}
@article {pmid16877320,
year = {2006},
author = {Bose, M and Slick, D and Sarto, MJ and Murphy, P and Roberts, D and Roberts, J and Barber, RD},
title = {Identification of SmtB/ArsR cis elements and proteins in archaea using the Prokaryotic InterGenic Exploration Database (PIGED).},
journal = {Archaea (Vancouver, B.C.)},
volume = {2},
number = {1},
pages = {39-49},
pmid = {16877320},
issn = {1472-3646},
mesh = {Archaea/*genetics ; Bacterial Proteins/analysis/*genetics ; Binding Sites ; DNA, Archaeal/metabolism ; DNA-Binding Proteins/analysis/*genetics ; Databases as Topic ; *Genes, Archaeal ; Phylogeny ; Prokaryotic Cells/metabolism ; Repressor Proteins/analysis/*genetics ; Trans-Activators/analysis/*genetics ; Winged-Helix Transcription Factors/physiology ; },
abstract = {Microbial genome sequencing projects have revealed an apparently wide distribution of SmtB/ArsR metal-responsive transcriptional regulators among prokaryotes. Using a position-dependent weight matrix approach, prokaryotic genome sequences were screened for SmtB/ArsR DNA binding sites using data derived from intergenic sequences upstream of orthologous genes encoding these regulators. Sixty SmtB/ArsR operators linked to metal detoxification genes, including nine among various archaeal species, are predicted among 230 annotated and draft prokaryotic genome sequences. Independent multiple sequence alignments of putative operator sites and corresponding winged helix-turn-helix motifs define sequence signatures for the DNA binding activity of this SmtB/ArsR subfamily. Prediction of an archaeal SmtB/ArsR based upon these signature sequences is confirmed using purified Methanosarcina acetivorans C2A protein and electrophoretic mobility shift assays. Tools used in this study have been incorporated into a web application, the Prokaryotic InterGenic Exploration Database (PIGED; http://bioinformatics.uwp.edu/~PIGED/home.htm), facilitating comparable studies. Use of this tool and establishment of orthology based on DNA binding signatures holds promise for deciphering potential cellular roles of various archaeal winged helix-turn-helix transcriptional regulators.},
}
@article {pmid16857943,
year = {2006},
author = {Erkel, C and Kube, M and Reinhardt, R and Liesack, W},
title = {Genome of Rice Cluster I archaea--the key methane producers in the rice rhizosphere.},
journal = {Science (New York, N.Y.)},
volume = {313},
number = {5785},
pages = {370-372},
doi = {10.1126/science.1127062},
pmid = {16857943},
issn = {1095-9203},
mesh = {Amino Acid Sequence ; Amino Acids/biosynthesis/metabolism ; Carbohydrate Metabolism ; DNA Repair ; Euryarchaeota/classification/*genetics/metabolism/physiology ; *Genome, Archaeal ; Genomics ; Glycolysis ; Methane/*biosynthesis ; Methanomicrobiales/classification/genetics/metabolism/physiology ; Methanosarcinales/classification/genetics/metabolism/physiology ; Molecular Sequence Data ; Oryza/*microbiology ; Oxidative Stress ; Pyruvic Acid/metabolism ; Sequence Alignment ; Sequence Analysis, DNA ; *Soil Microbiology ; Sulfates/metabolism ; Sulfur/metabolism ; },
abstract = {Rice fields are a global source of the greenhouse gas methane, which is produced by methanogenic archaea, and by methanogens of Rice Cluster I (RC-I) in particular. RC-I methanogens are not yet available in pure culture, and the mechanistic reasons for their prevalence in rice fields are unknown. We reconstructed a complete RC-I genome (3.18 megabases) using a metagenomic approach. Sequence analysis demonstrated an aerotolerant, H2/CO2-dependent lifestyle and enzymatic capacities for carbohydrate metabolism and assimilatory sulfate reduction, hitherto unknown among methanogens. These capacities and a unique set of antioxidant enzymes and DNA repair mechanisms as well as oxygen-insensitive enzymes provide RC-I with a selective advantage over other methanogens in its habitats, thereby explaining the prevalence of RC-I methanogens in the rice rhizosphere.},
}
@article {pmid16857336,
year = {2007},
author = {Schwarz, JI and Eckert, W and Conrad, R},
title = {Community structure of Archaea and Bacteria in a profundal lake sediment Lake Kinneret (Israel).},
journal = {Systematic and applied microbiology},
volume = {30},
number = {3},
pages = {239-254},
doi = {10.1016/j.syapm.2006.05.004},
pmid = {16857336},
issn = {0723-2020},
mesh = {Archaea/*classification/genetics ; Bacteria/*classification/genetics ; Biodiversity ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; DNA, Complementary ; DNA, Ribosomal/genetics ; Fresh Water ; Gene Dosage ; Genes, rRNA ; Geologic Sediments/*microbiology ; Molecular Sequence Data ; Phylogeny ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The microbial community structure of an anoxic profundal lake sediment, i.e., subtropical Lake Kinneret, was analysed with respect to its composition by culture-independent molecular methods including terminal restriction fragment length polymorphism (T-RFLP) analysis, comparative sequence analysis, and quantitative real-time PCR. In particular we were interested in the structure, species composition, and relative abundance of the overall microbial community in the methanogenic sediment layer (0-10 cm depth). Pairwise comparison of archaeal and bacterial 16S rRNA gene T-RFLP profiles obtained from three independent samplings indicated stability of the microbial community. The numbers of Archaea and Bacteria, quantified by real-time PCR, amounted to about 10(8) and 10(10) 16S rRNA gene copies cm(-3) sediment, respectively, suggesting that Archaea may account for only a minor fraction (approximately 1%) of the total prokaryotic community. Hydrogenotrophic Methanomicrobiales and acetoclastic Methanosaeta spp. dominated T-RFLP profiles of the archaeal community. T-RFLP profiles of the bacterial community were dominated by Deltaproteobacteria, sulphate reducers and syntrophs in particular. The second most abundant group was assigned to the Bacteroidetes-Chlorobi-group. Only one bacterial group, which was affiliated with halorespiring bacteria of subphylum II of the Chloroflexi, showed variation in abundance within the sediment samples investigated. Our study gives a comprehensive insight into the structure of the bacterial and archaeal community of a profundal lake sediment, indicating that sulphate reducers, syntrophs, bacteroidetes, halorespirers and methanogens are of particular importance in Lake Kinneret sediment.},
}
@article {pmid16844682,
year = {2006},
author = {Ferri-Fioni, ML and Fromant, M and Bouin, AP and Aubard, C and Lazennec, C and Plateau, P and Blanquet, S},
title = {Identification in archaea of a novel D-Tyr-tRNATyr deacylase.},
journal = {The Journal of biological chemistry},
volume = {281},
number = {37},
pages = {27575-27585},
doi = {10.1074/jbc.M605860200},
pmid = {16844682},
issn = {0021-9258},
mesh = {Amino Acid Sequence ; Aminoacyltransferases/*chemistry ; Archaea/*metabolism ; Archaeoglobus fulgidus/metabolism ; Catalysis ; Escherichia coli/metabolism ; Ions ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Pyrococcus abyssi/metabolism ; RNA, Transfer, Tyr/*chemistry ; Sequence Homology, Amino Acid ; Sulfolobus solfataricus/metabolism ; Zinc/chemistry ; },
abstract = {Most bacteria and eukarya contain an enzyme capable of specifically hydrolyzing D-aminoacyl-tRNA. Here, the archaea Sulfolobus solfataricus is shown to also contain an enzyme activity capable of recycling misaminoacylated D-Tyr-tRNATyr. N-terminal sequencing of this enzyme identifies open reading frame SS02234 (dtd2), the product of which does not present any sequence homology with the known D-Tyr-tRNATyr deacylases of bacteria or eukaryotes. On the other hand, homologs of dtd2 occur in archaea and plants. The Pyrococcus abyssi dtd2 ortholog (PAB2349) was isolated. It rescues the sensitivity to D-tyrosine of a mutant Escherichia coli strain lacking dtd, the gene of its endogeneous D-Tyr-tRNATyr deacylase. Moreover, in vitro, the PAB2349 product, which behaves as a monomer and carries 2 mol of zinc/mol of protein, catalyzes the cleavage of D-Tyr-tRNATyr. The three-dimensional structure of the product of the Archaeoglobus fulgidus dtd2 ortholog has been recently solved by others through a structural genomics approach (Protein Data Bank code 1YQE). This structure does not resemble that of Escherichia coli D-Tyr-tRNATyr deacylase. Instead, it displays homology with that of a bacterial peptidyl-tRNA hydrolase. We show, however, that the archaeal PAB2349 enzyme does not act against diacetyl-Lys-tRNALys, a model substrate of peptidyl-tRNA hydrolase. Based on the Protein Data Bank 1YQE structure, site-directed mutagenesis experiments were undertaken to remove zinc from the PAB2349 enzyme. Several residues involved in zinc binding and supporting the activity of the deacylase were identified. Taken together, these observations suggest evolutionary links between the various hydrolases in charge of the recycling of metabolically inactive tRNAs during translation.},
}
@article {pmid16829518,
year = {2006},
author = {Shin, JH and Kelman, Z},
title = {The replicative helicases of bacteria, archaea, and eukarya can unwind RNA-DNA hybrid substrates.},
journal = {The Journal of biological chemistry},
volume = {281},
number = {37},
pages = {26914-26921},
doi = {10.1074/jbc.M605518200},
pmid = {16829518},
issn = {0021-9258},
mesh = {Adenosine Triphosphatases/chemistry ; Archaeal Proteins/metabolism ; Biotinylation ; Cell Cycle Proteins/chemistry ; DNA/*chemistry ; DNA Helicases/*chemistry/metabolism ; Escherichia coli/metabolism ; Methanobacterium/metabolism ; Minichromosome Maintenance Complex Component 6 ; Nucleic Acid Denaturation ; RNA/*chemistry ; Schizosaccharomyces/metabolism ; Schizosaccharomyces pombe Proteins/chemistry ; Streptavidin/chemistry ; },
abstract = {Replicative helicases are hexameric enzymes that unwind DNA during chromosomal replication. They use energy from nucleoside triphosphate hydrolysis to translocate along one strand of the duplex DNA and displace the complementary strand. Here, the ability of a replicative helicase from each of the three domains, bacteria, archaea, and eukarya, to unwind RNA-containing substrate was determined. It is shown that all three helicases can unwind DNA-RNA hybrids while translocating along the single-stranded DNA. No unwinding could be observed when the helicases were provided with a single-stranded RNA overhang. Using DNA, RNA, and DNA-RNA chimeric oligonucleotides it was found that whereas the enzymes can bind both DNA and RNA, they could translocate only along DNA and only DNA stimulates the ATPase activity of the enzymes. Recent observations suggest that helicases may interact with enzymes participating in RNA metabolism and that RNA-DNA hybrids may be present on the chromosomes. Thus, the results presented here may suggest a new role for the replicative helicases during chromosomal replication or in other cellular processes.},
}
@article {pmid16824110,
year = {2006},
author = {Chaban, B and Voisin, S and Kelly, J and Logan, SM and Jarrell, KF},
title = {Identification of genes involved in the biosynthesis and attachment of Methanococcus voltae N-linked glycans: insight into N-linked glycosylation pathways in Archaea.},
journal = {Molecular microbiology},
volume = {61},
number = {1},
pages = {259-268},
doi = {10.1111/j.1365-2958.2006.05226.x},
pmid = {16824110},
issn = {0950-382X},
mesh = {Archaea/*genetics/metabolism/ultrastructure ; Archaeal Proteins/*genetics/metabolism ; Blotting, Western ; Carbohydrate Sequence ; Chromatography, Liquid ; Chromosome Mapping ; Electrophoresis, Polyacrylamide Gel ; Flagellin/chemistry/genetics/metabolism ; Gene Order ; Genes, Archaeal/genetics ; Glycosylation ; Mass Spectrometry ; Methanococcus/*genetics/metabolism/ultrastructure ; Microscopy, Electron ; Models, Biological ; Molecular Sequence Data ; Mutation ; Oligosaccharides/chemistry ; Polysaccharides/*biosynthesis ; Protein Processing, Post-Translational ; Recombinant Proteins/genetics/metabolism ; Signal Transduction/genetics ; },
abstract = {N-linked glycosylation is recognized as an important post-translational modification across all three domains of life. However, the understanding of the genetic pathways for the assembly and attachment of N-linked glycans in eukaryotic and bacterial systems far outweighs the knowledge of comparable processes in Archaea. The recent characterization of a novel trisaccharide [beta-ManpNAcA6Thr-(1-4)-beta-GlcpNAc3NAcA-(1-3)-beta-GlcpNAc]N-linked to asparagine residues in Methanococcus voltae flagellin and S-layer proteins affords new opportunities to investigate N-linked glycosylation pathways in Archaea. In this contribution, the insertional inactivation of several candidate genes within the M. voltae genome and their resulting effects on flagellin and S-layer glycosylation are reported. Two of the candidate genes were shown to have effects on flagellin and S-layer protein molecular mass and N-linked glycan structure. Further examination revealed inactivation of either of these two genes also had effects on flagella assembly. These genes, designated agl (archaeal glycosylation) genes, include a glycosyl transferase (aglA) involved in the attachment of the terminal sugar to the glycan and an STT3 oligosaccharyl transferase homologue (aglB) involved in the transfer of the complete glycan to the flagellin and S-layer proteins. These findings document the first experimental evidence for genes involved in any glycosylation process within the domain Archaea.},
}
@article {pmid16822522,
year = {2006},
author = {Gruic-Sovulj, I and Jaric, J and Dulic, M and Cindric, M and Weygand-Durasevic, I},
title = {Shuffling of discrete tRNASer regions reveals differently utilized identity elements in yeast and methanogenic archaea.},
journal = {Journal of molecular biology},
volume = {361},
number = {1},
pages = {128-139},
doi = {10.1016/j.jmb.2006.06.008},
pmid = {16822522},
issn = {0022-2836},
mesh = {Base Sequence ; *DNA Shuffling ; Methanococcus/*genetics ; Molecular Sequence Data ; RNA, Transfer, Ser/*genetics ; *Recombination, Genetic ; Saccharomyces cerevisiae/*genetics ; },
abstract = {Seryl-tRNA synthetases (SerRSs) from methanogenic archaea possess distinct evolutionary origin and show minimal sequence similarity with counterparts from bacteria, eukaryotes and other archaea. Here we show that SerRS from yeast Saccharomyces cerevisiae and archaeon Methanococcus maripaludis (ScSerRS and MmSerRS, respectively) display significantly different ability to serylate heterologous tRNA(Ser). Recognition in yeast was shown to be more stringent than in archaeon. While cross-aminoacylation of M. maripaludis tRNA(Ser) (MmtRNA(Ser)) by yeast SerRS barely occurs, yeast tRNA(Ser) (SctRNA(Ser)) was shown to be a good substrate for heterologous MmSerRS. To investigate the contribution of different tRNA regions for the recognition by yeast and archaeal SerRS, chimeric tRNAs bearing separated domains of SctRNA(Ser) in MmtRNA(Ser) framework were produced by in vitro transcription and subjected to kinetic and gel mobility shift analysis with both enzymes. Generally, the recognition in M. maripaludis seems to be relatively relaxed toward tertiary elements of tRNA(Ser) structure and relies on the direct recognition of identity nucleotides. On the other hand, expression of tRNA(Ser) identity elements in yeast seems to be more sensitive toward surrounding sequence context. In both systems variable arm of tRNA was recognized as a major identity region with a strong influence on SerRS:tRNA binding. Acceptor domain of SctRNA(Ser) was also shown to be important for serylation in yeast. We propose that cognate interactions between N-terminal domain of yeast SerRS and variable region of SctRNA(Ser) place the acceptor stem into the enzyme's active site and lead to increased affinity toward serine and efficient serylation of tRNA. The same effect was not observed in M. maripaludis. Unlike its yeast counterpart, MmSerRS forms only one type of covalent complex with MmtRNA(Ser), regardless of the tRNA/SerRS molar ratio. Stoichiometry of the complex, one tRNA per dimeric SerRS, was revealed by mass spectrometry. Our studies indicate that different SerRS:tRNA recognition mode is utilized by these two systems.},
}
@article {pmid16820449,
year = {2006},
author = {Sørensen, KB and Teske, A},
title = {Stratified communities of active Archaea in deep marine subsurface sediments.},
journal = {Applied and environmental microbiology},
volume = {72},
number = {7},
pages = {4596-4603},
pmid = {16820449},
issn = {0099-2240},
mesh = {Archaea/classification/*growth &amp; development ; DNA, Archaeal/analysis ; DNA, Ribosomal/analysis ; *Ecosystem ; Geologic Sediments/*microbiology ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Reverse Transcriptase Polymerase Chain Reaction ; Seawater/*microbiology ; Sequence Analysis, DNA ; },
abstract = {Archaeal 16S rRNA was extracted from samples of deep marine subsurface sediments from Peru Margin site 1227, Ocean Drilling Program leg 201. The amounts of archaeal 16S rRNA in each extract were quantified by serial dilution and reverse transcription (RT)-PCR. The results indicated a 1,000-fold variation in rRNA content with depth in the sediment, with the highest concentrations found near the sediment surface and in the sulfate-methane transition zone (SMTZ). The phylogenetic composition of the active archaeal population revealed by cloning and sequencing of RT-PCR products changed with depth. Several phylotypes affiliated with marine benthic group B (MBGB) dominated clone libraries from the upper part of the SMTZ and were detected only in this layer. Members of the miscellaneous crenarchaeotal group (MCG) dominated clone libraries from the other layers. These results demonstrate that archaeal communities change in activity and community composition over short distances in geochemically distinct zones of deep subseafloor sediments and that these changes are traceable in the rRNA pool. It was shown for the first time that members of both the MCG and MBGB Archaea are more active in the SMTZ than in layers above and below. This indicates that they benefit either directly or indirectly from the anaerobic oxidation of methane. They also appear to be ecophysiologically flexible, as they have been retrieved from a wide range of marine sediments of various geochemical properties.},
}
@article {pmid16806054,
year = {2006},
author = {Lewalter, K and Müller, V},
title = {Bioenergetics of archaea: ancient energy conserving mechanisms developed in the early history of life.},
journal = {Biochimica et biophysica acta},
volume = {1757},
number = {5-6},
pages = {437-445},
doi = {10.1016/j.bbabio.2006.04.027},
pmid = {16806054},
issn = {0006-3002},
mesh = {Amino Acid Sequence ; Archaea/genetics/*metabolism ; Archaeal Proteins/*physiology ; *Biological Evolution ; Crystallography, X-Ray ; Energy Metabolism/*physiology ; Models, Molecular ; Molecular Sequence Data ; Phylogeny ; Protein Binding ; Protein Subunits/physiology ; Proton-Translocating ATPases/*physiology ; Sequence Homology, Amino Acid ; },
abstract = {A key component in cellular bioenergetics is the ATP synthase. The enzyme from archaea represents a new class of ATPases, the A1AO ATP synthases. They are composed of two domains that function as a pair of rotary motors connected by a central and peripheral stalk(s). The structure of the chemically-driven motor (A1) was solved by small angle X-ray scattering in solution, and the structure of the first A1AO ATP synthases (from methanoarchaea) was obtained recently by single particle analyses. These studies revealed novel structural features such as a second peripheral stalk and a collar-like structure. Interestingly, the membrane-embedded electrically-driven motor (AO) is very different in archaea with sometimes novel, exceptional subunit composition.},
}
@article {pmid16801395,
year = {2006},
author = {Skophammer, RG and Herbold, CW and Rivera, MC and Servin, JA and Lake, JA},
title = {Evidence that the root of the tree of life is not within the Archaea.},
journal = {Molecular biology and evolution},
volume = {23},
number = {9},
pages = {1648-1651},
doi = {10.1093/molbev/msl046},
pmid = {16801395},
issn = {0737-4038},
support = {T32 HG002536/HG/NHGRI NIH HHS/United States ; },
mesh = {Amino Acid Sequence ; Archaea/*genetics ; Eukaryotic Cells ; *Evolution, Molecular ; *Genome, Archaeal ; Molecular Sequence Data ; Mutagenesis, Insertional ; *Phylogeny ; Sequence Deletion ; Sequence Homology, Amino Acid ; },
abstract = {The Archaea occupy uncommon and extreme habitats around the world. They manufacture unusual compounds, utilize novel metabolic pathways, and contain many unique genes. Many suspect, due to their novel properties, that the root of the tree of life may be within the Archaea, although there is little direct evidence for this root. Here, using gene insertions and deletions found within protein synthesis factors present in all prokaryotes and eukaryotes, we present statistically significant evidence that the root of life is outside the Archaea.},
}
@article {pmid16790020,
year = {2006},
author = {van de Werken, HJ and Verhees, CH and Akerboom, J and de Vos, WM and van der Oost, J},
title = {Identification of a glycolytic regulon in the archaea Pyrococcus and Thermococcus.},
journal = {FEMS microbiology letters},
volume = {260},
number = {1},
pages = {69-76},
doi = {10.1111/j.1574-6968.2006.00292.x},
pmid = {16790020},
issn = {0378-1097},
mesh = {Base Sequence ; Binding Sites ; Glycolysis/*genetics ; Molecular Sequence Data ; Promoter Regions, Genetic ; Pyrococcus/*genetics/metabolism ; *Regulon ; Thermococcus/*genetics/metabolism ; Transcription Initiation Site ; },
abstract = {The glycolytic pathway of the hyperthermophilic archaea that belong to the order Thermococcales (Pyrococcus, Thermococcus and Palaeococcus) differs significantly from the canonical Embden-Meyerhof pathway in bacteria and eukarya. This archaeal glycolysis variant consists of several novel enzymes, some of which catalyze unique conversions. Moreover, the enzymes appear not to be regulated allosterically, but rather at transcriptional level. To elucidate details of the gene expression control, the transcription initiation sites of the glycolytic genes in Pyrococcus furiosus have been mapped by primer extension analysis and the obtained promoter sequences have been compared with upstream regions of non-glycolytic genes. Apart from consensus sequences for the general transcription factors (TATA-box and BRE) this analysis revealed the presence of a potential transcription factor binding site (TATCAC-N(5)-GTGATA) in glycolytic and starch utilizing promoters of P. furiosus and several thermococcal species. The absence of this inverted repeat in Pyrococcus abyssi and Pyrococcus horikoshii probably reflects that their reduced catabolic capacity does not require this regulatory system. Moreover, this phyletic pattern revealed a TrmB-like regulator (PF0124 and TK1769) which may be involved in recognizing the repeat. This Thermococcales glycolytic regulon, with more than 20 genes, is the largest regulon that has yet been described for Archaea.},
}
@article {pmid16769689,
year = {2005},
author = {Minezaki, Y and Homma, K and Nishikawa, K},
title = {Genome-wide survey of transcription factors in prokaryotes reveals many bacteria-specific families not found in archaea.},
journal = {DNA research : an international journal for rapid publication of reports on genes and genomes},
volume = {12},
number = {5},
pages = {269-280},
doi = {10.1093/dnares/dsi016},
pmid = {16769689},
issn = {1756-1663},
mesh = {Algorithms ; Archaeal Proteins/genetics/*metabolism ; Bacterial Proteins/genetics/*metabolism ; DNA-Binding Proteins/genetics/*metabolism ; *Genome, Archaeal ; *Genome, Bacterial ; Protein Structure, Tertiary ; Transcription Factors/genetics/*metabolism ; },
abstract = {Assignment of all transcription factors (TFs) from genome sequence data is not a straightforward task due to the wide variation in TFs among different species. A DNA binding domain (DBD) and a contiguous non-DBD with a characteristic SCOP or Pfam domain combination are observed in most members of TF families. We found that most of the experimentally verified TFs in prokaryotes are detectable by a combination of SCOP or Pfam domains assigned to DBDs and non-DBDs. Based on this finding, we set up rules to detect TFs and classify them into 52 TF families. Application of the rules to 154 entirely sequenced prokaryotic genomes detected >18,000 TFs classified into families, which have been made publicly available from the 'GTOP_TF' database. Despite the rough proportionality of the number of TFs per genome with genome size, species with reduced genomes, i.e. obligatory parasites and symbionts, have only a few if any TFs, reflecting a nearly complete loss. Also the number of TFs is significantly lower in archaea than in bacteria. In addition, all but 1 of the 19 TF families present in archaea is present in bacteria, whereas 33 TF families are found exclusively in bacteria. This observation indicates that a number of new TF families have evolved in bacteria, making the transcription regulatory system more divergent in bacteria than in archaea.},
}
@article {pmid16765859,
year = {2006},
author = {Wright, AD and Toovey, AF and Pimm, CL},
title = {Molecular identification of methanogenic archaea from sheep in Queensland, Australia reveal more uncultured novel archaea.},
journal = {Anaerobe},
volume = {12},
number = {3},
pages = {134-139},
doi = {10.1016/j.anaerobe.2006.02.002},
pmid = {16765859},
issn = {1075-9964},
mesh = {Anaerobiosis ; Animals ; Archaea/genetics/*isolation &amp; purification/*metabolism ; Australia ; Methane/*metabolism ; Molecular Sequence Data ; Phylogeny ; RNA, Archaeal/genetics ; RNA, Ribosomal, 16S/genetics ; Rumen/microbiology ; Sheep, Domestic/*microbiology ; },
abstract = {Molecular diversity of rumen methanogens in sheep in Queensland, Australia was investigated using 16S rRNA gene libraries prepared from pooled rumen contents from nine merino sheep. A total of 78 clones were identified revealing 26 different sequences. Of these 26 sequences, eight sequences (15 clones) were 95-100% similar to cultivated methanogens belonging to the orders Methanobacteriales and Methanomicrobiales, and the remaining 18 phylotypes (63 clones) were 72-75% similar to Thermoplasma acidophilum and Thermoplasma volcanium. These unique sequences clustered within a distinct and strongly supported (100% bootstrap support) phylogenetic group, exclusively composed of sequences from uncharacterized archaea from very diverse anaerobic environments. Members of this unique group that were previously considered atypical for the rumen environment were the predominant clones.},
}
@article {pmid16762024,
year = {2006},
author = {Abu-Qarn, M and Eichler, J},
title = {Protein N-glycosylation in Archaea: defining Haloferax volcanii genes involved in S-layer glycoprotein glycosylation.},
journal = {Molecular microbiology},
volume = {61},
number = {2},
pages = {511-525},
doi = {10.1111/j.1365-2958.2006.05252.x},
pmid = {16762024},
issn = {0950-382X},
mesh = {Archaeal Proteins/genetics/*metabolism ; Bacterial Proteins/*genetics/*metabolism ; Gene Deletion ; Gene Expression Regulation, Archaeal ; Glycosylation ; Haloferax volcanii/*genetics/growth &amp; development/metabolism ; Hexosyltransferases/genetics/metabolism ; Lipids/chemistry ; Membrane Glycoproteins/*genetics/*metabolism ; Membrane Proteins/genetics/metabolism ; Open Reading Frames ; Polysaccharides/chemistry/metabolism ; Protein Subunits ; },
abstract = {In this study, characterization of the N-glycosylation process in the haloarchaea Haloferax volcanii was undertaken. Initially, putative Hfx. volcanii homologues of genes involved in eukaryal or bacterial N-glycosylation were identified by bioinformatics. Reverse transcription polymerase chain reaction (RT-PCR) confirmed that the proposed N-glycosylation genes are transcribed, indicative of true proteins being encoded. Where families of related gene sequences were detected, differential transcription of family members under a variety of physiological and environmental conditions was shown. Gene deletions point to certain genes, like alg11, as being essential yet revealed that others, such as the two versions of alg5, are not. Deletion of alg5-A did, however, lead to slower growth and interfered with surface (S)-layer glycoprotein glycosylation, as detected by modified migration on SDS-PAGE and glycostaining approaches. As deletion of stt3, the only component of the oligosaccharide transferase complex detected in Archaea, did not affect cell viability, it appears that N-glycosylation is not essential in Hfx. volcanii. Deletion of stt3 did, nonetheless, hinder both cell growth and S-layer glycoprotein glycosylation. Thus, with genes putatively involved in Hfx. volcanii protein glycosylation identified and the ability to address the roles played by the encoded polypeptides in modifying a reporter glycoprotein, the steps of the archaeal N-glycosylation pathway can be defined.},
}
@article {pmid16755286,
year = {2006},
author = {Albers, SV and Szabó, Z and Driessen, AJ},
title = {Protein secretion in the Archaea: multiple paths towards a unique cell surface.},
journal = {Nature reviews. Microbiology},
volume = {4},
number = {7},
pages = {537-547},
doi = {10.1038/nrmicro1440},
pmid = {16755286},
issn = {1740-1526},
mesh = {Archaea/chemistry/*metabolism ; Archaeal Proteins/*metabolism ; Cell Membrane/chemistry/*metabolism/ultrastructure ; Cell Surface Extensions/chemistry/metabolism/ultrastructure ; Models, Biological ; *Protein Transport ; },
abstract = {Archaea are similar to other prokaryotes in most aspects of cell structure but are unique with respect to the lipid composition of the cytoplasmic membrane and the structure of the cell surface. Membranes of archaea are composed of glycerol-ether lipids instead of glycerol-ester lipids and are based on isoprenoid side chains, whereas the cell walls are formed by surface-layer proteins. The unique cell surface of archaea requires distinct solutions to the problem of how proteins cross this barrier to be either secreted into the medium or assembled as appendages at the cell surface.},
}
@article {pmid16754611,
year = {2006},
author = {Gribaldo, S and Brochier-Armanet, C},
title = {The origin and evolution of Archaea: a state of the art.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {361},
number = {1470},
pages = {1007-1022},
pmid = {16754611},
issn = {0962-8436},
mesh = {*Biological Evolution ; Crenarchaeota/*genetics ; Euryarchaeota/*genetics ; Nuclear Proteins/genetics ; Phylogeny ; RNA, Ribosomal/genetics ; Ribosomal Proteins/genetics ; Signal Recognition Particle/genetics ; },
abstract = {Environmental surveys indicate that the Archaea are diverse and abundant not only in extreme environments, but also in soil, oceans and freshwater, where they may fulfil a key role in the biogeochemical cycles of the planet. Archaea display unique capacities, such as methanogenesis and survival at temperatures higher than 90 degrees C, that make them crucial for understanding the nature of the biota of early Earth. Molecular, genomics and phylogenetics data strengthen Woese's definition of Archaea as a third domain of life in addition to Bacteria and Eukarya. Phylogenomics analyses of the components of different molecular systems are highlighting a core of mainly vertically inherited genes in Archaea. This allows recovering a globally well-resolved picture of archaeal evolution, as opposed to what is observed for Bacteria and Eukarya. This may be due to the fact that no rapid divergence occurred at the emergence of present-day archaeal lineages. This phylogeny supports a hyperthermophilic and non-methanogenic ancestor to present-day archaeal lineages, and a profound divergence between two major phyla, the Crenarchaeota and the Euryarchaeota, that may not have an equivalent in the other two domains of life. Nanoarchaea may not represent a third and ancestral archaeal phylum, but a fast-evolving euryarchaeal lineage. Methanogenesis seems to have appeared only once and early in the evolution of Euryarchaeota. Filling up this picture of archaeal evolution by adding presently uncultivated species, and placing it back in geological time remain two essential goals for the future.},
}
@article {pmid16736576,
year = {2006},
author = {Huang, YP and Liu, P and Liu, Y and Shen, YF and Shen, P},
title = {[Function of promoter DNA fragments from halophilic archaea in Escherichia coli].},
journal = {Wei sheng wu xue bao = Acta microbiologica Sinica},
volume = {46},
number = {2},
pages = {200-204},
pmid = {16736576},
issn = {0001-6209},
mesh = {DNA, Archaeal/*genetics ; Escherichia coli/*genetics/growth &amp; development/metabolism ; Genes, Reporter ; Halobacterium salinarum/*genetics ; *Promoter Regions, Genetic ; Transcription, Genetic ; },
abstract = {RM07 and RM13 DNA fragments could function as promoter in Escherichia coli, which were isolated from an archaeon Halobacterium halobium R1. In the present study, promoter activities of these two fragments were confirmed by beta-galactosidase activity analysis and microcalorimetric studies. They were cloned into promoter-probe vector pYLZ-2 respectively. Four recombinant strains TE07, TE07-2, TE131 and TE132 were obtained, and all fragments were found to be active in E. coli DH5alpha. The beta-galactosidase activity of TE132 was higher than that of TE07-2. Both TE07 and TE131 had weak beta-galactosidase activity. Then the heat output of E. coli DH5alpha and its transformants had been detected by a microcalorimetric method at 37 degrees C. Compared with E. coli DH5alpha, the growth rate constant of E. coli T2 (pYLZ-2), TE07, TE07-2, TE131 and TE132 strain was reduced 6.5%, 11%, 41.1%, 47.5% and 42.7% respectively. When IPTG was added to LB medium, beta-galactosidase activity and heat output had been enhanced slightly in all strains. The results suggested that there was close correspondence between promoter activity and microcalorimetric results, and the heat output of growth was mainly affected by gene expression in E. coli. The higher beta-galactosidase activity of E. coli was, the lower its growth rate constant was. At the meantime, Microcalorimetric studies implied that 700bps of RM13 (RM131) fragment would have stronger promoter activity than RM13. Microcalorimetry may be used as a new approach for analyzing the regulation of foreign gene expression.},
}
@article {pmid16736575,
year = {2006},
author = {Zhu, JY and Hu, YH and Liu, J and Huang, YP and Shen, P},
title = {[Analysis of promoter sequence and its activity of homologues gene rad25 of eukaryotes from halophilic archaea].},
journal = {Wei sheng wu xue bao = Acta microbiologica Sinica},
volume = {46},
number = {2},
pages = {196-199},
pmid = {16736575},
issn = {0001-6209},
mesh = {Archaeal Proteins/*genetics ; Base Sequence ; DNA Helicases/*genetics ; Eukaryotic Cells/*enzymology ; Halobacterium salinarum/enzymology/*genetics ; Haloferax volcanii/genetics ; Molecular Sequence Data ; *Promoter Regions, Genetic ; },
abstract = {The transcriptional product in Halobacterium halobium R1 similar to eukaryotic gene rad25 was analyzed by RT-PCR. Using bgaH as the reporter genes, the promoter function of eukaryotic rad25-like DNA fragment in halophilic archaea was investigated by promoter probe analysis. The important functional regions, which could influence the promoter activity of rad25-like gene, were identified by deletion analysis of the promoter sequence in Haloferax volcanii. It is found that the DNA fragment of promoter similar to eukaryotic gene rad25 contains the typical characteristic sequence of archaeal promoter. These results indicate that rad25-like gene in Halobacterium halobium R1 is active and may play a role on the NER pathway as the eukaryotic pattern.},
}
@article {pmid16736571,
year = {2006},
author = {Cui, HL and Yang, Y and Dilbr, T and Zhou, PJ and Liu, SJ},
title = {[Biodiversity of halophilic archaea isolated from two salt lakes in Xin-Jiang region of China].},
journal = {Wei sheng wu xue bao = Acta microbiologica Sinica},
volume = {46},
number = {2},
pages = {171-176},
pmid = {16736571},
issn = {0001-6209},
mesh = {*Biodiversity ; China ; DNA, Archaeal/genetics ; DNA, Ribosomal/genetics ; Halobacteriaceae/classification/genetics/*isolation &amp; purification ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sodium Chloride/*metabolism ; *Water Microbiology ; },
abstract = {There are more than 1000 salt lakes situated in northern and western regions of China and 790 of these salt lakes are in Xinjiang Uigur Autonomous Region and Qinghai, Tibet, Inner Mongolia. To better understand halophilic archaeal diversity of salt lakes in Xinjiang, water and sediment samples were collected from two salt lakes, namely Aibi salt lake and Aiding salt lake, and the halophilic archaeal diversity of these samples was determined. Totally eighty-six halophilic archeal strains, of which 56 isolated from Aibi salt lake and 30 isolated from Aiding salt lake, were isolated respectively using CM agar medium. All the strains were subjected to 16S rRNA gene sequencing analysis. Similarity analysis based on 16S rRNA gene sequences of all these strains indicated that the isolates from Aibi salt lake belong to 11 different species of genera Haloarcula, Halobacterium, Halorubrum, Haloterrigena, Natrinema and Natronorubrum, and that the isolates from Aiding salt lake belong to 8 different species of genera Haloarcula, Halobiforma, Halorubrum, Haloterrigena, Natrinema. Among the 86 strains, members of Natronorubrum Natrinema, Halorubrum and Haloterrigena, are dominant groups in Aibi salt lake. However, the dominant group in Aibi salt lake are the members of Natrinema, Halorubrum and Haloterrigena. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strains ABH13, ABH 14, ABH 15, ABH 18, ABH 31 and ABH 33 may represent a novel species of Natronorubrum; ABH12, ABH32 and AD30 two novel species of Halorubrum; ABH17 and ABH25, ABH51, ABH52, ABH56 two novel species of Haloterrigena respectively; strain ABH19 a novel species of Haloarcula; strain ABHO7 a novel species of Halobacterium. The Shannon-Wiener's index of Aibi salt lake is 1.899, the same index of Aiding salt lake is 1.317, which indicated that the biodiversity of halophilic archaea from Aibi salt lake was slightly higher than that of Aiding salt lake. Different characteristics in pH of salt concentrations, average annual precipitation, annual evaporation and mankind's impact on two salt lakes might play important roles on halophilic archaeal diversity of two salt lakes.},
}
@article {pmid16730457,
year = {2006},
author = {Djuranovic, S and Rockel, B and Lupas, AN and Martin, J},
title = {Characterization of AMA, a new AAA protein from Archaeoglobus and methanogenic archaea.},
journal = {Journal of structural biology},
volume = {156},
number = {1},
pages = {130-138},
doi = {10.1016/j.jsb.2006.03.010},
pmid = {16730457},
issn = {1047-8477},
mesh = {Adenosine Triphosphatases/*chemistry/genetics/isolation &amp; purification/*metabolism/ultrastructure ; Amino Acid Motifs ; Amino Acid Sequence ; Archaea/*enzymology ; Archaeal Proteins/*chemistry/genetics/isolation &amp; purification/*metabolism/ultrastructure ; Archaeoglobus/*enzymology ; Circular Dichroism ; Cloning, Molecular ; Enzyme Stability ; Molecular Sequence Data ; Molecular Weight ; Phylogeny ; Protein Binding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Recombinant Proteins/metabolism ; Sequence Homology, Amino Acid ; Temperature ; },
abstract = {We have previously reported a new group of AAA proteins, which is only found in Archaeoglobus and methanogenic archaea (AMA). The proteins are phylogenetically basal to the metalloprotease clade and their N-terminal domain is homologous to the beta-clam part of the N-domain of CDC48-like proteins. Here we report the biochemical and biophysical characterization of Archaeoglobus fulgidus AMA, and of its isolated N-terminal (AMA-N) and ATPase (AMA-DeltaN) domains. AfAMA forms hexameric complexes, as does AMA-N, while AMA-DeltaN only forms dimers. The ability to hexamerize is dependent on the integrity of a GYPL motif in AMA-N, which resembles the pore motif of FtsH and HslU. While the physiological function of AMA is unknown, we show that it has ATP-dependent chaperone activity and can prevent the thermal aggregation of proteins in vitro. The ability to interact with non-native proteins resides in the N-domain and is energy-independent.},
}
@article {pmid16715049,
year = {2006},
author = {Cavicchioli, R},
title = {Cold-adapted archaea.},
journal = {Nature reviews. Microbiology},
volume = {4},
number = {5},
pages = {331-343},
doi = {10.1038/nrmicro1390},
pmid = {16715049},
issn = {1740-1526},
mesh = {*Adaptation, Biological ; Archaea/*physiology ; Biodiversity ; *Cold Temperature ; Ecosystem ; },
abstract = {Many archaea are extremophiles. They thrive at high temperatures, at high pressure and in concentrated acidic environments. Nevertheless, the largest proportion and greatest diversity of archaea exist in cold environments. Most of the Earth's biosphere is cold, and archaea represent a significant fraction of the biomass. Although psychrophilic archaea have long been the neglected majority, the study of these microorganisms is beginning to come of age. This review casts a spotlight on the ecology, adaptation biology and unique science that is being realized from studies on cold-adapted archaea.},
}
@article {pmid16701621,
year = {2006},
author = {Silva, AJ and Hirasawa, JS and Varesche, MB and Foresti, E and Zaiat, M},
title = {Evaluation of support materials for the immobilization of sulfate-reducing bacteria and methanogenic archaea.},
journal = {Anaerobe},
volume = {12},
number = {2},
pages = {93-98},
doi = {10.1016/j.anaerobe.2005.12.003},
pmid = {16701621},
issn = {1075-9964},
mesh = {Aluminum Oxide ; Bacteria, Anaerobic/*growth &amp; development/ultrastructure ; Bacterial Adhesion ; Biofilms/*growth &amp; development ; Biomass ; Bioreactors/*microbiology ; Carbon ; Euryarchaeota/*growth &amp; development/ultrastructure ; In Situ Hybridization, Fluorescence ; Indoles/metabolism ; Microbiological Techniques/*instrumentation ; Microscopy, Electron, Scanning ; Oxygen Consumption ; Polyethylene ; Polyurethanes ; Sulfates/metabolism ; Time Factors ; },
abstract = {This paper reports on the adhesion of sulfate-reducing bacteria (SRB) and methanogenic archaea on polyurethane foam (PU), vegetal carbon (VC), low-density polyethylene (PE) and alumina-based ceramics (CE). Anaerobic differential reactors fed with a sulfate-rich synthetic wastewater were used to evaluate the formation of a biofilm. The PU presented the highest specific biomass concentration throughout the experiment, achieving 872 mg TVS/g support, while 84 mg TVS/g support was the maximum value obtained for the other materials. FISH results showed that bacterial cells rather than archaeal cells were predominant on the biofilms. These cells, detected with EUB338 probe, accounted for 76.2% (+/-1.6%), 79.7% (+/-1.3%), 84.4% (+/-1.4%) and 60.2% (+/-1.0%) in PU, VC, PE and CE, respectively, of the 4'6-diamidino-2-phenylindole (DAPI)-stained cells. From these percentages, 44.8% (+/-2.1%), 55.4% (+/-1.2%), 32.7% (+/-1.4%) and 18.1% (+/-1.1%), respectively, represented the SRB group. Archaeal cells, detected with ARC915 probe, accounted for 33.1% (+/-1.6%), 25.4% (+/-1.3%), 22.6% (+/-1.1%) and 41.9% (+/-1.0%) in PU, VC, PE and CE, respectively, of the DAPI-stained cells. Sulfate reduction efficiencies of 39% and 45% and mean chemical oxygen demand (COD) removal efficiencies of 86% and 90% were achieved for PU and VC, respectively. The other two supports, PE and CE, provided mean COD removal efficiencies of 84% and 86%, respectively. However, no sulfate reduction was observed with these supports.},
}
@article {pmid16701533,
year = {2004},
author = {Shin, EC and Choi, BR and Lim, WJ and Hong, SY and An, CL and Cho, KM and Kim, YK and An, JM and Kang, JM and Lee, SS and Kim, H and Yun, HD},
title = {Phylogenetic analysis of archaea in three fractions of cow rumen based on the 16S rDNA sequence.},
journal = {Anaerobe},
volume = {10},
number = {6},
pages = {313-319},
doi = {10.1016/j.anaerobe.2004.08.002},
pmid = {16701533},
issn = {1075-9964},
abstract = {Phylogenetic analysis of archaea in the rumen ecosystem was analysed by PCR of 16S rDNA from the bovine rumen using archaea-specific primers. The libraries were constructed from rumen fluid (AF), rumen solid (AS), and rumen epithelium (AE) from a rumen-fistulated Korean cow (Hanwoo). The 45 AF clones could be divided into three groups and the largest group was affiliated with the Methanomicrobiaceae family (96% of clones). The AF clones contained a high proportion of unidentifiable clones (67%). The 39 AE clones could be divided into two groups and the largest group was also affiliated with the Methanomicrobiaceae family (95% of clones). The AE clones contained a low proportion of unidentifiable clones (5%). The 20 AS clones could be divided into two groups that were affiliated with either the Methanobacteriaceae family (55%) or the Methanomicrobiaceae family (45%). The AS clones contained a moderate proportion of unidentifiable clones (40%). The predominant family of whole rumen archaea was found to belong to the Methanomicrobiaceae (85%). Methanomicrobiaceae were predominant in the rumen epithelium and the rumen fluid while Methanobacteriaceae were predominant in the rumen solid. One clone from the rumen fluid and two clones from the rumen epithelium contained rDNA sequences of Non-Thermophilic-Crenarchaeota (NTC) and Thermophilic-Crenarchaeota (TC), respectively, which have not previously been described from the rumen.},
}
@article {pmid16701495,
year = {2004},
author = {Sossa, K and Alarcón, M and Aspé, E and Urrutia, H},
title = {Effect of ammonia on the methanogenic activity of methylaminotrophic methane producing Archaea enriched biofilm.},
journal = {Anaerobe},
volume = {10},
number = {1},
pages = {13-18},
doi = {10.1016/j.anaerobe.2003.10.004},
pmid = {16701495},
issn = {1075-9964},
abstract = {Ammonia is a metabolic product in the decomposition of protein wastes, and has a recognized inhibitory effect on methanogenesis; this effect has been slightly quantified on methanogenic biofilms and particularly those populated by methanogenic Archaea which produce ammonia as a catabolic product from methylated amines. This paper presents studies on the effect of ammonia on maximum methanogenic activity of anaerobic biofilms enriched by methylaminotrophic methane producing Archaea (mMPA). The effect of unionized free ammonia on the specific maximum methanogenic activity of a mMPA enriched biofilm was studied, using 250 mL flasks containing ceramic rings colonized by 30 day-old experimental biofilm and adding 48.8 (control system), 73.8, 98.8, 148.8, 248.8, 448.8 and 848.8 mg NH(3)-N/L. The systems were maintained for ten days at a pH of 7.5 and temperature of 37 degrees C. The results showed that at 848.8 mg NH(3)-N/L, biofilm methane production required 36 h adaptation period, prior to entering into maximum production phase. The highest maximum methanogenic activity reached a value of 2.337+/-0.213 g COD methane/g VSS *day when 48.8 mg NH(3)-N/L was added, and inhibition was clearly observed in those systems above 148.8 mg NH(3)-N/L, producing under 1.658+/-0.185 g COD methane/g VSS *day. The lowest methanogenic activity reached was 0.639+/-0.162 g COD methane/g VSS *day at the system added with 848.8 mg NH(3)-N/L. When applying the Luong and non-competitive inhibition models, the best fit was obtained with the non-competitive model, which predicted 50% inhibition of methanogenic activity at 365.288 mg NH(3)-N/L.},
}
@article {pmid16645313,
year = {2005},
author = {Müller, V and Lemker, T and Lingl, A and Weidner, C and Coskun, U and Grüber, G},
title = {Bioenergetics of archaea: ATP synthesis under harsh environmental conditions.},
journal = {Journal of molecular microbiology and biotechnology},
volume = {10},
number = {2-4},
pages = {167-180},
doi = {10.1159/000091563},
pmid = {16645313},
issn = {1464-1801},
mesh = {Adenosine Triphosphate/*metabolism ; Archaea/*physiology ; Archaeal Proteins/chemistry/metabolism ; Biological Evolution ; Dimerization ; *Energy Metabolism ; Hydrogen-Ion Concentration ; Protein Binding ; Protein Conformation ; Protein Subunits/chemistry/metabolism ; Proton-Translocating ATPases/chemistry/*metabolism ; *Temperature ; },
abstract = {Archaea are a heterogeneous group of microorganisms that often thrive under harsh environmental conditions such as high temperatures, extreme pHs and high salinity. As other living cells, they use chemiosmotic mechanisms along with substrate level phosphorylation to conserve energy in form of ATP. Because some archaea are rooted close to the origin in the tree of life, these unusual mechanisms are considered to have developed very early in the history of life and, therefore, may represent first energy-conserving mechanisms. A key component in cellular bioenergetics is the ATP synthase. The enzyme from archaea represents a new class of ATPases, the A1A0 ATP synthases. They are composed of two domains that function as a pair of rotary motors connected by a central and peripheral stalk(s). The structure of the chemically-driven motor (A1) was solved by small-angle X-ray scattering in solution, and the structure of the first A1A0 ATP synthases was obtained recently by single particle analyses. These studies revealed novel structural features such as a second peripheral stalk and a collar-like structure. In addition, the membrane-embedded electrically-driven motor (A0) is very different in archaea with sometimes novel, exceptional subunit composition and coupling stoichiometries that may reflect the differences in energy-conserving mechanisms as well as adaptation to temperatures at or above 100 degrees C.},
}
@article {pmid16629380,
year = {2006},
author = {Dave, BP and Anshuman, K and Hajela, P},
title = {Siderophores of halophilic archaea and their chemical characterization.},
journal = {Indian journal of experimental biology},
volume = {44},
number = {4},
pages = {340-344},
pmid = {16629380},
issn = {0019-5189},
mesh = {Halobacterium/*chemistry/metabolism ; Siderophores/*chemistry/*metabolism ; },
abstract = {Nine halophilic archaea viz., Halobacterium salinarum, Halobacterium sp.1, Halobacterium sp.2, Halobaculum sp., Halococcus saccharolyticus, Halorubrum saccharovorum, Haloterrigena turkmenica, Halogeometricum sp. and Natrialba sp. isolated from marine salterns around Bhavnagar coast were screened for siderophore production. Five isolates viz., Halococcus saccharolyticus, Halorubrum saccharovorum, Haloterrigena turkmenica, Halogeometricum sp. and Natrialba sp. produced siderophores as evidenced by positive reaction in FeCl3 test, CAS assay and CAS agar plate test. Determination of chemical nature of siderophores by chemical assays and bioassays identified them as carboxylates. Quantification of siderophores indicated Halorubrum saccharovorum to be the maximum siderophore producer (2.62 RE mg/ml) and Halococcus saccharolyticus to be the least (1.33 RE mg/ml). The present study is the first report on siderophore production in Indian haloarchaeal strains. Mechanism of iron assimilation in four non-siderophore isolates still needs to be investigated further.},
}
@article {pmid16621512,
year = {2006},
author = {Conrad, R and Erkel, C and Liesack, W},
title = {Rice Cluster I methanogens, an important group of Archaea producing greenhouse gas in soil.},
journal = {Current opinion in biotechnology},
volume = {17},
number = {3},
pages = {262-267},
doi = {10.1016/j.copbio.2006.04.002},
pmid = {16621512},
issn = {0958-1669},
mesh = {Agriculture/methods ; Ecology ; Euryarchaeota/*physiology ; Methane/*metabolism ; Oryza/microbiology ; *Soil Microbiology ; },
abstract = {Methane, which is an important greenhouse gas, is to a large part produced by methanogenic archaea in anoxic soils and sediments. Rice Cluster I methanogens have been characterized on the basis of their 16S rRNA and mcrA gene sequences, and were found to form a separate lineage within the phylogenetic radiation of Methanosarcinales and Methanomicrobiales. As isolation has not been achieved until recently, our knowledge of distribution, physiology and environmental significance of Rice Cluster I is solely based on molecular biology techniques. Rice Cluster I seems to be widely distributed, particularly in rice fields, possibly occupying different niches among the methane producers. One niche seems to be methane production on roots driven by plant photosynthesis, contributing substantially to the release of methane from rice fields into the atmosphere.},
}
@article {pmid16621083,
year = {2006},
author = {Angelov, A and Liebl, W},
title = {Insights into extreme thermoacidophily based on genome analysis of Picrophilus torridus and other thermoacidophilic archaea.},
journal = {Journal of biotechnology},
volume = {126},
number = {1},
pages = {3-10},
doi = {10.1016/j.jbiotec.2006.02.017},
pmid = {16621083},
issn = {0168-1656},
mesh = {Acclimatization/*genetics ; Electron Transport/genetics/physiology ; Gene Transfer, Horizontal/*genetics ; Hydrogen-Ion Concentration ; Membrane Transport Proteins/genetics ; Phylogeny ; RNA, Ribosomal, 16S/classification ; Sulfolobus/*genetics/physiology ; Thermoplasmales/*genetics/physiology ; },
abstract = {Thermoacidophiles are prokaryotic microorganisms with the stunning capability to survive and multiply at extremely low pH and simultaneously at high temperatures. The mechanisms by which these organisms, exclusively members of the Archaea, cope with their harsh surroundings are poorly understood. The genome sequences of several representatives of the thermoacidophilic genera Picrophilus, Thermoplasma and Sulfolobus have recently become available. Genome-wide comparison has revealed a number of features as possible facets of the overall acidophilic survival strategy of the most thermoacidophilic organisms known, such as a high ratio of secondary over primary transport systems, the composition of the respiratory chain, and the frequent genetic input via lateral gene transfer (LGT) during evolution.},
}
@article {pmid16615999,
year = {2006},
author = {Huang, H and Liu, J and de Marco, A},
title = {Induced fit of passenger proteins fused to Archaea maltose binding proteins.},
journal = {Biochemical and biophysical research communications},
volume = {344},
number = {1},
pages = {25-29},
doi = {10.1016/j.bbrc.2006.03.151},
pmid = {16615999},
issn = {0006-291X},
mesh = {Archaeal Proteins/*chemistry/genetics/isolation &amp; purification ; Carrier Proteins/*chemistry/genetics/isolation &amp; purification ; Escherichia coli/genetics/metabolism ; Glutathione Transferase/chemistry/genetics/isolation &amp; purification ; Green Fluorescent Proteins/chemistry/genetics/isolation &amp; purification ; *Heating ; Maltose-Binding Proteins ; Protein Folding ; Recombinant Fusion Proteins/biosynthesis/*chemistry/*isolation &amp; purification ; Solubility ; },
abstract = {Maltose binding proteins (MBPs) are used as carriers for improving the solubility of passenger proteins. Our results indicate that the higher solubility of the fusions correlates with their elevated heat stability. Fusions of the otherwise thermo-sensitive GFP with MBPs from Archaea, but not GST-GFP and Escherichia coli MBP-GFP, maintained their fluorescence and structure after 10min incubation at 100 degrees C and could be purified by heating the bacteria lysate, with yields even higher than those obtained using metal affinity chromatography. Furthermore, only correctly folded proteins could stand the heating treatment and, therefore, the heat-purification method can be used as a quality control step to select homogeneous monodispersed material whereas soluble aggregates are removed by precipitation.},
}
@article {pmid16613609,
year = {2006},
author = {Oren, A and Pri-El, N and Shapiro, O and Siboni, N},
title = {Buoyancy studies in natural communities of square gas-vacuolate archaea in saltern crystallizer ponds.},
journal = {Saline systems},
volume = {2},
number = {},
pages = {4},
pmid = {16613609},
issn = {1746-1448},
abstract = {BACKGROUND: Possession of gas vesicles is generally considered to be advantageous to halophilic archaea: the vesicles are assumed to enable the cells to float, and thus reach high oxygen concentrations at the surface of the brine.<br><br>RESULTS: We studied the possible ecological advantage of gas vesicles in a dense community of flat square extremely halophilic archaea in the saltern crystallizer ponds of Eilat, Israel. We found that in this environment, the cells' content of gas vesicles was insufficient to provide positive buoyancy. Instead, sinking/floating velocities were too low to permit vertical redistribution.<br><br>CONCLUSION: The hypothesis that the gas vesicles enable the square archaea to float to the surface of the brines in which they live was not supported by experimental evidence. Presence of the vesicles, which are mainly located close to the cell periphery, may provide an advantage as they may aid the cells to position themselves parallel to the surface, thereby increasing the efficiency of light harvesting by the retinal pigments in the membrane.},
}
@article {pmid16597851,
year = {2006},
author = {Vianna, ME and Conrads, G and Gomes, BP and Horz, HP},
title = {Identification and quantification of archaea involved in primary endodontic infections.},
journal = {Journal of clinical microbiology},
volume = {44},
number = {4},
pages = {1274-1282},
pmid = {16597851},
issn = {0095-1137},
mesh = {Archaea/classification/genetics/*isolation &amp; purification/metabolism ; DNA, Archaeal/analysis ; DNA, Ribosomal/analysis ; Dental Pulp Cavity/*microbiology ; Endodontics ; Humans ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; },
abstract = {Members of the domain Archaea, one of the three domains of life, are a highly diverse group of prokaryotes, distinct from bacteria and eukaryotes. Despite their abundance and ubiquity on earth, including their close association with humans, animals, and plants, so far no pathogenic archaea have been described. As some archaea live in close proximity to anaerobic bacteria, for instance, in the human gut system and in periodontal pockets, the aim of our study was to assess whether archaea might possibly be involved in human endodontic infections, which are commonly polymicrobial. We analyzed 20 necrotic uniradicular teeth with radiographic evidence of apical periodontitis and with no previous endodontic treatment. Using real-time quantitative PCR based on the functional gene mcrA (encoding the methyl coenzyme M reductase, specific to methanogenic archaea) and on archaeal 16S rRNA genes, we found five cases to be positive. Direct sequencing of PCR products from both genes showed that the archaeal community was dominated by a Methanobrevibacter oralis-like phylotype. The size of the archaeal population at the diseased sites ranged from 1.3 x 10(5) to 6.8 x 10(5) 16S rRNA gene target molecule numbers and accounted for up to 2.5% of the total prokaryotic community (i.e., bacteria plus archaea). Our findings show that archaea can be intimately connected with infectious diseases and thus support the hypothesis that members of the domain Archaea may have a role as human pathogens.},
}
@article {pmid16584891,
year = {2006},
author = {Summer, H and Bruderer, R and Weber-Ban, E},
title = {Characterization of a new AAA+ protein from archaea.},
journal = {Journal of structural biology},
volume = {156},
number = {1},
pages = {120-129},
doi = {10.1016/j.jsb.2006.01.010},
pmid = {16584891},
issn = {1047-8477},
mesh = {Adenosine Triphosphatases/analysis/*chemistry/isolation &amp; purification/*metabolism/ultrastructure ; Adenosine Triphosphate/metabolism ; Amino Acid Sequence ; Archaeal Proteins/*chemistry/isolation &amp; purification/*metabolism/ultrastructure ; Archaeoglobus fulgidus/enzymology/genetics ; Circular Dichroism ; Enzyme Stability ; Escherichia coli/genetics ; Hydrolysis ; Kinetics ; Molecular Sequence Data ; Molecular Weight ; Phylogeny ; Protein Binding ; Protein Structure, Tertiary ; Sequence Homology, Amino Acid ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; Temperature ; },
abstract = {We investigated a new archaeal member of the AAA+ protein family (ATPases associated with various cellular activities) which is found in all methanogenic archaea and the sulphate-reducer Archaeoglobus fulgidus. These proteins cluster to COG1223 predicted to form a subgroup of the AAA+ ATPases. The gene from A. fulgidus codes for a protein of 40 kDa monomeric molecular weight, which we overexpressed in Escherichia coli and purified to homogeneity. The protein forms ring-shaped complexes with a diameter of 125A as determined by electron microscopy. Using sedimentation equilibrium analysis we demonstrate that it assembles into hexamers over a wide concentration range both in presence and absence of ATP. As suggested by homology to other members of the AAA+ family, the complex binds and hydrolyzes ATP. Michaelis-Menten analysis revealed a k(cat) of 118 min(-1) and a K(M) of 1.4 mM at 78 degrees C. This hyperthermophilic archaeal ATPase is stable to 86 degrees C and the ATPase activity is maximal at this temperature. The protein is most homologous to the AAA-domain of FtsH from bacteria, while the N-terminal domain shows predicted structural homology to members of the CDC48 family of AAA proteins. Possible roles of this new AAA+ protein are discussed.},
}
@article {pmid16579455,
year = {2006},
author = {Pan, HL and Zhou, C and Wang, HL and Xue, YF and Ma, YH},
title = {[Diversity of halophilic archaea in hypersaline lakes of Inner Mongolia, China].},
journal = {Wei sheng wu xue bao = Acta microbiologica Sinica},
volume = {46},
number = {1},
pages = {1-6},
pmid = {16579455},
issn = {0001-6209},
mesh = {Biodiversity ; China ; *DNA, Ribosomal ; Halobacteriales/classification/*genetics/isolation &amp; purification/metabolism ; *Phylogeny ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S ; Restriction Mapping ; Sequence Analysis, DNA ; Sodium Chloride/metabolism ; *Water Microbiology ; },
abstract = {The aims of this work were to explore the diversity of halophilic archaea in hypersaline lakes of Inner Mongolia, China and to collect novel halophilic archaea. One hundred and sixty-five halophilic archaea were isolated from the three different types of hypersaline lakes (Erliannor, shangmatala and Xilin soda lake) in Inner Mongolia. By analysis of the restriction patterns of amplified 16S rDNA (ARDRA) with the enzyme Afa I and Hae II, respectively, the isolates were clustered into 14 genotypes, and the representatives of each genotype were randomly chosen for the determination of 16S rDNA sequence. The phylogenetic analysis revealed that all of the isolates were clustered into 10 groups: Halorubrum, Natronococcus, Natronorubrum, Haloterrigena, Halorhabdus, Halobiforma, Haloarcula, Haloferax and other two unknown groups. Dominant isolates were related to Halorubrum spp. in all three lakes. Some of the isolates studied showed less affiliation with known taxa (<98% sequence similarity) and may represent novel taxa. Two isolates HXH33 and HSH33 showed very less affiliation with known genus (< 93% sequence similarity) and may represent two new genera. These results suggest that diverse archaea exist in and the unknown archaea thrive in the hypersaline lakes of Inner Mongolia.},
}
@article {pmid16535736,
year = {1997},
author = {Janssen, PH and Frenzel, P},
title = {Inhibition of methanogenesis by methyl fluoride: studies of pure and defined mixed cultures of anaerobic bacteria and archaea.},
journal = {Applied and environmental microbiology},
volume = {63},
number = {11},
pages = {4552-4557},
pmid = {16535736},
issn = {0099-2240},
abstract = {Methyl fluoride (fluoromethane [CH(inf3)F]) has been used as a selective inhibitor of CH(inf4) oxidation by aerobic methanotrophic bacteria in studies of CH(inf4) emission from natural systems. In such studies, CH(inf3)F also diffuses into the anaerobic zones where CH(inf4) is produced. The effects of CH(inf3)F on pure and defined mixed cultures of anaerobic microorganisms were investigated. About 1 kPa of CH(inf3)F, similar to the amounts used in inhibition experiments, inhibited growth of and CH(inf4) production by pure cultures of aceticlastic methanogens (Methanosaeta spp. and Methanosarcina spp.) and by a methanogenic mixed culture of anaerobic microorganisms in which acetate was produced as an intermediate. With greater quantities of CH(inf3)F, hydrogenotrophic methanogens were also inhibited. At a partial pressure of CH(inf3)F of 1 kPa, homoacetogenic, sulfate-reducing, and fermentative bacteria and a methanogenic mixed culture of anaerobic microorganisms based on hydrogen syntrophy were not inhibited. The inhibition by CH(inf3)F of the growth and CH(inf4) production of Methanosarcina mazei growing on acetate was reversible. CH(inf3)F inhibited only acetate utilization by Methanosarcina barkeri, which is able to use acetate and hydrogen simultaneously, when both acetate and hydrogen were present. These findings suggest that the use of CH(inf3)F as a selective inhibitor of aerobic CH(inf4) oxidation in undefined systems must be interpreted with great care. However, by a careful choice of concentrations, CH(inf3)F may be useful for the rapid determination of the role of acetate as a CH(inf4) precursor.},
}
@article {pmid16516228,
year = {2006},
author = {Guy, CP and Haldenby, S and Brindley, A and Walsh, DA and Briggs, GS and Warren, MJ and Allers, T and Bolt, EL},
title = {Interactions of RadB, a DNA repair protein in archaea, with DNA and ATP.},
journal = {Journal of molecular biology},
volume = {358},
number = {1},
pages = {46-56},
doi = {10.1016/j.jmb.2006.02.010},
pmid = {16516228},
issn = {0022-2836},
support = {//Wellcome Trust/United Kingdom ; },
mesh = {Adenosine Triphosphate/*metabolism ; Amino Acid Sequence ; Amino Acid Substitution/genetics ; *Archaea ; Archaeal Proteins/chemistry/*metabolism ; DNA/*metabolism ; DNA Damage ; *DNA Repair/radiation effects ; DNA-Binding Proteins/chemistry/*metabolism ; Evolution, Molecular ; Haloferax volcanii/cytology/radiation effects ; Models, Molecular ; Molecular Sequence Data ; Phylogeny ; Protein Conformation ; Recombination, Genetic ; Ultraviolet Rays ; },
abstract = {The RecA family of recombinases (RecA, Rad51, RadA and UvsX) catalyse strand-exchange between homologous DNA molecules by utilising conserved DNA-binding modules and a common core ATPase domain. RadB was identified in archaea as a Rad51-like protein on the basis of conserved ATPase sequences. However, RadB does not catalyse strand exchange and does not turn over ATP efficiently. RadB does bind DNA, and here we report a triplet of residues (Lys-His-Arg) that is highly conserved at the RadB C terminus, and is crucial for DNA binding. This is consistent with the motif forming a "basic patch" of highly conserved residues identified in an atomic structure of RadB from Thermococcus kodakaraensis. As the triplet motif is conserved at the C terminus of XRCC2 also, a mammalian Rad51-paralogue, we present a phylogenetic analysis that clarifies the relationship between RadB, Rad51-paralogues and recombinases. We investigate interactions between RadB and ATP using genetics and biochemistry; ATP binding by RadB is needed to promote survival of Haloferax volcanii after UV irradiation, and ATP, but not other NTPs, induces pronounced conformational change in RadB. This is the first genetic analysis of radB, and establishes its importance for maintaining genome stability in archaea. ATP-induced conformational change in RadB may explain previous reports that RadB controls Holliday junction resolution by Hjc, depending on the presence or the absence of ATP.},
}
@article {pmid16508994,
year = {2006},
author = {Liu, CQ and Plumb, J and Hendry, P},
title = {Rapid specific detection and quantification of bacteria and archaea involved in mineral sulfide bioleaching using real-time PCR.},
journal = {Biotechnology and bioengineering},
volume = {94},
number = {2},
pages = {330-336},
doi = {10.1002/bit.20845},
pmid = {16508994},
issn = {0006-3592},
mesh = {Archaea/*genetics/isolation &amp; purification ; Bacteria/*genetics/isolation &amp; purification ; Colony Count, Microbial ; DNA, Bacterial/*analysis ; Minerals/metabolism ; Polymerase Chain Reaction/*methods ; RNA, Ribosomal, 16S/genetics ; Reproducibility of Results ; Sulfides/*metabolism ; },
abstract = {A SybrGreen real-time PCR assay was developed to detect and quantify both total and selected 16S rDNA species of bacteria and archaea involved in the bioleaching of metals from sulfide ores. A set of specific and universal primers based on 16S rDNA sequences was designed and validated for specific detection and quantification of DNA isolated from representative strains of Acidianus brierleyi, Sulfolobus sp., Sulfobacillus thermosulfidooxidans, Sulfobacillus acidophilus, Acidithiobacillus caldus, and Leptospirillum ferrooxidans. An artificial sequence based on 16S rDNA was constructed to quantify total 16S rDNA in mixed DNA samples. The real-time PCR assay was further validated using a mixture of 16S rDNA amplicons derived from the six different species, each added at a known amount. Finally, the real-time PCR assay was used to monitor the change of 16S rDNA copies of four bioleaching strains inoculated into chalcopyrite airlift column reactors operated at different temperatures. The growth dynamics of these strains correlated well with the expected effects of temperature in the chalcopyrite-leaching environment. The suitability of this method for monitoring microbial populations in industrial bioleaching environments is discussed.},
}
@article {pmid16505362,
year = {2006},
author = {Biddle, JF and Lipp, JS and Lever, MA and Lloyd, KG and Sørensen, KB and Anderson, R and Fredricks, HF and Elvert, M and Kelly, TJ and Schrag, DP and Sogin, ML and Brenchley, JE and Teske, A and House, CH and Hinrichs, KU},
title = {Heterotrophic Archaea dominate sedimentary subsurface ecosystems off Peru.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {103},
number = {10},
pages = {3846-3851},
pmid = {16505362},
issn = {0027-8424},
mesh = {Anaerobiosis ; Archaea/classification/genetics/*isolation &amp; purification/metabolism ; Carbon/metabolism ; *Ecosystem ; Energy Metabolism ; Geologic Sediments/*microbiology ; Lipids/chemistry/isolation &amp; purification ; Marine Biology ; Molecular Sequence Data ; Peru ; Phylogeny ; RNA, Archaeal/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics/isolation &amp; purification ; },
abstract = {Studies of deeply buried, sedimentary microbial communities and associated biogeochemical processes during Ocean Drilling Program Leg 201 showed elevated prokaryotic cell numbers in sediment layers where methane is consumed anaerobically at the expense of sulfate. Here, we show that extractable archaeal rRNA, selecting only for active community members in these ecosystems, is dominated by sequences of uncultivated Archaea affiliated with the Marine Benthic Group B and the Miscellaneous Crenarchaeotal Group, whereas known methanotrophic Archaea are not detectable. Carbon flow reconstructions based on stable isotopic compositions of whole archaeal cells, intact archaeal membrane lipids, and other sedimentary carbon pools indicate that these Archaea assimilate sedimentary organic compounds other than methane even though methanotrophy accounts for a major fraction of carbon cycled in these ecosystems. Oxidation of methane by members of Marine Benthic Group B and the Miscellaneous Crenarchaeotal Group without assimilation of methane-carbon provides a plausible explanation. Maintenance energies of these subsurface communities appear to be orders of magnitude lower than minimum values known from laboratory observations, and ecosystem-level carbon budgets suggest that community turnover times are on the order of 100-2,000 years. Our study provides clues about the metabolic functionality of two cosmopolitan groups of uncultured Archaea.},
}
@article {pmid16487318,
year = {2006},
author = {Thomas, JR and Bolhuis, A},
title = {The tatC gene cluster is essential for viability in halophilic archaea.},
journal = {FEMS microbiology letters},
volume = {256},
number = {1},
pages = {44-49},
doi = {10.1111/j.1574-6968.2006.00107.x},
pmid = {16487318},
issn = {0378-1097},
support = {C19762/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {DNA Primers/chemistry ; Escherichia coli Proteins/genetics/*physiology ; Gene Order/genetics ; Halobacteriales/genetics/*physiology ; Membrane Transport Proteins/genetics/*physiology ; Microbial Viability/*genetics ; Multigene Family/genetics/*physiology ; Plasmids ; Polymerase Chain Reaction/methods ; Time Factors ; },
abstract = {In prokaryotes the twin-arginine translocase (Tat) is a unique transport system for the export of folded proteins. The Tat pathway is usually involved in the export of a small proportion of extracytoplasmic proteins. An exception is found in halophilic archaea, in which the majority of secretory proteins have been predicted to be Tat-dependent. All haloarchaea analysed to date contain two genes encoding homologues of the Tat-component TatC. In all of these cases both genes are located adjacently on the chromosome, indicating that they form a functional unit. We show that this gene cluster is essential for viability in haloarchaea, which is in complete contrast to all other prokaryotes that have been tested thus far.},
}
@article {pmid16482157,
year = {2006},
author = {Frigaard, NU and Martinez, A and Mincer, TJ and DeLong, EF},
title = {Proteorhodopsin lateral gene transfer between marine planktonic Bacteria and Archaea.},
journal = {Nature},
volume = {439},
number = {7078},
pages = {847-850},
doi = {10.1038/nature04435},
pmid = {16482157},
issn = {1476-4687},
mesh = {Archaea/classification/*genetics ; Bacteria/*genetics ; Gene Transfer, Horizontal/*genetics ; Genes, Archaeal/genetics ; Genes, Bacterial/genetics ; Genes, rRNA/genetics ; Genome ; Genomic Library ; Marine Biology ; Molecular Sequence Data ; Photic Stimulation ; Phylogeny ; Plankton/*genetics ; Rhodopsin/*genetics ; Rhodopsins, Microbial ; Seawater/*microbiology ; Sunlight ; Synteny ; },
abstract = {Planktonic Bacteria, Archaea and Eukarya reside and compete in the ocean's photic zone under the pervasive influence of light. Bacteria in this environment were recently shown to contain photoproteins called proteorhodopsins, thought to contribute to cellular energy metabolism by catalysing light-driven proton translocation across the cell membrane. So far, proteorhodopsin genes have been well documented only in proteobacteria and a few other bacterial groups. Here we report the presence and distribution of proteorhodopsin genes in Archaea affiliated with the order Thermoplasmatales, in the ocean's upper water column. The genomic context and phylogenetic relationships of the archaeal and proteobacterial proteorhodopsins indicate its probable lateral transfer between planktonic Bacteria and Archaea. About 10% of the euryarchaeotes in the photic zone contained the proteorhodopsin gene adjacent to their small-subunit ribosomal RNA. The archaeal proteorhodopsins were also found in other genomic regions, in the same or in different microbial lineages. Although euryarchaeotes were distributed throughout the water column, their proteorhodopsins were found only in the photic zone. The cosmopolitan phylogenetic distribution of proteorhodopsins reflects their significant light-dependent fitness contributions, which drive the photoprotein's lateral acquisition and retention, but constrain its dispersal to the photic zone.},
}
@article {pmid16478446,
year = {2006},
author = {Wu, XL and Friedrich, MW and Conrad, R},
title = {Diversity and ubiquity of thermophilic methanogenic archaea in temperate anoxic soils.},
journal = {Environmental microbiology},
volume = {8},
number = {3},
pages = {394-404},
doi = {10.1111/j.1462-2920.2005.00904.x},
pmid = {16478446},
issn = {1462-2912},
mesh = {Anaerobiosis ; Archaea/*classification/genetics/*isolation &amp; purification ; *Biodiversity ; China ; DNA Fingerprinting ; DNA, Archaeal/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Ecosystem ; Methane/*biosynthesis ; Methanomicrobiales/classification/genetics/isolation &amp; purification ; Methanosarcinaceae/classification/genetics/isolation &amp; purification ; Molecular Sequence Data ; Phylogeny ; Polymorphism, Restriction Fragment Length ; Sequence Analysis, DNA ; *Soil Microbiology ; Temperature ; },
abstract = {Temperate rice field soil from Vercelli (Italy) contains moderately thermophilic methanogens of the yet uncultivated rice cluster I (RC-I), which become prevalent upon incubation at temperatures of 45-50 degrees C. We studied whether such thermophilic methanogens were ubiquitously present in anoxic soils. Incubation of different rice field soils (from Italy, China and the Philippines) and flooded riparian soils (from the Netherlands) at 45 degrees C resulted in vigorous CH(4) production after a lag phase of about 10 days. The archaeal community structure in the soils was analysed by terminal restriction fragment length polymorphism (T-RFLP) targeting the SSU rRNA genes retrieved from the soil, and by cloning and sequencing. Clones of RC-I methanogens mostly exhibited T-RF of 393 bp, but also terminal restriction fragment (T-RF) of 158 and 258 bp length, indicating a larger diversity than previously assumed. No RC-I methanogens were initially found in flooded riparian soils. However, these archaea became abundant upon incubation of the soil at 45 degrees C. Thermophilic RC-I methanogens were also found in the rice field soils from Pavia, Pila and Gapan. However, the archaeal communities in these soils also contained other methanogenic archaea at high temperature. Rice field soil from Buggalon, on the other hand, only contained thermophilic Methanomicrobiales rather than RC-I methanogens, and rice field soil from Jurong mostly Methanomicrobiales and only a few RC-I methanogens. The archaeal community of rice field soil from Zhenjiang almost exclusively consisted of Methanosarcinaceae when incubated at high temperature. Our results show that moderately thermophilic methanogens are common in temperate soils. However, RC-I methanogens are not always dominating or ubiquitous.},
}
@article {pmid16465452,
year = {2006},
author = {Reed, AJ and Lutz, RA and Vetriani, C},
title = {Vertical distribution and diversity of bacteria and archaea in sulfide and methane-rich cold seep sediments located at the base of the Florida Escarpment.},
journal = {Extremophiles : life under extreme conditions},
volume = {10},
number = {3},
pages = {199-211},
pmid = {16465452},
issn = {1431-0651},
mesh = {Archaea/genetics/*isolation &amp; purification ; Bacteria/genetics/*isolation &amp; purification ; Cold Temperature ; DNA, Ribosomal/genetics ; Florida ; Genetic Variation/genetics ; Genome, Archaeal/genetics ; Genome, Bacterial/genetics ; Geologic Sediments/*chemistry/*microbiology ; Methane/*analysis ; Phylogeny ; Sulfides/*analysis ; },
abstract = {The bacterial and archaeal communities of the sediments at the base of the Florida Escarpment (Gulf of Mexico, USA) were investigated using molecular phylogenetic analysis. The total microbial community DNA of each of three vertical zones (top, middle and bottom) of a sediment core was extracted and the 16S rRNA genes were amplified by PCR, cloned and sequenced. Shannon-Weaver Diversity measures of bacteria were high in all three zones. For the archaea, diversity was generally low, but increased with depth. The archaeal clonal libraries were dominated by representatives of four groups of organisms involved in the anaerobic oxidation of methane (ANME groups). Phylogenetic analysis of bacteria suggests the dominance of epsilon-proteobacteria in the top zone, the epsilon-, delta- and gamma-proteobacteria in the middle zone and the delta-proteobacteria in the bottom zone of the core. Members of the Cytophaga-Flexibacter-Bacteroidetes group, the Chloroflexi/green non-sulfur bacteria, the Gram+ (Firmicutes), the Planctomyces, candidate division WS3 and Fusobacterium were also detected. Our data suggest that the community structure and diversity of microorganisms can shift greatly within small vertical distances, possibly in response to changes in the physical and chemical conditions.},
}
@article {pmid16461723,
year = {2006},
author = {Karr, EA and Ng, JM and Belchik, SM and Sattley, WM and Madigan, MT and Achenbach, LA},
title = {Biodiversity of methanogenic and other archaea in the permanently frozen Lake Fryxell, Antarctica.},
journal = {Applied and environmental microbiology},
volume = {72},
number = {2},
pages = {1663-1666},
pmid = {16461723},
issn = {0099-2240},
mesh = {Antarctic Regions ; Archaea/*genetics/isolation &amp; purification/metabolism ; Base Sequence ; Biodiversity ; Crenarchaeota/genetics/isolation &amp; purification/metabolism ; DNA, Archaeal/genetics ; Ecosystem ; Euryarchaeota/genetics/isolation &amp; purification/metabolism ; Fresh Water/*microbiology ; Genes, Archaeal ; Geologic Sediments/microbiology ; Methane/biosynthesis ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; RNA, Archaeal/genetics ; RNA, Ribosomal, 16S/genetics ; Sulfides/metabolism ; },
abstract = {Archaea were detected in molecular diversity studies of the permanently frozen Lake Fryxell, Antarctica. Two clusters of methanogens were detected in the sediments, and another cluster of possibly methanotrophic Euryarchaeota was detected in the anoxic water column just above the sediments. One crenarchaeote was detected in water just below the oxycline. The Archaea present in Lake Fryxell are likely involved in the major biogeochemical cycles that occur there.},
}
@article {pmid16428816,
year = {2006},
author = {Kato, N and Yurimoto, H and Thauer, RK},
title = {The physiological role of the ribulose monophosphate pathway in bacteria and archaea.},
journal = {Bioscience, biotechnology, and biochemistry},
volume = {70},
number = {1},
pages = {10-21},
doi = {10.1271/bbb.70.10},
pmid = {16428816},
issn = {0916-8451},
mesh = {Aldehyde-Lyases/genetics/metabolism ; Aldose-Ketose Isomerases/genetics/metabolism ; Archaea/classification/genetics/*metabolism ; Bacteria/classification/genetics/*metabolism ; Phylogeny ; Ribulosephosphates/chemistry/*metabolism ; },
abstract = {3-Hexulose-6-phosphate synthase (HPS) and 6-phospho-3-hexuloisomerase (PHI) are the key enzymes of the ribulose monophosphate pathway. This pathway, which was originally found in methylotrophic bacteria, is now recognized as a widespread prokaryotic pathway involved in formaldehyde fixation and detoxification. Recent progress, involving biochemical and genetic approaches in elucidating the physiological functions of HPS and PHI in methylotrophic as well as non-methylotrophic bacteria are described in this review. HPS and PHI orthologs are also found in a variety of archaeal strains. Some archaeal HPS orthologs are fused with other genes to form single ORF (e.g., the hps-phi gene of Pyrococcus spp. and the faeB-hpsB gene of Methanosarcina spp). These fused gene products exhibit functions corresponding to the individual enzyme activities, and are more efficient than equivalent systems made up of discrete enzymes. Recently, a novel metabolic function for HPS and PHI has been proposed in which these enzymes catalyze the reverse reaction for the biosynthesis of pentose phosphate in some archaeal strains. Thus the enzyme system plays a different role in bacteria and archaea by catalyzing the forward and reverse reactions respectively.},
}
@article {pmid16371361,
year = {2006},
author = {Kupke, T and Schwarz, W},
title = {4'-phosphopantetheine biosynthesis in Archaea.},
journal = {The Journal of biological chemistry},
volume = {281},
number = {9},
pages = {5435-5444},
doi = {10.1074/jbc.M510056200},
pmid = {16371361},
issn = {0021-9258},
mesh = {Amino Acid Sequence ; Archaeal Proteins/chemistry/genetics/*metabolism ; Base Sequence ; Binding Sites ; Carboxy-Lyases/chemistry/genetics/*metabolism ; Cloning, Molecular ; Humans ; Methanococcales/*metabolism ; Molecular Sequence Data ; Molecular Structure ; *Multienzyme Complexes ; Pantetheine/*analogs &amp; derivatives/metabolism ; Peptide Synthases/chemistry/genetics/*metabolism ; Sequence Alignment ; },
abstract = {Coenzyme A as the principal acyl carrier is required for many synthetic and degradative reactions in intermediary metabolism. It is synthesized in five steps from pantothenate, and recently the CoaA biosynthetic genes of eubacteria, plants, and human were all identified and cloned. In most bacteria, the so-called Dfp proteins catalyze the synthesis of the coenzyme A precursor 4'-phosphopantetheine. Dfp proteins are bifunctional enzymes catalyzing the synthesis of 4'-phosphopantothenoylcysteine (CoaB activity) and its decarboxylation to 4'-phosphopantetheine (CoaC activity). Here, we demonstrate the functional characterization of the CoaB and CoaC domains of an archaebacterial Dfp protein. Both domains of the Methanocaldococcus jannaschii Dfp protein were purified as His tag proteins, and their enzymatic activities were then identified and characterized by site-directed mutagenesis. Although the nucleotide binding motif II of the CoaB domain resembles that of eukaryotic enzymes, Methanocaldococcus CoaB is a CTP- and not an ATP-dependent enzyme, as shown by detection of the 4'-phosphopantothenoyl-CMP intermediate. The proposed 4'-phosphopantothenoylcysteine binding clamp of the Methanocaldococcus CoaC activity differs significantly from those of other characterized CoaC proteins. In particular, the active site cysteine residue, which otherwise is involved in the reduction of an aminoenethiol reaction intermediate, is not present. Moreover, the conserved Asn residue of the PXMNXXMW motif, which contacts the carboxyl group of 4'-phosphopantothenoylcysteine, is exchanged for His.},
}
@article {pmid16332346,
year = {2005},
author = {Pasić, L and Bartual, SG and Ulrih, NP and Grabnar, M and Velikonja, BH},
title = {Diversity of halophilic archaea in the crystallizers of an Adriatic solar saltern.},
journal = {FEMS microbiology ecology},
volume = {54},
number = {3},
pages = {491-498},
doi = {10.1016/j.femsec.2005.06.004},
pmid = {16332346},
issn = {0168-6496},
mesh = {Bacteriorhodopsins/genetics ; Base Sequence ; DNA Primers ; Gene Library ; *Genetic Variation ; Halobacteriaceae/*genetics ; Likelihood Functions ; Mediterranean Sea ; Models, Genetic ; Molecular Sequence Data ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/analysis/*microbiology ; Sequence Analysis, DNA ; Slovenia ; },
abstract = {Haloarchaeal diversity in the crystallizers of Adriatic Secovlje salterns was investigated using gene fragments encoding 16S rRNA and bacteriorhodopsin as molecular markers. Screening of 180 clones from five gene libraries constructed for each gene targeted revealed 15 different 16S rRNA and 10 different bacteriorhodopsin phylotypes, indicating higher haloarchaeal diversity than previously reported in such hypersaline environments. Furthermore, results of rarefaction analysis indicated that analysis of an increasing number of clones would have revealed additional diversity. Finally, most sequences from the crystallizers grouped within the Halorubrum branch, whereas square-shaped 'Haloquadratum' relatives, repeatedly reported to dominate crystallizer communities, were rare. Presence of such special and diverse haloarchaeal community could be attributed to the Secovlje salterns rare continuous short-cycling salt production mechanism.},
}
@article {pmid16330755,
year = {2005},
author = {Mongodin, EF and Nelson, KE and Daugherty, S and Deboy, RT and Wister, J and Khouri, H and Weidman, J and Walsh, DA and Papke, RT and Sanchez Perez, G and Sharma, AK and Nesbø, CL and MacLeod, D and Bapteste, E and Doolittle, WF and Charlebois, RL and Legault, B and Rodriguez-Valera, F},
title = {The genome of Salinibacter ruber: convergence and gene exchange among hyperhalophilic bacteria and archaea.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {102},
number = {50},
pages = {18147-18152},
pmid = {16330755},
issn = {0027-8424},
mesh = {Adaptation, Physiological/genetics ; Archaea/*genetics ; Bacteroidetes/enzymology/*genetics ; Base Composition ; Base Sequence ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Genome, Bacterial/*genetics ; Likelihood Functions ; Models, Genetic ; Molecular Sequence Data ; *Phylogeny ; Rhodopsins, Microbial/*genetics ; Sequence Analysis, DNA ; },
abstract = {Saturated thalassic brines are among the most physically demanding habitats on Earth: few microbes survive in them. Salinibacter ruber is among these organisms and has been found repeatedly in significant numbers in climax saltern crystallizer communities. The phenotype of this bacterium is remarkably similar to that of the hyperhalophilic Archaea (Haloarchaea). The genome sequence suggests that this resemblance has arisen through convergence at the physiological level (different genes producing similar overall phenotype) and the molecular level (independent mutations yielding similar sequences or structures). Several genes and gene clusters also derive by lateral transfer from (or may have been laterally transferred to) haloarchaea. S. ruber encodes four rhodopsins. One resembles bacterial proteorhodopsins and three are of the haloarchaeal type, previously uncharacterized in a bacterial genome. The impact of these modular adaptive elements on the cell biology and ecology of S. ruber is substantial, affecting salt adaptation, bioenergetics, and photobiology.},
}
@article {pmid16329899,
year = {2005},
author = {Smirnov, A and Suzina, N and Chudinova, N and Kulakovskaya, T and Kulaev, I},
title = {Formation of insoluble magnesium phosphates during growth of the archaea Halorubrum distributum and Halobacterium salinarium and the bacterium Brevibacterium antiquum.},
journal = {FEMS microbiology ecology},
volume = {52},
number = {1},
pages = {129-137},
doi = {10.1016/j.femsec.2004.10.012},
pmid = {16329899},
issn = {0168-6496},
mesh = {Archaea/drug effects/growth &amp; development/*metabolism/ultrastructure ; Brevibacterium/drug effects/growth &amp; development/*metabolism/ultrastructure ; Carbonyl Cyanide p-Trifluoromethoxyphenylhydrazone/toxicity ; Cytoplasm/metabolism ; Magnesium Compounds/*metabolism ; Microscopy, Electron ; Phosphates/isolation &amp; purification/metabolism/*pharmacokinetics ; Sodium Chloride/metabolism ; Spectrophotometry, Atomic ; Time Factors ; Uncoupling Agents/toxicity ; },
abstract = {Stationary phase cells of the halophilic archaea Halobacterium salinarium and Halorubrum distributum, growing at 3-4 M NaCl, and of the halotolerant bacterium Brevibacterium antiquum, growing with and without 2.6 NaCl, took up approximately 90% of the phosphate from the culture media containing 2.3 and 11.5 mM phosphate. The uptake was blocked by the uncoupler FCCP. In B. antiquum, EDTA inhibited the phosphate uptake. The content of polyphosphates in the cells was significantly lower than the content of orthophosphate. At a high phosphate concentration, up to 80% of the phosphate taken up from the culture medium was accumulated as Mg(2)PO(4)OH x 4H(2)O in H. salinarium and H. distributum and as NH(4)MgPO(4) x 6H(2)O in B. antiquum. Consolidation of the cytoplasm and enlargement of the nucleoid zone were observed in the cells during phosphate accumulation. At phosphate surplus, part of the H. salinarium and H. distributum cell population was lysed. The cells of B. antiquum were not lysed and phosphate crystals were observed in the cytoplasm.},
}
@article {pmid16325203,
year = {2006},
author = {Kuratani, M and Sakai, H and Takahashi, M and Yanagisawa, T and Kobayashi, T and Murayama, K and Chen, L and Liu, ZJ and Wang, BC and Kuroishi, C and Kuramitsu, S and Terada, T and Bessho, Y and Shirouzu, M and Sekine, S and Yokoyama, S},
title = {Crystal structures of tyrosyl-tRNA synthetases from Archaea.},
journal = {Journal of molecular biology},
volume = {355},
number = {3},
pages = {395-408},
doi = {10.1016/j.jmb.2005.10.073},
pmid = {16325203},
issn = {0022-2836},
mesh = {Adenosine Monophosphate/analogs &amp; derivatives/chemistry ; Aeropyrum/*enzymology ; Amino Acid Sequence ; Archaeoglobus fulgidus/*enzymology ; Binding Sites ; Crystallography, X-Ray ; Hydrogen Bonding ; Models, Molecular ; Molecular Sequence Data ; Peptides/chemistry ; Proline/chemistry ; Protein Conformation ; Pyrococcus horikoshii/*enzymology ; Tyrosine/analogs &amp; derivatives/chemistry ; Tyrosine-tRNA Ligase/*chemistry ; },
abstract = {Tyrosyl-tRNA synthetase (TyrRS) catalyzes the tyrosylation of tRNA(Tyr) in a two-step reaction. TyrRS has the "HIGH" and "KMSKS" motifs, which play essential roles in the formation of the tyrosyl-adenylate from tyrosine and ATP. Here, we determined the crystal structures of Archaeoglobus fulgidus and Pyrococcus horikoshii TyrRSs in the l-tyrosine-bound form at 1.8A and 2.2A resolutions, respectively, and that of Aeropyrum pernix TyrRS in the substrate-free form at 2.2 A. The conformation of the KMSKS motif differs among the three TyrRSs. In the A.pernix TyrRS, the KMSKS loop conformation corresponds to the ATP-bound "closed" form. In contrast, the KMSKS loop of the P.horikoshii TyrRS forms a novel 3(10) helix, which appears to correspond to the "semi-closed" form. This conformation enlarges the entrance to the tyrosine-binding pocket, which facilitates the pyrophosphate ion release after the tyrosyl-adenylate formation, and probably is involved in the initial tRNA binding. The KMSSS loop of the A.fulgidus TyrRS is somewhat farther from the active site and is stabilized by hydrogen bonds. Based on the three structures, possible structural changes of the KMSKS motif during the tyrosine activation reaction are discussed. We suggest that the insertion sequence just before the KMSKS motif, which exists in some archaeal species, enhances the binding affinity of the TyrRS for its cognate tRNA. In addition, a non-proline cis peptide bond, which is involved in the tRNA binding, is conserved among the archaeal TyrRSs.},
}
@article {pmid16309392,
year = {2005},
author = {Meyerdierks, A and Kube, M and Lombardot, T and Knittel, K and Bauer, M and Glöckner, FO and Reinhardt, R and Amann, R},
title = {Insights into the genomes of archaea mediating the anaerobic oxidation of methane.},
journal = {Environmental microbiology},
volume = {7},
number = {12},
pages = {1937-1951},
doi = {10.1111/j.1462-2920.2005.00844.x},
pmid = {16309392},
issn = {1462-2912},
mesh = {Amino Acid Sequence ; Anaerobiosis ; Archaea/*genetics/metabolism ; Base Composition ; *Genome, Archaeal ; Geologic Sediments/microbiology ; Methane/*metabolism ; Molecular Sequence Data ; Multigene Family ; Oceans and Seas ; Operon ; Oregon ; Oxidation-Reduction ; RNA, Archaeal ; RNA, Ribosomal ; Russia ; Sequence Alignment ; Water Microbiology ; },
abstract = {The anaerobic oxidation of methane is a globally significant process which is mediated by consortia of yet uncultivated methanotrophic archaea (ANME) and sulfate-reducing bacteria. In order to gain deeper insights into genome characteristics of the different ANME groups, large-insert genomic libraries were constructed using DNA extracted from a methanotrophic microbial mat growing in the anoxic part of the Black Sea, and from sediments above gas hydrates at the Hydrate Ridge off the coast of Oregon. Analysis of these fosmid libraries with respect to archaeal 16S rRNA gene diversity revealed a single ANME-1b ribotype for the Black Sea libraries, whereas the sequences derived from the Hydrate Ridge library phylogenetically affiliated with the ANME-2a, ANME-2c and ANME-3 group. Genome walking for ANME-1b resulted in a contiguous 155 kb composite genome fragment. The comparison of a set of four genomic fragments belonging to the different ANME groups revealed differences in the rRNA operon structure and the average G+C content, with the ANME-2c contig showing the highest divergence within the set. A detailed analysis of the ANME contigs with respect to genes putatively involved in the anaerobic oxidation of methane led to the identification of: (i) a putative N5,N10-methenyltetrahydromethanopterin cyclohydrolase gene, (ii) a gene cluster supposedly encoding a novel type of heterodisulfide reductase/dehydrogenase complex and (iii) a gene cluster putatively encoding a new type of CO dehydrogenase/acetyl-CoA synthase enzyme complex.},
}
@article {pmid16306681,
year = {2005},
author = {Koga, Y and Morii, H},
title = {Recent advances in structural research on ether lipids from archaea including comparative and physiological aspects.},
journal = {Bioscience, biotechnology, and biochemistry},
volume = {69},
number = {11},
pages = {2019-2034},
doi = {10.1271/bbb.69.2019},
pmid = {16306681},
issn = {0916-8451},
mesh = {Adaptation, Physiological ; Archaea/*chemistry ; Cell Membrane Permeability ; Ethers/*chemistry ; Hot Temperature ; Lipids/*chemistry ; Membrane Lipids/*chemistry ; Molecular Structure ; Phase Transition ; },
abstract = {A great number of novel and unique chemical structures of archaeal polar lipids have been reported. Since 1993, when those lipids were reviewed in several review articles, a variety of core lipids and lipids with unique polar groups have been reported successively. We summarize new lipid structures from archaea elucidated after 1993. In addition to lipids from intact archaeal cells, more diverse structures of archaea-related lipids found in environmental samples are also reviewed. These lipids are assumed to be lipids from unidentified or ancient archaea or related organisms. In the second part of this paper, taxonomic and ecological aspects are discussed. Another aspect of archaeal lipid study has to do with its physiological significance, particularly the phase behavior and permeability of archaeal lipid membranes in relation to the thermophily of many archaea. In the last part of this review we discuss this problem.},
}
@article {pmid16291683,
year = {2005},
author = {Dilks, K and Giménez, MI and Pohlschröder, M},
title = {Genetic and biochemical analysis of the twin-arginine translocation pathway in halophilic archaea.},
journal = {Journal of bacteriology},
volume = {187},
number = {23},
pages = {8104-8113},
pmid = {16291683},
issn = {0021-9193},
support = {T32 GM007229/GM/NIGMS NIH HHS/United States ; T32-GM07229/GM/NIGMS NIH HHS/United States ; },
mesh = {Aerobiosis ; Amino Acid Sequence ; Archaeal Proteins/*metabolism ; Arginine/metabolism ; *Biological Transport ; Cell Wall/metabolism ; Cytoplasm/metabolism ; Genes, Archaeal/genetics ; Haloferax volcanii/growth &amp; development/*metabolism ; Molecular Sequence Data ; Sequence Alignment ; },
abstract = {The twin-arginine translocation (Tat) pathway is present in a wide variety of prokaryotes and is capable of exporting partially or fully folded proteins from the cytoplasm. Although diverse classes of proteins are transported via the Tat pathway, in most organisms it facilitates the secretion of a relatively small number of substrates compared to the Sec pathway. However, computational evidence suggests that haloarchaea route nearly all secreted proteins to the Tat pathway. We have expanded previous computational analyses of the haloarchaeal Tat pathway and initiated in vivo characterization of the Tat machinery in a model haloarchaeon, Haloferax volcanii. Consistent with the predicted usage of the this pathway in the haloarchaea, we determined that three of the four identified tat genes in Haloferax volcanii are essential for viability when grown aerobically in complex medium. This represents the first report of an organism that requires the Tat pathway for viability when grown under such conditions. Deletion of the nonessential gene had no effect on the secretion of a verified substrate of the Tat pathway. The two TatA paralogs TatAo and TatAt were detected in both the membrane and cytoplasm and could be copurified from the latter fraction. Using size exclusion chromatography to further characterize cytoplasmic and membrane TatA proteins, we find these proteins present in high-molecular-weight complexes in both cellular fractions.},
}
@article {pmid16282984,
year = {2005},
author = {Portnoy, V and Evguenieva-Hackenberg, E and Klein, F and Walter, P and Lorentzen, E and Klug, G and Schuster, G},
title = {RNA polyadenylation in Archaea: not observed in Haloferax while the exosome polynucleotidylates RNA in Sulfolobus.},
journal = {EMBO reports},
volume = {6},
number = {12},
pages = {1188-1193},
pmid = {16282984},
issn = {1469-221X},
mesh = {Exoribonucleases/*metabolism ; Haloferax/*metabolism ; Polyadenylation/*genetics ; Polyribonucleotide Nucleotidyltransferase/metabolism ; RNA, Archaeal/*metabolism ; RNA-Binding Proteins/*metabolism ; Sulfolobus/*metabolism ; },
abstract = {The addition of poly(A) tails to RNA is a phenomenon common to all organisms examined so far. No homologues of the known polyadenylating enzymes are found in Archaea and little is known concerning the mechanisms of messenger RNA degradation in these organisms. Hyperthermophiles of the genus Sulfolobus contain a protein complex with high similarity to the exosome, which is known to degrade RNA in eukaryotes. Halophilic Archaea, however, do not encode homologues of these eukaryotic exosome components. In this work, we analysed RNA polyadenylation and degradation in the archaea Sulfolobus solfataricus and Haloferax volcanii. No RNA polyadenylation was detected in the halophilic archaeon H. volcanii. However, RNA polynucleotidylation occurred in hyperthermophiles of the genus Sulfolobus and was mediated by the archaea exosome complex. Together, our results identify the first organism without RNA polyadenylation and show a polyadenylation activity of the archaea exosome.},
}
@article {pmid16280517,
year = {2005},
author = {Xue, Y and Fan, H and Ventosa, A and Grant, WD and Jones, BE and Cowan, DA and Ma, Y},
title = {Halalkalicoccus tibetensis gen. nov., sp. nov., representing a novel genus of haloalkaliphilic archaea.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {55},
number = {Pt 6},
pages = {2501-2505},
doi = {10.1099/ijs.0.63916-0},
pmid = {16280517},
issn = {1466-5026},
mesh = {Base Sequence ; China ; DNA, Archaeal/analysis/genetics ; Halobacteriaceae/genetics/*isolation &amp; purification ; Lipids/analysis ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/analysis/genetics ; Sequence Analysis, DNA ; Sodium Chloride/metabolism ; Water Microbiology ; },
abstract = {A haloalkaliphilic archaeon (strain DS12T) isolated from Lake Zabuye, the Tibetan Plateau, China, was characterized to elucidate its taxonomy. The strain was aerobic, chemo-organotrophic, and grew optimally at 40 degrees C, pH 9.5-10.0 and 3.4 M NaCl. Cells of strain DS12T were non-motile cocci and stained Gram-variable. The major polar lipids of strain DS12T were diphytanyl and phytanyl-sesterterpanyl diether derivatives of phosphatidylglycerol and phosphatidylglycerol phosphate methyl ester. No glycolipids were detected. Phylogenetic analysis revealed that the strain formed a distinct lineage within the family Halobacteriaceae. The low 16S rRNA gene sequence similarity values to its closest relatives (91.5-92.5 %) and its signature bases both suggest that the strain has no close affinity with any members of the family Halobacteriaceae with validly published names. Therefore, it is proposed that strain DS12T (=AS 1.3240T=JCM 11890T) represents the type strain of a novel species in a new genus, Halalkalicoccus tibetensis gen. nov., sp. nov.},
}
@article {pmid16269744,
year = {2005},
author = {Coombs, JM and Barkay, T},
title = {New findings on evolution of metal homeostasis genes: evidence from comparative genome analysis of bacteria and archaea.},
journal = {Applied and environmental microbiology},
volume = {71},
number = {11},
pages = {7083-7091},
pmid = {16269744},
issn = {0099-2240},
mesh = {Adenosine Triphosphatases/*genetics ; Amino Acid Sequence ; Archaea/genetics/metabolism ; Bacteria/genetics/metabolism ; Cation Transport Proteins/genetics ; Copper-Transporting ATPases ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genome, Archaeal ; *Genome, Bacterial ; Genomics ; Homeostasis ; Metals/*metabolism ; Molecular Sequence Data ; Phylogeny ; },
abstract = {In order to examine the natural history of metal homeostasis genes in prokaryotes, open reading frames with homology to characterized P(IB)-type ATPases from the genomes of 188 bacteria and 22 archaea were investigated. Major findings were as follows. First, a high diversity in N-terminal metal binding motifs was observed. These motifs were distributed throughout bacterial and archaeal lineages, suggesting multiple loss and acquisition events. Second, the CopA locus separated into two distinct phylogenetic clusters, CopA1, which contained ATPases with documented Cu(I) influx activity, and CopA2, which contained both efflux and influx transporters and spanned the entire diversity of the bacterial domain, suggesting that CopA2 is the ancestral locus. Finally, phylogentic incongruences between 16S rRNA and P(IB)-type ATPase gene trees identified at least 14 instances of lateral gene transfer (LGT) that had occurred among diverse microbes. Results from bootstrapped supported nodes indicated that (i) a majority of the transfers occurred among proteobacteria, most likely due to the phylogenetic relatedness of these organisms, and (ii) gram-positive bacteria with low moles percent G+C were often involved in instances of LGT. These results, together with our earlier work on the occurrence of LGT in subsurface bacteria (J. M. Coombs and T. Barkay, Appl. Environ. Microbiol. 70:1698-1707, 2004), indicate that LGT has had a minor role in the evolution of P(IB)-type ATPases, unlike other genes that specify survival in metal-stressed environments. This study demonstrates how examination of a specific locus across microbial genomes can contribute to the understanding of phenotypes that are critical to the interactions of microbes with their environment.},
}
@article {pmid16260307,
year = {2005},
author = {Friedrich, MW},
title = {Methyl-coenzyme M reductase genes: unique functional markers for methanogenic and anaerobic methane-oxidizing Archaea.},
journal = {Methods in enzymology},
volume = {397},
number = {},
pages = {428-442},
doi = {10.1016/S0076-6879(05)97026-2},
pmid = {16260307},
issn = {0076-6879},
mesh = {Archaea/*genetics ; Cloning, Molecular ; DNA, Archaeal/isolation &amp; purification ; Ecosystem ; Genes, Archaeal/*genetics ; Methanobacteriaceae/genetics ; Methanomicrobiales/genetics ; Methanosarcina barkeri/genetics ; Methanosarcinales/genetics ; Oxidoreductases/*genetics ; Phylogeny ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; Soil Microbiology ; },
abstract = {In many anoxic environments, methanogenesis is the predominant terminal electron accepting process involved in the mineralization of organic matter, which is catalyzed by methanogenic Archaea. These organisms represent a unique but phylogenetically diverse guild of prokaryotes, which can be conveniently tracked in the environment by targeting the mcrA gene as a functional marker. This gene encodes the alpha subunit of the methyl-coenzyme M reductase (MCR), which catalyzes the last step in methanogenesis and is present in all methanogens. Cultivation-independent analysis of methanogenic communities involves the polymerase chain reaction (PCR) amplification of the mcrA gene from extracted community DNA, comparative analysis of mcrA clone libraries, or PCR-based fingerprinting analysis by terminal restriction fragment polymorphism analysis (T-RFLP). It has also been suggested that anaerobic methane-oxidizing Archaea possess MCR, which facilitates detection of this novel group of "reverse methanogens" as well using the mcrA gene as a functional marker.},
}
@article {pmid16257573,
year = {2005},
author = {Rother, M and Metcalf, WW},
title = {Genetic technologies for Archaea.},
journal = {Current opinion in microbiology},
volume = {8},
number = {6},
pages = {745-751},
doi = {10.1016/j.mib.2005.10.010},
pmid = {16257573},
issn = {1369-5274},
mesh = {Archaea/*genetics/metabolism/*physiology ; Archaeal Proteins/genetics/*metabolism ; *Gene Expression Regulation, Archaeal ; *Genetic Techniques ; Hot Temperature ; Methane/metabolism ; },
abstract = {Members of the third domain of life, the Archaea, possess structural, physiological, biochemical and genetic features distinct from Bacteria and Eukarya and, therefore, have drawn considerable scientific interest. Physiological, biochemical and molecular analyses have revealed many novel biological processes in these important prokaryotes. However, assessment of the function of genes in vivo through genetic analysis has lagged behind because suitable systems for the creation of mutants in most Archaea were established only in the past decade. Among the Archaea, sufficiently sophisticated genetic systems now exist for some thermophilic sulfur-metabolizing Archaea, halophilic Archaea and methanogenic Archaea. Recently, there have been developments in genetic analysis of thermophilic and methanogenic Archaea and in the use of genetics to study the physiology, metabolism and regulatory mechanisms that direct gene expression in response to changes of environmental conditions in these important microorganisms.},
}
@article {pmid16257258,
year = {2005},
author = {Pohlschröder, M and Giménez, MI and Jarrell, KF},
title = {Protein transport in Archaea: Sec and twin arginine translocation pathways.},
journal = {Current opinion in microbiology},
volume = {8},
number = {6},
pages = {713-719},
doi = {10.1016/j.mib.2005.10.006},
pmid = {16257258},
issn = {1369-5274},
mesh = {Amino Acid Sequence ; Archaea/*metabolism ; Archaeal Proteins/chemistry/*metabolism ; Membrane Transport Proteins/chemistry/*metabolism ; Models, Molecular ; Molecular Sequence Data ; Protein Sorting Signals ; Protein Transport ; },
abstract = {The transport of proteins into and across hydrophobic membranes is an essential cellular process. The majority of proteins that are translocated in an unfolded conformation traverse the membrane by way of the universally conserved Sec pathway, whereas the twin arginine translocation pathway is responsible for the transport of folded proteins across the membrane. Structural, biochemical and genetic analyses of these processes in Archaea have revealed unique archaeal features, and have also provided a better understanding of these pathways in organisms of all domains. Further study of these pathways in Archaea might elucidate fundamental principles involved in each type of transport and could help determine their relative costs and benefits as well as evolutionary adaptations in protein secretion strategies.},
}
@article {pmid16257257,
year = {2005},
author = {Egorova, K and Antranikian, G},
title = {Industrial relevance of thermophilic Archaea.},
journal = {Current opinion in microbiology},
volume = {8},
number = {6},
pages = {649-655},
doi = {10.1016/j.mib.2005.10.015},
pmid = {16257257},
issn = {1369-5274},
mesh = {Archaea/*enzymology ; Archaeal Proteins/chemistry/metabolism ; Biotechnology/*methods ; Enzyme Stability ; Enzymes/*chemistry/*metabolism ; *Hot Temperature ; },
abstract = {The dramatic increase of newly isolated extremophilic microorganisms, analysis of their genomes and investigations of their enzymes by academic and industrial laboratories demonstrate the great potential of extremophiles in industrial (white) biotechnology. Enzymes derived from extremophiles (extremozymes) are superior to the traditional catalysts because they can perform industrial processes even under harsh conditions, under which conventional proteins are completely denatured. In particular, enzymes from thermophilic and hyperthermophilic Archaea have industrial relevance. Despite intensive investigations, our knowledge of the structure-function relationships of their enzymes is still limited. Information concerning the molecular properties of their enzymes and genes has to be obtained to be able to understand the mechanisms that are responsible for catalytic activity and stability at the boiling point of water.},
}
@article {pmid16256422,
year = {2005},
author = {Müller, V and Spanheimer, R and Santos, H},
title = {Stress response by solute accumulation in archaea.},
journal = {Current opinion in microbiology},
volume = {8},
number = {6},
pages = {729-736},
doi = {10.1016/j.mib.2005.10.011},
pmid = {16256422},
issn = {1369-5274},
mesh = {Amino Acids/metabolism ; Archaea/*metabolism/*physiology ; Betaine/metabolism ; *Gene Expression Regulation, Archaeal ; Glyceric Acids/metabolism ; *Heat-Shock Response ; Mannose/analogs &amp; derivatives/metabolism ; Osmolar Concentration ; Polymers/metabolism ; },
abstract = {The accumulation of organic solutes is a prerequisite for osmotic adjustment of all organisms. Archaea synthesize unusual solutes such as beta-amino acids, Nepsilon-acetyl-beta-lysine, mannosylglycerate and di-myo-inositol phosphate but, as in other cells, uptake of solutes such as glycine betaine is preferred over de novo synthesis. Study of the molecular basis of osmoadaptation and its regulation in archaea is still in its infancy, but genomics and functional genome analyses combined with classical biochemistry shed light on the processes that confer osmoadaptation in archaea. Most interestingly, some solutes are not only produced in response to salt but also to temperature stress.},
}
@article {pmid16256421,
year = {2005},
author = {Dennis, PP and Omer, A},
title = {Small non-coding RNAs in Archaea.},
journal = {Current opinion in microbiology},
volume = {8},
number = {6},
pages = {685-694},
doi = {10.1016/j.mib.2005.10.013},
pmid = {16256421},
issn = {1369-5274},
mesh = {Archaea/*genetics/metabolism ; Base Sequence ; Molecular Sequence Data ; Nucleic Acid Conformation ; RNA, Archaeal/chemistry/genetics/*metabolism ; RNA, Small Nucleolar/chemistry/genetics/*metabolism ; Structure-Activity Relationship ; Sulfolobus solfataricus/genetics ; },
abstract = {Biochemical and informatics analyses conducted over the past few years have revealed the presence of a plethora of small non-coding RNAs in various species of Archaea. A large proportion of these RNAs contain a common structural motif called the RNA kink turn (K-turn). The best-characterized are the C/D box and the H/ACA box guide small (s)RNAs. Both contain the K-turn fold and require the binding of the L7Ae protein to stabilize the structure of this crucial motif. These sRNAs assemble with L7Ae and several other proteins into complex and dynamic ribonucleoprotein machines that mediate guide-directed ribose methylation or pseudouridylation to specific locations in ribosomal or transfer RNA. Analyses of new archaeal sRNA libraries have identified additional classes of novel sRNAs; many of these contain the RNA K-turn motif and suggest that the RNAs might function as ribonucleoprotein complexes. Some have characteristics of small interfering RNAs or of micro RNAs that have been implicated in the post-transcriptional control of gene expression, whereas others appear to be involved in protein translocation or in ribosomal RNA processing and ribosome assembly. A complete understanding of the structure of the K-turn motif and its contribution to various RNA-RNA and RNA-protein interactions will be absolutely essential to fully elucidate the biological organization, activity and function of these novel archaeal ribonucleoprotein machines.},
}
@article {pmid16256419,
year = {2005},
author = {Siebers, B and Schönheit, P},
title = {Unusual pathways and enzymes of central carbohydrate metabolism in Archaea.},
journal = {Current opinion in microbiology},
volume = {8},
number = {6},
pages = {695-705},
doi = {10.1016/j.mib.2005.10.014},
pmid = {16256419},
issn = {1369-5274},
mesh = {Archaea/*enzymology/genetics ; Archaeal Proteins/genetics/*metabolism ; Gluconeogenesis ; Glucose/*metabolism ; Glycolysis ; },
abstract = {Sugar-utilizing hyperthermophilic and halophilic Archaea degrade glucose and glucose polymers to acetate or to CO2 using O2, nitrate, sulfur or sulfate as electron acceptors. Comparative analyses of glycolytic pathways in these organisms indicate a variety of differences from the classical Emden-Meyerhof and Entner-Doudoroff pathways that are operative in Bacteria and Eukarya, respectively. The archaeal pathways are characterized by the presence of numerous novel enzymes and enzyme families that catalyze, for example, the phosphorylation of glucose and of fructose 6-phosphate, the isomerization of glucose 6-phosphate, the cleavage of fructose 1,6-bisphosphate, the oxidation of glyceraldehyde 3-phosphate and the conversion of acetyl-CoA to acetate. Recent major advances in deciphering the complexity of archaeal central carbohydrate metabolism were gained by combination of classical biochemical and genomic-based approaches.},
}
@article {pmid16246618,
year = {2005},
author = {Reeve, JN and Schmitz, RA},
title = {Biology, biochemistry and the molecular machinery of Archaea.},
journal = {Current opinion in microbiology},
volume = {8},
number = {6},
pages = {627-629},
doi = {10.1016/j.mib.2005.10.017},
pmid = {16246618},
issn = {1369-5274},
mesh = {*Archaea/classification/genetics/metabolism/physiology ; Archaeal Proteins/genetics/metabolism ; DNA, Archaeal/genetics ; Gene Expression Regulation, Archaeal ; },
}
@article {pmid16246148,
year = {2005},
author = {Bolt, EL},
title = {Helicases that interact with replication forks: new candidates from archaea.},
journal = {Biochemical Society transactions},
volume = {33},
number = {Pt 6},
pages = {1471-1473},
doi = {10.1042/BST0331471},
pmid = {16246148},
issn = {0300-5127},
mesh = {Archaea/*enzymology ; Archaeal Proteins/*metabolism ; DNA Helicases/*metabolism ; *DNA Replication ; Escherichia coli/genetics/metabolism ; *Nucleic Acid Conformation ; Yeasts/genetics/metabolism ; },
abstract = {Overcoming DNA replication fork blocks is essential for completing genome duplication and cell division. Archaea and eukaryotes drive replication using essentially the same protein machinery. Archaea may be a valuable resource for identifying new helicase components at advancing forks and/or in replication-restart pathways. As described here, these may be relevant to understanding genome instability in metazoans.},
}
@article {pmid16243779,
year = {2005},
author = {Sugano, A and Tsuchimoto, H and Cho, TC and Kimura, M and Asakawa, S},
title = {Succession of methanogenic archaea in rice straw incorporated into a Japanese rice field: estimation by PCR-DGGE and sequence analyses.},
journal = {Archaea (Vancouver, B.C.)},
volume = {1},
number = {6},
pages = {391-397},
pmid = {16243779},
issn = {1472-3646},
mesh = {Archaea/classification/genetics/*isolation &amp; purification/metabolism ; Biodegradation, Environmental ; Methane/biosynthesis ; Methanomicrobiales/classification/isolation &amp; purification ; Methanosarcinales/classification/isolation &amp; purification ; Molecular Sequence Data ; Oryza/metabolism/microbiology ; Plant Stems/metabolism/microbiology ; *Soil Microbiology ; Species Specificity ; },
abstract = {The succession and phylogenetic profiles of methanogenic archaeal communities associated with rice straw decomposition in rice-field soil were studied by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) analysis followed by 16S rDNA sequencing. Nylon bags containing either leaf sheaths or blades were buried in the plowed layer of a Japanese rice field under drained conditions during the off-crop season and under flooded conditions after transplanting. In addition, rice straw samples that had been buried in the rice field under drained conditions during the off-crop season were temporarily removed during spring plowing and then re-buried in the same rice field under flooded conditions at transplanting. Populations of methanogenic archaea were examined by amplification of the 16S rRNA genes in the DNA extracted from the rice straw samples. No PCR product was produced for samples of leaf sheath or blade prior to burial or after burial under drained conditions, indicating that the methanogen population was very small during decomposition of rice straw under oxic conditions. Many common bands were observed in rice straw samples of leaf sheath and blade during decomposition of rice straw under flooded conditions. Cluster analysis based on DGGE patterns divided methanogenic archaeal communities into two groups before and after the mid-season drainage. Sequence analysis of DGGE bands that were commonly present were closely related to Methanomicrobiales and Rice cluster I. Methanomicrobiales, Rice cluster I and Methanosarcinales were major members before the mid-season drainage, whereas the DGGE bands that characterized methanogenic archaeal communities after the mid-season drainage were closely related to Methanomicrobiales. These results indicate that mid-season drainage affected the methanogenic archaeal communities irrespective of their location on rice straw (sheath and blade) and the previous history of decomposition during the off-crop season.},
}
@article {pmid16242993,
year = {2005},
author = {Shima, S and Thauer, RK},
title = {Methyl-coenzyme M reductase and the anaerobic oxidation of methane in methanotrophic Archaea.},
journal = {Current opinion in microbiology},
volume = {8},
number = {6},
pages = {643-648},
doi = {10.1016/j.mib.2005.10.002},
pmid = {16242993},
issn = {1369-5274},
mesh = {Anaerobiosis ; Archaea/*enzymology/genetics/growth &amp; development ; Geologic Sediments/*microbiology ; Methane/*metabolism ; Oxidation-Reduction ; Oxidoreductases/genetics/*metabolism ; },
abstract = {Recent biochemical and metagenomic data indicate that not yet cultured Archaea that are closely related to methanogenic Archaea of the order of Methanosarcinales are involved in the anaerobic oxidation of methane in marine sediments. The DNA from the methanotrophic Archaea has been shown to harbor gene homologues for methyl-coenzyme M reductase, which in methanogenic Archaea catalyses the methane-forming reaction. In microbial mats catalyzing anaerobic oxidation of methane, this nickel enzyme has been shown to be present in concentrations of up to 10% of the total extracted proteins.},
}
@article {pmid16242992,
year = {2005},
author = {Martin, W},
title = {Archaebacteria (Archaea) and the origin of the eukaryotic nucleus.},
journal = {Current opinion in microbiology},
volume = {8},
number = {6},
pages = {630-637},
doi = {10.1016/j.mib.2005.10.004},
pmid = {16242992},
issn = {1369-5274},
mesh = {Archaea/*genetics ; Bacteria/*genetics ; *Biological Evolution ; Cell Nucleus/*genetics ; Eukaryotic Cells/*ultrastructure ; },
abstract = {The eukaryotic nucleus is a unique structure. Because it lacks an obvious homologue or precursor among prokaryotes, ideas about its evolutionary origin are diverse. Current attempts to derive the nuclear membrane focus on invaginations of the plasma membrane in a prokaryote, endosymbiosis of an archaebacterium within a eubacterial host, or the origin of a genuinely new membrane system following the origin of mitochondria in an archaebacterial host. Recent reports point to ways in which different ideas regarding the origin of the nucleus might someday be discriminated.},
}
@article {pmid16242031,
year = {2005},
author = {Silverman, BD},
title = {Asymmetry in the burial of hydrophobic residues along the histone chains of eukarya, archaea and a transcription factor.},
journal = {BMC structural biology},
volume = {5},
number = {},
pages = {20},
pmid = {16242031},
issn = {1472-6807},
mesh = {Animals ; Archaeal Proteins/chemistry ; Biophysics/methods ; Dimerization ; Drosophila melanogaster ; Euryarchaeota/metabolism ; Histones/*chemistry ; Models, Molecular ; Models, Statistical ; Nucleosomes/metabolism ; Protein Binding ; Protein Conformation ; Protein Denaturation ; Protein Folding ; Protein Structure, Tertiary ; Transcription Factors/*chemistry ; },
abstract = {BACKGROUND: The histone fold is a common structural motif of proteins involved in the chromatin packaging of DNA and in transcription regulation. This single chain fold is stabilized by either homo- or hetero-dimer formation in archaea and eukarya. X-ray structures at atomic resolution have shown the eukaryotic nucleosome core particle to consist of a central tetramer of two bound H3-H4 dimers flanked by two H2A-H2B dimers. The c-terminal region of the H3 histone fold involved in coupling the two eukaryotic dimers of the tetramer, through a four-fold helical bundle, had previously been shown to be a region of reduced burial of hydrophobic residues within the dimers, and thereby provide a rationale for the observed reduced stability of the H3-H4 dimer compared with that of the H2A-H2B dimer. Furthermore, comparison between eukaryal and archaeal histones had suggested that this asymmetry in the distribution of hydrophobic residues along the H3 histone chains could be due to selective evolution that enhanced the coupling between the eukaryotic dimers of the tetramer.<br><br>RESULTS AND DISCUSSION: The present work describes calculations utilizing the X-ray structures at atomic resolution of a hyperthermophile from Methanopyrus kandleri (HMk) and a eukaryotic transcription factor from Drosophila melanogaster (DRm), that are structurally homologous to the eukaryotic (H3-H4)2 tetramer. The results for several other related structures are also described. Reduced burial of hydrophobic residues, at the homologous H3 c-terminal regions of these structures, is found to parallel the burial at the c-terminal regions of the H3 histones and is, thereby, expected to affect dimer stability and the processes involving histone structural rearrangement. Significantly different sequence homology between the two histones of the HMk doublet with other archaeal sequences is observed, and how this might have occurred during selection to enhance tetramer stability is described.},
}
@article {pmid16236543,
year = {2005},
author = {Robertson, CE and Harris, JK and Spear, JR and Pace, NR},
title = {Phylogenetic diversity and ecology of environmental Archaea.},
journal = {Current opinion in microbiology},
volume = {8},
number = {6},
pages = {638-642},
doi = {10.1016/j.mib.2005.10.003},
pmid = {16236543},
issn = {1369-5274},
mesh = {Archaea/*classification/genetics/*physiology ; Biodiversity ; *Ecosystem ; *Environmental Microbiology ; Genes, Archaeal ; Genes, rRNA ; *Phylogeny ; },
abstract = {On the basis of culture studies, Archaea were thought to be synonymous with extreme environments. However, the large numbers of environmental rRNA gene sequences currently flooding into databases such as GenBank show that these organisms are present in almost all environments examined to date. Large sequence databases and new fast phylogenetic software allow more precise determination of the archaeal phylogenetic tree, but also indicate that our knowledge of archaeal diversity is incomplete. Although it is apparent that Archaea can be found in all environments, the chemistry of their ecological context is mostly unknown.},
}
@article {pmid16233774,
year = {2005},
author = {Usami, R and Fukushima, T and Mizuki, T and Yoshida, Y and Inoue, A and Horikoshi, K},
title = {Organic solvent tolerance of halophilic archaea, Haloarcula strains: effects of NaCl concentration on the tolerance and polar lipid composition.},
journal = {Journal of bioscience and bioengineering},
volume = {99},
number = {2},
pages = {169-174},
doi = {10.1263/jbb.99.169},
pmid = {16233774},
issn = {1389-1723},
mesh = {Cell Proliferation ; Cell Size/drug effects ; Cell Survival/drug effects ; Dose-Response Relationship, Drug ; Drug Resistance, Bacterial/drug effects/*physiology ; Halobacteriales/*cytology/drug effects/*physiology ; Hydrogen-Ion Concentration ; *Lipid Metabolism ; Organic Chemicals/*administration &amp; dosage ; Sodium Chloride/*administration &amp; dosage ; Solvents/*administration &amp; dosage ; Species Specificity ; },
abstract = {Strains of halophilic archaea, Haloarcula vallismortis and two Haloarcula strains OHF-1 and OHF-2, showed high tolerance to organic solvents at high media NaCl concentrations. For example, the lowest log Pow of the solvent which allowed growth (log Pow is the common logarithm of the partition coefficient of a given solvent in a mixture of n-octanol and water) for H. vallismortis was 5.1 at 20% NaCl and 4.4 at 30% NaCl. The solvent tolerance of Haloarcula argentinensis, on the other hand, was not affected by the NaCl concentration. Cells of strains OHF-1 and OHF-2 were of triangular or irregular morphology but became spherical in cultures in NaCl media overlaid with cyclohexane (log Pow=3.4), but returned to the triangular shape when the organic solvent evaporated from the medium. When cells of strains OHF-1, OHF-2, and H. argentinensis were grown in NaCl media in the presence of n-decane, they contained less phosphatidylglycerol and more phosphatidylglycerosulfate and phosphatidylglycerophosphate methyl ester than when grown without added n-decane. When the solvent was removed from the media after cultivation, the levels of these compounds returned to their initial ones.},
}
@article {pmid16233511,
year = {2003},
author = {Itoh, T},
title = {Taxonomy of nonmethanogenic hyperthermophilic and related thermophilic archaea.},
journal = {Journal of bioscience and bioengineering},
volume = {96},
number = {3},
pages = {203-212},
pmid = {16233511},
issn = {1389-1723},
abstract = {In view of the continuous increase in the number of described species of nonmethanogenic hyperthermophilic and related thermophilic archaea thriving in geothermally heated habitats (i.e., members of the orders Thermoproteales, Desulfurococcales, Sulfolobales, Thermoplasmatales, Thermococcales and Archaeoglobales), their current taxonomic status and taxonomic properties are reviewed. The introduction of 16S rRNA phylogeny has brought a more reliable taxonomic framework for these archaea, although, their phenotypic properties still remain as salient and descriptive features. Moreover, certain cellular components are potentially applicable to their taxonomic classification.},
}
@article {pmid16233230,
year = {2002},
author = {Sakuraba, H and Ohshima, T},
title = {Novel energy metabolism in anaerobic hyperthermophilic archaea: a modified Embden-Meyerhof pathway.},
journal = {Journal of bioscience and bioengineering},
volume = {93},
number = {5},
pages = {441-448},
doi = {10.1016/s1389-1723(02)80090-1},
pmid = {16233230},
issn = {1389-1723},
abstract = {Hyperthermophiles, a group of microorganisms whose optimum growth temperatures are above 80 degrees C, have been isolated mainly from marine and continental volcanic environments. They are viewed as potential sources of extraordinarily stable biomolecules with applications in novel industrial processes. Most hyperthermophiles belong to the domain Archaea, the third domain of life, and are considered to be the most ancient of all extant life forms. Recent studies have revealed unusual energy metabolic processes in hyperthermophilic archaea, e.g. a modified Embden-Meyerhof pathway, that have not been observed so far in organisms belonging to the Bacteria and Eucarya domains. Several novel enzymes--ADP-dependent glucokinase, ADP-dependent phosphofruktokinase, glyceraldehyde-3-phosphate ferredoxin oxidoreductase, phosphoenolpyruvate synthase, pyruvate: ferredoxin oxidoreductase, and ADP-forming acetyl-CoA synthetase--have been found to be involved in the modified Embden-Meyerhof pathway of the hyperthermophilic archaeon Pyrococcus furiosus. In addition, a novel regulation site for energy metabolism and a unique mode of ATP regeneration have been postulated to exist in the pathway of P. furiosus. The metabolic design observed in this microorganism might reflect the situation at an early stage of evolution. This review focuses mainly on the unique energy metabolism and related enzymes of P. furiosus that have recently been described.},
}
@article {pmid16232710,
year = {2000},
author = {Higashibata, H and Fujiwara, S and Ezaki, S and Takagi, M and Fukui, K and Imanaka, T},
title = {Effect of polyamines on histone-induced DNA compaction of hyperthermophilic archaea.},
journal = {Journal of bioscience and bioengineering},
volume = {89},
number = {1},
pages = {103-106},
doi = {10.1016/s1389-1723(00)88061-5},
pmid = {16232710},
issn = {1389-1723},
abstract = {The effect of polyamines on histone-mediated DNA compaction was examined in vitro with archaeal histone HpkA from Pyrococcus kodakaraensis KOD1. An agarose gel mobility-shift experiment indicated that histone-bound DNA (compacted DNA) was further compacted by addition of a polyamine (putrescine, spermidine, or spermine) or its acetylated form (N-acetylputrescine, N1-acetylspermidine, N8-acetylspermidine, or N1-acetylspermine) when the mixture was incubated at above 75 degrees C. Spermine was most effective in compaction enhancement among all the polyamines tested. A high concentration of potassium ion (1.0 M) did not stabilize the compacted form of DNA even though double-stranded DNA was stably maintained against thermal denaturation at elevated temperatures under this condition. It appears likely that multivalent polyamines have a nucleosome maintenance function in hyperthermophilic archaea in high-temperature environments.},
}
@article {pmid16221764,
year = {2005},
author = {Tocchini-Valentini, GD and Fruscoloni, P and Tocchini-Valentini, GP},
title = {Coevolution of tRNA intron motifs and tRNA endonuclease architecture in Archaea.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {102},
number = {43},
pages = {15418-15422},
pmid = {16221764},
issn = {0027-8424},
mesh = {Archaeal Proteins/*chemistry ; Dimerization ; Endoribonucleases/*chemistry ; *Introns ; Protein Folding ; Protein Subunits ; RNA Precursors/*chemistry ; RNA Splicing ; RNA, Archaeal/*chemistry ; },
abstract = {Members of the three kingdoms of life contain tRNA genes with introns. The introns in pre-tRNAs of Bacteria are self-splicing, whereas introns in archaeal and eukaryal pre-tRNAs are removed by splicing endonucleases. We have studied the structures of the endonucleases of Archaea and the architecture of the sites recognized in their pre-tRNA substrates. Three endonuclease structures are known in the Archaea: a homotetramer in some Euryarchaea, a homodimer in other Euryarchaea, and a heterotetramer in the Crenarchaeota. The homotetramer cleaves only the canonical bulge-helix-bulge structure in its substrates. Variants of the substrate structure, termed bulge-helix-loops, appear in the pre-tRNAs of the Crenarcheota and Nanoarcheota. These variant structures can be cleaved only by the homodimer or heterotetramer forms of the endonucleases. Thus, the structures of the endonucleases and their substrates appear to have evolved together.},
}
@article {pmid16218963,
year = {2005},
author = {Seedorf, H and Kahnt, J and Pierik, AJ and Thauer, RK},
title = {Si-face stereospecificity at C5 of coenzyme F420 for F420H2 oxidase from methanogenic Archaea as determined by mass spectrometry.},
journal = {The FEBS journal},
volume = {272},
number = {20},
pages = {5337-5342},
doi = {10.1111/j.1742-4658.2005.04931.x},
pmid = {16218963},
issn = {1742-464X},
mesh = {Euryarchaeota/*enzymology ; Flavin Mononucleotide/chemistry ; Molecular Structure ; NADH, NADPH Oxidoreductases/*chemistry ; Oxidation-Reduction ; Oxidoreductases Acting on CH-NH Group Donors/chemistry ; Pterins/chemistry ; Riboflavin/*analogs &amp; derivatives/chemistry ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/*methods ; Stereoisomerism ; },
abstract = {Coenzyme F420 is a 5-deazaflavin. Upon reduction, 1,5 dihydro-coenzyme F420 is formed with a prochiral centre at C5. All the coenzyme F420-dependent enzymes investigated to date have been shown to be Si-face stereospecific with respect to C5 of the deazaflavin, despite most F420-dependent enzymes being unrelated phylogenetically. In this study, we report that the recently discovered F420H2 oxidase from methanogenic Archaea is also Si-face stereospecific. The enzyme was found to catalyse the oxidation of (5S)-[5-2H1]F420H2 with O2 to [5-1H]F420 rather than to [5-2H]F420 as determined by MALDI-TOF MS. (5S)-[5-2H1]F420H2 was generated by stereospecific enzymatic reduction of F420 with (14a-2H2)-[14a-2H2] methylenetetrahydromethanopterin.},
}
@article {pmid16218868,
year = {2005},
author = {Hedderich, R and Hamann, N and Bennati, M},
title = {Heterodisulfide reductase from methanogenic archaea: a new catalytic role for an iron-sulfur cluster.},
journal = {Biological chemistry},
volume = {386},
number = {10},
pages = {961-970},
doi = {10.1515/BC.2005.112},
pmid = {16218868},
issn = {1431-6730},
mesh = {Binding Sites ; Catalysis ; Euryarchaeota/*enzymology ; Iron-Sulfur Proteins/*chemistry ; Methanobacteriaceae/enzymology ; Methanosarcina barkeri/enzymology ; Oxidoreductases/*chemistry/genetics ; Protein Subunits/chemistry ; Spectrum Analysis ; },
abstract = {Heterodisulfide reductase (HDR) from methanogenic archaea is an iron-sulfur protein that catalyzes reversible reduction of the heterodisulfide (CoM-S-S-CoB) of the methanogenic thiol-coenzymes, coenzyme M (CoM-SH) and coenzyme B (CoB-SH). Via the characterization of a paramagnetic reaction intermediate generated upon oxidation of the enzyme in the presence of coenzyme M, the enzyme was shown to contain a [4Fe-4S] cluster in its active site that catalyzes reduction of the disulfide substrate in two one-electron reduction steps. The formal thiyl radical generated by the initial one-electron reduction of the disulfide is stabilized via reduction and coordination of the resultant thiol to the [4Fe-4S] cluster.},
}
@article {pmid16213671,
year = {2005},
author = {Hummel, CS and Lancaster, KM and Crane, EJ},
title = {Determination of coenzyme A levels in Pyrococcus furiosus and other Archaea: implications for a general role for coenzyme A in thermophiles.},
journal = {FEMS microbiology letters},
volume = {252},
number = {2},
pages = {229-234},
doi = {10.1016/j.femsle.2005.09.004},
pmid = {16213671},
issn = {0378-1097},
mesh = {Amino Acid Sequence ; Coenzyme A/*analysis/*physiology ; Molecular Sequence Data ; Molecular Weight ; Oxidation-Reduction ; Oxidative Stress ; Oxidoreductases/chemistry/genetics ; Pyrococcus furiosus/*chemistry ; Sequence Homology, Amino Acid ; Sulfhydryl Compounds/analysis/metabolism ; Sulfolobus solfataricus/*chemistry ; Sulfur/metabolism ; Thermococcus/*chemistry ; },
abstract = {Physiologically significant levels of intracellular coenzyme A were identified in Pyrococcus furiosus, Thermococcus litoralis, and Sulfolobus solfataricus, suggesting a role for CoA as an important low molecular mass thiol in the thermophilic Archaea. In P. furiosus, cells grown in the presence of sulfur showed significantly higher levels of oxidized CoA compared with those grown in the absence of S(0). T. litoralis showed strikingly similar CoA levels, although with low disulfide levels in both the presence and absence of S(0). S. solfataricus showed similarly high levels of CoA thiol, with correspondingly low levels of the CoA disulfide. These results are consistent with the identification of a coenzyme A disulfide reductase (CoADR) in P. furiosus and horikoshii as well as the presence of CoADR homologues in the genomes of S. solfataricus and T. kodakaraensis.},
}
@article {pmid16212260,
year = {2005},
author = {Markov, AV and Kulikov, AM},
title = {[Homologous protein domains in superkingdoms Archaea, Bacteria, and Eukaryota and the problem of the origin of eukaryotes].},
journal = {Izvestiia Akademii nauk. Seriia biologicheskaia},
volume = {},
number = {4},
pages = {389-400},
pmid = {16212260},
issn = {1026-3470},
mesh = {Animals ; Archaea/*genetics/metabolism ; Archaeal Proteins/*genetics/metabolism ; Bacteria/*genetics/metabolism ; Bacterial Proteins/*genetics/metabolism ; Eukaryotic Cells/*physiology ; *Evolution, Molecular ; Mitochondria/genetics/metabolism ; Plastids/genetics/metabolism ; Protein Structure, Tertiary/physiology ; },
abstract = {The distribution of protein domains was analyzed in superkingdoms Archaea, Bacteria, and Eukaryota. About a half of eukaryotic domains have prokaryotic origin. Many domains related to information processing in the nucleocytoplasm were inherited from archaea. Sets of domains associated with metabolism and regulatory and signaling systems were inherited from bacteria. Many signaling and regulatory domains common for bacteria and eukaryotes were responsible for the cellular interaction of bacteria with other components of the microbial community but were involved in coordination of the activity of eukaryotic organelles and cells in multicellular organisms. Many eukaryotic domains of bacterial origin could not originate from ancestral mitochondria and plastids but rather were adopted from other bacteria. An archaeon with the induced incorporation of alien genetic material could be the ancestor of the eukaryotic nucleocytoplasm.},
}
@article {pmid16204562,
year = {2005},
author = {Lloyd, KG and Edgcomb, VP and Molyneaux, SJ and Böer, S and Wirsen, CO and Atkins, MS and Teske, A},
title = {Effects of dissolved sulfide, pH, and temperature on growth and survival of marine hyperthermophilic Archaea.},
journal = {Applied and environmental microbiology},
volume = {71},
number = {10},
pages = {6383-6387},
pmid = {16204562},
issn = {0099-2240},
mesh = {Archaeoglobus/drug effects/growth &amp; development/physiology ; Euryarchaeota/drug effects/*growth &amp; development/physiology ; Heat-Shock Response ; *Hot Temperature ; Hydrogen-Ion Concentration ; Seawater/*microbiology ; Sulfides/*pharmacology ; Thermococcus/drug effects/growth &amp; development/physiology ; },
abstract = {The ability of metabolically diverse hyperthermophilic archaea to withstand high temperatures, low pHs, high sulfide concentrations, and the absence of carbon and energy sources was investigated. Close relatives of our study organisms, Methanocaldococcus jannaschii, Archaeoglobus profundus, Thermococcus fumicolans, and Pyrococcus sp. strain GB-D, are commonly found in hydrothermal vent chimney walls and hot sediments and possibly deeper in the subsurface, where highly dynamic hydrothermal flow patterns and steep chemical and temperature gradients provide an ever-changing mosaic of microhabitats. These organisms (with the possible exception of Pyrococcus strain GB-D) tolerated greater extremes of low pH, high sulfide concentration, and high temperature when actively growing and metabolizing than when starved of carbon sources and electron donors/acceptors. Therefore these organisms must be actively metabolizing in the hydrothermal vent chimneys, sediments, and subsurface in order to withstand at least 24 h of exposure to extremes of pH, sulfide, and temperature that occur in these environments.},
}
@article {pmid16186749,
year = {2005},
author = {Siqueira, JF and Rôças, IN and Baumgartner, JC and Xia, T},
title = {Searching for Archaea in infections of endodontic origin.},
journal = {Journal of endodontics},
volume = {31},
number = {10},
pages = {719-722},
doi = {10.1097/01.don.0000155224.00781.6c},
pmid = {16186749},
issn = {0099-2399},
mesh = {Archaea/*isolation &amp; purification/pathogenicity ; Bacterial Typing Techniques ; DNA, Archaeal/analysis ; Dental Pulp Cavity/*microbiology ; Humans ; Periapical Periodontitis/*microbiology ; Polymerase Chain Reaction ; Spirochaetales/isolation &amp; purification ; },
abstract = {Archaea is a highly diverse group of prokaryotes, whose members have been traditionally recognized as extremophiles. Recently, some of these microorganisms have also been found to thrive in nonextreme environments, including the human body. Methanogenic archaea have been detected in samples from subgingival plaque associated with periodontal disease and a pathogenetic role is suspected. The purpose of this study was to survey samples taken from different types of endodontic infections for the presence of archaea. Samples were taken from untreated and treated root canals associated with asymptomatic chronic periradicular lesions as well as from cases diagnosed as acute periradicular abscesses. Overall, 96 samples were obtained. DNA from samples was extracted by using two different protocols and used as template for polymerase chain reaction amplification using oligonucleotide universal primers for the domains Archaea or Bacteria. Samples were also checked for the presence of spirochetes by making use of a group-specific primer. While bacteria were present in all samples, no case yielded archaeal DNA. Spirochetes occurred in a high number of cases. Our findings suggested that members of the Archaea domain are not members of the microbiota present in different types of endodontic infections and thereby may not be implicated in the etiology of apical periodontitis.},
}
@article {pmid16186488,
year = {2005},
author = {Francis, CA and Roberts, KJ and Beman, JM and Santoro, AE and Oakley, BB},
title = {Ubiquity and diversity of ammonia-oxidizing archaea in water columns and sediments of the ocean.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {102},
number = {41},
pages = {14683-14688},
pmid = {16186488},
issn = {0027-8424},
mesh = {Base Sequence ; Cloning, Molecular ; Cluster Analysis ; Crenarchaeota/*genetics/*metabolism ; DNA Primers ; *Genetic Variation ; Geologic Sediments/*microbiology ; Mediterranean Sea ; Molecular Sequence Data ; Oxidoreductases/genetics ; Pacific Ocean ; *Phylogeny ; Seawater/*microbiology ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {Nitrification, the microbial oxidation of ammonia to nitrite and nitrate, occurs in a wide variety of environments and plays a central role in the global nitrogen cycle. Catalyzed by the enzyme ammonia monooxygenase, the ability to oxidize ammonia was previously thought to be restricted to a few groups within the beta- and gamma-Proteobacteria. However, recent metagenomic studies have revealed the existence of unique ammonia monooxygenase alpha-subunit (amoA) genes derived from uncultivated, nonextremophilic Crenarchaeota. Here, we report molecular evidence for the widespread presence of ammonia-oxidizing archaea (AOA) in marine water columns and sediments. Using PCR primers designed to specifically target archaeal amoA, we find AOA to be pervasive in areas of the ocean that are critical for the global nitrogen cycle, including the base of the euphotic zone, suboxic water columns, and estuarine and coastal sediments. Diverse and distinct AOA communities are associated with each of these habitats, with little overlap between water columns and sediments. Within marine sediments, most AOA sequences are unique to individual sampling locations, whereas a small number of sequences are evidently cosmopolitan in distribution. Considering the abundance of nonextremophilic archaea in the ocean, our results suggest that AOA may play a significant, but previously unrecognized, role in the global nitrogen cycle.},
}
@article {pmid16181730,
year = {2005},
author = {Takemura, M},
title = {Evolutionary history of the retinoblastoma gene from archaea to eukarya.},
journal = {Bio Systems},
volume = {82},
number = {3},
pages = {266-272},
doi = {10.1016/j.biosystems.2005.08.005},
pmid = {16181730},
issn = {0303-2647},
mesh = {Amino Acid Sequence ; Animals ; *Biological Evolution ; Cell Cycle ; Cell Differentiation ; Computational Biology/*methods ; *Evolution, Molecular ; *Gene Expression Regulation ; Genes, Archaeal ; Humans ; Methanococcus/genetics ; Models, Biological ; Molecular Sequence Data ; Retinoblastoma Protein/*genetics/*physiology ; Saccharomyces cerevisiae/genetics ; Sequence Homology, Amino Acid ; Species Specificity ; Systems Biology/*methods ; },
abstract = {The retinoblastoma gene product (Rb protein) has a role in progression through the cell cycle, regulating the activities of several transcription factors such as E2F. Since its functional loss results in impaired differentiation in the nervous, hematopoietic, and muscular systems, the Rb protein is very important for cell regulation in multicellular eukaryotes. To gain an insight into the evolutionary history of the Rb gene, I have compared the amino acid sequences of Rb proteins in multicellular eukaryotes and unicellular organisms including yeast, archaeotes, and viruses. Two short amino acid sequences, in the N-terminal and pocket A regions of human Rb protein, found to be well conserved, also in a single protein of Saccharomyces cerevisiae. These sequences were also found in proteins of two archaeotes, Archaeoglobus fulgidus and Methanococcus jannaschii. Further, the most conserved sequence in the pocket B region among multicellular eukaryotic Rb proteins was also conserved in several poxviruses. From these data, I conclude that the pocket A and B regions, backbones of the Rb protein, are derived from different organisms, respectively, the ancestors of archaeote and poxvirus, and that the ancestral pocket B region has been lost during evolutionary history of unicellular eukaryotes.},
}
@article {pmid16164996,
year = {2005},
author = {Clouet-d'Orval, B and Gaspin, C and Mougin, A},
title = {Two different mechanisms for tRNA ribose methylation in Archaea: a short survey.},
journal = {Biochimie},
volume = {87},
number = {9-10},
pages = {889-895},
doi = {10.1016/j.biochi.2005.02.004},
pmid = {16164996},
issn = {0300-9084},
mesh = {Archaea/enzymology/*genetics ; Gene Expression Regulation, Archaeal ; Humans ; Methylation ; Nucleic Acid Conformation ; RNA, Antisense ; RNA, Archaeal/biosynthesis/*metabolism ; RNA, Transfer/*biosynthesis ; Ribose/*biosynthesis ; Sequence Alignment ; Site-Specific DNA-Methyltransferase (Adenine-Specific)/chemistry ; tRNA Methyltransferases/*metabolism ; },
abstract = {The biogenesis of tRNA involves multiple reactions including post-transcriptional modifications and pre-tRNA splicing. Among the three domains of life, only Archaea have two different mechanisms for tRNA ribose methylation: site-specific 2'-O-methyltransferases and C/D guided-RNA machinery. Recently, the first archaeal tRNA 2'-O-methyltransferase, aTrm56, has been characterized. This enzyme is found in all archaeal genomes sequenced so far except one and belongs to the SPOUT family (class IV) of RNA methyltransferases. Its substrate is the conserved C56 in the T-loop of archaeal tRNAs. In the crenarchaeon Pyrobaculum aerophylum, in which no homologue of this methyltransferase is found, a box C/D guide sRNP insures the ribose methylation of C56. Moreover, a new twist on tRNA processing is the finding, in most euryarchaeal tRNAtrp genes, of a box C/D guide RNA within their intron specifying methylation at two sites. Modification of tRNA is an integral part of the complex maturation process of primary tRNA transcripts. In addition to their role in modification, both modification enzymes and C/D guide RNPs may have a chaperone function insuring the precise folding of the mature, functional tRNA.},
}
@article {pmid16148304,
year = {2005},
author = {Eichler, J and Adams, MW},
title = {Posttranslational protein modification in Archaea.},
journal = {Microbiology and molecular biology reviews : MMBR},
volume = {69},
number = {3},
pages = {393-425},
pmid = {16148304},
issn = {1092-2172},
mesh = {Archaea/genetics/*metabolism ; Archaeal Proteins/genetics/*metabolism ; Carbohydrate Sequence ; Disulfides/metabolism ; Glycosylation ; Lipoproteins/metabolism ; Methylation ; Molecular Sequence Data ; Phosphorylation ; Protein Processing, Post-Translational/*physiology ; },
abstract = {One of the first hurdles to be negotiated in the postgenomic era involves the description of the entire protein content of the cell, the proteome. Such efforts are presently complicated by the various posttranslational modifications that proteins can experience, including glycosylation, lipid attachment, phosphorylation, methylation, disulfide bond formation, and proteolytic cleavage. Whereas these and other posttranslational protein modifications have been well characterized in Eucarya and Bacteria, posttranslational modification in Archaea has received far less attention. Although archaeal proteins can undergo posttranslational modifications reminiscent of what their eucaryal and bacterial counterparts experience, examination of archaeal posttranslational modification often reveals aspects not previously observed in the other two domains of life. In some cases, posttranslational modification allows a protein to survive the extreme conditions often encountered by Archaea. The various posttranslational modifications experienced by archaeal proteins, the molecular steps leading to these modifications, and the role played by posttranslational modification in Archaea form the focus of this review.},
}
@article {pmid16126291,
year = {2006},
author = {Crocetti, G and Murto, M and Björnsson, L},
title = {An update and optimisation of oligonucleotide probes targeting methanogenic Archaea for use in fluorescence in situ hybridisation (FISH).},
journal = {Journal of microbiological methods},
volume = {65},
number = {1},
pages = {194-201},
doi = {10.1016/j.mimet.2005.07.007},
pmid = {16126291},
issn = {0167-7012},
mesh = {Archaea/*genetics ; In Situ Hybridization, Fluorescence/*methods ; Oligonucleotide Probes/chemistry/*genetics ; Phylogeny ; RNA, Archaeal/chemistry/genetics ; RNA, Ribosomal, 16S/chemistry/genetics ; },
abstract = {Fluorescence in situ hybridisation (FISH) is a common and popular method used to investigate microbial populations in natural and engineered environments. DNA oligonucleotide probes require accurate determination of the optimal experimental conditions for their use in FISH. Oligonucleotides targeting the rRNA of methanogenic Archaea at various taxonomic levels have previously been published, although when applied in FISH, no optimisation data has been presented. In this study, 3000 Euryarchaeota 16S rRNA gene sequences were phylogenetically analysed and previously published oligonucleotides were evaluated for target group accuracy. Where necessary, modifications were introduced or new probes were designed. The updated set of probes was optimised for use in FISH for a more accurate detection of methanogenic Archaea.},
}
@article {pmid16111915,
year = {2005},
author = {Makarova, KS and Koonin, EV},
title = {Evolutionary and functional genomics of the Archaea.},
journal = {Current opinion in microbiology},
volume = {8},
number = {5},
pages = {586-594},
doi = {10.1016/j.mib.2005.08.003},
pmid = {16111915},
issn = {1369-5274},
support = {//Intramural NIH HHS/United States ; },
mesh = {Archaea/*genetics ; *Evolution, Molecular ; *Genome, Archaeal ; Nanoarchaeota/genetics ; },
abstract = {In the past two years, archaeal genomics has achieved several breakthroughs. On the evolutionary front the most exciting development was the sequencing and analysis of the genome of Nanoarchaeum equitans, a tiny parasitic organism that has only approximately 540 genes. The genome of Nanoarchaeum shows signs of extreme rearrangement including the virtual absence of conserved operons and the presence of several split genes. Nanoarchaeum is distantly related to other archaea, and it has been proposed to represent a deep archaeal branch that is distinct from Euryarchaeota and Crenarchaeota. This would imply that many features of its gene repertoire and genome organization might be ancestral. However, additional genome analysis has provided a more conservative suggestion - that Nanoarchaeum is a highly derived euryarchaeon. Also there have been substantial developments in functional genomics, including the discovery of the elusive aminoacyl-tRNA synthetase that is involved in both the biosynthesis of cysteine and its incorporation into proteins in methanogens, and the first experimental validation of the predicted archaeal exosome.},
}
@article {pmid16104851,
year = {2005},
author = {Golyshina, OV and Timmis, KN},
title = {Ferroplasma and relatives, recently discovered cell wall-lacking archaea making a living in extremely acid, heavy metal-rich environments.},
journal = {Environmental microbiology},
volume = {7},
number = {9},
pages = {1277-1288},
doi = {10.1111/j.1462-2920.2005.00861.x},
pmid = {16104851},
issn = {1462-2912},
mesh = {Acids/*analysis ; Cell Wall ; Environmental Pollutants/*analysis ; Iron/chemistry ; Metals, Heavy/*analysis ; Oxidation-Reduction ; *Soil Microbiology ; Thermoplasmales/*growth &amp; development/ultrastructure ; *Water Microbiology ; },
abstract = {For several decades, the bacterium Acidithiobacillus (previously Thiobacillus) has been considered to be the principal acidophilic sulfur- and iron-oxidizing microbe inhabiting acidic environments rich in ores of iron and other heavy metals, responsible for the metal solubilization and leaching from such ores, and has become the paradigm of such microbes. However, during the last few years, new studies of a number of acidic environments, particularly mining waste waters, acidic pools, etc., in diverse geographical locations have revealed the presence of new cell wall-lacking archaea related to the recently described, acidophilic, ferrous-iron oxidizing Ferroplasma acidiphilum. These mesophilic and moderately thermophilic microbes, representing the family Ferroplasmaceae, were numerically significant members of the microbial consortia of the habitats studied, are able to mobilize metals from sulfide ores, e.g. pyrite, arsenopyrite and copper-containing sulfides, and are more acid-resistant than iron and sulfur oxidizing bacteria exhibiting similar eco-physiological properties. Ferroplasma cell membranes contain novel caldarchaetidylglycerol tetraether lipids, which have extremely low proton permeabilities, as a result of the bulky isoprenoid core, and which are probably a major contributor to the extreme acid tolerance of these cell wall-less microbes. Surprisingly, several intracellular enzymes, including an ATP-dependent DNA ligase have pH optima close to that of the external environment rather than of the cytoplasm. Ferroplasma spp. are probably the major players in the biogeochemical cycling of sulfur and sulfide metals in highly acidic environments, and may have considerable potential for biotechnological applications such as biomining and biocatalysis under extreme conditions.},
}
@article {pmid16099988,
year = {2005},
author = {Lu, Y and Conrad, R},
title = {In situ stable isotope probing of methanogenic archaea in the rice rhizosphere.},
journal = {Science (New York, N.Y.)},
volume = {309},
number = {5737},
pages = {1088-1090},
doi = {10.1126/science.1113435},
pmid = {16099988},
issn = {1095-9203},
mesh = {Archaea/classification/genetics/growth &amp; development/*metabolism ; Carbon Dioxide/metabolism ; Carbon Isotopes/*metabolism ; Cloning, Molecular ; *Ecosystem ; Hydrogen/metabolism ; Methane/*metabolism ; Molecular Sequence Data ; Oryza/metabolism/*microbiology ; Photosynthesis ; Phylogeny ; Plant Roots/metabolism/microbiology ; Polymorphism, Restriction Fragment Length ; RNA, Archaeal/metabolism ; RNA, Ribosomal, 16S/genetics/metabolism ; *Soil Microbiology ; },
abstract = {Microorganisms living in anoxic rice soils contribute 10 to 25% of global methane emissions. The most important carbon source for CH4 production is plant-derived carbon that enters soil as root exudates and debris. Pulse labeling of rice plants with 13CO2 resulted in incorporation of 13C into the ribosomal RNA of Rice Cluster I Archaea in the soil, indicating that this archaeal group plays a key role in CH4 production from plant-derived carbon. This group of microorganisms has not yet been isolated but appears to be of global environmental importance.},
}
@article {pmid16000782,
year = {2005},
author = {Girguis, PR and Cozen, AE and DeLong, EF},
title = {Growth and population dynamics of anaerobic methane-oxidizing archaea and sulfate-reducing bacteria in a continuous-flow bioreactor.},
journal = {Applied and environmental microbiology},
volume = {71},
number = {7},
pages = {3725-3733},
pmid = {16000782},
issn = {0099-2240},
mesh = {Anaerobiosis ; Archaea/genetics/*growth &amp; development ; *Bioreactors ; Deltaproteobacteria/genetics/*growth &amp; development ; *Ecosystem ; Geologic Sediments ; Methane/*metabolism ; Oxidation-Reduction ; Polymerase Chain Reaction/methods ; Sulfur-Reducing Bacteria/genetics/*growth &amp; development ; },
abstract = {The consumption of methane in anoxic marine sediments is a biogeochemical phenomenon mediated by two archaeal groups (ANME-1 and ANME-2) that exist syntrophically with sulfate-reducing bacteria. These anaerobic methanotrophs have yet to be recovered in pure culture, and key aspects of their ecology and physiology remain poorly understood. To characterize the growth and physiology of these anaerobic methanotrophs and the syntrophic sulfate-reducing bacteria, we incubated marine sediments using an anoxic, continuous-flow bioreactor during two experiments at different advective porewater flow rates. We examined the growth kinetics of anaerobic methanotrophs and Desulfosarcina-like sulfate-reducing bacteria using quantitative PCR as a proxy for cell counts, and measured methane oxidation rates using membrane-inlet mass spectrometry. Our data show that the specific growth rates of ANME-1 and ANME-2 archaea differed in response to porewater flow rates. ANME-2 methanotrophs had the highest rates in lower-flow regimes (mu(ANME-2) = 0.167 . week(-1)), whereas ANME-1 methanotrophs had the highest rates in higher-flow regimes (mu(ANME-1) = 0.218 . week(-1)). In both incubations, Desulfosarcina-like sulfate-reducing bacterial growth rates were approximately 0.3 . week(-1), and their growth dynamics suggested that sulfate-reducing bacterial growth might be facilitated by, but not dependent upon, an established anaerobic methanotrophic population. ANME-1 growth rates corroborate field observations that ANME-1 archaea flourish in higher-flow regimes. Our growth and methane oxidation rates jointly demonstrate that anaerobic methanotrophs are capable of attaining substantial growth over a range of environmental conditions used in these experiments, including relatively low methane partial pressures.},
}
@article {pmid15999201,
year = {2005},
author = {Wallner, SR and Nestl, BM and Faber, K},
title = {Highly enantioselective stereo-inverting sec-alkylsulfatase activity of hyperthermophilic Archaea.},
journal = {Organic &amp; biomolecular chemistry},
volume = {3},
number = {14},
pages = {2652-2656},
doi = {10.1039/b504883d},
pmid = {15999201},
issn = {1477-0520},
mesh = {Archaea/*enzymology ; Molecular Conformation ; Molecular Structure ; Stereoisomerism ; Sulfatases/*chemistry/metabolism ; Temperature ; },
abstract = {rac-sec-Alkyl sulfate esters 1a-8a were resolved in low to excellent enantioselectivities with E-values up to >200 using whole cells of aerobically-grown hyperthermophilic sulfur-metabolizers, such as Sulfolobus solfataricus DSM 1617, Sulfolobus shibatae DSM 5389 and, most notably, Sulfolobus acidocaldarius DSM 639. Significantly enhanced selectivities were obtained using cells grown on sucrose-enriched Brock-medium. The stereochemical course of this biohydrolysis was shown to proceed with strict inversion of configuration, thus the preferred (R)-enantiomers were converted into the corresponding (S)-sec-alcohols to furnish a homochiral product mixture.},
}
@article {pmid15993370,
year = {2006},
author = {Koga, Y and Morii, H},
title = {Special methods for the analysis of ether lipid structure and metabolism in archaea.},
journal = {Analytical biochemistry},
volume = {348},
number = {1},
pages = {1-14},
doi = {10.1016/j.ab.2005.04.004},
pmid = {15993370},
issn = {0003-2697},
mesh = {Archaea/chemistry/classification/*metabolism ; Chromatography, Gas/methods ; Esters/*analysis/chemistry/metabolism ; Ethers/*analysis/chemistry/metabolism ; Hydrolysis ; Molecular Structure ; },
}
@article {pmid15987815,
year = {2005},
author = {Renalier, MH and Joseph, N and Gaspin, C and Thebault, P and Mougin, A},
title = {The Cm56 tRNA modification in archaea is catalyzed either by a specific 2'-O-methylase, or a C/D sRNP.},
journal = {RNA (New York, N.Y.)},
volume = {11},
number = {7},
pages = {1051-1063},
pmid = {15987815},
issn = {1355-8382},
mesh = {Amino Acid Sequence ; Catalysis ; Cloning, Molecular ; Consensus Sequence ; Cytosine/*metabolism ; Escherichia coli/genetics ; Genome, Archaeal ; Glutathione Transferase/metabolism ; Kinetics ; Molecular Sequence Data ; Molecular Weight ; Open Reading Frames ; Phylogeny ; Protein Structure, Secondary ; Pyrobaculum/genetics/metabolism ; Pyrococcus abyssi/enzymology/genetics ; RNA, Archaeal/chemistry/genetics/*metabolism ; RNA, Small Nucleolar/genetics/*metabolism ; RNA, Transfer/*chemistry/metabolism ; Recombinant Proteins/chemistry/isolation &amp; purification/metabolism ; Sequence Homology, Amino Acid ; Substrate Specificity ; Temperature ; tRNA Methyltransferases/*chemistry/classification/genetics/*metabolism ; },
abstract = {We identified the first archaeal tRNA ribose 2'-O-methylase, aTrm56, belonging to the Cluster of Orthologous Groups (COG) 1303 that contains archaeal genes only. The corresponding protein exhibits a SPOUT S-adenosylmethionine (AdoMet)-dependent methyltransferase domain found in bacterial and yeast G18 tRNA 2'-O-methylases (SpoU, Trm3). We cloned the Pyrococcus abyssi PAB1040 gene belonging to this COG, expressed and purified the corresponding protein, and showed that in vitro, it specifically catalyzes the AdoMet-dependent 2'-O-ribose methylation of C at position 56 in tRNA transcripts. This tRNA methylation is present only in archaea, and the gene for this enzyme is present in all the archaeal genomes sequenced up to now, except in the crenarchaeon Pyrobaculum aerophilum. In this archaea, the C56 2'-O-methylation is provided by a C/D sRNP. Our work is the first demonstration that, within the same kingdom, two different mechanisms are used to modify the same nucleoside in tRNAs.},
}
@article {pmid15986097,
year = {2005},
author = {Kilian, HG and Gruler, H and Bartkowiak, D and Kaufmann, D},
title = {Stationary cell size distributions and mean protein chain length distributions of Archaea, Bacteria and Eukaryotes described with an increment model in terms of irreversible thermodynamics.},
journal = {The European physical journal. E, Soft matter},
volume = {17},
number = {3},
pages = {307-325},
pmid = {15986097},
issn = {1292-8941},
mesh = {Archaea/*cytology/*physiology ; Bacteria/*cytology ; *Bacterial Physiological Phenomena ; *Cell Enlargement ; Computer Simulation ; Eukaryotic Cells/*cytology/*physiology ; *Models, Biological ; Thermodynamics ; },
abstract = {In terms of an increment model irreversible thermodynamics allows to formulate general relations of stationary cell size distributions observed in growing colonies. The treatment is based on the following key postulates: i) The growth dynamics covers a broad spectrum of fast and slow processes. ii) Slow processes are considered to install structural patterns that operate in short periods as temporary stationary states of reference in the sense of irreversible thermodynamics. iii) Distortion during growth is balanced out via the many fast processes until an optimized stationary state is achieved. The relation deduced identifies the numerous different stationary patterns as equivalents, predicting that they should fall on one master curve. Stationary cell size distributions of different cell types, like Hyperphilic archaea, E. coli (Prokaryotes) and S. cerevisiae (Eukaryotes), altogether taken from the literature, are in fact consistently described. As demanded by the model they agree together with the same master curve. Considering the "protein factories" as subsystems of cells the mean protein chain length distributions deduced from completely sequenced genomes should be optimized. In fact, the mean course can be described with analogous relations as used above. Moreover, the master curve fits well to the patterns of different species of Archaea, Bacteria and Eukaryotes. General consequences are discussed.},
}
@article {pmid15983865,
year = {2005},
author = {Calteau, A and Gouy, M and Perrière, G},
title = {Horizontal transfer of two operons coding for hydrogenases between bacteria and archaea.},
journal = {Journal of molecular evolution},
volume = {60},
number = {5},
pages = {557-565},
pmid = {15983865},
issn = {0022-2844},
mesh = {Archaea/*genetics ; Bacteria/*genetics ; Computational Biology ; Gene Components ; Gene Transfer, Horizontal/*genetics ; Hydrogenase/*genetics ; Likelihood Functions ; Models, Genetic ; Multigene Family/genetics ; Operon/*genetics ; *Phylogeny ; },
abstract = {Using a phylogenetic approach, we discovered three putative horizontal transfers between bacterial and archaeal species involving large clusters of genes. One transfer involves an operon of 13 genes, called mbx, which probably was transferred into the genome of Thermotoga maritima from a species belonging or close to the Pyrococcus genus. The two others implied an operon of six genes, called ech, transferred independently to the genomes of Thermoanaerobacter tengcongensis and Desulfovibrio gigas, from a species belonging or close to the Methanosarcina genus. All these transfers affected operons coding for multisubunit membrane-bound (NiFe) hydrogenases involved in the energy metabolism of the donor genomes. The functionality of the transferred operons has not been experimentally demonstrated for T. maritima, whereas in D. gigas and T. tengcongensis the encoded multisubunit hydrogenase could have a role in energy conservation. This report adds several cases of horizontal gene transfers among hydrogenases already described.},
}
@article {pmid15972818,
year = {2005},
author = {Díaz-Perales, A and Quesada, V and Peinado, JR and Ugalde, AP and Alvarez, J and Suárez, MF and Gomis-Rüth, FX and López-Otín, C},
title = {Identification and characterization of human archaemetzincin-1 and -2, two novel members of a family of metalloproteases widely distributed in Archaea.},
journal = {The Journal of biological chemistry},
volume = {280},
number = {34},
pages = {30367-30375},
doi = {10.1074/jbc.M504533200},
pmid = {15972818},
issn = {0021-9258},
mesh = {Amino Acid Motifs ; Amino Acid Sequence ; Archaea ; Base Sequence ; Blotting, Northern ; Catalysis ; Catalytic Domain ; Computational Biology ; DNA, Complementary/metabolism ; Evolution, Molecular ; Gene Expression Regulation, Developmental ; Genome, Archaeal ; Humans ; Hydrogen-Ion Concentration ; Hydrolysis ; Liver/metabolism ; Male ; Mass Spectrometry ; Metalloproteases/*chemistry/physiology ; Molecular Sequence Data ; Myocardium/metabolism ; Peptides/chemistry ; Phylogeny ; Protein Binding ; Protein Structure, Tertiary ; Recombinant Proteins/chemistry ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Testis/metabolism ; Tissue Distribution ; Trypsin/pharmacology ; },
abstract = {Systematic analysis of degradomes, the complete protease repertoires of organisms, has demonstrated the large and growing complexity of proteolytic systems operating in all cells and tissues. We report here the identification of two new human metalloproteases that have been called archaemetzincin-1 (AMZ1) and archaemetzincin-2 (AMZ2) to emphasize their close relationship to putative proteases predicted by bioinformatic analysis of archaeal genomes. Both human proteins contain a catalytic domain with a core motif (HEXXHXXGX3CX4CXMX17CXXC) that includes an archetypal zinc-binding site, the methionine residue characteristic of metzincins, and four conserved cysteine residues that are not present at the equivalent positions of other human metalloproteases. Analysis of genome sequence databases revealed that AMZs are widely distributed in Archaea and vertebrates and contribute to the defining of a new metalloprotease family that has been called archaemetzincin. However, AMZ-like sequences are absent in a number of model organisms from bacteria to nematodes. Phylogenetic analysis showed that these enzymes have undergone a complex evolutionary process involving a series of lateral gene transfer, gene loss, and genetic duplication events that have shaped this novel family of metalloproteases. Northern blot analysis showed that AMZ1 and AMZ2 exhibit distinct expression patterns in human tissues. AMZ1 is mainly detected in liver and heart whereas AMZ2 is predominantly expressed in testis and heart, although both are also detectable at lower levels in other tissues. Both human enzymes were produced in Escherichia coli, and the purified recombinant proteins hydrolyzed synthetic substrates and bioactive peptides, demonstrating that they are functional proteases. Finally, these activities were abolished by inhibitors of metalloproteases, providing further evidence that AMZs belong to this catalytic class of proteolytic enzymes.},
}
@article {pmid15937113,
year = {2005},
author = {Tocchini-Valentini, GD and Fruscoloni, P and Tocchini-Valentini, GP},
title = {Structure, function, and evolution of the tRNA endonucleases of Archaea: an example of subfunctionalization.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {102},
number = {25},
pages = {8933-8938},
pmid = {15937113},
issn = {0027-8424},
mesh = {Archaea/*enzymology/genetics ; Archaeal Proteins/genetics/metabolism ; Endoribonucleases/chemistry/*genetics/*metabolism ; *Evolution, Molecular ; Models, Molecular ; Protein Conformation ; RNA, Archaeal/genetics/metabolism ; RNA, Transfer/*genetics/*metabolism ; },
abstract = {We have detected two paralogs of the tRNA endonuclease gene of Methanocaldococcus jannaschii in the genome of the crenarchaeote Sulfolobus solfataricus. This finding has led to the discovery of a previously unrecognized oligomeric form of the enzyme. The two genes code for two different subunits, both of which are required for cleavage of the pre-tRNA substrate. Thus, there are now three forms of tRNA endonuclease in the Archaea: a homotetramer in some Euryarchaea, a homodimer in other Euryarchaea, and a heterotetramer in the Crenarchaea and the Nanoarchaea. The last-named enzyme, arising most likely by gene duplication and subsequent "subfunctionalization," requires the products of both genes to be active.},
}
@article {pmid15936779,
year = {2005},
author = {Yamada, T and Fujii, T and Kanai, T and Amo, T and Imanaka, T and Nishimasu, H and Wakagi, T and Shoun, H and Kamekura, M and Kamagata, Y and Kato, T and Kawashima, K},
title = {Expression of acetylcholine (ACh) and ACh-synthesizing activity in Archaea.},
journal = {Life sciences},
volume = {77},
number = {16},
pages = {1935-1944},
doi = {10.1016/j.lfs.2005.01.026},
pmid = {15936779},
issn = {0024-3205},
mesh = {Acetylcholine/*biosynthesis/*metabolism ; Archaea/*metabolism ; Choline O-Acetyltransferase/metabolism ; Chromatography, High Pressure Liquid ; *Gene Expression ; Radioimmunoassay ; Species Specificity ; },
abstract = {Acetylcholine (ACh) is known generally as the neurotransmitter in the mammalian central and peripheral cholinergic nervous systems. However, ACh is also widely expressed in non-neuronal animal tissues and in plants, fungi and bacteria, where it is likely involved in the transport of water, electrolytes and nutrients, and in modulating various other cell functions. We have investigated the expression of ACh and ACh-synthesizing activity in various strains of Archaea, which are situated between Bacteria and Eucarya in the universal phylogenetic tree. Using a sensitive and specific radioimmunoassay, differing levels of ACh were detected in the Hyperthermophiles Thermococcus kodakaraensis KOD1, Sulfolobus tokodaii strain 7 and Pyrobaculum calidifontis VA1; the Methanogens Methanothermobacter thermautotrophicus deltaH and Methanosarcina barkeri; and the Halophiles Halobacterium sp. NRC-1 and Haloferax volcanii. T. kodakaraensis KOD1 expressed the highest levels of ACh among the Archaea tested; moreover, the substance expressed was verified to be ACh using high-performance liquid chromatography with electrochemical detection. Varying degrees of ACh-synthesizing activity were also identified in all of the strains, and the activity of bromoACh-sensitive choline acetyltransferase, an enzyme responsible for ACh synthesis in the nervous system, was detected in T. kodakaraensis KOD1. Our findings demonstrate that ACh and ACh-synthesizing activity are both expressed in evolutionally old Archaea. In the context of the recent discovery of non-neuronal ACh in bacteria, fungi, plants and animals, these findings support the notion that ACh has been expressed in organisms from the origin of life on the earth, functioning as a local mediator as well as a neurotransmitter.},
}
@article {pmid15932645,
year = {2005},
author = {Brochier, C and Forterre, P and Gribaldo, S},
title = {An emerging phylogenetic core of Archaea: phylogenies of transcription and translation machineries converge following addition of new genome sequences.},
journal = {BMC evolutionary biology},
volume = {5},
number = {},
pages = {36},
pmid = {15932645},
issn = {1471-2148},
mesh = {Algorithms ; Animals ; Archaea/*genetics ; Computational Biology/*methods ; Evolution, Molecular ; Genes, Archaeal ; *Genome, Archaeal ; Likelihood Functions ; Phylogeny ; *Protein Biosynthesis ; Protein Structure, Tertiary ; RNA, Ribosomal/genetics ; Software ; *Transcription, Genetic ; },
abstract = {BACKGROUND: The concept of a genomic core, defined as the set of genes ubiquitous in all genomes of a monophyletic group, has become crucial in comparative and evolutionary genomics. However, it is still a matter of debate whether lateral gene transfers (LGT) may affect the components of genomic cores, preventing their use to retrace species evolution. We have recently reconstructed the phylogeny of Archaea by using two large concatenated datasets of core proteins involved in translation and transcription, respectively. The resulting trees were largely congruent, showing that informational gene components of the archaeal genomic core belonging to two distinct molecular systems contain a coherent signal for archaeal phylogeny. However, some incongruence remained between the two phylogenies. This may be due either to undetected LGT and/or to a lack of sufficient phylogenetic signal in the datasets.<br><br>RESULTS: We present evidence strongly favoring of the latter hypothesis. In fact, we have updated our transcription and translation datasets with five new archaeal genomes for a total of 6384 and 2928 amino acid positions, respectively, and 25 taxa. This increase in taxonomic sampling led to the nearly complete convergence of the transcription-based and translation-based trees on a single phylogenetic pattern for archaeal evolution. In fact, only a single incongruence persisted between the two phylogenies. This concerned Methanopyrus kandleri, whose placement remained strongly biased in the transcription tree due to its above average evolutionary rates, and could not be counterbalanced due to the lack of availability of closely related and/or slower-evolving relatives.<br><br>CONCLUSION: To our knowledge, this is the first report of evidence that the phylogenetic signal harbored by components of the archaeal translation apparatus is confirmed by additional markers belonging to a second molecular system (i.e. transcription). This rules out the risk of circularity when inferring species evolution by small subunit ribosomal RNA and ribosomal protein sequences, since it has been suggested that concerted LGT may affect these markers. Our results strongly support the existence of a core of proteins that has evolved mainly through vertical inheritance in Archaea, and carries a bona fide phylogenetic signal that can be used to retrace the evolutionary history of this domain. The identification and analysis of additional molecular markers not affected by LGT should continue defining the emerging picture of a genuine phylogenetic core for the third domain of life.},
}
@article {pmid15931166,
year = {2005},
author = {Schleper, C and Jurgens, G and Jonuscheit, M},
title = {Genomic studies of uncultivated archaea.},
journal = {Nature reviews. Microbiology},
volume = {3},
number = {6},
pages = {479-488},
doi = {10.1038/nrmicro1159},
pmid = {15931166},
issn = {1740-1526},
mesh = {Animals ; Archaea/classification/*genetics ; Biodiversity ; *Genome, Archaeal ; Phylogeny ; Plankton/classification/genetics ; RNA, Archaeal/genetics ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Archaea represent a considerable fraction of the prokaryotic world in marine and terrestrial ecosystems, indicating that organisms from this domain might have a large impact on global energy cycles. However, many novel archaeal lineages that have been detected by molecular phylogenetic approaches have remained elusive because no laboratory-cultivated strains are available. Environmental genomic analyses have recently provided clues about the potential metabolic strategies of several of the uncultivated and abundant archaeal species, including non-thermophilic terrestrial and marine crenarchaeota and methanotrophic euryarchaeota. These initial studies of natural archaeal populations also revealed an unexpected degree of genomic variation that indicates considerable heterogeneity among archaeal strains. Here, we review genomic studies of uncultivated archaea within a framework of the phylogenetic diversity and ecological distribution of this domain.},
}
@article {pmid15908961,
year = {2005},
author = {Dwivedi, S and Kruparani, SP and Sankaranarayanan, R},
title = {A D-amino acid editing module coupled to the translational apparatus in archaea.},
journal = {Nature structural &amp; molecular biology},
volume = {12},
number = {6},
pages = {556-557},
doi = {10.1038/nsmb943},
pmid = {15908961},
issn = {1545-9993},
mesh = {*Amino Acids ; Archaea/*genetics ; Binding Sites ; Crystallography, X-Ray/methods ; *Protein Biosynthesis ; *RNA Editing ; Stereoisomerism ; Threonine-tRNA Ligase/genetics ; },
abstract = {We report the crystal structure of an archaea-specific editing domain of threonyl-tRNA synthetase that reveals a marked structural similarity to D-amino acid deacylases found in eubacteria and eukaryotes. The domain can bind D-amino acids despite a low sequence identity to other D-amino acid deacylases. These results together indicate the presence of these deacylases in all three kingdoms of life. This underlines an important role they may have played in enforcing homochirality during translation.},
}
@article {pmid15876569,
year = {2005},
author = {Bapteste, E and Brochier, C and Boucher, Y},
title = {Higher-level classification of the Archaea: evolution of methanogenesis and methanogens.},
journal = {Archaea (Vancouver, B.C.)},
volume = {1},
number = {5},
pages = {353-363},
pmid = {15876569},
issn = {1472-3646},
mesh = {Archaea/*classification/genetics/metabolism ; Archaeal Proteins/*genetics/metabolism ; DNA, Archaeal/genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal/genetics ; Genes, Archaeal/genetics ; Methane/*metabolism ; Phylogeny ; Ribosomal Proteins/*genetics/metabolism ; },
abstract = {We used a phylogenetic approach to analyze the evolution of methanogenesis and methanogens. We show that 23 vertically transmitted ribosomal proteins do not support the monophyly of methanogens, and propose instead that there are two distantly related groups of extant archaea that produce methane, which we have named Class I and Class II. Based on this finding, we subsequently investigated the uniqueness of the origin of methanogenesis by studying both the enzymes of methanogenesis and the proteins that synthesize its specific coenzymes. We conclude that hydrogenotrophic methanogenesis appeared only once during evolution. Genes involved in the seven central steps of the methanogenic reduction of carbon dioxide (CO(2)) are ubiquitous in methanogens and share a common history. This suggests that, although extant methanogens produce methane from various substrates (CO(2), formate, acetate, methylated C-1 compounds), these archaea have a core of conserved enzymes that have undergone little evolutionary change. Furthermore, this core of methanogenesis enzymes seems to originate (as a whole) from the last ancestor of all methanogens and does not appear to have been horizontally transmitted to other organisms or between members of Class I and Class II. The observation of a unique and ancestral form of methanogenesis suggests that it was preserved in two independent lineages, with some instances of specialization or added metabolic flexibility. It was likely lost in the Halobacteriales, Thermoplasmatales and Archaeoglobales. Given that fossil evidence for methanogenesis dates back 2.8 billion years, a unique origin of this process makes the methanogenic archaea a very ancient taxon.},
}
@article {pmid15876568,
year = {2005},
author = {Soderberg, T},
title = {Biosynthesis of ribose-5-phosphate and erythrose-4-phosphate in archaea: a phylogenetic analysis of archaeal genomes.},
journal = {Archaea (Vancouver, B.C.)},
volume = {1},
number = {5},
pages = {347-352},
pmid = {15876568},
issn = {1472-3646},
mesh = {Amino Acids, Aromatic/biosynthesis ; Archaea/enzymology/*genetics/*metabolism ; Genes, Archaeal/genetics ; *Genome, Archaeal ; Pentose Phosphate Pathway/genetics ; Phylogeny ; Ribosemonophosphates/*biosynthesis/genetics ; Sugar Phosphates/*biosynthesis ; },
abstract = {A phylogenetic analysis of the genes encoding enzymes in the pentose phosphate pathway (PPP), the ribulose monophosphate (RuMP) pathway, and the chorismate pathway of aromatic amino acid biosynthesis, employing data from 13 complete archaeal genomes, provides a potential explanation for the enigmatic phylogenetic patterns of the PPP genes in archaea. Genomic and biochemical evidence suggests that three archaeal species (Methanocaldococcus jannaschii, Thermoplasma acidophilum and Thermoplasma volcanium) produce ribose-5-phosphate via the nonoxidative PPP (NOPPP), whereas nine species apparently lack an NOPPP but may employ a reverse RuMP pathway for pentose synthesis. One species (Halobacterium sp. NRC-1) lacks both the NOPPP and the RuMP pathway but may possess a modified oxidative PPP (OPPP), the details of which are not yet known. The presence of transketolase in several archaeal species that are missing the other two NOPPP genes can be explained by the existence of differing requirements for erythrose-4-phosphate (E4P) among archaea: six species use transketolase to make E4P as a precursor to aromatic amino acids, six species apparently have an alternate biosynthetic pathway and may not require the ability to make E4P, and one species (Pyrococcus horikoshii) probably does not synthesize aromatic amino acids at all.},
}
@article {pmid15870315,
year = {2005},
author = {Herndl, GJ and Reinthaler, T and Teira, E and van Aken, H and Veth, C and Pernthaler, A and Pernthaler, J},
title = {Contribution of Archaea to total prokaryotic production in the deep Atlantic Ocean.},
journal = {Applied and environmental microbiology},
volume = {71},
number = {5},
pages = {2303-2309},
pmid = {15870315},
issn = {0099-2240},
mesh = {Archaea/*growth &amp; development/isolation &amp; purification/metabolism ; Atlantic Ocean ; Bacteria/*growth &amp; development/isolation &amp; purification ; Carbon/metabolism ; Plankton/metabolism ; Seawater/*microbiology ; },
abstract = {Fluorescence in situ hybridization (FISH) in combination with polynucleotide probes revealed that the two major groups of planktonic Archaea (Crenarchaeota and Euryarchaeota) exhibit a different distribution pattern in the water column of the Pacific subtropical gyre and in the Antarctic Circumpolar Current system. While Euryarchaeota were found to be more dominant in nearsurface waters, Crenarchaeota were relatively more abundant in the mesopelagic and bathypelagic waters. We determined the abundance of archaea in the mesopelagic and bathypelagic North Atlantic along a south-north transect of more than 4,000 km. Using an improved catalyzed reporter deposition-FISH (CARD-FISH) method and specific oligonucleotide probes, we found that archaea were consistently more abundant than bacteria below a 100-m depth. Combining microautoradiography with CARD-FISH revealed a high fraction of metabolically active cells in the deep ocean. Even at a 3,000-m depth, about 16% of the bacteria were taking up leucine. The percentage of Euryarchaeota and Crenarchaeaota taking up leucine did not follow a specific trend, with depths ranging from 6 to 35% and 3 to 18%, respectively. The fraction of Crenarchaeota taking up inorganic carbon increased with depth, while Euryarchaeota taking up inorganic carbon decreased from 200 m to 3,000 m in depth. The ability of archaea to take up inorganic carbon was used as a proxy to estimate archaeal cell production and to compare this archaeal production with total prokaryotic production measured via leucine incorporation. We estimate that archaeal production in the mesopelagic and bathypelagic North Atlantic contributes between 13 to 27% to the total prokaryotic production in the oxygen minimum layer and 41 to 84% in the Labrador Sea Water, declining to 10 to 20% in the North Atlantic Deep Water. Thus, planktonic archaea are actively growing in the dark ocean although at lower growth rates than bacteria and might play a significant role in the oceanic carbon cycle.},
}
@article {pmid15869466,
year = {2005},
author = {Ahmed, H and Ettema, TJ and Tjaden, B and Geerling, AC and van der Oost, J and Siebers, B},
title = {The semi-phosphorylative Entner-Doudoroff pathway in hyperthermophilic archaea: a re-evaluation.},
journal = {The Biochemical journal},
volume = {390},
number = {Pt 2},
pages = {529-540},
pmid = {15869466},
issn = {1470-8728},
mesh = {Aldehyde-Lyases/genetics/metabolism ; Glyceraldehyde-3-Phosphate Dehydrogenases/genetics/metabolism ; Hydro-Lyases/genetics/metabolism ; Multigene Family/genetics ; Phosphotransferases (Alcohol Group Acceptor)/genetics/metabolism ; Sulfolobus/*enzymology/genetics/metabolism ; Thermoproteus/*enzymology/genetics ; },
abstract = {Biochemical studies have suggested that, in hyperthermophilic archaea, the metabolic conversion of glucose via the ED (Entner-Doudoroff) pathway generally proceeds via a non-phosphorylative variant. A key enzyme of the non-phosphorylating ED pathway of Sulfolobus solfataricus, KDG (2-keto-3-deoxygluconate) aldolase, has been cloned and characterized previously. In the present study, a comparative genomics analysis is described that reveals conserved ED gene clusters in both Thermoproteus tenax and S. solfataricus. The corresponding ED proteins from both archaea have been expressed in Escherichia coli and their specificity has been identified, revealing: (i) a novel type of gluconate dehydratase (gad gene), (ii) a bifunctional 2-keto-3-deoxy-(6-phospho)-gluconate aldolase (kdgA gene), (iii) a 2-keto-3-deoxygluconate kinase (kdgK gene) and, in S. solfataricus, (iv) a GAPN (non-phosphorylating glyceraldehyde-3-phosphate dehydrogenase; gapN gene). Extensive in vivo and in vitro enzymatic analyses indicate the operation of both the semi-phosphorylative and the non-phosphorylative ED pathway in T. tenax and S. solfataricus. The existence of this branched ED pathway is yet another example of the versatility and flexibility of the central carbohydrate metabolic pathways in the archaeal domain.},
}
@article {pmid15866034,
year = {2005},
author = {Walsby, AE},
title = {Archaea with square cells.},
journal = {Trends in microbiology},
volume = {13},
number = {5},
pages = {193-195},
doi = {10.1016/j.tim.2005.03.002},
pmid = {15866034},
issn = {0966-842X},
mesh = {Archaea/*cytology/physiology/ultrastructure ; Cell Culture Techniques/*methods ; Microscopy, Phase-Contrast ; Pyruvic Acid/metabolism ; },
abstract = {Two groups of microbiologists have independently isolated 'Walsby's square bacterium' from salt crystallizer ponds; its growth depends on pyruvate. Genetic analysis shows that the squares, discovered 25 years ago on the Sinai Peninsula, are archaea rather than bacteria. These transparent tile-like cells might have been dismissed as surface artefacts of salt crystals but for their gas vesicles--structures peculiar to prokaryotic organisms. Paradoxically, the square archaea are the dominant microorganisms in some hypersaline environments and might be globally important.},
}
@article {pmid15841343,
year = {2005},
author = {Itoh, T and Yamaguchi, T and Zhou, P and Takashina, T},
title = {Natronolimnobius baerhuensis gen. nov., sp. nov. and Natronolimnobius innermongolicus sp. nov., novel haloalkaliphilic archaea isolated from soda lakes in Inner Mongolia, China.},
journal = {Extremophiles : life under extreme conditions},
volume = {9},
number = {2},
pages = {111-116},
pmid = {15841343},
issn = {1431-0651},
mesh = {Archaea/*classification/*physiology ; Base Composition ; China ; Chromatography, Thin Layer ; DNA/chemistry ; DNA, Archaeal ; DNA, Ribosomal ; Genes, rRNA ; Glycolipids/chemistry ; Hydrogen-Ion Concentration ; Lipids/chemistry ; Phenotype ; Phospholipids/chemistry ; Phylogeny ; RNA, Ribosomal, 16S/chemistry ; Sodium Chloride/pharmacology ; Species Specificity ; Temperature ; Water ; },
abstract = {Three novel isolates of haloalkaliphilic archaea, strains IHC-005T, IHC-010, and N-1311T, from soda lakes in Inner Mongolia, China, were characterized to elucidate their taxonomic positions. The three strains were aerobic, Gram-negative chemoorganotrophs growing optimally at 37-45 degrees C, pH 9.0-9.5, and 15-20% NaCl. Cells of strains IHC-005T/IHC-010 were motile rods, while those of strain N-1311T were non-motile pleomorphic flats or cocci. The three strains contained diphytanyl and phytanyl-sesterterpanyl diether derivatives of phosphatidylglycerol and phosphatidylglycerophosphate methyl ester. No glycolipids were detected. On phylogenetic analysis of 16S rRNA gene sequences, they formed an independent cluster in the Natro group of the family Halobacteriaceae. Comparison of their morphological, physiological, and biochemical properties, DNA G + C content and 16S rRNA gene sequences, and DNA-DNA hybridization study support the view that strains IHC-005T/IHC-010 and strain N-1311T represent separate species. Therefore, we propose Natronolimnobius baerhuensis gen. nov., sp. nov. for strains IHC-005T (=CGMCC 1.3597T =JCM 12253T)/IHC-010 (=CGMCC 1.3598 = JCM 12254) and Natronolimnobius innermongolicus sp. nov. for N-1311T (=CGMCC 1.2124T =JCM 12255T).},
}
@article {pmid15819852,
year = {2005},
author = {Nercessian, O and Fouquet, Y and Pierre, C and Prieur, D and Jeanthon, C},
title = {Diversity of Bacteria and Archaea associated with a carbonate-rich metalliferous sediment sample from the Rainbow vent field on the Mid-Atlantic Ridge.},
journal = {Environmental microbiology},
volume = {7},
number = {5},
pages = {698-714},
doi = {10.1111/j.1462-2920.2005.00744.x},
pmid = {15819852},
issn = {1462-2912},
mesh = {Archaea/genetics/*isolation &amp; purification ; Atlantic Ocean ; Bacteria/genetics/*isolation &amp; purification ; Base Sequence ; Carbon Isotopes/analysis ; Carbonates/*analysis ; Cloning, Molecular ; DNA, Archaeal/chemistry/genetics ; DNA, Bacterial/chemistry/genetics ; Genetic Variation ; Geologic Sediments/chemistry/*microbiology ; Hot Temperature ; Minerals/analysis ; Molecular Sequence Data ; Oxygen Isotopes/analysis ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/chemistry/genetics ; Sequence Alignment ; },
abstract = {Two sediment cores were collected in an inactive area of the deep-sea hydrothermal vent field Rainbow (36 degrees N on the Mid-Atlantic Ridge). Metals and carbonates were abundant throughout the cores; calcite (CaCO3) was found throughout the cores while dolomite [CaMg(CO3)2] and siderite (FeCO3) were only found in deeper layers. Using polymerase chain reaction (PCR)-amplified 16S rRNA gene sequence analysis, we examined the bacterial and archaeal diversity in a sediment layer that contained the three carbonates. The retrieved bacterial and archaeal sequences were new and less than 4% of the sequences exhibited 94% or more identity with that of cultured organisms. The analysis of the composition of the bacterial library revealed a high diversity of sequences. Half of the bacterial clones was affiliated to the gamma-Proteobacteria. Most of them had environmental sequences retrieved from deep-sea sediments as closest relatives, some of which being distantly related to free-living and symbiotic sulfur-oxidizers. Other sequences clustered in the alpha-, delta- and epsilon-Proteobacteria, the 'Bacteroidetes', the 'Planctomycetes', the 'Nitrospirae', the 'Actinobacteria', the 'Chlorobi ' and the 'Verrumicrobia'. Based on clonal abundance and sequence comparisons, phylotype groups putatively involved in the oxydation of sulfur compounds appeared to dominate in the studied sample. The majority of the archaeal sequences clustered in an euryarchaeotic lineage recently identified in the walls of black smokers suggesting a possible thermophilic way of life of these uncultured microorganisms. Oxygen isotopic composition of siderite and dolomite indicated that they were formed at 67 degrees C and 94 degrees C respectively. Together with chemical and microbiological data, this suggested that hydrothermal fluids may have circulated through this sediment.},
}
@article {pmid15816932,
year = {2005},
author = {Kemnitz, D and Kolb, S and Conrad, R},
title = {Phenotypic characterization of Rice Cluster III archaea without prior isolation by applying quantitative polymerase chain reaction to an enrichment culture.},
journal = {Environmental microbiology},
volume = {7},
number = {4},
pages = {553-565},
doi = {10.1111/j.1462-2920.2005.00723.x},
pmid = {15816932},
issn = {1462-2912},
mesh = {Acetates/metabolism ; Anaerobiosis ; Anti-Bacterial Agents/pharmacology ; Archaea/*classification/cytology/genetics/*physiology ; Bacteria/*classification/genetics ; DNA Fingerprinting ; DNA, Archaeal/analysis/chemistry/genetics/isolation &amp; purification ; DNA, Bacterial/analysis/chemistry/genetics/isolation &amp; purification ; DNA, Ribosomal/analysis/chemistry/genetics/isolation &amp; purification ; Gene Dosage ; Genes, rRNA ; Hydrogen-Ion Concentration ; In Situ Hybridization, Fluorescence ; Methane/metabolism ; Microscopy, Fluorescence ; Molecular Sequence Data ; Organic Chemicals/metabolism ; Peptones/metabolism ; Phylogeny ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; Temperature ; },
abstract = {A so far uncultured member of the Euryarchaeota was enriched from an anoxic riparian soil and phenotypically characterized using quantitative polymerase chain reaction (qPCR; "real-time PCR"). The microorganism is related to the Thermoplasmatales and belongs to Rice Cluster III (RC-III). Enrichment cultures utilized yeast extract (YE) by transiently accumulating acetate as major fermentation product, which was subsequently converted to methane. The abundance of RC-III archaea within the enrichment cultures was quantified by analysis of the terminal restriction fragment length polymorphism (T-RFLP) and by qPCR. We developed qPCR assays targeting the 16S rRNA genes (16S rDNA) specific for RC-III as well as for the Archaea in general. The enrichment cultures consisted of a mixed methanogenic community of Bacteria and Archaea, the latter consisting of up to 60% of members of RC-III. The other archaea belonged to Methanosarcinaceae, Methanomicrobiaceae and Methanobacteriaceae. The enriched RC-III archaea were represented by two sequences (LL25A, LL37A) that were highly similar to each other and to those detected in the soil inoculum (>98% similarity). However, the 16S rDNA copy numbers of RC-III archaea were about 1000-fold lower than those of Bacteria. Nevertheless, we were able to estimate growth parameters and physiological properties of one of the enriched RC-III archaea (LL25A) by measuring the increase of 16S rDNA copy numbers specific for this group under different growth conditions. The enriched RC-III archaeon grew optimally at temperatures between 20 and 30 degrees C and neutral pH using YE, meat extract, peptone or tryptone under anoxic conditions. Doubling time was approximately 3 days. No proliferation was detected on carbohydrates, amino acids, fatty acids, glycerol, alcohols, aromatic compounds, purine and pyrimidine bases or pyruvate. Various exogenous electron acceptors (e.g. ferric iron, S(0)) did not support growth on YE. Proliferation of the enriched RC-III archaeon was hardly affected by the antibiotics ampicillin, kanamycin and streptomycin. These findings suggest that the enriched archaeon is a mesophilic anaerobe, which can grow heterotrophically on peptides. Further enrichment on peptone and kanamycin eventually allowed the microscopic detection of coccoid cells stained by fluorescence in situ hybridization (FISH).},
}
@article {pmid15812059,
year = {2005},
author = {Galand, PE and Fritze, H and Conrad, R and Yrjälä, K},
title = {Pathways for methanogenesis and diversity of methanogenic archaea in three boreal peatland ecosystems.},
journal = {Applied and environmental microbiology},
volume = {71},
number = {4},
pages = {2195-2198},
pmid = {15812059},
issn = {0099-2240},
mesh = {DNA, Archaeal/analysis ; *Ecosystem ; *Genetic Variation ; Methane/*metabolism ; Methanosarcinales/*classification/genetics/isolation &amp; purification/metabolism ; Molecular Sequence Data ; Oxidoreductases/genetics/metabolism ; Phylogeny ; Sequence Analysis, DNA ; *Soil Microbiology ; },
abstract = {The main objectives of this study were to uncover the pathways used for methanogenesis in three different boreal peatland ecosystems and to describe the methanogenic populations involved. The mesotrophic fen had the lowest proportion of CH4 produced from H2-CO2. The oligotrophic fen was the most hydrogenotrophic, followed by the ombrotrophic bog. Each site was characterized by a specific group of methanogenic sequences belonging to Methanosaeta spp. (mesotrophic fen), rice cluster-I (oligotrophic fen), and fen cluster (ombrotrophic bog).},
}
@article {pmid15810434,
year = {2004},
author = {Hall, TA and Brown, JW},
title = {Interactions between RNase P protein subunits in archaea.},
journal = {Archaea (Vancouver, B.C.)},
volume = {1},
number = {4},
pages = {247-254},
pmid = {15810434},
issn = {1472-3646},
support = {GM52894/GM/NIGMS NIH HHS/United States ; },
mesh = {Methanobacteriaceae/*enzymology ; Protein Binding ; *Protein Interaction Mapping ; Protein Subunits/genetics/*metabolism ; Ribonuclease P/genetics/*metabolism ; Two-Hybrid System Techniques ; },
abstract = {A yeast two-hybrid system was used to identify protein-protein interactions between the ribonuclease P (RNase P) protein subunits Mth11p, Mth687p, Mth688p and Mth1618p from the archaeon Methanothermobacter thermoautotrophicus. Clear interactions between Mth688p and Mth687p, and between Mth1618p and Mth11p, were confirmed by HIS3 and LacZ reporter expression. Weaker interactions of Mth687p and Mth688p with Mth 11p, and Mth11p with itself, are also suggested. These interactions resemble, and confirm, those previously seen among the homologs of these proteins in the more complex yeast RNase P holoenzyme.},
}
@article {pmid15808741,
year = {2005},
author = {Londei, P},
title = {Evolution of translational initiation: new insights from the archaea.},
journal = {FEMS microbiology reviews},
volume = {29},
number = {2},
pages = {185-200},
doi = {10.1016/j.femsre.2004.10.002},
pmid = {15808741},
issn = {0168-6445},
mesh = {Archaea/*genetics ; *Codon, Initiator ; *Evolution, Molecular ; Genes, Archaeal ; *Protein Biosynthesis ; RNA, Messenger/genetics/metabolism ; },
abstract = {Recent in silico and experimental data have shed new light on the mechanism and components of translational initiation in archaea. The available data about the structure of archaeal mRNAs, mRNA/ribosome interaction and archaeal translation initiation factors are reviewed and analyzed in the conceptual framework of the evolution of translational initiation. A model of the initiation step of translation in the Last Universal Common Ancestor of extant cells is presented and discussed.},
}
@article {pmid15805780,
year = {2005},
author = {Veloso, F and Riadi, G and Aliaga, D and Lieph, R and Holmes, DS},
title = {Large-scale, multi-genome analysis of alternate open reading frames in bacteria and archaea.},
journal = {Omics : a journal of integrative biology},
volume = {9},
number = {1},
pages = {91-105},
doi = {10.1089/omi.2005.9.91},
pmid = {15805780},
issn = {1536-2310},
mesh = {Algorithms ; Base Composition ; Codon ; Codon, Terminator ; Genes, Archaeal/genetics ; Genes, Bacterial/genetics ; Genetic Techniques ; *Genome, Archaeal ; *Genome, Bacterial ; Genomics/*methods ; Leucine/metabolism ; *Models, Genetic ; Models, Statistical ; *Open Reading Frames ; Protein Biosynthesis ; Sequence Analysis, DNA ; Transcription, Genetic ; },
abstract = {Analysis of over 300,000 annotated genes in 105 bacterial and archaeal genomes reveals an unexpectedly high frequency of large (>300 nucleotides) alternate open reading frames (ORFs). Especially notable is the very high frequency of alternate ORFs in frames +3 and -1 (where the annotated gene is defined as frame +1). The occurrence of alternate ORFs is correlated with genomic G+C content and is strongly influenced by synonymous codon usage bias. The frequency of alternate ORFs in frame -1 is also influenced by the occurrence of codons encoding leucine and serine in frame +1. Although some alternate ORFs have been shown to encode proteins, many others are probably not expressed because they lack appropriate signals for transcription and translation. These latter can be mis-annotated by automatic gene finding programs leading to errors in public databases. Especially prone to mis-annotation is frame -1, because it exhibits a potential codon usage and theoretical capacity to encode proteins with an amino acid composition most similar to real genes. Some alternate ORFs are conserved across bacterial or archaeal species, and can give rise to misannotated "conserved hypothetical" genes, while others are unique to a genome and are misidentified as "hypothetical orphan" genes, contributing significantly to the orphan gene paradox.},
}
@article {pmid15804412,
year = {2005},
author = {Pollack, JD and Li, Q and Pearl, DK},
title = {Taxonomic utility of a phylogenetic analysis of phosphoglycerate kinase proteins of Archaea, Bacteria, and Eukaryota: insights by Bayesian analyses.},
journal = {Molecular phylogenetics and evolution},
volume = {35},
number = {2},
pages = {420-430},
doi = {10.1016/j.ympev.2005.02.002},
pmid = {15804412},
issn = {1055-7903},
mesh = {Archaea/*classification/*genetics ; Archaeal Proteins/*genetics ; Bacteria/*classification/*genetics ; Bacterial Proteins/*genetics ; Bayes Theorem ; Phosphoglycerate Kinase/*genetics ; *Phylogeny ; },
abstract = {We studied 131 protein sequences of the essentially ubiquitous glycolytic enzyme 3-phosphoglycerate kinase (3-PGK) by Bayesian analyses in three Domains: 15 Archaea, 83 Bacteria, and 33 Eukaryota. The posterior distribution of phylogenetic trees developed were based on a uniform prior, the WAG model of protein evolution, Metropolis-Hastings sampling in a Markov chain Monte Carlo analysis, and a package of diagnostics to critically evaluate the validity of the analyses. The 15 Archaea separated with high posterior probability. The archaean Phyla Euryarchaeota and the apparently Euryarchaeota derived Crenarchaeota were monophyletic. The 33 Eukaryota separated into two main groups: the non-chlorophyllous forms with coherent sub-groupings of Euglenozoa, Alveolata, Fungi, and Metazoa and all the chlorophyllous species studied: the Plantae (Viridaeplantae), chlorophyllous Stramenopiles, and the chlorophyllous Bacteria. This association supports other opinions concerning the related lineage of cyanobacteria and the Plantae. The 3-PGK sequences from 83 Bacteria in almost every instance associated by their recognized taxal group: alpha-, beta-, gamma-, epsilon-proteobacteria, Chlamydia, Actinobacteridae, and Firmicutes. Firmicutes sequences were subdivided into three apparently monophyletic groups: the anaerobic Clostridia, the spore-forming Bacillales and a group containing the Mollicutes, Lactobacillales and non-spore-forming Bacillales. The 3-PGK-gene tree assemblage was notable both for its pervasive clustering in three Domains according to recognized taxonomic groupings of Class, Order, Family, and Genus. The 3-PGK enzyme or 3-PGK-like activity may have played a central role in the metabolism of the Universal Ancestor.},
}
@article {pmid15803666,
year = {2003},
author = {Ronimus, RS and Morgan, HW},
title = {Distribution and phylogenies of enzymes of the Embden-Meyerhof-Parnas pathway from archaea and hyperthermophilic bacteria support a gluconeogenic origin of metabolism.},
journal = {Archaea (Vancouver, B.C.)},
volume = {1},
number = {3},
pages = {199-221},
pmid = {15803666},
issn = {1472-3646},
mesh = {Archaea/classification/*enzymology/*genetics ; Bacteria/classification/*enzymology/*genetics ; Biological Evolution ; Gluconeogenesis/*genetics ; Glycolysis/genetics ; Hot Temperature ; Models, Biological ; Phylogeny ; },
abstract = {Enzymes of the gluconeogenic/glycolytic pathway (the Embden-Meyerhof-Parnas (EMP) pathway), the reductive tricarboxylic acid cycle, the reductive pentose phosphate cycle and the Entner-Doudoroff pathway are widely distributed and are often considered to be central to the origins of metabolism. In particular, several enzymes of the lower portion of the EMP pathway (the so-called trunk pathway), including triosephosphate isomerase (TPI; EC 5.3.1.1), glyceraldehyde-3-phosphate dehydrogenase (GAPDH; EC 1.2.1.12/13), phosphoglycerate kinase (PGK; EC 2.7.2.3) and enolase (EC 4.2.1.11), are extremely well conserved and universally distributed among the three domains of life. In this paper, the distribution of enzymes of gluconeogenesis/glycolysis in hyperthermophiles--microorganisms that many believe represent the least evolved organisms on the planet--is reviewed. In addition, the phylogenies of the trunk pathway enzymes (TPIs, GAPDHs, PGKs and enolases) are examined. The enzymes catalyzing each of the six-carbon transformations in the upper portion of the EMP pathway, with the possible exception of aldolase, are all derived from multiple gene sequence families. In contrast, single sequence families can account for the archaeal and hyperthermophilic bacterial enzyme activities of the lower portion of the EMP pathway. The universal distribution of the trunk pathway enzymes, in combination with their phylogenies, supports the notion that the EMP pathway evolved in the direction of gluconeogenesis, i.e., from the bottom up.},
}
@article {pmid15803657,
year = {2002},
author = {Kloda, A and Martinac, B},
title = {Common evolutionary origins of mechanosensitive ion channels in Archaea, Bacteria and cell-walled Eukarya.},
journal = {Archaea (Vancouver, B.C.)},
volume = {1},
number = {1},
pages = {35-44},
pmid = {15803657},
issn = {1472-3646},
mesh = {Animals ; Archaea/classification/*genetics ; Bacteria/classification/*genetics ; Cell Wall/metabolism ; Eukaryotic Cells/physiology ; *Evolution, Molecular ; Ion Channels/*genetics/physiology ; Phylogeny ; },
abstract = {The ubiquity of mechanosensitive (MS) channels triggered a search for their functional homologs in Archaea. Archaeal MS channels were found to share a common ancestral origin with bacterial MS channels of large and small conductance, and sequence homology with several proteins that most likely function as MS ion channels in prokaryotic and eukaryotic cell-walled organisms. Although bacterial and archaeal MS channels differ in conductive and mechanosensitive properties, they share similar gating mechanisms triggered by mechanical force transmitted via the lipid bilayer. In this review, we suggest that MS channels of Archaea can bridge the evolutionary gap between bacterial and eukaryotic MS channels, and that MS channels of Bacteria, Archaea and cell-walled Eukarya may serve similar physiological functions and may have evolved to protect the fragile cellular membranes in these organisms from excessive dilation and rupture upon osmotic challenge.},
}
@article {pmid15803645,
year = {2002},
author = {Schiraldi, C and Giuliano, M and De Rosa, M},
title = {Perspectives on biotechnological applications of archaea.},
journal = {Archaea (Vancouver, B.C.)},
volume = {1},
number = {2},
pages = {75-86},
pmid = {15803645},
issn = {1472-3646},
mesh = {Archaea/genetics/*physiology ; Biotechnology/*methods ; Enzymes/metabolism ; Hot Temperature ; Species Specificity ; },
abstract = {Many archaea colonize extreme environments. They include hyperthermophiles, sulfur-metabolizing thermophiles, extreme halophiles and methanogens. Because extremophilic microorganisms have unusual properties, they are a potentially valuable resource in the development of novel biotechnological processes. Despite extensive research, however, there are few existing industrial applications of either archaeal biomass or archaeal enzymes. This review summarizes current knowledge about the biotechnological uses of archaea and archaeal enzymes with special attention to potential applications that are the subject of current experimental evaluation. Topics covered include cultivation methods, recent achievements in genomics, which are of key importance for the development of new biotechnological tools, and the application of wild-type biomasses, engineered microorganisms, enzymes and specific metabolites in particular bioprocesses of industrial interest.},
}
@article {pmid15790858,
year = {2005},
author = {Sauerwald, A and Zhu, W and Major, TA and Roy, H and Palioura, S and Jahn, D and Whitman, WB and Yates, JR and Ibba, M and Söll, D},
title = {RNA-dependent cysteine biosynthesis in archaea.},
journal = {Science (New York, N.Y.)},
volume = {307},
number = {5717},
pages = {1969-1972},
doi = {10.1126/science.1108329},
pmid = {15790858},
issn = {1095-9203},
mesh = {Adenosine Triphosphate/metabolism ; Amino Acyl-tRNA Synthetases/genetics/isolation &amp; purification/*metabolism ; Archaea/enzymology/genetics/metabolism ; Cysteine/*biosynthesis ; Methanococcales/enzymology/genetics/*metabolism ; Methanococcus/enzymology/genetics/*metabolism ; Oxidation-Reduction ; Phosphoserine/metabolism ; RNA, Archaeal/*metabolism ; RNA, Transfer, Amino Acyl/metabolism ; RNA, Transfer, Cys/metabolism ; },
abstract = {Several methanogenic archaea lack cysteinyl-transfer RNA (tRNA) synthetase (CysRS), the essential enzyme that provides Cys-tRNA(Cys) for translation in most organisms. Partial purification of the corresponding activity from Methanocaldococcus jannaschii indicated that tRNA(Cys) becomes acylated with O-phosphoserine (Sep) but not with cysteine. Further analyses identified a class II-type O-phosphoseryl-tRNA synthetase (SepRS) and Sep-tRNA:Cys-tRNA synthase (SepCysS). SepRS specifically forms Sep-tRNA(Cys), which is then converted to Cys-tRNA(Cys) by SepCysS. Comparative genomic analyses suggest that this pathway, encoded in all organisms lacking CysRS, can also act as the sole route for cysteine biosynthesis. This was proven for Methanococcus maripaludis, where deletion of the SepRS-encoding gene resulted in cysteine auxotrophy. As the conversions of Sep-tRNA to Cys-tRNA or to selenocysteinyl-tRNA are chemically analogous, the catalytic activity of SepCysS provides a means by which both cysteine and selenocysteine may have originally been added to the genetic code.},
}
@article {pmid15761691,
year = {2005},
author = {Wang, P and Xiao, X and Wang, F},
title = {Phylogenetic analysis of Archaea in the deep-sea sediments of west Pacific Warm Pool.},
journal = {Extremophiles : life under extreme conditions},
volume = {9},
number = {3},
pages = {209-217},
pmid = {15761691},
issn = {1431-0651},
mesh = {Archaea/*classification/genetics/isolation &amp; purification ; Bacteria/classification/genetics/isolation &amp; purification ; Base Sequence ; DNA Primers ; Geologic Sediments/*microbiology ; Pacific Ocean ; Polymerase Chain Reaction ; Seawater/*microbiology ; },
abstract = {Archaea are known to play important roles in carbon cycling in marine sediments. The main compositions of archaeal community in five deep-sea sediment samples collected from west Pacific Warm Pool area (WP-0, WP-1, WP-2, WP-3, WP-4), and in five sediment layers (1 cm-, 3 cm-, 6 cm-, 10 cm-, 12 cm- layer) of the 12 cm sediment core of WP-0 were checked and compared by denaturing gradient gel electrophoresis and 16 S rRNA gene sequencing. It was revealed that all the deep-sea sediment samples checked contained members of non-thermophilic marine group I crenarchaeota as the predominant archaeal group. To further detect groups of archaea possibly relating with C1 metabolism, PCR amplification was carried out using primers targeting methane-oxidizing archaea. Although no methane-oxidizing archaea was detected, a group of novel archaea (named as WPA) was instead identified from all these five WP samples by clone analysis. They could be placed in the euryarchaeota kingdom, separated into two distinct groups, the main group was peripherally related with methanogens, the other group related with Thermoplasma. The vertical distributions of WPA, archaea and bacteria along the WP-0 sediment column were determined by quantitative-PCR. It was found that bacteria dominated at all depths, the numbers of bacteria were 10-10(4) times more than those of archaea. The proportion of archaea versus bacteria had a depth related increasing tendency, it was lowest at the first layer (0.01%), reached highest at the 12 cm- layer (10%). WPA only constituted a small proportion of the archaeal community (0.05% to 5%) of west Pacific Warm Pool sediment.},
}
@article {pmid15693955,
year = {2005},
author = {Chistoserdova, L and Vorholt, JA and Lidstrom, ME},
title = {A genomic view of methane oxidation by aerobic bacteria and anaerobic archaea.},
journal = {Genome biology},
volume = {6},
number = {2},
pages = {208},
pmid = {15693955},
issn = {1474-760X},
mesh = {Anaerobiosis ; Archaea/enzymology/*genetics ; Bacteria, Aerobic/enzymology/genetics ; Environment ; Genomics ; Methane/*metabolism ; Methylococcus capsulatus/enzymology/*genetics ; Oxidation-Reduction ; Proteomics ; },
abstract = {Recent sequencing of the genome and proteomic analysis of a model aerobic methanotrophic bacterium, Methylococcus capsulatus (Bath) has revealed a highly versatile metabolic potential. In parallel, environmental genomics has provided glimpses into anaerobic methane oxidation by certain archaea, further supporting the hypothesis of reverse methanogenesis.},
}
@article {pmid15693614,
year = {2004},
author = {Bauer, M and Lombardot, T and Teeling, H and Ward, NL and Amann, RI and Glöckner, FO},
title = {Archaea-like genes for C1-transfer enzymes in Planctomycetes: phylogenetic implications of their unexpected presence in this phylum.},
journal = {Journal of molecular evolution},
volume = {59},
number = {5},
pages = {571-586},
pmid = {15693614},
issn = {0022-2844},
mesh = {Amidohydrolases/chemistry/genetics ; Amino Acid Sequence ; Archaea/*enzymology/*genetics ; Bacteria/*enzymology/*genetics ; Catalysis ; Conserved Sequence ; Genes, Archaeal/*genetics ; Genes, Bacterial/*genetics ; Genome, Bacterial ; Methylobacterium extorquens/chemistry/genetics ; Molecular Sequence Data ; *Phylogeny ; Sequence Alignment ; },
abstract = {The unexpected presence of archaea-like genes for tetrahydromethanopterin (H4MPT)-dependent enzymes in the completely sequence geiome of the aerobic marine planctomycete Pirellula sp. strain 1 ("Rhodopirellula baltica") and in the currently sequenced genome of the aerobic freshwater planctomycete Gemmata obscuriglobus strain UQM2246 revives the discussion on the origin of these genes in the bacterial domain. We compared the genomic arrangement of these genes in Planctomyetes and methylotrophic proteobacteria and perormed a phylogenetic analysis of the encoded protein sequences to address the question whether the genes have been present in the common ancestor of Bacteria and Archaea or were transferred laterally from the archaeal to the bacterial domain and herein. Although this question could not be solved using the data presented here, some constraints on the evolution of the genes involved in archaeal and)acterial H4MPT-dependent C1-transfer may be proposed: (i) lateral gene transfer (LGT) from Archea to a common ancestor of Proteobacteria and Planctomycetes seems more likely than the presence of the genes in the common ancestor of Bacteria and Archaea; (ii) a single event of interdomain LGT can e favored over two independent events; and (iii) the irchacal donor of the genes might have been a repesentative of the Methanosarcinales. In the bacterial domain, the acquired genes evolved according to distinct environmental and metabolic constraints, reflected by specific rearrangements of gene order, gene recruitment, and gene duplication, with subsequent functional specialization. During the course of evolution, genes were lost from some planctomycete genomes or replaced by orthologous genes from proteobacterial lineages.},
}
@article {pmid15676200,
year = {2005},
author = {Jupraputtasri, W and Boonapatcharoen, N and Cheevadhanarak, S and Chaiprasert, P and Tanticharoen, M and Techkarnjanaruk, S},
title = {Use of an alternative Archaea-specific probe for methanogen detection.},
journal = {Journal of microbiological methods},
volume = {61},
number = {1},
pages = {95-104},
doi = {10.1016/j.mimet.2004.11.017},
pmid = {15676200},
issn = {0167-7012},
mesh = {Base Sequence ; DNA Probes/chemistry/genetics ; DNA, Archaeal/chemistry/genetics ; Euryarchaeota/classification/*genetics/*isolation &amp; purification ; In Situ Hybridization, Fluorescence/*methods ; Microscopy, Fluorescence ; Molecular Sequence Data ; RNA, Ribosomal, 16S/chemistry/genetics ; Sequence Alignment ; Sewage/microbiology ; },
abstract = {An alternative 16S rRNA-targeted oligonucleotide probe specific for Archaea was developed and used for detection of methanogens in anaerobic reactors. The designed probe was checked for its specificity by computer-aided comparative sequence analysis. For in situ application, optimal stringency conditions were adjusted by performing whole cell hybridization using target and nontarget organisms. Anaerobic sludge samples were examined by in situ hybridization for methanogenic populations. The relative abundance of methanogens was monitored with epifluorescence microscopy. Individual cells could be visualized with strong fluorescence signals after hybridization with the newly developed probe.},
}
@article {pmid15659670,
year = {2005},
author = {Robinson, JL and Pyzyna, B and Atrasz, RG and Henderson, CA and Morrill, KL and Burd, AM and Desoucy, E and Fogleman, RE and Naylor, JB and Steele, SM and Elliott, DR and Leyva, KJ and Shand, RF},
title = {Growth kinetics of extremely halophilic archaea (family halobacteriaceae) as revealed by arrhenius plots.},
journal = {Journal of bacteriology},
volume = {187},
number = {3},
pages = {923-929},
pmid = {15659670},
issn = {0021-9193},
support = {GM05600-02/GM/NIGMS NIH HHS/United States ; },
mesh = {Halobacteriaceae/classification/*growth &amp; development ; Hot Temperature ; Kinetics ; Osmolar Concentration ; Sodium Chloride ; Thermodynamics ; },
abstract = {Members of the family Halobacteriaceae in the domain Archaea are obligate extreme halophiles. They occupy a variety of hypersaline environments, and their cellular biochemistry functions in a nearly saturated salty milieu. Despite extensive study, a detailed analysis of their growth kinetics is missing. To remedy this, Arrhenius plots for 14 type species of the family were generated. These organisms had maximum growth temperatures ranging from 49 to 58 degrees C. Nine of the organisms exhibited a single temperature optimum, while five grew optimally at more than one temperature. Generation times at these optimal temperatures ranged from 1.5 h (Haloterrigena turkmenica) to 3.0 h (Haloarcula vallismortis and Halorubrum saccharovorum). All shared an inflection point at 31 +/- 4 degrees C, and the temperature characteristics for 12 of the 14 type species were nearly parallel. The other two species (Natronomonas pharaonis and Natronorubrum bangense) had significantly different temperature characteristics, suggesting that the physiology of these strains is different. In addition, these data show that the type species for the family Halobacteriaceae share similar growth kinetics and are capable of much faster growth at higher temperatures than those previously reported.},
}
@article {pmid15659155,
year = {2005},
author = {Cobucci-Ponzano, B and Rossi, M and Moracci, M},
title = {Recoding in archaea.},
journal = {Molecular microbiology},
volume = {55},
number = {2},
pages = {339-348},
doi = {10.1111/j.1365-2958.2004.04400.x},
pmid = {15659155},
issn = {0950-382X},
mesh = {Archaea/chemistry/*genetics/metabolism ; *Codon, Terminator ; Frameshifting, Ribosomal ; Lysine/*analogs &amp; derivatives ; *Protein Biosynthesis ; Selenocysteine ; },
abstract = {Standard decoding of the genetic information into polypeptides is performed by one of the most sophisticated cell machineries, the translating ribosome, which, by following the genetic code, ensures the correspondence between the mature mRNA and the protein sequence. However, the expression of a minority of genes requires programmed deviations from the standard decoding rules, globally named recoding. This includes ribosome programmed -/+1 frameshifting, ribosome hopping, and stop codon readthrough. Recoding in Archaea was unequivocally demonstrated only for the translation of the UGA stop codon into the amino acid selenocysteine. However, a new recoding event leading to the 22nd amino acid pyrrolysine and the preliminary reports on a gene regulated by programmed -1 frameshifting have been recently described in Archaea. Therefore, it appears that the study of this phenomenon in Archaea is still at its dawn and that most of the genes whose expression is regulated by recoding are still uncharacterized.},
}
@article {pmid15652813,
year = {2005},
author = {Joo, WA and Kim, CW},
title = {Proteomics of Halophilic archaea.},
journal = {Journal of chromatography. B, Analytical technologies in the biomedical and life sciences},
volume = {815},
number = {1-2},
pages = {237-250},
doi = {10.1016/j.jchromb.2004.10.041},
pmid = {15652813},
issn = {1570-0232},
mesh = {Amino Acid Sequence ; Archaeal Proteins/*analysis/genetics ; Computational Biology ; Electrophoresis, Gel, Two-Dimensional ; Electrophoresis, Polyacrylamide Gel ; Gene Expression Regulation, Archaeal ; *Genome, Archaeal ; Halobacterium salinarum/*chemistry/genetics/metabolism ; Isoelectric Focusing ; Molecular Sequence Data ; Proteomics/*methods ; Ribosomal Protein L3 ; Ribosomal Proteins/chemistry ; },
abstract = {Halophilic archaea is a member of the Halobacteriacea family, the only family in the Halobacteriales order. Most Halophilic archaea require 1.5M NaCl both to grow and retain the structural integrity of the cells. The proteins of these organisms have thus been adapted to be active and stable in the hypersaline condition. Consequently, the unique properties of these biocatalysts have resulted in several novel applications in industrial processes. Halophilic archaea are also to be useful for bioremediation of hypersaline environment. Proteome data have expended enormously with the significant advance recently achieved in two-dimensional gel electrophoresis (2-DE) and mass spectrometry (MS). The whole genome sequencing of Halobacterium species NRC-1 was completed and this would also provide tremendous help to analyze the protein mass data from the similar strain Halobacterium salinarum. Proteomics coupled with genomic databases now has become a basic tool to understand or identify the function of genes and proteins. In addition, the bioinformatics approach will facilitate to predict the function of novel proteins of Halophilic archaea. This review will discuss current proteome study of Halophilic archaea and introduce the efficient procedures for screening, predicting, and confirming the function of novel halophilic enzymes.},
}
@article {pmid15643935,
year = {2005},
author = {Torarinsson, E and Klenk, HP and Garrett, RA},
title = {Divergent transcriptional and translational signals in Archaea.},
journal = {Environmental microbiology},
volume = {7},
number = {1},
pages = {47-54},
doi = {10.1111/j.1462-2920.2004.00674.x},
pmid = {15643935},
issn = {1462-2912},
mesh = {Archaea/classification/*genetics ; Archaeal Proteins/chemistry/genetics ; Base Sequence ; *Codon, Initiator ; DNA, Archaeal/analysis ; DNA, Ribosomal/analysis ; *Gene Expression Regulation, Archaeal ; Genome, Archaeal ; Genomics ; Molecular Sequence Data ; Phylogeny ; Promoter Regions, Genetic ; *Protein Biosynthesis ; RNA, Ribosomal, 16S/genetics ; *Transcription, Genetic ; },
abstract = {Many Archaea, in contrast to bacteria, produce a high proportion of leaderless transcripts, show a wide variation in their consensus Shine-Dalgarno (S-D) sequences and frequently use GUG and UUG start codons. In order to understand the basis for these differences, 18 complete archaeal genomes were examined for sequence signals that are positionally conserved upstream from genes. These functional motifs include box A promoter sequences for leaderless transcripts and S-D sequences for transcripts with leaders. Most of the box A sequences were preceded by a BRE-like motif and followed by a previously undetected A/T peak centred on position -10. Moreover, the sequence of the predominant S-D motifs in an archaeon is shown to depend on the precise number of nucleotides between the conserved anti-S-D CCUCC sequence and the 3'-terminal nucleotide of 16S RNA. Correlations with phylogenetic trees, constructed for the 18 Archaea, reveal that usage of high levels of both S-D motifs, and GUG and UUG start codons occurs exclusively in the shorter branched Archaea. High levels of leaderless transcripts are found in the longer branched Archaea.},
}
@article {pmid15640223,
year = {2005},
author = {Knittel, K and Lösekann, T and Boetius, A and Kort, R and Amann, R},
title = {Diversity and distribution of methanotrophic archaea at cold seeps.},
journal = {Applied and environmental microbiology},
volume = {71},
number = {1},
pages = {467-479},
pmid = {15640223},
issn = {0099-2240},
mesh = {Archaea/*classification/genetics/*isolation &amp; purification/metabolism ; *Cold Temperature ; DNA, Archaeal/analysis ; DNA, Ribosomal/analysis ; Geologic Sediments/*microbiology ; In Situ Hybridization, Fluorescence ; Methane/*metabolism ; Molecular Sequence Data ; Oregon ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; Sequence Analysis, DNA ; Thiotrichaceae/growth &amp; development ; Ukraine ; },
abstract = {In this study we investigated by using 16S rRNA-based methods the distribution and biomass of archaea in samples from (i) sediments above outcropping methane hydrate at Hydrate Ridge (Cascadia margin off Oregon) and (ii) massive microbial mats enclosing carbonate reefs (Crimea area, Black Sea). The archaeal diversity was low in both locations; there were only four (Hydrate Ridge) and five (Black Sea) different phylogenetic clusters of sequences, most of which belonged to the methanotrophic archaea (ANME). ANME group 2 (ANME-2) sequences were the most abundant and diverse sequences at Hydrate Ridge, whereas ANME-1 sequences dominated the Black Sea mats. Other seep-specific sequences belonged to the newly defined group ANME-3 (related to Methanococcoides spp.) and to the Crenarchaeota of marine benthic group B. Quantitative analysis of the samples by fluorescence in situ hybridization (FISH) showed that ANME-1 and ANME-2 co-occurred at the cold seep sites investigated. At Hydrate Ridge the surface sediments were dominated by aggregates consisting of ANME-2 and members of the Desulfosarcina-Desulfococcus branch (DSS) (ANME-2/DSS aggregates), which accounted for >90% of the total cell biomass. The numbers of ANME-1 cells increased strongly with depth; these cells accounted 1% of all single cells at the surface and more than 30% of all single cells (5% of the total cells) in 7- to 10-cm sediment horizons that were directly above layers of gas hydrate. In the Black Sea microbial mats ANME-1 accounted for about 50% of all cells. ANME-2/DSS aggregates occurred in microenvironments within the mat but accounted for only 1% of the total cells. FISH probes for the ANME-2a and ANME-2c subclusters were designed based on a comparative 16S rRNA analysis. In Hydrate Ridge sediments ANME-2a/DSS and ANME-2c/DSS aggregates differed significantly in morphology and abundance. The relative abundance values for these subgroups were remarkably different at Beggiatoa sites (80% ANME-2a, 20% ANME-2c) and Calyptogena sites (20% ANME-2a, 80% ANME-2c), indicating that there was preferential selection of the groups in the two habitats. These variations in the distribution, diversity, and morphology of methanotrophic consortia are discussed with respect to the presence of microbial ecotypes, niche formation, and biogeography.},
}
@article {pmid15638455,
year = {2004},
author = {Roberts, TH and Hejgaard, J and Saunders, NF and Cavicchioli, R and Curmi, PM},
title = {Serpins in unicellular Eukarya, Archaea, and Bacteria: sequence analysis and evolution.},
journal = {Journal of molecular evolution},
volume = {59},
number = {4},
pages = {437-447},
pmid = {15638455},
issn = {0022-2844},
mesh = {Amino Acid Sequence ; Animals ; Archaea/enzymology/*genetics ; Bacteria/enzymology/*genetics ; Conserved Sequence ; Entamoeba histolytica/enzymology/genetics ; Eukaryotic Cells/chemistry ; *Evolution, Molecular ; Humans ; Molecular Sequence Data ; Phylogeny ; Protein Structure, Tertiary ; Sequence Alignment ; Sequence Analysis, Protein ; Serpins/*chemistry/*genetics ; alpha 1-Antitrypsin/chemistry/genetics ; },
abstract = {Most serpins irreversibly inactivate specific serine proteinases of the chymotrypsin family. Inhibitory serpins are unusual proteins in that their native structure is metastable, and rapid conversion to a relaxed state is required to trap target enzymes in a covalent complex. The evolutionary origin of the serpin fold is unresolved, and while serpins in animals are known to be involved in the regulation of a remarkable diversity of metabolic processes, the physiological functions of homologues from other phyla are unknown. Addressing these questions, here we analyze serpin genes identified in unicellular eukaryotes: the green alga Chlamydomonas reinhardtii, the dinoflagellate Alexandrium tamarense, and the human pathogens Entamoeba spp., Eimera tenella, Toxoplasma gondii, and Giardia lamblia. We compare these sequences to others, particularly those in the complete genome sequences of Archaea, where serpins were found in only 4 of 13 genera, and Bacteria, in only 9 of 56 genera. The serpins from unicellular organisms appear to be phylogenetically distinct from all of the clades of higher eukaryotic serpins. Most of the sequences from unicellular organisms have the characteristics of inhibitory serpins, and where multiple serpin genes are found in one genome, variability is displayed in the region of the reactive-center loop important for specificity. All the unicellular eukaryotic serpins have large hydrophobic or positively charged residues at the putative PI position. In contrast, none of the prokaryotic serpins has a residue of these types at the predicted P1 position, but many have smaller, neutral residues. Serpin evolution is discussed.},
}
@article {pmid15632422,
year = {2005},
author = {Gregor, D and Pfeifer, F},
title = {In vivo analyses of constitutive and regulated promoters in halophilic archaea.},
journal = {Microbiology (Reading, England)},
volume = {151},
number = {Pt 1},
pages = {25-33},
doi = {10.1099/mic.0.27541-0},
pmid = {15632422},
issn = {1350-0872},
mesh = {Archaeal Proteins/genetics/*metabolism ; Base Sequence ; *Gene Expression Regulation, Archaeal ; Halobacterium salinarum/genetics/*growth &amp; development/metabolism ; Haloferax mediterranei/genetics/*growth &amp; development/metabolism ; Molecular Sequence Data ; *Promoter Regions, Genetic ; Proteins/genetics/*metabolism ; TATA Box ; Transcription, Genetic ; Transformation, Genetic ; },
abstract = {The two gvpA promoters P(cA) and P(pA) of Halobacterium salinarum, and the P(mcA) promoter of Haloferax mediterranei were investigated with respect to growth-phase-dependent expression and regulation in Haloferax volcanii transformants using the bgaH reading frame encoding BgaH, an enzyme with beta-galactosidase activity, as reporter. For comparison, the P(fdx) promoter of the ferredoxin gene of Hbt. salinarum and the P(bgaH) promoter of Haloferax lucentense (formerly Haloferax alicantei) were analysed. P(fdx), driving the expression of a house-keeping gene, was highly active during the exponential growth phase, whereas P(bgaH) and the three gvpA promoters yielded the largest activities during the stationary growth phase. Compared to P(fdx), the basal promoter activities of P(pA) and P(mcA) were rather low, and larger activities were only detected in the presence of the endogenous transcriptional activator protein GvpE. The P(cA) promoter does not yield a detectable basal promoter activity and is only active in the presence of the homologous cGvpE. To investigate whether the P(cA)-TATA box and the BRE element were the reason for the lack of the basal P(cA) activity, these elements and also sequences further upstream were substituted with the respective sequences of the stronger P(pA) promoter and investigated in Hfx. volcanii transformants. All these promoter chimera did not yield a detectable basal promoter activity. However, whenever the P(pA)-BRE element was substituted for the P(cA)-BRE, an enhanced cGvpE-mediated activation was observed. The promoter chimeras harbouring P(pA)-BRE plus 5 (or more) bp further upstream also gained activation by the heterologous pGvpE and mcGvpE proteins. The sequence required for the GvpE-mediated activation was determined by a 4 bp scanning mutagenesis with the 45 bp region upstream of P(mcA)-BRE. None of these alterations influenced the basal promoter activity, but the sequence TGAAACGG-n4-TGAACCAA was important for the GvpE-mediated activation of P(mcA).},
}
@article {pmid15630514,
year = {2005},
author = {Lange, M and Westermann, P and Ahring, BK},
title = {Archaea in protozoa and metazoa.},
journal = {Applied microbiology and biotechnology},
volume = {66},
number = {5},
pages = {465-474},
doi = {10.1007/s00253-004-1790-4},
pmid = {15630514},
issn = {0175-7598},
mesh = {Animals ; Archaea/classification/*physiology ; Eukaryota/*microbiology ; Eukaryotic Cells/microbiology ; Humans ; },
abstract = {The presence of Archaea is currently being explored in various environments, including extreme geographic positions and eukaryotic habitats. Methanogens are the dominating archaeal organisms found in most animals, from unicellular protozoa to humans. Many methanogens can contribute to the removal of hydrogen, thereby improving the efficiency of fermentation or the reductive capacity of energy-yielding reactions. They may also be involved in tissue damage in periodontal patients. Recent molecular studies demonstrated the presence of Archaea other than methanogens in some animals-but so far, not in humans. The roles of these microorganisms have not yet been established. In the present review, we present the state of the art regarding the archaeal microflora in animals.},
}
@article {pmid15628843,
year = {2005},
author = {Marg, BL and Schweimer, K and Sticht, H and Oesterhelt, D},
title = {A two-alpha-helix extra domain mediates the halophilic character of a plant-type ferredoxin from halophilic archaea.},
journal = {Biochemistry},
volume = {44},
number = {1},
pages = {29-39},
doi = {10.1021/bi0485169},
pmid = {15628843},
issn = {0006-2960},
mesh = {Amino Acid Sequence ; Base Sequence ; Calorimetry ; Circular Dichroism ; Cloning, Molecular ; DNA Primers ; Escherichia coli ; Ferredoxins/*chemistry ; Halobacterium salinarum/*chemistry ; Magnetic Resonance Spectroscopy ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Protein Denaturation ; Protein Structure, Secondary ; Recombinant Proteins/chemistry ; Sequence Alignment ; Sequence Homology, Amino Acid ; Spectrophotometry ; Thermodynamics ; },
abstract = {The [2Fe-2S] ferredoxin (HsFdx) of the halophilic archaeon Halobacterium salinarum exhibits a high degree of sequence conservation with plant-type ferredoxins except for an insertion of 30 amino acids near its N-terminus which is extremely rich in acidic amino acids. Unfolding studies reveal that HsFdx has an unfolding temperature of approximately 85 degrees C in 4.3 M NaCl, but of only 50 degrees C in low salinity, revealing its halophilic character. The three-dimensional structure of HsFdx was determined by NMR spectroscopy, resulting in a backbone rmsd of 0.6 A for the diamagnetic regions of the protein. Whereas the overall structure of HsFdx is very similar to that of the plant-type ferredoxins, two additional alpha-helices are found in the acidic extra domain. (15)N NMR relaxation studies indicate that HsFdx is rigid, and the flexibility of residues is similar throughout the molecule. Monitoring protein denaturation by NMR did not reveal differences between the core fold and the acidic domain, suggesting a cooperative unfolding of both parts of the molecule. A mutant of the HsFdx in which the acidic domain is replaced with a short loop of the nonhalophilic Anabaena ferredoxin shows a considerably changed expression pattern. The halophilic wild-type protein is readily expressed in large amounts in H. salinarum, but not in Escherichia coli, whereas the mutant ferredoxin could only be overexpressed in E. coli. The salt concentration was also found to play a critical role for the efficiency of cluster reconstitution: the cluster of HsFdx could be reconstituted only in a solution containing molar concentrations of NaCl, while the reconstitution of the cluster in the mutant protein proceeds efficiently in low salt. These findings suggest that the acidic domain mediates the halophilic character which is reflected in its thermostability, the exclusive expression in H. salinarum, and the ability to efficiently reconstitute the iron-sulfur cluster only at high salt concentrations.},
}
@article {pmid15614732,
year = {2004},
author = {Celestino, PB and de Carvalho, LR and de Freitas, LM and Dorella, FA and Martins, NF and Pacheco, LG and Miyoshi, A and Azevedo, V},
title = {Update of microbial genome programs for bacteria and archaea.},
journal = {Genetics and molecular research : GMR},
volume = {3},
number = {3},
pages = {421-431},
pmid = {15614732},
issn = {1676-5680},
mesh = {Brazil ; *Genome, Archaeal ; *Genome, Bacterial ; Genomics/*trends ; },
abstract = {Since the Haemophilus influenzae genome sequence was completed in 1995, 172 other prokaryotic genomes have been completely sequenced, while 508 projects are underway. Besides pathogens, organisms important in several other fields, such as biotechnology and bioremediation, have also been sequenced. Institutions choose the organisms they wish to sequence according to the importance that these species represent to them, the availability of the microbes, and based on the similarity of a species of interest with others that have been sequenced previously. Improvements in sequencing techniques and in associated methodologies have been achieved; however, scientists need to continue working on the development of this field. In Brazil, a multicentered, centrally coordinated and research-focused network was adopted and successfully used for the sequencing of several important organisms. We analyzed the current status of microbial genomes, the trends for criteria used to choose new sequencing projects, the future of microbial sequencing, and the Brazilian genome network.},
}
@article {pmid15612937,
year = {2005},
author = {Blount, ZD and Grogan, DW},
title = {New insertion sequences of Sulfolobus: functional properties and implications for genome evolution in hyperthermophilic archaea.},
journal = {Molecular microbiology},
volume = {55},
number = {1},
pages = {312-325},
doi = {10.1111/j.1365-2958.2004.04391.x},
pmid = {15612937},
issn = {0950-382X},
mesh = {Archaeal Proteins/genetics/metabolism ; Base Sequence ; *Chromosomes, Archaeal ; DNA Transposable Elements/*genetics ; DNA, Archaeal/chemistry/isolation &amp; purification ; *Evolution, Molecular ; Molecular Sequence Data ; Phylogeny ; Promoter Regions, Genetic ; Recombination, Genetic ; Repetitive Sequences, Nucleic Acid ; Sequence Alignment ; Sequence Analysis, DNA ; Sequence Homology ; Sulfolobus/*genetics ; },
abstract = {Analyses of complete genomes indicate that insertion sequences (ISs) are abundant and widespread in hyperthermophilic archaea, but few experimental studies have measured their activities in these hosts. As a way to investigate the impact of ISs on Sulfolobus genomes, we identified seven transpositionally active ISs in a widely distributed Sulfolobus species, and measured their functional properties. Six of the seven were found to be distinct from previously described ISs of Sulfolobus, and one of the six could not be assigned to any known IS family. A type II 'Miniature Inverted-repeat Transposable Element' (MITE) related to one of the ISs was also recovered. Rates of transposition of the different ISs into the pyrEF region of their host strains varied over a 250-fold range. The Sulfolobus ISs also differed with respect to target-site selectivity, although several shared an apparent preference for the pyrEF promoter region. Despite the number of distinct ISs assayed and their molecular diversity, only one demonstrated precise excision from the chromosomal target region. The fact that this IS is the only one lacking inverted repeats and target-site duplication suggests that the observed precise excision may be promoted by the IS itself. Sequence searches revealed previously unidentified partial copies of the newly identified ISs in the Sulfolobus tokodaii and Sulfolobus solfataricus genomes. The structures of these fragmentary copies suggest several distinct molecular mechanisms which, in the absence of precise excision, inactivate ISs and gradually eliminate the defective copies from Sulfolobus genomes.},
}
@article {pmid15574514,
year = {2005},
author = {Di Segni, G and Borghese, L and Sebastiani, S and Tocchini-Valentini, GP},
title = {A pre-tRNA carrying intron features typical of Archaea is spliced in yeast.},
journal = {RNA (New York, N.Y.)},
volume = {11},
number = {1},
pages = {70-76},
pmid = {15574514},
issn = {1355-8382},
mesh = {Base Sequence ; Chimera/genetics ; Genes, Fungal ; Introns ; Molecular Sequence Data ; Nucleic Acid Conformation ; RNA Precursors/chemistry/*genetics/*metabolism ; RNA Splicing ; RNA, Archaeal/chemistry/genetics/metabolism ; RNA, Transfer, Tyr/chemistry/genetics/metabolism ; Saccharomyces cerevisiae/genetics/metabolism ; Species Specificity ; Suppression, Genetic ; },
abstract = {Archaeal pre-tRNAs are characterized by the presence of the bulge-helix-bulge (BHB) structure in the intron stem-and-loop region. A chimeric pre-tRNA was constructed bearing an intron of the archaeal type and the mature domain of the Saccharomyces cerevisiae suppressor SUP4 tRNA(Tyr). This pre-tRNA(ArchEuka) is correctly cleaved in several cell-free extracts and by purified splicing endonucleases. It is also cleaved and ligated in S. cerevisiae cells, providing efficient suppression of nonsense mutations in various genes.},
}
@article {pmid15570068,
year = {2004},
author = {Guy, CP and Majerník, AI and Chong, JP and Bolt, EL},
title = {A novel nuclease-ATPase (Nar71) from archaea is part of a proposed thermophilic DNA repair system.},
journal = {Nucleic acids research},
volume = {32},
number = {21},
pages = {6176-6186},
pmid = {15570068},
issn = {1362-4962},
mesh = {Adenosine Triphosphatases/chemistry/genetics/*metabolism ; Amino Acid Sequence ; Amino Acid Substitution ; Catalysis ; *DNA Repair ; DNA, Single-Stranded/metabolism ; Deoxyribonucleases/chemistry/genetics/*metabolism ; Methanobacteriaceae/*enzymology/genetics ; Molecular Sequence Data ; Open Reading Frames ; },
abstract = {We have identified a novel structure-specific nuclease in highly fractionated extracts of the thermophilic archaeon Methanothermobacter thermautotrophicus (Mth). The 71 kDa protein product of open reading frame mth1090 is a nuclease with ATPase activity, which we call Nar71 (Nuclease-ATPase in Repair, 71 kDa). The nar71 gene is located in a gene neighbourhood proposed by genomics to encode a novel DNA repair system conserved in thermophiles. The biochemical characterization of Nar71 presented here is the first analysis from within this neighbourhood, and it supports the insight from genomics. Nuclease activity of Nar71 is specific for 3' flaps and flayed duplexes, targeting single-stranded DNA (ssDNA) regions. This activity requires Mg2+ or Mn2+ and is greatly reduced in ATP. In ATP, Nar71 displaces ssDNA, also with high specificity for 3' flap and flayed duplex DNA. Strand displacement is weak compared with nuclease activity, but in ATPS it is abolished, suggesting that Nar71 couples ATP hydrolysis to DNA strand separation. ATPase assays confirmed that Nar71 is stimulated by ssDNA, though not double-stranded DNA. Mutation of Lys-117 in Nar71 abolished ATPase and nuclease activity, and we describe a separation-of-function mutant (K68A) that has lost ATPase activity but retains nuclease activity. A model of possible Nar71 function in DNA repair is presented.},
}
@article {pmid15558824,
year = {2004},
author = {Kanokratana, P and Chanapan, S and Pootanakit, K and Eurwilaichitr, L},
title = {Diversity and abundance of Bacteria and Archaea in the Bor Khlueng Hot Spring in Thailand.},
journal = {Journal of basic microbiology},
volume = {44},
number = {6},
pages = {430-444},
doi = {10.1002/jobm.200410388},
pmid = {15558824},
issn = {0233-111X},
mesh = {Archaea/*classification/*isolation &amp; purification ; Bacteria/*classification/*isolation &amp; purification ; Biodiversity ; DNA Fingerprinting ; DNA, Archaeal/chemistry/isolation &amp; purification ; DNA, Bacterial/chemistry/isolation &amp; purification ; Genes, rRNA ; Geologic Sediments/microbiology ; Hot Springs/*microbiology ; Mineral Waters/microbiology ; Molecular Sequence Data ; Phylogeny ; Polymorphism, Restriction Fragment Length ; RNA, Archaeal/genetics ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Thailand ; *Water Microbiology ; },
abstract = {The prokaryotic diversity in the Bor Khlueng hot spring in Ratchaburi province, Thailand was investigated by a culture-independent molecular approach. This hydrothermal pool is located in the central part of Thailand and contains sulfide-rich mineral water that is believed to relieve muscle ache and pain. The water flow year-round with temperature ranging between 50-57 degrees C. Community DNA was extracted directly from sediment samples by coring to depth of approximately 20-30 cm. Small-subunit rRNA genes (16S rDNA) were amplified by PCR using primers specific for the domains Archaea and Bacteria. The PCR products were cloned and sequenced. For the bacterial rDNA clone library, 200 clones were randomly selected for further analyses. After restriction fragment length polymorphism (RFLP) analysis of rDNA clones and exclusion of chimeric sequences 36 phylotypes were obtained. The Bor Khlueng phylotypes spanned a wide range within the domain Bacteria, occupying eleven major lineages (phyla). Almost a quarter (23%) of the clones were classified as Acidobacteria. The other clones were grouped into the Bacteriodetes (19%), Nitrospirae (13%), Proteobacteria (12%), Deinococcus-Thermus lineage (11%), planctomycetes (6%), and Verrucomicrobia (5%). The four remaining phyla, 5% each, were assigned to Actinobacteria, Chloroflexi, Cyanobacteria, and the candidate division "OP10". For the archaeal 16S rRNA gene sequence library, 25 distinct phylotypes were obtained, 17 clones were found to be associated with Crenarahaeota and 8 clones were associated with Euryarachaeota. The findings of the molecular survey of this so far not investigated site showed that Bor Khlueng hot spring is a potential rich source of unique bacterial and archaeal species. The great majority (approximately 80%) of the prokaryotic sequences detected in Bor Khlueng were unknown.},
}
@article {pmid15556475,
year = {2004},
author = {Pérez-Rueda, E and Collado-Vides, J and Segovia, L},
title = {Phylogenetic distribution of DNA-binding transcription factors in bacteria and archaea.},
journal = {Computational biology and chemistry},
volume = {28},
number = {5-6},
pages = {341-350},
doi = {10.1016/j.compbiolchem.2004.09.004},
pmid = {15556475},
issn = {1476-9271},
mesh = {Amino Acid Sequence ; Archaea/*genetics/metabolism ; Bacteria/*genetics/metabolism ; DNA/chemistry/*genetics/metabolism ; Molecular Sequence Data ; Phylogeny ; Sequence Homology, Amino Acid ; Transcription Factors, General/genetics/*metabolism ; },
abstract = {We have addressed the distribution and abundance of 75 transcription factor (TF) families in complete genomes from 90 different bacterial and archaeal species. We found that the proportion of TFs increases with genome size. The deficit of TFs in some genomes might be compensated by the presence of proteins organizing and compacting DNA, such as histone-like proteins. Nine families are represented in all the bacteria and archaea we analyzed, whereas 17 families are specific to bacteria, providing evidence for regulon specialization at an early stage of evolution between the bacterial and archeal lineages. Ten of the 17 families identified in bacteria belong exclusively to the proteobacteria defining a specific signature for this taxonomical group. In bacteria, 10 families are lost mostly in intracellular pathogens and endosymbionts, while 9 families seem to have been horizontally transferred to archaea. The winged helix-turn-helix (HTH) is by far the most abundant structure (motif) in prokaryotes, and might have been the earliest HTH motif to appear as shown by its distribution and abundance in both bacterial and archaeal cellular domains. Horizontal gene transfer and lineage-specific gene losses suggest a progressive elimination of TFs in the course of archaeal and bacterial evolution. This analysis provides a framework for discussing the selective forces directing the evolution of the transcriptional machinery in prokaryotes.},
}
@article {pmid15554970,
year = {2004},
author = {Levin, I and Giladi, M and Altman-Price, N and Ortenberg, R and Mevarech, M},
title = {An alternative pathway for reduced folate biosynthesis in bacteria and halophilic archaea.},
journal = {Molecular microbiology},
volume = {54},
number = {5},
pages = {1307-1318},
doi = {10.1111/j.1365-2958.2004.04339.x},
pmid = {15554970},
issn = {0950-382X},
mesh = {Amino Acid Sequence ; Archaea/*genetics/metabolism ; Archaeal Proteins/genetics/physiology ; Bacteria/*genetics/metabolism ; Bacterial Proteins/genetics/physiology ; Conserved Sequence ; Dihydropteroate Synthase/chemistry/genetics/isolation &amp; purification/metabolism ; Escherichia coli/genetics/physiology ; Flavoproteins/chemistry/isolation &amp; purification ; Folic Acid/*biosynthesis ; Gene Deletion ; Genetic Complementation Test ; Haloarcula marismortui/genetics/metabolism ; Halobacterium salinarum/genetics/metabolism ; Haloferax volcanii/genetics/physiology ; Helicobacter pylori/genetics/physiology ; Molecular Sequence Data ; Peptide Synthases/genetics/metabolism ; Protein Structure, Tertiary/genetics/physiology ; Recombinant Proteins/chemistry/genetics/isolation &amp; purification/metabolism ; Sequence Alignment ; Sequence Homology, Amino Acid ; Tetrahydrofolate Dehydrogenase/genetics/metabolism ; },
abstract = {Whereas tetrahydrofolate is an essential cofactor in all bacteria, the gene that encodes the enzyme dihydrofolate reductase (DHFR) could not be identified in many of the bacteria whose genomes have been entirely sequenced. In this communication we show that the halophilic archaea Halobacterium salinarum and Haloarcula marismortui contain genes coding for proteins with an N-terminal domain homologous to dihydrofolate synthase (FolC) and a C-terminal domain homologous to dihydropteroate synthase (FolP). These genes are able to complement a Haloferax volcanii mutant that lacks DHFR. We also show that the Helicobacter pylori dihydropteroate synthase can complement an Escherichia coli mutant that lacks DHFR. Activity resides in an N-terminal segment that is homologous to the polypeptide linker that connects the dihydrofolate synthase and dihydropteroate synthase domains in the haloarchaeal enzymes. The purified recombinant H. pylori dihydropteroate synthase was found to be a flavoprotein.},
}
@article {pmid15546717,
year = {2004},
author = {Zimmerman, S and Innocenti, A and Casini, A and Ferry, JG and Scozzafava, A and Supuran, CT},
title = {Carbonic anhydrase inhibitors. Inhibition of the prokariotic beta and gamma-class enzymes from Archaea with sulfonamides.},
journal = {Bioorganic &amp; medicinal chemistry letters},
volume = {14},
number = {24},
pages = {6001-6006},
doi = {10.1016/j.bmcl.2004.09.085},
pmid = {15546717},
issn = {0960-894X},
support = {GM44661/GM/NIGMS NIH HHS/United States ; },
mesh = {Archaea/*enzymology ; Carbonic Anhydrase Inhibitors/chemistry/*pharmacology ; Carbonic Anhydrases/*classification/*drug effects ; Humans ; Isoenzymes/antagonists &amp; inhibitors ; Molecular Structure ; Structure-Activity Relationship ; Sulfonamides/chemistry/*pharmacology ; },
abstract = {A detailed inhibition study of carbonic anhydrases (CAs, EC 4.2.1.1) belonging to the beta- and gamma-families from Archaea with sulfonamides has been performed. Compounds included in this study were the clinically used sulfonamide CA inhibitors, such as acetazolamide, methazolamide, ethoxzolamide, topiramate, valdecoxib, celecoxib, dorzolamide, sulfanilamide, dichlorophanamide, as well as sulfanilamide analogs, halogenated sulfanilamides, and some 1,3-benzenedisulfonamide derivatives. The two gamma-CAs from Methanosarcina thermophila (Zn-Cam and Co-Cam) showed very different inhibitory properties with these compounds, as compared to the alpha-CA isozymes hCA I, II, and IX, and the beta-CA from Methanobacterium thermoautotrophicum (Cab). The best Zn-Cam inhibitors were sulfamic acid and acetazolamide, with inhibition constants in the range of 63-96 nM, whereas other investigated aromatic/heterocylic sulfonamides showed a rather levelled behavior, with KIs in the range of 0.12-1.70 microM. The best Co-Cam inhibitors were topiramate and p-aminoethyl-benzenesulfonamide, with KIs in the range of 0.12-0.13 microM, whereas the worst one was homosulfanilamide (KI of 8.50 microM). In the case of Cab, the inhibitory power of these compounds varied to a much larger extent, with sulfamic acid and sulfamide showing millimolar affinities (KIs in the range of 44-103 mM), whereas the best inhibitor was ethoxzolamide, with a KI of 5.35 microM. Most of these sulfonamides showed inhibition constants in the range of 12-100 microM against Cab. Thus, the three CA families investigated up to now possess a very diverse affinity for sulfonamides, the inhibitors with important medicinal, and environmental applications.},
}
@article {pmid15541397,
year = {2004},
author = {Fujiwara, S and Yamanaka, A and Hirooka, K and Kobayashi, A and Imanaka, T and Fukusaki, E},
title = {Temperature-dependent modulation of farnesyl diphosphate/geranylgeranyl diphosphate synthase from hyperthermophilic archaea.},
journal = {Biochemical and biophysical research communications},
volume = {325},
number = {3},
pages = {1066-1074},
doi = {10.1016/j.bbrc.2004.10.129},
pmid = {15541397},
issn = {0006-291X},
mesh = {Alkyl and Aryl Transferases/*chemistry/classification/genetics ; Amino Acid Sequence ; Archaea/enzymology/genetics ; Enzyme Activation ; Enzyme Stability ; Gene Expression Regulation, Archaeal/physiology ; Gene Expression Regulation, Enzymologic/physiology ; Geranyltranstransferase ; Isoenzymes/chemistry/genetics ; Kinetics ; Molecular Sequence Data ; Protein Denaturation ; Recombinant Proteins/chemistry/metabolism ; Sequence Homology, Amino Acid ; *Temperature ; Thermococcus/*enzymology/genetics ; },
abstract = {Enzyme characteristics of trans-prenyl diphosphate synthase (Tk-IdsA) from Thermococcus kodakaraensis, which catalyzes the consecutive trans-condensation of isopentenyl diphosphate (C(5)) units with allylic diphosphate, were examined. Product analysis revealed that Tk-IdsA is a bifunctional enzyme, farnesyl diphosphate (FPP, C(15))/geranylgeranyl diphosphate (GGPP, C(20)) synthase, and mainly yields both C(15) and C(20). The FPP/GGPP product ratio increases with the rise of the reaction temperature. The kinetic parameters obtained at 70 and 90 degrees C demonstrated that the rise of the temperature elevates the k(0) value for the C(10) allylic substrate to more than those for the C(5) and C(15) allylic substrates. These data suggest that Tk-IdsA contributes to adjust the membrane composition to the cell growth temperature by modulating its substrate and product specificities. Mutation study indicated that the aromatic side chain of Tyr-81 acts as a steric hindrance to terminate the chain elongation and defines the final product length.},
}
@article {pmid15537007,
year = {2004},
author = {Jun, HB and Park, SM and Park, NB and Lee, SH},
title = {Nitrogen removal and sludge reduction in a symbiotic activated sludge system between anaerobic archaea and bacteria.},
journal = {Water science and technology : a journal of the International Association on Water Pollution Research},
volume = {50},
number = {6},
pages = {189-197},
pmid = {15537007},
issn = {0273-1223},
mesh = {Anaerobiosis ; Archaea/growth &amp; development/*metabolism ; *Bioreactors ; Kinetics ; Nitrates/analysis/chemistry/metabolism ; Nitrites/chemistry/metabolism ; Nitrogen/*isolation &amp; purification/metabolism ; Oxygen/metabolism ; Sewage/chemistry/*microbiology ; Waste Disposal, Fluid/*methods ; },
abstract = {The possible symbiosis between bacteria and anaerobic archaea was investigated in intermittent aeration (I/A) systems. Archaea solution added to I/A reactor might play an important role in biological activities as well as in improvement of mineralization of organic matter. I/A reactor with archaea solution (I/A-arch) could increase both nitrification and denitrification rate and also reduce the sludge yield remarkably. These results indicate the possibility of the symbiotic activated sludge system with anaerobic archaea by controlling the DO level in the aeration tank. In this study, DO was controlled by intermittent aeration schemes and a successful symbiotic activated sludge system was achieved to reach the following conclusions. 1) SOUR of I/A-arch system was 2.9 mg-O2/g-VSS x min. SOUR and nitrification rate of the sludge from I/A-arch was higher than those from the I/A and A/S reactors. 2) Removal efficiencies of organic matter (TCOD(Cr)) in I/A-arch, I/A and conventional activated sludge (A/S) reactors were 93, 90 and 87%, respectively. 3) Nitrification occurred successfully in each reactor, while denitrification rate was much higher in the I/A-arch reactor. Efficiencies of TN removal in A/I-arch, I/A and A/S reactors were 75, 63 and 33%, respectively. 4) Observed yield coefficients of I/A-arch, I/A and A/S reactors were 0.28, 0.41 and 0.37 g-VSS/g-COD.},
}
@article {pmid15528644,
year = {2004},
author = {Cabello, P and Roldán, MD and Moreno-Vivián, C},
title = {Nitrate reduction and the nitrogen cycle in archaea.},
journal = {Microbiology (Reading, England)},
volume = {150},
number = {Pt 11},
pages = {3527-3546},
doi = {10.1099/mic.0.27303-0},
pmid = {15528644},
issn = {1350-0872},
mesh = {Archaea/genetics/*metabolism ; Nitrates/*metabolism ; Nitrogen/metabolism ; Nitrogen Compounds/*metabolism ; Nitrogen Fixation ; Oxidation-Reduction ; },
abstract = {The nitrogen cycle (N-cycle) in the biosphere, mainly driven by prokaryotes, involves different reductive or oxidative reactions used either for assimilatory purposes or in respiratory processes for energy conservation. As the N-cycle has important agricultural and environmental implications, bacterial nitrogen metabolism has become a major research topic in recent years. Archaea are able to perform different reductive pathways of the N-cycle, including both assimilatory processes, such as nitrate assimilation and N(2) fixation, and dissimilatory reactions, such as nitrate respiration and denitrification. However, nitrogen metabolism is much less known in archaea than in bacteria. The availability of the complete genome sequences of several members of the eury- and crenarchaeota has enabled new approaches to the understanding of archaeal physiology and biochemistry, including metabolic reactions involving nitrogen compounds. Comparative studies reveal that significant differences exist in the structure and regulation of some enzymes involved in nitrogen metabolism in archaea, giving rise to important conclusions and new perspectives regarding the evolution, function and physiological relevance of the different N-cycle processes. This review discusses the advances that have been made in understanding nitrate reduction and other aspects of the inorganic nitrogen metabolism in archaea.},
}
@article {pmid15528557,
year = {2004},
author = {Leuko, S and Legat, A and Fendrihan, S and Stan-Lotter, H},
title = {Evaluation of the LIVE/DEAD BacLight kit for detection of extremophilic archaea and visualization of microorganisms in environmental hypersaline samples.},
journal = {Applied and environmental microbiology},
volume = {70},
number = {11},
pages = {6884-6886},
pmid = {15528557},
issn = {0099-2240},
support = {P 16260/FWF_/Austrian Science Fund FWF/Austria ; },
mesh = {Archaea/*growth &amp; development/*isolation &amp; purification/metabolism ; Colony Count, Microbial ; Hydrogen-Ion Concentration ; *Microbiological Techniques ; Organic Chemicals/metabolism ; Reagent Kits, Diagnostic ; Sodium Chloride/*metabolism ; Staining and Labeling ; },
abstract = {Extremophilic archaea were stained with the LIVE/DEAD BacLight kit under conditions of high ionic strength and over a pH range of 2.0 to 9.3. The reliability of the kit was tested with haloarchaea following permeabilization of the cells. Microorganisms in hypersaline environmental samples were detectable with the kit, which suggests its potential application to future extraterrestrial halites.},
}
@article {pmid15526152,
year = {2004},
author = {Ambrogelly, A and Kamtekar, S and Sauerwald, A and Ruan, B and Tumbula-Hansen, D and Kennedy, D and Ahel, I and Söll, D},
title = {Cys-tRNACys formation and cysteine biosynthesis in methanogenic archaea: two faces of the same problem?.},
journal = {Cellular and molecular life sciences : CMLS},
volume = {61},
number = {19-20},
pages = {2437-2445},
pmid = {15526152},
issn = {1420-682X},
mesh = {Archaea/*metabolism ; Binding Sites ; Cysteine/*biosynthesis/chemistry ; *Genes, Archaeal ; Methane/chemistry ; Models, Biological ; Models, Molecular ; Phylogeny ; Protein Biosynthesis ; Protein Conformation ; RNA/chemistry ; RNA, Transfer, Amino Acyl/*chemistry ; },
abstract = {Aminoacyl-tRNA (transfer RNA) synthetases are essential components of the cellular translation machinery as they provide the ribosome with aminoacyl-tRNAs. Aminoacyl-tRNA synthesis is generally well understood. However, the mechanism of Cys-tRNACys formation in three methanogenic archaea (Methanocaldococcus jannaschii, Methanothermobacter thermautotrophicus and Methanopyrus kandleri) is still unknown, since no recognizable gene for a canonical cysteinyl-tRNA synthetase could be identified in the genome sequences of these organisms. Here we review the different routes recently proposed for Cys-tRNACys formation and discuss its possible link with cysteine biosynthesis in these methanogenic archaea.},
}
@article {pmid15525705,
year = {2004},
author = {Rigden, DJ},
title = {Archaea recruited D-Tyr-tRNATyr deacylase for editing in Thr-tRNA synthetase.},
journal = {RNA (New York, N.Y.)},
volume = {10},
number = {12},
pages = {1845-1851},
pmid = {15525705},
issn = {1355-8382},
mesh = {Amino Acid Sequence ; Aminoacyltransferases/chemistry/genetics/*metabolism ; Archaea/*genetics/*metabolism ; Computational Biology ; Dimerization ; Evolution, Molecular ; Methanosarcina/genetics/metabolism ; Models, Molecular ; Molecular Sequence Data ; Protein Structure, Quaternary ; *RNA Editing ; Sequence Homology, Amino Acid ; Threonine-tRNA Ligase/chemistry/genetics/*metabolism ; },
abstract = {Aminoacyl-tRNA synthetases (AARSs) are key players in the maintenance of the genetic code through correct pairing of amino acids with their cognate tRNA molecules. To this end, some AARSs, as well as seeking to recognize the correct amino acid during synthesis of aminoacyl-tRNA, enhance specificity through recognition of mischarged aminoacyl-tRNA molecules in a separate editing reaction. Recently, an editing domain, of uncertain provenance, idiosyncratic to some archaeal ThrRSs has been characterized. Here, sequence analyses and molecular modeling are reported that clearly show a relationship of the archaea-specific ThrRS editing domains with d-Tyr-tRNATyr deacylases (DTDs). The model enables the identification of the catalytic site and other substrate binding residues, as well as the proposal of a likely catalytic mechanism. Interestingly, typical DTD sequences, common in bacteria and eukaryotes, are entirely absent in archaea, consistent with an evolutionary scheme in which DTD was co-opted to serve as a ThrRS editing domain in archaea soon after their divergence from eukaryotes. A group of present-day archaebacteria contain a ThrRS obtained from a bacterium by horizontal gene transfer. In some of these cases a vestigial version of the original archaeal ThrRS, of potentially novel function, is maintained.},
}
@article {pmid15522433,
year = {2004},
author = {Stuart, ES and Morshed, F and Sremac, M and DasSarma, S},
title = {Cassette-based presentation of SIV epitopes with recombinant gas vesicles from halophilic archaea.},
journal = {Journal of biotechnology},
volume = {114},
number = {3},
pages = {225-237},
doi = {10.1016/j.jbiotec.2004.01.005},
pmid = {15522433},
issn = {0168-1656},
support = {AI42556/AI/NIAID NIH HHS/United States ; AI49772/AI/NIAID NIH HHS/United States ; },
mesh = {Animals ; Cytoplasmic Vesicles/*genetics ; Epitopes/*genetics/immunology ; Halobacterium/genetics/*physiology ; Immune Sera/immunology ; Immunologic Memory ; Mice ; Mice, Inbred BALB C ; Proteins/genetics/metabolism ; Rabbits ; Recombinant Proteins/genetics/immunology/metabolism ; Simian Immunodeficiency Virus/*immunology ; Viral Vaccines/genetics/immunology ; },
abstract = {In earlier studies we demonstrated recombinant gas vesicles from Halobacterium sp. NRC-1, expressing a model six amino acid insert, or native vesicles displaying chemically coupled TNP, each were immunogenic, and antigenic. Long-lived responses displaying immunologic memory were elicited without exogenous adjuvant. Here we report the generation and expression of cassettes containing SIV derived DNA. The results indicate a cassette-based display/delivery system derived from recombinant halobacterial gas vesicle genes is highly feasible. Data specifically support four conclusions: (i) Recombinants carrying up to 705 bp of SIV DNA inserted into the gvpC gene form functional gas vesicles; (ii) SIV peptides contained as part of the expressed recombinant, surface exposed GvpC protein are recognized by antibody elicited in monkeys exposed to native SIV in vivo; (iii) in the absence of adjuvant, mice immunized with the recombinant gas vesicle (r-GV) preparations mount a solid, titratable antibody response to the test SIV insert that is long lived and exhibits immunologic memory; (iv) recombinant organelles, created through the generation of cassettes encoding epitopes inserted into the gvpC DNA, can be used to construct a multiepitope display (MED) library, a potentially cost effective vehicle to express and deliver peptides of SIV, HIV or other pathogens.},
}
@article {pmid15522081,
year = {2004},
author = {Ziesche, SM and Omer, AD and Dennis, PP},
title = {RNA-guided nucleotide modification of ribosomal and non-ribosomal RNAs in Archaea.},
journal = {Molecular microbiology},
volume = {54},
number = {4},
pages = {980-993},
doi = {10.1111/j.1365-2958.2004.04319.x},
pmid = {15522081},
issn = {0950-382X},
mesh = {Archaeal Proteins/genetics/metabolism ; Base Sequence ; Methylation ; Nucleic Acid Conformation ; RNA, Archaeal/*genetics/*metabolism ; RNA, Ribosomal/*genetics/*metabolism ; RNA, Transfer, Amino Acyl/metabolism ; Recombinant Proteins/genetics/metabolism ; Ribonucleoproteins/metabolism ; Sulfolobus acidocaldarius/genetics ; },
abstract = {Archaea use ribonucleoprotein (RNP) machines similar to those found in the eukaryotic nucleolus to methylate ribose residues in nascent ribosomal RNA. The archaeal complex required for this 2'-O-ribose-methylation consists of the C/D box sRNA guide and three proteins, the core RNA-binding aL7a protein, the aNop56 protein and the methyltransferase aFib protein. These RNP machines were reconstituted in vitro from purified recombinant components, and shown to have methylation activity when provided with a simple target oligonucleotide, complementary to the sRNA guide sequence. To obtain a better understanding of the versatility and specificity of this reaction, the activity of reconstituted particles on more complex target substrates, including 5S RNA, tRNA(Gln) and 'double target' oligonucleotides that exhibit either direct or reverse complementarity to both the D' and D box guides, has been examined. The natural 5S and tRNA(Gln) substrates were efficiently methylated in vitro, as long as the complementarity between guide and target was about 10 base pairs in length, and lacked mismatches. Maximal activity of double guide sRNAs required that both methylation sites be present in cis on the target RNA.},
}
@article {pmid19712361,
year = {2004},
author = {Ishii, K and Mussmann, M and MacGregor, BJ and Amann, R},
title = {An improved fluorescence in situ hybridization protocol for the identification of bacteria and archaea in marine sediments.},
journal = {FEMS microbiology ecology},
volume = {50},
number = {3},
pages = {203-213},
doi = {10.1016/j.femsec.2004.06.015},
pmid = {19712361},
issn = {1574-6941},
mesh = {Archaea/*genetics/*isolation &amp; purification ; Bacteria/*genetics/*isolation &amp; purification ; Enzyme Inhibitors/pharmacology ; Geologic Sediments/*microbiology ; Germany ; Hydrogen Peroxide/pharmacology ; In Situ Hybridization, Fluorescence/*methods ; Methanol/pharmacology ; Peroxidases/antagonists &amp; inhibitors ; Sensitivity and Specificity ; },
abstract = {In situ identification of prokaryotic cells in subsurface sediments is hampered by the low cellular rRNA contents of the target organisms. Fluorescence in situ hybridization with catalyzed reporter deposition (CARD-FISH) has the potential to overcome this limitation, and was therefore optimized for a 40 cm deep sediment core sampled from a tidal sandy flat of the German Wadden Sea. Treatment with methanol and H(2)O(2) inactivated endogenous peroxidases and effectively reduced the background signal. Percentage of DAPI stained cells detected with the probe combination EUB(I-III), targeting nearly all the Bacteria, were comparable for CARD-FISH with a horseradish peroxidase (HRP)-labeled probe and FISH with a fluorescently monolabeled probe in the 2-3 cm depth interval (92% and 82%, respectively), but significantly higher with the HRP-labeled probe at 35-40 cm, the deepest layer sampled (63% with HRP vs. 26% with monolabeled probe). With CARD-FISH Alphaproteobacteria and the Desulfobulbaceae group of sulfate-reducing bacteria were detected only in the upper layers. In contrast, Desulfosarcinales, the Bacteroidetes group, Planctomycetes, Betaproteobacteria, and Gammaproteobacteria were found at all depths. Archaea were detectable with ARCH915-HRP after achromopeptidase treatment. Surprisingly, aggregates of Bacteria and Archaea were found, below 12 cm depth, that strongly resemble consortia involved in anoxic oxidation of methane that have previously been found in sediments near methane hydrate deposits. With the optimized CARD-FISH protocol, microbial populations could also be detected in deeper sediment horizons. Furthermore, the intensity of the CARD-FISH signals improved detection of rare organisms such as Archaea.},
}
@article {pmid15475349,
year = {2004},
author = {Ring, G and Eichler, J},
title = {In the Archaea Haloferax volcanii, membrane protein biogenesis and protein synthesis rates are affected by decreased ribosomal binding to the translocon.},
journal = {The Journal of biological chemistry},
volume = {279},
number = {51},
pages = {53160-53166},
doi = {10.1074/jbc.M410590200},
pmid = {15475349},
issn = {0021-9258},
mesh = {Archaea/metabolism ; Archaeal Proteins/chemistry/*physiology ; Cell Membrane/metabolism ; Cellulose/chemistry ; Cytoplasm/metabolism ; Densitometry ; Electrophoresis, Polyacrylamide Gel ; Endoplasmic Reticulum/metabolism ; Haloferax volcanii/*metabolism ; Kinetics ; Membrane Proteins/metabolism ; Protein Binding ; Protein Biosynthesis ; Protein Structure, Tertiary ; Protein Transport ; Proteins/*metabolism ; Puromycin/pharmacology ; RNA/metabolism ; RNA, Ribosomal/chemistry ; Ribosomes/chemistry/*metabolism ; Salts/pharmacology ; Subcellular Fractions ; Time Factors ; },
abstract = {In the haloarchaea Haloferax volcanii, ribosomes are found in the cytoplasm and membrane-bound at similar levels. Transformation of H. volcanii to express chimeras of the translocon components SecY and SecE fused to a cellulose-binding domain substantially decreased ribosomal membrane binding, relative to non-transformed cells, likely due to steric hindrance by the cellulose-binding domain. Treatment of cells with the polypeptide synthesis terminator puromycin, with or without low salt washes previously shown to prevent in vitro ribosomal membrane binding in halophilic archaea, did not lead to release of translocon-bound ribosomes, indicating that ribosome release is not directly related to the translation status of a given ribosome. Release was, however, achieved during cell starvation or stationary growth, pointing at a regulated manner of ribosomal release in H. volcanii. Decreased ribosomal binding selectively affected membrane protein levels, suggesting that membrane insertion occurs co-translationally in Archaea. In the presence of chimera-incorporating sterically hindered translocons, the reduced ability of ribosomes to bind in the transformed cells modulated protein synthesis rates over time, suggesting that these cells manage to compensate for the reduction in ribosome binding. Possible strategies for this compensation, such as a shift to a post-translational mode of membrane protein insertion or maintained ribosomal membrane-binding, are discussed.},
}
@article {pmid15474942,
year = {2005},
author = {Martone, CB and Pérez Borla, O and Sánchez, JJ},
title = {Fishery by-product as a nutrient source for bacteria and archaea growth media.},
journal = {Bioresource technology},
volume = {96},
number = {3},
pages = {383-387},
doi = {10.1016/j.biortech.2004.04.008},
pmid = {15474942},
issn = {0960-8524},
mesh = {Analysis of Variance ; Animals ; Archaea/*growth &amp; development ; Bacteria/*growth &amp; development ; Colony Count, Microbial ; Culture Media/*metabolism ; Fisheries ; Gadiformes/*metabolism ; Nephelometry and Turbidimetry ; Nucleic Acids/metabolism ; Protein Hydrolysates/isolation &amp; purification/*metabolism ; Waste Products ; },
abstract = {A highly soluble fish protein hydrolysates (FPH) with an 80% protein (peptide size between 1.5 and 20 kDa) and a low free amino acid content was obtained from hake (Merluccius hubssi) filleting waste [Lat. Am. Appl. Res. 30 (2000) 241]. Assays with Halobacterium salinarum, Escherichia coli, Bacillus subtilis and Staphylococcus epidermidis were performed in order to test that FPH as nutrient source for archaea and eubacteria culture media. Cell growth was evaluated by plate count, and by monitoring turbidity and nucleic acids content in liquid cultures. Neither cell growth nor generation times resulting from control and FPH cultures exhibited statistically significant differences at alpha: 0.05 suggesting that FPH can be used as an alternative substrate for microorganism cultural purposes.},
}
@article {pmid15381435,
year = {2004},
author = {Fischer, M and Schott, AK and Römisch, W and Ramsperger, A and Augustin, M and Fidler, A and Bacher, A and Richter, G and Huber, R and Eisenreich, W},
title = {Evolution of vitamin B2 biosynthesis. A novel class of riboflavin synthase in Archaea.},
journal = {Journal of molecular biology},
volume = {343},
number = {1},
pages = {267-278},
doi = {10.1016/j.jmb.2004.08.016},
pmid = {15381435},
issn = {0022-2836},
mesh = {Amino Acid Sequence ; Archaea/*enzymology/*genetics ; Base Sequence ; Codon ; Conserved Sequence ; Evolution, Molecular ; Kinetics ; Magnetic Resonance Spectroscopy ; Methanococcus/enzymology/genetics ; Molecular Sequence Data ; Molecular Weight ; Open Reading Frames ; Phylogeny ; Recombinant Proteins/chemistry/isolation &amp; purification/metabolism ; Riboflavin/*biosynthesis/chemistry/genetics/isolation &amp; purification ; Sequence Analysis, Protein ; Sequence Homology, Amino Acid ; Spectrometry, Mass, Electrospray Ionization ; Substrate Specificity ; Temperature ; Ultracentrifugation ; },
abstract = {The open reading frame MJ1184 of Methanococcus jannaschii with similarity to riboflavin synthase of Methanothermobacter thermoautotrophicus was cloned into an expression vector but was poorly expressed in an Escherichia coli host strain. However, a synthetic open reading frame that was optimized for expression in E.coli directed the synthesis of abundant amounts of a protein with an apparent subunit mass of 17.5 kDa. The protein was purified to apparent homogeneity. Hydrodynamic studies indicated a relative mass of 88 kDa suggesting a homopentamer structure. The enzyme was shown to catalyze the formation of riboflavin from 6,7-dimethyl-8-ribityllumazine at a rate of 24 nmol mg(-1) min(-1) at 40 degrees C. Divalent metal ions, preferably manganese or magnesium, are required for maximum activity. In contrast to pentameric archaeal type riboflavin synthases, orthologs from plants, fungi and eubacteria are trimeric proteins characterized by an internal sequence repeat with similar folding patterns. In these organisms the reaction is achieved by binding the two substrate molecules in an antiparallel orientation. With the enzyme of M.jannaschii, 13C NMR spectroscopy with 13C-labeled 6,7-dimethyl-8-ribityllumazine samples as substrates showed that the regiochemistry of the dismutation reaction is the same as observed in eubacteria and eukaryotes, however, in a non-pseudo-c2 symmetric environment. Whereas the riboflavin synthases of M.jannaschii and M.thermoautotrophicus are devoid of similarity with those of eubacteria and eukaryotes, they have significant sequence similarity with 6,7-dimethyl-8-ribityllumazine synthases catalyzing the penultimate step of riboflavin biosynthesis. 6,7-Dimethyl-8-ribityllumazine synthase and the archaeal riboflavin synthase appear to have diverged early in the evolution of Archaea from a common ancestor. Some Archaea have eubacterial type riboflavin synthases which may have been acquired by lateral gene transfer.},
}
@article {pmid15378928,
year = {2004},
author = {Tarasov, VY and Pyatibratov, MG and Beznosov, SN and Fedorov, OV},
title = {On the supramolecular organization of the flagellar filament in archaea.},
journal = {Doklady. Biochemistry and biophysics},
volume = {396},
number = {},
pages = {203-205},
pmid = {15378928},
issn = {1607-6729},
mesh = {Flagella/chemistry/genetics/*ultrastructure ; Flagellin/chemistry/genetics/ultrastructure ; Halobacterium salinarum/chemistry/genetics/*ultrastructure ; Mutation/genetics ; RNA, Archaeal/genetics/metabolism ; RNA, Messenger/genetics/metabolism ; },
}
@article {pmid15376975,
year = {2004},
author = {Suzuki, K and Mori, K},
title = {[Cultivation and preservation of bacteria and archaea].},
journal = {Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme},
volume = {49},
number = {11 Suppl},
pages = {1565-1571},
pmid = {15376975},
issn = {0039-9450},
mesh = {Archaea/*cytology ; Bacteria, Anaerobic/*cytology ; Cell Culture Techniques/instrumentation/*methods ; Specimen Handling/instrumentation/*methods ; },
}
@article {pmid15375115,
year = {2004},
author = {Finn, MW and Tabita, FR},
title = {Modified pathway to synthesize ribulose 1,5-bisphosphate in methanogenic archaea.},
journal = {Journal of bacteriology},
volume = {186},
number = {19},
pages = {6360-6366},
pmid = {15375115},
issn = {0021-9193},
support = {R01 GM024497/GM/NIGMS NIH HHS/United States ; R01 GM045404/GM/NIGMS NIH HHS/United States ; GM24497/GM/NIGMS NIH HHS/United States ; GM45404/GM/NIGMS NIH HHS/United States ; },
mesh = {Carbon Dioxide/metabolism ; Catalysis ; Methanococcus/*metabolism ; NAD/pharmacology ; Pentose Phosphate Pathway ; Pyrophosphatases/metabolism ; Ribulosephosphates/*biosynthesis ; },
abstract = {Several sequencing projects unexpectedly uncovered the presence of genes that encode ribulose 1,5-bisphosphate (RuBP) carboxylase/oxygenase (RubisCO) in anaerobic archaea. RubisCO is the key enzyme of the Calvin-Benson-Bassham (CBB) reductive pentose phosphate pathway, a scheme that does not appear to contribute greatly, if at all, to net CO2 assimilation in these organisms. Recombinant forms of the archaeal enzymes do, however, catalyze a bona fide RuBP-dependent CO2 fixation reaction, and it was recently shown that Methanocaldococcus (Methanococcus) jannaschii and other anaerobic archaea synthesize catalytically active RubisCO in vivo. To complete the CBB pathway, there is a need for an enzyme, i.e., phosphoribulokinase (PRK), to catalyze the formation of RuBP, the substrate for the RubisCO reaction. Homology searches, as well as direct enzymatic assays with M. jannaschii, failed to reveal the presence of PRK. The apparent lack of PRK raised the possibility that either there is an alternative pathway to generate RuBP or RubisCO might use an alternative substrate in vivo. In the present study, direct enzymatic assays performed with alternative substrates and extracts of M. jannsachii provided evidence for a previously uncharacterized pathway for RuBP synthesis from 5-phospho-D-ribose-1-pyrophosphate (PRPP) in M. jannaschii and other methanogenic archaea. Proteins and genes involved in the catalytic conversion of PRPP to RuBP were identified in M. jannaschii (Mj0601) and Methanosarcina acetivorans (Ma2851), and recombinant Ma2851 was active in extracts of Escherichia coli. Thus, in this work we identified a novel means to synthesize the CO2 acceptor and substrate for RubisCO in the absence of a detectable kinase, such as PRK. We suggest that the conversion of PRPP to RuBP might be an evolutional link between purine recycling pathways and the CBB scheme.},
}
@article {pmid15353266,
year = {2004},
author = {Roberts, MF},
title = {Osmoadaptation and osmoregulation in archaea: update 2004.},
journal = {Frontiers in bioscience : a journal and virtual library},
volume = {9},
number = {},
pages = {1999-2019},
doi = {10.2741/1366},
pmid = {15353266},
issn = {1093-9946},
mesh = {Adaptation, Physiological ; Animals ; Archaea/*metabolism/*physiology ; Archaeal Proteins/chemistry ; Heat-Shock Proteins/metabolism ; Ions ; Methanococcus/metabolism ; Osmolar Concentration ; Osmotic Pressure ; Potassium/metabolism ; Potassium Channels/metabolism ; Sodium Chloride/*metabolism/pharmacology ; Solutions ; Water/metabolism ; Water-Electrolyte Balance ; },
abstract = {The response of archaea to changes in external NaCl is reviewed and compared to what is known about osmoadaptation and osmoregulation in bacteria and eukaryotes. Cells placed in altered external NaCl exhibit short term and long term responses. The earliest events are likely to be water movement through aquaporin-like channels (efflux if external NaCl has been increased, influx into the cell if the external NaCl has been decreased) and ion movement (e.g., K+ moving in the direction opposite to water flow) through channels sensitive to osmotic pressure. A brief discussion of recent structures of homologues of these membrane proteins is presented. Accumulation of organic solutes, either by uptake from the medium or de novo synthesis, is triggered after these initial changes. Archaea have some unique organic solutes (osmolytes) that are not used by other organisms. These as well as other more common solutes have a role in stabilizing macromolecules from denaturation. Many osmolytes are distinguished by their stability in the cell and their lack of strong interactions with cellular components. A cell may respond by accumulating one or more temporary osmolytes, then over time readjust the intracellular solute distribution to what is optimal for cell growth under the new conditions. Coupled with the movement and accumulation of solutes is the induction of stress proteins (e.g., chaperonins) and, in some cases, transcriptional regulation of key enzymes. The response to NaCl stress of Methanococcus thermolithotrophicus is presented as an example of how one particular archaeon responds and adapts to altered osmotic pressure. The detailed response of many other archaea to osmotic stress will be needed in order to identify features (aside from some of the organic osmolytes) unique to the organisms in this kingdom.},
}
@article {pmid15345465,
year = {2004},
author = {Slobodkina, GB and Chernyh, NA and Slobodkin, AI and Subbotina, IV and Bonch-Osmolovskaya, EA and Lebedinsky, AV},
title = {PCR-based identification of hyperthermophilic archaea of the family Thermococcaceae.},
journal = {Applied and environmental microbiology},
volume = {70},
number = {9},
pages = {5701-5703},
pmid = {15345465},
issn = {0099-2240},
mesh = {Bacteria/genetics ; Base Sequence ; DNA Primers ; Geography ; Polymerase Chain Reaction/methods ; Sequence Alignment ; Sequence Homology, Nucleic Acid ; Thermococcaceae/*genetics/*isolation &amp; purification ; },
abstract = {A method for rapid detection and identification of hyperthermophilic archaea of the family Thermococcaceae based on PCR amplification of 16S rRNA gene fragments with primers TcPc 173F (5'-TCCCCCATAGGYCTGRGGTACTGGAAGGTC-3') and TcPc 589R (5'-GCCGTGRGATTTCGCCAGGGACTTACGGGC-3') was developed and used for identification of new isolates.},
}
@article {pmid15337158,
year = {2004},
author = {Kelman, LM and Kelman, Z},
title = {Multiple origins of replication in archaea.},
journal = {Trends in microbiology},
volume = {12},
number = {9},
pages = {399-401},
doi = {10.1016/j.tim.2004.07.001},
pmid = {15337158},
issn = {0966-842X},
mesh = {Archaea/*genetics/metabolism ; Archaeal Proteins/genetics/metabolism ; Centromere/genetics ; Chromosomes, Archaeal/genetics ; DNA Replication/genetics ; DNA, Archaeal/genetics ; *Replication Origin ; Sulfolobus/genetics ; },
abstract = {Until recently, the only archaeon for which a bona fide origin of replication was reported was Pyrococcus abyssi, where a single origin was identified. Although several in silico analyses have suggested that some archaeal species might contain more than one origin, this has only been demonstrated recently. Two studies have shown that multiple origins of replication function in two archaeal species. One study identified two origins of replication in the archaeon Sulfolobus solfataricus, whereas a second study used a different technique to show that both S. solfataricus and Sulfolobus acidocaldarius have three functional origins. These are the first reports of archaea having multiple origins. This finding has implications for research on the mechanisms of DNA replication and evolution.},
}
@article {pmid15333948,
year = {2004},
author = {Dwivedi, S and Kruparani, SP and Sankaranarayanan, R},
title = {Cloning, expression, purification, crystallization and preliminary X-ray crystallographic investigations of a unique editing domain from archaebacteria.},
journal = {Acta crystallographica. Section D, Biological crystallography},
volume = {60},
number = {Pt 9},
pages = {1662-1664},
doi = {10.1107/S0907444904017329},
pmid = {15333948},
issn = {0907-4449},
mesh = {Cloning, Molecular ; Crystallization ; Crystallography, X-Ray ; Molecular Weight ; Plasmids/genetics ; Pyrococcus/*chemistry/*genetics ; Reverse Transcriptase Polymerase Chain Reaction ; Threonine-tRNA Ligase/*chemistry/genetics ; },
abstract = {Threonyl-tRNA synthetase (ThrRS) faces a crucial double-discrimination problem during the translation of genetic code. Most ThrRSs from the archaeal kingdom possess a unique editing domain that differs from those of eubacteria and eukaryotes. In order to understand the structural basis of the editing mechanism in archaea, the editing module of ThrRS from Pyrococcus abyssi comprising of the first 183 amino-acid residues was cloned, expressed, purified and crystallized. The crystals belong to the trigonal space group P3(1(2))21, with one molecule in the asymmetric unit.},
}
@article {pmid15305922,
year = {2004},
author = {Treusch, AH and Kletzin, A and Raddatz, G and Ochsenreiter, T and Quaiser, A and Meurer, G and Schuster, SC and Schleper, C},
title = {Characterization of large-insert DNA libraries from soil for environmental genomic studies of Archaea.},
journal = {Environmental microbiology},
volume = {6},
number = {9},
pages = {970-980},
doi = {10.1111/j.1462-2920.2004.00663.x},
pmid = {15305922},
issn = {1462-2912},
mesh = {Adenosine Triphosphatases ; Archaea/*genetics ; Bacterial Proteins/*genetics ; Base Composition ; Base Sequence ; Cell Cycle Proteins/genetics ; DNA, Ribosomal/genetics ; Ecosystem ; *Gene Library ; *Genome, Bacterial ; Likelihood Functions ; Models, Genetic ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, DNA ; *Soil Microbiology ; Species Specificity ; Valosin Containing Protein ; },
abstract = {Complex genomic libraries are increasingly being used to retrieve complete genes, operons or large genomic fragments directly from environmental samples, without the need to cultivate the respective microorganisms. We report on the construction of three large-insert fosmid libraries in total covering 3 Gbp of community DNA from two different soil samples, a sandy ecosystem and a mixed forest soil. In a fosmid end sequencing approach including 5376 sequence tags of approximately 700 bp length, we show that mostly bacterial and, to a much lesser extent, archaeal and eukaryotic genome fragments (approximately 1% each) have been captured in our libraries. The diversity of putative protein-encoding genes, as reflected by their distribution into different COG clusters, was comparable to that encoded in complete genomes of cultivated microorganisms. A huge variety of genomic fragments has been captured in our libraries, as seen by comparison with sequences in the public databases and by the large variation in G+C contents. We dissect differences between the libraries, which relate to the different ecosystems analysed and to biases introduced by different DNA preparations. Furthermore, a range of taxonomic marker genes (other than 16S rRNA) has been identified that allows the assignment of genome fragments to specific lineages. The complete sequences of two genome fragments identified as being affiliated with Archaea, based on a gene encoding a CDC48 homologue and a thermosome subunit, respectively, are presented and discussed. We thereby extend the genomic information of uncultivated crenarchaeota from soil and offer hints to specific metabolic traits present in this group.},
}
@article {pmid15292191,
year = {2004},
author = {De Felice, M and Esposito, L and Pucci, B and De Falco, M and Rossi, M and Pisani, FM},
title = {A CDC6-like factor from the archaea Sulfolobus solfataricus promotes binding of the mini-chromosome maintenance complex to DNA.},
journal = {The Journal of biological chemistry},
volume = {279},
number = {41},
pages = {43008-43012},
doi = {10.1074/jbc.M406693200},
pmid = {15292191},
issn = {0021-9258},
mesh = {Adenosine Triphosphate/chemistry/metabolism ; Archaea/metabolism ; Archaeal Proteins/metabolism ; Cell Cycle Proteins/*chemistry/physiology ; Chromosomes, Archaeal ; DNA Replication ; DNA, Archaeal/chemistry/metabolism ; DNA-Binding Proteins/*chemistry/physiology ; Dose-Response Relationship, Drug ; Immunoprecipitation ; Minichromosome Maintenance 1 Protein/metabolism ; Oligonucleotides/chemistry ; Protein Binding ; Saccharomyces cerevisiae Proteins/*chemistry/physiology ; Sulfolobus/*metabolism ; },
abstract = {The archaeal replication apparatus appears to be a simplified version of the eukaryotic one with fewer polypeptides and simpler protein complexes. Herein, we report evidence that a Cdc6-like factor from the hyperthermophilic crenarchaea Sulfolobus solfataricus stimulates binding of the homohexameric MCM-like complex to bubble- and fork-containing DNA oligonucleotides that mimic early replication intermediates. This function does not require the Cdc6 ATP and DNA binding activities. These findings may provide important clues to understanding how the DNA replication initiation process has evolved in the more complex eukaryotic organisms.},
}
@article {pmid15287974,
year = {2004},
author = {Bonneau, R and Baliga, NS and Deutsch, EW and Shannon, P and Hood, L},
title = {Comprehensive de novo structure prediction in a systems-biology context for the archaea Halobacterium sp. NRC-1.},
journal = {Genome biology},
volume = {5},
number = {8},
pages = {R52},
pmid = {15287974},
issn = {1474-760X},
mesh = {Archaeal Proteins/*chemistry/genetics/*metabolism ; Bacteriophages/genetics/physiology ; Chemotaxis ; *Computational Biology ; Databases, Genetic ; Evolution, Molecular ; Genome, Archaeal ; Genomics ; Halobacterium/*chemistry/classification/genetics/*metabolism ; Oligonucleotide Array Sequence Analysis ; Protein Binding ; Protein Structure, Tertiary ; *Proteomics ; RNA, Messenger/genetics/metabolism ; Software ; Structure-Activity Relationship ; *Systems Biology ; Transcription Factors/chemistry/genetics/metabolism ; },
abstract = {BACKGROUND: Large fractions of all fully sequenced genomes code for proteins of unknown function. Annotating these proteins of unknown function remains a critical bottleneck for systems biology and is crucial to understanding the biological relevance of genome-wide changes in mRNA and protein expression, protein-protein and protein-DNA interactions. The work reported here demonstrates that de novo structure prediction is now a viable option for providing general function information for many proteins of unknown function.<br><br>RESULTS: We have used Rosetta de novo structure prediction to predict three-dimensional structures for 1,185 proteins and protein domains (<150 residues in length) found in Halobacterium NRC-1, a widely studied halophilic archaeon. Predicted structures were searched against the Protein Data Bank to identify fold similarities and extrapolate putative functions. They were analyzed in the context of a predicted association network composed of several sources of functional associations such as: predicted protein interactions, predicted operons, phylogenetic profile similarity and domain fusion. To illustrate this approach, we highlight three cases where our combined procedure has provided novel insights into our understanding of chemotaxis, possible prophage remnants in Halobacterium NRC-1 and archaeal transcriptional regulators.<br><br>CONCLUSIONS: Simultaneous analysis of the association network, coordinated mRNA level changes in microarray experiments and genome-wide structure prediction has allowed us to glean significant biological insights into the roles of several Halobacterium NRC-1 proteins of previously unknown function, and significantly reduce the number of proteins encoded in the genome of this haloarchaeon for which no annotation is available.},
}
@article {pmid15274916,
year = {2004},
author = {Nishimasu, H and Fushinobu, S and Shoun, H and Wakagi, T},
title = {The first crystal structure of the novel class of fructose-1,6-bisphosphatase present in thermophilic archaea.},
journal = {Structure (London, England : 1993)},
volume = {12},
number = {6},
pages = {949-959},
doi = {10.1016/j.str.2004.03.026},
pmid = {15274916},
issn = {0969-2126},
mesh = {Amino Acid Sequence ; Archaea/*enzymology ; Binding Sites ; Catalysis ; Catalytic Domain ; Crystallography, X-Ray ; Dose-Response Relationship, Drug ; Electrons ; Escherichia coli/metabolism ; Fructose-Bisphosphatase/*chemistry ; Ions ; Kinetics ; Ligands ; Lithium/chemistry ; Magnesium/chemistry ; Models, Molecular ; Molecular Sequence Data ; Mutagenesis, Site-Directed ; Mutation ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Recombinant Proteins/chemistry ; Sequence Homology, Amino Acid ; Substrate Specificity ; Temperature ; },
abstract = {As the first structure of the novel class of fructose-1,6-bisphosphatase (FBPase) present in thermophilic archaea, we solved the crystal structure of the ST0318 gene product (St-Fbp) of Sulfolobus tokodaii strain 7. The St-Fbp structure comprises a homooctamer of the 422 point-group. The protein folds as a four-layer alpha-beta-beta-alpha sandwich with a novel topology, which is completely different from the sugar phosphatase fold. The structure contains an unhydrolyzed FBP molecule in the open-keto form, as well as four hexacoordinated magnesium ions around the 1-phosphoryl group of FBP. The arrangement of the catalytic side chains and metal ligands is consistent with the three-metal ion assisted catalysis proposed for conventional FBPases. The structure provides an insight into the structural basis of the strict substrate specificity of St-Fbp.},
}
@article {pmid15240874,
year = {2004},
author = {Korencic, D and Ahel, I and Schelert, J and Sacher, M and Ruan, B and Stathopoulos, C and Blum, P and Ibba, M and Söll, D},
title = {A freestanding proofreading domain is required for protein synthesis quality control in Archaea.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {101},
number = {28},
pages = {10260-10265},
pmid = {15240874},
issn = {0027-8424},
mesh = {Acylation ; Amino Acid Sequence ; Chimera ; Gene Deletion ; *Gene Expression Regulation, Archaeal ; Hydrolysis ; Molecular Sequence Data ; Protein Biosynthesis ; Protein Structure, Tertiary ; *RNA Editing ; RNA, Transfer, Amino Acyl/metabolism ; Sequence Homology, Amino Acid ; Serine/metabolism ; Sulfolobus/*genetics/growth &amp; development/metabolism ; Threonine/metabolism ; Threonine-tRNA Ligase/chemistry/*genetics/*metabolism ; },
abstract = {Threonyl-tRNA synthetase (ThrRS) participates in protein synthesis quality control by selectively editing the misacylated species Ser-tRNA(Thr). In bacteria and eukaryotes the editing function of ThrRS resides in a highly conserved N-terminal domain distant from the active site. Most archaeal ThrRS proteins are devoid of this editing domain, suggesting evolutionary divergence of quality-control mechanisms. Here we show that archaeal editing of Ser-tRNAThr is catalyzed by a domain unrelated to, and absent from, bacterial and eukaryotic ThrRSs. Despite the lack of sequence homology, the archaeal and bacterial editing domains are both reliant on a pair of essential histidine residues suggestive of a common catalytic mechanism. Whereas the archaeal editing module is most commonly part of full-length ThrRS, several crenarchaeal species contain individual genes encoding the catalytic (ThrRS-cat) and editing domains (ThrRS-ed). Sulfolobus solfataricus ThrRS-cat was shown to synthesize both Thr-tRNAThr and Ser-tRNAThr and to lack editing activity against Ser-tRNAThr. In contrast, ThrRS-ed lacks aminoacylation activity but can act as an autonomous protein in trans to hydrolyze specifically Ser-tRNAThr, or it can be fused to ThrRS-cat to provide the same function in cis. Deletion analyses indicate that ThrRS-ed is dispensable for growth of S. solfataricus under standard conditions but is required for normal growth in media with elevated serine levels. The growth phenotype of the ThrRS-ed deletion strain suggests that retention of the discontinuous ThrRS quaternary structure relates to specific physiological requirements still evident in certain Archaea.},
}
@article {pmid15240332,
year = {2004},
author = {Teira, E and Reinthaler, T and Pernthaler, A and Pernthaler, J and Herndl, GJ},
title = {Combining catalyzed reporter deposition-fluorescence in situ hybridization and microautoradiography to detect substrate utilization by bacteria and Archaea in the deep ocean.},
journal = {Applied and environmental microbiology},
volume = {70},
number = {7},
pages = {4411-4414},
pmid = {15240332},
issn = {0099-2240},
mesh = {Archaea/*metabolism ; Autoradiography/*methods ; Bacteria/*metabolism ; Catalysis ; In Situ Hybridization, Fluorescence/*methods ; Seawater/*microbiology ; },
abstract = {The recently developed CARD-FISH protocol was refined for the detection of marine Archaea by replacing the lysozyme permeabilization treatment with proteinase K. This modification resulted in about twofold-higher detection rates for Archaea in deep waters. Using this method in combination with microautoradiography, we found that Archaea are more abundant than Bacteria (42% versus 32% of 4',6'-diamidino-2-phenylindole counts) in the deep waters of the North Atlantic and that a larger fraction of Archaea than of Bacteria takes up l-aspartic acid (19% versus 10%).},
}
@article {pmid15215500,
year = {2004},
author = {Fujishige, N and Nishimura, N and Iuchi, S and Kunii, T and Shinozaki, K and Hirayama, T},
title = {A novel Arabidopsis gene required for ethanol tolerance is conserved among plants and archaea.},
journal = {Plant &amp; cell physiology},
volume = {45},
number = {6},
pages = {659-666},
doi = {10.1093/pcp/pch086},
pmid = {15215500},
issn = {0032-0781},
mesh = {Acetaldehyde/metabolism/toxicity ; Amino Acid Motifs/genetics ; Amino Acid Sequence/genetics ; Arabidopsis/drug effects/*genetics/metabolism ; Arabidopsis Proteins/*genetics/isolation &amp; purification/metabolism ; Archaea/drug effects/genetics/*metabolism ; Base Sequence/genetics ; Conserved Sequence/genetics ; DNA, Complementary/analysis/genetics ; Drug Tolerance/*genetics ; Escherichia coli/drug effects/genetics/metabolism ; Ethanol/*metabolism/toxicity ; Evolution, Molecular ; Gene Expression Regulation, Plant/genetics ; Molecular Sequence Data ; Sequence Homology, Amino Acid ; Sequence Homology, Nucleic Acid ; Yeasts/drug effects/genetics/metabolism ; },
abstract = {A novel ethanol-hypersensitive mutant, gek1, of Arabidopsis shows 10-100 times greater sensitivity to ethanol compared to the wild type, while it grows normally in the absence of ethanol, and responds normally to other alcohols and to environmental stresses such as heat shock and high salinity. Mapping of the gek1 locus indicated it is a previously unreported locus. In order to address the GEK1 function, we identified the GEK1 gene by means of map-based cloning. The GEK1 gene encodes a novel protein without any known functional motifs. Transgenic Arabidopsis plants overexpressing GEK1 displayed an enhanced tolerance to ethanol and acetaldehyde, suggesting that GEK1 is directly involved in the tolerance to those chemicals. By contrast, expression of GEK1 in E. coli and yeasts did not increase their tolerance to ethanol or acetaldehyde. Interestingly, a similarity search revealed that GEK1-related genes are conserved only in plants and archaea. These results might suggest that plants, and presumably archaea, have a novel mechanism for protection from acetaldehyde toxicity.},
}
@article {pmid15210688,
year = {2004},
author = {Armengaud, J and Urbonavicius, J and Fernandez, B and Chaussinand, G and Bujnicki, JM and Grosjean, H},
title = {N2-methylation of guanosine at position 10 in tRNA is catalyzed by a THUMP domain-containing, S-adenosylmethionine-dependent methyltransferase, conserved in Archaea and Eukaryota.},
journal = {The Journal of biological chemistry},
volume = {279},
number = {35},
pages = {37142-37152},
doi = {10.1074/jbc.M403845200},
pmid = {15210688},
issn = {0021-9258},
mesh = {Amino Acid Sequence ; Archaea ; Calorimetry, Differential Scanning ; Catalysis ; Catalytic Domain ; Chromatography, Gel ; DNA Methylation ; Databases as Topic ; Electrophoresis, Polyacrylamide Gel ; Eukaryotic Cells/metabolism ; Guanosine/*chemistry ; Methylation ; Methyltransferases/*chemistry ; Models, Molecular ; Molecular Sequence Data ; Plasmids/metabolism ; Protein Structure, Quaternary ; Protein Structure, Tertiary ; RNA/chemistry ; RNA, Transfer/*chemistry/metabolism ; Recombinant Proteins/chemistry/metabolism ; S-Adenosylmethionine/*chemistry ; Sequence Homology, Amino Acid ; Temperature ; Time Factors ; tRNA Methyltransferases/*chemistry ; },
abstract = {In sequenced genomes, genes belonging to the cluster of orthologous group COG1041 are exclusively, and almost ubiquitously, found in Eukaryota and Archaea but never in Bacteria. The corresponding gene products exhibit a characteristic Rossmann fold, S-adenosylmethionine-dependent methyltransferase domain in the C terminus and a predicted RNA-binding THUMP (thiouridine synthases, RNA methyltransferases, and pseudouridine synthases) domain in the N terminus. Recombinant PAB1283 protein from the archaeon Pyrococcus abyssi GE5, a member of COG1041, was purified and shown to behave as a monomeric 39-kDa entity. This protein (EC 2.1.1.32), now renamed (Pab)Trm-G10, which is extremely thermostable, forms a 1:1 complex with tRNA and catalyzes the adenosylmethionine-dependent methylation of the exocyclic amino group (N(2)) of guanosine located at position 10. Depending on the experimental conditions used, as well as the tRNA substrate tested, the enzymatic reaction leads to the formation of either N(2)-monomethyl (m(2)G) or N(2)-dimethylguanosine (m(2)(2)G). Interestingly, (Pab)Trm-G10 exhibits different domain organization and different catalytic site architecture from another, earlier characterized, tRNA-dimethyltransferase from Pyrococcus furiosus ((Pfu)Trm-G26, also known as (Pfu)Trm1, a member of COG1867) that catalyzes an identical two-step dimethylation of guanosine but at position 26 in tRNAs and is also conserved among all sequenced Eukaryota and Archaea. The co-occurrence of these two guanosine dimethyltransferases in both Archaea and Eukaryota but not in Bacteria is a hallmark of distinct tRNAs maturation strategies between these domains of life.},
}
@article {pmid15196459,
year = {2004},
author = {Ouhammouch, M},
title = {Transcriptional regulation in Archaea.},
journal = {Current opinion in genetics &amp; development},
volume = {14},
number = {2},
pages = {133-138},
doi = {10.1016/j.gde.2004.01.002},
pmid = {15196459},
issn = {0959-437X},
mesh = {Archaea/*genetics/physiology ; Down-Regulation/physiology ; Gene Expression Regulation, Archaeal/*physiology ; Genomics ; Transcription, Genetic/*physiology ; Up-Regulation ; },
abstract = {During the past few decades, it has become clear that microorganisms can thrive under the most diverse conditions, including extremes of temperature, pressure, salinity and pH. Most of these extremophilic organisms belong to the third domain of life, that of the Archaea. The organisms of this domain are of particular interest because most informational systems that are associated with archaeal genomes and their expression are reminiscent of those seen in Eucarya, whereas, most of their metabolic aspects are similar to those of Bacteria. A better understanding of the regulatory mechanisms of gene expression in Archaea will, therefore, help to integrate the body of knowledge regarding the regulatory mechanisms that underlie gene expression in all three domains of life.},
}
@article {pmid15187186,
year = {2004},
author = {Szurmant, H and Ordal, GW},
title = {Diversity in chemotaxis mechanisms among the bacteria and archaea.},
journal = {Microbiology and molecular biology reviews : MMBR},
volume = {68},
number = {2},
pages = {301-319},
pmid = {15187186},
issn = {1092-2172},
support = {R01 GM054365/GM/NIGMS NIH HHS/United States ; R01 GM54365/GM/NIGMS NIH HHS/United States ; },
mesh = {Archaea/genetics/*metabolism ; Archaeal Proteins/genetics/*metabolism ; Bacteria/genetics/*metabolism ; Bacterial Proteins/genetics/*metabolism ; *Chemotaxis/genetics ; Forecasting ; Gene Dosage ; Gene Expression Regulation, Bacterial ; *Genetic Variation ; Models, Biological ; Phylogeny ; Signal Transduction ; },
abstract = {The study of chemotaxis describes the cellular processes that control the movement of organisms toward favorable environments. In bacteria and archaea, motility is controlled by a two-component system involving a histidine kinase that senses the environment and a response regulator, a very common type of signal transduction in prokaryotes. Most insights into the processes involved have come from studies of Escherichia coli over the last three decades. However, in the last 10 years, with the sequencing of many prokaryotic genomes, it has become clear that E. coli represents a streamlined example of bacterial chemotaxis. While general features of excitation remain conserved among bacteria and archaea, specific features, such as adaptational processes and hydrolysis of the intracellular signal CheY-P, are quite diverse. The Bacillus subtilis chemotaxis system is considerably more complex and appears to be similar to the one that existed when the bacteria and archaea separated during evolution, so that understanding this mechanism should provide insight into the variety of mechanisms used today by the broad sweep of chemotactic bacteria and archaea. However, processes even beyond those used in E. coli and B. subtilis have been discovered in other organisms. This review emphasizes those used by B. subtilis and these other organisms but also gives an account of the mechanism in E. coli.},
}
@article {pmid15168616,
year = {2004},
author = {Serrano, A and Perez-Castiñeira, JR and Baltscheffsky, H and Baltscheffsky, M},
title = {Proton-pumping inorganic pyrophosphatases in some archaea and other extremophilic prokaryotes.},
journal = {Journal of bioenergetics and biomembranes},
volume = {36},
number = {1},
pages = {127-133},
doi = {10.1023/b:jobb.0000019604.49875.b3},
pmid = {15168616},
issn = {0145-479X},
mesh = {Amino Acid Sequence ; Archaea/*enzymology ; Cell Membrane/chemistry/*physiology ; Enzyme Activation ; Enzyme Stability ; Inorganic Pyrophosphatase/*chemistry/genetics/*metabolism ; Molecular Conformation ; Molecular Sequence Data ; Prokaryotic Cells/*enzymology ; Protein Structure, Tertiary ; Sequence Homology, Amino Acid ; Temperature ; },
abstract = {Comparative studies between the proton-pumping, membrane-bound inorganic pyrophosphatases (H(+)-PPases) from hyperthermophilic and thermophilic prokaryotes and those from mesophilic organisms can now be performed because of very recent sequence data. Typical overall factors that contribute to protein thermostability are found in H(+)-PPases from extremophiles; nevertheless, putative active site motifs of this class of enzymes may be identical over the whole range of average growth temperatures of the compared prokaryotes. Heterologous expression in yeast of H(+)-PPases from organisms spanning a wide range of thermal habitats has allowed the biochemical comparison among these proteins within the same system, ensuring that differences observed are due to intrinsic characteristics of the proteins and not to their interactions with different cellular environments. On the other hand, the availability of H(+)-PPase sequences from a variety of sources have permitted molecular phylogenetic studies of this class of proton pumps, thus providing information about their general structural and functional properties. A great step forward may be expected when one of the several groups now attempting crystallization and 3D structural determination of H(+)-PPases will be successful.},
}
@article {pmid15168612,
year = {2004},
author = {Kletzin, A and Urich, T and Müller, F and Bandeiras, TM and Gomes, CM},
title = {Dissimilatory oxidation and reduction of elemental sulfur in thermophilic archaea.},
journal = {Journal of bioenergetics and biomembranes},
volume = {36},
number = {1},
pages = {77-91},
pmid = {15168612},
issn = {0145-479X},
mesh = {Archaea/*physiology ; Cell Membrane/*physiology ; Energy Transfer/*physiology ; Oxidation-Reduction ; Oxidoreductases/*metabolism ; Signal Transduction/physiology ; Sulfur/*metabolism ; },
abstract = {The oxidation and reduction of elemental sulfur and reduced inorganic sulfur species are some of the most important energy-yielding reactions for microorganisms living in volcanic hot springs, solfataras, and submarine hydrothermal vents, including both heterotrophic, mixotrophic, and chemolithoautotrophic, carbon dioxide-fixing species. Elemental sulfur is the electron donor in aerobic archaea like Acidianus and Sulfolobus. It is oxidized via sulfite and thiosulfate in a pathway involving both soluble and membrane-bound enzymes. This pathway was recently found to be coupled to the aerobic respiratory chain, eliciting a link between sulfur oxidation and oxygen reduction at the level of the respiratory heme copper oxidase. In contrast, elemental sulfur is the electron acceptor in a short electron transport chain consisting of a membrane-bound hydrogenase and a sulfur reductase in (facultatively) anaerobic chemolithotrophic archaea Acidianus and Pyrodictium species. It is also the electron acceptor in organoheterotrophic anaerobic species like Pyrococcus and Thermococcus, however, an electron transport chain has not been described as yet. The current knowledge on the composition and properties of the aerobic and anaerobic pathways of dissimilatory elemental sulfur metabolism in thermophilic archaea is summarized in this contribution.},
}
@article {pmid15168611,
year = {2004},
author = {Hedderich, R},
title = {Energy-converting [NiFe] hydrogenases from archaea and extremophiles: ancestors of complex I.},
journal = {Journal of bioenergetics and biomembranes},
volume = {36},
number = {1},
pages = {65-75},
pmid = {15168611},
issn = {0145-479X},
mesh = {Archaea/*physiology ; Cell Membrane/*physiology ; Conserved Sequence ; Electron Transport Complex I/*chemistry/*metabolism ; Energy Transfer/*physiology ; Evolution, Molecular ; Halobacteriales/physiology ; Hydrogenase/*chemistry/*metabolism ; Oxidation-Reduction ; Sequence Homology, Amino Acid ; },
abstract = {[NiFe] hydrogenases are well-characterized enzymes that have a key function in the H2 metabolism of various microorganisms. In the recent years a subfamily of [NiFe] hydrogenases with unique properties has been identified. The members of this family form multisubunit membrane-bound enzyme complexes composed of at least four hydrophilic and two integral membrane proteins. These six conserved subunits, which built the core of these hydrogenases, have closely related counterparts in energy-conserving NADH:quinone oxidoreductases (complex I). However, the reaction catalyzed by these hydrogenases differs significantly from the reaction catalyzed by complex I. For some of these hydrogenases the physiological role is to catalyze the reduction of H+ with electrons derived from reduced ferredoxins or poly-ferredoxins. This exergonic reaction is coupled to energy conservation by means of electron-transport phosphorylation. Other members of this hydrogenase family mainly function to provide the cell with reduced ferredoxin with H2 as electron donor in a reaction driven by reverse electron transport. As complex I these hydrogenases function as ion pumps and have therefore been designated as energy-converting [NiFe] hydrogenases.},
}
@article {pmid15168605,
year = {2004},
author = {Albers, SV and Koning, SM and Konings, WN and Driessen, AJ},
title = {Insights into ABC transport in archaea.},
journal = {Journal of bioenergetics and biomembranes},
volume = {36},
number = {1},
pages = {5-15},
pmid = {15168605},
issn = {0145-479X},
mesh = {ATP-Binding Cassette Transporters/*chemistry/genetics/*metabolism ; Amino Acid Sequence ; Archaea/*physiology ; Archaeal Proteins/chemistry/genetics/metabolism ; Biological Transport, Active/physiology ; Cell Membrane/*physiology ; Gene Expression Regulation, Archaeal/*physiology ; Molecular Sequence Data ; Protein Binding ; Protein Sorting Signals/*physiology ; Pyrococcus/physiology ; Sequence Homology, Amino Acid ; Signal Transduction/*physiology ; },
abstract = {In archaea, ATP-binding cassette (ABC) transporters play a crucial role in substrate uptake, export, and osmoregulation. Archael substrate-binding-protein-dependent ABC transporters are equipped with a very high affinity for their cognate substrates which provide these organisms with the ability to efficiently scavenge substrates from their environment even when present only at low concentration. Further adaptations to the archaeal way of life are especially found in the domain organization and anchoring of the substrate-binding proteins to the membrane. Examination of the signal peptides of binding proteins of 14 archael genomes showed clear differences between euryarchaeotes and crenarchaeotes. Furthermore, a profiling and comparison of ABC transporters in the three sequenced pyrococcal strains was performed.},
}
@article {pmid15168604,
year = {2004},
author = {Schäfer, G},
title = {Introduction. Extremophilic archaea and bacteria.},
journal = {Journal of bioenergetics and biomembranes},
volume = {36},
number = {1},
pages = {3-4},
pmid = {15168604},
issn = {0145-479X},
mesh = {Archaea/*physiology ; Archaeal Proteins/metabolism ; *Bacterial Physiological Phenomena ; Bacterial Proteins/metabolism ; Biological Transport, Active/physiology ; Cell Membrane/*physiology ; Energy Metabolism/*physiology ; Gene Expression Regulation, Archaeal/*physiology ; Gene Expression Regulation, Bacterial/*physiology ; Signal Transduction/*physiology ; },
}
@article {pmid15168532,
year = {2004},
author = {Tamura, N and Tamura, T},
title = {[Proteases in Archaea].},
journal = {Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme},
volume = {49},
number = {7 Suppl},
pages = {1075-1076},
pmid = {15168532},
issn = {0039-9450},
mesh = {ATP-Dependent Proteases ; Adenosine Triphosphatases/physiology ; Adenosine Triphosphate/metabolism ; Bacterial Proteins/metabolism ; Cysteine Endopeptidases/*physiology ; Heat-Shock Proteins/*physiology ; Multienzyme Complexes/*physiology ; Proteasome Endopeptidase Complex ; Serine Endopeptidases/*physiology ; Thermoplasma/*enzymology/genetics/*metabolism ; },
}
@article {pmid15168171,
year = {2004},
author = {Rusch, A and Amend, JP},
title = {Order-specific 16S rRNA-targeted oligonucleotide probes for (hyper)thermophilic archaea and bacteria.},
journal = {Extremophiles : life under extreme conditions},
volume = {8},
number = {5},
pages = {357-366},
pmid = {15168171},
issn = {1431-0651},
mesh = {Archaea/genetics ; Bacteria/genetics ; DNA Primers/genetics ; DNA Probes ; DNA, Archaeal/*genetics ; DNA, Bacterial/*genetics ; Genome, Bacterial ; In Situ Hybridization, Fluorescence ; Microscopy, Fluorescence ; Nucleic Acid Hybridization ; Oligonucleotides/*genetics ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA ; },
abstract = {New oligonucleotide probes were designed and evaluated for application in fluorescence in situ hybridization (FISH) studies on (hyper)thermophilic microbial communities--Arglo32, Tcoc164, and Aqui1197 target the 16S rRNA of Archaeoglobales, Thermococcales, and Aquificales, respectively. Both sequence information and experimental evaluation showed high coverage and specificity of all three probes. The signal intensity of Aqui1197 was improved by addition of a newly designed, unlabeled "helper" oligonucleotide, hAqui1045. It was shown that in addition to its function as a probe for Aquificales, Aqui1197 is suitable as a supplementary probe to extend the coverage of the domain-specific bacterial probe EUB338. In sediments from two hydrothermal seeps on Vulcano Island, Italy, the microbial community structure was analyzed by FISH with both established and the new oligonucleotide probes, showing the applicability of Arglo32, Tcoc164, and Aqui1197/hAqui1045 to natural samples. At both sites, all major groups of (hyper)thermophiles, except for methanogens, were detected: Crenarchaeota (19%, 16%), Thermococcales (14%, 22%), Archaeoglobales (14%, 12%), Aquificales (5%, 8%), Thermotoga/Thermosipho spp. (12%, 9%), Thermus sp. (12%, none), and thermophilic Bacillus sp. (12%, 8%).},
}
@article {pmid15166024,
year = {2004},
author = {Martínez-Bueno, M and Molina-Henares, AJ and Pareja, E and Ramos, JL and Tobes, R},
title = {BacTregulators: a database of transcriptional regulators in bacteria and archaea.},
journal = {Bioinformatics (Oxford, England)},
volume = {20},
number = {16},
pages = {2787-2791},
doi = {10.1093/bioinformatics/bth330},
pmid = {15166024},
issn = {1367-4803},
mesh = {Archaea/genetics/metabolism ; Archaeal Proteins/*genetics ; Bacteria/genetics/metabolism ; Bacterial Proteins/*genetics ; Database Management Systems ; *Databases, Genetic ; Documentation/*methods ; Gene Expression Regulation, Archaeal/genetics ; Gene Expression Regulation, Bacterial/genetics ; Information Storage and Retrieval/*methods ; Internet ; Sequence Analysis, DNA/*methods ; Transcription Factors/classification/*genetics ; },
abstract = {MOTIVATION: The BacTregulators database is intended to collect and to integrate information on proteins belonging to defined families of transcriptional regulators in prokaryotes.<br><br>RESULTS: The BacTregulators database currently contains data on two families of transcriptional regulators: AraC-XylS and TetR. The proteins included in the BacTregulators database have been identified by screening 123 genomes from archaea and bacteria and the SWISS-PROT and TrEMBL databases with profiles defining each family. As the result of an integration process, we have included 1326 different protein sequences from the AraC-XylS family and 1487 different protein sequences from the TetR family. The definition of an entry in BacTregulators is based on protein sequence, source organism, genome element and position in this genome element. The BacTregulators site allows the user to retrieve protein sequences, functional features and experimental evidence supporting the functions, references and the three-dimensional structure of the regulator when available. BacTregulators supplies an innovative tool that allows the researcher to obtain an integrated report that shows the data corresponding to other entries which are related by sequence similarity to the query entry. BacTregulators detects and classifies the regulators belonging to AraC-XylS and TetR families present in prokaryotic genomes, and thus contributes to a more accurate annotation of regulators in genomes. The information collected on each protein in the family can be useful to characterize a new regulator or compile information on the biological properties of a known regulator.<br><br>AVAILABILITY: The BacTregulators is available at www.bactregulators.org},
}
@article {pmid15162961,
year = {2004},
author = {Koga, Y},
title = {[Diversification of Bacteria, Archaea, and Eucarya--a hypothesis based on the enantiomeric glycerophospholipids].},
journal = {Seikagaku. The Journal of Japanese Biochemical Society},
volume = {76},
number = {4},
pages = {349-358},
pmid = {15162961},
issn = {0037-1017},
mesh = {*Archaea/cytology/genetics/metabolism ; *Bacteria/cytology/genetics/metabolism ; *Biological Evolution ; *Eukaryotic Cells/cytology/metabolism ; *Glycerophospholipids/metabolism ; Membrane Lipids/metabolism ; Phylogeny ; Stereoisomerism ; },
}
@article {pmid15150699,
year = {2004},
author = {Wan, XF and Bridges, SM and Boyle, JA},
title = {Revealing gene transcription and translation initiation patterns in archaea, using an interactive clustering model.},
journal = {Extremophiles : life under extreme conditions},
volume = {8},
number = {4},
pages = {291-299},
pmid = {15150699},
issn = {1431-0651},
mesh = {Archaea/*genetics ; Databases, Nucleic Acid ; *Gene Expression Regulation, Archaeal ; *Genes, Archaeal ; Halobacterium/genetics ; Multigene Family ; Open Reading Frames ; *Protein Biosynthesis ; Ribosomes/metabolism ; Sulfolobus/genetics ; *Transcription, Genetic ; },
abstract = {An interactive clustering model based on positional weight matrices is described and results obtained using the model to analyze gene regulation patterns in archaea are presented. The 5' flanking sequences of ORFs identified in four archaea, Sulfolobus solfataricus, Pyrobaculum aerophilum, Halobacterium sp. NRC-1, and Pyrococcus abyssi, were clustered using the model. Three regular patterns of clusters were identified for most ORFs. One showed genes with only a ribosome-binding site; another showed genes with a transcriptional regulatory region located at a constant location with respect to the start codon. A third pattern combined the previous two. Both P. aerophilum and Halobacterium sp. NRC-1 exhibited clusters of genes that lacked any regular pattern. Halobacterium sp. NRC-1 also presented regular features not seen in the other organisms. This group of archaea seems to use a combination of eubacterial and eukaryotic regulatory features as well as some unique to individual species. Our results suggest that interactive clustering may be used to examine the divergence of the gene regulatory machinery in archaea and to identify the presence of archaea-specific gene regulation patterns.},
}
@article {pmid15145058,
year = {2004},
author = {Fuglsang, A},
title = {Compositional nonrandomness upstream of start codons in archaebacteria.},
journal = {Gene},
volume = {332},
number = {},
pages = {89-95},
doi = {10.1016/j.gene.2004.02.022},
pmid = {15145058},
issn = {0378-1119},
mesh = {5' Flanking Region/*genetics ; Algorithms ; Archaea/*genetics ; Archaeal Proteins/genetics ; Base Composition ; Base Sequence ; Codon, Initiator/*genetics ; Genome, Archaeal ; Statistics as Topic ; },
abstract = {Since the regions directing transcriptional and translational initiation in archaebacteria are poorly characterized, the purpose of this study was to characterize them using measurements of nonrandomness upstream of start codons on eight fully sequenced archaebacterial genomes. Two distinctly different regions with conservation were identified. The location of the first corresponded well to the classical Shine-Dalgarno region (phi peak), and the other was located approximately 20-35 nucleotides upstream of start codons (alpha region), but both regions are not present in all strains. The composition of the region around the phi peak showed an overrepresentation of guanine, whereas composition in the alpha region had an overrepresentation of adenine and thymine. It is furthermore shown that the alpha region surprisingly is associated with start codon usage and other characteristics of the genes. The alpha region is likely to correspond to TATA-boxes and thereby indicates use of leaderless (or short-leadered) transcripts.},
}
@article {pmid15133100,
year = {2004},
author = {Maggio-Hall, LA and Claas, KR and Escalante-Semerena, JC},
title = {The last step in coenzyme B(12) synthesis is localized to the cell membrane in bacteria and archaea.},
journal = {Microbiology (Reading, England)},
volume = {150},
number = {Pt 5},
pages = {1385-1395},
doi = {10.1099/mic.0.26952-0},
pmid = {15133100},
issn = {1350-0872},
support = {R01 GM040313/GM/NIGMS NIH HHS/United States ; GM40413/GM/NIGMS NIH HHS/United States ; GM08349/GM/NIGMS NIH HHS/United States ; },
mesh = {Archaeal Proteins/genetics/metabolism ; Bacterial Proteins/genetics/metabolism ; Cell Membrane/*enzymology ; Cobamides/*biosynthesis/metabolism ; Escherichia coli/*enzymology ; Membrane Proteins/genetics/metabolism ; Methanobacterium/*enzymology ; Nitrogenous Group Transferases/genetics/*metabolism ; Recombinant Fusion Proteins/genetics/metabolism ; Salmonella enterica/*enzymology ; Ultracentrifugation ; },
abstract = {In Salmonella enterica, the last step of the synthesis of adenosylcobamide is catalysed by the cobalamin synthase enzyme encoded by the cobS gene of this bacterium. Overexpression of the S. enterica cobS gene in Escherichia coli elicited the accumulation of the phage shock protein PspA, a protein whose expression has been linked to membrane stress. Resolution of inner and outer membranes of S. enterica by isopycnic density ultracentrifugation showed CobS activity associated with the inner membrane, a result that was confirmed using antibodies against CobS. Computer analysis of the predicted amino acid sequence of CobS suggested it was an integral membrane protein. Results of experiments performed with strains carrying plasmids encoding CobS-alkaline phosphatase or CobS-beta-galactosidase protein fusions were consistent with the membrane localization of the CobS protein. Modifications to the predicted model were made based on data obtained from experiments using protein fusions. The function encoded by the cobS orthologue in the methanogenic archaeon Methanobacterium thermoautotrophicum strain deltaH compensated for the lack of CobS during cobalamin synthesis in cobS strains of S. enterica. Cobalamin synthase activity was also detected in a membrane preparation of M. thermoautotrophicum. It was concluded that the assembly of the nucleotide loop of adenosylcobamides in archaea and bacteria is a membrane-associated process. Possible reasons for the association of adenosylcobamide biosynthetic enzymes with the cell membrane are discussed.},
}
@article {pmid15131255,
year = {2004},
author = {Friedrich-Heineken, E and Hübscher, U},
title = {The Fen1 extrahelical 3'-flap pocket is conserved from archaea to human and regulates DNA substrate specificity.},
journal = {Nucleic acids research},
volume = {32},
number = {8},
pages = {2520-2528},
pmid = {15131255},
issn = {1362-4962},
mesh = {Amino Acid Sequence ; Archaeoglobus fulgidus/*enzymology ; Base Sequence ; *Conserved Sequence ; DNA/genetics/*metabolism ; Flap Endonucleases/*chemistry/genetics/*metabolism ; Humans ; Molecular Sequence Data ; Mutation/genetics ; Proliferating Cell Nuclear Antigen/metabolism ; Protein Binding ; Substrate Specificity ; },
abstract = {Fen1 is a key enzyme for the maintenance of genetic stability in archaea and eukaryotes and is classified as a tumor suppressor. Very recent structural data obtained from Archaeoglobus fulgidus Fen1 suggest that an extrahelical 3'-flap pocket is responsible for substrate specificity, by binding to the unpaired 3'-flap and by opening and kinking the DNA. Since the extrahelical 3'-flap pocket in archaeal Fen1 contains seven amino acids that are conserved to a great extent in human Fen1, we have mutated the four conserved or all seven amino acids in the human Fen1 extrahelical 3'-flap pocket to alanine. Our data suggest that the human extrahelical 3'-flap pocket mutants have lost substrate specificity to the double-flap DNA. Moreover, loss of high affinity for the unpaired 3'-flap suggests that the extrahelical 3'-flap pocket is essential for recognition and processing of the 'physiological' template. Human PCNA could stimulate the human Fen1 extrahelical 3'-flap pocket mutants but not restore their specificity. Thus the substrate specificity of Fen1 has been functionally conserved over a billion years from archaea to human.},
}
@article {pmid15130130,
year = {2004},
author = {Lange, U and Hausner, W},
title = {Transcriptional fidelity and proofreading in Archaea and implications for the mechanism of TFS-induced RNA cleavage.},
journal = {Molecular microbiology},
volume = {52},
number = {4},
pages = {1133-1143},
doi = {10.1111/j.1365-2958.2004.04039.x},
pmid = {15130130},
issn = {0950-382X},
mesh = {Archaea/genetics/*metabolism ; Archaeal Proteins/*metabolism ; Base Sequence ; DNA Footprinting ; DNA-Directed RNA Polymerases/*metabolism ; Exodeoxyribonucleases/metabolism ; Methanococcus/genetics/metabolism ; RNA, Archaeal/chemistry/*metabolism ; RNA, Messenger/chemistry/metabolism ; Ribonucleases/metabolism ; Templates, Genetic ; Transcription Factors/*metabolism ; *Transcription, Genetic ; },
abstract = {We have addressed the question whether TFS, a protein that stimulates the intrinsic cleavage activity of the archaeal RNA polymerase, is able to improve the fidelity of transcription in Methanococcus. Using non-specific transcription experiments, we could demonstrate that misincorporation of non-templated nucleotides is reduced in the presence of TFS. A more detailed analysis revealed that elongation complexes containing a misincorporated nucleotide were arrested, but could be reactivated by TFS. RNase as well as exonuclease III footprinting experiments demonstrated that this arrest was not combined with extended backtracking. Analysis of paused elongation complexes demonstrated that TFS is able to induce a cleavage resynthesis cycle in such complexes, which resulted in the accumulation of dinucleotides corresponding to the last two nucleotides of the transcript. Further analysis of cleavage products revealed that, even under conditions that strongly promote misincorporation, still 50% of the released dinucleotides were correctly incorporated. Therefore, we assume that pausing of elongation complexes is an important determinant of TFS-induced RNA cleavage from the 3' end. As the incorporation rate of wrong nucleotides is about 700-fold reduced, it is possible that this delay also provides an appropriate time window for cleavage induction in order to maintain transcriptional fidelity by preventing misincorporation.},
}
@article {pmid15125206,
year = {2004},
author = {Shatalkin, AI},
title = {[Highest level of division in classification of organisms. 2. Archaebacteria, eubacteria and eukaryotes].},
journal = {Zhurnal obshchei biologii},
volume = {65},
number = {2},
pages = {99-115},
pmid = {15125206},
issn = {0044-4596},
mesh = {Archaea/*classification/cytology/physiology ; Bacteria/*classification/cytology ; Bacterial Physiological Phenomena ; Biological Evolution ; Eukaryotic Cells/*classification/cytology/parasitology ; Gene Expression ; },
abstract = {In three-domain system of organic world archaebacteria are considered as the third form of life alongside with eubacteria and eukaryotes. The author gives brief characteristics of all three groups with special focus on such diagnostic attributes as: plasmatic membrane and cellular wall, flagella, protein transcription, replication, topoisomerases, transcription, translation, glycosylation, chaperons and chaperonins, proteasomes and exosomes, histones, ATP-ases. The three-domain system has been proposed by several scientists but principal ideas were put by C. Woese. The systematics according Woese should reflect contemporary level of our knowledge of organisms. In the historical plan it once had to refuse dividing the organic world into plants and animals but accept the division into prokaryotes and eukaryotes. The science however goes further and turns now to the new level of generalizations based on the molecular aspects of cellular structures and processes. From this point of view, both plants and animals are uniform. As to prokaryotes they appeared to be non-monolithic group because of essentially different transcriptional and translational mechanisms. Therefore the detachment of archaebacteria as an independent group was the important step in the development of systematics. At the same time the three-domain system of organisms is typological and requires correction according to data on phylogenetic relatedness of these groups.},
}
@article {pmid15119824,
year = {2004},
author = {Grogan, DW},
title = {Stability and repair of DNA in hyperthermophilic Archaea.},
journal = {Current issues in molecular biology},
volume = {6},
number = {2},
pages = {137-144},
pmid = {15119824},
issn = {1467-3037},
mesh = {Archaea/*genetics/physiology ; Base Pair Mismatch/physiology ; DNA/*physiology ; DNA Repair/*physiology ; Hot Temperature ; },
abstract = {Evolutionary and physiological considerations argue that study of hyperthermophilic archaea should reveal new molecular aspects of DNA stabilization and repair. So far, these unusual prokaryotes have yielded a number of genes and enzymatic activities consistent with known mechanisms of excision repair, photo-reversal, and trans-lesion synthesis. However, other DNA enzymes of hyperthermophilic archaea show novel biochemical properties which may be related to DNA stability or repair at extremely high temperature but which remain difficult to evaluate rigorously in vivo. Perhaps the most striking feature of the hyperthermophilic archaea is that all of them whose genomes have been sequenced lack key genes of both the nucleotide excision repair and DNA mismatch repair pathways, which are otherwise highly conserved in biology. Although the growth properties of these micro-organisms hinder experimentation, there is evidence that some systems of excision repair and mutation avoidance operate in Sulfolobus spp. It will therefore be of strategic significance in the next few years to formulate and test hypotheses in Sulfolobus spp. and other hyperthermophilic archaea regarding mechanisms and gene products involved in the repair of UV photoproducts and DNA mismatches.},
}
@article {pmid15112239,
year = {2004},
author = {Martin, W},
title = {Pathogenic archaebacteria: do they not exist because archaebacteria use different vitamins?.},
journal = {BioEssays : news and reviews in molecular, cellular and developmental biology},
volume = {26},
number = {5},
pages = {592-3; author reply 593},
doi = {10.1002/bies.20044},
pmid = {15112239},
issn = {0265-9247},
mesh = {Animals ; Archaea/*metabolism/*pathogenicity ; Eukaryotic Cells/metabolism/microbiology ; Humans ; Vitamins/*metabolism ; },
}
@article {pmid15096613,
year = {2004},
author = {Freitas, TA and Hou, S and Dioum, EM and Saito, JA and Newhouse, J and Gonzalez, G and Gilles-Gonzalez, MA and Alam, M},
title = {Ancestral hemoglobins in Archaea.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {101},
number = {17},
pages = {6675-6680},
pmid = {15096613},
issn = {0027-8424},
support = {R01 HL064038/HL/NHLBI NIH HHS/United States ; HL-64038/HL/NHLBI NIH HHS/United States ; },
mesh = {Amino Acid Sequence ; Archaea/*chemistry ; Base Sequence ; Carbon Monoxide/metabolism ; DNA Primers ; Hemoglobins/*chemistry/genetics/metabolism ; Models, Molecular ; Molecular Sequence Data ; Nitric Oxide/metabolism ; Oxygen/metabolism ; Phylogeny ; Protein Binding ; Protein Conformation ; Sequence Homology, Amino Acid ; Spectrophotometry, Ultraviolet ; },
abstract = {Hemoglobins are ubiquitous in Eukarya and Bacteria but, until now, have not been found in Archaea. A phylogenetic analysis of the recently revealed microbial family of globin-coupled heme-based sensors suggests that these sensors descended from an ancient globin-only progenitor, or a protoglobin (Pgb). Here, we report the discovery and characterization of two Pgbs from the Archaea: ApPgb from the obligately aerobic hyperthermophile Aeropyrum pernix, and MaPgb from the strictly anaerobic methanogen Methanosarcina acetivorans. Both ApPgb and MaPgb bind molecular oxygen, nitric oxide, and carbon monoxide by means of a heme moiety that is coordinated to the protein through the F8 histidine (histidine 120). We postulate that these archaeal globins are the ancestors of contemporary hemoglobins.},
}
@article {pmid15074036,
year = {2004},
author = {Iudina, TG and Briukhanov, AL and Netrusov, AI},
title = {[Susceptibility of archaea to the antibiotic effect of the parasporal inclusion proteins from Bacillus thuringiensis subspecies].},
journal = {Mikrobiologiia},
volume = {73},
number = {1},
pages = {25-30},
pmid = {15074036},
issn = {0026-3656},
mesh = {Archaea/*drug effects/growth &amp; development ; Bacillus thuringiensis/chemistry/*metabolism ; Bacterial Proteins/isolation &amp; purification/*pharmacology ; Inclusion Bodies/metabolism ; Methanosarcina barkeri/drug effects ; Microbial Sensitivity Tests ; Species Specificity ; Spores, Bacterial/metabolism ; },
abstract = {The proteins of parasporal inclusions from three Bacillus thuringiensis subspecies (kurstaki, amagiensis, and monterrey) inhibited growth of methanogenic archaea of two species belonging to two genera, Methanobrevibacter arboriphilus and Methanosarcina barkeri. The minimal inhibitory concentrations of these proteins were 20 to 50 micrograms/ml. Lysozyme exhibited similar bactericidal effect on archaea. The perspective of comparative studies on the effect of polyfunctional proteins on bacteria and archaea is discussed.},
}
@article {pmid15067114,
year = {2004},
author = {Lepp, PW and Brinig, MM and Ouverney, CC and Palm, K and Armitage, GC and Relman, DA},
title = {Methanogenic Archaea and human periodontal disease.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {101},
number = {16},
pages = {6176-6181},
pmid = {15067114},
issn = {0027-8424},
support = {R01 DE013541/DE/NIDCR NIH HHS/United States ; R01-DE13541/DE/NIDCR NIH HHS/United States ; },
mesh = {Archaea/classification/genetics/*pathogenicity ; Base Sequence ; DNA Primers ; Humans ; Molecular Sequence Data ; Periodontal Diseases/*microbiology ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal/genetics ; },
abstract = {Archaea have been isolated from the human colon, vagina, and oral cavity, but have not been established as causes of human disease. In this study, we reveal a relationship between the severity of periodontal disease and the relative abundance of archaeal small subunit ribosomal RNA genes (SSU rDNA) in the subgingival crevice by using quantitative PCR. Furthermore, the relative abundance of archaeal small subunit rDNA decreased at treated sites in association with clinical improvement. Archaea were harbored by 36% of periodontitis patients and were restricted to subgingival sites with periodontal disease. The presence of archaeal cells at these sites was confirmed by fluorescent in situ hybridization. The archaeal community at diseased sites was dominated by a Methanobrevibacter oralis-like phylotype and a distinct Methanobrevibacter subpopulation related to archaea that inhabit the gut of numerous animals. We hypothesize that methanogens participate in syntrophic relationships in the subgingival crevice that promote colonization by secondary fermenters during periodontitis. Because they are potential alternative syntrophic partners, our finding of larger Treponema populations sites without archaea provides further support for this hypothesis.},
}
@article {pmid15066859,
year = {2004},
author = {Edgcomb, VP and Molyneaux, SJ and Saito, MA and Lloyd, K and Böer, S and Wirsen, CO and Atkins, MS and Teske, A},
title = {Sulfide ameliorates metal toxicity for deep-sea hydrothermal vent archaea.},
journal = {Applied and environmental microbiology},
volume = {70},
number = {4},
pages = {2551-2555},
pmid = {15066859},
issn = {0099-2240},
mesh = {Anaerobiosis ; Archaea/*drug effects/growth &amp; development ; Hot Temperature ; Metals, Heavy/*toxicity ; Methanococcales/drug effects/growth &amp; development ; Pyrococcus/drug effects/growth &amp; development ; Seawater/*microbiology ; Sulfides/*pharmacology ; Thermococcus/drug effects/growth &amp; development ; Water Pollutants, Chemical/toxicity ; },
abstract = {The chemical stress factors for microbial life at deep-sea hydrothermal vents include high concentrations of heavy metals and sulfide. Three hyperthermophilic vent archaea, the sulfur-reducing heterotrophs Thermococcus fumicolans and Pyrococcus strain GB-D and the chemolithoautotrophic methanogen Methanocaldococcus jannaschii, were tested for survival tolerance to heavy metals (Zn, Co, and Cu) and sulfide. The sulfide addition consistently ameliorated the high toxicity of free metal cations by the formation of dissolved metal-sulfide complexes as well as solid precipitates. Thus, chemical speciation of heavy metals with sulfide allows hydrothermal vent archaea to tolerate otherwise toxic metal concentrations in their natural environment.},
}
@article {pmid15066817,
year = {2004},
author = {Elshahed, MS and Najar, FZ and Roe, BA and Oren, A and Dewers, TA and Krumholz, LR},
title = {Survey of archaeal diversity reveals an abundance of halophilic Archaea in a low-salt, sulfide- and sulfur-rich spring.},
journal = {Applied and environmental microbiology},
volume = {70},
number = {4},
pages = {2230-2239},
pmid = {15066817},
issn = {0099-2240},
mesh = {Archaea/*genetics/isolation &amp; purification/*metabolism ; Base Sequence ; Cloning, Molecular ; Crenarchaeota/genetics/isolation &amp; purification/metabolism ; DNA, Archaeal/genetics ; Fresh Water/analysis/*microbiology ; Genetic Variation ; Halobacteriales/genetics/isolation &amp; purification/metabolism ; Molecular Sequence Data ; Oklahoma ; Phylogeny ; Sodium Chloride/analysis ; Sulfides/analysis ; Sulfur/analysis ; },
abstract = {The archaeal community in a sulfide- and sulfur-rich spring with a stream water salinity of 0.7 to 1.0% in southwestern Oklahoma was studied by cloning and sequencing of 16S rRNA genes. Two clone libraries were constructed from sediments obtained at the hydrocarbon-exposed source of the spring and the microbial mats underlying the water flowing from the spring source. Analysis of 113 clones from the source library and 65 clones from the mat library revealed that the majority of clones belonged to the kingdom Euryarchaeota, while Crenarchaeota represented less than 10% of clones. Euryarchaeotal clones belonged to the orders Methanomicrobiales, Methanosarcinales, and Halobacteriales, as well as several previously described lineages with no pure-culture representatives. Those within the Halobacteriales represented 36% of the mat library and 4% of the source library. All cultivated members of this order are obligately aerobic halophiles. The majority of halobacterial clones encountered were not affiliated with any of the currently described genera of the family Halobacteriaceae. Measurement of the salinity at various locations at the spring, as well as along vertical gradients, revealed that soils adjacent to spring mats have a much higher salinity (NaCl concentrations as high as 32%) and a lower moisture content than the spring water, presumably due to evaporation. By use of a high-salt-plus-antibiotic medium, several halobacterial isolates were obtained from the microbial mats. Analysis of 16S rRNA genes indicated that all the isolates were members of the genus Haloferax. All isolates obtained grew at a wide range of salt concentrations, ranging from 6% to saturation, and all were able to reduce elemental sulfur to sulfide. We reason that the unexpected abundance of halophilic Archaea in such a low-salt, highly reduced environment could be explained by their relatively low salt requirement, which could be satisfied in specific locations of the shallow spring via evaporation, and their ability to grow under the prevalent anaerobic conditions in the spring, utilizing zero-valent sulfur compounds as electron acceptors. This study demonstrates that members of the Halobacteriales are not restricted to their typical high-salt habitats, and we propose a role for the Halobacteriales in sulfur reduction in natural ecosystems.},
}
@article {pmid15066037,
year = {2004},
author = {Boucher, Y and Kamekura, M and Doolittle, WF},
title = {Origins and evolution of isoprenoid lipid biosynthesis in archaea.},
journal = {Molecular microbiology},
volume = {52},
number = {2},
pages = {515-527},
doi = {10.1111/j.1365-2958.2004.03992.x},
pmid = {15066037},
issn = {0950-382X},
mesh = {Alkyl and Aryl Transferases/genetics/metabolism ; Archaea/chemistry/enzymology/genetics/*metabolism ; Archaeal Proteins/*genetics ; *Biological Evolution ; Genome, Archaeal ; Glycerolphosphate Dehydrogenase/genetics/metabolism ; Glycerophosphates/metabolism ; Lipids/*biosynthesis/chemistry ; Membrane Lipids/*biosynthesis/chemistry/metabolism ; Mevalonic Acid/metabolism ; Molecular Sequence Data ; Phylogeny ; Terpenes/*metabolism ; },
abstract = {A characteristic feature of the domain archaea are the lipids forming the hydrophobic core of their cell membrane. These unique lipids are composed of isoprenoid side-chains stereospecifically ether linked to sn-glycerol-1-phosphate. Recently, considerable progress has been made in characterizing the enzymes responsible for the synthesis of archaeal lipids. However, little is known about their evolution. To better understand how this unique biosynthetic apparatus came to be, large-scale database surveys and phylogenetic analyses were performed. All characterized enzymes involved in the biosynthesis of isoprenoid side-chains and the glycerol phosphate backbone along with their assembly in ether lipids were included in these analyses. The sequence data available in public databases was complemented by an in-depth sampling of isoprenoid lipid biosynthesis genes from multiple genera of the archaeal order Halobacteriales, allowing us to look at the evolution of these enzymes on a smaller phylogenetic scale. This investigation of the isoprenoid biosynthesis apparatus of archaea on small and large phylogenetic scales reveals that it evolved through a combination of evolutionary processes, including the co-option of ancestral enzymes, modification of enzymatic specificity, orthologous and non-orthologous gene displacement, integration of components from eukaryotes and bacteria and lateral gene transfer within and between archaeal orders.},
}
@article {pmid15049918,
year = {2004},
author = {Kemnitz, D and Chin, KJ and Bodelier, P and Conrad, R},
title = {Community analysis of methanogenic archaea within a riparian flooding gradient.},
journal = {Environmental microbiology},
volume = {6},
number = {5},
pages = {449-461},
doi = {10.1111/j.1462-2920.2004.00573.x},
pmid = {15049918},
issn = {1462-2912},
mesh = {Archaea/classification/*genetics/metabolism ; DNA, Ribosomal/analysis ; *Ecosystem ; Fresh Water ; Methane/*metabolism ; Molecular Sequence Data ; Netherlands ; Phylogeny ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal/analysis ; *Soil Microbiology ; },
abstract = {Anoxic soils in river floodplains (or riparian soils) are a source of methane emission. However, little is known about the ecology and community structure of archaeal methanogenic microbes, which are a crucial component of methane flux in those habitats. We studied the archaeal community in the vertical profile of four different sites along the River Waal in the Netherlands. These sites differ in their annual flooding regime ranging from never or seldom to permanently flooded. The archaeal community structure has been characterized by terminal restriction fragment length polymorphism (T-RFLP) and comparative sequence analysis of the archaeal SSU rRNA gene and the mcrA gene. The latter gene codes for the alpha-subunit of methyl-coenzyme M reductase. Additionally, the potential methanogenic activity was determined by incubation of soil slurries under anoxic conditions. The community composition differed only slightly with the depth of the soil (0-20 cm). However, the diversity of archaeal SSU rRNA genes increased with the frequency of flooding. Terminal restriction fragment length polymorphism analysis of mcrA gene amplicons confirmed the results concerning methanogenic archaea. In the never and rarely flooded soils, crenarchaeotal sequences were the dominant group. In the frequently and permanently flooded soils, Methanomicrobiaceae, Methanobacteriaceae, Methanosarcinaceae and the uncultured Rice Clusters IV and VI (Crenarchaeota) were detectable independently from duration of anoxic conditions. Methanosaetaceae, on the other hand, were only found in the permanently and frequently flooded soils under conditions where concentrations of acetate were < 30 microM. The results indicate that methanogens as well as other archaea occupy characteristic niches according to the flooding conditions in the field. Methanosaetaceae, in particular, seem to be adapted (or proliferate at) to low acetate concentrations.},
}
@article {pmid15049143,
year = {2004},
author = {Tsujimura, M and Kawarabayasi, Y},
title = {[Comprehensive expression of thermo-stable proteins in acidothermophilic archaea].},
journal = {Seikagaku. The Journal of Japanese Biochemical Society},
volume = {76},
number = {2},
pages = {149-154},
pmid = {15049143},
issn = {0037-1017},
mesh = {Archaea/*genetics ; Archaeal Proteins/*genetics ; Escherichia coli/genetics ; *Gene Expression Regulation, Archaeal ; Genetic Vectors ; Genome, Archaeal ; },
}
@article {pmid15046578,
year = {2004},
author = {Leduc, D and Graziani, S and Meslet-Cladiere, L and Sodolescu, A and Liebl, U and Myllykallio, H},
title = {Two distinct pathways for thymidylate (dTMP) synthesis in (hyper)thermophilic Bacteria and Archaea.},
journal = {Biochemical Society transactions},
volume = {32},
number = {Pt 2},
pages = {231-235},
doi = {10.1042/bst0320231},
pmid = {15046578},
issn = {0300-5127},
mesh = {Archaea/*physiology ; *Bacterial Physiological Phenomena ; Catalysis ; DNA/biosynthesis/metabolism ; Flavins/chemistry ; *Genome, Archaeal ; Genome, Bacterial ; Hot Temperature ; Models, Genetic ; Models, Molecular ; Phylogeny ; Protein Structure, Tertiary ; Pyrococcus/metabolism ; Temperature ; Thermotoga maritima/genetics ; Thymidine Monophosphate/*biosynthesis/*chemistry ; Thymidylate Synthase/chemistry ; },
abstract = {The hyperthermophilic anaerobic archaeon Pyrococcus abyssi, which lacks thymidine kinase, incorporates label from extracellular uracil, but not from thymidine, into its DNA. This implies that P. abyssi must synthesize dTMP (thymidylate), an essential precursor for DNA synthesis, de novo. However, iterative similarity searches of the three completed Pyrococcus genomes fail to detect candidate genes for canonical thymidylate synthase ThyA, suggesting the presence of alternative pathways for dTMP synthesis. Indeed, by identifying a novel class of flavin-dependent thymidylate synthases, ThyX, we have recently proven that two distinct pathways for de novo synthesis of dTMP are operational in the microbial world. While both thyX and thyA can be found in hyperthermophilic micro-organisms, the phylogenetic distribution of thyX among hyperthermophiles is wider than that of thyA. In this contribution, we discuss the differences in the distinct mechanisms of dTMP synthesis, with a special emphasis on hyperthermophilic micro-organisms.},
}
@article {pmid15046566,
year = {2004},
author = {Klenk, HP and Spitzer, M and Ochsenreiter, T and Fuellen, G},
title = {Phylogenomics of hyperthermophilic Archaea and Bacteria.},
journal = {Biochemical Society transactions},
volume = {32},
number = {Pt 2},
pages = {175-178},
doi = {10.1042/bst0320175},
pmid = {15046566},
issn = {0300-5127},
mesh = {Escherichia coli/genetics ; Evolution, Molecular ; *Genome, Archaeal ; *Genome, Bacterial ; Hot Temperature ; Phylogeny ; },
abstract = {The location of hyperthermophilic organisms in the tree of life has been the source of many exciting discussions during the last two decades. It inspired not only novel hypotheses for the early evolution of the organisms, but also the isolation of many new species of Archaea and Bacteria from hot environments, as well as microbial genome sequencing and phylogenomic analyses. In view of the new wealth of genetic information generated from several analysed genomes of the hyperthermophiles, we can only conclude that the question of their exact phylogenetic location and evolutionary origin is presently as open as ever before.},
}
@article {pmid15043055,
year = {2004},
author = {Shenroy, AR and Visweswariah, SS},
title = {Class III nucleotide cyclases in bacteria and archaebacteria: lineage-specific expansion of adenylyl cyclases and a dearth of guanylyl cyclases.},
journal = {FEBS letters},
volume = {561},
number = {1-3},
pages = {11-21},
doi = {10.1016/s0014-5793(04)00128-0},
pmid = {15043055},
issn = {0014-5793},
mesh = {Adenylyl Cyclases/*genetics ; Archaea/enzymology ; Bacteria/enzymology ; Bacterial Proteins/*genetics ; *Evolution, Molecular ; Guanylate Cyclase/*genetics ; Isoenzymes/*genetics ; Phylogeny ; Plasmids ; Protein Structure, Tertiary ; Substrate Specificity/genetics ; },
abstract = {The Class III nucleotide cyclases are found in bacteria, eukaryotes and archaebacteria. Our survey of the bacterial and archaebacterial genome and plasmid sequences identified 193 Class III cyclase genes in only 29 species, of which we predict the majority to be adenylyl cyclases. Interestingly, several putative cyclase genes were found to have non-conserved substrate specifying residues. Ancestors of the eukaryotic C1-C2 domain containing soluble adenylyl cyclases as well as the protist guanylyl cyclases were found in bacteria. Diverse domains were fused to the cyclase domain and phylogenetic analysis indicated that most proteins within a single cluster have similar domain compositions, emphasising the ancient evolutionary origin and versatility of the cyclase domain.},
}
@article {pmid15042434,
year = {2004},
author = {Krader, P and Emerson, D},
title = {Identification of archaea and some extremophilic bacteria using matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry.},
journal = {Extremophiles : life under extreme conditions},
volume = {8},
number = {4},
pages = {259-268},
pmid = {15042434},
issn = {1431-0651},
mesh = {Archaea/*chemistry/classification/growth &amp; development ; Bacteria/*chemistry/classification/growth &amp; development ; Databases, Factual ; Halobacterium salinarum/chemistry/growth &amp; development ; Phylogeny ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods ; },
abstract = {Archaea and a number of groups of environmentally important bacteria, e.g., sulfate-reducing bacteria, anoxygenic phototrophs, and some thermophiles, are difficult to characterize using current methods developed for phenotypically differentiating heterotrophic bacteria. We have evaluated matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF-MS) as a rapid method for identifying different groups of extremophilic prokaryotes using a linear mass spectrometer (Micromass, UK). The instrument is designed to acquire mass-spectral patterns from prokaryotic cell-wall components between masses of 500 and 10,000 Da in a statistically robust manner and create a database that can be used for identification. We have tested 28 archaea (10 genera, 20 spp.) and 42 bacteria (25 genera, 37 spp.) and found that all species yield reproducible, unique mass-spectral profiles. As a whole, the profiles for the archaea had fewer peaks and showed less differentiation compared to the bacteria, perhaps reflecting fundamental differences in cell-wall structure. The halophilic archaea all had consistent patterns that showed little differentiation; however, the software was able to consistently distinguish Halobacterium salinarium, Halococcus dombrowski, and Haloarcula marismortui from one another, although it could not always correctly distinguish four strains of Hb. salinarium from one another. The method was able to reliably identify 10(5) cells of either Albidovulum inexpectatum or Thermococcus litoralis and could detect as low as 10(3) cells. We found that the matrix, alpha-cyano-4-hydroxy-cinnamic acid yielded better spectra for archaea than 5-chloro-2-mercapto-benzothiazole. Overall, the method was rapid, required a minimum of sample processing, and was capable of distinguishing and identifying a very diverse group of prokaryotes.},
}
@article {pmid15037064,
year = {2004},
author = {Ring, G and Eichler, J},
title = {Membrane binding of ribosomes occurs at SecYE-based sites in the Archaea Haloferax volcanii.},
journal = {Journal of molecular biology},
volume = {336},
number = {5},
pages = {997-1010},
doi = {10.1016/j.jmb.2004.01.008},
pmid = {15037064},
issn = {0022-2836},
mesh = {Archaea/chemistry/genetics/ultrastructure ; Binding Sites ; Carrier Proteins/*metabolism ; Cell Membrane/*metabolism ; Cellulose/metabolism/pharmacology ; Haloferax volcanii/*chemistry/*genetics/ultrastructure ; Liposomes ; Membrane Proteins/*metabolism ; Receptors, Cytoplasmic and Nuclear/metabolism ; Ribosomes/*metabolism ; Sodium Chloride/pharmacology ; },
abstract = {Whereas ribosomes bind to membranes at eukaryal Sec61alphabetagamma and bacterial SecYEG sites, ribosomal membrane binding has yet to be studied in Archaea. Accordingly, functional ribosomes and inverted membrane vesicles were prepared from the halophilic archaea Haloferax volcanii. The ability of the ribosomes to bind to the membranes was determined using a flotation approach. Proteolytic pretreatment of the vesicles, as well as quantitative analyses, revealed the existence of a proteinaceous ribosome receptor, with the affinity of binding being comparable to that found in Eukarya and Bacteria. Inverted membrane vesicles prepared from cells expressing chimeras of SecE or SecY fused to a cytoplasmically oriented cellulose-binding domain displayed reduced ribosome binding due to steric hindrance. Pretreatment with cellulose drastically reduced ribosome binding to chimera-containing but not wild-type vesicles. Thus, as in Eukarya and Bacteria, ribosome binding in Archaea occurs at Sec-based sites. However, unlike the situation in the other domains of Life, ribosome binding in haloarchaea requires molar concentrations of salt. Structural information on ribosome-Sec complexes may provide insight into this high salt-dependent binding.},
}
@article {pmid15034136,
year = {2004},
author = {Inagaki, Y and Susko, E and Fast, NM and Roger, AJ},
title = {Covarion shifts cause a long-branch attraction artifact that unites microsporidia and archaebacteria in EF-1alpha phylogenies.},
journal = {Molecular biology and evolution},
volume = {21},
number = {7},
pages = {1340-1349},
doi = {10.1093/molbev/msh130},
pmid = {15034136},
issn = {0737-4038},
mesh = {Animals ; Archaea/*classification/genetics ; *Artifacts ; Microsporidia/*classification/genetics ; Peptide Elongation Factor 1/*classification/genetics ; *Phylogeny ; },
abstract = {Microsporidia branch at the base of eukaryotic phylogenies inferred from translation elongation factor 1alpha (EF-1alpha) sequences. Because these parasitic eukaryotes are fungi (or close relatives of fungi), it is widely accepted that fast-evolving microsporidian sequences are artifactually "attracted" to the long branch leading to the archaebacterial (outgroup) sequences ("long-branch attraction," or "LBA"). However, no previous studies have explicitly determined the reason(s) why the artifactual allegiance of microsporidia and archaebacteria ("M + A") is recovered by all phylogenetic methods, including maximum likelihood, a method that is supposed to be resistant to classical LBA. Here we show that the M + A affinity can be attributed to those alignment sites associated with large differences in evolutionary site rates between the eukaryotic and archaebacterial subtrees. Therefore, failure to model the significant evolutionary rate distribution differences (covarion shifts) between the ingroup and outgroup sequences is apparently responsible for the artifactual basal position of microsporidia in phylogenetic analyses of EF-1alpha sequences. Currently, no evolutionary model that accounts for discrete changes in the site rate distribution on particular branches is available for either protein or nucleotide level phylogenetic analysis, so the same artifacts may affect many other "deep" phylogenies. Furthermore, given the relative similarity of the site rate patterns of microsporidian and archaebacterial EF-1alpha proteins ("parallel site rate variation"), we suggest that the microsporidian orthologs may have lost some eukaryotic EF-1alpha-specific nontranslational functions, exemplifying the extreme degree of reduction in this parasitic lineage.},
}
@article {pmid15031730,
year = {2004},
author = {Laksanalamai, P and Whitehead, TA and Robb, FT},
title = {Minimal protein-folding systems in hyperthermophilic archaea.},
journal = {Nature reviews. Microbiology},
volume = {2},
number = {4},
pages = {315-324},
doi = {10.1038/nrmicro866},
pmid = {15031730},
issn = {1740-1526},
mesh = {Amino Acid Sequence ; Archaea/genetics/*physiology ; Archaeal Proteins/genetics/*physiology ; Genome, Archaeal ; Heat-Shock Proteins/physiology ; Heat-Shock Response/physiology ; Models, Molecular ; Molecular Chaperones/physiology ; Molecular Sequence Data ; Phylogeny ; Protein Folding ; },
}
@article {pmid15030489,
year = {2004},
author = {Lichi, T and Ring, G and Eichler, J},
title = {Membrane binding of SRP pathway components in the halophilic archaea Haloferax volcanii.},
journal = {European journal of biochemistry},
volume = {271},
number = {7},
pages = {1382-1390},
doi = {10.1111/j.1432-1033.2004.04050.x},
pmid = {15030489},
issn = {0014-2956},
mesh = {Amino Acid Sequence ; Archaea/metabolism ; Arginine/chemistry ; Bacterial Proteins/chemistry ; Cell Membrane/*metabolism ; Cytoplasm/metabolism ; Endopeptidase K/chemistry ; Escherichia coli/metabolism ; Haloferax volcanii/*metabolism ; Immunoblotting ; Lysine/chemistry ; Molecular Sequence Data ; Plasmids/metabolism ; Protein Binding ; Protein Structure, Tertiary ; Receptors, Cytoplasmic and Nuclear/chemistry ; Signal Recognition Particle/*metabolism ; Subcellular Fractions/metabolism ; Time Factors ; },
abstract = {Across evolution, the signal recognition particle pathway targets extra-cytoplasmic proteins to membranous translocation sites. Whereas the pathway has been extensively studied in Eukarya and Bacteria, little is known of this system in Archaea. In the following, membrane association of FtsY, the prokaryal signal recognition particle receptor, and SRP54, a central component of the signal recognition particle, was addressed in the halophilic archaea Haloferax volcanii. Purified H. volcanii FtsY, the FtsY C-terminal GTP-binding domain (NG domain) or SRP54, were combined separately or in different combinations with H. volcanii inverted membrane vesicles and examined by gradient floatation to differentiate between soluble and membrane-bound protein. Such studies revealed that both FtsY and the FtsY NG domain bound to H. volcanii vesicles in a manner unaffected by proteolytic pretreatment of the membranes, implying that in Archaea, FtsY association is mediated through the membrane lipids. Indeed, membrane association of FtsY was also detected in intact H. volcanii cells. The contribution of the NG domain to FtsY binding in halophilic archaea may be considerable, given the low number of basic charges found at the start of the N-terminal acidic domain of haloarchaeal FtsY proteins (the region of the protein thought to mediate FtsY-membrane association in Bacteria). Moreover, FtsY, but not the NG domain, was shown to mediate membrane association of H. volcanii SRP54, a protein that did not otherwise interact with the membrane.},
}
@article {pmid15019782,
year = {2004},
author = {Shuttleworth, G and Fogg, MJ and Kurpiewski, MR and Jen-Jacobson, L and Connolly, BA},
title = {Recognition of the pro-mutagenic base uracil by family B DNA polymerases from archaea.},
journal = {Journal of molecular biology},
volume = {337},
number = {3},
pages = {621-634},
doi = {10.1016/j.jmb.2004.01.021},
pmid = {15019782},
issn = {0022-2836},
support = {BBS/B/05060/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; R01 GM029207/GM/NIGMS NIH HHS/United States ; R37 GM029207/GM/NIGMS NIH HHS/United States ; },
mesh = {Archaea/*genetics ; Base Sequence ; DNA Replication ; DNA, Single-Stranded ; DNA-Directed DNA Polymerase/*metabolism ; Mutagenesis ; Oligodeoxyribonucleotides/metabolism ; Protein Binding ; Templates, Genetic ; Thermodynamics ; Uracil/*metabolism ; },
abstract = {Archaeal family B DNA polymerases contain a specialised pocket that binds tightly to template-strand uracil, causing the stalling of DNA replication. The mechanism of this unique "template-strand proof-reading" has been studied using equilibrium binding measurements, DNA footprinting, van't Hoff analysis and calorimetry. Binding assays have shown that the polymerase preferentially binds to uracil in single as opposed to double-stranded DNA. Tightest binding is observed using primer-templates that contain uracil four bases in front of the primer-template junction, corresponding to the observed stalling position. Ethylation interference analysis of primer-templates shows that the two phosphates, immediately flanking the uracil (NpUpN), are important for binding; contacts are also made to phosphates in the primer-strand. Microcalorimetry and van't Hoff analysis have given a fuller understanding of the thermodynamic parameters involved in uracil recognition. All the results are consistent with a "read-ahead" mechanism, in which the replicating polymerase scans the template, ahead of the replication fork, for the presence of uracil and halts polymerisation on detecting this base. Post-stalling events, serving to eliminate uracil, await full elucidation.},
}
@article {pmid15014152,
year = {2004},
author = {Genschel, U},
title = {Coenzyme A biosynthesis: reconstruction of the pathway in archaea and an evolutionary scenario based on comparative genomics.},
journal = {Molecular biology and evolution},
volume = {21},
number = {7},
pages = {1242-1251},
doi = {10.1093/molbev/msh119},
pmid = {15014152},
issn = {0737-4038},
mesh = {Archaea/enzymology/*genetics ; Carboxy-Lyases/genetics ; Coenzyme A/*biosynthesis/genetics ; Escherichia coli/enzymology/genetics ; *Evolution, Molecular ; *Genomics ; Humans ; Pantothenic Acid/biosynthesis/genetics ; Peptide Synthases/genetics ; *Phylogeny ; },
abstract = {Coenzyme A (CoA) holds a central position in cellular metabolism and therefore can be assumed to be an ancient molecule. Starting from the known E. coli and human enzymes required for the biosynthesis of CoA, phylogenetic profiles and chromosomal proximity methods enabled an almost complete reconstruction of archaeal CoA biosynthesis. This includes the identification of strong candidates for archaeal pantothenate synthetase and pantothenate kinase, which are unrelated to the corresponding bacterial or eukaryotic enzymes. According to this reconstruction, the topology of CoA synthesis from common precursors is essentially conserved across the three domains of life. The CoA pathway is conserved to varying degrees in eukaryotic pathogens like Giardia lamblia or Plasmodium falciparum, indicating that these pathogens have individual uptake-mechanisms for different CoA precursors. Phylogenetic analysis and phyletic distribution of the CoA biosynthetic enzymes suggest that the enzymes required for the synthesis of phosphopantothenate were recruited independently in the bacterial and archaeal lineages by convergent evolution, and that eukaryotes inherited the genes for the synthesis of pantothenate (vitamin B5) from bacteria. Homologues to bacterial enzymes involved in pantothenate biosynthesis are present in a subset of archaeal genomes. The phylogenies of these enzymes indicate that they were acquired from bacterial thermophiles through horizontal gene transfer. Monophyly can be inferred for each of the enzymes catalyzing the four ultimate steps of CoA synthesis, the conversion of phosphopantothenate into CoA. The results support the notion that CoA was initially synthesized from a prebiotic precursor, most likely pantothenate or a related compound.},
}
@article {pmid15006762,
year = {2004},
author = {Pritchett, MA and Zhang, JK and Metcalf, WW},
title = {Development of a markerless genetic exchange method for Methanosarcina acetivorans C2A and its use in construction of new genetic tools for methanogenic archaea.},
journal = {Applied and environmental microbiology},
volume = {70},
number = {3},
pages = {1425-1433},
pmid = {15006762},
issn = {0099-2240},
mesh = {Alleles ; Base Sequence ; DNA, Archaeal/genetics ; Drug Resistance, Microbial/genetics ; Escherichia coli/genetics ; Genes, Archaeal ; Genes, Reporter ; Genetic Markers ; *Genetic Techniques ; Genetic Vectors ; Hypoxanthine Phosphoribosyltransferase/genetics ; Methanosarcina/drug effects/enzymology/*genetics ; Mutation ; Plasmids/genetics ; Recombination, Genetic ; },
abstract = {A new genetic technique for constructing mutants of Methanosarcina acetivorans C2A by using hpt as a counterselectable marker was developed. Mutants with lesions in the hpt gene, encoding hypoxanthine phosphoribosyltransferase, were shown to be >35-fold more resistant to the toxic base analog 8-aza-2,6-diaminopurine (8ADP) than was the wild type. Reintroduction of the hpt gene into a Delta hpt host restored 8ADP sensitivity and provided the basis for a two-step strategy involving plasmid integration and excision for recombination of mutant alleles onto the M. acetivorans chromosome. We have designated this method markerless exchange because, although selectable markers are used during the process, they are removed in the final mutants. Thus, the method can be repeated many times in the same cell line. The method was validated by construction of Delta proC Delta hpt mutants, which were recovered at a frequency of 22%. Additionally, a Methanosarcina-Escherichia shuttle vector, encoding the Escherichia coli proC gene as a new selectable marker, was constructed for use in proC hosts. Finally, the markerless exchange method was used to recombine a series of uidA reporter gene fusions into the M. acetivorans proC locus. In vitro assay of beta-glucuronidase activity in extracts of these recombinants demonstrated, for the first time, the utility of uidA as a reporter gene in Methanosarcina: A >5,000-fold range of promoter activities could be measured by using uidA: the methyl-coenzyme M reductase operon fusion displayed approximately 300-fold-higher activity than did the serC gene fusion, which in turn had 16-fold-higher activity than did a fusion to the unknown orf2 gene.},
}
@article {pmid14991422,
year = {2004},
author = {Jolivet, E and Corre, E and L'Haridon, S and Forterre, P and Prieur, D},
title = {Thermococcus marinus sp. nov. and Thermococcus radiotolerans sp. nov., two hyperthermophilic archaea from deep-sea hydrothermal vents that resist ionizing radiation.},
journal = {Extremophiles : life under extreme conditions},
volume = {8},
number = {3},
pages = {219-227},
pmid = {14991422},
issn = {1431-0651},
mesh = {Base Composition ; Base Sequence ; DNA, Archaeal/chemistry/genetics ; DNA, Ribosomal/genetics ; Drug Resistance ; Gamma Rays ; Hot Temperature ; Hydrogen-Ion Concentration ; Microscopy, Electron ; Molecular Sequence Data ; Phenotype ; Phylogeny ; Radiation Tolerance ; Seawater/microbiology ; Sodium Chloride ; Species Specificity ; Thermococcus/classification/genetics/*isolation &amp; purification/*radiation effects ; },
abstract = {Enrichments for anaerobic, organotrophic hyperthermophiles were performed with hydrothermal chimney samples collected from the Mid-Atlantic Ridge at a depth of 3,550 m (23 degrees 22'N, 44 degrees 57'W) and the Guaymas Basin (27 degrees 01'N, 111 degrees 24'W) at a depth of 2,616 m. Positive enrichments were submitted to gamma-irradiation at doses of 20 and 30 kGy. Two hyperthermophilic, anaerobic, sulfur-metabolizing archaea were isolated. Strain EJ1T was isolated from chimney samples collected from the Mid-Atlantic Ridge after gamma-irradiation at 20 kGy, and strain EJ2T was isolated from the Guaymas Basin after gamma-irradiation at 30 kGy. Only strain EJ2T was motile, and both formed regular cocci. These new strains grew between 55 and 95 degrees C with the optimal temperature being 88 degrees C. The optimal pH for growth was 6.0, and the optimal NaCl concentration for growth was around 20 g l(-1). These strains were obligate anaerobic heterotrophs that utilized yeast extract, tryptone, and peptone as a carbon source for growth. Ten amino acids were essential for the growth of strain EJ1), such as arginine, aspartic acid, isoleucine, leucine, methionine, phenylalanine, proline, threonine, tyrosine, and valine, while strain EJ2T was unable to grow on a mixture of amino acids. Elemental sulfur or cystine was required for EJ2T growth and was reduced to hydrogen sulfide. Rifampicin inhibited growth for both strains EJ1T and EJ2T. The G + C contents of the genomic DNA were 52.3 and 54.5 mol% for EJ1T and EJ2T, respectively. As determined by 16S rRNA gene sequence analysis, these strains were more closely related to Thermococcus gorgonarius, T. celer, T. guaymasensis, T. profundus, and T. hydrothermalis. However, no significant homology was observed between them with DNA-DNA hybridization. These novel organisms also possess phenotypic traits that differ from those of its closest phylogenetic relatives. Therefore, it is proposed that these isolates, which are amongst the most radioresistant hyperthermophilic archaea known to date with T. gammatolerans (Jolivet et al. 2003a), should be described as novel species T. marinus sp. nov. and T. radiotolerans sp. nov. The type strain of T. marinus is strain EJ1T (= DSM 15227T = JCM 11825T) and the type strain of T. radiotolerans is strain EJ2T (= DSM 15228T = JCM 11826T).},
}
@article {pmid14990804,
year = {2004},
author = {Woodson, JD and Escalante-Semerena, JC},
title = {CbiZ, an amidohydrolase enzyme required for salvaging the coenzyme B12 precursor cobinamide in archaea.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {101},
number = {10},
pages = {3591-3596},
pmid = {14990804},
issn = {0027-8424},
support = {R01 GM040313/GM/NIGMS NIH HHS/United States ; R37 GM040313/GM/NIGMS NIH HHS/United States ; GM40313/GM/NIGMS NIH HHS/United States ; },
mesh = {Aminohydrolases/genetics/*metabolism ; Cobamides/*metabolism ; Genes, Archaeal ; Genetic Complementation Test ; Halobacterium/genetics/*metabolism ; Methanosarcina/genetics/*metabolism ; Molecular Sequence Data ; Mutation ; Recombinant Proteins/genetics/metabolism ; Salmonella enterica/genetics/metabolism ; Species Specificity ; Vitamin B 12/*analogs &amp; derivatives/metabolism ; },
abstract = {The existence of a pathway for salvaging the coenzyme B(12) precursor dicyanocobinamide (Cbi) from the environment was established by genetic and biochemical means. The pathway requires the function of a previously unidentified amidohydrolase enzyme that converts adenosylcobinamide to adenosylcobyric acid, a bona fide intermediate of the de novo coenzyme B(12) biosynthetic route. The cbiZ gene of the methanogenic archaeon Methanosarcina mazei strain Göl was cloned, was overproduced in Escherichia coli, and the recombinant protein was isolated to homogeneity. HPLC, UV-visible spectroscopy, MS, and bioassay data established adenosylcobyric as the corrinoid product of the CbiZ-catalyzed reaction. Inactivation of the cbiZ gene in the extremely halophilic archaeon Halobacterium sp. strain NRC-1 blocked the ability of this archaeon to salvage Cbi. cbiZ function restored Cbi salvaging in a strain of the bacterium Salmonella enterica, whose Cbi-salvaging pathway was blocked. The salvaging of Cbi through the CbiZ enzyme appears to be an archaeal strategy because all of the genomes of B(12)-producing archaea have a cbiZ ortholog. Reasons for the evolution of two distinct pathways for Cbi salvaging in prokaryotes are discussed.},
}
@article {pmid14990749,
year = {2004},
author = {Constantinesco, F and Forterre, P and Koonin, EV and Aravind, L and Elie, C},
title = {A bipolar DNA helicase gene, herA, clusters with rad50, mre11 and nurA genes in thermophilic archaea.},
journal = {Nucleic acids research},
volume = {32},
number = {4},
pages = {1439-1447},
pmid = {14990749},
issn = {1362-4962},
mesh = {Amino Acid Sequence ; Archaeal Proteins/*genetics ; DNA Helicases/classification/*genetics/metabolism ; Endodeoxyribonucleases/*genetics ; Exodeoxyribonucleases/*genetics ; *Genes, Archaeal ; Hot Temperature ; Molecular Sequence Data ; Operon ; Sequence Alignment ; Sulfolobus acidocaldarius/genetics ; Transcription, Genetic ; },
abstract = {We showed previously that rad50 and mre11 genes of thermophilic archaea are organized in an operon-like structure with a third gene (nurA) encoding a 5' to 3' exonuclease. Here, we show that the rad50, mre11 and nurA genes from the hyperthermophilic archaeon Sulfolobus acidocaldarius are co-transcribed with a fourth gene encoding a DNA helicase. This enzyme (HerA) is the prototype of a new class of DNA helicases able to utilize either 3' or 5' single-stranded DNA extensions for loading and subsequent DNA duplex unwinding. To our knowledge, DNA helicases capable of translocating along the DNA in both directions have not been identified previously. Sequence analysis of HerA shows that it is a member of the TrwB, FtsK and VirB4/VirD4 families of the PilT class NTPases. HerA homologs are found in all thermophilic archaeal species and, in all cases except one, the rad50, mre11, nurA and herA genes are grouped together. These results suggest that the archaeal Rad50-Mre11 complex might act in association with a 5' to 3' exonuclease (NurA) and a bipolar DNA helicase (HerA) indicating a probable involvement in the initiation step of homologous recombination.},
}
@article {pmid14977583,
year = {2004},
author = {Maupin-Furlow, JA and Gil, MA and Karadzic, IM and Kirkland, PA and Reuter, CJ},
title = {Proteasomes: perspectives from the Archaea.},
journal = {Frontiers in bioscience : a journal and virtual library},
volume = {9},
number = {},
pages = {1743-1758},
doi = {10.2741/1363},
pmid = {14977583},
issn = {1093-9946},
support = {R01GM57498/GM/NIGMS NIH HHS/United States ; },
mesh = {Archaea/*enzymology/metabolism ; Archaeal Proteins/chemistry/*physiology ; Cysteine Endopeptidases/chemistry/*physiology ; Energy Metabolism ; Multienzyme Complexes/chemistry/*physiology ; Proteasome Endopeptidase Complex ; Protein Subunits/metabolism ; },
abstract = {The development of whole systems approaches to microbiology (e.g. genomics and proteomics) has facilitated a global view of archaeal physiology. Surprisingly, as archaea respond to environmental signals, the majority of protein concentration changes that occur are not reflected at the mRNA level. This incongruity highlights the importance of post-transcription control mechanisms in these organisms. One of the central players in proteolysis is the proteasome, a multicatalytic energy-dependent protease. Proteasomes serve both proteolytic and non-proteolytic roles in protein quality control and in the regulation of cell function. The proteolytic active sites of these enzymes are housed within a central chamber of an elaborate nanocompartment termed the 20S proteasome or core particle. Axial gates, positioned at each end of this particle, restrict the type of substrate that can access the proteolytic active sites. Assortments of regulatory AAA complexes are predicted to recognize/bind and unfold substrate proteins, open the axial gates, and translocate substrate into the 20S core particle.},
}
@article {pmid14977547,
year = {2004},
author = {Macario, AJ and Malz, M and Conway de Macario, E},
title = {Evolution of assisted protein folding: the distribution of the main chaperoning systems within the phylogenetic domain archaea.},
journal = {Frontiers in bioscience : a journal and virtual library},
volume = {9},
number = {},
pages = {1318-1332},
doi = {10.2741/1328},
pmid = {14977547},
issn = {1093-9946},
mesh = {Archaea/*classification ; Archaeal Proteins/*classification ; Bacteria/classification ; Biological Evolution ; Chaperonin 10/classification ; Chaperonin 60/classification ; Molecular Chaperones/*classification ; *Phylogeny ; Protein Folding ; },
abstract = {Newly made proteins must achieve a functional shape, the native configuration, before they can play their physiological roles in the cell. Proteins must also travel to the locale (e.g., the mitochondrion) in the cell where their functions are required. In these processes of folding into the native configuration and translocation to the place of work, proteins may be assisted by molecules called molecular chaperones. Stressors can unfold (denature) proteins, and genetic defects can cause misfolding and, in addition, both abnormalities can lead to polypeptide aggregation. Chaperones play a role in assisting refolding of partially denatured or misfolded proteins, thus preventing aggregation. Clearly, molecular chaperones are key cell components under normal, physiological circumstances, as well as in potentially harmful situations resulting from environmental or inherited factors. Hence, molecular chaperones constitute attractive targets for a variety of efforts aiming at improving the cell's performance, particularly under stress, to prevent disease, or at least to slow down its progression and to contain the deleterious effects of stress. In our efforts in this direction, we have undertaken to investigate the chaperoning systems of cells belonging to the phylogenetic domain Archaea. The findings reported here pertain to the distribution of the molecular chaperone machine, the chaperonins, and the prefoldins, among archaea. The genes hsp70(dnaK), hsp40(dnaJ), and grpE encoding the components of the molecular chaperone machine were present only in some archeaeal species: this contrasts with bacteria and eucarya, which do have the genes with no known exception. The group I, or bacterial, chaperonin-genes groEL and groES occured in the genomes of Methanosarcina species but were not found in any of the other archaea whose genomes have been sequenced. While all the archaea studied had between one and three chaperonins of group II (thermosome subunits), Methanosarcina acetivorans was exceptional since it had five of these chaperonins. This is the largest number of group II chaperonins ever found in a prokaryote. Furthermore, two of the M. acetivorans chaperonins were different from, albeit related to, the other known archaeal and eucaryal chaperonins of group II. Prefoldins were found in all archaea examined. Overall, the results provide clues to the evolution of the chaperoning systems, which must have played a critical role in survival since life started. Also, the data suggest new avenues of research for elucidating the evolution of assisted protein folding and for uncovering roles and interactions not yet described for these molecules.},
}
@article {pmid14976868,
year = {2003},
author = {Zorzopulos, J},
title = {Birth of the domains Bacteria, Archaea and Eucarya and of major taxa within them: a hypothesis.},
journal = {Revista Argentina de microbiologia},
volume = {35},
number = {4},
pages = {175-182},
pmid = {14976868},
issn = {0325-7541},
mesh = {Animals ; Archaea/*classification/genetics/ultrastructure ; Bacteria/*classification/genetics/ultrastructure ; *Biological Evolution ; Cell Fusion ; Cell Wall/ultrastructure ; DNA/genetics ; Gene Pool ; *Models, Biological ; Phenotype ; Photosynthesis/genetics ; Phylogeny ; Plants/*classification/genetics ; Recombination, Genetic ; },
abstract = {A hypothesis to explain how the birth of the Bacteria, Archaea and Eucarya domains and of major taxa within them took place is presented. It is proposed that the birth of each domain was an independent event consisting in the genetic isolation of a particular cell from a very diverse pool of "primitive cells". Cells within this pool have a dynamic pattern of cell fusion followed by mostly illegitimate DNA recombination. It is postulated that genetic isolation was achieved: a) by evolution of the peptidoglycan layer in Bacteria, b) by evolution of a glycoproteic cell wall in Archaea, and c) by evolution of the nuclear membrane in Eucarya. It is also postulated that, within each domain, branching was a consequence of sporadic events of fusion between two cells of different phylogenetic lineages, followed by mostly illegitimate DNA recombination and cell wall regeneration. The two fusing cells may have belonged to the same domain, to different domains or even one may have belonged to one of the domains and the other to the pool of "primitive cells". In this last case, new complex phenotypes, previously absent from all the domains, were suddenly introduced in one of them (e.g.: photosynthesis in Bacteria, methanogenesis in Archaea). A corollary of this theory is that genes should have a phylogenetic tree with defined nodes while organisms are characterized by discontinuities instead of nodes.},
}
@article {pmid14976258,
year = {2004},
author = {Forbes, AJ and Patrie, SM and Taylor, GK and Kim, YB and Jiang, L and Kelleher, NL},
title = {Targeted analysis and discovery of posttranslational modifications in proteins from methanogenic archaea by top-down MS.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {101},
number = {9},
pages = {2678-2683},
pmid = {14976258},
issn = {0027-8424},
support = {R01 GM067193/GM/NIGMS NIH HHS/United States ; GM 067193/GM/NIGMS NIH HHS/United States ; },
mesh = {Amino Acid Sequence ; Archaeal Proteins/chemistry/isolation &amp; purification/*metabolism ; Automation ; Fourier Analysis ; Methanococcus/*metabolism ; Models, Biological ; Molecular Sequence Data ; Molecular Weight ; *Protein Processing, Post-Translational ; },
abstract = {For more complete characterization of DNA-predicted proteins (including their posttranslational modifications) a "top-down" approach using high-resolution tandem MS is forwarded here by its application to methanogens in both hypothesis-driven and discovery modes, with the latter dependent on new automation benchmarks for intact proteins. With proteins isolated from ribosomes and whole-cell lysates of Methanococcus jannaschii (approximately 1,800 genes) using a 2D protein fractionation method, 72 gene products were identified and characterized with 100% sequence coverage via automated fragmentation of intact protein ions in a custom quadrupole/Fourier transform hybrid mass spectrometer. Three incorrect start sites and two modifications were found, with one of each determined for MJ0556, a 20-kDa protein with an unknown methylation at approximately 50% occupancy in stationary phase cells. The separation approach combined with the quadrupole/Fourier transform hybrid mass spectrometer allowed targeted and efficient comparison of histones from M. jannaschii, Methanosarcina acetivorans (largest Archaeal genome, 5.8 Mb), and yeast. This finding revealed a striking difference in the posttranslational regulation of DNA packaging in Eukarya vs. the Archaea. This study illustrates a significant evolutionary step for the MS tools available for characterization of WT proteins from complex proteomes without proteolysis.},
}
@article {pmid14960362,
year = {2004},
author = {Xiaohui, C and Jin, W},
title = {A unique ATG triplet downstream of gene start in archaea: implications for translation initiation and evolution.},
journal = {Gene},
volume = {327},
number = {1},
pages = {75-79},
doi = {10.1016/j.gene.2003.11.001},
pmid = {14960362},
issn = {0378-1119},
mesh = {Archaea/*genetics ; Base Sequence ; Codon, Initiator/*genetics ; Evolution, Molecular ; Genes, Archaeal/*genetics ; Genome, Archaeal ; Protein Biosynthesis ; },
abstract = {Searching for unique features of archaeal genome may shed light on the mechanism of gene regulation in primitive life forms. Statistical analysis of ATG frequency on the complete genome sequences of 16 archaea, 20 bacteria and 2 eukaryotes revealed that most of the archaeal genomes have a remarkably high ATG frequency at the position of nine nucleotide (nt) downstream of the translation initiation site (the first nucleotide of the translation initiation codon is designated as 0). To understand the role of this unique ATG in archaea, we further analyzed the ATG-initiated genes and non-ATG-initiated genes separately, and the results indicated that only the non-ATG-initiated genes contribute to the high ATG frequency at position +9. This led us to speculate that the in-frame ATG at +9 may serve as a remedial initiation site for archaea in case of initiation failure at the regular site. In addition, it seems that this phenomenon does not result from the harsh environment that archaea are usually viable according to the fact that no considerably high ATG frequency at +9 was observed in all the four thermophilic bacteria that also live in harsh environment. We proposed that the high ATG frequency at position +9 might reflect the decreased efficiency of the translation initiation machinery in archaea. Since archaea evolve very slowly, this unique characteristic of high ATG frequency at position +9 may present the primitive state of the Universal Ancestor.},
}
@article {pmid14871864,
year = {2004},
author = {Shmuely, H and Dinitz, E and Dahan, I and Eichler, J and Fischer, D and Shaanan, B},
title = {Poorly conserved ORFs in the genome of the archaea Halobacterium sp. NRC-1 correspond to expressed proteins.},
journal = {Bioinformatics (Oxford, England)},
volume = {20},
number = {8},
pages = {1248-1253},
doi = {10.1093/bioinformatics/bth075},
pmid = {14871864},
issn = {1367-4803},
mesh = {Bacterial Proteins/*genetics ; Chromosome Mapping/*methods ; Conserved Sequence/*genetics ; Gene Expression Profiling/*methods ; Genome, Archaeal ; Genome, Bacterial ; Halobacterium/*genetics ; Open Reading Frames/*genetics ; Sequence Alignment/methods ; Sequence Analysis, DNA/*methods ; },
abstract = {MOTIVATION: A large fraction of open reading frames (ORFs) identified as 'hypothetical' proteins correspond to either 'conserved hypothetical' proteins, representing sequences homologous to ORFs of unknown function from other organisms, or to hypothetical proteins lacking any significant sequence similarity to other ORFs in the databases. Elucidating the functions and three-dimensional structures of such orphan ORFs, termed ORFans or poorly conserved ORFs (PCOs), is essential for understanding biodiversity. However, it has been claimed that many ORFans may not encode for expressed proteins.<br><br>RESULTS: A genome-wide experimental study of 'paralogous PCOs' in the halophilic archaea Halobacterium sp. NRC-1 was conducted. Paralogous PCOs are ORFs with at least one homolog in the same organism, but with no clear homologs in other organisms. The results reveal that mRNA is synthesized for a majority of the Halobacterium sp. NRC-1 paralogous PCO families, including those comprising relatively short proteins, strongly suggesting that these Halobacterium sp. NRC-1 paralogous PCOs correspond to true, expressed proteins. Hence, further computational and experimental studies aimed at characterizing PCOs in this and other organisms are merited. Such efforts could shed light on PCOs' functions and origins, thereby serving to elucidate the vast diversity observed in the genetic material.},
}
@article {pmid14762828,
year = {2004},
author = {Sakuraba, H and Goda, S and Ohshima, T},
title = {Unique sugar metabolism and novel enzymes of hyperthermophilic archaea.},
journal = {Chemical record (New York, N.Y.)},
volume = {3},
number = {5},
pages = {281-287},
doi = {10.1002/tcr.10066},
pmid = {14762828},
issn = {1527-8999},
mesh = {Amino Acid Sequence ; Archaea/*enzymology/genetics/metabolism ; *Carbohydrate Metabolism ; Glucokinase/genetics ; Models, Molecular ; Molecular Sequence Data ; Phosphotransferases (Alcohol Group Acceptor)/genetics ; Phylogeny ; Sequence Alignment ; Sequence Homology, Amino Acid ; },
abstract = {Hyperthermophiles are a group of microorganisms that have their optimum growth temperature above 80 degrees C. More than 60 species of the hyperthermophiles have been isolated from marine and continental volcanic environments. Most hyperthermophiles belong to Archaea, the third domain of life, and are considered to be the most ancient of all extant life forms. Recent studies have revealed the presence of unusual sugar metabolic processes in hyperthermophilic archaea, for example, a modified Embden-Meyerhof pathway, that has so far not been observed in bacteria and eucarya. Several novel enzymes, such as ADP-dependent glucokinase, ADP-dependent phosphofructokinase, glyceraldehyde-3-phosphate ferredoxin oxidoreductase, phosphoenolpyruvate synthase, pyruvate : ferredoxin oxidoreductase, and ADP-forming acetyl-CoA synthetase, have been found to be involved in a modified Embden-Meyerhof pathway of the hyperthermophilic archaeon Pyrococcus furiosus. In addition, a unique mode of ATP regeneration has been postulated to exist in the pathway of P. furiosus. The metabolic design observed in this microorganism might reflect the situation at an early stage of evolution.},
}
@article {pmid14743312,
year = {2004},
author = {Vaughan, S and Wickstead, B and Gull, K and Addinall, SG},
title = {Molecular evolution of FtsZ protein sequences encoded within the genomes of archaea, bacteria, and eukaryota.},
journal = {Journal of molecular evolution},
volume = {58},
number = {1},
pages = {19-29},
pmid = {14743312},
issn = {0022-2844},
mesh = {Amino Acid Sequence ; Animals ; Archaea/*genetics ; Bacteria/*genetics ; Bacterial Proteins/*genetics ; Cytoskeletal Proteins/*genetics ; Databases, Genetic ; Fungi/genetics ; Gene Duplication ; Molecular Sequence Data ; *Phylogeny ; Plants/genetics ; Protein Conformation ; Sequence Alignment ; *Sequence Homology ; Tubulin/*genetics ; },
abstract = {The FtsZ protein is a polymer-forming GTPase which drives bacterial cell division and is structurally and functionally related to eukaryotic tubulins. We have searched for FtsZ-related sequences in all freely accessible databases, then used strict criteria based on the tertiary structure of FtsZ and its well-characterized in vitro and in vivo properties to determine which sequences represent genuine homologues of FtsZ. We have identified 225 full-length FtsZ homologues, which we have used to document, phylum by phylum, the primary sequence characteristics of FtsZ homologues from the Bacteria, Archaea, and Eukaryota. We provide evidence for at least five independent ftsZ gene-duplication events in the bacterial kingdom and suggest the existence of three ancestoral euryarchaeal FtsZ paralogues. In addition, we identify "FtsZ-like" sequences from Bacteria and Archaea that, while showing significant sequence similarity to FtsZs, are unlikely to bind and hydrolyze GTP.},
}
@article {pmid14718158,
year = {2004},
author = {Liberi, G and Foiani, M},
title = {Initiation of DNA replication: a new hint from archaea.},
journal = {Cell},
volume = {116},
number = {1},
pages = {3-4},
doi = {10.1016/s0092-8674(03)01072-9},
pmid = {14718158},
issn = {0092-8674},
mesh = {Archaea/*genetics ; Cell Cycle Proteins/genetics ; Cell Division/genetics ; Chromosomes/*genetics ; DNA Replication/*genetics ; DNA-Binding Proteins/genetics ; Eukaryotic Cells/metabolism ; Origin Recognition Complex ; *Saccharomyces cerevisiae Proteins ; },
abstract = {In this issue, Robinson and coworkers provide new insights into the mechanisms of initiation of chromosome replication in Archea. This and other studies, focused on model organisms, will certainly help to understand how the replication process has evolved in Eukaryotes.},
}
@article {pmid14686932,
year = {2004},
author = {Lyon, EJ and Shima, S and Buurman, G and Chowdhuri, S and Batschauer, A and Steinbach, K and Thauer, RK},
title = {UV-A/blue-light inactivation of the 'metal-free' hydrogenase (Hmd) from methanogenic archaea.},
journal = {European journal of biochemistry},
volume = {271},
number = {1},
pages = {195-204},
doi = {10.1046/j.1432-1033.2003.03920.x},
pmid = {14686932},
issn = {0014-2956},
mesh = {Archaeal Proteins/antagonists &amp; inhibitors/isolation &amp; purification/radiation effects ; Chromatography, Gel ; Hydrogenase/antagonists &amp; inhibitors/isolation &amp; purification/*radiation effects ; Iron/analysis ; Kinetics ; Light ; Methanobacteriaceae/*enzymology ; Methanobacterium/*enzymology ; Spectrophotometry ; *Ultraviolet Rays ; },
abstract = {H2-forming methylenetetrahydromethanopterin dehydrogenase (Hmd) is an unusual hydrogenase present in many methanogenic archaea. The homodimeric enzyme dubbed 'metal-free' hydrogenase does not contain iron-sulfur clusters or nickel and thus differs from [Ni-Fe] and [Fe-Fe] hydrogenases, which are all iron-sulfur proteins. Hmd preparations were found to contain up to 1 mol iron per 40 kDa subunit, but the iron was considered to be a contaminant as none of the catalytic and spectroscopic properties of the enzyme indicated that it was an essential component. Hmd does, however, harbour a low molecular mass cofactor of yet unknown structure. We report here that the iron found in Hmd is most probably functional after all. Further investigation was initiated by the discovery that Hmd is inactivated upon exposure to UV-A (320-400 nm) or blue-light (400-500 nm). Enzyme purified in the dark exhibited an absorption spectrum with a maximum at approximately 360 nm and which mirrored its sensitivity towards light. In UV-A/blue-light the enzyme was bleached. The cofactor extracted from active Hmd was also light sensitive. It showed an UV/visible spectrum similar to that of the active enzyme and was bleached upon exposure to light. Photobleached cofactor no longer had the ability to reconstitute active Hmd from the apoenzyme. When purified in the dark, Hmd consistently contained per monomer about one Fe, which was tightly bound to the cofactor. The iron was released from the enzyme and from the cofactor upon light inactivation. Hmd activity was inhibited by high concentrations of CO and CO protected the enzyme from light inactivation indicating that the iron in Hmd is of functional importance. Therefore, reference to Hmd as 'metal-free' hydrogenase is no longer appropriate.},
}
@article {pmid14679228,
year = {2004},
author = {Ding, YH and Ferry, JG},
title = {Flavin mononucleotide-binding flavoprotein family in the domain Archaea.},
journal = {Journal of bacteriology},
volume = {186},
number = {1},
pages = {90-97},
pmid = {14679228},
issn = {0021-9193},
mesh = {Amino Acid Sequence ; Archaea/genetics/*metabolism/physiology ; Archaeal Proteins/chemistry/genetics/*metabolism ; Archaeoglobus fulgidus/genetics/metabolism/physiology ; Binding Sites ; Carrier Proteins/chemistry/genetics/*metabolism ; Escherichia coli/genetics/metabolism ; Ferredoxin-NADP Reductase/metabolism ; Flavin Mononucleotide/*metabolism ; Flavoproteins/chemistry/genetics/*metabolism ; Methane/metabolism ; Molecular Sequence Data ; Oxidation-Reduction ; Oxidative Stress ; },
abstract = {The protein (AfpA, for archaeoflavoprotein) encoded by AF1518 in the genome of Archaeoglobus fulgidus was produced in Escherichia coli and characterized. AfpA was found to be a homodimer with a native molecular mass of 43 kDa and containing two noncovalently bound flavin mononucleotides (FMNs). The cell extract of A. fulgidus catalyzed the CO-dependent reduction of AfpA that was stimulated by the addition of ferredoxin. Ferredoxin was found to be a direct electron donor to purified AfpA, whereas rubredoxin was unable to substitute. Neither NADH nor NADPH was an electron donor. Ferricyanide, 2,6-dichlorophenolindophenol, several quinones, ferric citrate, bovine cytochrome c, and O(2) accepted electrons from reduced AfpA, whereas coenzyme F(420) did not. The rate of cytochrome c reduction was enhanced in the presence of O(2) suggesting that superoxide is a product of the interaction of reduced AfpA with O(2). Although AF1518 was previously annotated as encoding a decarboxylase involved in coenzyme A biosynthesis, the results establish that AfpA is an electron carrier protein with ferredoxin as the physiological electron donor. The genomes of several diverse Archaea contained afpA homologs clustered with open reading frames annotated as homologs of genes encoding reductases involved in the oxidative stress response of anaerobes from the domain Bacteria. A potential role for AfpA in coupling electron flow from ferredoxin to the putative reductases is discussed. A search of the databases suggests that AfpA is the prototype of a previously unrecognized flavoprotein family unique to the domain Archaea for which the name archaeoflavoprotein is proposed.},
}
@article {pmid14673752,
year = {2003},
author = {Hamana, K and Tanaka, T and Hosoya, R and Niitsu, M and Itoh, T},
title = {Cellular polyamines of the acidophilic, thermophilic and thermoacidophilic archaebacteria, Acidilobus, Ferroplasma, Pyrobaculum, Pyrococcus, Staphylothermus, Thermococcus, Thermodiscus and Vulcanisaeta.},
journal = {The Journal of general and applied microbiology},
volume = {49},
number = {5},
pages = {287-293},
doi = {10.2323/jgam.49.287},
pmid = {14673752},
issn = {0022-1260},
mesh = {Chromatography, High Pressure Liquid/methods ; Crenarchaeota/*chemistry/classification ; Euryarchaeota/*chemistry/classification ; Polyamines/*analysis/isolation &amp; purification ; },
abstract = {Cellular polyamines of newly isolated acidophilic, thermophilic and thermoacidophilic archaebacteria were investigated for the chemotaxonomic significance of polyamine distribution profiles. In addition to spermidine, spermine and agmatine, a quaternary branched penta-amine, N(4)-bis(aminopropyl)spermidine, was found in thermophilic Thermococcus waiotapuensis, Thermococcus aegaeus and Pyrococcus glycovorans belonging to the order Thermococcales. An acidophilic euryarchaeon, Ferroplasma acidiphilum located in the order Thermoplasmatales, contained spermidine and agmatine. Norspermidine, spermidine, norspermine and spermine were found in thermoacidophilic Acidilobus aceticus and thermophilic Thermodiscus maritimus located in the order Desulfurococcales, and in thermophilic Pyrobaculum arsenaticum, Pyrobaculum oguniense, Vulcanisaeta distributa and Vulcanisaeta souniana belonging to the order Thermoproteales; however, the four genera differ on their tetra- and penta-amine levels. Thermophilic Staphylothermus hellenicus belonging to Desulfurococcales contained caldopentamine, caldohexamine and N1-acetylcaldopentamine in addition to norspermidine, spermidine and norspermine. This is the first report on the occurrence of acetylated penta-amine in nature.},
}
@article {pmid14669915,
year = {2003},
author = {Yang, Y and Huang, YP and Shen, P},
title = {The 492-bp RM07 DNA fragment from the halophilic Archaea confers promoter activity in all three domains of life.},
journal = {Current microbiology},
volume = {47},
number = {5},
pages = {388-394},
doi = {10.1007/s00284-003-4034-4},
pmid = {14669915},
issn = {0343-8651},
mesh = {Artificial Gene Fusion ; Base Sequence ; Chloramphenicol O-Acetyltransferase/genetics/physiology ; DNA, Archaeal/chemistry/*genetics ; Drug Resistance, Fungal ; Escherichia coli/genetics ; Genes, Reporter ; Gentamicins/pharmacology ; Halobacterium salinarum/*genetics/*physiology ; Haloferax volcanii/genetics ; Molecular Sequence Data ; Mutagenesis, Site-Directed ; *Promoter Regions, Genetic ; RNA, Archaeal/isolation &amp; purification ; Reverse Transcriptase Polymerase Chain Reaction ; Saccharomyces cerevisiae/genetics ; Sequence Deletion ; Transformation, Genetic ; beta-Galactosidase/genetics/physiology ; },
abstract = {A 492-bp DNA fragment, designated RM07, was isolated from the chromosomal DNA of the halophilic Archaea, Halobacterium halobium, and was shown to confer promoter activity in Escherichia coli. Sequence analysis revealed that RM07 contained three consensus sequences of the archaeal distal promoter element as well as the typical -35 and -10 box sequences of bacterial promoters. Promoter probe analysis confirmed that RM07 conferred promoter activity in all three domains of life: Archaea (Haloferax volcanii), Eukarya (Saccharomyces cerevisiae) and Bacteria (Escherichia coli). Deletion analysis and site-directed mutagenesis further identified the functional regions within RM07 required for promoter activity. This is the first report of a DNA fragment from Archaea that confers promoter activity in all three domains of life, suggesting that the promoter structure and activity may be viewed as a bridge narrowing the gaps among the different domains of life.},
}
@article {pmid14645280,
year = {2003},
author = {Woodson, JD and Zayas, CL and Escalante-Semerena, JC},
title = {A new pathway for salvaging the coenzyme B12 precursor cobinamide in archaea requires cobinamide-phosphate synthase (CbiB) enzyme activity.},
journal = {Journal of bacteriology},
volume = {185},
number = {24},
pages = {7193-7201},
pmid = {14645280},
issn = {0021-9193},
support = {F31-GM64009/GM/NIGMS NIH HHS/United States ; GM40313/GM/NIGMS NIH HHS/United States ; R01 GM040313/GM/NIGMS NIH HHS/United States ; F31 GM064009/GM/NIGMS NIH HHS/United States ; R37 GM040313/GM/NIGMS NIH HHS/United States ; },
mesh = {Amidohydrolases/genetics/*metabolism ; Archaeal Proteins/genetics/metabolism ; Cobamides/biosynthesis/chemistry/*metabolism ; Genes, Archaeal ; Genetic Complementation Test ; Halobacterium/genetics/*metabolism ; },
abstract = {The ability of archaea to salvage cobinamide has been under question because archaeal genomes lack orthologs to the bacterial nucleoside triphosphate:5'-deoxycobinamide kinase enzyme (cobU in Salmonella enterica). The latter activity is required for cobinamide salvaging in bacteria. This paper reports evidence that archaea salvage cobinamide from the environment by using a pathway different from the one used by bacteria. These studies demanded the functional characterization of two genes whose putative function had been annotated based solely on their homology to the bacterial genes encoding adenosylcobyric acid and adenosylcobinamide-phosphate synthases (cbiP and cbiB, respectively) of S. enterica. A cbiP mutant strain of the archaeon Halobacterium sp. strain NRC-1 was auxotrophic for adenosylcobyric acid, a known intermediate of the de novo cobamide biosynthesis pathway, but efficiently salvaged cobinamide from the environment, suggesting the existence of a salvaging pathway in this archaeon. A cbiB mutant strain of Halobacterium was auxotrophic for adenosylcobinamide-GDP, a known de novo intermediate, and did not salvage cobinamide. The results of the nutritional analyses of the cbiP and cbiB mutants suggested that the entry point for cobinamide salvaging is adenosylcobyric acid. The data are consistent with a salvaging pathway for cobinamide in which an amidohydrolase enzyme cleaves off the aminopropanol moiety of adenosylcobinamide to yield adenosylcobyric acid, which is converted by the adenosylcobinamide-phosphate synthase enzyme to adenosylcobinamide-phosphate, a known intermediate of the de novo biosynthetic pathway. The existence of an adenosylcobinamide amidohydrolase enzyme would explain the lack of an adenosylcobinamide kinase in archaea.},
}
@article {pmid14641908,
year = {2003},
author = {Studholme, DJ and Pau, RN},
title = {A DNA element recognised by the molybdenum-responsive transcription factor ModE is conserved in Proteobacteria, green sulphur bacteria and Archaea.},
journal = {BMC microbiology},
volume = {3},
number = {},
pages = {24},
pmid = {14641908},
issn = {1471-2180},
mesh = {Archaea/*genetics ; *Bacterial Proteins ; Base Sequence ; Binding Sites ; Chlorobi/*genetics ; *Conserved Sequence ; DNA, Archaeal/metabolism ; DNA, Bacterial/metabolism ; *Escherichia coli Proteins ; Molybdenum/metabolism ; Proteobacteria/*genetics ; Transcription Factors/chemistry/*metabolism ; },
abstract = {BACKGROUND: The transition metal molybdenum is essential for life. Escherichia coli imports this metal into the cell in the form of molybdate ions, which are taken up via an ABC transport system. In E. coli and other Proteobacteria molybdenum metabolism and homeostasis are regulated by the molybdate-responsive transcription factor ModE.<br><br>RESULTS: Orthologues of ModE are widespread amongst diverse prokaryotes, but not ubiquitous. We identified probable ModE-binding sites upstream of genes implicated in molybdenum metabolism in green sulphur bacteria and methanogenic Archaea as well as in Proteobacteria. We also present evidence of horizontal transfer of nitrogen fixation genes between green sulphur bacteria and methanogenic Archaea.<br><br>CONCLUSIONS: Whereas most of the archaeal helix-turn-helix-containing transcription factors belong to families that are Archaea-specific, ModE is unusual in that it is found in both Archaea and Bacteria. Moreover, its cognate upstream DNA recognition sequence is also conserved between Archaea and Bacteria, despite the fundamental differences in their core transcription machinery. ModE is the third example of a transcriptional regulator with a binding signal that is conserved in Bacteria and Archaea.},
}
@article {pmid14638414,
year = {2003},
author = {Radianingtyas, H and Wright, PC},
title = {Alcohol dehydrogenases from thermophilic and hyperthermophilic archaea and bacteria.},
journal = {FEMS microbiology reviews},
volume = {27},
number = {5},
pages = {593-616},
doi = {10.1016/S0168-6445(03)00068-8},
pmid = {14638414},
issn = {0168-6445},
mesh = {Alcohol Dehydrogenase/*genetics/*metabolism ; Amino Acid Sequence ; Archaea/*enzymology/*genetics ; Bacteria/*enzymology/*genetics ; Molecular Sequence Data ; },
abstract = {Many studies have been undertaken to characterise alcohol dehydrogenases (ADHs) from thermophiles and hyperthermophiles, mainly to better understand their activities and thermostability. To date, there are 20 thermophilic archaeal and 17 thermophilic bacterial strains known to have ADHs or similar enzymes, including the hypothetical proteins. Some of these thermophiles are found to have multiple ADHs, sometimes of different types. A rigid delineation of amino acid sequences amongst currently elucidated thermophilic ADHs and similar proteins is phylogenetically apparent. All are NAD(P)-dependent, with one exception that utilises the cofactor F(420) instead. Within the NAD(P)-dependent group, the thermophilic ADHs are orderly clustered as zinc-dependent ADHs, short-chain ADHs, and iron-containing/activated ADHs. Distance matrix calculations reveal that thermophilic ADHs within one type are homologous, with those derived from a single genus often showing high similarities. Elucidation of the enzyme activity and stability, coupled with structure analysis, provides excellent information to explain the relationship between them, and thermophilic ADHs diversity.},
}
@article {pmid14627803,
year = {2003},
author = {Santoro, SW and Anderson, JC and Lakshman, V and Schultz, PG},
title = {An archaebacteria-derived glutamyl-tRNA synthetase and tRNA pair for unnatural amino acid mutagenesis of proteins in Escherichia coli.},
journal = {Nucleic acids research},
volume = {31},
number = {23},
pages = {6700-6709},
pmid = {14627803},
issn = {1362-4962},
support = {R01 GM062159/GM/NIGMS NIH HHS/United States ; GM62159/GM/NIGMS NIH HHS/United States ; },
mesh = {Acylation ; *Amino Acid Substitution ; Archaea/*enzymology/*genetics ; Base Sequence ; Codon, Nonsense/genetics ; Consensus Sequence ; Escherichia coli Proteins/biosynthesis/*chemistry/*genetics ; Glutamate-tRNA Ligase/genetics/*metabolism ; Molecular Sequence Data ; Mutagenesis ; Nucleic Acid Conformation ; Pyrococcus horikoshii/enzymology ; RNA, Transfer, Glu/genetics/*metabolism ; },
abstract = {The addition of novel amino acids to the genetic code of Escherichia coli involves the generation of an aminoacyl-tRNA synthetase and tRNA pair that is 'orthogonal', meaning that it functions independently of the synthetases and tRNAs endogenous to E.coli. The amino acid specificity of the orthogonal synthetase is then modified to charge the corresponding orthogonal tRNA with an unnatural amino acid that is subsequently incorporated into a polypeptide in response to a nonsense or missense codon. Here we report the development of an orthogonal glutamic acid synthetase and tRNA pair. The tRNA is derived from the consensus sequence obtained from a multiple sequence alignment of archaeal tRNA(Glu) sequences. The glutamyl-tRNA synthetase is from the achaebacterium Pyrococcus horikoshii. The new orthogonal pair suppresses amber nonsense codons with an efficiency roughly comparable to that of the orthogonal tyrosine pair derived from Methanococcus jannaschii, which has been used to selectively incorporate a variety of unnatural amino acids into proteins in E.coli. Development of the glutamic acid orthogonal pair increases the potential diversity of unnatural amino acid structures that may be incorporated into proteins in E.coli.},
}
@article {pmid14624007,
year = {2003},
author = {Marck, C and Grosjean, H},
title = {Identification of BHB splicing motifs in intron-containing tRNAs from 18 archaea: evolutionary implications.},
journal = {RNA (New York, N.Y.)},
volume = {9},
number = {12},
pages = {1516-1531},
pmid = {14624007},
issn = {1355-8382},
mesh = {Base Sequence ; *Evolution, Molecular ; Exons ; *Introns ; Molecular Sequence Data ; Nucleic Acid Conformation ; *RNA Splicing ; RNA, Archaeal/*chemistry/genetics ; RNA, Transfer/*chemistry/genetics ; },
abstract = {Most introns of archaeal tRNA genes (tDNAs) are located in the anticodon loop, between nucleotides 37 and 38, the unique location of their eukaryotic counterparts. However, in several Archaea, mostly in Crenarchaeota, introns have been found at many other positions of the tDNAs. In the present work, we revisit and extend all previous findings concerning the identification, exact location, size, and possible fit to the proposed bulge-helix-bulge structural motif (BHB, now renamed hBHBh') of the sequences spanning intron-exon junctions in intron-containing tRNAs of 18 archaea. A total of 103 introns were found located at the usual position 37/38 and 33 introns at 14 other different positions, that is, in the anticodon stem and loop, in the D-and T-loops, in the V-arm, or in the amino acid arm. For introns located at 37/38 and elsewhere in the pre-tRNA, canonical hBHBh' motifs were not always found. Instead, a relaxed hBH or HBh' motif including the constant central 4-bp helix H flanked by one helix (h or h') on either side generating only one bulge could be disclosed. Also, for introns located elsewhere than at position 37/38, the hBHBh' (or HBh') structure competes with the three-dimensional structure of the mature tRNA, attesting to important structural rearrangements during the complex multistep maturation-splicing processes. A homotetramer-type of splicing endonuclease (like in all Crenarchaeota) instead of a homodimeric-type of enzyme (as in most Euryarchaeota) appears to best fit the requirement for splicing introns at relaxed hBH or HBh' motifs, and may represent the most primitive form of this enzyme.},
}
@article {pmid19719570,
year = {2003},
author = {Huang, LN and Chen, YQ and Zhou, H and Luo, S and Lan, CY and Qu, LH},
title = {Characterization of methanogenic Archaea in the leachate of a closed municipal solid waste landfill.},
journal = {FEMS microbiology ecology},
volume = {46},
number = {2},
pages = {171-177},
doi = {10.1016/S0168-6496(03)00218-6},
pmid = {19719570},
issn = {1574-6941},
abstract = {Cultivation-independent molecular approaches were used to investigate the phylogenetic composition of Archaea and the relative abundance of phylogenetically defined groups of methanogens in the leachate of a closed municipal solid waste landfill. Cloning and phylogenetic analysis of archaeal 16S rRNA gene sequences (16S rDNA) revealed that the landfill leachate harbored a diverse Archaea community, with sequence types distributed within the two archaeal kingdoms of the Euryarchaeota and the Crenarchaeota. Of the 80 clones examined, 51 were phylogenetically associated with well-defined methanogen lineages covering two major methanogenic phenotypes; 20 were related to Thermoplasma and were grouped with some novel archaeal rRNA gene sequences recently recovered from various anaerobic habitats; finally, five belonged to Crenarchaeota and were not closely related to any hitherto cultivated species. Most of the methanogen-like clones were affiliated with the hydrogenotrophic Methanomicrobiales and the methylotrophic and acetoclastic Methanosarcinales. Quantitative oligonucleotide hybridization experiments showed that methanogens in the leachate accounted for only a very small fraction of the total community (approximately 2%) and that Methanomicrobiales and Methanosarcinales constituted the majority of the total methanogenic population.},
}
@article {pmid14592760,
year = {2003},
author = {Bettstetter, M and Peng, X and Garrett, RA and Prangishvili, D},
title = {AFV1, a novel virus infecting hyperthermophilic archaea of the genus acidianus.},
journal = {Virology},
volume = {315},
number = {1},
pages = {68-79},
doi = {10.1016/s0042-6822(03)00481-1},
pmid = {14592760},
issn = {0042-6822},
mesh = {Acidianus/growth &amp; development/*virology ; Base Sequence ; Genome, Viral ; *Hot Temperature ; Lipothrixviridae/*classification/genetics/*isolation &amp; purification/ultrastructure ; Microscopy, Electron ; Molecular Sequence Data ; Open Reading Frames ; Sequence Analysis, DNA ; Viral Proteins/chemistry/genetics/metabolism ; Virion/ultrastructure ; },
abstract = {We describe a novel virus, AFV1, of the hyperthermophilic archaeal genus Acidianus. Filamentous virions are covered with a lipid envelope and contain at least five different proteins with molecular masses in the range of 23-130 kDa and a 20.8-kb-long linear double-stranded DNA. The virus has been assigned to the family Lipothrixviridae on the basis of morphotypic characteristics. Host range is confined to several strains of Acidianus and the virus persists in its hosts in a stable carrier state. The latent period of virus infection is about 4 h. Viral DNA was sequenced and sequence similarities were found to the lipothrixvirus SIFV, the rudiviruses SIRV1 and SIRV2, as well as to conjugative plasmids and chromosomes of the genus Sulfolobus. Exceptionally for the linear genomes of archaeal viruses, many short direct repeats, with the sequence TTGTT or close variants thereof, are closely clustered over 300 bp at each end of the genome. They are reminiscent of the telomeric ends of linear eukaryal chromosomes.},
}
@article {pmid14579252,
year = {2003},
author = {Cavicchioli, R and Curmi, PM and Saunders, N and Thomas, T},
title = {Pathogenic archaea: do they exist?.},
journal = {BioEssays : news and reviews in molecular, cellular and developmental biology},
volume = {25},
number = {11},
pages = {1119-1128},
doi = {10.1002/bies.10354},
pmid = {14579252},
issn = {0265-9247},
mesh = {Animals ; Archaea/classification/*physiology ; Humans ; Phylogeny ; Toxins, Biological ; Virulence ; },
abstract = {Archaea are microorganisms that are distinct from bacteria and eukaryotes. They are prevalent in extreme environments, and yet found in most ecosystems. They are a natural component of the microbiota of most, if not all, humans and other animals. Despite their ubiquity and close association with humans, animals and plants, no pathogenic archaea have been identified. Because no archaeal pathogens have yet been identified, there is a general assumption that archaeal pathogens do not exist. This review examines whether this is a good assumption by investigating the potential for archaea to be or become pathogens. This is achieved by addressing: the diversity of archaea versus known pathogens, opportunities for archaea to demonstrate pathogenicity and be detected as pathogens, reports linking archaea with disease, and immune responses to archaea. In addition, molecular and genomic data are examined for the presence of systems utilised in pathogenesis. The view of this report is that, although archaea can presently be described as non-pathogenic, they have the potential to be (discovered as) pathogens. The present optimistic view that there are no archaeal pathogens is tainted by a severe lack of relevant knowledge, which may have important consequences in the future.},
}
@article {pmid14571983,
year = {2003},
author = {Chen, AC and Ueda, K and Sekiguchi, Y and Ohashi, A and Harada, H},
title = {Molecular detection and direct enumeration of methanogenic Archaea and methanotrophic Bacteria in domestic solid waste landfill soils.},
journal = {Biotechnology letters},
volume = {25},
number = {18},
pages = {1563-1569},
doi = {10.1023/a:1025461915495},
pmid = {14571983},
issn = {0141-5492},
mesh = {Archaea/genetics/isolation &amp; purification ; Colony Count, Microbial/*methods ; Gene Expression Profiling/methods ; In Situ Hybridization, Fluorescence/*methods ; Methanobacterium/*genetics/*isolation &amp; purification ; RNA, Ribosomal, 16S/*analysis/*genetics ; Refuse Disposal/methods ; Sewage/*microbiology ; *Soil Microbiology ; },
abstract = {Methane oxidizing and producing activities of cover soil (10, 30 cm depth) and burial waste (1, 3 m depth) were evaluated: top cover soil (10 cm) had the highest methane oxidizing activity, while 1 m depth buried waste showed the highest methane producing potential. All the sequences of the 1 m sample were found to be closely related to 16S rDNAs of mainly hydrogenotrophic methanogens known, such as genera Methanosarcina, Methanoculleus, and Methanobacterium. We developed a modified fluorescence in situ hybridization (FISH) direct counting method for landfill samples, resulting in the detection of approx. 1% of total cells as archaeal cells (presumably methanogens). However, probe-positive cells could not be found with probes for methanotrophs by the methods.},
}
@article {pmid14568143,
year = {2003},
author = {Makarova, KS and Koonin, EV},
title = {Filling a gap in the central metabolism of archaea: prediction of a novel aconitase by comparative-genomic analysis.},
journal = {FEMS microbiology letters},
volume = {227},
number = {1},
pages = {17-23},
doi = {10.1016/S0378-1097(03)00596-2},
pmid = {14568143},
issn = {0378-1097},
mesh = {Aconitate Hydratase/chemistry/*genetics/metabolism ; Archaea/classification/*genetics/metabolism ; DNA, Archaeal/analysis ; Databases, Factual ; *Genome, Archaeal ; Multigene Family ; Phylogeny ; },
abstract = {Aconitase, an essential enzyme of the tricarboxylic acid cycle (TCA), so far has been identified only in a minority of archaeal genomes. This enzyme belongs to the aconitase A family, which is represented in most bacteria and eukaryotes. Using iterative sequence database search, we linked two previously uncharacterized protein families (COG1679 and COG1786), respectively, to the three Fe-S-cluster-associated aconitase domains and the swiveling domain, the four domains that are present in all known aconitase families. The respective genes are often found in one predicted operon and, moreover, are fused in several species, suggesting a functional and physical interaction. We predict that these proteins together comprise a previously undetected, distinct aconitase family, which we designated aconitase X. Aconitase X is encoded in the genomes of many archaea and some proteobacteria. Among archaea, the pattern of aconitase X occurrence complements that of aconitase A such that together the two enzymes account for aconitase activity in all archaea. Phylogenetic analysis indicates that aconitase X is likely to be the ancestral archaeal form, with non-orthologous displacement in some of the archaea apparently brought about by horizontal transfer of the gene for bacterial aconitase A. The prediction of aconitase X completes the TCA cycle for Methanothermobacter thermoautotrophicus and Archaeoglobus fulgidus and suggests that most archaea have a full TCA cycle.},
}
@article {pmid14551194,
year = {2004},
author = {Hansen, T and Wendorff, D and Schönheit, P},
title = {Bifunctional phosphoglucose/phosphomannose isomerases from the Archaea Aeropyrum pernix and Thermoplasma acidophilum constitute a novel enzyme family within the phosphoglucose isomerase superfamily.},
journal = {The Journal of biological chemistry},
volume = {279},
number = {3},
pages = {2262-2272},
doi = {10.1074/jbc.M309849200},
pmid = {14551194},
issn = {0021-9258},
mesh = {Aeropyrum/*enzymology ; Amino Acid Sequence ; Catalysis ; Circular Dichroism ; Enzyme Stability ; Glucose-6-Phosphate Isomerase/chemistry/genetics/*metabolism ; Mannose-6-Phosphate Isomerase/chemistry/genetics/*metabolism ; Molecular Sequence Data ; Substrate Specificity ; Thermoplasma/*enzymology ; },
abstract = {The hyperthermophilic crenarchaeon Aeropyrum pernix contains phosphoglucose isomerase (PGI) activity. However, obvious homologs with significant identity to known PGIs could not be identified in the sequenced genome of this organism. The PGI activity from A. pernix was purified and characterized. Kinetic analysis revealed that, unlike all known PGIs, the enzyme catalyzed reversible isomerization not only of glucose 6-phosphate but also of epimeric mannose 6-phosphate at similar catalytic efficiency, thus defining the protein as bifunctional phosphoglucose/phosphomannose isomerase (PGI/PMI). The gene pgi/pmi encoding PGI/PMI (open reading frame APE0768) was identified by matrix-assisted laser desorption ionization time-of-flight analyses; the gene was overexpressed in Escherichia coli as functional PGI/PMI. Putative PGI/PMI homologs were identified in several (hyper)thermophilic archaea and two bacteria. The homolog from Thermoplasma acidophilum (Ta1419) was overexpressed in E. coli, and the recombinant enzyme was characterized as bifunctional PGI/PMI. PGI/PMIs showed low sequence identity to the PGI superfamily and formed a distinct phylogenetic cluster. However, secondary structure predictions and the presence of several conserved amino acids potentially involved in catalysis indicate some structural and functional similarity to the PGI superfamily. Thus, we propose that bifunctional PGI/PMI constitutes a novel protein family within the PGI superfamily.},
}
@article {pmid14532061,
year = {2003},
author = {Pflüger, K and Baumann, S and Gottschalk, G and Lin, W and Santos, H and Müller, V},
title = {Lysine-2,3-aminomutase and beta-lysine acetyltransferase genes of methanogenic archaea are salt induced and are essential for the biosynthesis of Nepsilon-acetyl-beta-lysine and growth at high salinity.},
journal = {Applied and environmental microbiology},
volume = {69},
number = {10},
pages = {6047-6055},
pmid = {14532061},
issn = {0099-2240},
mesh = {Acetyltransferases/genetics/*metabolism ; Amino Acid Sequence ; Enzyme Induction ; Gene Deletion ; Gene Expression Regulation, Archaeal ; Genes, Essential ; Intramolecular Transferases/genetics/*metabolism ; Lysine/*analogs &amp; derivatives/*metabolism ; Methane/metabolism ; Methanococcus/drug effects/*enzymology/genetics/growth &amp; development ; Methanosarcina/drug effects/*enzymology/genetics/growth &amp; development ; Methanosarcina barkeri/enzymology/genetics/growth &amp; development ; Molecular Sequence Data ; Sequence Analysis, DNA ; Sodium Chloride/*pharmacology ; },
abstract = {The compatible solute N(epsilon)-acetyl-beta-lysine is unique to methanogenic archaea and is produced under salt stress only. However, the molecular basis for the salt-dependent regulation of N(epsilon)-acetyl-beta-lysine formation is unknown. Genes potentially encoding lysine-2,3-aminomutase (ablA) and beta-lysine acetyltransferase (ablB), which are assumed to catalyze N(epsilon)-acetyl-beta-lysine formation from alpha-lysine, were identified on the chromosomes of the methanogenic archaea Methanosarcina mazei Gö1, Methanosarcina acetivorans, Methanosarcina barkeri, Methanococcus jannaschii, and Methanococcus maripaludis. The order of the two genes was identical in the five organisms, and the deduced proteins were very similar, indicating a high degree of conservation of structure and function. Northern blot analysis revealed that the two genes are organized in an operon (termed the abl operon) in M. mazei Gö1. Expression of the abl operon was strictly salt dependent. The abl operon was deleted in the genetically tractable M. maripaludis. Delta(abl) mutants of M. maripaludis no longer produced N(epsilon)-acetyl-beta-lysine and were incapable of growth at high salt concentrations, indicating that the abl operon is essential for N(epsilon)-acetyl-beta-lysine synthesis. These experiments revealed the first genes involved in the biosynthesis of compatible solutes in methanogens.},
}
@article {pmid14499933,
year = {2003},
author = {Snyder, JC and Stedman, K and Rice, G and Wiedenheft, B and Spuhler, J and Young, MJ},
title = {Viruses of hyperthermophilic Archaea.},
journal = {Research in microbiology},
volume = {154},
number = {7},
pages = {474-482},
doi = {10.1016/S0923-2508(03)00127-X},
pmid = {14499933},
issn = {0923-2508},
mesh = {Archaea/*virology ; Archaeal Viruses/*isolation &amp; purification ; Crenarchaeota/virology ; *Hot Temperature ; },
abstract = {The viruses of Archaea are likely to be useful tools for studying host evolution, host biochemical pathways, and as tools for the biotechnology industry. Many of the viruses isolated from Archaea show distinct morphologies and genes. The euryarchaeal viruses show morphologies similar to the head-and-tail phage isolated from Bacteria; however, sequence analysis of viral genomes from Crenarchaea shows little or no similarity to previously isolated viruses. Because viruses adapt to host organism characteristics, viruses may lead to important discoveries in archaeal biochemistry, genetics, and evolution.},
}
@article {pmid12957937,
year = {2003},
author = {Hallam, SJ and Girguis, PR and Preston, CM and Richardson, PM and DeLong, EF},
title = {Identification of methyl coenzyme M reductase A (mcrA) genes associated with methane-oxidizing archaea.},
journal = {Applied and environmental microbiology},
volume = {69},
number = {9},
pages = {5483-5491},
pmid = {12957937},
issn = {0099-2240},
mesh = {Amino Acid Sequence ; Archaea/enzymology/*genetics ; Cosmids ; DNA, Archaeal/genetics ; DNA, Ribosomal/genetics ; Gene Library ; Genes, Archaeal ; Genetic Variation ; Methane/*metabolism ; Molecular Sequence Data ; Oxidation-Reduction ; Oxidoreductases/chemistry/*genetics ; Polymerase Chain Reaction/methods ; RNA, Ribosomal, 16S/genetics ; Sequence Alignment ; Sequence Homology, Amino Acid ; },
abstract = {Phylogenetic and stable-isotope analyses implicated two methanogen-like archaeal groups, ANME-1 and ANME-2, as key participants in the process of anaerobic methane oxidation. Although nothing is known about anaerobic methane oxidation at the molecular level, the evolutionary relationship between methane-oxidizing archaea (MOA) and methanogenic archaea raises the possibility that MOA have co-opted key elements of the methanogenic pathway, reversing many of its steps to oxidize methane anaerobically. In order to explore this hypothesis, the existence and genomic conservation of methyl coenzyme M reductase (MCR), the enzyme catalyzing the terminal step in methanogenesis, was studied in ANME-1 and ANME-2 archaea isolated from various marine environments. Clone libraries targeting a conserved region of the alpha subunit of MCR (mcrA) were generated and compared from environmental samples, laboratory-incubated microcosms, and fosmid libraries. Four out of five novel mcrA types identified from these sources were associated with ANME-1 or ANME-2 group members. Assignment of mcrA types to specific phylogenetic groups was based on environmental clone recoveries, selective enrichment of specific MOA and mcrA types in a microcosm, phylogenetic congruence between mcrA and small-subunit rRNA tree topologies, and genomic context derived from fosmid sequences. Analysis of the ANME-1 and ANME-2 mcrA sequences suggested the potential for catalytic activity based on conservation of active-site amino acids. These results provide a basis for identifying methanotrophic archaea with mcrA sequences and define a functional genomic link between methanogenic and methanotrophic archaea.},
}
@article {pmid12957936,
year = {2003},
author = {Girguis, PR and Orphan, VJ and Hallam, SJ and DeLong, EF},
title = {Growth and methane oxidation rates of anaerobic methanotrophic archaea in a continuous-flow bioreactor.},
journal = {Applied and environmental microbiology},
volume = {69},
number = {9},
pages = {5472-5482},
pmid = {12957936},
issn = {0099-2240},
mesh = {5'-Nucleotidase/genetics ; Anaerobiosis ; Archaea/classification/*growth &amp; development/isolation &amp; purification/metabolism ; Base Sequence ; *Bioreactors ; DNA Primers ; Equipment Design ; Fresh Water/microbiology ; Geologic Sediments/microbiology ; Methane/*metabolism ; Oxidation-Reduction ; Phylogeny ; Seawater/microbiology ; },
abstract = {Anaerobic methanotrophic archaea have recently been identified in anoxic marine sediments, but have not yet been recovered in pure culture. Physiological studies on freshly collected samples containing archaea and their sulfate-reducing syntrophic partners have been conducted, but sample availability and viability can limit the scope of these experiments. To better study microbial anaerobic methane oxidation, we developed a novel continuous-flow anaerobic methane incubation system (AMIS) that simulates the majority of in situ conditions and supports the metabolism and growth of anaerobic methanotrophic archaea. We incubated sediments collected from within and outside a methane cold seep in Monterey Canyon, Calif., for 24 weeks on the AMIS system. Anaerobic methane oxidation was measured in all sediments after incubation on AMIS, and quantitative molecular techniques verified the increases in methane-oxidizing archaeal populations in both seep and nonseep sediments. Our results demonstrate that the AMIS system stimulated the maintenance and growth of anaerobic methanotrophic archaea, and possibly their syntrophic, sulfate-reducing partners. Our data demonstrate the utility of combining physiological and molecular techniques to quantify the growth and metabolic activity of anaerobic microbial consortia. Further experiments with the AMIS system should provide a better understanding of the biological mechanisms of methane oxidation in anoxic marine environments. The AMIS may also enable the enrichment, purification, and isolation of methanotrophic archaea as pure cultures or defined syntrophic consortia.},
}
@article {pmid12951519,
year = {2003},
author = {Usami, R and Fukushima, T and Mizuki, T and Inoue, A and Yoshida, Y and Horikoshi, K},
title = {Organic solvent tolerance of halophilic archaea.},
journal = {Bioscience, biotechnology, and biochemistry},
volume = {67},
number = {8},
pages = {1809-1812},
doi = {10.1271/bbb.67.1809},
pmid = {12951519},
issn = {0916-8451},
mesh = {Alkanes/chemistry/*pharmacology ; Culture Media ; Ether/analogs &amp; derivatives/*pharmacology ; Halobacteriaceae/drug effects/genetics/*growth &amp; development ; Solvents ; Species Specificity ; },
abstract = {Organic solvent tolerance was tested in type strains of type species of the sixteen genera of Halobacteriaceae, the halophilic archaea. Most of the strains were observed to grow in the presence of hexylether (log Pow=5.1), but none grew in the presence of n-octane (log Pow=4.9) except Halogeometricum borinquense JCM 10706T and Halorubrum saccharovorum JCM 8865T. On the other hand, two strains, Haloarcula spp. OHF-1 and 2 isolated from a French solar salt were found to show stronger tolerance even to isooctane (log Pow=4.8). Growth of some strains was retarded by the presence of n-decane but reached to the same cell densities at late stationary phase. Final cell densities of some strains were greatly repressed by the presence of the solvent.},
}
@article {pmid12949100,
year = {2003},
author = {Noon, KR and Guymon, R and Crain, PF and McCloskey, JA and Thomm, M and Lim, J and Cavicchioli, R},
title = {Influence of temperature on tRNA modification in archaea: Methanococcoides burtonii (optimum growth temperature [Topt], 23 degrees C) and Stetteria hydrogenophila (Topt, 95 degrees C).},
journal = {Journal of bacteriology},
volume = {185},
number = {18},
pages = {5483-5490},
pmid = {12949100},
issn = {0021-9193},
mesh = {Cell Division/physiology ; Chromatography, Liquid/methods ; Desulfurococcaceae/*genetics/growth &amp; development ; Guanosine/metabolism ; Mass Spectrometry/methods ; Methanosarcinaceae/*genetics/growth &amp; development ; Nucleosides/analysis/chemistry ; RNA Processing, Post-Transcriptional/*physiology ; RNA, Transfer/chemistry/genetics/*metabolism ; Ribose/metabolism ; Species Specificity ; *Temperature ; Uridine/*analogs &amp; derivatives/metabolism ; },
abstract = {We report the first study of tRNA modification in psychrotolerant archaea, specifically in the archaeon Methanococcoides burtonii grown at 4 and 23 degrees C. For comparison, unfractionated tRNA from the archaeal hyperthermophile Stetteria hydrogenophila cultured at 93 degrees C was examined. Analysis of modified nucleosides using liquid chromatography-electrospray ionization mass spectrometry revealed striking differences in levels and identities of tRNA modifications between the two organisms. Although the modification levels in M. burtonii tRNA are the lowest in any organism of which we are aware, it contains more than one residue per tRNA molecule of dihydrouridine, a molecule associated with maintenance of polynucleotide flexibility at low temperatures. No differences in either identities or levels of modifications, including dihydrouridine, as a function of culture temperature were observed, in contrast to selected tRNA modifications previously reported for archaeal hyperthermophiles. By contrast, S. hydrogenophila tRNA was found to contain a remarkable structural diversity of 31 modified nucleosides, including nine methylated guanosines, with eight different nucleoside species methylated at O-2' of ribose, known to be an effective stabilizing motif in RNA. These results show that some aspects of tRNA modification in archaea are strongly associated with environmental temperature and support the thesis that posttranscriptional modification is a universal natural mechanism for control of RNA molecular structure that operates across a wide temperature range in archaea as well as bacteria.},
}
@article {pmid12921536,
year = {2003},
author = {Verhees, CH and Kengen, SW and Tuininga, JE and Schut, GJ and Adams, MW and De Vos, WM and Van Der Oost, J},
title = {The unique features of glycolytic pathways in Archaea.},
journal = {The Biochemical journal},
volume = {375},
number = {Pt 2},
pages = {231-246},
pmid = {12921536},
issn = {1470-8728},
mesh = {Adenosine Diphosphate/metabolism ; Archaea/enzymology/genetics/*metabolism ; Evolution, Molecular ; Glucose/*metabolism ; *Glycolysis ; Phosphotransferases/genetics/metabolism ; Phylogeny ; Species Specificity ; },
abstract = {An early divergence in evolution has resulted in two prokaryotic domains, the Bacteria and the Archaea. Whereas the central metabolic routes of bacteria and eukaryotes are generally well-conserved, variant pathways have developed in Archaea involving several novel enzymes with a distinct control. A spectacular example of convergent evolution concerns the glucose-degrading pathways of saccharolytic archaea. The identification, characterization and comparison of the glycolytic enzymes of a variety of phylogenetic lineages have revealed a mosaic of canonical and novel enzymes in the archaeal variants of the Embden-Meyerhof and the Entner-Doudoroff pathways. By means of integrating results from biochemical and genetic studies with recently obtained comparative and functional genomics data, the structure and function of the archaeal glycolytic routes, the participating enzymes and their regulation are re-evaluated.},
}
@article {pmid12919411,
year = {2003},
author = {Cifuentes, A and Antón, J and De Wit, R and Rodríguez-Valera, F},
title = {Diversity of bacteria and Archaea in sulphate-reducing enrichment cultures inoculated from serial dilution of Zostera noltii rhizosphere samples.},
journal = {Environmental microbiology},
volume = {5},
number = {9},
pages = {754-764},
doi = {10.1046/j.1470-2920.2003.00470.x},
pmid = {12919411},
issn = {1462-2912},
mesh = {Acetates/metabolism ; Archaea/*classification/growth &amp; development/isolation &amp; purification ; Bacteria/*classification/growth &amp; development/isolation &amp; purification ; Base Sequence ; DNA, Archaeal/chemistry/isolation &amp; purification ; DNA, Bacterial/chemistry/isolation &amp; purification ; DNA, Ribosomal/chemistry/isolation &amp; purification ; *Ecosystem ; Fructose/metabolism ; Lactic Acid/metabolism ; Molecular Sequence Data ; Organic Chemicals/metabolism ; Plant Roots/*microbiology ; Quaternary Ammonium Compounds/metabolism ; RNA, Ribosomal, 16S/chemistry ; *Soil Microbiology ; Sucrose/metabolism ; Sulfates/*metabolism ; Zosteraceae/*microbiology ; },
abstract = {We have analysed the diversity of culturable sulphate-reducing bacteria (SRB) in Zostera noltii colonized sediments from Bassin d'Arcachon (France). Four organic substrates have been tested as well as the combination of H2 and CO2 to select for lithotrophic SRB. All energy sources were supplied in parallel cultures that were amended with yeast extract plus NH4+ and prepared without a source of combined nitrogen, the latter to select for diazotrophic SRB. The 10 different enrichment media were inoculated from serial dilution of rhizosphere samples. The highest dilution cultures yielding positive growth (i.e. 10-7) were studied by molecular techniques (16S rDNA clone libraries, RISA and ARDRA). Lactate as a single organic substrate in combination with a source of combined nitrogen resulted in selection of members of the Desulfovibrionaceae. Surprisingly, when lactate was added without a source of combined nitrogen, Desulfobacteriaceae were selected. A strong influence of the presence or absence of combined nitrogen was also observed for the substrates sucrose and fructose. Whereas the liquid culture growing on sucrose and NH4+ systematically yielded 16S rDNA clones related to an environmental unidentified green sulphur bacterium (OPS185), on plates we were able to isolate a SRB related to Desulfovibrio dechloracetivorans, which likely represents a non-described species. Under diazotrophic conditions, sucrose selected for SRB clones related to the cluster formed by Desulfovibrio zosterae, Desulfovibrio salexigens and Desulfovibrio bastinii. The corresponding isolate obtained on plates showed only low sequence similarity with this closest neighbour (93.8%), and we suggest that it also represents a non-described species. Surprisingly, a 16S rDNA sequence corresponding to an archaeon, i.e. a non-extremophile Crenoarchaeota, was retrieved from several of the SRB enrichment cultures even after subsequent transfers.},
}
@article {pmid12918383,
year = {2001},
author = {Glazunov, EA and Kil, Y and Lantsov, VA},
title = {Two types of temperature dependence of homologous recombinases in archaea: the properties of the Desulfurococcus amylolyticus recombinase.},
journal = {Doklady biological sciences : proceedings of the Academy of Sciences of the USSR, Biological sciences sections},
volume = {379},
number = {},
pages = {389-392},
pmid = {12918383},
issn = {0012-4966},
mesh = {Adenosine Triphosphate/metabolism ; Archaea/*enzymology ; Archaeal Proteins/*chemistry ; Catalysis ; DNA Nucleotidyltransferases/*chemistry ; DNA-Binding Proteins/*chemistry ; Desulfurococcaceae/*enzymology ; Hydrolysis ; Kinetics ; Recombinases ; Temperature ; Time Factors ; },
}
@article {pmid12914937,
year = {2003},
author = {Gruber, T and Köhrer, C and Lung, B and Shcherbakov, D and Piendl, W},
title = {Affinity of ribosomal protein S8 from mesophilic and (hyper)thermophilic archaea and bacteria for 16S rRNA correlates with the growth temperatures of the organisms.},
journal = {FEBS letters},
volume = {549},
number = {1-3},
pages = {123-128},
doi = {10.1016/s0014-5793(03)00760-9},
pmid = {12914937},
issn = {0014-5793},
mesh = {Amino Acid Sequence ; Archaea/chemistry/genetics/*growth &amp; development ; Bacteria/chemistry/genetics/*growth &amp; development ; Escherichia coli/chemistry/genetics/growth &amp; development ; Methanococcus/chemistry/genetics/growth &amp; development ; Protein Binding ; RNA Stability ; RNA, Ribosomal, 16S/chemistry/*metabolism ; Ribosomal Proteins/*metabolism ; Sequence Alignment ; Temperature ; Thermus thermophilus/chemistry/genetics/growth &amp; development ; },
abstract = {The ribosomal protein S8 plays a pivotal role in the assembly of the 30S ribosomal subunit. Using filter binding assays, S8 proteins from mesophilic, and (hyper)thermophilic species of the archaeal genus Methanococcus and from the bacteria Escherichia coli and Thermus thermophilus were tested for their affinity to their specific 16S rRNA target site. S8 proteins from hyperthermophiles exhibit a 100-fold and S8 from thermophiles exhibit a 10-fold higher affinity than their mesophilic counterparts. Thus, there is a striking correlation of affinity of S8 proteins for their specific RNA binding site and the optimal growth temperatures of the respective organisms. The stability of individual rRNA-protein complexes might modulate the stability of the ribosome, providing a maximum of thermostability and flexibility at the growth temperature of the organism.},
}
@article {pmid12914651,
year = {2003},
author = {Makarova, KS and Koonin, EV},
title = {Comparative genomics of Archaea: how much have we learned in six years, and what's next?.},
journal = {Genome biology},
volume = {4},
number = {8},
pages = {115},
pmid = {12914651},
issn = {1474-760X},
mesh = {Evolution, Molecular ; *Genome, Archaeal ; Genomics/*methods ; },
abstract = {Archaea comprise one of the three distinct domains of life (with bacteria and eukaryotes). With 16 complete archaeal genomes sequenced to date, comparative genomics has revealed a conserved core of 313 genes that are represented in all sequenced archaeal genomes, plus a variable 'shell' that is prone to lineage-specific gene loss and horizontal gene exchange. The majority of archaeal genes have not been experimentally characterized, but novel functional pathways have been predicted.},
}
@article {pmid12903279,
year = {2000},
author = {Ishikura, H and Nagaoka, Y and Yokozawa, J and Umehara, T and Kuno, A and Hasegawa, T},
title = {Threonyl-tRNA synthetase of archaea: importance of the discriminator base in the aminoacylation of threonine tRNA.},
journal = {Nucleic acids symposium series},
volume = {},
number = {44},
pages = {83-84},
doi = {10.1093/nass/44.1.83},
pmid = {12903279},
issn = {0261-3166},
mesh = {Escherichia coli/metabolism ; Haloferax volcanii/genetics/metabolism ; Mutation ; RNA, Archaeal/genetics/metabolism ; RNA, Bacterial/metabolism ; RNA, Transfer, Amino Acyl/genetics/*metabolism ; Species Specificity ; Substrate Specificity ; Threonine-tRNA Ligase/*metabolism ; },
abstract = {To investigate the contribution of the discriminator base of archaeal tRNA(Thr) in aminoacylation by threonyl-tRNA synthetase (ThrRS), cross-species aminoacylation between Escherichia coli and Haloferax volcanii, halophilic archaea, was studied. It was found that E. coli ThrRS threonylated the H. volcanii tRNA(Thr) but that E. coli threonine tRNA was not aminoacylated by H. volcanii ThrRS. Results of a threonylation experiment using in vitro mutants of E. coli threonine tRNA showed that only the mutant tRNA(Thr) having U73 was threonylated by H. volcanii ThrRS. These findings indicate that the discriminator base U73 of H. volcanii tRNA(Thr) is a strong determinant for the recognition by ThrRS.},
}
@article {pmid12901014,
year = {2003},
author = {Perevalova, AA and Lebedinskiĭ, AV and Bonch-Osmolovskaia, EA and Chernykh, NA},
title = {[Detection of hyperthermophilic archaea of the genus Desulforococcus by hybridization with oligonucleotide probes].},
journal = {Mikrobiologiia},
volume = {72},
number = {3},
pages = {383-389},
pmid = {12901014},
issn = {0026-3656},
mesh = {DNA Primers ; DNA, Archaeal/analysis ; Deoxyuracil Nucleotides ; Desulfurococcaceae/genetics/*isolation &amp; purification ; Dideoxynucleotides ; Digoxigenin/*analogs &amp; derivatives ; *Oligonucleotide Probes ; Polymerase Chain Reaction ; RNA, Archaeal/analysis ; RNA, Ribosomal, 16S/analysis ; Russia ; Species Specificity ; Staining and Labeling ; Water Microbiology ; },
abstract = {Based on the analysis of nucleotide sequences of 16S rRNA, oligonucleotide probes were designed for the detection and identification of representatives of the genus Desulfurococcus (kingdom Crenarchaeota of the domain Archaea). The detection procedure included obtaining of PCR products on DNA isolated from pure cultures, enrichments, or natural samples with a Crenarchaeota-specific primer pair designed: Cren 7F (5'-TTCCGGTTGATCCYGCCGGACC-3') and Cren 518R (5'-GCTGGTWTTACCGCGGCGGCTGA-3'). The PCR products were hybridized with Dig-11-dUTP-labeled oligonucleotide probes targeting the genus Desulfurococcus (Dco 198, 5'-CGTTAACYCCYGCCACACC-3) and its species D. mobilis (Dco_mob 198, 5'-CGTTAACCCCTGCCACACC-3') and D. amylolyticus (Dco_amy 198, 5'-CGTTAACCCCCGCCACACC-3'). With the use of these primers and probes, four new strains isolated from hydrotherms of Kamchatka and Kunashir Island were identified as members of the species Desulfurococcus amylolyticus. Desulfurococcus representatives were detected in several natural samples, including a sample taken from a marine hydrotherm at the Kunashir Island; this demonstrates that representatives of this genus occur not only in terrestrial but also in marine environments.},
}
@article {pmid12881573,
year = {2003},
author = {Whitaker, RJ and Grogan, DW and Taylor, JW},
title = {Geographic barriers isolate endemic populations of hyperthermophilic archaea.},
journal = {Science (New York, N.Y.)},
volume = {301},
number = {5635},
pages = {976-978},
doi = {10.1126/science.1086909},
pmid = {12881573},
issn = {1095-9203},
mesh = {Analysis of Variance ; Biological Evolution ; *Ecosystem ; Genes, Archaeal ; Genes, rRNA ; Genetic Drift ; Genetic Variation ; Genetics, Population ; Genotype ; Geography ; Geologic Sediments/*microbiology ; Hot Temperature ; Hydrogen-Ion Concentration ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, DNA ; Sulfolobus/genetics/isolation &amp; purification/*physiology ; Temperature ; *Water Microbiology ; },
abstract = {Barriers to dispersal between populations allow them to diverge through local adaptation or random genetic drift. High-resolution multilocus sequence analysis revealed that, on a global scale, populations of hyperthermophilic microorganisms are isolated from one another by geographic barriers and have diverged over the course of their recent evolutionary history. The identification of a biogeographic pattern in the archaeon Sulfolobus challenges the current model of microbial biodiversity in which unrestricted dispersal constrains the development of global species richness.},
}
@article {pmid12868410,
year = {2003},
author = {Sakuraba, H and Ohshima, T},
title = {[Modified Embden-Meyerhof pathway of hyperthermophilic Archaea].},
journal = {Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme},
volume = {48},
number = {9},
pages = {1256-1262},
pmid = {12868410},
issn = {0039-9450},
mesh = {Adenosine Triphosphate/metabolism ; Amino Acid Sequence ; Energy Metabolism/genetics ; Glucokinase/chemistry/genetics/physiology ; *Glycolysis/genetics ; Molecular Sequence Data ; Phosphotransferases (Alcohol Group Acceptor)/genetics/physiology ; Pyrococcus furiosus/*enzymology/genetics/*metabolism ; Sequence Homology, Amino Acid ; },
}
@article {pmid12853641,
year = {2003},
author = {Inagaki, Y and Blouin, C and Susko, E and Roger, AJ},
title = {Assessing functional divergence in EF-1alpha and its paralogs in eukaryotes and archaebacteria.},
journal = {Nucleic acids research},
volume = {31},
number = {14},
pages = {4227-4237},
pmid = {12853641},
issn = {1362-4962},
support = {AI147079/AI/NIAID NIH HHS/United States ; },
mesh = {Amino Acid Sequence ; Animals ; Archaea/genetics ; Bacteria/genetics ; Binding Sites/genetics ; DNA, Complementary/chemistry/genetics ; DNA, Protozoan/chemistry/genetics ; Dictyostelium/genetics ; Diplomonadida/genetics ; Eukaryotic Cells/*metabolism ; Genetic Variation ; Giardia lamblia/genetics ; Molecular Sequence Data ; Peptide Elongation Factor 1/chemistry/*genetics ; Phylogeny ; Protein Conformation ; Protein Structure, Tertiary ; Sequence Alignment ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Trichomonas vaginalis/genetics ; Trypanosoma brucei brucei/genetics ; },
abstract = {A number of methods have recently been published that use phylogenetic information extracted from large multiple sequence alignments to detect sites that have changed properties in related protein families. In this study we use such methods to assess functional divergence between eukaryotic EF-1alpha (eEF-1alpha), archaebacterial EF-1alpha (aEF-1alpha) and two eukaryote-specific EF-1alpha paralogs-eukaryotic release factor 3 (eRF3) and Hsp70 subfamily B suppressor 1 (HBS1). Overall, the evolutionary modes of aEF-1alpha, HBS1 and eRF3 appear to significantly differ from that of eEF-1alpha. However, functionally divergent (FD) sites detected between aEF-1alpha and eEF-1alpha only weakly overlap with sites implicated as putative EF-1beta or aminoacyl-tRNA (aa-tRNA) binding residues in EF-1alpha, as expected based on the shared ancestral primary translational functions of these two orthologs. In contrast, FD sites detected between eEF-1alpha and its paralogs significantly overlap with the putative EF-1beta and/or aa-tRNA binding sites in EF-1alpha. In eRF3 and HBS1, these sites appear to be released from functional constraints, indicating that they bind neither eEF-1beta nor aa-tRNA. These results are consistent with experimental observations that eRF3 does not bind to aa-tRNA, but do not support the 'EF-1alpha-like' function recently proposed for HBS1. We re-assess the available genetic data for HBS1 in light of our analyses, and propose that this protein may function in stop codon-independent peptide release.},
}
@article {pmid12836705,
year = {2002},
author = {Sokabe, M and Kawamura, T and Sakai, N and Yao, M and Watanabe, N and Tanaka, I},
title = {The X-ray crystal structure of pyrrolidone-carboxylate peptidase from hyperthermophilic archaea Pyrococcus horikoshii.},
journal = {Journal of structural and functional genomics},
volume = {2},
number = {3},
pages = {145-154},
pmid = {12836705},
issn = {1345-711X},
mesh = {Amino Acid Sequence ; Archaeal Proteins/*chemistry ; Bacillus/enzymology ; Bacterial Proteins/chemistry ; Crystallography, X-Ray ; Cysteine Endopeptidases/chemistry ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Pyrococcus/*enzymology ; Pyrococcus furiosus/enzymology ; Pyroglutamyl-Peptidase I/*chemistry ; Recombinant Fusion Proteins/chemistry ; Sequence Alignment ; Sequence Homology, Amino Acid ; Structure-Activity Relationship ; Thermococcus/enzymology ; },
abstract = {The crystal structure of pyrrolidone-carboxylate peptidase (PCP) from hyperthermophilic archaea Pyrococcus horikoshii (PhoPCP) has been determined at 1.6-A resolution by X-ray crystallography. PCP belongs to the C15 family of cysteine protease, and specifically removes the amino terminal pyroglutamate residue from a wide range of N-terminal-blocking peptides. The crystal structure is very similar to that of other hyperthermophiles, Pyrococcus furiosus and Thermococcus litoralis, and even that from the mesophile, Bacillus amyloliquefaciens. The inter-subunit disulfide bonds, which have been proposed as one of the thermostabilizing factors of the PCP from such hyperthermophiles, was not present in PhoPCP. The result suggests that the thermostability of PhoPCP may be obtained by the accumulation of many weak factors.},
}
@article {pmid12836292,
year = {2001},
author = {Yokozawa, J and Nagaoka, Y and Umehara, T and Iwaki, J and Kawarabayasi, Y and Koyama, Y and Sako, Y and Wakagi, T and Kuno, A and Hasegawa, T},
title = {Recognition of tRNA by aminoacyl-tRNA synthetase from hyperthermophilic archaea, Aeropyrum pernix K1.},
journal = {Nucleic acids research. Supplement (2001)},
volume = {},
number = {1},
pages = {117-118},
doi = {10.1093/nass/1.1.117},
pmid = {12836292},
mesh = {Desulfurococcaceae/*enzymology ; Enzyme Stability ; Hot Temperature ; RNA, Archaeal/metabolism ; RNA, Bacterial/metabolism ; RNA, Transfer, Thr/*metabolism ; Substrate Specificity ; Threonine-tRNA Ligase/*metabolism ; },
abstract = {To study the recognition sites of tRNA for archaeal aminoacyl-tRNA synthetase, several aminoacyl-tRNA synthetase genes from hyperthermophilic archaeon, Aeropyrum pernix K1 were cloned and expressed. All the expressed enzymes showed extreme thermostability. Expressed threonyl-tRNA synthetase threonylated not only archaeal (A. pernix and Haloferax volcanii) threonine tRNAs but also Escherichia coli threonine tRNA. However, threonyl-tRNA synthetase from H. volcanii did not threonylate E. coli threonine tRNA.},
}
@article {pmid12816550,
year = {2003},
author = {Faguy, DM},
title = {Lateral gene transfer (LGT) between Archaea and Escherichia coli is a contributor to the emergence of novel infectious disease.},
journal = {BMC infectious diseases},
volume = {3},
number = {},
pages = {13},
pmid = {12816550},
issn = {1471-2334},
mesh = {Archaea/*genetics ; Escherichia coli/*genetics/pathogenicity ; *Gene Transfer, Horizontal ; Transduction, Genetic ; Transformation, Bacterial/genetics ; Transformation, Genetic ; Virulence/genetics ; },
abstract = {BACKGROUND: Lateral gene transfer is the major mechanism for acquisition of new virulence genes in pathogens. Recent whole genome analyses have suggested massive gene transfer between widely divergent organisms.<br><br>Archeal-like genes acting as virulence genes are present in several pathogens and genomes contain a number of archaeal-like genes of unknown function. Archaea, by virtue of their very different evolutionary history and different environment, provide a pool of potential virulence genes to bacterial pathogens.<br><br>TESTING THE HYPOTHESIS: We can test this hypothesis by 1)identifying genes likely to have been transferred (directly or indirectly) to E. coli O157:H7 from archaea; 2)investigating the distribution of similar genes in pathogens and non-pathogens and 3)performing rigorous phylogenetic analyses on putative transfers.<br><br>Although this hypothesis focuses on archaea and E. coli, it will serve as a model having broad applicability to a number of pathogenic systems. Since no archaea are known vertebrate pathogens, archaeal-like transferred genes that are associated with virulence in bacteria represent a clear model for the emergence of virulence genes.},
}
@article {pmid12809505,
year = {2003},
author = {Lipman, RS and Chen, J and Evilia, C and Vitseva, O and Hou, YM},
title = {Association of an aminoacyl-tRNA synthetase with a putative metabolic protein in archaea.},
journal = {Biochemistry},
volume = {42},
number = {24},
pages = {7487-7496},
doi = {10.1021/bi0344533},
pmid = {12809505},
issn = {0006-2960},
mesh = {Amino Acid Sequence ; Amino Acid Substitution ; Amino Acyl-tRNA Synthetases/isolation &amp; purification/*metabolism ; Archaeal Proteins/genetics/isolation &amp; purification/*metabolism ; Electrophoretic Mobility Shift Assay ; Humans ; Kinetics ; Methanococcaceae/*enzymology ; Molecular Sequence Data ; Oxidoreductases/genetics ; Protein Binding ; Protein Structure, Tertiary ; RNA, Transfer/metabolism ; Recombinant Proteins/genetics/isolation &amp; purification/metabolism ; Repetitive Sequences, Amino Acid ; Sequence Alignment ; Sequence Homology, Amino Acid ; },
abstract = {Aminoacyl-tRNA synthetases are essential enzymes that catalyze attachment of amino acids to tRNAs for decoding of genetic information. In higher eukaryotes, several synthetases associate with non-synthetase proteins to form a high-molecular mass complex that may improve the efficiency of protein synthesis. This multi-synthetase complex is not found in bacteria. Here we describe the isolation of a non-synthetase protein from the archaeon Methanocaldococcus jannaschii that was copurified with prolyl-tRNA synthetase (ProRS). This protein, Mj1338, also interacts with several other tRNA synthetases and has an affinity for general tRNA, suggesting the possibility of forming a multi-synthetase complex. However, unlike the non-synthetase proteins in the eukaryotic complex, the protein Mj1338 is predicted to be a metabolic protein, related to members of the family of H(2)-forming N(5),N(10)-methylene tetrahydromethanopterin (5,10-CH(2)-H(4)MP) dehydrogenases that are involved in the one-carbon metabolism of the archaeon. The association of Mj1338 with ProRS, and with other components of the protein synthesis machinery, thus suggests the possibility of a closer link between metabolism and decoding in archaea than in eukarya or bacteria.},
}
@article {pmid12805271,
year = {2003},
author = {Saunders, NF and Thomas, T and Curmi, PM and Mattick, JS and Kuczek, E and Slade, R and Davis, J and Franzmann, PD and Boone, D and Rusterholtz, K and Feldman, R and Gates, C and Bench, S and Sowers, K and Kadner, K and Aerts, A and Dehal, P and Detter, C and Glavina, T and Lucas, S and Richardson, P and Larimer, F and Hauser, L and Land, M and Cavicchioli, R},
title = {Mechanisms of thermal adaptation revealed from the genomes of the Antarctic Archaea Methanogenium frigidum and Methanococcoides burtonii.},
journal = {Genome research},
volume = {13},
number = {7},
pages = {1580-1588},
pmid = {12805271},
issn = {1088-9051},
mesh = {Adaptation, Physiological/*genetics ; Amino Acid Sequence ; Archaeal Proteins/genetics ; Bacterial Proteins/genetics ; Base Composition ; *Cold Temperature ; DNA-Binding Proteins/genetics ; Genes, Archaeal/genetics ; *Genome, Archaeal ; Methanomicrobiaceae/*genetics ; Methanosarcinaceae/*genetics ; Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; RNA, Transfer/chemistry/genetics ; RNA-Binding Proteins/genetics ; Sequence Homology, Amino Acid ; },
abstract = {We generated draft genome sequences for two cold-adapted Archaea, Methanogenium frigidum and Methanococcoides burtonii, to identify genotypic characteristics that distinguish them from Archaea with a higher optimal growth temperature (OGT). Comparative genomics revealed trends in amino acid and tRNA composition, and structural features of proteins. Proteins from the cold-adapted Archaea are characterized by a higher content of noncharged polar amino acids, particularly Gln and Thr and a lower content of hydrophobic amino acids, particularly Leu. Sequence data from nine methanogen genomes (OGT 15 degrees -98 degrees C) were used to generate 1111 modeled protein structures. Analysis of the models from the cold-adapted Archaea showed a strong tendency in the solvent-accessible area for more Gln, Thr, and hydrophobic residues and fewer charged residues. A cold shock domain (CSD) protein (CspA homolog) was identified in M. frigidum, two hypothetical proteins with CSD-folds in M. burtonii, and a unique winged helix DNA-binding domain protein in M. burtonii. This suggests that these types of nucleic acid binding proteins have a critical role in cold-adapted Archaea. Structural analysis of tRNA sequences from the Archaea indicated that GC content is the major factor influencing tRNA stability in hyperthermophiles, but not in the psychrophiles, mesophiles or moderate thermophiles. Below an OGT of 60 degrees C, the GC content in tRNA was largely unchanged, indicating that any requirement for flexibility of tRNA in psychrophiles is mediated by other means. This is the first time that comparisons have been performed with genome data from Archaea spanning the growth temperature extremes from psychrophiles to hyperthermophiles.},
}
@article {pmid12798234,
year = {2003},
author = {Prangishvili, D},
title = {Evolutionary insights from studies on viruses of hyperthermophilic archaea.},
journal = {Research in microbiology},
volume = {154},
number = {4},
pages = {289-294},
doi = {10.1016/S0923-2508(03)00073-1},
pmid = {12798234},
issn = {0923-2508},
mesh = {Archaea/*virology ; Archaeal Viruses/physiology/*ultrastructure ; *Biological Evolution ; Hot Temperature ; Sulfolobus/virology ; Thermoproteaceae/virology ; },
abstract = {The morphological diversity of viruses which parasitize hyperthermophilic archaea thriving at temperatures > or = 80 degrees C appears to exceed that of viruses of prokaryotes living at lower temperatures. Based on assumptions of the existence of viruses in the prebiotic phase of evolution and hot origins of cellular life, we suggest that this remarkable diversity could have its source in ancestral diversity of viral morphotypes in hot environments. Attempts are made to trace evolutionary relationships of viruses of hyperthermophilic archaea with other viruses.},
}
@article {pmid12788726,
year = {2003},
author = {Empadinhas, N and Albuquerque, L and Henne, A and Santos, H and da Costa, MS},
title = {The bacterium Thermus thermophilus, like hyperthermophilic archaea, uses a two-step pathway for the synthesis of mannosylglycerate.},
journal = {Applied and environmental microbiology},
volume = {69},
number = {6},
pages = {3272-3279},
pmid = {12788726},
issn = {0099-2240},
mesh = {Amino Acid Sequence ; DNA, Archaeal/analysis ; DNA, Bacterial/analysis ; Glyceric Acids ; Hot Temperature ; Mannose/*analogs &amp; derivatives/*biosynthesis ; Mannosyltransferases/genetics/*metabolism ; Molecular Sequence Data ; Phosphotransferases (Alcohol Group Acceptor)/genetics/*metabolism ; Pyrococcus/enzymology ; Recombinant Proteins/genetics/metabolism ; Sequence Analysis, DNA ; Thermus thermophilus/*enzymology/genetics/metabolism ; },
abstract = {The biosynthetic pathway for the synthesis of the compatible solute alpha-mannosylglycerate (MG) in the thermophilic bacterium Thermus thermophilus HB27 was identified based on the activities of recombinant mannosyl-3-phosphoglycerate synthase (MPGS) (EC 2.4.1.217) and mannosyl-3-phosphoglycerate phosphatase (MPGP) (EC 3.1.3.70). The sequences of homologous genes from the archaeon Pyrococcus horikoshii were used to identify MPGS and MPGP genes in T. thermophilus HB27 genome. Both genes were separately cloned and overexpressed in Escherichia coli, yielding 3 to 4 mg of pure recombinant protein per liter of culture. The molecular masses were 43.6 and 28.1 kDa for MPGS and MPGP, respectively. The recombinant MPGS catalyzed the synthesis of alpha-mannosyl-3-phosphoglycerate (MPG) from GDP-mannose and D-3-phosphoglycerate, while the recombinant MPGP catalyzed the dephosphorylation of MPG to MG. The recombinant MPGS had optimal activity at 80 to 90 degrees C and a pH optimum near 7.0; MPGP had maximal activity between 90 and 95 degrees C and at pH 6.0. The activities of both enzymes were strictly dependent on divalent cations; Mn(2+) was most effective for MPGS, while Mn(2+), Co(2+), Mg(2+), and to a lesser extent Ni(2+) activated MPGP. The organization of MG biosynthetic genes in T. thermophilus HB27 is different from the P. horikoshii operon-like structure, since the genes involved in the conversion of fructose-6-phosphate to GDP-mannose are not found immediately downstream of the contiguous MPGS and MPGP genes. The biosynthesis of MG in the thermophilic bacterium T. thermophilus HB27, proceeding through a phosphorylated intermediate, is similar to the system found in hyperthermophilic archaea.},
}
@article {pmid12787364,
year = {2003},
author = {Christensen, SK and Gerdes, K},
title = {RelE toxins from bacteria and Archaea cleave mRNAs on translating ribosomes, which are rescued by tmRNA.},
journal = {Molecular microbiology},
volume = {48},
number = {5},
pages = {1389-1400},
doi = {10.1046/j.1365-2958.2003.03512.x},
pmid = {12787364},
issn = {0950-382X},
mesh = {Archaea/genetics/*metabolism ; Archaeal Proteins/genetics/metabolism ; Bacterial Toxins/genetics/*metabolism ; Base Sequence ; Escherichia coli Proteins/genetics/*metabolism ; Gene Expression Regulation, Archaeal ; Gene Expression Regulation, Bacterial ; Gram-Positive Bacteria/genetics/*metabolism ; Molecular Sequence Data ; *Protein Biosynthesis ; RNA, Bacterial/*metabolism ; RNA, Messenger/*metabolism ; Ribosomes/*metabolism ; Toxins, Biological/genetics/metabolism ; },
abstract = {RelE of Escherichia coli is a global inhibitor of translation that is activated by nutritional stress. Activation of RelE depends on Lon-mediated degradation of RelB, the antagonist that neutralizes RelE. In vitro, RelE cleaves synthetic mRNAs positioned at the ribosomal A-site. We show here that in vivo overexpression of RelE confers cleavage of mRNA and tmRNA in their coding regions. RelE-mediated cleavage depended on translation of the RNAs and occurred at both sense and stop codons. RelE cleavage of mRNA and tmRNA was also induced by amino acid starvation. An ssrA deletion strain was hypersensitive to RelE, whereas overproduction of tmRNA counteracted RelE toxicity. After neutralization of RelE by RelB, rapid recovery of translation required tmRNA, indicating that tmRNA alleviated RelE toxicity by rescuing ribosomes stalled on damaged mRNAs. RelE proteins from Gram-positive Bacteria and Archaea cleaved tmRNA with a pattern similar to that of E. coli RelE, suggesting that the function and target of RelE may be conserved across the prokaryotic domains.},
}
@article {pmid12783513,
year = {2003},
author = {Montenegro, E and Gabler, B and Paradies, G and Seemann, M and Helmchen, G},
title = {Determination of the configuration of an archaea membrane lipid containing cyclopentane rings by total synthesis.},
journal = {Angewandte Chemie (International ed. in English)},
volume = {42},
number = {21},
pages = {2419-2421},
doi = {10.1002/anie.200250629},
pmid = {12783513},
issn = {1433-7851},
mesh = {Archaea/*chemistry ; Membrane Lipids/*chemistry ; Molecular Conformation ; Nuclear Magnetic Resonance, Biomolecular ; },
}
@article {pmid12777534,
year = {2003},
author = {Rest, JS and Mindell, DP},
title = {Retroids in archaea: phylogeny and lateral origins.},
journal = {Molecular biology and evolution},
volume = {20},
number = {7},
pages = {1134-1142},
doi = {10.1093/molbev/msg135},
pmid = {12777534},
issn = {0737-4038},
support = {T32-HG00040/HG/NHGRI NIH HHS/United States ; },
mesh = {Archaea/classification/enzymology/*genetics ; Bacteria/classification/enzymology/*genetics ; Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genome, Archaeal ; *Genome, Bacterial ; Open Reading Frames ; Phylogeny ; RNA-Directed DNA Polymerase/*genetics ; },
abstract = {Until recently, none of the diverse elements bearing reverse transcriptase (retroids) have been known from Archaea. However, in the recently published genomes of the acetate-utilizing archaeal methanogens, Methanosarcina acetivorans and M. mazei, several open reading frames (ORFs) are annotated as reverse transcriptase (RT). These annotations led us to the characterization of a retron and 13 retrointrons, including three twintrons, clustered at seven loci of the M. acetivorans genome, and four retrointrons at two loci of the M. mazei genome. Based on a phylogeny of the RT ORFs, we infer four lateral gene transfers (LGT) of these retroids from Bacteria to Archaea and of retrointron mobility within the Archaea genomes. Our phylogenetic analysis also identifies several novel retrons from GenBank in the bacterial groups Firmicutes, Fusobacteria, Cyanobacteria and beta-Proteobacteria, as well as in M. acetivorans. The discovery of retrointrons in Archaea as a consequence of LGT from Bacteria suggests that they did not originate in the progenote and parallels the "mitochondrial seed" theory of the origin of spliceosomes. Extending the known phylogenetic distribution of retroids to Archaea is consistent with the view that they have played a significant role in evolution of genomes throughout the tree of life.},
}
@article {pmid19719617,
year = {2003},
author = {Purdy, KJ and Munson, MA and Cresswell-Maynard, T and Nedwell, DB and Embley, TM},
title = {Use of 16S rRNA-targeted oligonucleotide probes to investigate function and phylogeny of sulphate-reducing bacteria and methanogenic archaea in a UK estuary.},
journal = {FEMS microbiology ecology},
volume = {44},
number = {3},
pages = {361-371},
doi = {10.1016/S0168-6496(03)00078-3},
pmid = {19719617},
issn = {0168-6496},
abstract = {Abstract Sulphate-reducing bacteria (SRB) and methanogenic archaea (MA) are important anaerobic terminal oxidisers of organic matter. However, we have little knowledge about the distribution and types of SRB and MA in the environment or the functional role they play in situ. Here we have utilised sediment slurry microcosms amended with ecologically significant substrates, including acetate and hydrogen, and specific functional inhibitors, to identify the important SRB and MA groups in two contrasting sites on a UK estuary. Substrate and inhibitor additions had significant effects on methane production and on acetate and sulphate consumption in the slurries. By using specific 16S-targeted oligonucleotide probes we were able to link specific SRB and MA groups to the use of the added substrates. Acetate consumption in the freshwater-dominated sediments was mediated by Methanosarcinales under low-sulphate conditions and Desulfobacter under the high-sulphate conditions that simulated a tidal incursion. In the marine-dominated sediments, acetate consumption was linked to Desulfobacter. Addition of trimethylamine, a non-competitive substrate for methanogenesis, led to a large increase in Methanosarcinales signal in marine slurries. Desulfobulbus was linked to non-sulphate-dependent H(2) consumption in the freshwater sediments. The addition of sulphate to freshwater sediments inhibited methane production and reduced signal from probes targeted to Methanosarcinales and Methanomicrobiales, while the addition of molybdate to marine sediments inhibited Desulfobulbus and Desulfobacterium. These data complement our understanding of the ecophysiology of the organisms detected and make a firm connection between the capabilities of species, as observed in the laboratory, to their roles in the environment.},
}
@article {pmid12773188,
year = {2003},
author = {Allers, T and Ngo, HP},
title = {Genetic analysis of homologous recombination in Archaea: Haloferax volcanii as a model organism.},
journal = {Biochemical Society transactions},
volume = {31},
number = {Pt 3},
pages = {706-710},
doi = {10.1042/bst0310706},
pmid = {12773188},
issn = {0300-5127},
mesh = {Crossing Over, Genetic/genetics ; Haloferax volcanii/*genetics ; Models, Genetic ; Recombination, Genetic/*genetics ; Sequence Deletion ; },
abstract = {Homologous recombination is a fundamental cellular process that rearranges genes both within and between chromosomes, promotes repair of damaged DNA and underpins replication. Much of our understanding of recombination stems from pioneering studies of bacterial and eukaryotic systems such as Escherichia coli and Saccharomyces cerevisiae. Since most archaeal species are extremophilic and difficult to cultivate, current knowledge of recombination in the Archaea is confined largely to comparative genomics and biochemistry. A clear view of what we can learn will not emerge until genetic and molecular systems have been established. We are developing such systems using Haloferax volcanii as a model organism, as it can be cultivated in the laboratory with ease and offers great potential for establishing tractable and informative genetic systems.},
}
@article {pmid12773187,
year = {2003},
author = {Bolt, EL and Guy, CP},
title = {Homologous recombination in Archaea: new Holliday junction helicases.},
journal = {Biochemical Society transactions},
volume = {31},
number = {Pt 3},
pages = {703-705},
doi = {10.1042/bst0310703},
pmid = {12773187},
issn = {0300-5127},
mesh = {Archaea/*genetics ; DNA Helicases/*genetics/*metabolism ; DNA, Archaeal/genetics ; DNA, Cruciform/genetics ; Recombination, Genetic/*genetics ; },
abstract = {Homologous recombination (HR) maintains genome stability by promoting high fidelity DNA repair. Several recent reports have established that the primary function of HR enzymes is to underpin DNA replication, resetting forks that are blocked or collapsed at sites of DNA damage remote from replication origins. These functions are crucial to ensuring that genomes are transmitted successfully into subsequent generations of cells. Enzymes of HR have been unearthed in all three domains of life: bacteria, Archaea and eukarya. Helicases that specifically unwind branched DNA molecules are pivotal in linking HR and DNA replication in bacteria. However, knowledge of helicases with these functions in eukaryotes is vague and is wholly absent in Archaea. We are using the archaeal species Methanothermobacter thermautotrophicus to identify new DNA helicases of homologous recombination.},
}
@article {pmid12773182,
year = {2003},
author = {Lund, PA and Large, AT and Kapatai, G},
title = {The chaperonins: perspectives from the Archaea.},
journal = {Biochemical Society transactions},
volume = {31},
number = {Pt 3},
pages = {681-685},
doi = {10.1042/bst0310681},
pmid = {12773182},
issn = {0300-5127},
mesh = {Archaea/*physiology ; Archaeal Proteins/physiology ; Bacterial Physiological Phenomena ; Chaperonins/*chemistry/classification/*physiology ; Eukaryotic Cells ; Mitochondria/physiology ; Models, Molecular ; Protein Conformation ; },
abstract = {Heat-shock protein (Hsp) 60 chaperones are almost ubiquitous and almost always essential. They can be divided on the basis of sequence homology into two broad types: group I (found in bacteria, mitochondria and chloroplasts) and group II (found in Archaea and the eukaryotic cytosol). Of the two, the group I chaperones are the better understood. Data on their structure, mechanism of action and cellular role will be briefly presented. The group II chaperones are less well studied. In eukaryotes they form large complexes with 8-fold symmetry containing eight different subunits, all of which are essential. They appear to have a major role in the folding of actin and tubulin, although they may also act on other substrates. No crystal structures are available for these complexes. The situation in the Archaea is simpler, with organisms containing between one and three genes for these chaperones. A 2.6 A structure exists for one archaeal group II chaperone complex. Some progress has been made in defining the reaction cycle of the archaeal group II chaperones and this has shown that they have some properties distinct from the group I chaperones. To date, the in vivo role and importance of the archaeal group II Hsp60 chaperones has not been determined. We have now shown that in the halophilic archaeon Haloferax volcanii not all the genes for these proteins are essential. Further analysis of these proteins in the Archaea should be very productive in yielding more information about these important chaperones and their cellular functions.},
}
@article {pmid12756329,
year = {2003},
author = {Kaya, Y and Ofengand, J},
title = {A novel unanticipated type of pseudouridine synthase with homologs in bacteria, archaea, and eukarya.},
journal = {RNA (New York, N.Y.)},
volume = {9},
number = {6},
pages = {711-721},
pmid = {12756329},
issn = {1355-8382},
support = {R01 GM058879/GM/NIGMS NIH HHS/United States ; GM58879/GM/NIGMS NIH HHS/United States ; },
mesh = {Amino Acid Motifs ; Amino Acid Sequence ; Archaea/*enzymology ; Aspartic Acid/physiology ; Bacteria/*enzymology ; Base Sequence ; Escherichia coli/enzymology/genetics ; Escherichia coli Proteins/chemistry/*classification/genetics/physiology ; Eukaryotic Cells/*enzymology ; Gene Deletion ; Genes, Bacterial ; Genome ; Hydro-Lyases/chemistry/*classification/genetics/physiology ; Molecular Sequence Data ; Pseudouridine/analysis/biosynthesis ; RNA, Transfer, Glu/biosynthesis/chemistry ; Sequence Analysis, RNA ; Sequence Homology, Amino Acid ; Substrate Specificity ; },
abstract = {Putative pseudouridine synthase genes are members of a class consisting of four subgroups that possess characteristic amino acid sequence motifs. These genes have been found in all organisms sequenced to date. In Escherichia coli, 10 such genes have been identified, and the 10 synthase gene products have been shown to function in making all of the pseudouridines found in tRNA and ribosomal RNA except for tRNA(Glu) pseudouridine13. In this work, a protein able to make this pseudouridine was purified by standard biochemical procedures. Amino-terminal sequencing of the isolated protein identified the synthase as YgbO. Deletion of the ygbO gene caused the loss of tRNA(Glu) pseudouridine13 and plasmid-borne restoration of the structural gene restored pseudouridine13. Reaction of the overexpressed gene product, renamed TruD, with a tRNA(Glu) transcript made in vitro also yielded only pseudouridine13. A search of the database detected 58 homologs of TruD spanning all three phylogenetic domains, including ancient organisms. Thus, we have identified a new wide-spread class of pseudouridine synthase with no sequence homology to the previously known four subgroups. The only completely conserved sequence motif in all 59 organisms that contained aspartate was GXKD, in motif II. This aspartate was essential for in vitro activity.},
}
@article {pmid12732960,
year = {2003},
author = {Giménez, MI and Sánchez, JJ and De Castro, RE},
title = {Detection of an intracellular protease inhibitor in archaea.},
journal = {Current microbiology},
volume = {46},
number = {5},
pages = {334-339},
doi = {10.1007/s00284-002-3861-z},
pmid = {12732960},
issn = {0343-8651},
mesh = {Cell Membrane/metabolism ; Culture Media ; Cytosol/metabolism ; Halobacteriaceae/enzymology/*growth &amp; development/metabolism ; Metalloendopeptidases/metabolism ; Protease Inhibitors/*metabolism ; Serine Endopeptidases/metabolism ; },
abstract = {Proteolytic activity and a subtilisin inhibitor (NSI) were detected in Natrialba magadii cells. The proteolytic activity was due to two different proteases: a approximately 90-kDa metallo protease (NMP) produced during exponential growth and a 246-kDa serine protease (NSP) detected in the stationary phase. Both proteases were detected in the cytosolic fraction. NSI activity was maximal during early stages of growth and decreased in the stationary phase. NSI is a 35-kDa thermosensitive protein; it inhibits NSP activity but has no effect on NMP, and it was detected as a soluble or membrane-bound protein depending on the growth phase. Our results suggest that NSI may regulate NSP activity in vivo and that this protease may have a role in stationary phase cells. To our knowledge, this is the first report on the occurrence of protease inhibitors in Archaea.},
}
@article {pmid12730164,
year = {2003},
author = {Finn, MW and Tabita, FR},
title = {Synthesis of catalytically active form III ribulose 1,5-bisphosphate carboxylase/oxygenase in archaea.},
journal = {Journal of bacteriology},
volume = {185},
number = {10},
pages = {3049-3059},
pmid = {12730164},
issn = {0021-9193},
support = {R01 GM024497/GM/NIGMS NIH HHS/United States ; GM24497/GM/NIGMS NIH HHS/United States ; },
mesh = {Amino Acid Sequence ; Archaea/enzymology/genetics/*metabolism ; Archaeal Proteins/genetics/isolation &amp; purification/*metabolism ; Blotting, Western ; Carbon Dioxide/metabolism ; Catalysis ; Cell Division/physiology ; Enzyme Activation ; Gene Deletion ; Genetic Complementation Test ; Molecular Sequence Data ; Recombinant Proteins/genetics/metabolism ; Rhodobacter capsulatus/genetics/metabolism ; Rhodobacter sphaeroides/genetics/metabolism ; Ribulose-Bisphosphate Carboxylase/genetics/isolation &amp; purification/*metabolism ; Sequence Homology, Amino Acid ; },
abstract = {Ribulose 1,5 bisphosphate carboxylase/oxygenase (RubisCO) catalyzes the biological reduction and assimilation of carbon dioxide gas to organic carbon; it is the key enzyme responsible for the bulk of organic matter found on earth. Until recently it was believed that there are only two forms of RubisCO, form I and form II. However, the recent completion of several genome-sequencing projects uncovered open reading frames resembling RubisCO in the third domain of life, the archaea. Previous work and homology comparisons suggest that these enzymes represent a third form of RubisCO, form III. While earlier work indicated that two structurally distinct recombinant archaeal RubisCO proteins catalyzed bona fide RubisCO reactions, it was not established that the rbcL genes of anaerobic archaea can be transcribed and translated to an active enzyme in the native organisms. In this report, it is shown not only that Methanococcus jannaschii, Archaeoglobus fulgidus, Methanosarcina acetivorans, and Methanosarcina barkeri possess open reading frames with the residues required for catalysis but also that the RubisCO protein from these archaea accumulates in an active form under normal growth conditions. In addition, the form III RubisCO gene (rbcL) from M. acetivorans was shown to complement RubisCO deletion strains of Rhodobacter capsulatus and Rhodobacter sphaeroides under both photoheterotrophic and photoautotrophic growth conditions. These studies thus indicate for the first time that archaeal form III RubisCO functions in a physiologically significant fashion to fix CO(2). Furthermore, recombinant M. jannaschii, M. acetivorans, and A. fulgidus RubisCO possess unique properties with respect to quaternary structure, temperature optima, and activity in the presence of molecular oxygen compared to the previously described Thermococcus kodakaraensis and halophile proteins.},
}
@article {pmid19719655,
year = {2003},
author = {Koizumi, Y and Takii, S and Nishino, M and Nakajima, T},
title = {Vertical distributions of sulfate-reducing bacteria and methane-producing archaea quantified by oligonucleotide probe hybridization in the profundal sediment of a mesotrophic lake.},
journal = {FEMS microbiology ecology},
volume = {44},
number = {1},
pages = {101-108},
doi = {10.1016/S0168-6496(02)00463-4},
pmid = {19719655},
issn = {1574-6941},
abstract = {Abstract Vertical distributions of sulfate-reducing bacteria and methane-producing archaea were investigated in the profundal sediment of a freshwater lake using membrane-immobilized small subunit rRNA hybridization with group- and genus-specific oligonucleotide probes. The annual average of the relative abundance of small subunit rRNA hybridized with all probes for sulfate-reducing bacteria to total small subunit rRNA was 2.3% at 0-2 cm and increased with depth up to 22.9% at 8-14 cm where sulfate concentration was less than 10 nmol ml(-1) in interstitial water, suggesting that these bacteria may survive on alternative metabolisms. The signal of probe Dsv687 (the family Desulfovibrionaceae and some Geobacteraceae) was the main factor in this increase. The relative abundance of methane-producing archaea to total small subunit rRNA was highest (7.8%) at 8-14 cm, dominated by the order Methanosarcinales. The metabolic rates measured in the sediments demonstrated that the peaks of sulfate reduction and methane production were separated vertically, and were not linked to their small subunit rRNA distributions. Our data indicate that sulfate-reducing bacteria can coexist with methane-producing archaea from 0 to 20 cm in the freshwater lake sediment.},
}
@article {pmid12694910,
year = {2003},
author = {Ye, X and Ou, J and Ni, L and Shi, W and Shen, P},
title = {Characterization of a novel plasmid from extremely halophilic Archaea: nucleotide sequence and function analysis.},
journal = {FEMS microbiology letters},
volume = {221},
number = {1},
pages = {53-57},
doi = {10.1016/S0378-1097(03)00175-7},
pmid = {12694910},
issn = {0378-1097},
mesh = {Archaeal Proteins/genetics ; Base Composition ; Cloning, Molecular ; Culture Media ; DNA Replication ; Halobacterium salinarum/genetics/*growth &amp; development ; Molecular Sequence Data ; Open Reading Frames ; Plasmids/*genetics ; Sequence Analysis, DNA ; Sodium Chloride ; },
abstract = {We determined the complete nucleotide sequence of the 16341 bp plasmid pHH205 of the extremely halophilic archaeon Halobacterium salinarum J7. The plasmid has a G+C content of 61.1%. A number of direct and inverted repeat sequences were found in pHH205, while no insertion sequences were found. Thirty-eight large open reading frames (ORFs) were identified in both strands, and most of them had no significant similarities to known proteins. A putative protein encoded by ORF31 showed 20-41% homology to some hypothetical proteins, which are annotated in several archaeal genome databases as predicted nucleic acid-binding proteins containing PIN domain. Sequence analysis using the GC skew procedure predicted a possible origin of replication. A 4.8 kb PvuII-SnaBI fragment containing both this region and ORF31 was shown to be able to restore replicate of pWL102, a replicon-deficient plasmid in Haloferax volcanii and in H. salinarum R1. Several methods failed to completely cure H. salinarum J7 of pHH205, suggesting that the plasmid probably played an important role in the growth and metabolism of the host. Our work describes a novel haloarchaeal replicon, which may be useful in the construction of cloning and shuttle vectors.},
}
@article {pmid12694610,
year = {2003},
author = {Praetorius-Ibba, M and Ibba, M},
title = {Aminoacyl-tRNA synthesis in archaea: different but not unique.},
journal = {Molecular microbiology},
volume = {48},
number = {3},
pages = {631-637},
doi = {10.1046/j.1365-2958.2003.03330.x},
pmid = {12694610},
issn = {0950-382X},
mesh = {Archaea/genetics/*metabolism ; Codon ; Lysine/*analogs &amp; derivatives/genetics/metabolism ; Lysine-tRNA Ligase/metabolism ; RNA, Transfer, Amino Acyl/*biosynthesis ; Selenocysteine/genetics/metabolism ; Transferases/metabolism ; },
abstract = {Accurate aminoacyl-tRNA synthesis is essential for correct translation of the genetic code in all organisms. Whereas many aspects of this process are conserved, others display a surprisingly high level of divergence from the canonical Escherichia coli model system. These differences are most pronounced in archaea where novel mechanisms have recently been described for aminoacylating tRNAs with asparagine, cysteine, glutamine and lysine. Whereas these mechanisms were initially assumed to be uniquely archaeal, both the alternative asparagine and lysine pathways have subsequently been demonstrated in numerous bacteria. Similarly, studies of the means by which archaea insert the rare amino acid selenocysteine in response to UGA stop codons have helped provide a better understanding of both archaeal and eukaryal selenoprotein synthesis. Most recently a new co-translationally inserted amino acid, pyrrolysine, has been found in archaea although again there is some suggestion that it may also be present in bacteria. Thus, whereas archaea contain a preponderance of non-canonical aminoacyl-tRNA synthesis systems most are also found elsewhere albeit less frequently.},
}
@article {pmid12694609,
year = {2003},
author = {Omer, AD and Ziesche, S and Decatur, WA and Fournier, MJ and Dennis, PP},
title = {RNA-modifying machines in archaea.},
journal = {Molecular microbiology},
volume = {48},
number = {3},
pages = {617-629},
doi = {10.1046/j.1365-2958.2003.03483.x},
pmid = {12694609},
issn = {0950-382X},
support = {GM19351/GM/NIGMS NIH HHS/United States ; },
mesh = {Amino Acid Sequence ; Archaea/chemistry/*genetics/physiology ; Archaeal Proteins/chemistry/metabolism ; Humans ; Models, Molecular ; Molecular Sequence Data ; *Nucleic Acid Conformation ; Protein Structure, Secondary ; RNA, Archaeal/genetics/*metabolism ; RNA-Binding Proteins/chemistry/metabolism ; Sequence Alignment ; },
abstract = {It has been known for nearly half a century that coding and non-coding RNAs (mRNA, and tRNAs and rRNAs respectively) play critical roles in the process of information transfer from DNA to protein. What is both surprising and exciting, are the discoveries in the last decade that cells, particularly eukaryotic cells, contain a plethora of non-coding RNAs and that these RNAs can either possess catalytic activity or can function as integral components of dynamic ribonucleoprotein machines. These machines appear to mediate diverse, complex and essential processes such as intron excision, RNA modification and editing, protein targeting, DNA packaging, etc. Archaea have been shown to possess RNP complexes; some of these are authentic homologues of the eukaryotic complexes that function as machines in the processing, modification and assembly of rRNA into ribosomal subunits. Deciphering how these RNA-containing machines function will require a dissection and analysis of the component parts, an understanding of how the parts fit together and an ability to reassemble the parts into complexes that can function in vitro. This article summarizes our current knowledge about small-non-coding RNAs in Archaea, their roles in ribosome biogenesis and their relationships to the complexes that have been identified in eukaryotic cells.},
}
@article {pmid12694608,
year = {2003},
author = {Kelman, LM and Kelman, Z},
title = {Archaea: an archetype for replication initiation studies?.},
journal = {Molecular microbiology},
volume = {48},
number = {3},
pages = {605-615},
doi = {10.1046/j.1365-2958.2003.03369.x},
pmid = {12694608},
issn = {0950-382X},
mesh = {Archaea/genetics/*physiology ; Archaeal Proteins/metabolism ; DNA Helicases/chemistry/metabolism ; *DNA Replication ; DNA, Archaeal/*metabolism ; DNA-Binding Proteins/chemistry/metabolism ; Models, Genetic ; Models, Molecular ; Protein Structure, Tertiary ; Replication Origin ; },
abstract = {Whereas the process of DNA replication is fundamentally conserved in the three domains of life, the archaeal system is closer to that of eukarya than bacteria. In the time since the complete genome sequences of several members of the archaeal domain became available, there has been a burst of research on archaeal DNA replication. These studies have led to both expected and surprising findings. This review summarizes the search for origins of replication in archaea, and our current knowledge of initiation, the process by which replication origins are recognized, the DNA molecule is unwound and the replicative helicase is loaded onto the DNA in preparation for DNA synthesis. The similarities and differences of the initiation process in archea, bacteria and eukarya are also summarized.},
}
@article {pmid12686546,
year = {2003},
author = {Brindley, AA and Raux, E and Leech, HK and Schubert, HL and Warren, MJ},
title = {A story of chelatase evolution: identification and characterization of a small 13-15-kDa "ancestral" cobaltochelatase (CbiXS) in the archaea.},
journal = {The Journal of biological chemistry},
volume = {278},
number = {25},
pages = {22388-22395},
doi = {10.1074/jbc.M302468200},
pmid = {12686546},
issn = {0021-9258},
mesh = {Amino Acid Sequence ; Archaea/*enzymology ; *Bacterial Proteins ; Circular Dichroism ; Conserved Sequence ; *Evolution, Molecular ; Lyases/chemistry/*genetics ; Molecular Conformation ; Molecular Sequence Data ; Molecular Weight ; Protein Conformation ; Sequence Alignment ; Sequence Homology, Amino Acid ; Spectrophotometry, Ultraviolet ; },
abstract = {The cobaltochelatase required for the synthesis of vitamin B12 (cobalamin) in the archaeal kingdom has been identified as CbiX through similarity searching with the CbiX from Bacillus megaterium. However, the CbiX proteins in the archaea are much shorter than the CbiX proteins found in eubacteria, typically containing less than half the number of amino acids in their primary structure. For this reason the shorter CbiX proteins have been termed CbiXS and the longer versions CbiXL. The CbiXS proteins from Methanosarcina barkeri and Methanobacter thermoautotrophicum were overproduced in Escherichia coli as recombinant proteins and characterized. Through complementation studies of a defined chelatase-deficient strain of E. coli and by direct in vitro assays the function of CbiXS as a sirohydrochlorin cobaltochelatase has been demonstrated. On the basis of sequence alignments and conserved active site residues we suggest that CbiXS may represent a primordial chelatase, giving rise to larger chelatases such as CbiXL, SirB, CbiK, and HemH through gene duplication and subsequent variation and selection. A classification scheme for chelatases is proposed.},
}
@article {pmid12672112,
year = {2003},
author = {Tietze, M and Beuchle, A and Lamla, I and Orth, N and Dehler, M and Greiner, G and Beifuss, U},
title = {Redox potentials of methanophenazine and CoB-S-S-CoM, factors involved in electron transport in Methanogenic archaea.},
journal = {Chembiochem : a European journal of chemical biology},
volume = {4},
number = {4},
pages = {333-335},
doi = {10.1002/cbic.200390053},
pmid = {12672112},
issn = {1439-4227},
mesh = {*Electron Transport ; Hydrogen-Ion Concentration ; Mesna/analogs &amp; derivatives/*chemistry ; Methanosarcina/*chemistry ; Organophosphates/*chemistry ; Oxidation-Reduction ; Phenazines/*chemistry ; },
}
@article {pmid12654928,
year = {2003},
author = {Johnsen, U and Hansen, T and Schonheit, P},
title = {Comparative analysis of pyruvate kinases from the hyperthermophilic archaea Archaeoglobus fulgidus, Aeropyrum pernix, and Pyrobaculum aerophilum and the hyperthermophilic bacterium Thermotoga maritima: unusual regulatory properties in hyperthermophilic archaea.},
journal = {The Journal of biological chemistry},
volume = {278},
number = {28},
pages = {25417-25427},
doi = {10.1074/jbc.M210288200},
pmid = {12654928},
issn = {0021-9258},
mesh = {Adenosine Diphosphate/pharmacology ; Allosteric Site ; Amino Acid Sequence ; Archaeal Proteins/*physiology ; Archaeoglobus fulgidus/*enzymology ; Catalysis ; Cations ; Circular Dichroism ; Cloning, Molecular ; Desulfurococcaceae/*enzymology ; Dose-Response Relationship, Drug ; Hydrogen-Ion Concentration ; Ions ; Kinetics ; Molecular Sequence Data ; Open Reading Frames ; Phylogeny ; Potassium/metabolism ; Pyruvate Kinase/*chemistry/physiology ; Recombinant Proteins/metabolism ; Sequence Homology, Amino Acid ; Temperature ; Thermoproteaceae/*enzymology ; Thermotoga maritima/*enzymology ; Time Factors ; },
abstract = {Pyruvate kinases (PK, EC 2.7.1.40) from three hyperthermophilic archaea (Archaeoglobus fulgidus strain 7324, Aeropyrum pernix, and Pyrobaculum aerophilum) and from the hyperthermophilic bacterium Thermotoga maritima were compared with respect to their thermophilic, kinetic, and regulatory properties. PKs from the archaea are 200-kDa homotetramers composed of 50-kDa subunits. The enzymes required divalent cations, Mg2+ and Mn2+ being most effective, but were independent of K+. Temperature optima for activity were 85 degrees C (A. fulgidus) and above 98 degrees C (A. pernix and P. aerophilum). The PKs were highly thermostable up to 110 degrees C (A. pernix) and showed melting temperatures for thermal unfolding at 93 degrees C (A. fulgidus) or above 98 degrees C (A. pernix and P. aerophilum). All archaeal PKs exhibited sigmoidal saturation kinetics with phosphoenolpyruvate (PEP) and ADP indicating positive homotropic cooperative response with both substrates. Classic heterotropic allosteric regulators of PKs from eukarya and bacteria, e.g. fructose 1,6-bisphosphate or AMP, did not affect PK activity of hyperthermophilic archaea, suggesting the absence of heterotropic allosteric regulation. PK from the bacterium T. maritima is also a homotetramer of 50-kDa subunits. The enzyme was independent of K+ ions, had a temperature optimum of 80 degrees C, was highly thermostable up to 90 degrees C, and had a melting temperature above 98 degrees C. The enzyme showed cooperative response to PEP and ADP. In contrast to its archaeal counterparts, the T. maritima enzyme exhibited the classic allosteric response to the activator AMP and to the inhibitor ATP. Sequences of hyperthermophilic PKs showed significant similarity to characterized PKs from bacteria and eukarya. Phylogenetic analysis of PK sequences of all three domains indicates a distinct archaeal cluster that includes the PK from the hyperthermophilic bacterium T. maritima.},
}
@article {pmid12651013,
year = {2003},
author = {Wu, X and Oppermann, U},
title = {High-level expression and rapid purification of rare-codon genes from hyperthermophilic archaea by the GST gene fusion system.},
journal = {Journal of chromatography. B, Analytical technologies in the biomedical and life sciences},
volume = {786},
number = {1-2},
pages = {177-185},
doi = {10.1016/s1570-0232(02)00810-3},
pmid = {12651013},
issn = {1570-0232},
mesh = {Archaea/*genetics ; *Artificial Gene Fusion ; Base Sequence ; *Codon ; DNA Primers ; *Genes, Archaeal ; Mass Spectrometry ; Recombinant Proteins/genetics/isolation &amp; purification ; },
abstract = {In this study, we compared two gene fusion expression strategies using two rare codon genes (Ssh10b and MtGrxM) from archaea as a model system. Both genes can be highly expressed as N- or C-terminal fusion partners to GST or the intein/chitin-binding tag. However, the fusion protein with intein tag could not be cleaved, even under stringent conditions, possibly due to steric hindrance, thus preventing further purification. In contrast, the GST fusion system could increase protein expression level and the corresponding fusion protein could be easily cleaved by thrombin. After binding to glutathione sepharose, the fusion protein was cleaved on column, and a roughly purified protein fraction was eluted. This fraction was purified by heating at 80 degrees C for 10 min, followed by centrifugation. The correct total mass and N-terminal primary structure were confirmed by mass spectrometry and Edman degradation. Both constructs were used for in vitro expression, and similar results were obtained, indicating higher expression levels of the GST tag vs. intein/chitin tag. Taken together, our results suggest that the GST fusion system can be used as a considerable alternative to synthetic genes for the expression of rare codon genes. The affinity chromatography purification followed by a heating step is an efficient and convenient method for thermostable protein purification.},
}
@article {pmid12626506,
year = {2003},
author = {Dörr, C and Zaparty, M and Tjaden, B and Brinkmann, H and Siebers, B},
title = {The hexokinase of the hyperthermophile Thermoproteus tenax. ATP-dependent hexokinases and ADP-dependent glucokinases, teo alternatives for glucose phosphorylation in Archaea.},
journal = {The Journal of biological chemistry},
volume = {278},
number = {21},
pages = {18744-18753},
doi = {10.1074/jbc.M301914200},
pmid = {12626506},
issn = {0021-9258},
mesh = {Adenosine Diphosphate/*pharmacology ; Adenosine Triphosphate/*pharmacology ; Amino Acid Sequence ; Base Sequence ; Blotting, Northern ; Cations, Divalent ; Fructose/metabolism ; Genes, Bacterial ; Glucokinase/chemistry/genetics/*metabolism ; Glucose/metabolism ; Hexokinase/chemistry/genetics/*metabolism ; Magnesium/pharmacology ; Manganese/pharmacology ; Mannose/metabolism ; Molecular Sequence Data ; Molecular Weight ; Phosphorylation ; Phylogeny ; Promoter Regions, Genetic ; RNA, Messenger/analysis ; Recombinant Proteins/metabolism ; Substrate Specificity ; Thermoproteaceae/*enzymology/genetics ; },
abstract = {The phosphorylation of glucose by different sugar kinases plays an essential role in Archaea because of the absence of a phosphoenolpyruvate-dependent transferase system characteristic for Bacteria. In the genome of the hyperthermophilic Archaeon Thermoproteus tenax a gene was identified with sequence similarity to glucokinases of the so-called ROK family (repressor protein, open reading frame, sugar kinase). The T. tenax enzyme, like the recently described ATP-dependent "glucokinase" from Aeropyrum pernix, shows the typical broad substrate specificity of hexokinases catalyzing not only phosphorylation of glucose but also of other hexoses such as fructose, mannose, or 2-deoxyglucose, and thus both enzymes represent true hexokinases. The T. tenax hexokinase shows strikingly low if at all any regulatory properties and thus fulfills no important control function at the beginning of the variant of the Embden-Meyerhof-Parnas pathway in T. tenax. Transcript analyses reveal that the hxk gene of T. tenax is cotranscribed with an upstream located orfX, which codes for an 11-kDa protein of unknown function. Growth-dependent studies and promoter analyses suggest that post-transcriptional RNA processing might be involved in the generation of the monocistronic hxk message, which is observed only under heterotrophic growth conditions. Data base searches revealed T. tenax hexokinase homologs in some archaeal, few eukaryal, and many bacterial genomes. Phylogenetic analyses confirm that the archaeal hexokinase is a member of the so-called ROK family, which, however, should be referred to as ROK group because it represents a group within the bacterial glucokinase fructokinase subfamily II of the hexokinase family. Thus, archaeal hexokinases represent a second major group of glucose-phosphorylating enzymes in Archaea beside the recently described archaeal ADP-dependent glucokinases, which were recognized as members of the ribokinase family. The distribution of the two types of sugar kinases, differing in their cosubstrate as well as substrate specificity, within Archaea is discussed on the basis of physiological constraints of the respective organisms.},
}
@article {pmid12621493,
year = {2003},
author = {Ansorg, R and Rath, PM and Runde, V and Beelen, DW},
title = {Influence of intestinal decontamination using metronidazole on the detection of methanogenic Archaea in bone marrow transplant recipients.},
journal = {Bone marrow transplantation},
volume = {31},
number = {2},
pages = {117-119},
doi = {10.1038/sj.bmt.1703797},
pmid = {12621493},
issn = {0268-3369},
mesh = {Adult ; Anti-Bacterial Agents/*therapeutic use ; Archaea/drug effects/*isolation &amp; purification ; Bacteria, Anaerobic/drug effects/isolation &amp; purification ; Bone Marrow Transplantation/*physiology ; Decontamination/methods ; Euryarchaeota/drug effects/isolation &amp; purification ; Feces/*microbiology ; Female ; Humans ; Intestines/*microbiology ; Male ; Methane/*analysis ; Metronidazole/*therapeutic use ; Middle Aged ; },
abstract = {Methane-forming microbes of the phylogenetic domain Archaea are part of the strictly anaerobic microflora of the human intestine. In bone marrow transplant (BMT) recipients, the regimen of intestinal decontamination with metronidazole is targeted to anaerobic bacteria. The effect on the anaerobic methanoarchaea, however, is unknown. Therefore, the faeces of patients undergoing BMT were investigated for methane production. The anoxic Hungate technique and an archaeal growth medium were used to culture faecal specimens. Methane production was measured in the head space of the culture bottles by gas chromatography using a thermal conductivity detector. In a testing serial specimen of 100 patients, 13 patients were found to bear methanogens, and 11 of these patients received metronidazole. The methane-producing faecal specimens occurred before metronidazole use in three patients, during the first week in five patients, and after cessation in three patients. No specimen of the 11 patients that was obtained during the 2nd-5th week of gut decontamination showed methane production. It is concluded that use of metronidazole directed against faecal anaerobic bacteria also suppresses or eliminates faecal methanogenic Archaea.},
}
@article {pmid12620867,
year = {2003},
author = {Behrens, S and Rühland, C and Inácio, J and Huber, H and Fonseca, A and Spencer-Martins, I and Fuchs, BM and Amann, R},
title = {In situ accessibility of small-subunit rRNA of members of the domains Bacteria, Archaea, and Eucarya to Cy3-labeled oligonucleotide probes.},
journal = {Applied and environmental microbiology},
volume = {69},
number = {3},
pages = {1748-1758},
pmid = {12620867},
issn = {0099-2240},
mesh = {Bacteria/*genetics ; Carbocyanines/metabolism ; Crenarchaeota/*genetics ; Escherichia coli/genetics ; Flow Cytometry ; Fluorescent Dyes/metabolism ; In Situ Hybridization, Fluorescence ; Oligonucleotide Probes/*genetics ; RNA, Ribosomal, 16S/*genetics ; RNA, Ribosomal, 18S/*genetics ; Saccharomyces cerevisiae/*genetics ; },
abstract = {Low accessibility of the rRNA is together with cell wall impermeability and low cellular ribosome content a frequent reason for failure of whole-cell fluorescence hybridization with fluorescently labeled oligonucleotide probes. In this study we compare accessibility data for the 16S rRNA of Escherichia coli (gamma Proteobacteria, Bacteria) with the phylogenetically distantly related organisms Pirellula sp. strain 1 (Planctomycetes, Bacteria) and Metallosphaera sedula (Crenarchaeota, Archaea) and the 18S rRNA accessibility of Saccharomyces cerevisiae (Eucarya). For a total of 537 Cy3-labeled probes, the signal intensities of hybridized cells were quantified under standardized conditions by flow cytometry. The relative probe-conferred fluorescence intensities are shown on color-coded small-subunit rRNA secondary-structure models. For Pirellula sp., most of the probes belong to class II and III (72% of the whole data set), whereas most of the probes targeting sites on M. sedula were grouped into class V and VI (46% of the whole data set). For E. coli, 45% of all probes of the data set belong to class III and IV. A consensus model for the accessibility of the small-subunit rRNA to oligonucleotide probes is proposed which uses 60 homolog target sites of the three prokaryotic 16S rRNA molecules. In general, open regions were localized around helices 13 and 14 including target positions 285 to 338, whereas helix 22 (positions 585 to 656) and the 3' half of helix 47 (positions 1320 to 1345) were generally inaccessible. Finally, the 16S rRNA consensus model was compared to data on the in situ accessibility of the 18S rRNA of S. cerevisiae.},
}
@article {pmid12620859,
year = {2003},
author = {Schouten, S and Wakeham, SG and Hopmans, EC and Sinninghe Damsté, JS},
title = {Biogeochemical evidence that thermophilic archaea mediate the anaerobic oxidation of methane.},
journal = {Applied and environmental microbiology},
volume = {69},
number = {3},
pages = {1680-1686},
pmid = {12620859},
issn = {0099-2240},
mesh = {Anaerobiosis ; Archaea/growth &amp; development/*metabolism ; Biomarkers ; Carbon Isotopes/metabolism ; Chromatography, High Pressure Liquid ; *Hot Temperature ; Lipid Metabolism ; Mass Spectrometry ; Methane/*metabolism ; Oxidation-Reduction ; Seawater/*microbiology ; },
abstract = {Distributions and isotopic analyses of lipids from sediment cores at a hydrothermally active site in the Guaymas Basin with a steep sedimentary temperature gradient revealed the presence of archaea that oxidize methane anaerobically. The presence of strongly (13)C-depleted lipids at greater depths in the sediments suggests that microbes involved in anaerobic oxidation of methane are present and presumably active at environmental temperatures of >30 degrees C, indicating that this process can occur not only at cold seeps but also at hydrothermal sites. The distribution of the membrane tetraether lipids of the methanotrophic archaea shows that these organisms have adapted their membrane composition to these high environmental temperatures.},
}
@article {pmid19719676,
year = {2003},
author = {Bomberg, M and Jurgens, G and Saano, A and Sen, R and Timonen, S},
title = {Nested PCR detection of Archaea in defined compartments of pine mycorrhizospheres developed in boreal forest humus microcosms.},
journal = {FEMS microbiology ecology},
volume = {43},
number = {2},
pages = {163-171},
doi = {10.1111/j.1574-6941.2003.tb01055.x},
pmid = {19719676},
issn = {1574-6941},
abstract = {Archaea colonising defined compartments of Scots pine Suillus bovinus or Paxillus involutus mycorrhizospheres developed in forest humus-containing microcosms were investigated by nested polymerase chain reaction (PCR), cloning, restriction fragment length polymorphism (RFLP) and sequencing. Archaea representing six RFLP groups were detected in the system. Sequence analysis of clones representing the different RFLP types confirmed the presence of novel Finnish forest soil Crenarchaeota. Archaeal sequences were identified from mycorrhizas of both P. involutus and S. bovinus, at the margins of the external mycelium and in uncolonised humus but not from non-mycorrhizal short roots. Fungal and compartment-specific crenarchaeal occupation of mycorrhizospheres is discussed in relation to bacterial community distribution in similar systems.},
}
@article {pmid12610721,
year = {2003},
author = {Hügler, M and Huber, H and Stetter, KO and Fuchs, G},
title = {Autotrophic CO2 fixation pathways in archaea (Crenarchaeota).},
journal = {Archives of microbiology},
volume = {179},
number = {3},
pages = {160-173},
doi = {10.1007/s00203-002-0512-5},
pmid = {12610721},
issn = {0302-8933},
mesh = {Carbon Dioxide/*metabolism ; Citric Acid Cycle ; Crenarchaeota/classification/genetics/growth &amp; development/*metabolism ; Models, Biological ; Phylogeny ; },
abstract = {Representative autotrophic and thermophilic archaeal species of different families of Crenarchaeota were examined for key enzymes of the known autotrophic CO(2) fixation pathways. Pyrobaculum islandicum (Thermoproteaceae) contained key enzymes of the reductive citric acid cycle. This finding is consistent with the operation of this pathway in the related Thermoproteus neutrophilus. Pyrodictium abyssi and Pyrodictium occultum (Pyrodictiaceae) contained ribulose 1,5-bisphosphate carboxylase, which was active in boiling water. Yet, phosphoribulokinase activity was not detectable. Operation of the Calvin cycle remains to be demonstrated. Ignicoccus islandicus and Ignicoccus pacificus (Desulfurococcaceae) contained pyruvate oxidoreductase as potential carboxylating enzyme, but apparently lacked key enzymes of known pathways; their mode of autotrophic CO(2) fixation is at issue. Metallosphaera sedula, Acidianus ambivalens and Sulfolobus sp. strain VE6 (Sulfolobaceae) contained key enzymes of a 3-hydroxypropionate cycle. This finding is in line with the demonstration of acetyl-coenzyme A (CoA) and propionyl-CoA carboxylase activities in the related Acidianus brierleyi and Sulfolobus metallicus. Enzymes of central carbon metabolism in Metallosphaera sedula were studied in more detail. Enzyme activities of the 3-hydroxypropionate cycle were strongly up-regulated during autotrophic growth, supporting their role in CO(2) fixation. However, formation of acetyl-CoA from succinyl-CoA could not be demonstrated, suggesting a modified pathway of acetyl-CoA regeneration. We conclude that Crenarchaeota exhibit a mosaic of three or possibly four autotrophic pathways. The distribution of the pathways so far correlates with the 16S-rRNA-based taxa of the Crenarchaeota.},
}
@article {pmid12606030,
year = {2003},
author = {Fox, JD and Routzahn, KM and Bucher, MH and Waugh, DS},
title = {Maltodextrin-binding proteins from diverse bacteria and archaea are potent solubility enhancers.},
journal = {FEBS letters},
volume = {537},
number = {1-3},
pages = {53-57},
doi = {10.1016/s0014-5793(03)00070-x},
pmid = {12606030},
issn = {0014-5793},
mesh = {Archaeal Proteins/chemistry/*metabolism ; Bacterial Proteins/chemistry/*metabolism ; Carrier Proteins/chemistry/*metabolism ; Cloning, Molecular ; Escherichia coli/metabolism ; Glutathione Transferase/metabolism ; History, Ancient ; Recombinant Fusion Proteins/metabolism ; Solubility ; Species Specificity ; },
abstract = {Escherichia coli maltose-binding protein (MBP) is frequently used as an affinity tag to facilitate the purification of recombinant proteins. An important additional attribute of MBP is its remarkable ability to enhance the solubility of its fusion partners. MBPs are present in a wide variety of microorganisms including both mesophilic and thermophilic bacteria and archaea. In the present study, we compared the ability of MBPs from six diverse microorganisms (E. coli, Pyrococcus furiosus, Thermococcus litoralis, Vibrio cholerae, Thermotoga maritima, and Yersinia pestis) to promote the solubility of eight different aggregation-prone proteins in E. coli. In contrast to glutathione S-transferase (GST), all of these MBPs proved to be effective solubility enhancers and some of them were even more potent solubilizing agents than E. coli MBP.},
}
@article {pmid12603336,
year = {2003},
author = {Haase, I and Mörtl, S and Köhler, P and Bacher, A and Fischer, M},
title = {Biosynthesis of riboflavin in archaea. 6,7-dimethyl-8-ribityllumazine synthase of Methanococcus jannaschii.},
journal = {European journal of biochemistry},
volume = {270},
number = {5},
pages = {1025-1032},
doi = {10.1046/j.1432-1033.2003.03478.x},
pmid = {12603336},
issn = {0014-2956},
mesh = {Amino Acid Sequence ; Methanococcus/enzymology/*metabolism ; Molecular Sequence Data ; Multienzyme Complexes/chemistry/genetics/*metabolism ; Phylogeny ; Riboflavin/*biosynthesis ; Sequence Homology, Amino Acid ; Spectrometry, Mass, Electrospray Ionization ; Ultracentrifugation ; },
abstract = {Heterologous expression of the putative open reading frame MJ0303 of Methanococcus jannaschii provided a recombinant protein catalysing the formation of the riboflavin precursor, 6,7-dimethyl-8-ribityllumazine, by condensation of 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione and 3,4-dihydroxy-2-butanone 4-phosphate. Steady state kinetic analysis at 37 degrees C and pH 7.0 indicated a catalytic rate of 11 nmol.mg-1.min-1; Km values for 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione and 3,4-dihydroxybutanone 4-phosphate were 12.5 and 52 micro m, respectively. The enzyme sediments at an apparent velocity of about 12 S. Sedimentation equilibrium analysis indicated a molecular mass around 1 MDa but was hampered by nonideal solute behaviour. Negative-stained electron micrographs showed predominantly spherical particles with a diameter of about 150 A. The data suggest that the enzyme from M. jannaschii can form capsids with icosahedral 532 symmetry consisting of 60 subunits.},
}
@article {pmid12589784,
year = {2003},
author = {Conway de Macario, E and Maeder, DL and Macario, AJ},
title = {Breaking the mould: archaea with all four chaperoning systems.},
journal = {Biochemical and biophysical research communications},
volume = {301},
number = {4},
pages = {811-812},
doi = {10.1016/s0006-291x(03)00047-0},
pmid = {12589784},
issn = {0006-291X},
mesh = {Archaeal Proteins/genetics ; Biological Evolution ; Genes, Archaeal ; Methanosarcina/*genetics ; Molecular Chaperones/*genetics ; Phylogeny ; RNA, Archaeal/genetics ; },
}
@article {pmid12588294,
year = {2003},
author = {Toro, N},
title = {Bacteria and Archaea Group II introns: additional mobile genetic elements in the environment.},
journal = {Environmental microbiology},
volume = {5},
number = {3},
pages = {143-151},
doi = {10.1046/j.1462-2920.2003.00398.x},
pmid = {12588294},
issn = {1462-2912},
mesh = {Archaea/genetics ; Archaeal Proteins/genetics ; Bacteria/*genetics ; Bacterial Proteins/genetics ; *DNA Transposable Elements ; Environmental Microbiology ; Evolution, Molecular ; Introns/*genetics ; },
abstract = {Self-splicing group II introns are present in the organelles of lower eukaryotes, plants and Bacteria and have been found recently in Archaea. It is generally accepted that group II introns originated in bacteria before spreading to mitochondria and chloroplasts. These introns are thought to be related to the progenitors of spliceosomal introns. Group II introns are also mobile genetic elements. In bacteria, they appear to spread using either other mobile genetic elements or low-expression regions as target sites. Bacteria and Archaea genome sequence annotations have revealed the diversity of group II intron classes and that they are involved in vertical and horizontal inheritance.},
}
@article {pmid12586394,
year = {2003},
author = {Giraldo, R},
title = {Common domains in the initiators of DNA replication in Bacteria, Archaea and Eukarya: combined structural, functional and phylogenetic perspectives.},
journal = {FEMS microbiology reviews},
volume = {26},
number = {5},
pages = {533-554},
doi = {10.1111/j.1574-6976.2003.tb00629.x},
pmid = {12586394},
issn = {0168-6445},
mesh = {Amino Acid Sequence ; Animals ; Archaea/*genetics ; DNA Replication/*physiology ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; DNA-Binding Proteins/*chemistry/genetics/physiology ; Eukaryotic Cells ; Gram-Negative Bacteria/*genetics ; Models, Molecular ; Phylogeny ; Protein Structure, Tertiary ; *Replication Origin ; Sequence Alignment ; },
abstract = {Although DNA replication is the universal process for the transmission of genetic information in all living organisms, until very recently evidence was lacking for a related structure and function in the proteins (initiators) that trigger replication in the three 'Life Domains' (Bacteria, Archaea and Eukarya). In this article new data concerning the presence of common features in the initiators of chromosomal replication in bacteria, archaea and eukaryotes are reviewed. Initiators are discussed in the light of: (i) The structure and function of their conserved ATPases Associated with various cellular Activities (AAA+) and winged-helix domains. (ii) The nature of the macromolecular assemblies that they constitute at the replication origins. (iii) Their possible phylogenetic relationship, attempting to sketch the essentials of a hypothetical DNA replication initiator in the micro-organism proposed to be the ancestor of all living cells.},
}
@article {pmid12583906,
year = {2003},
author = {Contursi, P and Cannio, R and Prato, S and Fiorentino, G and Rossi, M and Bartolucci, S},
title = {Development of a genetic system for hyperthermophilic Archaea: expression of a moderate thermophilic bacterial alcohol dehydrogenase gene in Sulfolobus solfataricus.},
journal = {FEMS microbiology letters},
volume = {218},
number = {1},
pages = {115-120},
doi = {10.1111/j.1574-6968.2003.tb11506.x},
pmid = {12583906},
issn = {0378-1097},
mesh = {Alcohol Dehydrogenase/*genetics ; Cloning, Molecular ; *Gene Expression Regulation, Archaeal ; *Gene Expression Regulation, Enzymologic ; Genetic Vectors ; Geobacillus stearothermophilus/*genetics ; Mutagenesis ; Plasmids ; Promoter Regions, Genetic ; Sulfolobus/enzymology/*genetics ; Transcription, Genetic ; Transformation, Genetic ; },
abstract = {The Escherichia coli/Sulfolobus solfataricus shuttle vector pEXSs was used as a cloning vehicle for the gene transfer and expression of two bacterial genes in Sulfolobus solfataricus. The alcohol dehydrogenase (adh) from the moderate thermophilic Bacillus stearothermophilus (strain LLDR) and a mutagenised version encoding a less thermostable ADH enzyme were the selected genes. S. solfataricus adh promoter and aspartate aminotransferase terminator were used to drive the heterologous gene expression and to guarantee the correct termination of the transcripts, respectively. The constructed vectors were found to be able to carry these 'passenger' genes without undergoing any rearrangements. The active transcription of bacillar mRNAs was ascertained in vivo by RT-PCR. Transformed S. solfataricus expressed functional exogenous ADHs that showed unaffected kinetic and chemical-physical features.},
}
@article {pmid12566448,
year = {2003},
author = {Irihimovitch, V and Eichler, J},
title = {Post-translational secretion of fusion proteins in the halophilic archaea Haloferax volcanii.},
journal = {The Journal of biological chemistry},
volume = {278},
number = {15},
pages = {12881-12887},
doi = {10.1074/jbc.M210762200},
pmid = {12566448},
issn = {0021-9258},
mesh = {Amino Acid Sequence ; Archaeal Proteins/chemistry/*metabolism ; Binding Sites ; Haloferax volcanii/*metabolism ; Molecular Sequence Data ; Protein Precursors/chemistry/metabolism ; Protein Processing, Post-Translational ; Recombinant Fusion Proteins/chemistry/*metabolism ; },
abstract = {Although protein secretion occurs post-translationally in bacteria and is mainly a cotranslational event in Eukarya, the relationship between the translation and translocation of secreted proteins in Archaea is not known. To address this question, the signal peptide-encoding region of the surface layer glycoprotein gene from the Haloarchaea Haloferax volcanii was fused either to the cellulose-binding domain of the Clostridium thermocellum cellulosome or to the cytoplasmic enzyme dihydrofolate reductase from H. volcanii. Signal peptide-cleaved mature versions of both the cellulose-binding domain and dihydrofolate reductase could be detected in the growth medium of transformed H. volcanii cells. Immunoblot analysis revealed, however, the presence of full-length signal peptide-bearing forms of both proteins inside the cytoplasm of the transformed cells. Proteinase accessibility assays confirmed that the presence of cell-associated signal peptide-bearing proteins was not due to medium contamination. Moreover, the pulse-radiolabeled signal peptide cellulose-binding domain chimera could be chased from the cytoplasm into the growth medium even following treatment with anisomycin, an antibiotic inhibitor of haloarchaeal protein translation. Thus, these results provide evidence that, in Archaea, at least some secreted proteins are first synthesized inside the cell and only then translocated across the plasma membrane into the medium.},
}
@article {pmid12560992,
year = {2003},
author = {Scholten, JC and Murrell, JC and Kelly, DP},
title = {Growth of sulfate-reducing bacteria and methanogenic archaea with methylated sulfur compounds: a commentary on the thermodynamic aspects.},
journal = {Archives of microbiology},
volume = {179},
number = {2},
pages = {135-144},
doi = {10.1007/s00203-002-0509-0},
pmid = {12560992},
issn = {0302-8933},
mesh = {3-Mercaptopropionic Acid/metabolism ; Archaea/*growth &amp; development/*metabolism ; Biodegradation, Environmental ; Methane/classification/metabolism ; Methylation ; Sulfhydryl Compounds/metabolism ; Sulfides/classification/metabolism ; Sulfonium Compounds/metabolism ; Sulfur Compounds/classification/*metabolism ; Sulfur-Reducing Bacteria/*growth &amp; development/*metabolism ; Thermodynamics ; },
abstract = {Methylated sulfur compounds such as dimethylsulfoniopropionate, dimethylsulfide, methanethiol, and other methylated sulfur compounds can act as sources of carbon and energy for the growth under anoxic conditions of a number of sulfate-reducing bacteria and methanogenic archaea. We summarise the range of degradative reactions that do or might occur in such organisms, and present thermodynamic data for these processes. These data enable estimates of the feasibility of the reactions as growth-supporting systems, and of the possible maximum growth yields of the bacteria and archaea catalysing them. We compare our new estimates with the few data that are currently available from the literature, and show that some published growth-yield assessments need reevaluation.},
}
@article {pmid12560482,
year = {2003},
author = {Rozhdestvensky, TS and Tang, TH and Tchirkova, IV and Brosius, J and Bachellerie, JP and Hüttenhofer, A},
title = {Binding of L7Ae protein to the K-turn of archaeal snoRNAs: a shared RNA binding motif for C/D and H/ACA box snoRNAs in Archaea.},
journal = {Nucleic acids research},
volume = {31},
number = {3},
pages = {869-877},
pmid = {12560482},
issn = {1362-4962},
mesh = {Archaea/genetics ; Archaeal Proteins/*metabolism ; Base Sequence ; Binding Sites ; Conserved Sequence ; Molecular Sequence Data ; Mutation ; Nucleic Acid Conformation ; RNA, Archaeal/*chemistry/genetics/*metabolism ; RNA, Small Nucleolar/*chemistry/genetics/*metabolism ; RNA-Binding Proteins/metabolism ; Ribosomal Proteins/*metabolism ; },
abstract = {Small nucleolar RNAs (designated as snoRNAs in Eukarya or sRNAs in Archaea) can be grouped into H/ACA or C/D box snoRNA (sRNA) subclasses. In Eukarya, H/ACA snoRNAs assemble into a ribonucleoprotein (RNP) complex comprising four proteins: Cbf5p, Gar1p, Nop10p and Nhp2p. A homolog for the Nhp2p protein has not been identified within archaeal H/ACA RNPs thus far, while potential orthologs have been identified for the other three proteins. Nhp2p is related, particularly in the middle portion of the protein sequence, to the archaeal ribosomal protein and C/D box protein L7Ae. This finding suggests that L7Ae may be able to substitute for the Nhp2p protein in archaeal H/ACA sRNAs. By band shift assays, we have analyzed in vitro the interaction between H/ACA box sRNAs and protein L7Ae from the archaeon Archaeoglobus fulgidus. We present evidence that L7Ae forms specific complexes with three different H/ACA sRNAs, designated as Afu-4, Afu-46 and Afu-190 with an apparent K(d) ranging from 28 to 100 nM. By chemical and enzymatic probing we show that distinct bases located within bulges or loops of H/ACA sRNAs interact with the L7Ae protein. These findings are corroborated by mutational analysis of the L7Ae binding site. Thereby, the RNA motif required for L7Ae binding exhibits a structure, designated as the K-turn, which is present in all C/D box sRNAs. We also identified four H/ACA RNAs from the archaeal species Pyrococcus which exhibit the K-turn motif at a similar position in their structure. These findings suggest a triple role for L7Ae protein in Archaea, e.g. in ribosomes as well as H/ACA and C/D box sRNP biogenesis and function by binding to the K-turn motif.},
}
@article {pmid12557560,
year = {2002},
author = {Li, Y and Xiang, H and Tan, H},
title = {[Halocin: protein antibiotics produced by extremely halophilic archaea].},
journal = {Wei sheng wu xue bao = Acta microbiologica Sinica},
volume = {42},
number = {4},
pages = {502-505},
pmid = {12557560},
issn = {0001-6209},
mesh = {Antimicrobial Cationic Peptides ; Archaea/*metabolism ; *Archaeal Proteins/chemistry/genetics/isolation &amp; purification ; *Bacteriocins/chemistry/genetics/isolation &amp; purification ; Genes, Archaeal ; Halobacteriaceae/*chemistry ; Open Reading Frames ; Peptides/chemistry/genetics/isolation &amp; purification ; },
}
@article {pmid12554871,
year = {2003},
author = {Dai, L and Zimmerly, S},
title = {ORF-less and reverse-transcriptase-encoding group II introns in archaebacteria, with a pattern of homing into related group II intron ORFs.},
journal = {RNA (New York, N.Y.)},
volume = {9},
number = {1},
pages = {14-19},
pmid = {12554871},
issn = {1355-8382},
mesh = {Amino Acid Sequence ; Base Sequence ; *Introns ; Methanosarcina/genetics ; Molecular Sequence Data ; *Open Reading Frames ; RNA, Archaeal ; RNA-Directed DNA Polymerase/*genetics ; },
abstract = {Although group II intron retroelements are prevalent in eubacteria, they have not been identified in archaebacteria in the first 10 genomes sequenced. However, the recently sequenced archael genome of Methanosarcina acetivorans contains 21 group II introns, including 7 introns that do not encode reverse transcriptase ORFs. To our knowledge, these are the first retroelements identified in archaebacteria, and the first ORF-less group II introns in bacteria. Furthermore, the insertion pattern of the introns is highly unusual. The introns appear to insert site-specifically into ORFs of other group II introns, forming nested clusters of up to four introns, but there are no flanking exons that could encode a functional protein after the introns have been spliced out.},
}
@article {pmid12549077,
year = {2001},
author = {He, Z and Li, Y and Zhou, P},
title = {[Study on reclassification of extremely thermoacidophilic archaea strain S5].},
journal = {Wei sheng wu xue bao = Acta microbiologica Sinica},
volume = {41},
number = {3},
pages = {259-264},
pmid = {12549077},
issn = {0001-6209},
mesh = {Acidianus/*classification/genetics/isolation &amp; purification/ultrastructure ; Base Sequence ; DNA, Archaeal/*genetics ; Hot Springs/microbiology ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA ; Sulfolobales/*classification/genetics/isolation &amp; purification ; *Terminology as Topic ; Water Microbiology ; },
abstract = {The further study on thermoacidophilic archaea strain S5, with has been identified as Sulfosphaerellus thermoacidophilum gen.nov.,sp.nov, has shown it was able to grow facultatively aerobically by means of two sulfur-metabolizing modes of chemolithotrophy which is the characteristic of Acidianus. And the 16SrRNA gene of strain S5 was amplified, cloned and sequenced, a phylogenetic tree was constructed on the 16SrRNA gene sequences. The tree clearly indicated that strain S5 formed the same lineage with Acidianus brierleyi. Thus strain S5 should be the member of Acidianus. However, there are only 44%, 22% and 23% genomic DNA similarity between S5 and A. brierleyi. A. infernus and A. ambivalens, respectively. And the G + C content of S5 DNA is 38%, which is 5% ~ 7% higher than the reported G + C contents of the other Acidianus species (31% or 32.7%) . In addition, strain S5 is a strictly chemolithoautotrophs, which is obviously different from facultative chemolithotrophs of A brierleyi. Based on the observed differences, strain S5 represents a new species within the genus Acidianus. A new species name, Acidianus tengchongenses, was proposed for it. The type strain is designated S5.},
}
@article {pmid12540534,
year = {2003},
author = {Eckburg, PB and Lepp, PW and Relman, DA},
title = {Archaea and their potential role in human disease.},
journal = {Infection and immunity},
volume = {71},
number = {2},
pages = {591-596},
pmid = {12540534},
issn = {0019-9567},
mesh = {Archaea/*pathogenicity ; Disease/*etiology ; Humans ; Virulence ; },
}
@article {pmid12540196,
year = {2002},
author = {Hickey, AJ and Conway de Macario, E and Macario, AJ},
title = {Transcription in the archaea: basal factors, regulation, and stress-gene expression.},
journal = {Critical reviews in biochemistry and molecular biology},
volume = {37},
number = {6},
pages = {537-599},
doi = {10.1080/10409230290771555},
pmid = {12540196},
issn = {1040-9238},
mesh = {Archaea/enzymology/*genetics/physiology ; *Gene Expression Regulation, Archaeal ; HSP70 Heat-Shock Proteins/*genetics ; *Transcription, Genetic ; },
abstract = {A brief survey is presented of salient findings on transcription in the Archaea, focussing on stress genes of the hsp70(dnaK locus, which code for the molecular chaperones Hsp70(DnaK), Hsp40(DnaJ), and GrpE. Archaeal basal factors and some recently characterized regulators pertinent to non-stress genes are presented first to show their similarities and differences with equivalents in organisms of the other two phylogenetic domains, Bacteria and Eucarya, and to reveal clues on how these or similar factors might transcribe and regulate the archaeal stress genes. The second part of the article deals with the hsp70(dnaK)-locus genes, particularly those from Methanosarcina mazeii, because they are virtually the only ones within the methanogenic Archaea whose patterns of constitutive and stress-induced expressions have been studied. Therefore, these genes provide a standardized model system to elucidate transcription initiation and regulation at the molecular level in this phylogenetic group. Promoters, and other cis-acting sites that are, or might be, involved in stress-gene expression are described. Conformational changes of basal transcription factors after interaction with stress-gene promoters are discussed that suggest ways for generating a large diversity of initiation complexes using a few factors and DNA sites in different combinations. Likewise, the effects of stress on DNA topology and on TBP-TFB-promoter complex formation and tightness are described, which might also contribute to the generation of transcription-initiation complex diversity. This diversity would be key to differential gene expression, namely, which genes are transcribed, when (basal, steady expression vs. sporadic stress-induced expression), and to what level. Future research should investigate this diversity, and the mechanism of complex formation and action at the atomic, molecular, and supramolecular levels, to elucidate the dynamics of transcription initiation in real time.},
}
@article {pmid12532352,
year = {2003},
author = {Schiller, SM and Naumann, R and Lovejoy, K and Kunz, H and Knoll, W},
title = {Archaea analogue thiolipids for tethered bilayer lipid membranes on ultrasmooth gold surfaces.},
journal = {Angewandte Chemie (International ed. in English)},
volume = {42},
number = {2},
pages = {208-211},
doi = {10.1002/anie.200390080},
pmid = {12532352},
issn = {1433-7851},
mesh = {Archaea/*chemistry ; *Gold ; Lipid Bilayers/*chemistry ; Molecular Conformation ; Spectroscopy, Fourier Transform Infrared ; Sulfhydryl Compounds/*chemistry ; Surface Properties ; },
}
@article {pmid12529358,
year = {2003},
author = {Sakuraba, H and Tsuge, H and Shimoya, I and Kawakami, R and Goda, S and Kawarabayasi, Y and Katunuma, N and Ago, H and Miyano, M and Ohshima, T},
title = {The first crystal structure of archaeal aldolase. Unique tetrameric structure of 2-deoxy-d-ribose-5-phosphate aldolase from the hyperthermophilic archaea Aeropyrum pernix.},
journal = {The Journal of biological chemistry},
volume = {278},
number = {12},
pages = {10799-10806},
doi = {10.1074/jbc.M212449200},
pmid = {12529358},
issn = {0021-9258},
mesh = {Amino Acid Sequence ; Archaea/*enzymology ; Archaeal Proteins/*chemistry ; Enzyme Stability ; Escherichia coli/enzymology ; Fructose-Bisphosphate Aldolase/*chemistry/genetics ; Hydrogen-Ion Concentration ; Molecular Sequence Data ; Protein Subunits ; Recombinant Proteins/chemistry ; Ribosemonophosphates/*metabolism ; },
abstract = {A gene encoding a 2-deoxy-d-ribose-5-phosphate aldolase (DERA) homolog was identified in the hyperthermophilic Archaea Aeropyrum pernix. The gene was overexpressed in Escherichia coli, and the produced enzyme was purified and characterized. The enzyme is an extremely thermostable DERA; its activity was not lost after incubation at 100 degrees C for 10 min. The enzyme has a molecular mass of approximately 93 kDa and consists of four subunits with an identical molecular mass of 24 kDa. This is the first report of the presence of tetrameric DERA. The three-dimensional structure of the enzyme was determined by x-ray analysis. The subunit folds into an alpha/beta-barrel. The asymmetric unit consists of two homologous subunits, and a crystallographic 2-fold axis generates the functional tetramer. The main chain coordinate of the monomer of the A. pernix enzyme is quite similar to that of the E. coli enzyme. There was no significant difference in hydrophobic interactions and the number of ion pairs between the monomeric structures of the two enzymes. However, a significant difference in the quaternary structure was observed. The area of the subunit-subunit interface in the dimer of the A. pernix enzyme is much larger compared with the E. coli enzyme. In addition, the A. pernix enzyme is 10 amino acids longer than the E. coli enzyme in the N-terminal region and has an additional N-terminal helix. The N-terminal helix produces a unique dimer-dimer interface. This promotes the formation of a functional tetramer of the A. pernix enzyme and strengthens the hydrophobic intersubunit interactions. These structural features are considered to be responsible for the extremely high stability of the A. pernix enzyme. This is the first description of the structure of hyperthermophilic DERA and of aldolase from the Archaea domain.},
}
@article {pmid12501361,
year = {1999},
author = {Chagan, I and Tokura, M and Jouany, JP and Ushida, K},
title = {Detection of methanogenic archaea associated with rumen ciliate protozoa.},
journal = {The Journal of general and applied microbiology},
volume = {45},
number = {6},
pages = {305-308},
doi = {10.2323/jgam.45.305},
pmid = {12501361},
issn = {1349-8037},
}
@article {pmid12486065,
year = {2003},
author = {Zhulin, IB and Nikolskaya, AN and Galperin, MY},
title = {Common extracellular sensory domains in transmembrane receptors for diverse signal transduction pathways in bacteria and archaea.},
journal = {Journal of bacteriology},
volume = {185},
number = {1},
pages = {285-294},
pmid = {12486065},
issn = {0021-9193},
mesh = {Adenylyl Cyclases/chemistry/genetics ; Amino Acid Sequence ; Archaea/*chemistry/genetics/metabolism ; Archaeal Proteins/metabolism ; Bacteria/*chemistry/genetics/metabolism ; Bacterial Proteins/metabolism ; Chemotaxis ; Computational Biology ; Databases, Genetic ; Guanylate Cyclase/chemistry/genetics ; Histidine Kinase ; Molecular Sequence Data ; Protein Kinases/chemistry/genetics ; Receptors, Cell Surface/*chemistry/genetics ; Sequence Alignment ; *Signal Transduction ; },
abstract = {Transmembrane receptors in microorganisms, such as sensory histidine kinases and methyl-accepting chemotaxis proteins, are molecular devices for monitoring environmental changes. We report here that sensory domain sharing is widespread among different classes of transmembrane receptors. We have identified two novel conserved extracellular sensory domains, named CHASE2 and CHASE3, that are found in at least four classes of transmembrane receptors: histidine kinases, adenylate cyclases, predicted diguanylate cyclases, and either serine/threonine protein kinases (CHASE2) or methyl-accepting chemotaxis proteins (CHASE3). Three other extracellular sensory domains were shared by at least two different classes of transmembrane receptors: histidine kinases and either diguanylate cyclases, adenylate cyclases, or phosphodiesterases. These observations suggest that microorganisms use similar conserved domains to sense similar environmental signals and transmit this information via different signal transduction pathways to different regulatory circuits: transcriptional regulation (histidine kinases), chemotaxis (methyl-accepting proteins), catabolite repression (adenylate cyclases), and modulation of enzyme activity (diguanylate cyclases and phosphodiesterases). The variety of signaling pathways using the CHASE-type domains indicates that these domains sense some critically important extracellular signals.},
}
@article {pmid12482750,
year = {2003},
author = {Chandu, D and Kumar, A and Nandi, D},
title = {PepN, the major Suc-LLVY-AMC-hydrolyzing enzyme in Escherichia coli, displays functional similarity with downstream processing enzymes in Archaea and eukarya. Implications in cytosolic protein degradation.},
journal = {The Journal of biological chemistry},
volume = {278},
number = {8},
pages = {5548-5556},
doi = {10.1074/jbc.M207926200},
pmid = {12482750},
issn = {0021-9258},
mesh = {Amino Acid Sequence ; Aminopeptidases/metabolism ; Animals ; Archaea/*enzymology ; Bacteria/enzymology ; Bacterial Proteins/genetics/isolation &amp; purification/*metabolism ; Base Sequence ; Chromatography, Affinity ; Chromatography, DEAE-Cellulose ; Chromatography, Gel ; Coumarins/metabolism ; DNA Primers ; Escherichia coli/*enzymology ; Escherichia coli Proteins/genetics/isolation &amp; purification/metabolism ; Eukaryotic Cells/enzymology ; Mice ; Molecular Sequence Data ; Oligopeptides/metabolism ; Plasmids ; Polymerase Chain Reaction ; Sequence Alignment ; Sequence Homology, Amino Acid ; Substrate Specificity ; },
abstract = {Succinyl-Leu-Leu-Val-Tyr-7-amido-4-methylcoumarin (Suc-LLVY-AMC), a fluorogenic endopeptidase substrate, is used to detect 20 S proteasomal activity from Archaea to mammals. An o-phenanthroline-sensitive Suc-LLVY-AMC hydrolyzing activity was detected in Escherichia coli although it lacks 20 S proteasomes. We identified PepN, previously characterized as the sole alanine aminopeptidase in E. coli, to be responsible for the hydrolysis of Suc-LLVY-AMC. PepN is an aminoendopeptidase. First, extracts from an ethyl methanesulfonate-derived PepN mutant, 9218, did not cleave Suc-LLVY-AMC and L-Ala-para-nitroanilide (pNA). Second, biochemically purified PepN cleaves a wide variety of both aminopeptidase and endopeptidase substrates, and L-Ala-pNA is cleaved more efficiently than other substrates. Studies with bestatin, an aminopeptidase-specific inhibitor, suggest differences in the mechanisms of cleavage of aminopeptidase and endopeptidase substrates. Third, PepN hydrolyzes whole proteins, casein and albumin. Finally, an E. coli strain with a targeted deletion in PepN also lacks the ability to cleave Suc-LLVY-AMC and L-Ala-pNA, and expression of wild type PepN in this mutant rescues both activities. In addition, we identified a low molecular weight Suc-LLVY-AMC-cleaving peptidase in Mycobacterium smegmatis, a eubacteria harboring 20 S proteasomes, to be an aminopeptidase homologous to E. coli PepN, by mass spectrometry analysis. "Sequence-based homologues" of PepN include well characterized aminopeptidases, e.g. Tricorn interacting factors F2 and F3 in Archaea and puromycin-sensitive aminopeptidase in mammals. However, our results suggest that eubacterial PepN and its homologues displaying aminoendopeptidase activities may be "functionally similar" to enzymes important in downstream processing of proteins in the cytosol: Tricorn-F1-F2-F3 complex in Archaea and TPPII/Multicorn in eukaryotes.},
}
@article {pmid19709303,
year = {2002},
author = {Galand, PE and Saarnio, S and Fritze, H and Yrjälä, K},
title = {Depth related diversity of methanogen Archaea in Finnish oligotrophic fen.},
journal = {FEMS microbiology ecology},
volume = {42},
number = {3},
pages = {441-449},
doi = {10.1111/j.1574-6941.2002.tb01033.x},
pmid = {19709303},
issn = {1574-6941},
abstract = {The annual rate of CH4 release and potential CH4 production has recently been studied in the Salmisuo fen in eastern Finland but the microbiota responsible for the CH4 production has not been examined. The diversity of the methane producing Archaea was analysed, at different depths, in the most representative microsite (Eriophorum lawn) of the fen. Methanogen populations were studied using primers amplifying a region of the methyl-coenzyme M reductase gene. PCR products were analysed by denaturing gradient gel electrophoresis and restriction fragment length polymorphism (RFLP) analysis of clone libraries. A representative of each RFLP group was sequenced. The study revealed a change of the methanogen populations with depth. Sequences from the upper layers of the fen grouped in a novel 'Fen cluster' and were related to Methanomicrobiales. Sequences retrieved from the deeper layers of the fen were related to Methanosarcinales via the Rice Cluster-I.},
}
@article {pmid12450849,
year = {2002},
author = {Fairley, DJ and Boyd, DR and Sharma, ND and Allen, CC and Morgan, P and Larkin, MJ},
title = {Aerobic metabolism of 4-hydroxybenzoic acid in Archaea via an unusual pathway involving an intramolecular migration (NIH shift).},
journal = {Applied and environmental microbiology},
volume = {68},
number = {12},
pages = {6246-6255},
pmid = {12450849},
issn = {0099-2240},
mesh = {2,2'-Dipyridyl/metabolism ; Aerobiosis ; Biotransformation ; *Gentisates ; Haloarcula/growth &amp; development/*metabolism ; Hydroxybenzoates/metabolism ; Magnetic Resonance Spectroscopy ; Parabens/*metabolism ; },
abstract = {A novel haloarchaeal strain, Haloarcula sp. strain D1, grew aerobically on 4-hydroxybenzoic acid (4HBA) as a sole carbon and energy source and is the first member of the domain Archaea reported to do so. Unusually, D1 metabolized 4HBA via gentisic acid rather than via protocatechuic acid, hydroquinone, or catechol. Gentisate was detected in 4HBA-grown cultures, and gentisate 1,2-dioxygenase activity was induced in 4HBA-grown cells. Stoichiometric accumulation of gentisate from 4HBA was demonstrated in 4HBA-grown cell suspensions containing 2,2'-dipyridyl (which strongly inhibits gentisate 1,2-dioxygenase). To establish whether initial 1-hydroxylation of 4HBA with concomitant 1,2-carboxyl group migration to yield gentisate occurred, 2,6-dideutero-4HBA was synthesized and used as a substrate. Deuterated gentisate was recovered from cell suspensions and identified as 3-deutero-gentisate, using gas chromatography-mass spectrometry and proton nuclear magnetic resonance spectroscopy. This structural isomer would be expected only if a 1,2-carboxyl group migration had taken place, and it provides compelling evidence that the 4HBA pathway in Haloarcula sp. strain D1 involves a hydroxylation-induced intramolecular migration. To our knowledge, this is the first report of a pathway which involves such a transformation (called an NIH shift) in the domain Archaea.},
}
@article {pmid12448707,
year = {2002},
author = {Serour, E and Antranikian, G},
title = {Novel thermoactive glucoamylases from the thermoacidophilic Archaea Thermoplasma acidophilum, Picrophilus torridus and Picrophilus oshimae.},
journal = {Antonie van Leeuwenhoek},
volume = {81},
number = {1-4},
pages = {73-83},
doi = {10.1023/a:1020525525490},
pmid = {12448707},
issn = {0003-6072},
mesh = {Enzyme Stability ; Glucan 1,4-alpha-Glucosidase/isolation &amp; purification/*metabolism ; Hydrogen-Ion Concentration ; Starch/metabolism ; Temperature ; Thermoplasma/*enzymology/growth &amp; development ; Thermoplasmales/*enzymology/growth &amp; development ; },
abstract = {The thermoacidophilic Archaea Thermoplasma acidophilum (optimal growth at 60 degrees C and pH 1-2), Picrophilus torridus and Picrophilus oshimae (optimal growth at 60 degrees C and pH 0.7) were able to utilize starch as sole carbon source. During growth these microorganisms secreted heat and acid-stable glucoamylases into the culture fluid. Applying SDS gel electrophoresis activity bands were detected with appearent molecular mass (Mw) of 141.0, 95.0 kDa for T. acidophilum, 133.0, 90.0 kDa for P. torridus and 140.0, 85.0 kDa for P. oshimae. The purified enzymes were incubated with various polymeric substrates such as starch, pullulan, panose and isomaltose. The product pattern, analyzed by HPLC, showed that in all cases glucose was formed as the sole product of hydrolysis. The purified glucoamylases were optimally active at pH 2.0 and 90 degrees C and have an isoelectric points (pI) between 4.5 and 4.8. Enzymatic activity was detected even at pH 1.0 and 100 degrees C. The glucoamylases were thermostable at elevated temperature with a half-life of 24 h at 90 degrees C for both P. torridus and T acidophilum, and 20 h at 90 degrees C for P oshimae. The enzyme system of T acidophilum has a lower Km value for soluble starch (1.06 mg/ml) than the enzymes from P. oshimae and P. torridus (4.35 mg/ml and 2.5 mg/ml), respectively. Enzyme activity was not affected by Na+, Mg++, Ca++, Ni++, Zn++, Fe++, EDTA and DTT.},
}
@article {pmid12448706,
year = {2002},
author = {Konings, WN and Albers, SV and Koning, S and Driessen, AJ},
title = {The cell membrane plays a crucial role in survival of bacteria and archaea in extreme environments.},
journal = {Antonie van Leeuwenhoek},
volume = {81},
number = {1-4},
pages = {61-72},
doi = {10.1023/a:1020573408652},
pmid = {12448706},
issn = {0003-6072},
mesh = {Archaea/*growth &amp; development ; Bacteria/*growth &amp; development ; Biological Transport ; Cell Membrane/*physiology ; Cell Membrane Permeability ; Energy Metabolism ; *Temperature ; },
abstract = {The cytoplasmic membrane of bacteria and archaea determine to a large extent the composition of the cytoplasm. Since the ion and in particular the proton and/or the sodium ion electrochemical gradients across the membranes are crucial for the bioenergetic conditions of these microorganisms, strategies are needed to restrict the permeation of these ions across their cytoplasmic membrane. The proton and sodium permeabilities of all biological membranes increase with the temperature. Psychrophilic and mesophilic bacteria, and mesophilic, (hyper)thermophilic and halophilic archaea are capable of adjusting the lipid composition of their membranes in such a way that the proton permeability at the respective growth temperature remains low and constant (homeo-proton permeability). Thermophilic bacteria, however, have more difficulties to restrict the proton permeation across their membrane at high temperatures and these organisms have to rely on the less permeable sodium ions for maintaining a high sodium-motive force for driving their energy requiring membrane-bound processes. Transport of solutes across the bacterial and archaeal membrane is mainly catalyzed by primary ATP driven transport systems or by proton or sodium motive force driven secondary transport systems. Unlike most bacteria, hyperthermophilic bacteria and archaea prefer primary ATP-driven uptake systems for their carbon and energy sources. Several high-affinity ABC transporters for sugars from hyperthermophiles have been identified and characterized. The activities of these ABC transporters allow these organisms to thrive in their nutrient-poor environments.},
}
@article {pmid12446147,
year = {2002},
author = {White, MF and Bell, SD},
title = {Holding it together: chromatin in the Archaea.},
journal = {Trends in genetics : TIG},
volume = {18},
number = {12},
pages = {621-626},
doi = {10.1016/s0168-9525(02)02808-1},
pmid = {12446147},
issn = {0168-9525},
mesh = {Amino Acid Sequence ; Archaeal Proteins/genetics/physiology ; Chromatin/*chemistry/*genetics/physiology ; DNA/metabolism ; DNA-Binding Proteins/genetics/physiology ; Eukaryotic Cells/chemistry/physiology ; Histones/chemistry/genetics/physiology ; Molecular Sequence Data ; Sulfolobus/*chemistry/*genetics/physiology ; },
abstract = {Recently, several advances have been made in the understanding of the form and function of archaeal chromatin. Remarkable parallels can be drawn between the structure and modification of chromatin components in the archaeal and the eukaryotic domains of life. Indeed, it now appears that key components of the hugely complex eukaryotic chromatin regulatory machinery were established before the divergence of the archaeal and eukaryotic lineages.},
}
@article {pmid12441648,
year = {2002},
author = {Horiike, T and Hamada, K and Shinozawa, T},
title = {Origin of eukaryotic cell nuclei by symbiosis of Archaea in Bacteria supported by the newly clarified origin of functional genes.},
journal = {Genes &amp; genetic systems},
volume = {77},
number = {5},
pages = {369-376},
doi = {10.1266/ggs.77.369},
pmid = {12441648},
issn = {1341-7568},
mesh = {Archaea/genetics/*physiology ; Bacteria/*genetics ; *Biological Evolution ; Cell Nucleus/*physiology ; Eukaryotic Cells/*physiology ; Gene Transfer, Horizontal ; Open Reading Frames ; Saccharomyces cerevisiae/genetics ; },
abstract = {In the previous report, we demonstrated the origin of eukaryotic cell nuclei as the symbiosis of Archaea in Bacteria by the newly developed "Homology-Hit Analysis". In that case, we counted yeast Open Reading Frames (ORFs) showing the highest similarity to a bacterial ORF as orthologous ORFs (Orthologous ORFs were produced by speciation from a common ancestor, and have the highest similarity to each other.) by comparing whole ORFs of yeast with those of individual bacteria. However, we could not count all yeast ORFs showing the highest similarity to a bacterial ORF in functional categories of yeast. Therefore, the origin of ORFs in the functional categories of yeast could not be inferred strictly. Here, we have improved the method for detecting orthologous ORFs. In this method, we count the numbers of ORF with the highest similarity between individual yeast functional categories and individual bacteria as orthologous ORFs. By this method, it was possible to detect the correct orthologous ORFs and to infer the origins of the functional categories in eukaryotic cells. As a result, two categories, assembly of protein complexes and DNA repair were newly judged to be of Archaeal origin, while five categories, lipid (fatty-acid and isoprenoid) metabolism, protein folding and stabilization, signal transduction, organization of the plasma membrane and organization of the cytoplasm, were newly judged to be of Bacterial origin. On the other hand, the origins of two categories (meiosis and cellular import, which were determined in the previous analysis) could not be judged. It is considered that functional categories related to the nucleus have origins common to Archaea, while those related to the cytoplasm have origins common to Bacteria. From these data including the origin of plasma membrane, it was further clarified that cell nucleus originated by the symbiosis of Archaea in Bacteria.},
}
@article {pmid12440773,
year = {2002},
author = {Deppenmeier, U},
title = {Redox-driven proton translocation in methanogenic Archaea.},
journal = {Cellular and molecular life sciences : CMLS},
volume = {59},
number = {9},
pages = {1513-1533},
doi = {10.1007/s00018-002-8526-3},
pmid = {12440773},
issn = {1420-682X},
mesh = {Amino Acid Sequence ; Animals ; Archaeal Proteins/genetics/metabolism ; Carbon Dioxide/metabolism ; Electron Transport/*physiology ; Ion Transport ; Membrane Proteins/genetics/metabolism ; Methanosarcina/*enzymology/genetics ; Molecular Sequence Data ; Molecular Structure ; Operon/genetics ; Oxidation-Reduction ; Oxidoreductases/genetics/metabolism ; *Protons ; },
abstract = {Methanogenic archaea of the genus Methanosarcina are able to utilize H2 + CO2, methylated C1 compounds or acetate as energy and carbon source, thereby producing methane as the major end product. The methanogenic pathways lead to the formation of a mixed disulfide derived from coenzyme M and coenzyme B. This disulfide is of major importance for methanogens because it is the terminal electron acceptor of a branched respiratory chain. Molecular hydrogen, reduced coenzyme F420 or reduced ferredoxin are used as electron donors. Four enzymes are involved in the membrane-bound electron transport system of Methanosarcina species, all of which are involved in the generation of an electrochemical proton gradient that is used for ATP synthesis. This review focuses on the membrane-bound electron transport chains of Methanosarcina species with respect to the biochemical and genetic characteristics of the unusual energy transducing enzymes. Furthermore, the review addresses questions concerning the relationship between methanogenic proteins and components of respiratory chains found in bacteria and eukarya.},
}
@article {pmid12424340,
year = {2002},
author = {Szeto, TH and Rowland, SL and Rothfield, LI and King, GF},
title = {Membrane localization of MinD is mediated by a C-terminal motif that is conserved across eubacteria, archaea, and chloroplasts.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {99},
number = {24},
pages = {15693-15698},
pmid = {12424340},
issn = {0027-8424},
support = {R01 GM060632/GM/NIGMS NIH HHS/United States ; R37 GM060632/GM/NIGMS NIH HHS/United States ; GM-48583/GM/NIGMS NIH HHS/United States ; GM-60632/GM/NIGMS NIH HHS/United States ; },
mesh = {Adenosine Triphosphatases/*chemistry/genetics ; Amino Acid Motifs ; Amino Acid Sequence ; Archaea/*enzymology ; Archaeal Proteins/*chemistry ; Bacteria/*enzymology ; Bacterial Proteins/*chemistry ; Cell Membrane/*enzymology ; Chloroplasts/*enzymology ; Escherichia coli Proteins/*chemistry/genetics ; Evolution, Molecular ; Membrane Proteins/*chemistry ; Models, Molecular ; Molecular Sequence Data ; Mutagenesis, Site-Directed ; Plant Proteins/*chemistry ; Protein Structure, Secondary ; Protein Transport ; Sequence Alignment ; Sequence Homology, Amino Acid ; Species Specificity ; },
abstract = {MinD is a widely conserved ATPase that has been demonstrated to play a pivotal role in selection of the division site in eubacteria and chloroplasts. It is a member of the large ParA superfamily of ATPases that are characterized by a deviant Walker-type ATP-binding motif. MinD localizes to the cytoplasmic face of the inner membrane in Escherichia coli, and its association with the inner membrane is a prerequisite for membrane recruitment of the septation inhibitor MinC. However, the mechanism by which MinD associates with the membrane has proved enigmatic; it seems to lack a transmembrane domain and the amino acid sequence is devoid of hydrophobic tracts that might predispose the protein to interaction with lipids. In this study, we show that the extreme C-terminal region of MinD contains a highly conserved 8- to 12-residue sequence motif that is essential for membrane localization of the protein. We provide evidence that this motif forms an amphipathic helix that most likely mediates a direct interaction between MinD and membrane phospholipids. A model is proposed whereby the membrane-targeting motif mediates the rapid cycles of membrane attachment-release-reattachment that are presumed to occur during pole-to-pole oscillation of MinD in E. coli.},
}
@article {pmid12419895,
year = {2002},
author = {Komori, K and Fujikane, R and Shinagawa, H and Ishino, Y},
title = {Novel endonuclease in Archaea cleaving DNA with various branched structure.},
journal = {Genes &amp; genetic systems},
volume = {77},
number = {4},
pages = {227-241},
doi = {10.1266/ggs.77.227},
pmid = {12419895},
issn = {1341-7568},
mesh = {Amino Acid Sequence ; DNA/*metabolism ; DNA Repair/*genetics/physiology ; DNA Replication/physiology ; DNA-Binding Proteins/genetics ; Endodeoxyribonucleases/genetics ; Endonucleases/*genetics/metabolism ; Holliday Junction Resolvases ; Molecular Sequence Data ; Pyrococcus furiosus/enzymology/*genetics ; },
abstract = {We identified a novel structure-specific endonuclease in Pyrococcus furiosus. This nuclease contains two distinct domains, which are similar to the DEAH helicase family at the N-terminal two-third and the XPF endonuclease superfamily at the C-terminal one-third of the protein, respectively. The C-terminal domain has an endonuclease activity cleaving the DNA strand at the 5'-side of nicked or flapped positions in the duplex DNA. The nuclease also incises in the proximity of the 5'-side of a branch point in the template strand for leading synthesis in the fork-structured DNA. The N-terminal helicase may work cooperatively to change the fork structure suitable for cleavage by the C-terminal endonuclease. This protein, designated as Hef (helicase-associated endonuclease for fork-structured DNA), may be a prototypical enzyme for resolving stalled forks during DNA replication, as well as working at nucleotide excision repair.},
}
@article {pmid12409299,
year = {2003},
author = {Thore, S and Mayer, C and Sauter, C and Weeks, S and Suck, D},
title = {Crystal structures of the Pyrococcus abyssi Sm core and its complex with RNA. Common features of RNA binding in archaea and eukarya.},
journal = {The Journal of biological chemistry},
volume = {278},
number = {2},
pages = {1239-1247},
doi = {10.1074/jbc.M207685200},
pmid = {12409299},
issn = {0021-9258},
mesh = {Amino Acid Sequence ; Archaeal Proteins/*chemistry/metabolism ; Binding Sites ; Crystallization ; Models, Molecular ; Molecular Sequence Data ; Protein Structure, Secondary ; Pyrococcus/*chemistry ; RNA/chemistry/*metabolism ; Ribonucleoproteins, Small Nuclear/*chemistry/metabolism ; },
abstract = {The Sm proteins are conserved in all three domains of life and are always associated with U-rich RNA sequences. Their proposed function is to mediate RNA-RNA interactions. We present here the crystal structures of Pyrococcus abyssi Sm protein (PA-Sm1) and its complex with a uridine heptamer. The overall structure of the protein complex, a heptameric ring with a central cavity, is similar to that proposed for the eukaryotic Sm core complex and found for other archaeal Sm proteins. RNA molecules bind to the protein at two different sites. They interact specifically inside the ring with three highly conserved residues, defining the uridine-binding pocket. In addition, nucleotides also interact on the surface formed by the N-terminal alpha-helix as well as a conserved aromatic residue in beta-strand 2 of the PA-Sm1 protein. The mutation of this conserved aromatic residue shows the importance of this second site for the discrimination between RNA sequences. Given the high structural homology between archaeal and eukaryotic Sm proteins, the PA-Sm1.RNA complex provides a model for how the small nuclear RNA contacts the Sm proteins in the Sm core. In addition, it suggests how Sm proteins might exert their function as modulators of RNA-RNA interactions.},
}
@article {pmid12403461,
year = {2002},
author = {Marck, C and Grosjean, H},
title = {tRNomics: analysis of tRNA genes from 50 genomes of Eukarya, Archaea, and Bacteria reveals anticodon-sparing strategies and domain-specific features.},
journal = {RNA (New York, N.Y.)},
volume = {8},
number = {10},
pages = {1189-1232},
pmid = {12403461},
issn = {1355-8382},
mesh = {Amino Acid Sequence ; Animals ; Archaea/*genetics ; Bacteria/*genetics ; Base Composition ; Base Pairing ; Base Sequence ; Codon ; Conserved Sequence ; Eukaryotic Cells/*physiology ; *Genome ; Humans ; Molecular Sequence Data ; Nucleic Acid Conformation ; Phylogeny ; RNA Processing, Post-Transcriptional ; RNA, Transfer/chemistry/*genetics ; RNA, Transfer, Ile ; Transcription, Genetic ; },
abstract = {From 50 genomes of the three domains of life (7 eukarya, 13 archaea, and 30 bacteria), we extracted, analyzed, and compared over 4,000 sequences corresponding to cytoplasmic, nonorganellar tRNAs. For each genome, the complete set of tRNAs required to read the 61 sense codons was identified, which permitted revelation of three major anticodon-sparing strategies. Other features and sequence peculiarities analyzed are the following: (1) fit to the standard cloverleaf structure, (2) characteristic consensus sequences for elongator and initiator tDNAs, (3) frequencies of bases at each sequence position, (4) type and frequencies of conserved 2D and 3D base pairs, (5) anticodon/tDNA usages and anticodon-sparing strategies, (6) identification of the tRNA-Ile with anticodon CAU reading AUA, (7) size of variable arm, (8) occurrence and location of introns, (9) occurrence of 3'-CCA and 5'-extra G encoded at the tDNA level, and (10) distribution of the tRNA genes in genomes and their mode of transcription. Among all tRNA isoacceptors, we found that initiator tDNA-iMet is the most conserved across the three domains, yet domain-specific signatures exist. Also, according to which tRNA feature is considered (5'-extra G encoded in tDNAs-His, AUA codon read by tRNA-Ile with anticodon CAU, presence of intron, absence of "two-out-of-three" reading mode and short V-arm in tDNA-Tyr) Archaea sequester either with Bacteria or Eukarya. No common features between Eukarya and Bacteria not shared with Archaea could be unveiled. Thus, from the tRNomic point of view, Archaea appears as an "intermediate domain" between Eukarya and Bacteria.},
}
@article {pmid12382111,
year = {2002},
author = {Neef, K and Birkenbihl, RP and Kemper, B},
title = {Holliday junction-resolving enzymes from eight hyperthermophilic archaea differ in reactions with cruciform DNA.},
journal = {Extremophiles : life under extreme conditions},
volume = {6},
number = {5},
pages = {359-367},
doi = {10.1007/s00792-002-0265-8},
pmid = {12382111},
issn = {1431-0651},
mesh = {Amino Acid Sequence ; Archaea/enzymology/*genetics/physiology ; Archaeal Proteins/isolation &amp; purification/metabolism ; Cloning, Molecular ; DNA, Archaeal/*metabolism ; Endodeoxyribonucleases/isolation &amp; purification/*metabolism ; Holliday Junction Resolvases ; *Hot Temperature ; *Models, Genetic ; Molecular Sequence Data ; Nucleic Acid Conformation ; Phylogeny ; Recombinant Fusion Proteins/isolation &amp; purification/metabolism ; Recombination, Genetic ; Sequence Alignment ; Sequence Homology, Amino Acid ; Substrate Specificity ; },
abstract = {Holliday junction-resolving enzymes have been identified in a broad variety of organisms and tissues. In this study, six new Holliday junction-cleaving enzymes (Hjcs) were obtained from hyperthermophilic crenarchaeal and euryarchaeal species, including Pyrococcus horikoshii, Pyrococcus abyssi, Methanococcus jannaschii, Methanobacterium thermautotrophicum, Archaeoglobus fulgidus, and Aeropyrum pernix. The genes were cloned and overexpressed in Escherichia coli, and the respective proteins were purified from crude extracts to homogeneity. For an initial characterization of the enzymatic activities, synthetic heat-stable fixed and mobile cruciform DNA substrates were used at 75 degrees C. The Hjcs from Pyrococcus furiosus, Sulfolobus solfataricus, and the archaeal virus SIRV2 were included in the study for comparison. Despite their sequence homology, the enzymes showed marked differences in their reactions with individual cruciform DNAs. While the fixed cruciform structure was cleaved by all enzymes at only one major position, the mobile cruciform structure displayed different cleavage patterns for individual Hjcs, each with several cleavage positions. Furthermore, a strong bias for cleavage of one direction across the junction was observed with the fixed cruciform DNA for all enzymes. In contrast, the mobile cruciform DNA displayed different preferences, depending on the enzyme used.},
}
@article {pmid12370012,
year = {2002},
author = {Yonath, A},
title = {High-resolution structures of large ribosomal subunits from mesophilic eubacteria and halophilic archaea at various functional States.},
journal = {Current protein &amp; peptide science},
volume = {3},
number = {1},
pages = {67-78},
doi = {10.2174/1389203023380828},
pmid = {12370012},
issn = {1389-2037},
support = {GM 34360/GM/NIGMS NIH HHS/United States ; },
mesh = {Anti-Bacterial Agents/metabolism ; Bacterial Proteins/chemistry ; Crystallography, X-Ray ; Deinococcus/chemistry/genetics ; Haloarcula marismortui/chemistry/genetics ; Macromolecular Substances ; Models, Molecular ; Nucleic Acid Conformation ; Peptidyl Transferases/metabolism ; Protein Conformation ; Protein Synthesis Inhibitors/pharmacology ; RNA, Bacterial/chemistry ; RNA, Ribosomal/chemistry ; RNA, Transfer/chemistry ; Ribosomal Proteins/chemistry ; Ribosomes/*chemistry ; Thermus thermophilus/chemistry/genetics ; },
abstract = {Structural analysis of the recently determined high resolution structures of the small and the large ribosomal subunits from three bacterial sources, assisted by the medium resolution structure of a complex of the entire ribosome with three tRNAs, led to a quantum jump in our understanding of the process of the translation of the genetic code into proteins. Results of these studies highlighted dynamic aspects of protein biosynthesis; illuminated the modes of action of several antibiotics; indicated strategies adopted by ribosomes for maximizing their functional activity and revealed a wealth of architectural elements, including long tails of proteins penetrating the particle s cores and stabilizing the intricate folds of the RNA chains. Binding of substrate analogues showed that the decoding and the peptide-bond formation are accomplished mainly by RNA. However, several proteins may be functionally relevant in directing the mRNA and in mediating the proper orientation of the tRNA molecules within the ribosomal rRNA frame. Elements involved in intersubunit contacts or in substrate binding are inherently flexible, but maintain well-ordered characteristic conformations in unbound particles. The ribosomes utilize this conformational variability for optimizing their efficiency and minimizing non-productive interactions, hence disorder of functionally relevant features may be linked to less active conformations or to far from physiological conditions. Clinically relevant antibiotics bind almost exclusively to rRNA. In the small subunit they affect the decoding accuracy or limit conformational mobility and in the large subunit they either interfere with substrate binding, by interacting with components of the peptidyl transferase cavity, or hinder the progression of the growing peptide chain.},
}
@article {pmid12368242,
year = {2002},
author = {Rodionov, DA and Mironov, AA and Gelfand, MS},
title = {Conservation of the biotin regulon and the BirA regulatory signal in Eubacteria and Archaea.},
journal = {Genome research},
volume = {12},
number = {10},
pages = {1507-1516},
pmid = {12368242},
issn = {1088-9051},
mesh = {Archaeal Proteins/*genetics ; Biotin/*genetics ; Carbon-Nitrogen Ligases/*genetics ; Chromosome Mapping/methods/statistics &amp; numerical data ; Computational Biology/methods/statistics &amp; numerical data ; Conserved Sequence/genetics/*physiology ; Escherichia coli Proteins/*genetics ; Gene Order/genetics ; Genes, Archaeal/genetics ; Genes, Bacterial/genetics ; Likelihood Functions ; Regulon/*genetics ; Repressor Proteins/*genetics ; Signal Transduction/*genetics ; Transcription Factors/*genetics ; },
abstract = {Biotin is a necessary cofactor of numerous biotin-dependent carboxylases in a variety of microorganisms. The strict control of biotin biosynthesis in Escherichia coli is mediated by the bifunctional BirA protein, which acts both as a biotin-protein ligase and as a transcriptional repressor of the biotin operon. Little is known about regulation of biotin biosynthesis in other bacteria. Using comparative genomics and phylogenetic analysis, we describe the biotin biosynthetic pathway and the BirA regulon in most available bacterial genomes. Existence of an N-terminal DNA-binding domain in BirA strictly correlates with the presence of putative BirA-binding sites upstream of biotin operons. The predicted BirA-binding sites are well conserved among various eubacterial and archaeal genomes. The possible role of the hypothetical genes bioY and yhfS-yhfT, newly identified members of the BirA regulon, in the biotin metabolism is discussed. Based on analysis of co-occurrence of the biotin biosynthetic genes and bioY in complete genomes, we predict involvement of the transmembrane protein BioY in biotin transport. Various nonorthologous substitutes of the bioC-coupled gene bioH from E. coli, observed in several genomes, possibly represent the existence of different pathways for pimeloyl-CoA biosynthesis. Another interesting result of analysis of operon structures and BirA sites is that some biotin-dependent carboxylases from Rhodobacter capsulatus, actinomycetes, and archaea are possibly coregulated with BirA. BirA is the first example of a transcriptional regulator with a conserved binding signal in eubacteria and archaea.},
}
@article {pmid12324325,
year = {2002},
author = {Cardona, ST and Chávez, FP and Jerez, CA},
title = {The exopolyphosphatase gene from sulfolobus solfataricus: characterization of the first gene found to be involved in polyphosphate metabolism in archaea.},
journal = {Applied and environmental microbiology},
volume = {68},
number = {10},
pages = {4812-4819},
pmid = {12324325},
issn = {0099-2240},
mesh = {Acid Anhydride Hydrolases/*genetics/metabolism ; Amino Acid Sequence ; Cloning, Molecular ; Escherichia coli/genetics ; Gene Expression Regulation, Archaeal ; Molecular Sequence Data ; Open Reading Frames ; Polyphosphates/*metabolism ; Sequence Alignment ; Sulfolobus/*enzymology/genetics ; },
abstract = {Inorganic polyphosphate (polyP) polymers are widely distributed in all kinds of organisms. Although the presence of polyP in members of the domain Archaea has been described, at present nothing is known about the enzymology of polyP metabolism or the genes involved in this domain. We have cloned, sequenced, and overexpressed an exopolyphosphatase (PPX) gene (ppx) from thermophilic Sulfolobus solfataricus. The gene codes for a functional PPX and possesses an open reading frame for 417 amino acids (calculated mass, 47.9 kDa). The purified recombinant PPX was highly active, degrading long-chain polyP (700 to 800 residues) in vitro at 50 to 60 degrees C. The putative PPXs present in known archaeal genomes showed the highest similarity to yeast PPXs. In contrast, informatic analysis revealed that the deduced amino acid sequence of S. solfataricus PPX showed the highest similarity (25 to 45%) to sequences of members of the bacterial PPXs, possessing all of their conserved motifs. To our knowledge, this is the first report of an enzyme characterized to be involved in polyP metabolism in members of the Archaea.},
}
@article {pmid12236465,
year = {2002},
author = {Hickey, AJ and Conway de Macario, E and Macario, AJ},
title = {Transcription in the archaea: basal factors, regulation, and stress gene expression.},
journal = {Critical reviews in biochemistry and molecular biology},
volume = {37},
number = {4},
pages = {199-258},
doi = {10.1080/10409230290771500},
pmid = {12236465},
issn = {1040-9238},
mesh = {Archaea/*genetics/metabolism ; Archaeal Proteins/chemistry/genetics/metabolism ; Base Sequence ; DNA, Archaeal/genetics/metabolism ; DNA-Directed RNA Polymerases/chemistry/genetics/metabolism ; Gene Expression Regulation, Archaeal ; Genes, Archaeal ; Heat-Shock Proteins/chemistry/genetics/metabolism ; Methanosarcina/genetics/metabolism ; Models, Genetic ; Molecular Chaperones/chemistry/genetics/metabolism ; TATA-Box Binding Protein/chemistry/genetics/metabolism ; Transcription Factors/chemistry/genetics/metabolism ; Transcription, Genetic ; },
abstract = {A brief survey is presented of salient findings on transcription in the Archaea, focussing on stress genes of the hsp70(dnaK) locus, which code for the molecular chaperones Hsp70(DnaK), Hsp40(DnaJ), and GrpE. Archaeal basal factors and some recently characterized regulators pertinent to non-stress genes are presented first to show their similarities and differences with equivalents in organisms of the other two phylogenetic domains, Bacteria and Eucarya, and to reveal clues on how these or similar factors might transcribe and regulate the archaeal stress genes. The second part of the article deals with the hsp70(dnaK)-locus genes, particularly those from Methanosarcina mazeii, because they are virtually the only ones within the methanogenic Archaea whose patterns of constitutive and stress-induced expressions have been studied. Therefore, these genes, provide a standardized model system to elucidate transcription initiation and regulation at the molecular level in this phylogenetic group. Promoters, and other cis-acting sites that are, or might be, involved in stress-gene expression are described. Conformational changes of basal transcription factors after interaction with stress-gene promoters are discussed that suggest ways for generating a large diversity of initiation complexes using a few factors and DNA sites in different combinations. Likewise, the effects of stress on DNA topology and on TBP-TFB-promoter complex formation and tightness are described, which might also contribute to the generation of transcription-initiation complex diversity. This diversity would be key to differential gene expression, namely, which genes are transcribed, when (basal, steady expression vs. sporadic stress-induced expression), and to what level. Future research should investigate this diversity, and the mechanism of complex formation and action at the atomic, molecular, and supramolecular levels to elucidate the dynamics of transcription initiation in real time.},
}
@article {pmid12215811,
year = {2002},
author = {Ochsenreiter, T and Pfeifer, F and Schleper, C},
title = {Diversity of Archaea in hypersaline environments characterized by molecular-phylogenetic and cultivation studies.},
journal = {Extremophiles : life under extreme conditions},
volume = {6},
number = {4},
pages = {267-274},
doi = {10.1007/s00792-001-0253-4},
pmid = {12215811},
issn = {1431-0651},
mesh = {Archaea/*classification/genetics ; DNA, Ribosomal/genetics ; *Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Sodium Chloride ; },
abstract = {The diversity of Archaea from three different hypersaline environments was analyzed and compared by polymerase chain reaction (PCR)-based molecular phylogenetic techniques and cultivation approaches. The samples originated from a crystallization pond of a solar saltern in Spain (FC); an alkaline lake in Nevada, USA, (EMF); and a small pond from a slag heap of a potassium mine in Germany (DIE). Except for two 16S rDNA sequences that were related to crenarchaeota from soil and did not apparently belong to the indigenous halophilic community, all sequences recovered from environmental DNA or cultivated strains grouped within the Halobacteriaceae. Mostly 16S rDNA sequences related to the genera Halorubrum and Haloarcula were detected in sample FC, and organisms belonging to these genera were also recovered by cultivation. In contrast, sequences related to five different groups of halophilic archaea were amplified from sample DIE (including novel lineages with only uncultivated phylotypes), but the organisms that were cultivated from this sample fell into different groups (i.e., Natronococcus, Halorubrum, or unaffiliated) and did not overlap with those predicted using the culture-independent approach. With respect to the highly alkaline sample, EMF, four groups were predicted from the environmental 16S rDNA sequences, two of which (Natronomonas and Haloarcula) were also recovered through cultivation together with Natronococcus isolates. In summary, we found that halophilic archaea dominate the archaeal populations in these three hypersaline environments and show that culturability of the organisms predicted by molecular surveys might strongly depend on the habitat chosen. While a number of novel halophilic archaea have been isolated, we have not been able to cultivate representatives of the new lineages that were detected in this and several other environmental studies.},
}
@article {pmid12215443,
year = {2002},
author = {Andreu, JM and Oliva, MA and Monasterio, O},
title = {Reversible unfolding of FtsZ cell division proteins from archaea and bacteria. Comparison with eukaryotic tubulin folding and assembly.},
journal = {The Journal of biological chemistry},
volume = {277},
number = {45},
pages = {43262-43270},
doi = {10.1074/jbc.M206723200},
pmid = {12215443},
issn = {0021-9258},
mesh = {Amino Acid Sequence ; Archaeal Proteins/*chemistry/*metabolism/ultrastructure ; Bacterial Proteins/*chemistry/*metabolism ; Circular Dichroism ; *Cytoskeletal Proteins ; Escherichia coli/*metabolism ; Escherichia coli Proteins/chemistry/metabolism ; GTP Phosphohydrolases/metabolism ; Kinetics ; Methanococcus/*metabolism ; Molecular Sequence Data ; Protein Conformation ; Protein Denaturation ; Protein Folding ; Protein Structure, Secondary ; },
abstract = {The stability, refolding, and assembly properties of FtsZ cell division proteins from Methanococcus jannaschii and Escherichia coli have been investigated. Their guanidinium chloride unfolding has been studied by circular dichroism spectroscopy. FtsZ from E. coli and tubulin released the bound guanine nucleotide, coinciding with an initial unfolding stage at low denaturant concentrations, followed by unfolding of the apoprotein. FtsZ from M. jannaschii released its nucleotide without any detectable secondary structural change. It unfolded in an apparently two-state transition at larger denaturant concentrations. Isolated FtsZ polypeptide chains were capable of spontaneous refolding and GTP-dependent assembly. The homologous eukaryotic tubulin monomers misfold in solution, but fold within the cytosolic chaperonin CCT. Analysis of the extensive tubulin loop insertions in the FtsZ/tubulin common core and of the intermolecular contacts in model microtubules and tubulin-CCT complexes shows a loop insertion present at every element of lateral protofilament contact and at every contact of tubulin with CCT (except at loop T7). The polymers formed by purified FtsZ have a distinct limited protofilament association in comparison with microtubules. We propose that the loop insertions of tubulin and its CCT-assisted folding coevolved with the lateral association interfaces responsible for extended two-dimensional polymerization into microtubule polymers.},
}
@article {pmid12200440,
year = {2002},
author = {Fischer, M and Romisch, W and Schiffmann, S and Kelly, M and Oschkinat, H and Steinbacher, S and Huber, R and Eisenreich, W and Richter, G and Bacher, A},
title = {Biosynthesis of riboflavin in archaea studies on the mechanism of 3,4-dihydroxy-2-butanone-4-phosphate synthase of Methanococcus jannaschii.},
journal = {The Journal of biological chemistry},
volume = {277},
number = {44},
pages = {41410-41416},
doi = {10.1074/jbc.M206863200},
pmid = {12200440},
issn = {0021-9258},
mesh = {Amino Acid Sequence ; Base Sequence ; Magnetic Resonance Spectroscopy ; Methanococcus/*metabolism ; Molecular Sequence Data ; Riboflavin/*biosynthesis ; Sugar Phosphates/*metabolism ; },
abstract = {The hypothetical protein predicted by the open reading frame MJ0055 of Methanococcus jannaschii was expressed in a recombinant Escherichia coli strain under the control of a synthetic gene optimized for translation in an eubacterial host. The recombinant protein catalyzes the formation of the riboflavin precursor 3,4-dihydroxy-2-butanone 4-phosphate from ribulose 5-phosphate at a rate of 174 nmol mg(-1) min(-1) at 37 degrees C. The homodimeric 51.6-kDa protein requires divalent metal ions, preferentially magnesium, for activity. The reaction involves an intramolecular skeletal rearrangement as shown by (13)C NMR spectroscopy using [U-(13)C(5)]ribulose 5-phosphate as substrate. A cluster of charged amino acid residues comprising arginine 25, glutamates 26 and 28, and aspartates 21 and 30 is essential for catalytic activity. Histidine 164 and glutamate 185 were also shown to be essential for catalytic activity.},
}
@article {pmid12192854,
year = {2002},
author = {Zhou, MX and Xiang, H and Tan, HR},
title = {[Development of the genetic transformation system in extremely halophilic archaea].},
journal = {Sheng wu gong cheng xue bao = Chinese journal of biotechnology},
volume = {18},
number = {3},
pages = {267-271},
pmid = {12192854},
issn = {1000-3061},
mesh = {Archaea/*genetics ; Cloning, Molecular ; Genetic Vectors ; *Transformation, Genetic ; },
abstract = {The development of the genetic transformation systems in extremely halophilic Archaea was reviewed in this paper. Included are the screening of selectable markers for resistance to antibiotics, the development of gene cloning and expression vectors, and the modifications of the host organisms.},
}
@article {pmid12192072,
year = {2002},
author = {Mamat, B and Roth, A and Grimm, C and Ermler, U and Tziatzios, C and Schubert, D and Thauer, RK and Shima, S},
title = {Crystal structures and enzymatic properties of three formyltransferases from archaea: environmental adaptation and evolutionary relationship.},
journal = {Protein science : a publication of the Protein Society},
volume = {11},
number = {9},
pages = {2168-2178},
pmid = {12192072},
issn = {0961-8368},
mesh = {Archaeoglobus fulgidus/*enzymology ; Crystallography, X-Ray ; Environment ; Euryarchaeota/*enzymology ; *Evolution, Molecular ; Hydroxymethyl and Formyl Transferases/*chemistry/classification/genetics/*metabolism ; Methanosarcina barkeri/*enzymology ; Models, Molecular ; Phylogeny ; Protein Structure, Quaternary ; Protein Subunits ; Temperature ; Ultracentrifugation ; },
abstract = {Formyltransferase catalyzes the reversible formation of formylmethanofuran from N(5)-formyltetrahydromethanopterin and methanofuran, a reaction involved in the C1 metabolism of methanogenic and sulfate-reducing archaea. The crystal structure of the homotetrameric enzyme from Methanopyrus kandleri (growth temperature optimum 98 degrees C) has recently been solved at 1.65 A resolution. We report here the crystal structures of the formyltransferase from Methanosarcina barkeri (growth temperature optimum 37 degrees C) and from Archaeoglobus fulgidus (growth temperature optimum 83 degrees C) at 1.9 A and 2.0 A resolution, respectively. Comparison of the structures of the three enzymes revealed very similar folds. The most striking difference found was the negative surface charge, which was -32 for the M. kandleri enzyme, only -8 for the M. barkeri enzyme, and -11 for the A. fulgidus enzyme. The hydrophobic surface fraction was 50% for the M. kandleri enzyme, 56% for the M. barkeri enzyme, and 57% for the A. fulgidus enzyme. These differences most likely reflect the adaptation of the enzyme to different cytoplasmic concentrations of potassium cyclic 2,3-diphosphoglycerate, which are very high in M. kandleri (>1 M) and relatively low in M. barkeri and A. fulgidus. Formyltransferase is in a monomer/dimer/tetramer equilibrium that is dependent on the salt concentration. Only the dimers and tetramers are active, and only the tetramers are thermostable. The enzyme from M. kandleri is a tetramer, which is active and thermostable only at high concentrations of potassium phosphate (>1 M) or potassium cyclic 2,3-diphosphoglycerate. Conversely, the enzyme from M. barkeri and A. fulgidus already showed these properties, activity and stability, at much lower concentrations of these strong salting-out salts.},
}
@article {pmid12177347,
year = {2002},
author = {Griffiths, E and Gupta, RS},
title = {Protein signatures distinctive of chlamydial species: horizontal transfers of cell wall biosynthesis genes glmU from archaea to chlamydiae and murA between chlamydiae and Streptomyces.},
journal = {Microbiology (Reading, England)},
volume = {148},
number = {Pt 8},
pages = {2541-2549},
doi = {10.1099/00221287-148-8-2541},
pmid = {12177347},
issn = {1350-0872},
mesh = {Alkyl and Aryl Transferases/*genetics ; Archaea/*genetics ; Cell Wall/*genetics/physiology ; Chlamydiales/classification/*genetics ; Conserved Sequence ; DNA, Bacterial/analysis ; Gene Deletion ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genome, Bacterial ; Molecular Sequence Data ; Nucleotidyltransferases/*genetics/physiology ; Phylogeny ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Streptomyces/classification/*genetics ; },
abstract = {Chlamydiae are major human and animal pathogens. Based on alignments of different protein sequences, a number of conserved indels (insertion/deletions) were identified that appear to be unique and distinctive characteristics of the chlamydial species. The identified signatures include one 16 aa and two single aa inserts in the enzyme UDP-N-acetylglucosamine 1-carboxyvinyltransferase (MurA), a 1 aa insert in protein synthesis elongation factor P (EF-P), a 1 aa insert in the Mg(2+) transport protein (MgtE), a 1 aa insert in the carboxy-terminal protease and a 1 aa deletion in the tRNA (guanine-N(1)-)-methyltransferase (TrmD) protein. The homologues of these proteins are found in all major groups of bacteria and the observed indels are present in all available chlamydial sequences but not in any other species (except for the large insert in MurA in Streptomyces). The validity of three of these signatures (MurA, EF-P and MgtE) was tested by PCR amplifying the signature regions from several chlamydial species for which no sequence information was available. All Chlamydiaceae species for which specific fragments could be amplified (Chlamydia suis, Chlamydophila abortus, Chlamydophila psittaci, Chlamydophila felis) contained the expected signatures. Additionally, a fragment of the murA gene from Waddlia chondrophila and the efp gene from Simkania negevensis, two chlamydia-like species, were also cloned and sequenced. The presence of respective indels in these species provides strong evidence that they are specifically related to the traditional chlamydial species, and that these signatures may be distinctive of the entire Chlamydiales order. A 17 aa conserved indel was also identified in the cell wall biosynthesis enzyme UDP-N-acetylglucosamine pyrophosphorylase (GlmU), which is shared by all archaeal and chlamydial homologues. The gene for this protein is indicated to have been horizontally transferred from an archaeon to a common ancestor of the chlamydiae. The results also support a lateral transfer of the murA gene between chlamydiae and STREPTOMYCES: The large inserts in these peptidoglycan synthesis related genes in chlamydiae could account for their unusual cell-wall characteristics. These signatures are also potentially useful for screening of the chlamydiae species.},
}
@article {pmid12167361,
year = {2002},
author = {Forterre, P and Brochier, C and Philippe, H},
title = {Evolution of the Archaea.},
journal = {Theoretical population biology},
volume = {61},
number = {4},
pages = {409-422},
doi = {10.1006/tpbi.2002.1592},
pmid = {12167361},
issn = {0040-5809},
mesh = {Archaea/classification/*genetics/ultrastructure ; *Biological Evolution ; Genome, Archaeal ; Microscopy, Electron ; },
abstract = {Archaea, members of the third domain of life, are bacterial-looking prokaryotes that harbour many unique genotypic and phenotypic properties, testifying for their peculiar evolutionary status. The archaeal ancestor was probably a hyperthermophilic anaerobe. Two archaeal phyla are presently recognized, the Euryarchaeota and the Crenarchaeota. Methanogenesis was the main invention that occurred in the euryarchaeal phylum and is now shared by several archaeal groups. Adaptation to aerobic conditions occurred several times independently in both Euryarchaeota and Crenarchaeota. Recently, many new groups of Archaea that have not yet been cultured have been detected by PCR amplification of 16S ribosomal RNA from environmental samples. The phenotypic and genotypic characterization of these new groups is now a top priority for further studies on archaeal evolution.},
}
@article {pmid12167359,
year = {2002},
author = {Karlin, S and Brocchieri, L and Trent, J and Blaisdell, BE and Mrázek, J},
title = {Heterogeneity of genome and proteome content in bacteria, archaea, and eukaryotes.},
journal = {Theoretical population biology},
volume = {61},
number = {4},
pages = {367-390},
doi = {10.1006/tpbi.2002.1606},
pmid = {12167359},
issn = {0040-5809},
support = {5R01GM10452-40/GM/NIGMS NIH HHS/United States ; 5R01HG00335-15/HG/NHGRI NIH HHS/United States ; },
mesh = {Amino Acids/chemistry ; Animals ; Archaea/genetics/*metabolism ; Bacteria/genetics/*metabolism ; *Eukaryotic Cells ; *Genome ; Humans ; Proteins/chemistry ; *Proteome ; },
abstract = {Our analysis compares bacteria, archaea, and eukaryota with respect to a wide assortment of genome and proteome properties. These properties include ribosomal protein gene distributions, chaperone protein contrasts, major variation of transcription/translation factors, gene encoding pathways of energy metabolism, and predicted protein expression levels. Significant differences within and between the three domains of life include protein lengths, information processing procedures, many metabolic and lipid biosynthesis pathways, cellular controls, and regulatory proteins. Differences among genomes are influenced by lifestyle, habitat, physiology, energy sources, and other factors.},
}
@article {pmid12151216,
year = {2002},
author = {Makarova, KS and Aravind, L and Koonin, EV},
title = {SWIM, a novel Zn-chelating domain present in bacteria, archaea and eukaryotes.},
journal = {Trends in biochemical sciences},
volume = {27},
number = {8},
pages = {384-386},
doi = {10.1016/s0968-0004(02)02140-0},
pmid = {12151216},
issn = {0968-0004},
mesh = {Amino Acid Sequence ; Animals ; Archaeal Proteins/chemistry/*metabolism ; Bacterial Proteins/chemistry/*metabolism ; Binding Sites ; *Cell Cycle Proteins ; Cyclin-Dependent Kinase Inhibitor Proteins ; DNA/metabolism ; DNA-Binding Proteins/*metabolism ; Eukaryotic Cells/chemistry ; Fungal Proteins/chemistry/metabolism ; *MAP Kinase Kinase Kinase 1 ; Molecular Sequence Data ; *Nuclear Proteins ; Plant Proteins/chemistry/metabolism ; Protein Serine-Threonine Kinases/chemistry/*metabolism ; Protein Structure, Tertiary ; *Repressor Proteins ; *Saccharomyces cerevisiae Proteins ; Sequence Homology, Amino Acid ; Transcription Factors/*metabolism ; Transposases/chemistry/metabolism ; Vertebrates ; Zinc/*metabolism ; },
abstract = {A previously undetected domain with a CxCx(n)CxH pattern of predicted zinc-chelating residues was identified in a variety of prokaryotic and eukaryotic proteins. These include bacterial ATPases of the SWI2/SNF2 family, plant MuDR transposases and transposase-derived Far1 nuclear proteins, and vertebrate MEK kinase-1. This domain was designated SWIM after SWI2/SNF2 and MuDR, and is predicted to have DNA-binding and protein-protein interaction functions in different contexts.},
}
@article {pmid12125824,
year = {2002},
author = {Deppenmeier, U and Johann, A and Hartsch, T and Merkl, R and Schmitz, RA and Martinez-Arias, R and Henne, A and Wiezer, A and Bäumer, S and Jacobi, C and Brüggemann, H and Lienard, T and Christmann, A and Bömeke, M and Steckel, S and Bhattacharyya, A and Lykidis, A and Overbeek, R and Klenk, HP and Gunsalus, RP and Fritz, HJ and Gottschalk, G},
title = {The genome of Methanosarcina mazei: evidence for lateral gene transfer between bacteria and archaea.},
journal = {Journal of molecular microbiology and biotechnology},
volume = {4},
number = {4},
pages = {453-461},
pmid = {12125824},
issn = {1464-1801},
mesh = {Archaea/*genetics ; Bacteria/classification/*genetics ; Gene Transfer Techniques ; *Genome, Archaeal ; Methanosarcina/classification/*genetics/metabolism ; Open Reading Frames ; Phylogeny ; },
abstract = {The Archaeon Methanosarcina mazei and related species are of great ecological importance as they are the only organisms fermenting acetate, methylamines and methanol to methane, carbon dioxide and ammonia (in case of methylamines). Since acetate is the precursor of 60% of the methane produced on earth these organisms contribute significantly to the production of this greenhouse gas, e.g. in rice paddies. The 4,096,345 base pairs circular chromosome of M. mazei is more than twice as large as the genomes of the methanogenic Archaea currently completely sequenced (Bult et al., 1996; Smith et al., 1997). 3,371 open reading frames (ORFs) were identified. Based on currently available sequence data 376 of these ORFs are Methanosarcina-specific and 1,043 ORFs find their closest homologue in the bacterial domain. 544 of these ORFs reach significant similarity values only in the bacterial domain. They include 56 of the 102 transposases, and proteins involved in gluconeogenesis, proline biosynthesis, transport processes, DNA-repair, environmental sensing, gene regulation, and stress response. Striking examples are the occurrence of the bacterial GroEL/GroES chaperone system and the presence of tetrahydrofolate-dependent enzymes. These findings might indicate that lateral gene transfer has played an important evolutionary role in forging the physiology of this metabolically versatile methanogen.},
}
@article {pmid12123460,
year = {2002},
author = {Plösser, P and Pfeifer, F},
title = {A bZIP protein from halophilic archaea: structural features and dimer formation of cGvpE from Halobacterium salinarum.},
journal = {Molecular microbiology},
volume = {45},
number = {2},
pages = {511-520},
doi = {10.1046/j.1365-2958.2002.03031.x},
pmid = {12123460},
issn = {0950-382X},
mesh = {Amino Acid Sequence ; Amino Acid Substitution ; Archaeal Proteins/*chemistry/genetics ; DNA-Binding Proteins/*chemistry/genetics ; Dimerization ; Genes, Reporter ; Halobacterium salinarum/chemistry ; Haloferax volcanii/*chemistry/genetics ; *Leucine Zippers/genetics ; Models, Molecular ; Molecular Sequence Data ; Mutation, Missense ; Protein Conformation ; Protein Structure, Tertiary ; Recombinant Fusion Proteins/chemistry ; Structure-Activity Relationship ; Trans-Activators/*chemistry/genetics ; },
abstract = {The cGvpE protein of Halobacterium salinarum PHH4 has been identified as transcriptional activator for the promoter of the c-gvpA gene encoding the major gas vesicle structural protein cGvpA. Molecular modelling of the carboxy-terminal region of cGvpE suggests that this protein resembles a basic leucine-zipper protein, and mutations in the putative DNA binding domain DNAB completely abolish the activator function in Haloferax volcanii transformants. Mutations in the key residues of the putative leucine-zipper region AH6 of cGvpE confirmed that the three residues V159, L166 and L173 were essential for the activator function of cGvpE at the c-gvpA promoter, whereas the cysteine residue C180 could be altered to a leucine or an aspartate residue without the loss of this function. Mutations in basic residues of helix AH4 demonstrated the importance of the lysine K104 for the activator function of cGvpE. A cGvpE protein containing a his-tag at the C-terminus was still able to activate the expression of c-gvpA in vivo. The cGvpE his-purified from Hf. volcanii formed a dimer in Blue-native polyacrylamide gels that could be resolved into monomers by SDS-polyacrylamide gel electrophoresis (SDS-PAGE). Dimers of cGvpE were already seen using SDS-PAGE, but not with cGvpE mutant proteins containing the alterations L166E or L173E/C180L in the leucine zipper. These results imply that the hydrophobic surface of helix AH6 is indeed required for the establishment of cGvpE dimers.},
}
@article {pmid12119099,
year = {2002},
author = {Ideno, A and Maruyama, T},
title = {Expression of long- and short-type FK506 binding proteins in hyperthermophilic archaea.},
journal = {Gene},
volume = {292},
number = {1-2},
pages = {57-63},
doi = {10.1016/s0378-1119(02)00674-1},
pmid = {12119099},
issn = {0378-1119},
mesh = {Catalysis ; Citrate (si)-Synthase/chemistry/metabolism ; Gene Expression Regulation, Archaeal ; Isoenzymes/genetics/metabolism ; Methanococcus/enzymology/*genetics/growth &amp; development ; Molecular Chaperones/metabolism ; Peptidylprolyl Isomerase/metabolism ; Protein Folding ; Tacrolimus Binding Proteins/genetics/*metabolism ; Temperature ; Transcription, Genetic ; },
abstract = {It has been reported that the hyperthermophilic archaeon, Methanococcus jannaschii, possesses two FKBP (FK506 binding protein) genes in the genome, one being 26 kDa FKBP (long-type FKBP) and the other, 18 kDa FKBP (short-type FKBP). FKBP is a family of peptidyl-prolyl cis-trans isomerases (PPIases). In order to clarify the difference between their roles in archaeal cells, they were expressed in Escherichia coli, and their PPIase and chaperone-like protein-folding activities were investigated. The catalytic efficiency of the PPIase activity of the long-type FKBP was significantly lower than that of short-type FKBP (less than 1/1000) which is comparable to that of human FKBP12. Both FKBPs showed chaperone-like protein-folding activity to enhance the refolding yield of an unfolded protein (Thermoplasma citrate synthase) in vitro. The chaperone-like protein-folding activity of the short type was higher than that of the long type. While the intracellular content of long-type FKBP in M. jannaschii tended to increase, that of short-type FKBP obviously decreased at growth temperatures higher than the optimum of 85 degrees C. In Pyrococcus horikoshii, another hyperthermophilic archaeon, the intracellular content of long-type FKBP did not change with temperature (80-102 degrees C). These results suggest that long-type FKBP functions at any temperature in the cells as a chaperone to maintain the folding states of intracellular proteins. On the other hand, short-type FKBP may be required at lower temperatures. Peptidyl-prolyl cis-trans isomerization is known to be a rate-limiting step in protein-folding and is slower at low temperature. Since the PPIase activity of short-type FKBP was much stronger than that of the long type, it may be required to accelerate the folding of intracellular proteins and for the hyperthermophilic cell to live at low growth temperatures.},
}
@article {pmid12116647,
year = {2001},
author = {DeLong, EF and Pace, NR},
title = {Environmental diversity of bacteria and archaea.},
journal = {Systematic biology},
volume = {50},
number = {4},
pages = {470-478},
pmid = {12116647},
issn = {1063-5157},
mesh = {Archaea/classification/*genetics ; Bacteria/classification/*genetics ; Ecosystem ; Environmental Microbiology ; Genetic Variation ; Phylogeny ; },
abstract = {The microbial way of life spans at least 3.8 billion years of evolution. Microbial organisms are pervasive, ubiquitous, and essential components of all ecosystems. The geochemical composition of Earth's biosphere has been molded largely by microbial activities. Yet, despite the predominance of microbes during the course of life's history, general principles and theory of microbial evolution and ecology are not well developed. Until recently, investigators had no idea how accurately cultivated microorganisms represented overall microbial diversity. The development of molecular phylogenetics has recently enabled characterization of naturally occurring microbial biota without cultivation. Free from the biases of culture-based studies, molecular phylogenetic surveys have revealed a vast array of new microbial groups. Many of these new microbes are widespread and abundant among contemporary microbiota and fall within novel divisions that branch deep within the tree of life. The breadth and extent of extant microbial diversity has become much clearer. A remaining challenge for microbial biologists is to better characterize the biological properties of these newly described microbial taxa. This more comprehensive picture will provide much better perspective on the natural history, ecology, and evolution of extant microbial life.},
}
@article {pmid12112867,
year = {2002},
author = {Imanaka, T and Atomi, H},
title = {Catalyzing "hot" reactions: enzymes from hyperthermophilic Archaea.},
journal = {Chemical record (New York, N.Y.)},
volume = {2},
number = {3},
pages = {149-163},
doi = {10.1002/tcr.10023},
pmid = {12112867},
issn = {1527-8999},
mesh = {DNA Ligases/*chemistry ; DNA-Directed DNA Polymerase/*chemistry ; Enzyme Stability ; Glutamate Dehydrogenase/*chemistry ; Hot Temperature ; Models, Molecular ; O(6)-Methylguanine-DNA Methyltransferase/*chemistry ; Ribulose-Bisphosphate Carboxylase/chemistry ; Thermococcus/*enzymology/growth &amp; development ; },
abstract = {We reflect on some of our studies on the hyperthermophilic archaeon, Thermococcus kodakaraensis KOD1 and its enzymes. The strain can grow at temperatures up to the boiling point and also represents one of the simplest forms of life. As expected, all enzymes displayed remarkable thermostability, and we have determined some of the basic principles that govern this feature. To our delight, many of the enzymes exhibited unique biochemical properties and novel structures not found in mesophilic proteins. Here, we focus on a few enzymes that are useful in application, and whose three-dimensional structures are characteristic of thermostable enzymes.},
}
@article {pmid12098796,
year = {2000},
author = {Xie, T and Sheng, QH and Ding, DF},
title = {Reconstruction of ABC Transporter Pathways of Archaea and Comparison of Their Genomes.},
journal = {Sheng wu hua xue yu sheng wu wu li xue bao Acta biochimica et biophysica Sinica},
volume = {32},
number = {2},
pages = {169-174},
pmid = {12098796},
issn = {0582-9879},
abstract = {Reconstruction and comparison of metabolic pathway and regulatory network is an advanced task in genome function prediction. In this study, many bioinformatic tools were employed to reconstruct all ABC transporter pathways and predict their functional features of an archaeon, Pyrococcus abyssi, on genome scale. The comparison between ABC transporter pathways of P.abyssi and those of another archaeon, M.jannaschii, revealed that there was no peptide uptake ABC transporter system in M.jannaschii. This may result from their different metabolic types.},
}
@article {pmid12089140,
year = {2002},
author = {Takahashi, Y and Tokumoto, U},
title = {A third bacterial system for the assembly of iron-sulfur clusters with homologs in archaea and plastids.},
journal = {The Journal of biological chemistry},
volume = {277},
number = {32},
pages = {28380-28383},
doi = {10.1074/jbc.C200365200},
pmid = {12089140},
issn = {0021-9258},
mesh = {Archaea/*metabolism ; Bacterial Proteins/*metabolism ; Escherichia coli/metabolism ; Iron/metabolism ; Iron-Sulfur Proteins/*metabolism ; Models, Genetic ; Models, Molecular ; Mutagenesis, Site-Directed ; Mutation ; Phenotype ; Plasmids/metabolism ; Plastids/*metabolism ; Sulfur/metabolism ; },
abstract = {The assembly of iron-sulfur (Fe-S) clusters is mediated by complex machinery. In several proteobacteria, this process involves ISC (Fe-S cluster assembly) machinery composed of at least six components also conserved in mitochondria from lower to higher eukaryotes. In nitrogen-fixing bacteria, another system, termed NIF (nitrogen fixation), is required for the maturation of nitrogenase. Here we report the identification of a third system, designated the SUF machinery, the components of which are encoded in Escherichia coli by an unassigned operon, sufABCDSE. We have analyzed spontaneous pseudorevertants isolated from a mutant strain lacking all the components of the ISC machinery. The suppressor mutations in the revertants have been localized to the regulatory region of the suf operon; overexpression of this operon restores the growth phenotypes and activity of Fe-S proteins in mutant cells lacking ISC. Disruption of the suf operon alone does not cause any major defects, but synthetic lethality was observed when both the isc and suf operons were inactivated. These results indicate that proteins encoded by the suf operon participate in the ISC-independent minor pathway for the assembly of Fe-S clusters. The genes homologous to sufBC are present in a wide range of bacteria, Archaea, and plastids, suggesting that this type of system is almost ubiquitous in nature.},
}
@article {pmid12076796,
year = {2002},
author = {van der Oost, J and Huynen, MA and Verhees, CH},
title = {Molecular characterization of phosphoglycerate mutase in archaea.},
journal = {FEMS microbiology letters},
volume = {212},
number = {1},
pages = {111-120},
doi = {10.1111/j.1574-6968.2002.tb11253.x},
pmid = {12076796},
issn = {0378-1097},
mesh = {Amino Acid Sequence ; Archaea/enzymology/genetics ; Escherichia coli/enzymology/genetics/growth &amp; development ; Methanococcus/*enzymology/genetics/growth &amp; development ; Molecular Sequence Data ; Phosphoglycerate Mutase/chemistry/*genetics/*metabolism ; Phylogeny ; Pyrococcus furiosus/*enzymology/genetics/growth &amp; development ; Sequence Alignment ; Substrate Specificity ; },
abstract = {The interconversion of 3-phosphoglycerate and 2-phosphoglycerate during glycolysis and gluconeogenesis is catalyzed by phosphoglycerate mutase (PGM). In bacteria and eukaryotes two structurally distinct enzymes have been found, a cofactor-dependent and a cofactor-independent (iPGM) type. Sequence analysis of archaeal genomes did not find PGMs of either kind, but identified a new family of proteins, distantly related to iPGMs. In this study, these predicted archaeal PGMs from Pyrococcus furiosus and Methanococcus jannaschii have been functionally produced in Escherichia coli, and characterization of the purified proteins has confirmed that they are iPGMs. Analysis of the available microbial genomes indicates that this new type of iPGM is widely distributed among archaea and also encoded in several bacteria. In addition, as has been demonstrated in certain bacteria, some archaea appear to possess an alternative, cofactor-dependent PGM.},
}
@article {pmid12069685,
year = {2002},
author = {Konrad, Z and Eichler, J},
title = {Lipid modification of proteins in Archaea: attachment of a mevalonic acid-based lipid moiety to the surface-layer glycoprotein of Haloferax volcanii follows protein translocation.},
journal = {The Biochemical journal},
volume = {366},
number = {Pt 3},
pages = {959-964},
pmid = {12069685},
issn = {0264-6021},
mesh = {Acids/pharmacology ; Archaea/*metabolism ; Cell Membrane/metabolism ; Glycoproteins/chemistry/metabolism ; Haloferax/*metabolism ; *Lipid Metabolism ; Magnesium/metabolism ; Mevalonic Acid/*metabolism ; Peptides/chemistry ; Protein Prenylation ; Protein Processing, Post-Translational ; Protein Transport ; Time Factors ; },
abstract = {Once the newly synthesized surface (S)-layer glycoprotein of the halophilic archaeaon Haloferax volcanii has traversed the plasma membrane, the protein undergoes a membrane-related, Mg(2+)-dependent maturation event, revealed as an increase in the apparent molecular mass and hydrophobicity of the protein. To test whether lipid modification of the S-layer glycoprotein could explain these observations, H. volcanii cells were incubated with a radiolabelled precursor of isoprene, [(3)H]mevalonic acid. In Archaea, isoprenoids serve as the major hydrophobic component of archaeal membrane lipids and have been shown to modify other haloarchaeal S-layer glycoproteins, although little is known of the mechanism, site or purpose of such modification. In the present study we report that the H. volcanii S-layer glycoprotein is modified by a derivative of mevalonic acid and that maturation of the protein was prevented upon treatment with mevinolin (lovastatin), an inhibitor of mevalonic acid biosynthesis. These findings suggest that lipid modification of S-layer glycoproteins is a general property of halophilic archaea and, like S-layer glycoprotein glycosylation, lipid-modification of the S-layer glycoproteins takes place on the external cell surface, i.e. following protein translocation across the membrane.},
}
@article {pmid12065581,
year = {2002},
author = {Rashid, N and Imanaka, H and Kanai, T and Fukui, T and Atomi, H and Imanaka, T},
title = {A novel candidate for the true fructose-1,6-bisphosphatase in archaea.},
journal = {The Journal of biological chemistry},
volume = {277},
number = {34},
pages = {30649-30655},
doi = {10.1074/jbc.M202868200},
pmid = {12065581},
issn = {0021-9258},
mesh = {Amino Acid Sequence ; Archaea/*enzymology ; Archaeal Proteins/*metabolism ; Chromatography, High Pressure Liquid ; Cloning, Molecular ; Fructose-Bisphosphatase/chemistry/genetics/*metabolism ; Hydrogen-Ion Concentration ; Molecular Sequence Data ; Molecular Weight ; Temperature ; Transcription, Genetic ; },
abstract = {Fructose-1,6-bisphosphatase (FBPase) is one of the key enzymes of the gluconeogenic pathway. Although enzyme activity had been detected in Archaea, the corresponding gene had not been identified until a presumable inositol monophosphatase gene from Methanococcus jannaschii was found to encode a protein with both inositol monophosphatase and FBPase activities. Here we display that a gene from the hyperthermophilic archaeon, Thermococcus kodakaraensis KOD1, which does not correspond to the inositol monophosphatase gene from M. jannaschii, displays high FBPase activity. The FBPase from strain KOD1 was partially purified, its N-terminal amino acid sequence was determined, and the gene (Tk-fbp) was cloned. Tk-fbp encoded a protein of 375 amino acid residues with a molecular mass of 41,658 Da. The recombinant Tk-Fbp was purified and characterized. Tk-Fbp catalyzed the conversion of fructose 1,6-bisphosphate to fructose 6-phosphate following Michaelis-Menten kinetics with a K(m) value of 100 microm toward fructose 1,6-bisphosphate, and a k(cat) value of 17 s(-1) subunit(-1) at 95 degrees C. Unlike the inositol monophosphatase from M. jannaschii, Tk-Fbp displayed strict substrate specificity for fructose 1,6-bisphosphate. Activity was enhanced by Mg(2+) and dithioerythritol, and was slightly inhibited by fructose 2,6-bisphosphate. AMP did not inhibit the enzyme activity. We examined whether expression of Tk-fbp was regulated at the transcription level. High levels of Tk-fbp transcripts were detected in cells grown on pyruvate or amino acids, whereas no transcription was detected when starch was present in the medium. Orthologue genes corresponding to Tk-fbp with high similarity are present in all the complete genome sequences of thermophilic Archaea, including M. jannaschii, Pyrococcus furiosus, Sulfolobus solfataricus, and Archaeoglobus fulgidus, but are yet to be assigned any function. Taking into account the high FBPase activity of the protein, the strict substrate specificity, and its sugar-repressed gene expression, we propose that Tk-Fbp may represent the bona fide FBPase in Archaea.},
}
@article {pmid12058480,
year = {2002},
author = {Watanabe, Y and Yokobori, S and Kawarabayasi, Y},
title = {[Intron and pre-mRNA splicing of bacteria and Archaea].},
journal = {Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme},
volume = {47},
number = {7},
pages = {833-836},
pmid = {12058480},
issn = {0039-9450},
mesh = {Archaea/*genetics ; Bacteria/*genetics ; Base Sequence ; Introns/*genetics ; Molecular Sequence Data ; *RNA Splicing ; RNA, Archaeal/*genetics ; RNA, Bacterial/*genetics ; },
}
@article {pmid12052775,
year = {2002},
author = {Constantinesco, F and Forterre, P and Elie, C},
title = {NurA, a novel 5'-3' nuclease gene linked to rad50 and mre11 homologs of thermophilic Archaea.},
journal = {EMBO reports},
volume = {3},
number = {6},
pages = {537-542},
pmid = {12052775},
issn = {1469-221X},
mesh = {Amino Acid Sequence ; Archaeal Proteins/genetics ; Bacterial Proteins/genetics ; Endodeoxyribonucleases/genetics ; Exodeoxyribonucleases/*genetics ; Molecular Sequence Data ; Sequence Alignment ; Sulfolobus acidocaldarius/*enzymology/genetics ; },
abstract = {We isolated and characterized a new nuclease (NurA) exhibiting both single-stranded endonuclease activity and 5'-3' exonuclease activity on single-stranded and double-stranded DNA from the hyperthermophilic archaeon Sulfolobus acidocaldarius. Nuclease homologs are detected in all thermophilic archaea and, in most species, the nurA gene is organized in an operon-like structure with rad50 and mre11 archaeal homologs. This nuclease might thus act in concert with Rad50 and Mre11 proteins in archaeal recombination/repair. To our knowledge, this is the first report of a 5'-3' nuclease potentially associated with Rad50 and Mre11-like proteins that may lead to the processing of double-stranded breaks in 3' single-stranded tails.},
}
@article {pmid12046893,
year = {2002},
author = {Kloda, A and Martinac, B},
title = {Mechanosensitive channels of bacteria and archaea share a common ancestral origin.},
journal = {European biophysics journal : EBJ},
volume = {31},
number = {1},
pages = {14-25},
doi = {10.1007/s002490100160},
pmid = {12046893},
issn = {0175-7571},
mesh = {Amino Acid Sequence ; Archaea/classification/*genetics/*metabolism ; *Archaeal Proteins ; Bacteria/classification/*genetics/*metabolism ; Biophysical Phenomena ; Biophysics ; Escherichia coli Proteins/genetics/metabolism ; Ion Channel Gating ; Ion Channels/*genetics/*metabolism ; Mechanotransduction, Cellular ; Molecular Sequence Data ; Patch-Clamp Techniques ; Phylogeny ; Sequence Homology, Amino Acid ; },
abstract = {The ubiquity of mechanosensitive (MS) ion channels set off a search for their functional homologues in archaea, the third domain of life. A new MS channel was identified in the archaeon Methanococcus jannaschii by using the TM1 transmembrane domain of the bacterial MS channel of large conductance, MscL, as a genetic probe to search the archaeal genomic database for MS channel homologues. The hypothetical protein MJ0170 (MscMJ) was found to harbor two MscL-like TM1 structural motifs and showed a high degree of se quence and secondary structure conservation with MscS (YggB) homologues. The alignment of sequences of MscL, MscS and MscMJ homologues further revealed that bacterial and archaeal channels form a phylogenetic tree composed of three main branches and share a common ancestral origin. This suggests the evolution of prokaryotic MS channels via gene duplication of a MscL-like progenitor gene followed by divergence, fur ther indicating that the common ancestor of the prokaryotic MS channels most likely resembled MscL. When expressed in E. coli and functionally examined by the patch clamp, the MscMJ protein behaved as a MS channel with a conductance of 270 pS in 200 mM KCl and a cation selectivity (PK/PC]) of approximately 6. The structural and functional homologue of MscMJ, MscMJLR, was identified as a second type of MS channel in M. jannaschii. The channel has a conductance of approximately 2 nS, rectifies with voltage and shares cation selectivity with MscMJ. The stoichiometry of both types of MS channels revealed that the free energy of activation, deltaG0 approximately 7kT, obtained for MscMJ matches the one calculated for MscS, deltaG0 approximately 5kT, whereas the free energy of activation approximately deltaG0 approximately 18kT of MscMJLR resembles more the deltaG0 = 14-19kT reported for MscL. The presence of two types of MS channels discovered in the cell envelope of M. jannaschii indicates that multiplicity of MS channels in prokaryotes is a necessary element for their survival in the habitats frequently challenged by sudden changes in osmolarity. Further functional and phylogenetic study of MS channels from all three domains of the universal phylogenetic tree may help to understand the evolution and common biophysical principles that govern mechanosensory transduction.},
}
@article {pmid12038998,
year = {2002},
author = {Bertoldo, C and Antranikian, G},
title = {Starch-hydrolyzing enzymes from thermophilic archaea and bacteria.},
journal = {Current opinion in chemical biology},
volume = {6},
number = {2},
pages = {151-160},
doi = {10.1016/s1367-5931(02)00311-3},
pmid = {12038998},
issn = {1367-5931},
mesh = {Archaea/*enzymology ; Archaeal Proteins/genetics/metabolism ; Biotechnology ; Conserved Sequence ; Glycoside Hydrolases/genetics/*metabolism ; Starch/metabolism ; Temperature ; Thermus/*enzymology ; },
abstract = {Extremophlic microorganisms have developed a variety of molecular strategies in order to survive in harsh conditions. For the utilization of natural polymeric substrates such as starch, a number of extremophiles, belonging to different taxonomic groups, produce amylolytic enzymes. This class of enzyme is important not only for the study of biocatalysis and protein stability at extreme conditions but also for the many biotechnological opportunities they offer. In this review, we report on the different molecular properties of thermostable archaeal and bacterial enzymes including alpha-amylase, alpha-glucosidase, glucoamylase, pullulanase, and cyclodextrin glycosyltransferase. Comparison of the primary sequence of the pyrococcal pullulanase with other members of the glucosyl hydrolase family revealed that significant differences are responsible for the mode of action of these enzymes.},
}
@article {pmid12029131,
year = {2002},
author = {Srinivasan, G and James, CM and Krzycki, JA},
title = {Pyrrolysine encoded by UAG in Archaea: charging of a UAG-decoding specialized tRNA.},
journal = {Science (New York, N.Y.)},
volume = {296},
number = {5572},
pages = {1459-1462},
doi = {10.1126/science.1069588},
pmid = {12029131},
issn = {1095-9203},
mesh = {Amino Acid Sequence ; Amino Acyl-tRNA Synthetases/chemistry/*genetics/metabolism ; Anticodon ; Archaeal Proteins ; Base Sequence ; Catalytic Domain ; *Codon ; Codon, Terminator ; Kinetics ; Lysine/analogs &amp; derivatives/chemistry/*genetics/metabolism ; Methanosarcina barkeri/chemistry/enzymology/*genetics ; Methyltransferases/genetics/metabolism ; Molecular Sequence Data ; Nucleic Acid Conformation ; Protein Biosynthesis ; RNA, Archaeal/chemistry/genetics/metabolism ; RNA, Transfer/chemistry/*genetics/metabolism ; Recombinant Proteins/metabolism ; Sequence Alignment ; },
abstract = {Pyrrolysine is a lysine derivative encoded by the UAG codon in methylamine methyltransferase genes of Methanosarcina barkeri. Near a methyltransferase gene cluster is the pylT gene, which encodes an unusual transfer RNA (tRNA) with a CUA anticodon. The adjacent pylS gene encodes a class II aminoacyl-tRNA synthetase that charges the pylT-derived tRNA with lysine but is not closely related to known lysyl-tRNA synthetases. Homologs of pylS and pylT are found in a Gram-positive bacterium. Charging a tRNA(CUA) with lysine is a likely first step in translating UAG amber codons as pyrrolysine in certain methanogens. Our results indicate that pyrrolysine is the 22nd genetically encoded natural amino acid.},
}
@article {pmid12013435,
year = {2002},
author = {Siddiqui, KS and Cavicchioli, R and Thomas, T},
title = {Thermodynamic activation properties of elongation factor 2 (EF-2) proteins from psychrotolerant and thermophilic Archaea.},
journal = {Extremophiles : life under extreme conditions},
volume = {6},
number = {2},
pages = {143-150},
doi = {10.1007/s007920100237},
pmid = {12013435},
issn = {1431-0651},
mesh = {Archaeal Proteins/*chemistry/*metabolism ; Cold Temperature ; Drug Stability ; GTP Phosphohydrolases/chemistry/metabolism ; Methanosarcina/*metabolism ; Methanosarcinaceae/*metabolism ; Peptide Elongation Factor 2/*chemistry/*metabolism ; Protein Denaturation ; Solutions ; Species Specificity ; Thermodynamics ; },
abstract = {In this study, the thermodynamic activation parameters of cold-adapted proteins from Archaeaa are described for the first time for the irreversible protein unfolding and ribosome-dependent GTPase activity of elongation factor 2 (EF-2) from the psychrotolerant Methanococcoides burtonii and the thermophilic Methanosarcina thermophila. Thermolability of Methanococcoides burtonii EF-2 was demonstrated by a low activation free-energy of unfolding as a result of low activation-enthalpy. Although structural data for EF-2 are presently limited to protein homology modeling, the observed thermodynamic properties are consistent with a low number of noncovvalent bonds or an altered solvent interaction, causing a loss of entropy during the unfolding process. A physiological concentration of potassium aspartate or potassium glutamate was shown to stabilize both proteins against irreversible denaturation by strengthening noncovalent interactions, as indicated by increased activation enthalpies. The transition state of GTPase activity for Methanococcoides burtonii EF-2 was characterized by a lower activation enthalpy than for Methanosarcina thermophila EF-2. The relative entropy changes could be explained by differential displacement of water molecules during catalysis, resulting in similar activation free energies for both proteins. The presence of solutes was shown to facilitate the breaking of enthalpy-driven interactions and structuring of more water molecules during the reaction. By studying the thermodynamic activation parameters of both GTPase activity and unfolding and examining the effects of intracellular solutes and partner proteins (ribosomes), we were able to identify enthalpic and entropic properties that have evolved in the archaeal EF-2 proteins to enable Methanococcoides burtonii and Methanosarcina thermophila to adapt to their respective thermal environments.},
}
@article {pmid12006484,
year = {2002},
author = {Kokoeva, MV and Storch, KF and Klein, C and Oesterhelt, D},
title = {A novel mode of sensory transduction in archaea: binding protein-mediated chemotaxis towards osmoprotectants and amino acids.},
journal = {The EMBO journal},
volume = {21},
number = {10},
pages = {2312-2322},
pmid = {12006484},
issn = {0261-4189},
mesh = {Amino Acid Sequence ; Amino Acids/*pharmacology ; Archaea/drug effects/genetics/*physiology ; Chemotaxis/drug effects/*physiology ; Escherichia coli/genetics ; Genome, Archaeal ; Halobacterium salinarum/drug effects/genetics/*physiology ; Open Reading Frames/genetics ; Sequence Alignment ; Sequence Homology, Amino Acid ; Signal Transduction/*physiology ; },
abstract = {Directly upstream of the Halobacterium salinarum transducer genes basT and htpIV we identified two open reading frames (orfs) with significant homologies to genes encoding binding proteins for amino acids and compatible solutes, respectively. Behavioral testing of deletion mutants indicates that halobacterial chemotaxis towards branched-chain amino acids as well as compatible osmolytes of the betaine family requires both a binding and a transducer protein. We therefore named the binding/transducer proteins BasB/BasT for branched-chain and sulfur-containing amino acids and CosB/CosT for compatible solutes. Our data support a signaling mechanism with the binding proteins functioning as lipid-anchored receptors interacting with the extracellular domain of their cognate transducers. Inspection of the halobacterial genome suggests that BasB and CosB exclusively mediate chemotaxis responses without any additional role in transport, which is in contrast to bacterial binding proteins, which are always part of ABC transport systems. The CosB/CosT system is the first instance of a chemotaxis signaling pathway for organic osmolytes in the living world and natural abundance 13C-NMR analysis of cytoplasmic extracts suggests that H.salinarum utilizes these solutes for osmotic adaptation.},
}
@article {pmid12000316,
year = {2002},
author = {Gray, ND and Miskin, IP and Kornilova, O and Curtis, TP and Head, IM},
title = {Occurrence and activity of Archaea in aerated activated sludge wastewater treatment plants.},
journal = {Environmental microbiology},
volume = {4},
number = {3},
pages = {158-168},
doi = {10.1046/j.1462-2920.2002.00280.x},
pmid = {12000316},
issn = {1462-2912},
mesh = {Archaea/genetics/*growth &amp; development/metabolism ; Base Sequence ; DNA, Archaeal/chemistry/genetics ; Methane/metabolism ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/chemistry/genetics ; Sewage/*microbiology ; United Kingdom ; *Water Purification ; },
abstract = {The occurrence, distribution and activity of archaeal populations within two aerated, activated sludge wastewater treatment systems, one treating domestic waste and the second treating mixed domestic and industrial wastewater, were investigated by denaturing gradient gel electrophoresis (DGGE) analysis of polymerase chain reaction (PCR)-amplified ribosomal RNA gene fragments and process measurements. In the plant receiving mixed industrial and domestic waste the archaeal populations found in the mixed liquor were very similar to those in the influent sewage, though a small number of DGGE bands specific to the mixed liquor were identified. In contrast, the activated sludge treating principally domestic waste harboured distinct archaeal populations associated with the mixed liquor that were not prevalent in the influent sewage. We deduce that the Archaea in the plant treating mixed wastewater were derived principally from the influent, whereas those in the plant treating solely domestic waste were actively growing in the treatment plant. Archaeal 16S rRNA gene sequences related to the Methanosarcinales, Methanomicrobiales and the Methanobacteriales were detected. Methanogenesis was measured in activated sludge samples incubated under oxic and anoxic conditions, demonstrating that the methanogens present in both activated sludge plants were active only in anoxic incubations. The relatively low rates of methanogenesis measured indicated that, although active, the methanogens play a minor role in carbon turnover in activated sludge.},
}
@article {pmid11986665,
year = {2002},
author = {Huber, H and Hohn, MJ and Rachel, R and Fuchs, T and Wimmer, VC and Stetter, KO},
title = {A new phylum of Archaea represented by a nanosized hyperthermophilic symbiont.},
journal = {Nature},
volume = {417},
number = {6884},
pages = {63-67},
doi = {10.1038/417063a},
pmid = {11986665},
issn = {0028-0836},
mesh = {Archaea/*classification/genetics/*physiology/ultrastructure ; Base Sequence ; Biological Evolution ; Blotting, Southern ; Genome, Archaeal ; *Hot Temperature ; Microscopy, Electron ; Molecular Sequence Data ; Nucleic Acid Conformation ; RNA, Archaeal/chemistry/genetics ; RNA, Ribosomal/chemistry/genetics ; *Symbiosis ; Terminology as Topic ; },
abstract = {According to small subunit ribosomal RNA (ss rRNA) sequence comparisons all known Archaea belong to the phyla Crenarchaeota, Euryarchaeota, and--indicated only by environmental DNA sequences--to the 'Korarchaeota'. Here we report the cultivation of a new nanosized hyperthermophilic archaeon from a submarine hot vent. This archaeon cannot be attached to one of these groups and therefore must represent an unknown phylum which we name 'Nanoarchaeota' and species, which we name 'Nanoarchaeum equitans'. Cells of 'N. equitans' are spherical, and only about 400 nm in diameter. They grow attached to the surface of a specific archaeal host, a new member of the genus Ignicoccus. The distribution of the 'Nanoarchaeota' is so far unknown. Owing to their unusual ss rRNA sequence, members remained undetectable by commonly used ecological studies based on the polymerase chain reaction. 'N. equitans' harbours the smallest archaeal genome; it is only 0.5 megabases in size. This organism will provide insight into the evolution of thermophily, of tiny genomes and of interspecies communication.},
}
@article {pmid11980710,
year = {2002},
author = {Franzetti, B and Schoehn, G and Hernandez, JF and Jaquinod, M and Ruigrok, RW and Zaccai, G},
title = {Tetrahedral aminopeptidase: a novel large protease complex from archaea.},
journal = {The EMBO journal},
volume = {21},
number = {9},
pages = {2132-2138},
pmid = {11980710},
issn = {0261-4189},
mesh = {Amino Acid Sequence ; Aminopeptidases/*chemistry/physiology ; Archaeal Proteins/chemistry/physiology ; Haloarcula marismortui/*chemistry/physiology ; Ion Channels/chemistry/physiology/ultrastructure ; Macromolecular Substances ; Molecular Sequence Data ; Protein Structure, Quaternary ; Protein Subunits ; Sequence Alignment ; Substrate Specificity/physiology ; },
abstract = {A dodecameric protease complex with a tetrahedral shape (TET) was isolated from Haloarcula marismortui, a salt-loving archaeon. The 42 kDa monomers in the complex are homologous to metal-binding, bacterial aminopeptidases. TET has a broad aminopeptidase activity and can process peptides of up to 30-35 amino acids in length. TET has a central cavity that is accessible through four narrow channels (<17 A wide) and through four wider channels (21 A wide). This architecture is different from that of all the proteolytic complexes described to date that are made up by rings or barrels with a single central channel and only two openings.},
}
@article {pmid11952791,
year = {2002},
author = {Mander, GJ and Duin, EC and Linder, D and Stetter, KO and Hedderich, R},
title = {Purification and characterization of a membrane-bound enzyme complex from the sulfate-reducing archaeon Archaeoglobus fulgidus related to heterodisulfide reductase from methanogenic archaea.},
journal = {European journal of biochemistry},
volume = {269},
number = {7},
pages = {1895-1904},
doi = {10.1046/j.1432-1033.2002.02839.x},
pmid = {11952791},
issn = {0014-2956},
mesh = {Amino Acid Sequence ; Archaeoglobus/*enzymology ; Base Sequence ; Catalysis ; DNA, Archaeal ; Electron Spin Resonance Spectroscopy ; Heme/metabolism ; Molecular Sequence Data ; Multienzyme Complexes/chemistry/*isolation &amp; purification/metabolism ; Oxidation-Reduction ; Oxidoreductases/*metabolism ; Spectrophotometry, Ultraviolet ; },
abstract = {Heterodisulfide reductase (Hdr) is a unique disulfide reductase that plays a key role in the energy metabolism of methanogenic archaea. The genome of the sulfate-reducing archaeon Archaeoglobus fulgidus encodes several proteins of unknown function with high sequence similarity to the catalytic subunit of Hdr. Here we report on the purification of a multisubunit membrane-bound enzyme complex from A. fulgidus that contains a subunit related to the catalytic subunit of Hdr. The purified enzyme is a heme/iron-sulfur protein, as deduced by UV/Vis spectroscopy, EPR spectroscopy, and the primary structure. It is composed of four different subunits encoded by a putative transcription unit (AF499, AF501-AF503). A fifth protein (AF500) encoded by this transcription unit could not be detected in the purified enzyme preparation. Subunit AF502 is closely related to the catalytic subunit HdrD of Hdr from Methanosarcina barkeri. AF501 encodes a membrane-integral cytochrome, and AF500 encodes a second integral membrane protein. AF499 encodes an extracytoplasmic iron-sulfur protein, and AF503 encodes an extracytoplasmic c-type cytochrome with three heme c-binding motifs. All of the subunits show high sequence similarity to proteins encoded by the dsr locus of Allochromatium vinosum and to subunits of the Hmc complex from Desulfovibrio vulgaris. The heme groups of the enzyme are rapidly reduced by reduced 2,3-dimethyl-1,4-naphthoquinone (DMNH2), which indicates that the enzyme functions as a menaquinol-acceptor oxidoreductase. The physiological electron acceptor has not yet been identified. Redox titrations monitored by EPR spectroscopy were carried out to characterize the iron-sulfur clusters of the enzyme. In addition to EPR signals due to [4Fe-4S]+ clusters, signals of an unusual paramagnetic species with g values of 2.031, 1.994, and 1.951 were obtained. The paramagnetic species could be reduced in a one-electron transfer reaction, but could not be further oxidized, and shows EPR properties similar to those of a paramagnetic species recently identified in Hdr. In Hdr this paramagnetic species is specifically induced by the substrates of the enzyme and is thought to be an intermediate of the catalytic cycle. Hence, Hdr and the A. fulgidus enzyme not only share sequence similarity, but may also have a similar active site and a similar catalytic function.},
}
@article {pmid11941508,
year = {2002},
author = {Mahlert, F and Bauer, C and Jaun, B and Thauer, RK and Duin, EC},
title = {The nickel enzyme methyl-coenzyme M reductase from methanogenic archaea: In vitro induction of the nickel-based MCR-ox EPR signals from MCR-red2.},
journal = {Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry},
volume = {7},
number = {4-5},
pages = {500-513},
doi = {10.1007/s00775-001-0325-z},
pmid = {11941508},
issn = {0949-8257},
mesh = {Chloroform/chemistry ; Citric Acid/chemistry ; Electron Spin Resonance Spectroscopy ; Euryarchaeota/*enzymology ; Hydrogen-Ion Concentration ; Light ; Metalloporphyrins/chemistry ; Nickel ; Oxidation-Reduction ; Oxidoreductases/*chemistry/*metabolism ; Oxygen/chemistry ; Phosphothreonine/analogs &amp; derivatives/chemistry ; Spectrophotometry, Ultraviolet ; Sulfides/chemistry ; Sulfites/chemistry ; },
abstract = {Methyl-coenzyme M reductase (MCR) is a nickel enzyme catalyzing the formation of methane from methyl-coenzyme M and coenzyme B in all methanogenic archaea. The active purified enzyme exhibits the axial EPR signal MCR-red1 and in the presence of coenzyme M and coenzyme B the rhombic signal MCR-red2, both derived from Ni(I). Two other EPR-detectable states of the enzyme have been observed in vivo and in vitro designated MCR-ox1 and MCR-ox2 which have quite different nickel EPR signals and which are inactive. Until now the MCR-ox1 and MCR-ox2 states could only be induced in vivo. We report here that in vitro the MCR-red2 state is converted into the MCR-ox1 state by the addition of polysulfide and into a light-sensitive MCR-ox2 state by the addition of sulfite. In the presence of O(2) the MCR-red2 state was converted into a novel third state designated MCR-ox3 and exhibiting two EPR signals similar but not identical to MCR-ox1 and MCR-ox2. The formation of the MCR-ox states was dependent on the presence of coenzyme B. Investigations with the coenzyme B analogues S-methyl-coenzyme B and desulfa-methyl-coenzyme B indicate that for the induction of the MCR-ox states the thiol group of coenzyme B is probably not of importance. The results were obtained with purified active methyl-coenzyme M reductase isoenzyme I from Methanothermobacter marburgensis. They are discussed with respect to the nickel oxidation states in MCR-ox1, MCR-ox2 and MCR-ox3 and to a possible presence of a second redox active group in the active site. Electronic supplementary material to this paper can be obtained by using the Springer LINK server located at http://dx.doi.org/10.1007/s00775-001-0325-z.},
}
@article {pmid11935223,
year = {2002},
author = {Eschrich, D and Buchhaupt, M and Kötter, P and Entian, KD},
title = {Nep1p (Emg1p), a novel protein conserved in eukaryotes and archaea, is involved in ribosome biogenesis.},
journal = {Current genetics},
volume = {40},
number = {5},
pages = {326-338},
doi = {10.1007/s00294-001-0269-4},
pmid = {11935223},
issn = {0172-8083},
mesh = {Amino Acid Sequence ; Archaea ; Base Sequence ; Conserved Sequence ; Eukaryotic Cells ; HeLa Cells ; Humans ; Methylation ; Molecular Sequence Data ; RNA Processing, Post-Transcriptional ; Ribosomal Proteins/*genetics/physiology ; Ribosomes/*physiology ; Saccharomyces cerevisiae Proteins/*genetics/physiology ; },
abstract = {The essential Saccharomyces cerevisiae gene YLR186w [ NEP1 (nucleolar essential protein 1), also recently named EMG1 (essential for mitotic growth 1)] is highly conserved in eukaryotes and archaea. In S. cerevisiae, Nep1p is localized in the nucleus with a rod-shaped morphology, which first suggested a spindle/microtubule association for ScNEP1 (S. cerevisiae NEP1). However, in Candida albicans and in HeLa cells, Nep1p is a protein of the nucleoli. CaNEP1 (C. albicans NEP1) and HsNEP1 (Homo sapiens NEP1) heterologously complement the essential phenotype in a S. cerevisiae nep1 deletion mutant. However, the ScNEP1 spindle/microtubule phenotype is not found with HsNEP1 and CaNEP1, which shows that the spindle/microtubule association is specific for ScNep1p and that it is not the primary essential function of Nep1p. A temperature-sensitive ScNEP1 (ts1) allele was isolated and revealed a strongly increased sensitivity to paromomycin, a translational inhibitor which binds to RNA, indicating that ribosome biogenesis within the nucleolus is probably affected. This was confirmed by polysome profile and ribosomal subunit analysis, showing a ribosomal subunit imbalance with a decrease in 40S subunits, due to reduced amounts of native 18S rRNA. Furthermore, ScSAM2, encoding S-adenosylmethionine synthetase, was isolated as a multicopy-suppressor of the ScNEP1 (ts1) mutant allele and medium supplementation with S-adenosylmethionine restored its growth. For the first time, these results identified a novel protein with an essential function in ribosomal biogenesis which directly or indirectly interferes with a methylation reaction during the early steps of pre-rRNA processing necessary for the generation of 40S ribosomal subunits.},
}
@article {pmid11931543,
year = {2002},
author = {Pfeifer, F and Gregor, D and Hofacker, A and Plösser, P and Zimmermann, P},
title = {Regulation of gas vesicle formation in halophilic archaea.},
journal = {Journal of molecular microbiology and biotechnology},
volume = {4},
number = {3},
pages = {175-181},
pmid = {11931543},
issn = {1464-1801},
mesh = {Archaeal Proteins/genetics/*metabolism ; Base Sequence ; Cytoplasmic Vesicles/*physiology ; *Gene Expression Regulation, Archaeal ; Halobacterium/genetics/metabolism/*ultrastructure ; Membrane Proteins/genetics/*metabolism ; Molecular Sequence Data ; *Proteins ; },
abstract = {The halophilic archaea Halobacterium salinarum and Haloferax mediterranei produce gas vesicles depending on the growth phase and on environmental factors such as light, salt, or oxygen. Fourteen different gvp genes (gvpACNO and gvpDEFGHIJKLM) are involved in their formation, and the regulation of gvp gene expression occurs at the transcriptional and translational level. Haloferax volcanii offers a clean genetic background for the functional analysis of gas vesicle genes by transformation experiments. Such experiments show that the promoter of the gvpA gene encoding the major gas vesicle structural protein is activated by the endogenous basic leucine-zipper protein GvpE. On the other hand, the GvpD protein, which contains a p-loop motif, is involved either directly or indirectly in the repression of the gvpA promoter activity. Eight of the fourteen p-gvp genes (p-gvpAO and p-gvpFGJKLM) enable gas vesicle formation in Hf. volcanii transformants and thus constitute the minimal p-vac region.},
}
@article {pmid11911366,
year = {2002},
author = {Hansen, MA and Kirpekar, F and Ritterbusch, W and Vester, B},
title = {Posttranscriptional modifications in the A-loop of 23S rRNAs from selected archaea and eubacteria.},
journal = {RNA (New York, N.Y.)},
volume = {8},
number = {2},
pages = {202-213},
pmid = {11911366},
issn = {1355-8382},
mesh = {Bacillus subtilis/*genetics ; Base Sequence ; Escherichia coli/genetics ; Geobacillus stearothermophilus/*genetics ; Haloarcula marismortui/*genetics ; Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; Oligoribonucleotides/chemistry ; *RNA Processing, Post-Transcriptional ; RNA, Archaeal/chemistry/genetics ; RNA, Bacterial/chemistry/genetics ; RNA, Ribosomal, 23S/chemistry/*genetics ; Ribonucleases ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; Sulfolobus acidocaldarius/*genetics ; Transcription, Genetic ; },
abstract = {Posttranscriptional modifications were mapped in helices 90-92 of 23S rRNA from the following phylogenetically diverse organisms: Haloarcula marismortui, Sulfolobus acidocaldarius, Bacillus subtilis, and Bacillus stearothermophilus. Helix 92 is a component of the ribosomal A-site, which contacts the aminoacyl-tRNA during protein synthesis, implying that posttranscriptional modifications in helices 90-92 may be important for ribosome function. RNA fragments were isolated from 23S rRNA by site-directed RNase H digestion. A novel method of mapping modifications by analysis of short, nucleotide-specific, RNase digestion fragments with Matrix Assisted Laser Desorption/Ionization Mass Spectrometry (MALDI-MS) was utilized. The MALDI-MS data were complemented by two primer extension techniques using reverse transcriptase. One technique utilizes decreasing concentrations of deoxynucleotide triphosphates to map 2'-O-ribose methylations. In the other, the rRNA is chemically modified, followed by mild alkaline hydrolysis to map pseudouridines (psis). A total of 10 posttranscriptionally methylated nucleotides and 6 psis were detected in the five organisms. Eight of the methylated nucleotides and one psi have not been reported previously. The distribution of modified nucleotides and their locations on the surface of the ribosomal peptidyl transferase cleft suggests functional importance.},
}
@article {pmid11902154,
year = {2002},
author = {Koning, SM and Albers, SV and Konings, WN and Driessen, AJ},
title = {Sugar transport in (hyper)thermophilic archaea.},
journal = {Research in microbiology},
volume = {153},
number = {2},
pages = {61-67},
doi = {10.1016/s0923-2508(01)01289-x},
pmid = {11902154},
issn = {0923-2508},
mesh = {ATP-Binding Cassette Transporters/chemistry/*metabolism ; Amino Acid Sequence ; Archaea/*metabolism ; Archaeal Proteins/chemistry/*metabolism ; Biological Transport ; *Carbohydrate Metabolism ; *Hot Temperature ; Molecular Sequence Data ; },
abstract = {Hyperthermophilic archaea show important metabolic adaptations for growth on carbohydrates under hostile conditions. For carbohydrate uptake so far only ABC-type transporters have been described that are equipped with a uniquely high affinity as compared to mesophilic bacterial systems. This allows these organisms to efficiently scavenge all available carbohydrates from the extreme environment.},
}
@article {pmid11898861,
year = {2001},
author = {Kloda, A and Martinac, B},
title = {Mechanosensitive channels in archaea.},
journal = {Cell biochemistry and biophysics},
volume = {34},
number = {3},
pages = {349-381},
doi = {10.1385/CBB:34:3:349},
pmid = {11898861},
issn = {1085-9195},
mesh = {Amino Acid Motifs ; Amino Acid Sequence ; Archaea/*metabolism ; Biological Evolution ; Cell Membrane/metabolism ; Cell Wall/metabolism ; Cloning, Molecular ; Escherichia coli Proteins/metabolism ; Esters/metabolism ; Ethers/metabolism ; Hydrogen-Ion Concentration ; Ion Channels/*metabolism ; Lipid Bilayers ; Lipids/chemistry ; Methanococcus/metabolism ; Molecular Sequence Data ; Patch-Clamp Techniques ; Peptidoglycan/chemistry ; Phylogeny ; Pressure ; Protein Structure, Secondary ; Sequence Homology, Amino Acid ; Signal Transduction ; Time Factors ; },
abstract = {The ubiquity of mechanosensitive (MS) channels triggered a search for their functional homologues in Archaea, the third domain of the phylogenetic tree. Two types of MS channels have been identified in the cell membranes of Haloferax volcanii using the patch clamp technique. Recently MS channels were identified and cloned from two archaeal species occupying different environmental habitats. These studies demonstrate that archaeal MS channels share structural and functional homology with bacterial MS channels. The mechanical force transmitted via the lipid bilayer alone activates all to date known prokaryotic MS channels. This implies the existence of a common gating mechanism for bacterial as well as archaeal MS channels according to the bilayer model. Based on recent evidence that the bilayer model also applies to eukaryotic MS channels, mechanosensory transduction probably originated along with the appearance of the first life forms according to simple biophysical principles. In support of this hypothesis the phylogenetic analysis revealed that prokaryotic MS channels of large and small conductance originated from a common ancestral molecule resembling the bacterial MscL channel protein. Furthemore, bacterial and archaeal MS channels share common structural motifs with eukaryotic channels of diverse function indicating the importance of identified structures to the gating mechanism of this family of channels. The comparative approach used throughout this review should contribute towards understanding of the evolution and molecular basis of mechanosensory transduction in general.},
}
@article {pmid11898860,
year = {2001},
author = {Kloda, A and Martinac, B},
title = {Mechanosensitive channel of Thermoplasma, the cell wall-less archaea: cloning and molecular characterization.},
journal = {Cell biochemistry and biophysics},
volume = {34},
number = {3},
pages = {321-347},
doi = {10.1385/CBB:34:3:321},
pmid = {11898860},
issn = {1085-9195},
mesh = {Amino Acid Motifs ; Amino Acid Sequence ; Animals ; Blotting, Western ; Cell Membrane/metabolism ; Cell Wall/*physiology ; Cell-Free System ; Cloning, Molecular ; Dogs ; Electrophoresis, Polyacrylamide Gel ; Electrophysiology ; Escherichia coli/metabolism ; *Escherichia coli Proteins ; Gadolinium/pharmacology ; Ion Channels/*chemistry/*genetics/metabolism ; Liposomes/metabolism ; Molecular Sequence Data ; Pressure ; Protein Binding ; Protein Structure, Secondary ; Rabbits ; Sequence Homology, Amino Acid ; Thermoplasma/*metabolism/*physiology ; Time Factors ; },
abstract = {By using a functional approach of reconstituting detergent-solubilized membrane proteins into liposomes and following their function in patch-clamp experiments, we identified a novel mechanosensitive (MS) channel in the thermophilic cell wall-less archaeon Thermoplasma volcanium. Sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) of the enriched protein fractions revealed a band of approx 15 kDa comparable to MscL, the bacterial MS channel of large conductance. 20 N-terminal residues determined by protein microsequencing, matched the sequence to an unknown open reading frame in the genome of a related species Thermoplasma acidophilum. The protein encoded by the T. acidophilum gene was cloned and expressed in Escherichia coli and reconstituted into liposomes. When examined for function, the reconstituted protein exhibited properties typical of an MS ion channel: 1) activation by negative pressure applied to the patch-clamp pipet, 2) blockage by gadolinium, and 3) activation by the anionic amphipath trinitrophenol. In analogy to the nomenclature used for bacterial MS channels, the MS channel of T acidophilum was termed MscTA. Secondary structural analysis indicated that similar to MscL, the T. acidophilum MS protein may have two transmembrane domains, suggesting that MS channels of thermophilic Archaea belong to a family of structurally related MscL-like ion channels with two membrane-spanning regions. When the mscTA gene was expressed in the mscL- knockout strain and the MscTA protein reconstituted into liposomes, the gating of MscTA was characterized by very brief openings of variable conductance. In contrast, when the mscTA gene was expressed in the wild-type mscL+ strain of E. coli, the gating properties of the channel resembled MscL. However, the channel had reduced conductance and differed from MscL in its kinetics and in the free energy of activation, suggesting that MscTA and MscL can form functional complexes and/or modulate each other activity. Similar to MscL, MscTA exhibited an increase in activity in liposomes made of phospholipids having shorter acyl chain, suggesting a role of hydrophobic mismatch in the function of prokaryotic MS channels.},
}
@article {pmid11889103,
year = {2002},
author = {Graupner, M and Xu, H and White, RH},
title = {The pyrimidine nucleotide reductase step in riboflavin and F(420) biosynthesis in archaea proceeds by the eukaryotic route to riboflavin.},
journal = {Journal of bacteriology},
volume = {184},
number = {7},
pages = {1952-1957},
pmid = {11889103},
issn = {0021-9193},
mesh = {Archaeal Proteins/*metabolism ; Escherichia coli/genetics ; Methanococcus/enzymology/*metabolism ; Pyrimidines/metabolism ; Riboflavin/*analogs &amp; derivatives/*biosynthesis ; Ribonucleotide Reductases/*metabolism ; Substrate Specificity ; },
abstract = {The Methanococcus jannaschii gene MJ0671 was cloned and overexpressed in Escherichia coli, and its gene product was tested for its ability to catalyze the pyridine nucleotide-dependent reduction of either 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate (compound 3) to 2,5-diamino-6-ribitylamino-4(3H)-pyrimidinone 5'-phosphate (compound 4) or 5-amino-6-ribosylamino-2,4(1H,3H)-pyrimidinedione 5'-phosphate (compound 7) to 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione 5'-phosphate (compound 5). Only compound 3 was found to serve as a substrate for the enzyme. NADPH and NADH functioned equally well as the reductants. This specificity for the reduction of compound 3 was also confirmed by using cell extracts of M. jannaschii and Methanosarcina thermophila. Thus, this step in riboflavin biosynthesis in these archaea is the same as that found in yeasts. The absence of the other genes in the biosynthesis of riboflavin in Archaea is discussed.},
}
@article {pmid11884130,
year = {2002},
author = {Schierling, K and Rösch, S and Rupprecht, R and Schiffer, S and Marchfelder, A},
title = {tRNA 3' end maturation in archaea has eukaryotic features: the RNase Z from Haloferax volcanii.},
journal = {Journal of molecular biology},
volume = {316},
number = {4},
pages = {895-902},
doi = {10.1006/jmbi.2001.5395},
pmid = {11884130},
issn = {0022-2836},
mesh = {Anticodon/genetics ; Base Sequence ; Cell Nucleus/enzymology ; Endoribonucleases/isolation &amp; purification/*metabolism ; Eukaryotic Cells/*enzymology ; Evolution, Molecular ; Haloferax volcanii/*enzymology/*genetics ; Hydrogen-Ion Concentration ; Introns/genetics ; Mitochondria/enzymology ; Mutation/genetics ; Nucleic Acid Conformation ; Osmolar Concentration ; Potassium Chloride/pharmacology ; *RNA 3' End Processing ; RNA, Archaeal/chemistry/genetics/*metabolism ; RNA, Transfer/chemistry/genetics/*metabolism ; RNA, Transfer, Tyr/chemistry/genetics/metabolism ; Substrate Specificity ; Temperature ; },
abstract = {Here, we report the first characterization and partial purification of an archaeal tRNA 3' processing activity, the RNase Z from Haloferax volcanii. The activity identified here is an endonuclease, which cleaves tRNA precursors 3' to the discriminator. Thus tRNA 3' processing in archaea resembles the eukaryotic 3' processing pathway. The archaeal RNase Z has a KCl optimum at 5mM, which is in contrast to the intracellular KCl concentration being as high as 4M KCl. The archaeal RNase Z does process 5' extended and intron-containing pretRNAs but with a much lower efficiency than 5' matured, intronless pretRNAs. At least in vitro there is thus no defined order for 5' and 3' processing and splicing. A heterologous precursor tRNA is cleaved efficiently by the archaeal RNase Z. Experiments with precursors containing mutated tRNAs revealed that removal of the anticodon arm reduces cleavage efficiency only slightly, while removal of D and T arm reduces processing effciency drastically, even down to complete inhibition. Comparison with its nuclear and mitochondrial homologs revealed that the substrate specificity of the archaeal RNase Z is narrower than that of the nuclear RNase Z but broader than that of the mitochondrial RNase Z.},
}
@article {pmid11862546,
year = {2002},
author = {Mahlert, F and Grabarse, W and Kahnt, J and Thauer, RK and Duin, EC},
title = {The nickel enzyme methyl-coenzyme M reductase from methanogenic archaea: in vitro interconversions among the EPR detectable MCR-red1 and MCR-red2 states.},
journal = {Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry},
volume = {7},
number = {1-2},
pages = {101-112},
doi = {10.1007/s007750100270},
pmid = {11862546},
issn = {0949-8257},
mesh = {Electron Spin Resonance Spectroscopy/methods ; Enzyme Activation ; Enzyme Stability/physiology ; Hydrogen/metabolism ; Mesna/*analogs &amp; derivatives/*metabolism ; Metalloporphyrins/*metabolism ; Methanobacterium/*enzymology ; Nickel/*pharmacology ; Oxidation-Reduction/drug effects ; Oxidoreductases/*metabolism ; Spectrum Analysis/methods ; Titanium/pharmacology ; },
abstract = {Methyl-coenzyme M reductase (MCR) catalyzes the formation of methane from methyl-coenzyme M and coenzyme B in methanogenic archaea. The enzyme contains tightly bound the nickel porphinoid F430. The nickel enzyme has been shown to be active only when its prosthetic group is in the Ni(I) reduced state. In this state MCR exhibits the nickel-based EPR signal red1. We report here for the MCR from Methanothermobacter marburgensis that the EPR spectrum of the active enzyme changed upon addition or removal of coenzyme M, methyl coenzyme M and/or coenzyme B. In the presence of methyl-coenzyme M the red1 signal showed a more resolved 14N-superhyperfine splitting than in the presence of coenzyme M indicating a possible axial ligation of the substrate to the Ni(I). In the presence of methyl-coenzyme M and coenzyme B the red1 signal was the same as in the presence of methyl-coenzyme M alone. However, in the presence of coenzyme M and coenzyme B a highly rhombic EPR signal, MCR-red2, was induced, which was found to be light sensitive and appeared to be formed at the expense of the MCR-red1 signal. Upon addition of methyl-coenzyme M, the red2 signal disappeared and the red1 signal increased again. The red2 signal of MCR with 61Ni-labeled cofactor was significantly broadened indicating that the signal is nickel or nickel-ligand based.},
}
@article {pmid11857765,
year = {2002},
author = {Murae, T and Takamatsu, Y and Muraoka, R and Endoh, S and Yamauchi, N},
title = {Facile distinction of neutral and acidic tetraether lipids in archaea membrane by halogen atom adduct ions in electrospray ionization mass spectrometry.},
journal = {Journal of mass spectrometry : JMS},
volume = {37},
number = {2},
pages = {209-215},
doi = {10.1002/jms.276},
pmid = {11857765},
issn = {1076-5174},
mesh = {Animals ; Glyceryl Ethers/*analysis ; Halogens/*chemistry ; Ions/chemistry ; Membrane Lipids/*analysis ; Molecular Structure ; Spectrometry, Mass, Electrospray Ionization/*methods ; Sulfolobus/*chemistry ; Thermoplasma/*chemistry ; },
abstract = {Calditocaldarchaeol (neutral tetraether lipid) from Sulfolobus acidocaldarius (acidothermophilic archaea) and intact total lipid from the thermoacidophilic archaea Sulfolobus sp. was examined by electrospray ionization time-of-flight mass spectrometry in the negative-ion mode using high resolution. When the sample was injected as a solution in a 3:1 mixture of methanol (MeOH) and chloroform (CHCl(3)) using an infusion system, the total ether lipid afforded molecular-related ions as [M - H](-) for acidic polar lipids containing a phosphoric or sulfuric group, and as [M + Cl](-) ion for neutral glycolipids. The attachment of chloride was confirmed by the observation of [M + Br](-) ion, instead of [M + Cl](-) ion, when a 3:1 mixture of MeOH and CHBr(3) was used in place of MeOH-CHCl(3) as the solvent. The composition of tetraether neutral glycolipids that are different from each other only in the number of five-membered rings in the isoprenoid chain was determined on the basis of the isotope-resolved mass spectrum of [M + Cl](-) ions. As for acidic tetraether lipids, molecular-related ions [M - H](-)) were not observed when the 3:1 MeOH-CHBr(3) mixture was used as the solvent. These results together afforded a facile method of distinguishing neutral from acidic tetraether lipids in intact total lipids of acidothermophilic archaea. This method was applied to determine the difference of the number of five-membered rings in isoprenyl chains of neutral tetraether glycolipids yielded by the Sulfolobus sp. grown at different temperatures. Discrimination of neutral tetraether glycolipids from acidic tetraether lipids in the total lipids obtained from Thermoplasma sp. was also achieved by this method.},
}
@article {pmid11846768,
year = {2001},
author = {Roesser, M and Müller, V},
title = {Osmoadaptation in bacteria and archaea: common principles and differences.},
journal = {Environmental microbiology},
volume = {3},
number = {12},
pages = {743-754},
doi = {10.1046/j.1462-2920.2001.00252.x},
pmid = {11846768},
issn = {1462-2912},
mesh = {Adaptation, Physiological ; Archaea/*physiology ; *Bacterial Physiological Phenomena ; Homeostasis ; Molecular Structure ; Signal Transduction/physiology ; Solutions ; Water/*metabolism ; Water-Electrolyte Balance/*physiology ; },
abstract = {The availability of water is the most important prerequisite for life of any living cell, and exposure of cells to hypersaline conditions always threatens the cells with a drastic loss of water. To re-establish the essential turgor pressure, cells increase the water activity of their cytoplasm by accumulation of compatible solutes, either by synthesis or by uptake. The ability to respond to increasing osmolality is well conserved in all three lines of descent and, here, we compare the osmoadaptive strategies of Bacteria and Archaea. The temporal sequence of events after an osmotic upshock will be discussed, with a focus on the most rapid response, notably the mechanisms of transport activation at the protein level, and different signals for osmolality will be compared. The spectrum of compatible solutes used by different organisms is rather diverse and a comparison of 'bacterial' and 'archaeal' compatible solutes will be given.},
}
@article {pmid11842103,
year = {2002},
author = {Tang, TH and Rozhdestvensky, TS and d'Orval, BC and Bortolin, ML and Huber, H and Charpentier, B and Branlant, C and Bachellerie, JP and Brosius, J and Hüttenhofer, A},
title = {RNomics in Archaea reveals a further link between splicing of archaeal introns and rRNA processing.},
journal = {Nucleic acids research},
volume = {30},
number = {4},
pages = {921-930},
pmid = {11842103},
issn = {1362-4962},
mesh = {Archaeoglobus fulgidus/genetics/metabolism ; Base Sequence ; Electrophoretic Mobility Shift Assay ; *Introns ; Molecular Sequence Data ; Nucleic Acid Conformation ; RNA Precursors/chemistry/genetics/metabolism ; *RNA Splicing ; RNA, Archaeal/chemistry/genetics/*metabolism ; RNA, Ribosomal/chemistry/genetics/*metabolism ; RNA, Ribosomal, 16S/chemistry/genetics/metabolism ; RNA, Ribosomal, 23S/chemistry/genetics/metabolism ; Ribosomal Proteins/metabolism ; Sequence Homology, Nucleic Acid ; Sulfolobus/genetics/metabolism ; },
abstract = {The bulge-helix-bulge (BHB) motif recognised by the archaeal splicing endonuclease is also found in the long processing stems of archaeal rRNA precursors in which it is cleaved to generate pre-16S and pre-23S rRNAs. We show that in two species, Archaeoglobus fulgidus and Sulfolobus solfataricus, representatives from the two major archaeal kingdoms Euryarchaeota and Crenarchaeota, respectively, the pre-rRNA spacers cleaved at the BHB motifs surrounding pre-16S and pre-23S rRNAs subsequently become ligated. In addition, we present evidence that this is accompanied by circularization of ribosomal pre-16S and pre-23S rRNAs in both species. These data reveal a further link between intron splicing and pre-rRNA processing in Archaea, which might reflect a common evolutionary origin of the two processes. One spliced RNA species designated 16S-D RNA, resulting from religation at the BHB motif of 16S pre-rRNA, is a highly abundant and stable RNA which folds into a three-stem structure interrupted by two single-stranded regions as assessed by chemical probing. It spans a region of the pre-rRNA 5' external transcribed spacer exhibiting a highly conserved folding pattern in Archaea. Surprisingly, 16S-D RNA contains structural motifs found in archaeal C/D box small RNAs and binds to the L7Ae protein, a core component of archaeal C/D box RNPs. This supports the notion that it might have an important but still unknown role in pre-rRNA biogenesis or might even target RNA molecules other than rRNA.},
}
@article {pmid11837318,
year = {2002},
author = {Cavalier-Smith, T},
title = {The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {52},
number = {Pt 1},
pages = {7-76},
doi = {10.1099/00207713-52-1-7},
pmid = {11837318},
issn = {1466-5026},
mesh = {Archaea/*classification/*genetics ; Bacteria/*classification/*genetics ; *Biological Evolution ; Eukaryotic Cells ; *Phylogeny ; },
abstract = {Prokaryotes constitute a single kingdom, Bacteria, here divided into two new subkingdoms: Negibacteria, with a cell envelope of two distinct genetic membranes, and Unibacteria, comprising the new phyla Archaebacteria and Posibacteria, with only one. Other new bacterial taxa are established in a revised higher-level classification that recognizes only eight phyla and 29 classes. Morphological, palaeontological and molecular data are integrated into a unified picture of large-scale bacterial cell evolution despite occasional lateral gene transfers. Archaebacteria and eukaryotes comprise the clade neomura, with many common characters, notably obligately co-translational secretion of N-linked glycoproteins, signal recognition particle with 7S RNA and translation-arrest domain, protein-spliced tRNA introns, eight-subunit chaperonin, prefoldin, core histones, small nucleolar ribonucleoproteins (snoRNPs), exosomes and similar replication, repair, transcription and translation machinery. Eubacteria (posibacteria and negibacteria) are paraphyletic, neomura having arisen from Posibacteria within the new subphylum Actinobacteria (possibly from the new class Arabobacteria, from which eukaryotic cholesterol biosynthesis probably came). Replacement of eubacterial peptidoglycan by glycoproteins and adaptation to thermophily are the keys to neomuran origins. All 19 common neomuran character suites probably arose essentially simultaneously during the radical modification of an actinobacterium. At least 11 were arguably adaptations to thermophily. Most unique archaebacterial characters (prenyl ether lipids; flagellar shaft of glycoprotein, not flagellin; DNA-binding protein lob; specially modified tRNA; absence of Hsp90) were subsequent secondary adaptations to hyperthermophily and/or hyperacidity. The insertional origin of protein-spliced tRNA introns and an insertion in proton-pumping ATPase also support the origin of neomura from eubacteria. Molecular co-evolution between histones and DNA-handling proteins, and in novel protein initiation and secretion machineries, caused quantum evolutionary shifts in their properties in stem neomura. Proteasomes probably arose in the immediate common ancestor of neomura and Actinobacteria. Major gene losses (e.g. peptidoglycan synthesis, hsp90, secA) and genomic reduction were central to the origin of archaebacteria. Ancestral archaebacteria were probably heterotrophic, anaerobic, sulphur-dependent hyperthermoacidophiles; methanogenesis and halophily are secondarily derived. Multiple lateral gene transfers from eubacteria helped secondary archaebacterial adaptations to mesophily and genome re-expansion. The origin from a drastically altered actinobacterium of neomura, and the immediately subsequent simultaneous origins of archaebacteria and eukaryotes, are the most extreme and important cases of quantum evolution since cells began. All three strikingly exemplify De Beer's principle of mosaic evolution: the fact that, during major evolutionary transformations, some organismal characters are highly innovative and change remarkably swiftly, whereas others are largely static, remaining conservatively ancestral in nature. This phenotypic mosaicism creates character distributions among taxa that are puzzling to those mistakenly expecting uniform evolutionary rates among characters and lineages. The mixture of novel (neomuran or archaebacterial) and ancestral eubacteria-like characters in archaebacteria primarily reflects such vertical mosaic evolution, not chimaeric evolution by lateral gene transfer. No symbiogenesis occurred. Quantum evolution of the basic neomuran characters, and between sister paralogues in gene duplication trees, makes many sequence trees exaggerate greatly the apparent age of archaebacteria. Fossil evidence is compelling for the extreme antiquity of eubacteria [over 3500 million years (My)] but, like their eukaryote sisters, archaebacteria probably arose only 850 My ago. Negibacteria are the most ancient, radiating rapidly into six phyla. Evidence from molecular sequences, ultrastructure, evolution of photosynthesis, envelope structure and chemistry and motility mechanisms fits the view that the cenancestral cell was a photosynthetic negibacterium, specifically an anaerobic green non-sulphur bacterium, and that the universal tree is rooted at the divergence between sulphur and non-sulphur green bacteria. The negibacterial outer membrane was lost once only in the history of life, when Posibacteria arose about 2800 My ago after their ancestors diverged from Cyanobacteria.},
}
@article {pmid11823239,
year = {2002},
author = {Moissl, C and Rudolph, C and Huber, R},
title = {Natural communities of novel archaea and bacteria with a string-of-pearls-like morphology: molecular analysis of the bacterial partners.},
journal = {Applied and environmental microbiology},
volume = {68},
number = {2},
pages = {933-937},
pmid = {11823239},
issn = {0099-2240},
mesh = {Archaea/classification/genetics/*growth &amp; development/ultrastructure ; Bacteria/classification/genetics/*growth &amp; development/ultrastructure ; DNA, Archaeal/analysis/isolation &amp; purification ; DNA, Bacterial/analysis/isolation &amp; purification ; DNA, Ribosomal/analysis ; *Ecosystem ; Fresh Water/*microbiology ; In Situ Hybridization, Fluorescence ; Indoles/metabolism ; Molecular Sequence Data ; Oligonucleotide Probes ; Phylogeny ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; },
abstract = {A recently discovered bacterial/archaeal association, growing in a string-of-pearls-like structure, thrives in the cold (approximately 10 degrees C) sulfidic marsh water of the Sippenauer Moor near Regensburg, Bavaria, Germany. It forms characteristic, macroscopically visible globules, the pearls, containing microcolonies of novel euryarchaeota, which are surrounded by mainly filamentous bacteria (C. Rudolph, G. Wanner, and R. Huber, Appl. Environ. Microbiol. 67:2336-2344, 2001). Single pearls in series are connected by white threads. Here we report the first detailed molecular investigations of the taxonomic affiliation of the bacteria contributing to the strings of pearls. Phylogenetic analysis showed the dominance of a single phylotype (clone sipK4) within single pearls most closely related to Thiothrix unzii. The presence of Thiothrix sipK4 as a major constituent of single pearls and of the pearl-connecting white threads was verified by fluorescence in situ hybridization.},
}
@article {pmid11823205,
year = {2002},
author = {Pernthaler, A and Preston, CM and Pernthaler, J and DeLong, EF and Amann, R},
title = {Comparison of fluorescently labeled oligonucleotide and polynucleotide probes for the detection of pelagic marine bacteria and archaea.},
journal = {Applied and environmental microbiology},
volume = {68},
number = {2},
pages = {661-667},
pmid = {11823205},
issn = {0099-2240},
mesh = {Archaea/classification/genetics/*isolation &amp; purification ; Bacteria/classification/genetics/*isolation &amp; purification ; Carbocyanines/metabolism ; Fluorescein/metabolism ; Fluorescent Dyes/metabolism ; Image Processing, Computer-Assisted ; *In Situ Hybridization, Fluorescence ; Oligonucleotide Probes/*genetics ; Polyribonucleotides/*genetics ; RNA, Ribosomal/genetics ; Seawater/*microbiology ; },
abstract = {We compared the detection of bacteria and archaea in the coastal North Sea and at Monterey Bay, Calif., after fluorescence in situ hybridization (FISH) either with rRNA-targeted oligonucleotide probes monolabeled with the cyanin dye Cy3 (oligoFISH) or with fluorescein-labeled polyribonucleotide probes (polyFISH). During an annual cycle in German Bight surface waters, the percentages of bacteria visualized by polyFISH (annual mean, 77% of total counts) were significantly higher than those detected by oligoFISH (53%). The fraction of total bacteria visualized by oligoFISH declined during winter, whereas cell numbers determined by polyFISH remained constant throughout the year. Depth profiles from Monterey Bay showed large differences in the fraction of bacterial cells visualized by polyFISH and oligoFISH in the deeper water layers irrespective of the season. Image-analyzed microscopy indicated that the superior detection of cells by polyFISH with fluorescein-labeled probes in bacterioplankton samples was less a consequence of higher absolute fluorescence intensities but was rather related to quasi-linear bleaching dynamics and to a higher signal-to-background ratio. The relative abundances of archaea in North Sea and Monterey Bay spring samples as determined by oligoFISH were on average higher than those determined by polyFISH. However, simultaneous hybridizations with oligonucleotide probes for bacteria and archaea suggested that the oligoFISH probe ARCH915 unspecifically stained a population of bacteria. Using either FISH technique, blooms of archaea were observed in North Sea surface waters during the spring and summer months. Marine group II archaea (Euryarchaeota) reached >30% of total picoplankton abundances, as determined by polyFISH. We suggest that studies of pelagic microbial community structure using oligoFISH with monolabeled probes should focus on environments that yield detections > or =70% of total cell counts, e.g., coastal surface waters during spring and summer.},
}
@article {pmid11822685,
year = {2001},
author = {Lizama, C and Monteoliva-Sánchez, M and Prado, B and Ramos-Cormenzana, A and Weckesser, J and Campos, V},
title = {Taxonomic study of extreme halophilic archaea isolated from the "Salar de Atacama", Chile.},
journal = {Systematic and applied microbiology},
volume = {24},
number = {3},
pages = {464-474},
doi = {10.1078/0723-2020-00053},
pmid = {11822685},
issn = {0723-2020},
mesh = {Archaea/*classification/isolation &amp; purification ; Chile ; DNA, Archaeal/analysis ; Phenotype ; Phylogeny ; },
abstract = {A large number of halophilic bacteria were isolated in 1984-1992 from the Atacama Saltern (North of Chile). For this study 82 strains of extreme halophilic archaea were selected. The characterization was performed by using the phenotypic characters including morphological, physiological, biochemical, nutritional and antimicrobial susceptibility test. The results, together with those from reference strains, were subjected to numerical analysis, using the Simple Matching (S(SM)) coefficient and clustered by the unweighted pair group method of association (UPGMA). Fifteen phena were obtained at an 70% similarity level. The results obtained reveal a high diversity among the halophilic archaea isolated. Representative strains from the phena were chosen to determine their DNA base composition and the percentage of DNA-DNA similarity compared to reference strains. The 16S rRNA studies showed that some of these strains constitutes a new taxa of extreme halophilic archaea.},
}
@article {pmid11822455,
year = {2002},
author = {Blériot, Y and Untersteller, E and Fritz, B and Sinaÿ, P},
title = {Total synthesis of calditol: structural clarification of this typical component of Archaea order Sulfolobales.},
journal = {Chemistry (Weinheim an der Bergstrasse, Germany)},
volume = {8},
number = {1},
pages = {240-246},
doi = {10.1002/1521-3765(20020104)8:1&lt;240::aid-chem240&gt;3.0.co;2-g},
pmid = {11822455},
issn = {0947-6539},
mesh = {Acetates/*chemical synthesis/chemistry ; Alcohols/chemistry ; Biological Factors ; Carbonates/chemistry ; Cyclopentanes/chemical synthesis/chemistry ; Diglycerides/*chemical synthesis/*chemistry ; Lipids/chemistry ; Molecular Structure ; Nuclear Magnetic Resonance, Biomolecular ; Sorbitol/analogs &amp; derivatives/chemistry ; Stereoisomerism ; Sulfates/chemistry ; Sulfites/chemistry ; Sulfolobales/*chemistry ; },
abstract = {The original structure of calditol--that is, an open-chain branched nonitol--has recently been questioned by various research groups and cyclopentane-based structures have been proposed. To unambiguously clear up this confusion, four isomeric cyclopentane candidates 26-29 have been synthesized. Of these, compound 27 was found to be fully identical to the natural product present in Sulfolobus solfataricus (A.T.C.C. 49155). The synthesis of 27 uses a samarium-diiodide-induced pinacolization reaction of the ketoaldehyde 15 as the critical step.},
}
@article {pmid11806827,
year = {2002},
author = {Xie, G and Forst, C and Bonner, C and Jensen, RA},
title = {Significance of two distinct types of tryptophan synthase beta chain in Bacteria, Archaea and higher plants.},
journal = {Genome biology},
volume = {3},
number = {1},
pages = {RESEARCH0004},
pmid = {11806827},
issn = {1474-760X},
mesh = {Amino Acid Sequence ; Archaea/enzymology/*genetics ; Bacteria/enzymology/*genetics ; Isoenzymes/genetics ; Molecular Sequence Data ; Phylogeny ; Plants/enzymology/*genetics ; Protein Subunits ; Sequence Alignment ; Sequence Homology, Amino Acid ; Tryptophan Synthase/*genetics ; },
abstract = {BACKGROUND: Tryptophan synthase consists of two subunits, alpha and beta. Two distinct subgroups of beta chain exist. The major group (TrpEb_1) includes the well-studied beta chain of Salmonella typhimurium. The minor group of beta chain (TrpEb_2) is most frequently found in the Archaea. Most of the amino-acid residues important for catalysis are highly conserved between both TrpE subfamilies.<br><br>RESULTS: Conserved amino-acid residues of TrpEb_1 that make allosteric contact with the TrpEa subunit (the alpha chain) are absent in TrpEb_2. Representatives of Archaea, Bacteria and higher plants all exist that possess both TrpEb_1 and TrpEb_2. In those prokaryotes where two trpEb genes coexist, one is usually trpEb_1 and is adjacent to trpEa, whereas the second is trpEb_2 and is usually unlinked with other tryptophan-pathway genes.<br><br>CONCLUSIONS: TrpEb_1 is nearly always partnered with TrpEa in the tryptophan synthase reaction. However, by default at least six lineages of the Archaea are likely to use TrpEb_2 as the functional beta chain, as TrpEb_1 is absent. The six lineages show a distinctive divergence within the overall TrpEa phylogenetic tree, consistent with the lack of selection for amino-acid residues in TrpEa that are otherwise conserved for interfacing with TrpEb_1. We suggest that the standalone function of TrpEb_2 might be to catalyze the serine deaminase reaction, an established catalytic capability of tryptophan synthase beta chains. A coincident finding of interest is that the Archaea seem to use the citramalate pathway, rather than threonine deaminase (IlvA), to initiate the pathway of isoleucine biosynthesis.},
}
@article {pmid11790732,
year = {2002},
author = {Musfeldt, M and Schönheit, P},
title = {Novel type of ADP-forming acetyl coenzyme A synthetase in hyperthermophilic archaea: heterologous expression and characterization of isoenzymes from the sulfate reducer Archaeoglobus fulgidus and the methanogen Methanococcus jannaschii.},
journal = {Journal of bacteriology},
volume = {184},
number = {3},
pages = {636-644},
pmid = {11790732},
issn = {0021-9193},
mesh = {Archaeal Proteins/genetics/metabolism ; Archaeoglobus fulgidus/*enzymology/genetics ; Coenzyme A Ligases/genetics/*metabolism ; Enzyme Stability ; Escherichia coli/genetics ; Hot Temperature ; Isoenzymes/genetics ; Methane/metabolism ; Methanococcus/*enzymology/genetics ; Open Reading Frames ; Oxidation-Reduction ; RNA ; Recombinant Proteins/metabolism ; Substrate Specificity ; Sulfates/metabolism ; },
abstract = {Acetyl coenzyme A (CoA) synthetase (ADP forming) (ACD) represents a novel enzyme of acetate formation and energy conservation (acetyl-CoA + ADP + P(i) right harpoon over left harpoon acetate + ATP + CoA) in Archaea and eukaryotic protists. The only characterized ACD in archaea, two isoenzymes from the hyperthermophile Pyrococcus furiosus, constitute 145-kDa heterotetramers (alpha(2), beta(2)). The coding genes for the alpha and beta subunits are located at different sites in the P. furiosus chromosome. Based on significant sequence similarity of the P. furiosus genes, five open reading frames (ORFs) encoding putative ACD were identified in the genome of the hyperthermophilic sulfate-reducing archaeon Archaeoglobus fulgidus and one ORF was identified in the hyperthermophilic methanogen Methanococcus jannaschii. The ORFs constitute fusions of the homologous P. furiosus genes encoding the alpha and beta subunits. Two ORFs, AF1211 and AF1938, of A. fulgidus and ORF MJ0590 of M. jannaschii were cloned and functionally overexpressed in Escherichia coli. The purified recombinant proteins were characterized as distinctive isoenzymes of ACD with different substrate specificities. In contrast to the Pyrococcus ACD, the ACDs of Archaeoglobus and Methanococcus constitute homodimers of about 140 kDa composed of two identical 70-kDa subunits, which represent fusions of the homologous P. furiosus alpha and beta subunits in an alphabeta (AF1211 and MJ0590) or betaalpha (AF1938) orientation. The data indicate that A. fulgidus and M. jannaschii contains a novel type of ADP-forming acetyl-CoA synthetase in Archaea, in which the subunit polypeptides and their coding genes are fused.},
}
@article {pmid11788711,
year = {2002},
author = {Makarova, KS and Aravind, L and Grishin, NV and Rogozin, IB and Koonin, EV},
title = {A DNA repair system specific for thermophilic Archaea and bacteria predicted by genomic context analysis.},
journal = {Nucleic acids research},
volume = {30},
number = {2},
pages = {482-496},
pmid = {11788711},
issn = {1362-4962},
mesh = {Amino Acid Sequence ; Archaea/enzymology/*genetics ; Bacteria/enzymology/*genetics ; Conserved Sequence/genetics ; DNA Helicases/genetics ; DNA Repair/*genetics ; DNA-Directed DNA Polymerase/chemistry/genetics ; Databases, Nucleic Acid ; Evolution, Molecular ; Exonucleases/chemistry/genetics ; Gene Order/genetics ; Gene Transfer, Horizontal ; Genes, Archaeal/*genetics ; Genes, Bacterial/*genetics ; *Genome, Archaeal ; *Genome, Bacterial ; Hydrolases/genetics ; Models, Molecular ; Molecular Sequence Data ; Operon/genetics ; Phylogeny ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Sequence Alignment ; Species Specificity ; },
abstract = {During a systematic analysis of conserved gene context in prokaryotic genomes, a previously undetected, complex, partially conserved neighborhood consisting of more than 20 genes was discovered in most Archaea (with the exception of Thermoplasma acidophilum and Halobacterium NRC-1) and some bacteria, including the hyperthermophiles Thermotoga maritima and Aquifex aeolicus. The gene composition and gene order in this neighborhood vary greatly between species, but all versions have a stable, conserved core that consists of five genes. One of the core genes encodes a predicted DNA helicase, often fused to a predicted HD-superfamily hydrolase, and another encodes a RecB family exonuclease; three core genes remain uncharacterized, but one of these might encode a nuclease of a new family. Two more genes that belong to this neighborhood and are present in most of the genomes in which the neighborhood was detected encode, respectively, a predicted HD-superfamily hydrolase (possibly a nuclease) of a distinct family and a predicted, novel DNA polymerase. Another characteristic feature of this neighborhood is the expansion of a superfamily of paralogous, uncharacterized proteins, which are encoded by at least 20-30% of the genes in the neighborhood. The functional features of the proteins encoded in this neighborhood suggest that they comprise a previously undetected DNA repair system, which, to our knowledge, is the first repair system largely specific for thermophiles to be identified. This hypothetical repair system might be functionally analogous to the bacterial-eukaryotic system of translesion, mutagenic repair whose central components are DNA polymerases of the UmuC-DinB-Rad30-Rev1 superfamily, which typically are missing in thermophiles.},
}
@article {pmid11778839,
year = {2001},
author = {Inagaki, F and Takai, K and Komatsu, T and Kanamatsu, T and Fujioka, K and Horikoshi, K},
title = {Archaeology of Archaea: geomicrobiological record of Pleistocene thermal events concealed in a deep-sea subseafloor environment.},
journal = {Extremophiles : life under extreme conditions},
volume = {5},
number = {6},
pages = {385-392},
doi = {10.1007/s007920100211},
pmid = {11778839},
issn = {1431-0651},
mesh = {Archaea/*genetics/*isolation &amp; purification ; Archaeology ; DNA, Archaeal/genetics ; DNA, Ribosomal/genetics ; Ecosystem ; Geologic Sediments/microbiology ; Geological Phenomena ; Geology ; Hot Temperature ; Molecular Sequence Data ; Pacific Ocean ; Paleontology ; Phylogeny ; Seawater/microbiology ; },
abstract = {A record of the history of the Earth is hidden in the Earth's crust, like the annual rings of an old tree. From very limited records retrieved from deep underground, one can infer the geographical, geological, and biological events that occurred throughout Earth's history. Here we report the discovery of vertically shifted community structures of Archaea in a typical oceanic subseafloor core sample (1410 cm long) recovered from the West Philippine Basin at a depth of 5719 m. Beneath a surface community of ubiquitous deep-sea archaea (marine crenarchaeotic group I; MGI), an unusual archaeal community consisting of extremophilic archaea, such as extreme halophiles and hyperthermophiles, was present. These organisms could not be cultivated, and may be microbial relicts more than 2 million years old. Our discovery of archaeal rDNA in this core sample, probably associated with the past terrestrial volcanic and submarine hydrothermal activities surrounding the West Philippine Basin, serves as potential geomicrobiological evidence reflecting novel records of geologic thermal events in the Pleistocene period concealed in the deep-sea subseafloor.},
}
@article {pmid11755525,
year = {2002},
author = {Watanabe, Y and Yokobori, S and Inaba, T and Yamagishi, A and Oshima, T and Kawarabayasi, Y and Kikuchi, H and Kita, K},
title = {Introns in protein-coding genes in Archaea.},
journal = {FEBS letters},
volume = {510},
number = {1-2},
pages = {27-30},
doi = {10.1016/s0014-5793(01)03219-7},
pmid = {11755525},
issn = {0014-5793},
mesh = {Amino Acid Sequence ; Archaeal Proteins/*genetics ; Base Sequence ; DNA, Archaeal ; Desulfurococcaceae/*genetics ; *Genes, Archaeal ; *Hydro-Lyases ; *Introns ; Microtubule-Associated Proteins/*genetics ; Molecular Sequence Data ; RNA Precursors ; RNA Splicing ; RNA-Binding Proteins/*genetics ; *Ribonucleoproteins, Small Nuclear ; *Saccharomyces cerevisiae Proteins ; Sequence Homology, Amino Acid ; Sulfolobus/*genetics ; },
abstract = {Introns in protein-coding genes are ubiquitous in eukaryotic cells, but pre-mRNA splicing has yet to be reported in archaeal and its viral genomes. We present evidence of introns in genes encoding a homolog of eukaryotic Cbf5p (centromere-binding factor 5; a subunit of a small nucleolar ribonucleoprotein) in three Archaea; Aeropyrum pernix, Sulfolobus solfataricus and Sulfolobus tokodaii. Splicing of pre-mRNAs in vivo was demonstrated by reverse transcriptase-mediated polymerase chain reaction. The exon-intron boundaries of these genes are predicted to be folded into a structure similar to the bulge-helix-bulge motif, suggesting that splicing of these pre-mRNAs probably depends on the splicing system elucidated for archaeal pre-tRNAs and rRNAs.},
}
@article {pmid19709178,
year = {2002},
author = {Oren, A},
title = {Molecular ecology of extremely halophilic Archaea and Bacteria.},
journal = {FEMS microbiology ecology},
volume = {39},
number = {1},
pages = {1-7},
doi = {10.1111/j.1574-6941.2002.tb00900.x},
pmid = {19709178},
issn = {1574-6941},
abstract = {Abstract Water bodies with NaCl concentrations approaching saturation are often populated by dense microbial communities. Red halophilic Archaea of the family Halobacteriaceae dominate in such environments. The application of molecular biological techniques, in particular the use of approaches based on the characterization of ribosomal RNA sequences, has greatly contributed to our understanding of the community structure of halophilic Archaea in hypersaline ecosystems. Analyses of lipids extracted from the environment have also provided useful information. This article reviews our present understanding of the community structure of halophilic Archaea in saltern crystallizer ponds, in the Dead Sea, in African hypersaline soda lakes, and in other hypersaline water bodies. It was recently shown that red heterotrophic Bacteria of the genus Salinibacter, which are no less salt-dependent and salt-tolerant than the most halophilic among the Archaea, may coexist with the halophilic archaeal community. Our latest insights into their distribution in hypersaline ecosystems are presented as well.},
}
@article {pmid11742691,
year = {2001},
author = {Lange, M and Ahring, BK},
title = {A comprehensive study into the molecular methodology and molecular biology of methanogenic Archaea.},
journal = {FEMS microbiology reviews},
volume = {25},
number = {5},
pages = {553-571},
doi = {10.1111/j.1574-6976.2001.tb00591.x},
pmid = {11742691},
issn = {0168-6445},
mesh = {Euryarchaeota/classification/*genetics ; Genetic Techniques ; *Genome, Archaeal ; },
abstract = {Methanogens belong to the kingdom of Euryarchaeota in the domain of Archaea. The Archaea differ from Bacteria in many aspects important to molecular work. Among these are cell wall composition, their sensitivity to antibiotics, their translation and transcription machinery, and their very strict demands to anaerobic culture conditions. These differences may, at least partly, be responsible for the delay in availability of genetic research tools for methanogens. At present, however, the research within genetics of methanogens and their gene regulation and expression is in rapid progress. Two complete methanogenic genomes have been sequenced and published and more are underway. Besides, sequences are known from a multitude of individual genes from methanogens. Standard methods for simple DNA and RNA work can normally be employed, but permeabilization of the cell wall may demand special procedures. Efficient genetic manipulation systems, including shuttle and integration vector systems, have appeared for mesophilic, but not for thermophilic species within the last few years and will have a major impact on future investigations of methanogenic molecular biology.},
}
@article {pmid11730135,
year = {2001},
author = {Nozhevnikova, AN and Simankova, MV and Parshina, SN and Kotsyurbenko, OR},
title = {Temperature characteristics of methanogenic archaea and acetogenic bacteria isolated from cold environments.},
journal = {Water science and technology : a journal of the International Association on Water Pollution Research},
volume = {44},
number = {8},
pages = {41-48},
pmid = {11730135},
issn = {0273-1223},
mesh = {Archaea/*physiology ; Bacteria, Anaerobic/*physiology ; Cold Temperature ; Ecosystem ; Methane ; Population Dynamics ; Temperature ; },
abstract = {In most terrestrial ecosystems of boreal and northern climate zones degradation of organic matter with methane production occurs at low temperature. Two psychrophilic methanogenic archaea and four acetogenic bacteria were described until now. Recently, we isolated 12 new strains of methanogenic archaea and 3 strains of acetogenic bacteria from different natural and man-made cold environments including tundra permafrost wet land, sediments of deep lakes, silt of sludge disposal pond, pig and cattle manure digested at 6 degrees C, and an anaerobic EGSB-reactor operated at 9 degrees C. The temperature characteristics of microorganisms isolated from cold environments are discussed. All isolates are able to grow below 10 degrees C, most of them grow at such low temperature as 1 degrees C. The upper temperature limit for most growing at low temperature acetogens is 30 degrees C, and the temperature optima is 20 degrees C and below. Most isolated methanogens have temperature optima around 25 degrees C, and upper temperature limits at 30-40 degrees C. Whether microorganisms able to grow at low temperature are classified as mesophiles, psychrophiles, or psychrotrophs (psychrotolerants) is an issue of this article. We propose to modify the basic temperature definition of anaerobic microorganisms growing at low temperature.},
}
@article {pmid11717274,
year = {2001},
author = {Thomas, NA and Jarrell, KF},
title = {Characterization of flagellum gene families of methanogenic archaea and localization of novel flagellum accessory proteins.},
journal = {Journal of bacteriology},
volume = {183},
number = {24},
pages = {7154-7164},
pmid = {11717274},
issn = {0021-9193},
mesh = {Amino Acid Sequence ; Archaeal Proteins/biosynthesis/*genetics ; Cell Compartmentation ; Escherichia coli/genetics ; Flagella/*genetics ; Flagellin/genetics ; *Genes, Archaeal ; Membrane Proteins/biosynthesis/genetics ; Methanococcus/*genetics ; Molecular Sequence Data ; *Multigene Family ; Protein Precursors/genetics ; Protein Sorting Signals/genetics ; Recombinant Proteins/biosynthesis ; Sequence Homology, Amino Acid ; Transcription, Genetic ; },
abstract = {Archaeal flagella are unique motility structures, and the absence of bacterial structural motility genes in the complete genome sequences of flagellated archaeal species suggests that archaeal flagellar biogenesis is likely mediated by novel components. In this study, a conserved flagellar gene family from each of Methanococcus voltae, Methanococcus maripaludis, Methanococcus thermolithotrophicus, and Methanococcus jannaschii has been characterized. These species possess multiple flagellin genes followed immediately by eight known and supposed flagellar accessory genes, flaCDEFGHIJ. Sequence analyses identified a conserved Walker box A motif in the putative nucleotide binding proteins FlaH and FlaI that may be involved in energy production for flagellin secretion or assembly. Northern blotting studies demonstrated that all the species have abundant polycistronic mRNAs corresponding to some of the structural flagellin genes, and in some cases several flagellar accessory genes were shown to be cotranscribed with the flagellin genes. Cloned flagellar accessory genes of M. voltae were successfully overexpressed as His-tagged proteins in Escherichia coli. These recombinant flagellar accessory proteins were affinity purified and used as antigens to raise polyclonal antibodies for localization studies. Immunoblotting of fractionated M. voltae cells demonstrated that FlaC, FlaD, FlaE, FlaH, and FlaI are all present in the cell as membrane-associated proteins but are not major components of isolated flagellar filaments. Interestingly, flaD was found to encode two proteins, each translated from a separate ribosome binding site. These protein expression data indicate for the first time that the putative flagellar accessory genes of M. voltae, and likely those of other archaeal species, do encode proteins that can be detected in the cell.},
}
@article {pmid11717273,
year = {2001},
author = {Verhees, CH and Tuininga, JE and Kengen, SW and Stams, AJ and van der Oost, J and de Vos, WM},
title = {ADP-dependent phosphofructokinases in mesophilic and thermophilic methanogenic archaea.},
journal = {Journal of bacteriology},
volume = {183},
number = {24},
pages = {7145-7153},
pmid = {11717273},
issn = {0021-9193},
mesh = {Amino Acid Sequence ; Archaeal Proteins/genetics/*metabolism ; Escherichia coli/genetics ; Evolution, Molecular ; Genes, Archaeal ; Genome, Archaeal ; Glycolysis ; Methane/metabolism ; Methanococcales/classification/*enzymology/genetics ; Methanosarcinales/classification/*enzymology/genetics ; Molecular Sequence Data ; Phosphotransferases (Alcohol Group Acceptor)/genetics/*metabolism ; Phylogeny ; Recombinant Proteins/biosynthesis ; Sequence Homology, Amino Acid ; Species Specificity ; },
abstract = {Phosphofructokinase (PFK) is a key enzyme of the glycolytic pathway in all domains of life. Two related PFKs, ATP-dependent and PP(i)-dependent PFK, have been distinguished in bacteria and eucarya, as well as in some archaea. Hyperthermophilic archaea of the order Thermococcales, including Pyrococcus and Thermococcus spp., have recently been demonstrated to possess a unique ADP-dependent PFK (ADP-PFK) that appears to be phylogenetically distinct. Here, we report the presence of ADP-PFKs in glycogen-producing members of the orders Methanococcales and Methanosarcinales, including both mesophilic and thermophilic representatives. To verify the substrate specificities of the methanogenic kinases, the gene encoding the ADP-PFK from Methanococcus jannaschii was functionally expressed in Escherichia coli, and the produced enzyme was purified and characterized in detail. Compared to its counterparts from the two members of the order Thermococcales, the M. jannaschii ADP-PFK has an extremely low K(m) for fructose 6-phosphate (9.6 microM), and it accepts both ADP and acetyl-phosphate as phosphoryl donors. Phylogenetic analysis of the ADP-PFK reveals it to be a key enzyme of the modified Embden-Meyerhof pathway of heterotrophic and chemolithoautotrophic archaea. Interestingly, uncharacterized homologs of this unusual kinase are present in several eucarya.},
}
@article {pmid11701313,
year = {2001},
author = {Ibba, M},
title = {Nonsense suppression in Archaea.},
journal = {Trends in biochemical sciences},
volume = {26},
number = {11},
pages = {645},
doi = {10.1016/s0968-0004(01)01996-x},
pmid = {11701313},
issn = {0968-0004},
mesh = {Archaea/*metabolism ; Codon, Nonsense/genetics/*physiology ; Methylamines/metabolism ; Methyltransferases/chemistry/*genetics/metabolism ; Multigene Family/physiology ; },
}
@article {pmid11684083,
year = {2001},
author = {Bujnicki, JM},
title = {In silico analysis of the tRNA:m1A58 methyltransferase family: homology-based fold prediction and identification of new members from Eubacteria and Archaea.},
journal = {FEBS letters},
volume = {507},
number = {2},
pages = {123-127},
doi = {10.1016/s0014-5793(01)02962-3},
pmid = {11684083},
issn = {0014-5793},
mesh = {Amino Acid Sequence ; Archaea/*enzymology ; Eubacterium/*enzymology ; Molecular Sequence Data ; *Protein Folding ; RNA, Transfer ; Sequence Analysis, Protein ; tRNA Methyltransferases/*chemistry/classification/physiology ; },
abstract = {The amino acid sequences of Gcd10p and Gcd14p, the two subunits of the tRNA:(1-methyladenosine-58; m(1)A58) methyltransferase (MTase) of Saccharomyces cerevisiae, have been analyzed using iterative sequence database searches and fold recognition programs. The results suggest that the 'catalytic' Gcd14p and 'substrate binding' Gcd10p are related to each other and to a group of prokaryotic open reading frames, which were previously annotated as hypothetical protein isoaspartate MTases in sequence databases. It is predicted that the prokaryotic proteins are genuine tRNA:m(1)A MTases based on similarity of their predicted active site to the Gcd14p family. In addition to the MTase domain, an additional domain was identified in the N-terminus of all these proteins that may be involved in interaction with tRNA. These results suggest that the eukaryotic tRNA:m(1)A58 MTase is a product of gene duplication and divergent evolution of a possibly homodimeric prokaryotic enzyme.},
}
@article {pmid11679338,
year = {2001},
author = {Lanoil, BD and Sassen, R and La Duc, MT and Sweet, ST and Nealson, KH},
title = {Bacteria and Archaea physically associated with Gulf of Mexico gas hydrates.},
journal = {Applied and environmental microbiology},
volume = {67},
number = {11},
pages = {5143-5153},
pmid = {11679338},
issn = {0099-2240},
mesh = {Archaea/classification/genetics/*isolation &amp; purification ; Bacteria/classification/genetics/*isolation &amp; purification ; Colony Count, Microbial ; DNA, Archaeal/analysis/genetics ; DNA, Bacterial/analysis/genetics ; Genes, rRNA ; Geologic Sediments/*chemistry/microbiology ; Hydrocarbons/*metabolism ; Methane/*metabolism ; Methanosarcinaceae/classification/genetics/isolation &amp; purification ; Molecular Sequence Data ; Phylogeny ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; Sequence Analysis, DNA ; },
abstract = {Although there is significant interest in the potential interactions of microbes with gas hydrate, no direct physical association between them has been demonstrated. We examined several intact samples of naturally occurring gas hydrate from the Gulf of Mexico for evidence of microbes. All samples were collected from anaerobic hemipelagic mud within the gas hydrate stability zone, at water depths in the ca. 540- to 2,000-m range. The delta(13)C of hydrate-bound methane varied from -45.1 per thousand Peedee belemnite (PDB) to -74.7 per thousand PDB, reflecting different gas origins. Stable isotope composition data indicated microbial consumption of methane or propane in some of the samples. Evidence of the presence of microbes was initially determined by 4,6-diamidino 2-phenylindole dihydrochloride (DAPI) total direct counts of hydrate-associated sediments (mean = 1.5 x 10(9) cells g(-1)) and gas hydrate (mean = 1.0 x 10(6) cells ml(-1)). Small-subunit rRNA phylogenetic characterization was performed to assess the composition of the microbial community in one gas hydrate sample (AT425) that had no detectable associated sediment and showed evidence of microbial methane consumption. Bacteria were moderately diverse within AT425 and were dominated by gene sequences related to several groups of Proteobacteria, as well as Actinobacteria and low-G + C Firmicutes. In contrast, there was low diversity of Archaea, nearly all of which were related to methanogenic Archaea, with the majority specifically related to Methanosaeta spp. The results of this study suggest that there is a direct association between microbes and gas hydrate, a finding that may have significance for hydrocarbon flux into the Gulf of Mexico and for life in extreme environments.},
}
@article {pmid11677685,
year = {2001},
author = {Leroux, MR},
title = {Protein folding and molecular chaperones in archaea.},
journal = {Advances in applied microbiology},
volume = {50},
number = {},
pages = {219-277},
doi = {10.1016/s0065-2164(01)50007-6},
pmid = {11677685},
issn = {0065-2164},
mesh = {Archaea/chemistry/*metabolism ; Archaeal Proteins/*chemistry/metabolism ; Heat-Shock Proteins/*chemistry/metabolism ; Molecular Chaperones/*metabolism ; Protein Conformation ; *Protein Folding ; },
}
@article {pmid11677684,
year = {2001},
author = {Soppa, J},
title = {Basal and regulated transcription in archaea.},
journal = {Advances in applied microbiology},
volume = {50},
number = {},
pages = {171-217},
doi = {10.1016/s0065-2164(01)50006-4},
pmid = {11677684},
issn = {0065-2164},
mesh = {Archaea/*genetics/metabolism ; Archaeal Proteins/genetics/*metabolism ; *Gene Expression Regulation, Archaeal ; *Transcription, Genetic ; },
}
@article {pmid11677683,
year = {2001},
author = {Seitz, EM and Haseltine, CA and Kowalczykowski, SC},
title = {DNA recombination and repair in the archaea.},
journal = {Advances in applied microbiology},
volume = {50},
number = {},
pages = {101-169},
doi = {10.1016/s0065-2164(01)50005-2},
pmid = {11677683},
issn = {0065-2164},
support = {GM07377/GM/NIGMS NIH HHS/United States ; GM41347/GM/NIGMS NIH HHS/United States ; GM62653/GM/NIGMS NIH HHS/United States ; },
mesh = {Amino Acid Sequence ; Archaea/*genetics/metabolism ; Archaeal Proteins/genetics/metabolism ; *DNA Repair ; DNA, Archaeal/*genetics ; Molecular Sequence Data ; *Recombination, Genetic ; },
}
@article {pmid11594597,
year = {2001},
author = {Xu, Y and Wang, Z and Xue, Y and Zhou, P and Ma, Y and Ventosa, A and Grant, WD},
title = {Natrialba hulunbeirensis sp. nov. and Natrialba chahannaoensis sp. nov., novel haloalkaliphilic archaea from soda lakes in Inner Mongolia Autonomous Region, China.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {51},
number = {Pt 5},
pages = {1693-1698},
doi = {10.1099/00207713-51-5-1693},
pmid = {11594597},
issn = {1466-5026},
mesh = {Base Composition ; China ; DNA, Archaeal/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Fresh Water/*microbiology ; Genes, rRNA ; Halobacteriaceae/*classification/genetics/isolation &amp; purification/physiology/ultrastructure ; Lipids/analysis ; Molecular Sequence Data ; Nucleic Acid Hybridization ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sodium Chloride ; },
abstract = {Two haloalkaliphilic archaeal strains, X21T and C112T, were isolated from soda lakes in Inner Mongolia Autonomous Region, China. Their morphology, physiology, biochemical features, polar lipid composition and 16S rRNA genes were characterized in order to elucidate their taxonomy. According to these data, strains X21T and C112T belong to the genus Natrialba, although there are clear differences with respect to their physiology and polar lipid composition between the two strains and the type species, Natrialba asiatica. On the basis of low DNA-DNA hybridizations, these two strains should be considered as new species of genus Natrialba. The names Natrialba hulunbeirensis sp. nov. (type strain X21T = AS 1.1986T = JCM 10989T) and Natrialba chahannaoensis sp. nov. (type strain C112T = AS 1.1977T = JCM 10990T) are proposed.},
}
@article {pmid11589580,
year = {2001},
author = {Gérard, E and Jolivet, E and Prieur, D and Forterre, P},
title = {DNA protection mechanisms are not involved in the radioresistance of the hyperthermophilic archaea Pyrococcus abyssi and P. furiosus.},
journal = {Molecular genetics and genomics : MGG},
volume = {266},
number = {1},
pages = {72-78},
doi = {10.1007/s004380100520},
pmid = {11589580},
issn = {1617-4615},
mesh = {DNA Damage ; DNA, Archaeal/*genetics ; Electrophoresis/methods ; Escherichia coli/radiation effects ; Gamma Rays ; Pyrococcus/genetics/*radiation effects ; Radiation Tolerance/*genetics ; Species Specificity ; },
abstract = {Hyperthermophilic archaea of the genus Pyrococcus are resistant to gamma radiation, suggesting that efficient mechanisms for DNA repair exist in these organisms. To determine whether protective mechanisms might also be implicated in this radioresistance, we have estimated the linear density of DNA double-stranded breaks caused by gamma irradiation in the genomic DNA of two Pyrococcus species, using Escherichia coli and the radioresistant bacterium Deinococcus radiodurans as controls. The linear density of double-stranded breaks was essentially the same in all four microorganisms when irradiation was carried under similar anaerobic conditions, indicating that no specific DNA protection mechanisms exist in Pyrococcus species. Using one- and two-dimensional gel electrophoresis we compared the protein patterns from Pyrococcus abyssi and P. furiosus cells that had or had not been exposed to gamma rays. We did not detect any significant protein induction following DNA damage in either species.},
}
@article {pmid11581661,
year = {2001},
author = {Meng, F and Cargile, BJ and Miller, LM and Forbes, AJ and Johnson, JR and Kelleher, NL},
title = {Informatics and multiplexing of intact protein identification in bacteria and the archaea.},
journal = {Nature biotechnology},
volume = {19},
number = {10},
pages = {952-957},
doi = {10.1038/nbt1001-952},
pmid = {11581661},
issn = {1087-0156},
support = {GM 51334/GM/NIGMS NIH HHS/United States ; K22 AI 01748-01/AI/NIAID NIH HHS/United States ; },
mesh = {Algorithms ; Alkaline Phosphatase ; Amino Acid Sequence ; Archaeal Proteins/*analysis/chemistry ; Bacterial Proteins/*analysis/chemistry ; *Computational Biology/methods ; Cyclin-Dependent Kinases/genetics ; Databases, Factual ; Information Storage and Retrieval ; Ions ; Mass Spectrometry ; Methanococcus/chemistry ; *Models, Statistical ; Molecular Sequence Data ; Mycoplasma pneumoniae/chemistry ; Probability ; },
abstract = {Although direct fragmentation of protein ions in a mass spectrometer is far more efficient than exhaustive mapping of 1-3 kDa peptides for complete characterization of primary structures predicted from sequenced genomes, the development of this approach is still in its infancy. Here we describe a statistical model (good to within approximately 5%) that shows that the database search specificity of this method requires only three of four fragment ions to match (at +/-0.1 Da) for a 99.8% probability of being correct in a database of 5,000 protein forms. Software developed for automated processing of protein ion fragmentation data and for probability-based retrieval of whole proteins is illustrated by identification of 18 archaeal and bacterial proteins with simultaneous mass-spectrometric (MS) mapping of their entire primary structures. Dissociation of two or three proteins at once for such identifications in parallel is also demonstrated, along with retention and exact localization of a phosphorylated serine residue through the fragmentation process. These conceptual and technical advances should assist future processing of whole proteins in a higher throughput format for more robust detection of co- and post-translational modifications.},
}
@article {pmid11576683,
year = {2001},
author = {du Plessis, CA and Barnard, P and Naldrett, K and de Kock, SH},
title = {Development of respirometry methods to assess the microbial activity of thermophilic bioleaching archaea.},
journal = {Journal of microbiological methods},
volume = {47},
number = {2},
pages = {189-198},
doi = {10.1016/s0167-7012(01)00300-1},
pmid = {11576683},
issn = {0167-7012},
mesh = {Archaea/drug effects/growth &amp; development/*metabolism ; Carbon Dioxide/metabolism ; Oxygen/metabolism ; *Oxygen Consumption/drug effects ; Sodium/metabolism/pharmacology ; Temperature ; Time Factors ; },
abstract = {Respirometry methods have been used for many years to assess the microbial activity of mainly heterotrophic bacteria. Using this technique, the consumption of oxygen and evolution of carbon dioxide for heterotrophic carbon catabolism can be used to assess microbial activity. In the case of autotrophic bioleaching bacteria, carbon dioxide is used as a carbon source resulting in the consumption of both oxygen and carbon dioxide. The use of such respirometry techniques at high temperatures (up to 80 degrees C) for the investigation of bioleaching Archaea, however, poses particular difficulties. At these elevated temperatures, the solubility of oxygen into the liquid phase is particularly poor. This work details specific methods by which high temperature constraints are overcome while monitoring the activity of thermophilic Archaea using a Micro-Oxymax respirometer (Columbus Instruments). The use of elevated headspace oxygen concentrations, in order to overcome low oxygen solubility, is demonstrated as well as the effect of such elevated oxygen concentrations on microbial oxygen consumption rates. The relative rates of oxygen and carbon dioxide consumption are also illustrated during the oxidation of a chalcopyrite concentrate. In addition, this paper details generic methods by which respirometry data can be used to quantify inhibitory effects of a compound such as Na(2)SO(4). The further use of such data in predicting minimum hydraulic reactor retention times for continuous culture bioleaching reactors, as a function of concentration of potentially inhibitory compounds, is also demonstrated.},
}
@article {pmid11568443,
year = {2001},
author = {Rother, M and Resch, A and Wilting, R and Böck, A},
title = {Selenoprotein synthesis in archaea.},
journal = {BioFactors (Oxford, England)},
volume = {14},
number = {1-4},
pages = {75-83},
doi = {10.1002/biof.5520140111},
pmid = {11568443},
issn = {0951-6433},
mesh = {Amino Acid Sequence ; Archaea/*genetics/metabolism ; Base Sequence ; Codon ; Methanococcus/genetics/metabolism ; Molecular Sequence Data ; Nucleic Acid Conformation ; Peptide Elongation Factors/chemistry/metabolism ; Protein Biosynthesis ; Proteins/*genetics ; RNA, Archaeal/genetics/metabolism ; RNA, Messenger/genetics/metabolism ; Selenocysteine/*metabolism ; Selenoproteins ; Sequence Alignment ; Sequence Homology, Amino Acid ; },
abstract = {The availability of the genome sequences from several archaea has facilitated the identification of the encoded selenoproteins and also of most of the components of the machinery for selenocysteine biosynthesis and insertion. Until now, selenoproteins have been identified solely in species of the genera Methanococcus (M.) and Methanopyrus. Apart from selenophosphate synthetase, they include only enzymes with a function in energy metabolism. Like in bacteria and eukarya, selenocysteine insertion is directed by a UGA codon in the mRNA and involves the action of a specific tRNA and of selenophosphate as the selenium donor. Major differences to the bacterial system, however, are that no homolog for the bacterial selenocysteine synthase was found and, especially, that the SECIS element of the mRNA is positioned in the 3' nontranslated region. The characterisation of a homolog for the bacterial SelB protein showed that it does not bind to the SECIS element necessitating the activity of at least a second protein. The use of the genetic system of M. maripaludis allowed the heterologous expression of a selenoprotein gene from M. jannaschii and will facilitate the elucidation of the mechanism of the selenocysteine insertion process in the future.},
}
@article {pmid11528391,
year = {2001},
author = {Podani, J and Oltvai, ZN and Jeong, H and Tombor, B and Barabási, AL and Szathmáry, E},
title = {Comparable system-level organization of Archaea and Eukaryotes.},
journal = {Nature genetics},
volume = {29},
number = {1},
pages = {54-56},
doi = {10.1038/ng708},
pmid = {11528391},
issn = {1061-4036},
mesh = {Archaea/*genetics/metabolism ; *Biological Evolution ; *Eukaryotic Cells/metabolism ; },
abstract = {A central and long-standing issue in evolutionary theory is the origin of the biological variation upon which natural selection acts. Some hypotheses suggest that evolutionary change represents an adaptation to the surrounding environment within the constraints of an organism's innate characteristics. Elucidation of the origin and evolutionary relationship of species has been complemented by nucleotide sequence and gene content analyses, with profound implications for recognizing life's major domains. Understanding of evolutionary relationships may be further expanded by comparing systemic higher-level organization among species. Here we employ multivariate analyses to evaluate the biochemical reaction pathways characterizing 43 species. Comparison of the information transfer pathways of Archaea and Eukaryotes indicates a close relationship between these domains. In addition, whereas eukaryotic metabolic enzymes are primarily of bacterial origin, the pathway-level organization of archaeal and eukaryotic metabolic networks is more closely related. Our analyses therefore suggest that during the symbiotic evolution of eukaryotes, incorporation of bacterial metabolic enzymes into the proto-archaeal proteome was constrained by the host's pre-existing metabolic architecture.},
}
@article {pmid11524131,
year = {2001},
author = {Kelly, DJ and Thomas, GH},
title = {The tripartite ATP-independent periplasmic (TRAP) transporters of bacteria and archaea.},
journal = {FEMS microbiology reviews},
volume = {25},
number = {4},
pages = {405-424},
doi = {10.1111/j.1574-6976.2001.tb00584.x},
pmid = {11524131},
issn = {0168-6445},
mesh = {Amino Acid Sequence ; Archaeal Proteins/chemistry/genetics/*metabolism ; Bacterial Proteins/chemistry/genetics/*metabolism ; *Biological Transport, Active ; Carrier Proteins/chemistry/genetics/*metabolism ; *Dicarboxylic Acid Transporters ; Dicarboxylic Acids/metabolism ; Evolution, Molecular ; Membrane Proteins/chemistry/genetics/*metabolism ; *Membrane Transport Proteins ; Molecular Sequence Data ; *Periplasmic Proteins ; },
abstract = {Until recently, extracytoplasmic solute receptor (ESR)-dependent uptake systems were invariably found to possess a conserved ATP-binding protein (the ATP-binding cassette protein or ABC protein), which couples ATP hydrolysis to the translocation of the solute across the cytoplasmic membrane. While it is clear that this class of ABC transporter is ubiquitous in prokaryotes, it is now firmly established that other, unrelated types of membrane transport systems exist which also have ESR components. These systems have been designated tripartite ATP-independent periplasmic (TRAP) transporters, and they form a distinct class of ESR-dependent secondary transporters where the driving force for solute accumulation is an electrochemical ion gradient and not ATP hydrolysis. Currently, the most well characterised TRAP transporter at the functional and molecular level is the high-affinity C4-dicarboxylate transport (Dct) system from Rhodobacter capsulatus. This consists of three proteins; an ESR (DctP) and small (DctQ) and large (DctM) integral membrane proteins. The characteristics of this system are discussed in detail. Homologues of the R. capsulatus DctPQM proteins are present in a diverse range of prokaryotes, both bacteria and archaea, but not in eukaryotes. The deduced structures and possible functions of these homologous systems are described. In addition to the DctP family, other types of ESRs can be associated with TRAP transporters. A conserved family of immunogenic extracytoplasmic proteins is shown to be invariably associated with TRAP systems that contain a large DctQM fusion protein. All of the currently known archaeal systems are of this type. It is concluded that TRAP transporters are a widespread and ancient type of solute uptake system that transport a potentially diverse range of solutes and most likely evolved by the addition of auxiliary proteins to a single secondary transporter.},
}
@article {pmid11523896,
year = {2001},
author = {Reich, CI and McNeil, LK and Brace, JL and Brucker, JK and Olsen, GJ},
title = {Archaeal RecA homologues: different response to DNA-damaging agents in mesophilic and thermophilic Archaea.},
journal = {Extremophiles : life under extreme conditions},
volume = {5},
number = {4},
pages = {265-275},
doi = {10.1007/s007920100197},
pmid = {11523896},
issn = {1431-0651},
mesh = {Archaea/*genetics/metabolism ; DNA Damage ; Gene Expression Regulation, Archaeal ; Genes, Archaeal ; Rec A Recombinases/analysis/*genetics/metabolism ; Recombination, Genetic ; },
abstract = {Two archaeal proteins, RadA and RadB, share similarity with the RecA/Rad51 family of recombinases, with RadA being the functional homologue. We have studied and compared the RadA and RadB proteins of mesophilic and thermophilic Archaea. In growing cells, RadA levels are similar in mesophilic Methanococcus species and the hyperthermophile Methanococcus jannaschii. Treatment of cells with mutagenic agents (methylmethane sulfonate or UV light) increased the expression of RadA (as evidenced by higher levels of both mRNA and protein) in all organisms tested, but the increase was greater in the mesophiles than in the thermophiles M. jannaschii and Sulfolobus solfataricus. Recombinantly expressed RadA proteins from the mesophile M. voltae and the thermophile M. jannaschii were similar in their ATPase- and DNA-binding activities. All the data are consistent with proposals that RadA plays the same role as eukaryotic Rad51. Surprisingly, the data also suggested that the thermophiles do not need more RadA protein or activity than the mesophiles. On the other hand, RadB is not coregulated with RadA, and its role remains unclear. Neither RadA nor RadB from a mesophile or from a thermophile rescued the UV-sensitive phenotype of an Escherichia coli recA- host.},
}
@article {pmid11523004,
year = {2001},
author = {Pérez-Rueda, E and Collado-Vides, J},
title = {Common history at the origin of the position-function correlation in transcriptional regulators in archaea and bacteria.},
journal = {Journal of molecular evolution},
volume = {53},
number = {3},
pages = {172-179},
doi = {10.1007/s002390010207},
pmid = {11523004},
issn = {0022-2844},
mesh = {Archaea/chemistry/*genetics/metabolism ; Archaeal Proteins/chemistry/genetics/metabolism ; Bacteria/chemistry/*genetics/metabolism ; Bacterial Proteins/chemistry/genetics/metabolism ; DNA-Binding Proteins/chemistry/genetics/metabolism ; *Evolution, Molecular ; *Helix-Turn-Helix Motifs/genetics ; Repressor Proteins/chemistry/genetics/metabolism ; Transcription Factors/chemistry/*genetics/metabolism ; },
abstract = {Regulatory proteins in Escherichia coli with a helix-turn-helix (HTH) DNA binding motif show a position-function correlation such that repressors have this motif predominantly at the N terminus, whereas activators have the motif at the C-terminus extreme. Using this initial collection we identified by sequence comparison the exhaustive set of transcriptional regulators in 17 bacterial and 6 archaeal genomes. This enlarged set shows the same position-function correlation. The main question we address is whether this correlation is the result of common origin in evolution or the result of convergence. Evidence is presented supporting a common history at the origin of this correlation. We show the existence of a supergroup of eight repressor protein families sharing a conserved extended sequence comprising the classic HTH. Two of these repressor families (MarR and AsnC) originated before the divergence of Archaea and Bacteria. They are proposed at the origin of HTH-bearing transcriptional regulators currently present in Bacteria. The group of LysR proteins, with the HTH also at the N terminus, offers a control to the argument, since it shows clearly distinctive structural, functional, and evolutionary properties. This group of activator proteins, suggested to have originated within the Bacteria, has an advantageous gene organization to facilitate its horizontal transfer-used to conquer some Archaea-as well as negative autoregulation convenient for homeostasis, all of which agrees with this being the largest family in Bacteria. These results suggest that if shuffling of motifs occurred in Bacteria, it occurred only early in the history of these proteins, as opposed to what is observed in eukaryotic regulators.},
}
@article {pmid11521661,
year = {2000},
author = {Vas, A and Leatherwood, J},
title = {Where does DNA replication start in archaea?.},
journal = {Genome biology},
volume = {1},
number = {3},
pages = {REVIEWS1020},
pmid = {11521661},
issn = {1474-760X},
mesh = {Archaea/*genetics ; Base Sequence ; DNA Replication/*genetics ; DNA, Archaeal/biosynthesis/genetics ; GC Rich Sequence/genetics ; Phylogeny ; Replication Origin/*genetics ; },
abstract = {Genome-wide measures of DNA strand composition have been used to find archaeal DNA replication origins. Archaea seem to replicate using a single origin (as do eubacteria) even though archaeal replication factors are more like those of eukaryotes.},
}
@article {pmid11513609,
year = {2001},
author = {Madern, D and Ebel, C and Dale, HA and Lien, T and Steen, IH and Birkeland, NK and Zaccai, G},
title = {Differences in the oligomeric states of the LDH-like L-MalDH from the hyperthermophilic archaea Methanococcus jannaschii and Archaeoglobus fulgidus.},
journal = {Biochemistry},
volume = {40},
number = {34},
pages = {10310-10316},
doi = {10.1021/bi010168c},
pmid = {11513609},
issn = {0006-2960},
mesh = {Amino Acid Sequence ; Archaeoglobus fulgidus/*enzymology ; Cloning, Molecular ; DNA Primers ; Enzyme Stability ; Hot Temperature ; Hydrogen-Ion Concentration ; Kinetics ; L-Lactate Dehydrogenase/*chemistry ; Macromolecular Substances ; Malate Dehydrogenase/*chemistry/genetics/metabolism ; Methanococcus/*enzymology ; Models, Molecular ; Molecular Sequence Data ; Neutrons ; Protein Structure, Secondary ; Recombinant Proteins/chemistry/metabolism ; Scattering, Radiation ; Sequence Alignment ; Sequence Homology, Amino Acid ; Species Specificity ; Ultracentrifugation ; },
abstract = {L-Malate (MalDH) and L-lactate (LDH) dehydrogenases belong to the same family of NAD-dependent enzymes. To gain insight into molecular relationships within this family, we studied two hyperthermophilic (LDH-like) L-MalDH (proteins with LDH-like structure and MalDH enzymatic activity) from the archaea Archaeoglobus fulgidus (Af) and Methanococcus jannaschii (Mj). The structural parameters of these enzymes determined by neutron scattering and analytical centrifugation showed that the Af (LDH-like) L-MalDH is a dimer whereas the Mj (LDH-like) L-MalDH is a tetramer. The effects of high temperature, cofactor binding, and high phosphate concentration were studied. They did not modify the oligomeric state of either enzyme. The enzymatic activity of the dimeric Af (LDH-like) L-MalDH is controlled by a pH-dependent transition at pH 7 without dissociation of the subunits. The data were analyzed in the light of the crystallographic structure of the LDH-like L-MalDH from Haloarcula marismortui. This showed that a specific loop at the dimer-dimer contact regions in these enzymes controls the tetramer formation.},
}
@article {pmid11497995,
year = {2001},
author = {Bell, SD and Magill, CP and Jackson, SP},
title = {Basal and regulated transcription in Archaea.},
journal = {Biochemical Society transactions},
volume = {29},
number = {Pt 4},
pages = {392-395},
doi = {10.1042/bst0290392},
pmid = {11497995},
issn = {0300-5127},
mesh = {Archaea/*genetics ; DNA-Binding Proteins/metabolism ; Gene Expression Regulation, Archaeal ; Promoter Regions, Genetic ; Protein Subunits ; RNA Polymerase II/*metabolism ; TATA-Box Binding Protein ; Transcription Factors/metabolism ; *Transcription, Genetic ; },
abstract = {The basal transcription machinery of Archaea is fundamentally related to the eucaryal RNA polymerase (RNAP) II apparatus. In addition to a 12-subunit RNAP, Archaea possess two general transcription factors, the activities of which are required for accurate and efficient in vitro transcription. These factors, TBP and TFB, are homologues of the eucaryal TATA-box binding protein and TFIIB respectively. Archaea also possess TFE, a homologue of the eucaryal RNAP II general transcription factor TFIIE. Although not absolutely required for transcription in vitro, TFE nonetheless plays a stimulatory role under conditions where promoter recognition by TBP is sub-optimal. The basal transcription apparatus of Archaea is closely related to that of Eucarya but archaeal transcriptional regulators resemble those of bacteria. The mode of action of two such regulators has been characterized to determine how these 'bacterial-like' regulators impinge on the 'eucaryal-like' basal machinery.},
}
@article {pmid11481493,
year = {2001},
author = {Hou, S and Freitas, T and Larsen, RW and Piatibratov, M and Sivozhelezov, V and Yamamoto, A and Meleshkevitch, EA and Zimmer, M and Ordal, GW and Alam, M},
title = {Globin-coupled sensors: a class of heme-containing sensors in Archaea and Bacteria.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {98},
number = {16},
pages = {9353-9358},
pmid = {11481493},
issn = {0027-8424},
mesh = {Amino Acid Sequence ; Archaea/*metabolism ; Bacteria/*metabolism ; Bacterial Proteins/chemistry/genetics/isolation &amp; purification/metabolism ; Base Sequence ; *Biosensing Techniques ; DNA Primers ; Globins/*metabolism ; Heme/*metabolism ; Heme-Binding Proteins ; Hemeproteins/chemistry/genetics/isolation &amp; purification/metabolism ; Models, Molecular ; Molecular Sequence Data ; Recombinant Proteins/chemistry/genetics/isolation &amp; purification/metabolism ; Sequence Homology, Amino Acid ; },
abstract = {The recently discovered prokaryotic signal transducer HemAT, which has been described in both Archaea and Bacteria, mediates aerotactic responses. The N-terminal regions of HemAT from the archaeon Halobacterium salinarum (HemAT-Hs) and from the Gram-positive bacterium Bacillus subtilis (HemAT-Bs) contain a myoglobin-like motif, display characteristic heme-protein absorption spectra, and bind oxygen reversibly. Recombinant HemAT-Hs and HemAT-Bs shorter than 195 and 176 residues, respectively, do not bind heme effectively. Sequence homology comparisons and three-dimensional modeling predict that His-123 is the proximal heme-binding residue in HemAT from both species. The work described here used site-specific mutagenesis and spectroscopy to confirm this prediction, thereby providing direct evidence for a functional domain of prokaryotic signal transducers that bind heme in a globin fold. We postulate that this domain is part of a globin-coupled sensor (GCS) motif that exists as a two-domain transducer having no similarity to the PER-ARNT-SIM (PAS)-domain superfamily transducers. Using the GCS motif, we have identified several two-domain sensors in a variety of prokaryotes. We have cloned, expressed, and purified two potential globin-coupled sensors and performed spectral analysis on them. Both bind heme and show myoglobin-like spectra. This observation suggests that the general function of GCS-type transducers is to bind diatomic oxygen and perhaps other gaseous ligands, and to transmit a conformational signal through a linked signaling domain.},
}
@article {pmid11472939,
year = {2001},
author = {Takai, K and Komatsu, T and Inagaki, F and Horikoshi, K},
title = {Distribution of archaea in a black smoker chimney structure.},
journal = {Applied and environmental microbiology},
volume = {67},
number = {8},
pages = {3618-3629},
pmid = {11472939},
issn = {0099-2240},
mesh = {Archaea/*classification/genetics/*growth &amp; development ; Colony Count, Microbial ; Culture Media ; DNA, Ribosomal/analysis ; *Ecosystem ; Hot Temperature ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal/genetics ; Ribotyping ; Seawater/chemistry/*microbiology ; Sequence Analysis, DNA ; Spectrum Analysis ; },
abstract = {Archaeal community structures in microhabitats in a deep-sea hydrothermal vent chimney structure were evaluated through the combined use of culture-independent molecular analyses and enrichment culture methods. A black smoker chimney was obtained from the PACMANUS site in the Manus Basin near Papua New Guinea, and subsamples were obtained from vertical and horizontal sections. The elemental composition of the chimney was analyzed in different subsamples by scanning electron microscopy and energy-dispersive X-ray spectroscopy, indicating that zinc and sulfur were major components while an increased amount of elemental oxygen in exterior materials represented the presence of oxidized materials on the outer surface of the chimney. Terminal restriction fragment length polymorphism analysis revealed that a shift in archaeal ribotype structure occurred in the chimney structure. Through sequencing of ribosomal DNA (rDNA) clones from archaeal rDNA clone libraries, it was demonstrated that the archaeal communities in the chimney structure consisted for the most part of hyperthermophilic members and extreme halophiles and that the distribution of such extremophiles in different microhabitats of the chimney varied. The results of the culture-dependent analysis supported in part the view that changes in archaeal community structures in these microhabitats are associated with the geochemical and physical dynamics in the black smoker chimney.},
}
@article {pmid11463914,
year = {2001},
author = {Orphan, VJ and House, CH and Hinrichs, KU and McKeegan, KD and DeLong, EF},
title = {Methane-consuming archaea revealed by directly coupled isotopic and phylogenetic analysis.},
journal = {Science (New York, N.Y.)},
volume = {293},
number = {5529},
pages = {484-487},
doi = {10.1126/science.1061338},
pmid = {11463914},
issn = {0036-8075},
mesh = {Anaerobiosis ; Carbon Isotopes/analysis ; Deltaproteobacteria/chemistry/classification/*metabolism ; Geologic Sediments/*microbiology ; In Situ Hybridization, Fluorescence ; Lipids/analysis ; Methane/*metabolism ; Methanosarcinales/chemistry/classification/*metabolism ; Oceans and Seas ; Oligonucleotide Probes ; Oxidation-Reduction ; Phylogeny ; RNA, Archaeal/genetics ; RNA, Bacterial/genetics ; RNA, Ribosomal/genetics ; Spectrometry, Mass, Secondary Ion ; Sulfates/metabolism ; },
abstract = {Microorganisms living in anoxic marine sediments consume more than 80% of the methane produced in the world's oceans. In addition to single-species aggregates, consortia of metabolically interdependent bacteria and archaea are found in methane-rich sediments. A combination of fluorescence in situ hybridization and secondary ion mass spectrometry shows that cells belonging to one specific archaeal group associated with the Methanosarcinales were all highly depleted in 13C (to values of -96 per thousand). This depletion indicates assimilation of isotopically light methane into specific archaeal cells. Additional microbial species apparently use other carbon sources, as indicated by significantly higher 13C/12C ratios in their cell carbon. Our results demonstrate the feasibility of simultaneous determination of the identity and the metabolic activity of naturally occurring microorganisms.},
}
@article {pmid11453458,
year = {2001},
author = {Cannio, R and Contursi, P and Rossi, M and Bartolucci, S},
title = {Thermoadaptation of a mesophilic hygromycin B phosphotransferase by directed evolution in hyperthermophilic Archaea: selection of a stable genetic marker for DNA transfer into Sulfolobus solfataricus.},
journal = {Extremophiles : life under extreme conditions},
volume = {5},
number = {3},
pages = {153-159},
doi = {10.1007/s007920100189},
pmid = {11453458},
issn = {1431-0651},
mesh = {*Adaptation, Biological ; Base Sequence ; *Directed Molecular Evolution ; Escherichia coli/enzymology/genetics ; Fuselloviridae/genetics ; Gene Expression ; Genes, Bacterial ; Genetic Markers ; Mutation ; Phosphotransferases (Alcohol Group Acceptor)/*genetics ; Plasmids/genetics ; Sulfolobus/*enzymology/*genetics/virology ; Temperature ; Transformation, Genetic ; },
abstract = {A mutated version of the hygromycin B phosphotransferase (hph(mut)) gene from Escherichia coli, isolated by directed evolution at 75 degrees C in transformants of a thermophilic strain of Sulfolobus solfataricus, was characterized with respect to its genetic stability in both the original mesophilic and the new thermophilic hosts. This gene was demonstrated to be able to express the hygromycin B resistance phenotype and to be steadily maintained and propagated also in other, more thermophilic strains of S. solfataricus, i.e., up to 82 degrees C. Furthermore, it may be transferred to S. solfataricus cells by cotransformation with pKMSD48, another extrachromosomal element derived from the virus SSV1 of Sulfolobus shibatae, without any loss of stability and without affecting the replication and infectivity of this viral DNA. The hph(mut) and the wild-type gene products were expressed at higher levels in E. coli and purified by specific affinity chromatography on immobilized hygromycin B. Comparative characterization revealed that the mutant enzyme had acquired significant thermoresistance and displayed higher thermal activity with augmented catalytic efficiency.},
}
@article {pmid11451450,
year = {2001},
author = {Graupner, M and White, RH},
title = {The first examples of (S)-2-hydroxyacid dehydrogenases catalyzing the transfer of the pro-4S hydrogen of NADH are found in the archaea.},
journal = {Biochimica et biophysica acta},
volume = {1548},
number = {1},
pages = {169-173},
doi = {10.1016/s0167-4838(01)00220-5},
pmid = {11451450},
issn = {0006-3002},
mesh = {Alcohol Oxidoreductases/chemistry/*metabolism ; Archaea/*enzymology ; Hydrogen/chemistry/metabolism ; Mitochondrial Proteins ; NAD/chemistry/*metabolism ; Oxidation-Reduction ; Stereoisomerism ; },
abstract = {Reduction of 2-oxoacids to the corresponding (S)-2-hydroxyacids is an important transformation in biochemistry. To date all (S)-2-hydroxyacid dehydrogenases belonging to the L-lactate/L-malate dehydrogenase family have been found to transfer the pro-4R hydrogen of either NADH or NADPH to C-2 of the 2-oxoacid substrates during their reduction. Here, we report that recombinantly generated (S)-2-hydroxyacid dehydrogenases present in the methanoarchaea Methanococcus jannaschii and Methanothermus fervidus use the pro-4S hydrogen of NADH to reduce a series of 2-oxoacids to the corresponding (S)-2-hydroxyacids. This information as well as the low sequence identity between these archaeal enzymes and the L-lactate/L-malate family of enzymes indicate that these enzymes are not evolutionary related and therefore constitute a new class of (S)-2-hydroxyacid dehydrogenases.},
}
@article {pmid11441180,
year = {2001},
author = {Kuypers, MM and Blokker, P and Erbacher, J and Kinkel, H and Pancost, RD and Schouten, S and Sinninghe Damste, JS},
title = {Massive expansion of marine archaea during a mid-Cretaceous oceanic anoxic event.},
journal = {Science (New York, N.Y.)},
volume = {293},
number = {5527},
pages = {92-95},
doi = {10.1126/science.1058424},
pmid = {11441180},
issn = {0036-8075},
mesh = {Adaptation, Physiological ; Animals ; Archaea/chemistry/*physiology ; Atlantic Ocean ; *Biological Evolution ; Carbon/metabolism ; Carbon Isotopes ; Cyanobacteria/chemistry/metabolism ; Eukaryota/chemistry/metabolism ; *Fossils ; Geologic Sediments/analysis/chemistry/microbiology ; Membrane Lipids/analysis ; Oxygen/*metabolism ; Plankton/metabolism ; Plants/chemistry/metabolism ; Temperature ; Time Factors ; },
abstract = {Biogeochemical and stable carbon isotopic analysis of black-shale sequences deposited during an Albian oceanic anoxic event (approximately 112 million years ago) indicate that up to 80 weight percent of sedimentary organic carbon is derived from marine, nonthermophilic archaea. The carbon-13 content of archaeal molecular fossils indicates that these archaea were living chemoautotrophically. Their massive expansion may have been a response to the strong stratification of the ocean during this anoxic event. Indeed, the sedimentary record of archaeal membrane lipids suggests that this anoxic event marks a time in Earth history at which certain hyperthermophilic archaea adapted to low-temperature environments.},
}
@article {pmid11441169,
year = {2001},
author = {Smith, DC},
title = {Marine biology. Expansion of the marine Archaea.},
journal = {Science (New York, N.Y.)},
volume = {293},
number = {5527},
pages = {56-57},
doi = {10.1126/science.1063491},
pmid = {11441169},
issn = {0036-8075},
mesh = {Archaea/chemistry/*physiology ; Atlantic Ocean ; *Biological Evolution ; Carbon/metabolism ; Carbon Dioxide/metabolism ; *Fossils ; Geologic Sediments/chemistry/microbiology ; Membrane Lipids/analysis ; Oxygen/metabolism ; Temperature ; Time Factors ; },
}
@article {pmid11431930,
year = {2001},
author = {Ishino, Y},
title = {[Studies on DNA replication mechanism and related proteins in Archaea].},
journal = {Nihon saikingaku zasshi. Japanese journal of bacteriology},
volume = {56},
number = {2},
pages = {435-454},
pmid = {11431930},
issn = {0021-4930},
mesh = {*Archaea/genetics ; *Archaeal Proteins ; DNA Helicases/physiology ; DNA Ligases/physiology ; DNA Primase/physiology ; *DNA Replication ; DNA Topoisomerases, Type I/physiology ; DNA Topoisomerases, Type II/physiology ; *DNA, Archaeal ; DNA-Binding Proteins/physiology ; DNA-Directed DNA Polymerase/physiology ; Humans ; Origin Recognition Complex ; Replication Origin ; },
}
@article {pmid11429452,
year = {2001},
author = {Gregor, D and Pfeifer, F},
title = {Use of a halobacterial bgaH reporter gene to analyse the regulation of gene expression in halophilic archaea.},
journal = {Microbiology (Reading, England)},
volume = {147},
number = {Pt 7},
pages = {1745-1754},
doi = {10.1099/00221287-147-7-1745},
pmid = {11429452},
issn = {1350-0872},
mesh = {Archaeal Proteins/*genetics/metabolism ; Base Sequence ; *Gene Expression Regulation, Archaeal ; Genes, Reporter/*genetics ; Halobacterium salinarum/*genetics/metabolism ; Haloferax/*genetics/metabolism ; Membrane Proteins/*genetics/metabolism ; Molecular Sequence Data ; Promoter Regions, Genetic/genetics ; *Proteins ; Recombinant Fusion Proteins/metabolism ; Transcription, Genetic ; Transformation, Bacterial ; beta-Galactosidase/*genetics/metabolism ; },
abstract = {The bgaH reading frame encoding a beta-galactosidase of 'Haloferax alicantei' was used as a reporter gene to investigate three different promoter regions derived from gvpA genes of Haloferax mediterranei (mc-gvpA) and Halobacterium salinarum (c-gvpA and p-gvpA) in Haloferax volcanii transformants. The fusion of bgaH at the start codon of each gvpA reading frame (A1-bgaH fusion genes) caused translational problems in some cases. Transformants containing constructs with fusions further downstream in the gvpA reading frame (A-bgaH) produced beta-galactosidase, and colonies on agar plates turned blue when sprayed with X-Gal. The beta-galactosidase activities quantified by standard ONPG assays correlated well with the mRNA data determined with transformants containing the respective gvpA genes: the cA-bgaH fusion gene was completely inactive, the mcA-bgaH transformants showed low amounts of products, whereas the pA-bgaH fusion gene was constitutively expressed in the respective transformants. The transcription of each A-bgaH gene was activated by the homologous transcriptional activator protein GvpE. The cGvpE, pGvpE and mcGvpE proteins were able to activate the promoter of pA-bgaH and mcA-bgaH, whereas the promoter of cA-bgaH was only activated by cGvpE. Among the three GvpE proteins tested, cGvpE appeared to be the strongest transcriptional activator.},
}
@article {pmid11425752,
year = {2001},
author = {Kashefi, K and Tor, JM and Nevin, KP and Lovley, DR},
title = {Reductive precipitation of gold by dissimilatory Fe(III)-reducing bacteria and archaea.},
journal = {Applied and environmental microbiology},
volume = {67},
number = {7},
pages = {3275-3279},
pmid = {11425752},
issn = {0099-2240},
mesh = {Archaea/chemistry/*metabolism ; Bacteria/growth &amp; development/*metabolism ; Chemical Precipitation ; Ferric Compounds/*metabolism ; Gold/*metabolism ; Oxidation-Reduction ; },
abstract = {Studies with a diversity of hyperthermophilic and mesophilic dissimilatory Fe(III)-reducing Bacteria and Archaea demonstrated that some of these organisms are capable of precipitating gold by reducing Au(III) to Au(0) with hydrogen as the electron donor. These studies suggest that models for the formation of gold deposits in both hydrothermal and cooler environments should consider the possibility that dissimilatory metal-reducing microorganisms can reductively precipitate gold from solution.},
}
@article {pmid11409546,
year = {2001},
author = {Bräsen, C and Schönheit, P},
title = {Mechanisms of acetate formation and acetate activation in halophilic archaea.},
journal = {Archives of microbiology},
volume = {175},
number = {5},
pages = {360-368},
doi = {10.1007/s002030100273},
pmid = {11409546},
issn = {0302-8933},
mesh = {Acetate-CoA Ligase/*metabolism ; Acetic Acid/*metabolism ; Acetyl Coenzyme A/metabolism ; Adenosine Diphosphate/metabolism ; Adenosine Monophosphate/metabolism ; Archaea/enzymology/*metabolism ; Coenzyme A Ligases/metabolism ; Enzyme Stability ; Glucose/metabolism ; Kinetics ; Substrate Specificity ; },
abstract = {The halophilic archaea Halococcus (Hc.) saccharolyticus, Haloferax (Hf.) volcanii, and Halorubrum (Hr.) saccharovorum were found to generate acetate during growth on glucose and to utilize acetate as a growth substrate. The mechanisms of acetate formation from acetyl-CoA and of acetate activation to acetyl-CoA were studied. Hc. saccharolyticus, exponentially growing on complex medium with glucose, formed acetate and contained ADP-forming acetyl-CoA synthetase (ADP-ACS) rather than acetate kinase and phosphate acetyltransferase or AMP-forming acetyl-CoA synthetase. In the stationary phase, the excreted acetate was completely consumed, and cells contained AMP-forming acetyl-CoA synthetase (AMP-ACS) and a significantly reduced ADP-ACS activity. Hc. saccharolyticus, grown on acetate as carbon and energy source, contained only AMP-ACS rather than ADP-ACS or acetate kinase. Cell suspensions of Hc. saccharolyticus metabolized acetate only when they contained AMP-ACS activity, i.e., when they were obtained after growth on acetate or from the stationary phase after growth on glucose. Suspensions of exponential glucose-grown cells, containing only ADP-ACS but not AMP-ACS, did not consume acetate. Similar results were obtained for the phylogenetic distantly related halophilic archaea Hf. volcanii and Hf. saccharovorum. We conclude that, in halophilic archaea, the formation of acetate from acetyl-CoA is catalyzed by ADP-ACS, whereas the activation of acetate to acetyl-CoA is mediated by an inducible AMP-ACS.},
}
@article {pmid11411682,
year = {2001},
author = {Hezayen, FF and Rehm, BH and Tindall, BJ and Steinbüchel, A},
title = {Transfer of Natrialba asiatica B1T to Natrialba taiwanensis sp. nov. and description of Natrialba aegyptiaca sp. nov., a novel extremely halophilic, aerobic, non-pigmented member of the Archaea from Egypt that produces extracellular poly(glutamic acid).},
journal = {International journal of systematic and evolutionary microbiology},
volume = {51},
number = {Pt 3},
pages = {1133-1142},
doi = {10.1099/00207713-51-3-1133},
pmid = {11411682},
issn = {1466-5026},
mesh = {DNA, Ribosomal/genetics ; Egypt ; Euryarchaeota/*classification/genetics/physiology ; Halobacteriaceae/*classification/genetics/physiology ; Lipids/analysis ; Molecular Sequence Data ; Nucleic Acid Hybridization ; *Phylogeny ; Polyglutamic Acid/*biosynthesis ; RNA, Ribosomal, 16S/genetics ; Temperature ; },
abstract = {A novel extremely halophilic member of the Archaea, strain 40T, was isolated from Egypt (Aswan). This isolate requires at least 1.6 M sodium chloride for growth and exhibits optimal growth between 37 and 42 degrees C. Determination of the entire 16S rRNA gene sequence revealed the highest similarity to the type strain of Natrialba asiatica (> 99%). Polar lipid analysis indicated that strain 40T and Natrialba asiatica have essentially identical compositions, indicating that the former is a member of genus Natrialba. However, physiological and biochemical data provided evidence that Natrialba asiatica strains B1T and 172P1T, as well as strain 40T, are sufficiently different to be divided in three different species. The G+C content of strain 40T was 61.5+/-0.6 mol%. In addition, DNA-DNA hybridization data supported the placement of the isolate in a new species in the genus Natrialba, Natrialba aegyptiaca sp. nov., and indicated that Natrialba asiatica strain B1T should also be placed in a separate species, Natrialba taiwanensis sp. nov. Morphological studies of strain 40T indicated clearly that this isolate appears in three completely different cell shapes (cocci, rods, tetrads) under different conditions of growth, including different sodium chloride concentrations and different growth temperatures. Another interesting property of strain 40T is the ability to produce an extracellular polymer, which was found to be composed predominantly of glutamic acid (85% w/w), representing poly(glutamic acid), carbohydrates (12.5% w/w) and unidentified compounds (2.5% w/w). Among the Archaea, production of an extracellular polysaccharide has been described for some members of the genera Haloferax and Haloarcula.},
}
@article {pmid11410351,
year = {2001},
author = {Tajima, K and Nagamine, T and Matsui, H and Nakamura, M and Aminov, RI},
title = {Phylogenetic analysis of archaeal 16S rRNA libraries from the rumen suggests the existence of a novel group of archaea not associated with known methanogens.},
journal = {FEMS microbiology letters},
volume = {200},
number = {1},
pages = {67-72},
doi = {10.1111/j.1574-6968.2001.tb10694.x},
pmid = {11410351},
issn = {0378-1097},
mesh = {Animals ; Archaea/*classification/genetics/isolation &amp; purification ; Bacteria/genetics ; Cattle ; Eukaryotic Cells ; Euryarchaeota/classification/genetics ; Evolution, Molecular ; Gene Library ; Molecular Sequence Data ; Nucleic Acid Conformation ; Phylogeny ; RNA, Archaeal/*genetics ; RNA, Ribosomal, 16S/*genetics ; Rumen/*microbiology ; Sequence Analysis, DNA ; },
abstract = {Molecular diversity of rumen archaea was analyzed by PCR amplification and sequencing of two 16S rRNA clone libraries prepared from the bovine rumen fluid using two different archaea-specific primer sets. The first library of 19 clones which was generated with primers D30 and D33, produced essentially two groups of sequences, one affiliated with Methanomicrobium mobile (21% of clones) and the other -- with the uncultured archaeal sequences from anaerobic digester, which are distantly associated with Thermoplasma (79% of clones). The second library of 25 clones, which was generated with primers 0025e Forward and 1492 Reverse, produced a higher degree of diversity: in addition to the previous two groups, with the M. mobile- (56%) and Thermoplasma-associated sequences (20%), four clones (16%) were identified as Methanobrevibacter spp. The remaining two sequences were associated with unidentified archaeal sequences from the rumen and swine waste. Phylogenetic placement of eight almost complete 16S rRNA sequences revealed the existence of a novel cluster of the rumen Euryarchaeota, which is not affiliated with the known methanogenic archaea.},
}
@article {pmid11403846,
year = {2001},
author = {Stuart, ES and Morshed, F and Sremac, M and DasSarma, S},
title = {Antigen presentation using novel particulate organelles from halophilic archaea.},
journal = {Journal of biotechnology},
volume = {88},
number = {2},
pages = {119-128},
doi = {10.1016/s0168-1656(01)00267-x},
pmid = {11403846},
issn = {0168-1656},
support = {AI42556/AI/NIAID NIH HHS/United States ; },
mesh = {Adjuvants, Immunologic ; Animals ; Antigens/*chemistry/immunology ; *Archaeal Proteins ; Bacterial Outer Membrane Proteins/genetics ; Halobacterium/*cytology/genetics ; Haptens/chemistry/immunology ; Immune Sera ; *Immunologic Memory ; *Membrane Proteins ; Mice ; Mice, Inbred BALB C ; Organelles/chemistry/*immunology ; Peptides/chemical synthesis/immunology ; Picrates/chemistry/immunology ; *Proteins ; Serum Albumin, Bovine/chemistry ; },
abstract = {A presentation vehicle was developed based on particulate gas vesicles produced by halophilic archaea. Gas vesicle epitope displays were prepared using standard coupling methods or recombinant DNA technology. When presented in the context of gas vesicle preparations, either the hapten, TNP, or a model six amino acid recombinant insert in the outer gas vesicle protein, GvpC was rendered immunogenic. Assays to quantify humoral responses indicated that each preparation elicited strong antibody responses in the absence of exogenous adjuvant. Thus, each preparation elicited a humoral response when injected into mice and this response was long lived and exhibited immunologic memory. Recombinant gas vesicle preparations therefore constitute a new, self-adjuvanting carrier/display vehicle for presentation of an array of peptidyl epitopes.},
}
@article {pmid11403394,
year = {2001},
author = {Luo, Y and Wasserfallen, A},
title = {Gene transfer systems and their applications in Archaea.},
journal = {Systematic and applied microbiology},
volume = {24},
number = {1},
pages = {15-25},
doi = {10.1078/0723-2020-00005},
pmid = {11403394},
issn = {0723-2020},
mesh = {Archaea/*genetics ; Conjugation, Genetic ; Crenarchaeota/genetics ; Euryarchaeota/genetics ; *Gene Transfer Techniques ; Transduction, Genetic ; Transformation, Bacterial ; },
abstract = {Members of the Archaea domain are extremely diverse in their adaptation to extreme environments, yet also widespread in "normal" habitats. Altogether, among the best characterized archaeal representatives all mechanisms of gene transfer such as transduction, conjugation, and transformation have been discovered, as briefly reviewed here. For some halophiles and mesophilic methanogens, usable genetic tools were developed for in vivo studies. However, on an individual basis no single organism has evolved into the "E. coli of Archaea" as far as genetics is concerned. Currently, and unfortunately, most of the genome sequences available are those of microorganisms which are either not amenable to gene transfer or not among the most promising candidates for genetic studies.},
}
@article {pmid11399068,
year = {2001},
author = {Collins, BM and Harrop, SJ and Kornfeld, GD and Dawes, IW and Curmi, PM and Mabbutt, BC},
title = {Crystal structure of a heptameric Sm-like protein complex from archaea: implications for the structure and evolution of snRNPs.},
journal = {Journal of molecular biology},
volume = {309},
number = {4},
pages = {915-923},
doi = {10.1006/jmbi.2001.4693},
pmid = {11399068},
issn = {0022-2836},
mesh = {Amino Acid Sequence ; Archaeal Proteins/*chemistry/genetics/metabolism ; Binding Sites ; Conserved Sequence ; Crystallography, X-Ray ; *Evolution, Molecular ; Gene Order ; Hydrogen Bonding ; Methanobacterium/*chemistry/genetics ; Models, Molecular ; Molecular Sequence Data ; Protein Structure, Quaternary ; Protein Structure, Tertiary ; Protein Subunits ; RNA/genetics/metabolism ; Ribonucleoproteins, Small Nuclear/*chemistry/genetics/metabolism ; Ribosomal Proteins/genetics ; Sequence Alignment ; },
abstract = {The Sm/Lsm proteins associate with small nuclear RNA to form the core of small nuclear ribonucleoproteins, required for processes as diverse as pre-mRNA splicing, mRNA degradation and telomere formation. The Lsm proteins from archaea are likely to represent the ancestral Sm/Lsm domain. Here, we present the crystal structure of the Lsm alpha protein from the thermophilic archaeon Methanobacterium thermoautotrophicum at 2.0 A resolution. The Lsm alpha protein crystallizes as a heptameric ring comprised of seven identical subunits interacting via beta-strand pairing and hydrophobic interactions. The heptamer can be viewed as a propeller-like structure in which each blade consists of a seven-stranded antiparallel beta-sheet formed from neighbouring subunits. There are seven slots on the inner surface of the heptamer ring, each of which is lined by Asp, Asn and Arg residues that are highly conserved in the Sm/Lsm sequences. These conserved slots are likely to form the RNA-binding site. In archaea, the gene encoding Lsm alpha is located next to the L37e ribosomal protein gene in a putative operon, suggesting a role for the Lsm alpha complex in ribosome function or biogenesis.},
}
@article {pmid11398459,
year = {2001},
author = {Bocs, C and Buhler, C and Forterre, P and Bergerat, A},
title = {DNA topoisomerases VI from hyperthermophilic archaea.},
journal = {Methods in enzymology},
volume = {334},
number = {},
pages = {172-179},
doi = {10.1016/s0076-6879(01)34466-x},
pmid = {11398459},
issn = {0076-6879},
mesh = {Ammonium Sulfate/chemistry ; Archaea/*enzymology ; Archaeal Proteins ; Chromatography, Gel ; *DNA Topoisomerases, Type II/chemistry/*isolation &amp; purification/metabolism ; Polyethylene Glycols/chemistry ; Pyrococcus furiosus/*enzymology ; Sepharose/analogs &amp; derivatives/chemistry ; },
}
@article {pmid11398457,
year = {2001},
author = {Déclais, AC and de La Tour, CB and Duguet, M},
title = {Reverse gyrases from bacteria and archaea.},
journal = {Methods in enzymology},
volume = {334},
number = {},
pages = {146-162},
doi = {10.1016/s0076-6879(01)34464-6},
pmid = {11398457},
issn = {0076-6879},
mesh = {Adenosine Triphosphatases/metabolism ; Amino Acid Motifs ; Archaea/*enzymology ; DNA Helicases/chemistry ; DNA Topoisomerases, Type I/metabolism ; DNA Topoisomerases, Type II/chemistry/*isolation &amp; purification/metabolism ; Escherichia coli/*enzymology ; Nucleic Acid Conformation ; Recombinant Proteins/isolation &amp; purification/metabolism ; },
}
@article {pmid11398412,
year = {2001},
author = {Piñar, G and Gurtner, C and Lubitz, W and Rölleke, S},
title = {Identification of archaea in objects of art by denaturing gradient gel electrophoresis analysis and shotgun cloning.},
journal = {Methods in enzymology},
volume = {336},
number = {},
pages = {356-366},
doi = {10.1016/s0076-6879(01)36601-6},
pmid = {11398412},
issn = {0076-6879},
mesh = {Archaea/*genetics/*isolation &amp; purification ; Archaeology ; *Art ; Base Sequence ; *Biofilms ; Cloning, Molecular ; DNA Primers/genetics ; DNA, Archaeal/genetics/isolation &amp; purification ; DNA, Ribosomal/genetics/isolation &amp; purification ; Electrophoresis, Polyacrylamide Gel ; Environmental Microbiology ; Paintings ; Polymerase Chain Reaction ; RNA, Archaeal/genetics ; RNA, Ribosomal, 16S/genetics ; },
}
@article {pmid11395490,
year = {2001},
author = {Franzetti, B and Schoehn, G and Ebel, C and Gagnon, J and Ruigrok, RW and Zaccai, G},
title = {Characterization of a novel complex from halophilic archaebacteria, which displays chaperone-like activities in vitro.},
journal = {The Journal of biological chemistry},
volume = {276},
number = {32},
pages = {29906-29914},
doi = {10.1074/jbc.M102098200},
pmid = {11395490},
issn = {0021-9258},
mesh = {Adenosine Triphosphatases/*chemistry/metabolism ; Amino Acid Sequence ; Archaea/*chemistry ; *Archaeal Proteins ; Chromatography, Gel ; Dose-Response Relationship, Drug ; Microscopy, Electron ; Microscopy, Fluorescence ; Models, Biological ; Molecular Chaperones/*chemistry/isolation &amp; purification/*metabolism ; Molecular Sequence Data ; Protein Binding ; Protein Conformation ; Protein Denaturation ; Protein Folding ; Spectrometry, Fluorescence ; Time Factors ; Ultracentrifugation ; },
abstract = {We isolated a protein, P45, from the extreme halophilic archaeon Haloarcula marismortui, which displays molecular chaperone activities in vitro. P45 is a weak ATPase that assembles into a large ring-shaped oligomeric complex comprising about 10 subunits. The protein shows no significant homology to any known protein. P45 forms complexes with halophilic malate dehydrogenase during its salt-dependent denaturation/renaturation and decreases the rate of deactivation of the enzyme in an ATP-dependent manner. Compared with other halophilic proteins, the P45 complex appears to be much less dependent on salt for its various activities or stability. In vivo experiments showed that P45 accumulates when cells are exposed to a low salt environment. We suggest, therefore, that P45 could protect halophilic proteins against denaturation under conditions of cellular hyposaline stress.},
}
@article {pmid11391463,
year = {2001},
author = {Chelius, MK and Triplett, EW},
title = {The Diversity of Archaea and Bacteria in Association with the Roots of Zea mays L.},
journal = {Microbial ecology},
volume = {41},
number = {3},
pages = {252-263},
doi = {10.1007/s002480000087},
pmid = {11391463},
issn = {1432-184X},
abstract = {The diversity of bacteria and archaea associating on the surface and interior of maize roots (Zea mays L.) was investigated. A bacterial 16S rDNA primer was designed to amplify bacterial sequences directly from maize roots by PCR to the exclusion of eukaryotic and chloroplast DNA. The mitochondrial sequence from maize was easily separated from the PCR-amplified bacterial sequences by size fractionation. The culturable component of the bacterial community was also assessed, reflecting a community composition different from that of the clone library. The phylogenetic overlap between organisms obtained by cultivation and those identified by direct PCR amplification of 16S rDNA was 48%. Only 4 bacterial divisions were found in the culture collection, which represented 27 phylotypes, whereas 6 divisions were identified in the clonal analysis, comprising 74 phylotypes, including a member of the OP10 candidate division originally described as a novel division level lineage in a Yellowstone hot spring. The predominant group in the culture collection was the actinobacteria and within the clone library, the a-proteobacteria predominated. The population of maize-associated proteobacteria resembled the proteobacterial population of a typical soil community within which resided a subset of specific plant-associated bacteria, such as Rhizobium- and Herbaspirillum-related phylotypes. The representation of phylotypes within other divisions (OP10 and Acidobacterium) suggests that maize roots support a distinct bacterial community. The diversity within the archaeal domain was low. Of the 50 clones screened, 6 unique sequence types were identified, and 5 of these were highly related to each other (sharing 98% sequence identity). The archaeal sequences clustered with good bootstrap support near Marine group I (crenarchaea) and with Marine group II (euryarchaea) uncultured archaea. The results suggest that maize supports a diverse root-associated microbial community composed of species that for the first time have been described as inhabitants of a plant-root environment.},
}
@article {pmid11381026,
year = {2001},
author = {Lecompte, O and Ripp, R and Puzos-Barbe, V and Duprat, S and Heilig, R and Dietrich, J and Thierry, JC and Poch, O},
title = {Genome evolution at the genus level: comparison of three complete genomes of hyperthermophilic archaea.},
journal = {Genome research},
volume = {11},
number = {6},
pages = {981-993},
pmid = {11381026},
issn = {1088-9051},
mesh = {Archaeal Proteins/genetics ; Chromosome Deletion ; Chromosomes, Archaeal/genetics ; *Evolution, Molecular ; Gene Amplification/genetics ; Genes, Archaeal/genetics ; *Genome, Archaeal ; *Hot Temperature ; Molecular Sequence Data ; Proteome/genetics ; Pyrococcus/*genetics ; Pyrococcus furiosus/*genetics ; Sequence Homology, Nucleic Acid ; Species Specificity ; },
abstract = {We have compared three complete genomes of closely related hyperthermophilic species of Archaea belonging to the Pyrococcus genus: Pyrococcus abyssi, Pyrococcus horikoshii, and Pyrococcus furiosus. At the genomic level, the comparison reveals a differential conservation among four regions of the Pyrococcus chromosomes correlated with the location of genetic elements mediating DNA reorganization. This discloses the relative contribution of the major mechanisms that promote genomic plasticity in these Archaea, namely rearrangements linked to the replication terminus, insertion sequence-mediated recombinations, and DNA integration within tRNA genes. The combination of these mechanisms leads to a high level of genomic plasticity in these hyperthermophilic Archaea, at least comparable to the plasticity observed between closely related bacteria. At the proteomic level, the comparison of the three Pyrococcus species sheds light on specific selection pressures acting both on their coding capacities and evolutionary rates. Indeed, thanks to two independent methods, the "reciprocal best hits" approach and a new distance ratio analysis, we detect the false orthology relationships within the Pyrococcus lineage. This reveals a high amount of differential gains and losses of genes since the divergence of the three closely related species. The resulting polymorphism is probably linked to an adaptation of these free-living organisms to differential environmental constraints. As a corollary, we delineate the set of orthologous genes shared by the three species, that is, the genes that may characterize the Pyrococcus genus. In this conserved core, the amino acid substitution rate is equal between P. abyssi and P. horikoshii for most of their shared proteins, even for fast-evolving ones. In contrast, strong discrepancies exist among the substitution rates observed in P. furiosus relative to the two other species, which is in disagreement with the molecular clock hypothesis.},
}
@article {pmid11359559,
year = {2001},
author = {Dennis, PP and Omer, A and Lowe, T},
title = {A guided tour: small RNA function in Archaea.},
journal = {Molecular microbiology},
volume = {40},
number = {3},
pages = {509-519},
doi = {10.1046/j.1365-2958.2001.02381.x},
pmid = {11359559},
issn = {0950-382X},
mesh = {Animals ; Base Sequence ; Binding Sites ; Evolution, Molecular ; Genome, Archaeal ; Methylation ; Molecular Sequence Data ; Phylogeny ; RNA, Archaeal/*physiology ; RNA, Transfer ; Temperature ; },
abstract = {In eukaryotes, the C/D box family of small nucleolar (sno)RNAs contain complementary guide regions that are used to direct 2'-O-ribose methylation to specific nucleotide positions within rRNA during the early stages of ribosome biogenesis. Direct cDNA cloning and computational genome searches have revealed homologues of C/D box snoRNAs (called sRNAs) in prokaryotic Archaea that grow at high temperature. The guide sequences within the sRNAs indicate that they are used to direct methylation to nucleotides in both rRNAs and tRNAs. The number of sRNA genes that are detectable within currently sequenced genomes correlates with the optimal growth temperature. We suggest that archaeal sRNAs may have two functions: to guide the deposition of methyl groups at the 2'-O position of ribose, which is an important determinant in RNA structural stability, and to serve as a molecular chaperones to help orchestrate the folding of rRNAs and tRNAs at high temperature.},
}
@article {pmid11344146,
year = {2001},
author = {Ehrenshaft, M and Daub, ME},
title = {Isolation of PDX2, a second novel gene in the pyridoxine biosynthesis pathway of eukaryotes, archaebacteria, and a subset of eubacteria.},
journal = {Journal of bacteriology},
volume = {183},
number = {11},
pages = {3383-3390},
pmid = {11344146},
issn = {0021-9193},
mesh = {Amino Acid Sequence ; Archaeal Proteins/genetics/metabolism ; Ascomycota/genetics/*metabolism ; Bacillus subtilis/genetics/metabolism ; Bacterial Proteins/genetics/metabolism ; Base Sequence ; Fungal Proteins/genetics/*isolation &amp; purification/metabolism ; Gene Targeting ; Genetic Complementation Test ; Molecular Sequence Data ; Mutation ; Mycobacterium leprae/genetics/metabolism ; Plant Proteins/chemistry/*genetics/metabolism ; Pyridoxine/*biosynthesis/genetics ; Pyrococcus/genetics/metabolism ; Sequence Analysis, DNA ; Sulfolobus/genetics/metabolism ; Transformation, Genetic ; Triticum/genetics/metabolism ; },
abstract = {In this paper we describe the isolation of a second gene in the newly identified pyridoxine biosynthesis pathway of archaebacteria, some eubacteria, fungi, and plants. Although pyridoxine biosynthesis has been thoroughly examined in Escherichia coli, recent characterization of the Cercospora nicotianae biosynthesis gene PDX1 led to the discovery that most organisms contain a pyridoxine synthesis gene not found in E. coli. PDX2 was isolated by a degenerate primer strategy based on conserved sequences of a gene specific to PDX1-containing organisms. The role of PDX2 in pyridoxine biosynthesis was confirmed by complementation of two C. nicotianae pyridoxine auxotrophs not mutant in PDX1. Also, targeted gene replacement of PDX2 in C. nicotianae results in pyridoxine auxotrophy. Comparable to PDX1, PDX2 homologues are not found in any of the organisms with homologues to the E. coli pyridoxine genes, but are found in the same archaebacteria, eubacteria, fungi, and plants that contain PDX1 homologues. PDX2 proteins are less well conserved than their PDX1 counterparts but contain several protein motifs that are conserved throughout all PDX2 proteins.},
}
@article {pmid11322875,
year = {2001},
author = {Madadi-Kahkesh, S and Duin, EC and Heim, S and Albracht, SP and Johnson, MK and Hedderich, R},
title = {A paramagnetic species with unique EPR characteristics in the active site of heterodisulfide reductase from methanogenic archaea.},
journal = {European journal of biochemistry},
volume = {268},
number = {9},
pages = {2566-2577},
doi = {10.1046/j.1432-1327.2001.02141.x},
pmid = {11322875},
issn = {0014-2956},
mesh = {Alkylating Agents/pharmacology ; Amino Acid Sequence ; Base Sequence ; Catalytic Domain ; DNA Primers/genetics ; Electron Spin Resonance Spectroscopy ; Enzyme Inhibitors/pharmacology ; Euryarchaeota/*enzymology/genetics ; Methanobacterium/enzymology/genetics ; Methanosarcina barkeri/enzymology/genetics ; Oxidation-Reduction ; Oxidoreductases/antagonists &amp; inhibitors/*chemistry/genetics/metabolism ; Phosphothreonine/*analogs &amp; derivatives/chemistry ; Protein Subunits ; Recombinant Proteins/chemistry/genetics ; },
abstract = {Heterodisulfide reductase (Hdr) from methanogenic archaea is an iron-sulfur protein that catalyses the reversible reduction of the heterodisulfide (CoM-S-S-CoB) of the methanogenic thiol coenzymes, coenzyme M (H-S-CoM) and coenzyme B (H-S-CoB). In EPR spectroscopic studies with the enzyme from Methanothermobacter marburgensis, we have identified a unique paramagnetic species that is formed upon reaction of the oxidized enzyme with H-S-CoM in the absence of H-S-CoB. This paramagnetic species can be reduced in a one-electron step with a midpoint-potential of -185 mV but not further oxidized. A broadening of the EPR signal in the 57Fe-enriched enzyme indicates that it is at least partially iron based. The g values (gxyz = 2.013, 1.991 and 1.938) and the midpoint potential argue against a conventional [2Fe-2S]+, [3Fe-4S]+, [4Fe-4S]+ or [4Fe-4S]3+ cluster. This species reacts with H-S-CoB to form an EPR silent form. Hence, we propose that only a half reaction is catalysed in the presence of H-S-CoM and that a reaction intermediate is trapped. This reaction intermediate is thought to be a [4Fe-4S]3+ cluster that is coordinated by one of the cysteines of a nearby active-site disulfide or by the sulfur of H-S-CoM. A paramagnetic species with similar EPR properties was also identified in Hdr from Methanosarcina barkeri.},
}
@article {pmid11320123,
year = {2001},
author = {Kim, DJ and Forst, S},
title = {Genomic analysis of the histidine kinase family in bacteria and archaea.},
journal = {Microbiology (Reading, England)},
volume = {147},
number = {Pt 5},
pages = {1197-1212},
doi = {10.1099/00221287-147-5-1197},
pmid = {11320123},
issn = {1350-0872},
mesh = {Amino Acid Sequence ; Archaea/*genetics ; Bacteria/*genetics ; Conserved Sequence ; Evolution, Molecular ; *Genome, Archaeal ; *Genome, Bacterial ; Histidine Kinase ; Molecular Sequence Data ; *Phylogeny ; Protein Kinases/*genetics ; Protein Structure, Tertiary ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; },
abstract = {Two-component signal transduction systems, consisting of histidine kinase (HK) sensors and DNA-binding response regulators, allow bacteria and archaea to respond to diverse environmental stimuli. HKs possess a conserved domain (H-box region) which contains the site of phosphorylation and an ATP-binding kinase domain. In this study, a genomic approach was taken to analyse the HK family in bacteria and archaea. Based on phylogenetic analysis, differences in the sequence and organization of the H-box and kinase domains, and the predicted secondary structure of the H-box region, five major HK types were identified. Of the 336 HKs analysed, 92% could be assigned to one of the five major HK types. The Type I HKs were found predominantly in bacteria while Type II HKs were not prevalent in bacteria but constituted the major type (13 of 15 HKs) in the archaeon Archaeoglobus fulgidus. Type III HKs were generally more prevalent in Gram-positive bacteria and were the major HK type (14 of 15 HKs) in the archaeon Methanobacterium thermoautotrophicum. Type IV HKs represented a minor type found in bacteria. The fifth HK type was composed of the chemosensor HKs, CheA. Several bacterial genomes contained all five HK types. In contrast, archaeal genomes either contained a specific HK type or lacked HKs altogether. These findings suggest that the different HK types originated in bacteria and that specific HK types were acquired in archaea by horizontal gene transfer.},
}
@article {pmid11319120,
year = {2001},
author = {Rudolph, C and Wanner, G and Huber, R},
title = {Natural communities of novel archaea and bacteria growing in cold sulfurous springs with a string-of-pearls-like morphology.},
journal = {Applied and environmental microbiology},
volume = {67},
number = {5},
pages = {2336-2344},
pmid = {11319120},
issn = {0099-2240},
mesh = {Archaea/classification/genetics/*growth &amp; development/ultrastructure ; Bacteria/classification/genetics/*growth &amp; development/ultrastructure ; Cold Temperature ; DNA, Ribosomal/analysis/genetics ; *Ecosystem ; Fresh Water/chemistry/*microbiology ; Genes, rRNA ; In Situ Hybridization, Fluorescence ; Microscopy, Electron, Scanning ; Molecular Sequence Data ; Phylogeny ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Sulfur/chemistry ; },
abstract = {We report the identification of novel archaea living in close association with bacteria in the cold (approximately 10 degrees C) sulfurous marsh water of the Sippenauer Moor near Regensburg, Bavaria, Germany. These microorganisms form a characteristic, macroscopically visible structure, morphologically comparable to a string of pearls. Tiny, whitish globules (the pearls; diameter, about 0.5 to 3.0 mm) are connected to each other by thin, white-colored threads. Fluorescent in situ hybridization (FISH) studies have revealed that the outer part of the pearls is mainly composed of bacteria, with a filamentous bacterium predominating. Internally, archaeal cocci are the predominant microorganisms, with up to 10(7) cells estimated to be present in a single pearl. The archaea appear to be embedded in a polymer of unknown chemical composition. According to FISH and 16S rRNA gene sequence analysis, the archaea are affiliated with the euryarchaeal kingdom. The new euryarchaeal sequence represents a deep phylogenetic branch within the 16S rRNA tree and does not show extensive similarity to any cultivated archaea or to 16S rRNA gene sequences from environmental samples.},
}
@article {pmid11297011,
year = {2001},
author = {Hamana, K and Itoh, T},
title = {Polyamines of the hyperthermophilic archaebacteria belonging to the genera Thermococcus and Methanothermus and two new genera Caldivirga and Palaeococcus.},
journal = {Microbios},
volume = {104},
number = {408},
pages = {105-114},
pmid = {11297011},
issn = {0026-2633},
mesh = {Polyamines/*analysis ; Thermococcus/*chemistry/classification ; },
abstract = {Cellular polyamines of eight new thermophilic archaebacteria were investigated to determine the chemotaxonomic significance of polyamine distribution profiles. Hyperthermoacidophilic Caldivirga maquilingensis belonging to the family Thermoproteaceae of the Crenarchaeota have a unique polyamine profile comprising spermidine, norspermidine and norspermine as the major polyamines. Within the order Thermococcales of the Euryarchaeota, the major polyamines of an extremely thermophilic terrestrial species of Thermococcus, T. zilligii, were spermidine and agmatine, whereas hyperthermophilic submarine species of Thermococcus and hyperthermophilic submarine Palaeococcus ferrophilus contained a quaternary branched penta-amine, N4-bis(aminopropyl)spermidine, as a major polyamine. A hyperthermophilic methanogen, Methanothermus sociabilis, belonging to Euryarchaeota, contained spermidine and spermine as the major polyamine.},
}
@article {pmid11296251,
year = {2001},
author = {Giraldo, R and Diaz-Orejas, R},
title = {Similarities between the DNA replication initiators of Gram-negative bacteria plasmids (RepA) and eukaryotes (Orc4p)/archaea (Cdc6p).},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {98},
number = {9},
pages = {4938-4943},
pmid = {11296251},
issn = {0027-8424},
mesh = {Amino Acid Sequence ; Archaea/*chemistry/genetics ; Cell Cycle Proteins/*chemistry/metabolism ; Chromatin/genetics/metabolism ; *DNA Helicases ; DNA Replication ; DNA-Binding Proteins/*chemistry/metabolism ; *Escherichia coli Proteins ; *Evolution, Molecular ; Gram-Negative Bacteria/*chemistry/genetics ; HSP70 Heat-Shock Proteins/metabolism ; Leucine Zippers ; Models, Molecular ; Molecular Sequence Data ; Origin Recognition Complex ; Phylogeny ; Plasmids/genetics ; Protein Binding ; Protein Folding ; Protein Structure, Tertiary ; Protein Subunits ; Proteins/*chemistry/metabolism ; Pseudomonas/chemistry/genetics ; Replication Origin/genetics ; Saccharomyces cerevisiae/*chemistry/genetics ; *Saccharomyces cerevisiae Proteins ; Sequence Alignment ; *Trans-Activators ; },
abstract = {The proteins responsible for the initiation of DNA replication are thought to be essentially unrelated in bacteria and archaea/eukaryotes. Here we show that RepA, the initiator from the Pseudomonas plasmid pPS10, and the C-terminal domain of ScOrc4p, a subunit of Saccharomyces cerevisiae (Sc) origin recognition complex (ORC), share sequence similarities. Based on biochemical and spectroscopic evidence, these similarities include common structural elements, such as a winged-helix domain and a leucine-zipper dimerization motif. We have also found that ScOrc4p, as previously described for RepA-type initiators, interacts with chaperones of the Hsp70 family both in vitro and in vivo, most probably to regulate the assembly of active ORC. In evolutionary terms, our results are compatible with the recruitment of the same protein module for initiation of DNA replication by the ancestors of present-day Gram-negative bacteria plasmids, archaea, and eukaryotes.},
}
@article {pmid11294844,
year = {2001},
author = {Berg, S and Edman, M and Li, L and Wikström, M and Wieslander, A},
title = {Sequence properties of the 1,2-diacylglycerol 3-glucosyltransferase from Acholeplasma laidlawii membranes. Recognition of a large group of lipid glycosyltransferases in eubacteria and archaea.},
journal = {The Journal of biological chemistry},
volume = {276},
number = {25},
pages = {22056-22063},
doi = {10.1074/jbc.M102576200},
pmid = {11294844},
issn = {0021-9258},
mesh = {Acholeplasma laidlawii/*enzymology ; Amino Acid Sequence ; Base Sequence ; Cell Membrane/enzymology ; Cloning, Molecular ; DNA Primers ; DNA, Complementary ; Glucosyltransferases/chemistry/genetics/*metabolism ; Molecular Sequence Data ; Sequence Homology, Amino Acid ; },
abstract = {Synthesis of the nonbilayer-prone alpha-monoglucosyldiacylglycerol (MGlcDAG) is crucial for bilayer packing properties and the lipid surface charge density in the membrane of Acholeplasma laidlawii. The gene for the responsible, membrane-bound glucosyltransferase (alMGS) (EC) was sequenced and functionally cloned in Escherichia coli, yielding MGlcDAG in the recombinants. Similar amino acid sequences were encoded in the genomes of several Gram-positive bacteria (especially pathogens), thermophiles, archaea, and a few eukaryotes. All of these contained the typical EX(7)E catalytic motif of the CAZy family 4 of alpha-glycosyltransferases. The synthesis of MGlcDAG by a close sequence analog from Streptococcus pneumoniae (spMGS) was verified by polymerase chain reaction cloning, corroborating a connection between sequence and functional similarity for these proteins. However, alMGS and spMGS varied in dependence on anionic phospholipid activators phosphatidylglycerol and cardiolipin, suggesting certain regulatory differences. Fold predictions strongly indicated a similarity for alMGS (and spMGS) with the two-domain structure of the E. coli MurG cell envelope glycosyltransferase and several amphipathic membrane-binding segments in various proteins. On the basis of this structure, the alMGS sequence charge distribution, and anionic phospholipid dependence, a model for the bilayer surface binding and activity is proposed for this regulatory enzyme.},
}
@article {pmid11282650,
year = {2001},
author = {Orphan, VJ and Hinrichs, KU and Ussler, W and Paull, CK and Taylor, LT and Sylva, SP and Hayes, JM and Delong, EF},
title = {Comparative analysis of methane-oxidizing archaea and sulfate-reducing bacteria in anoxic marine sediments.},
journal = {Applied and environmental microbiology},
volume = {67},
number = {4},
pages = {1922-1934},
pmid = {11282650},
issn = {0099-2240},
support = {R21 AG059422/AG/NIA NIH HHS/United States ; },
mesh = {Anaerobiosis ; Archaea/*classification/genetics/metabolism ; DNA, Ribosomal/analysis/genetics ; Geologic Sediments/*microbiology ; In Situ Hybridization, Fluorescence ; Lipids/analysis ; Methane/*metabolism ; Molecular Sequence Data ; Oxidation-Reduction ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; Sequence Analysis, DNA ; Sulfates/*metabolism ; Sulfur-Reducing Bacteria/*classification/genetics/metabolism ; },
abstract = {The oxidation of methane in anoxic marine sediments is thought to be mediated by a consortium of methane-consuming archaea and sulfate-reducing bacteria. In this study, we compared results of rRNA gene (rDNA) surveys and lipid analyses of archaea and bacteria associated with methane seep sediments from several different sites on the Californian continental margin. Two distinct archaeal lineages (ANME-1 and ANME-2), peripherally related to the order Methanosarcinales, were consistently associated with methane seep marine sediments. The same sediments contained abundant (13)C-depleted archaeal lipids, indicating that one or both of these archaeal groups are members of anaerobic methane-oxidizing consortia. (13)C-depleted lipids and the signature 16S rDNAs for these archaeal groups were absent in nearby control sediments. Concurrent surveys of bacterial rDNAs revealed a predominance of delta-proteobacteria, in particular, close relatives of Desulfosarcina variabilis. Biomarker analyses of the same sediments showed bacterial fatty acids with strong (13)C depletion that are likely products of these sulfate-reducing bacteria. Consistent with these observations, whole-cell fluorescent in situ hybridization revealed aggregations of ANME-2 archaea and sulfate-reducing Desulfosarcina and Desulfococcus species. Additionally, the presence of abundant (13)C-depleted ether lipids, presumed to be of bacterial origin but unrelated to ether lipids of members of the order Desulfosarcinales, suggests the participation of additional bacterial groups in the methane-oxidizing process. Although the Desulfosarcinales and ANME-2 consortia appear to participate in the anaerobic oxidation of methane in marine sediments, our data suggest that other bacteria and archaea are also involved in methane oxidation in these environments.},
}
@article {pmid11282647,
year = {2001},
author = {Braker, G and Ayala-del-Río, HL and Devol, AH and Fesefeldt, A and Tiedje, JM},
title = {Community structure of denitrifiers, bacteria, and archaea along redox gradients in Pacific Northwest marine sediments by terminal restriction fragment length polymorphism analysis of amplified nitrite reductase (nirS) and 16S rRNA genes.},
journal = {Applied and environmental microbiology},
volume = {67},
number = {4},
pages = {1893-1901},
pmid = {11282647},
issn = {0099-2240},
mesh = {Archaea/enzymology/*genetics ; Bacteria/enzymology/*genetics ; Ecosystem ; Genes, Archaeal ; Genes, Bacterial ; Genes, rRNA ; Geologic Sediments/*microbiology ; Molecular Sequence Data ; Nitrates/metabolism ; Nitrite Reductases/*genetics ; Nitrites/metabolism ; Oxidation-Reduction ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; Sequence Analysis, DNA ; Washington ; },
abstract = {Steep vertical gradients of oxidants (O(2) and NO(3)(-)) in Puget Sound and Washington continental margin sediments indicate that aerobic respiration and denitrification occur within the top few millimeters to centimeters. To systematically explore the underlying communities of denitrifiers, Bacteria, and Archaea along redox gradients at distant geographic locations, nitrite reductase (nirS) genes and bacterial and archaeal 16S rRNA genes (rDNAs) were PCR amplified and analyzed by terminal restriction fragment length polymorphism (T-RFLP) analysis. The suitablility of T-RFLP analysis for investigating communities of nirS-containing denitrifiers was established by the correspondence of dominant terminal restriction fragments (T-RFs) of nirS to computer-simulated T-RFs of nirS clones. These clones belonged to clusters II, III, and IV from the same cores and were analyzed in a previous study (G. Braker, J. Zhou, L. Wu, A. H. Devol, and J. M. Tiedje, Appl. Environ. Microbiol. 66:2096-2104, 2000). T-RFLP analysis of nirS and bacterial rDNA revealed a high level of functional and phylogenetic diversity, whereas the level of diversity of Archaea was lower. A comparison of T-RFLPs based on the presence or absence of T-RFs and correspondence analysis based on the frequencies and heights of T-RFs allowed us to group sediment samples according to the sampling location and thus clearly distinguish Puget Sound and the Washington margin populations. However, changes in community structure within sediment core sections during the transition from aerobic to anaerobic conditions were minor. Thus, within the top layers of marine sediments, redox gradients seem to result from the differential metabolic activities of populations of similar communities, probably through mixing by marine invertebrates rather than from the development of distinct communities.},
}
@article {pmid11282478,
year = {2001},
author = {Bell, SD and Jackson, SP},
title = {Mechanism and regulation of transcription in archaea.},
journal = {Current opinion in microbiology},
volume = {4},
number = {2},
pages = {208-213},
doi = {10.1016/s1369-5274(00)00190-9},
pmid = {11282478},
issn = {1369-5274},
mesh = {Archaea/*genetics ; Evolution, Molecular ; *Gene Expression Regulation, Archaeal ; Genes, Archaeal/genetics ; Transcription Factors ; },
abstract = {The archaeal basal transcription machinery resembles the core components of the eucaryal RNA polymerase II apparatus. Thus, studies of the archaeal basal machinery over the last few years have shed light on fundamentally conserved aspects of the mechanisms of transcription pre-initiation complex assembly in both eucarya and archaea. Intriguingly, it has become increasingly apparent that regulators of archaeal transcription resemble regulators initially identified in bacteria. The presence of these shared bacterial-archaeal regulators has given insight into the evolution of gene regulatory processes in all three domains of life.},
}
@article {pmid11265486,
year = {2001},
author = {Crowhurst, G and McHarg, J and Littlechild, JA},
title = {Phosphoglycerate kinases from bacteria and archaea.},
journal = {Methods in enzymology},
volume = {331},
number = {},
pages = {90-104},
doi = {10.1016/s0076-6879(01)31049-2},
pmid = {11265486},
issn = {0076-6879},
mesh = {Amino Acid Sequence ; Archaea/enzymology ; *Bacterial Proteins ; Chromatography, Gel/methods ; Chromatography, Ion Exchange/methods ; Cloning, Molecular ; Conserved Sequence ; Crystallization ; Escherichia coli/genetics ; Geobacillus stearothermophilus/*enzymology ; Models, Molecular ; Molecular Sequence Data ; Multienzyme Complexes/*chemistry/isolation &amp; purification ; Phosphoglycerate Kinase/*chemistry/*genetics/isolation &amp; purification ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Recombinant Proteins/chemistry/isolation &amp; purification ; Sequence Alignment ; Sequence Homology, Amino Acid ; Thermotoga maritima/*enzymology/genetics ; Thermus thermophilus/*enzymology/genetics ; Triose-Phosphate Isomerase/*chemistry/isolation &amp; purification ; },
}
@article {pmid11265473,
year = {2001},
author = {Danson, MJ and Hough, DW},
title = {Citrate synthase from hyperthermophilic Archaea.},
journal = {Methods in enzymology},
volume = {331},
number = {},
pages = {3-12},
doi = {10.1016/s0076-6879(01)31042-x},
pmid = {11265473},
issn = {0076-6879},
mesh = {Archaea/*enzymology/genetics ; Chromatography, Affinity/methods ; Citrate (si)-Synthase/chemistry/isolation &amp; purification/*metabolism ; Cloning, Molecular/methods ; Enzyme Stability ; Hot Temperature ; Recombinant Proteins/isolation &amp; purification/metabolism ; Thermodynamics ; },
}
@article {pmid11250035,
year = {2001},
author = {Amend, JP and Shock, EL},
title = {Energetics of overall metabolic reactions of thermophilic and hyperthermophilic Archaea and bacteria.},
journal = {FEMS microbiology reviews},
volume = {25},
number = {2},
pages = {175-243},
doi = {10.1111/j.1574-6976.2001.tb00576.x},
pmid = {11250035},
issn = {0168-6445},
mesh = {Archaea/*metabolism ; Bacteria/*metabolism ; *Energy Metabolism ; Environmental Microbiology ; Models, Chemical ; Oxidation-Reduction ; Temperature ; Thermodynamics ; },
abstract = {Thermophilic and hyperthermophilic Archaea and Bacteria have been isolated from marine hydrothermal systems, heated sediments, continental solfataras, hot springs, water heaters, and industrial waste. They catalyze a tremendous array of widely varying metabolic processes. As determined in the laboratory, electron donors in thermophilic and hyperthermophilic microbial redox reactions include H2, Fe(2+), H2S, S, S2O3(2-), S4O6(2-), sulfide minerals, CH4, various mono-, di-, and hydroxy-carboxylic acids, alcohols, amino acids, and complex organic substrates; electron acceptors include O2, Fe(3+), CO2, CO, NO3(-), NO2(-), NO, N2O, SO4(2-), SO3(2-), S2O3(2-), and S. Although many assimilatory and dissimilatory metabolic reactions have been identified for these groups of microorganisms, little attention has been paid to the energetics of these reactions. In this review, standard molal Gibbs free energies (DeltaGr(0)) as a function of temperature to 200 degrees C are tabulated for 370 organic and inorganic redox, disproportionation, dissociation, hydrolysis, and solubility reactions directly or indirectly involved in microbial metabolism. To calculate values of DeltaGr(0) for these and countless other reactions, the apparent standard molal Gibbs free energies of formation (DeltaG(0)) at temperatures to 200 degrees C are given for 307 solids, liquids, gases, and aqueous solutes. It is shown that values of DeltaGr(0) for many microbially mediated reactions are highly temperature dependent, and that adopting values determined at 25 degrees C for systems at elevated temperatures introduces significant and unnecessary errors. The metabolic processes considered here involve compounds that belong to the following chemical systems: H-O, H-O-N, H-O-S, H-O-N-S, H-O-C(inorganic), H-O-C, H-O-N-C, H-O-S-C, H-O-N-S-C(amino acids), H-O-S-C-metals/minerals, and H-O-P. For four metabolic reactions of particular interest in thermophily and hyperthermophily (knallgas reaction, anaerobic sulfur and nitrate reduction, and autotrophic methanogenesis), values of the overall Gibbs free energy (DeltaGr) as a function of temperature are calculated for a wide range of chemical compositions likely to be present in near-surface and deep hydrothermal and geothermal systems.},
}
@article {pmid11248186,
year = {2001},
author = {Gottschalk, G and Thauer, RK},
title = {The Na(+)-translocating methyltransferase complex from methanogenic archaea.},
journal = {Biochimica et biophysica acta},
volume = {1505},
number = {1},
pages = {28-36},
doi = {10.1016/s0005-2728(00)00274-7},
pmid = {11248186},
issn = {0006-3002},
mesh = {Amino Acid Sequence ; *Archaeal Proteins ; Bacterial Proteins/*metabolism ; Cations, Monovalent ; Cell Membrane/enzymology ; Corrinoids ; Euryarchaeota/*enzymology ; Methane/metabolism ; Methyltransferases/chemistry/*metabolism ; Models, Molecular ; Molecular Sequence Data ; Molecular Structure ; Multienzyme Complexes/chemistry/genetics/*metabolism ; Porphyrins/chemistry ; Protein Conformation ; Sodium/*metabolism ; },
abstract = {Methanogenic archaea are dependent on sodium ions for methane formation. A sodium ion-dependent step has been shown to be methyl transfer from N(5)-methyltetrahydromethanopterin to coenzyme M. This exergonic reaction (DeltaG degrees '=-30 kJ/mol) is catalyzed by a Na(+)-translocating membrane-associated multienzyme complex composed of eight different subunits, MtrA-H. Subunit MtrA harbors a cob(I)amide prosthetic group which is methylated and demethylated in the catalytic cycle, demethylation being sodium ion-dependent. Based on the finding that in the cob(II)amide oxidation state the corrinoid is bound in a base-off/His-on configuration it is proposed that methyl transfer from MtrA to coenzyme M is associated with a conformational change of the protein and that this change drives the electrogenic translocation of the sodium ions.},
}
@article {pmid11239791,
year = {2001},
author = {Eichler, J and Moll, R},
title = {The signal recognition particle of Archaea.},
journal = {Trends in microbiology},
volume = {9},
number = {3},
pages = {130-136},
doi = {10.1016/s0966-842x(01)01954-0},
pmid = {11239791},
issn = {0966-842X},
mesh = {Amino Acid Sequence ; Animals ; Archaea/*metabolism ; Cell Membrane/metabolism ; Molecular Sequence Data ; Protein Biosynthesis ; Signal Recognition Particle/chemistry/genetics/*metabolism ; },
abstract = {It is becoming increasingly clear that similarities exist in the manner in which extracytoplasmic proteins are targeted to complexes responsible for translocating these proteins across membranes in each of the three domains of life. In Eukarya and Bacteria, the signal recognition particle (SRP) directs nascent polypeptides to membrane-embedded translocation sites. In Archaea, the SRP protein targeting pathway apparently represents an intermediate between the bacterial and eukaryal systems. Understanding the archaeal SRP pathway could therefore reveal universal aspects of targeting not detected in current comparisons of the eukaryal and bacterial systems while possibly identifying aspects of the process either not previously reported or unique to Archaea.},
}
@article {pmid11230537,
year = {2001},
author = {Nesbo, CL and L'Haridon, S and Stetter, KO and Doolittle, WF},
title = {Phylogenetic analyses of two "archaeal" genes in thermotoga maritima reveal multiple transfers between archaea and bacteria.},
journal = {Molecular biology and evolution},
volume = {18},
number = {3},
pages = {362-375},
doi = {10.1093/oxfordjournals.molbev.a003812},
pmid = {11230537},
issn = {0737-4038},
mesh = {Bacteria/*genetics ; Base Sequence ; DNA Primers ; *Gene Transfer, Horizontal ; *Genes, Archaeal ; Likelihood Functions ; Molecular Sequence Data ; *Phylogeny ; RNA, Ribosomal/genetics ; Sequence Homology, Nucleic Acid ; Thermotoga maritima/*genetics ; },
abstract = {The genome sequence of Thermotoga maritima revealed that 24% of its open reading frames (ORFs) showed the highest similarity scores to archaeal genes in BLAST analyses. Here we screened 16 strains from the genus Thermotoga and other related Thermotogales for the occurrence of two of these "archaeal" genes: the gene encoding the large subunit of glutamate synthase (gltB) and the myo-inositol 1P synthase gene (ino1). Both genes were restricted to the Thermotoga species within the Thermotogales. The distribution of the two genes, along with results from phylogenetic analyses, showed that they were acquired from Archaea during the divergence of the Thermotogales. Database searches revealed that three other bacteria-Dehalococcoides ethenogenes, Sinorhizobium meliloti, and Clostridium difficile-possess archaeal-type gltBs, and the phylogenetic analyses confirmed at least two lateral gene transfer (LGT) events between Bacteria and Archaea. These LGT events were also strongly supported by gene structure data, as the three domains in bacterial-type gltB are homologous to three independent ORFs in Archaea and Bacteria with archaeal-type gltBs. The ino1 gene has a scattered distribution among Bacteria, and apart from the Thermotoga strains it is found only in Aquifex aeolicus, D. ethenogenes, and some high-G+C Gram-positive bacteria. Phylogenetic analysis of the ino1 sequences revealed three highly supported prokaryotic clades, all containing a mixture of archaeal and bacterial sequences, and suggested that all bacterial ino1 genes had been recruited from archaeal donors. The Thermotoga strains and A. aeolicus acquired this gene independently from different archaeal species. Although transfer of genes from hyperthermophilic Archaea may have facilitated the evolution of bacterial hyperthermophily, between-domain transfers also affect mesophilic species. For hyperthermophiles, we hypothesize that LGT may be as much a consequence as the cause of adaptation to hyperthermophily.},
}
@article {pmid11208800,
year = {2001},
author = {Chung, YJ and Krueger, C and Metzgar, D and Saier, MH},
title = {Size comparisons among integral membrane transport protein homologues in bacteria, Archaea, and Eucarya.},
journal = {Journal of bacteriology},
volume = {183},
number = {3},
pages = {1012-1021},
pmid = {11208800},
issn = {0021-9193},
support = {R01 GM055434/GM/NIGMS NIH HHS/United States ; 2RO1 AI14176/AI/NIAID NIH HHS/United States ; 9RO1 GM55434/GM/NIGMS NIH HHS/United States ; },
mesh = {ATP-Binding Cassette Transporters/chemistry ; *Archaea ; *Bacteria ; Biological Transport ; Carrier Proteins/*chemistry/genetics ; Cytoplasm/enzymology ; *Eukaryotic Cells ; *Evolution, Molecular ; Ion Channels/*chemistry/genetics ; Membrane Proteins/*chemistry/genetics ; Particle Size ; Sequence Alignment ; Sequence Homology ; },
abstract = {Integral membrane proteins from over 20 ubiquitous families of channels, secondary carriers, and primary active transporters were analyzed for average size differences between homologues from the three domains of life: Bacteria, Archaea, and Eucarya. The results showed that while eucaryotic homologues are consistently larger than their bacterial counterparts, archaeal homologues are significantly smaller. These size differences proved to be due primarily to variations in the sizes of hydrophilic domains localized to the N termini, the C termini, or specific loops between transmembrane alpha-helical spanners, depending on the family. Within the Eucarya domain, plant homologues proved to be substantially smaller than their animal and fungal counterparts. By contrast, extracytoplasmic receptors of ABC-type uptake systems in Archaea proved to be larger on average than those of their bacterial homologues, while cytoplasmic enzymes from different organisms exhibited little or no significant size differences. These observations presumably reflect evolutionary pressure and molecular mechanisms that must have been operative since these groups of organisms diverged from each other.},
}
@article {pmid11207731,
year = {1999},
author = {Lehmann-Richter, S and Grosskopf, R and Liesack, W and Frenzel, P and Conrad, R},
title = {Methanogenic archaea and CO2-dependent methanogenesis on washed rice roots.},
journal = {Environmental microbiology},
volume = {1},
number = {2},
pages = {159-166},
doi = {10.1046/j.1462-2920.1999.00019.x},
pmid = {11207731},
issn = {1462-2912},
mesh = {Acetates/metabolism ; Carbon Dioxide/*metabolism ; Culture Media ; Euryarchaeota/*classification/genetics/*metabolism ; Genes, rRNA ; Methane/*metabolism ; Molecular Sequence Data ; Oryza/*microbiology ; Plant Roots/*microbiology ; RNA, Ribosomal/genetics ; Sequence Analysis, DNA ; },
abstract = {Washed excised roots of rice (Oryza sativa) immediately started to produce CH4 when they were incubated in phosphate buffer under anoxic conditions (N2 atmosphere), with initial rates varying between 2 and 70nmolh(-1)g(-1) dry weight of root material (mean +/- SE: 20.3 +/- 5.9 nmol h(-1) g(-1) dry weight; n = 18). Production of CH4 continued for at least 500 h, with rates usually decreasing slowly. CH4 production was not significantly affected by methyl fluoride, an inhibitor of acetoclastic methanogenesis. Less than 0.5% of added [2-14C]-acetate was converted to 14CH4, and conversion of 14CO2 to 14CH4 indicated that CH4 was almost exclusively produced from CO2. Occasionally, however, especially when the roots were incubated without additional buffer, CH4 production started to accelerate after about 200h reaching rates of > 100 nmol h(-1) g(-1) dry weight. Methyl fluoride inhibited methanogenesis by more than 20% only in these cases, and the conversion of 14CO2 to 14CH4 decreased. These results indicate that CO2-dependent rather than acetoclastic methanogenesis was primarily responsible for CH4 production in anoxically incubated rice roots. Determination of most probable numbers of methanogens on washed roots showed highest numbers (10(6)g(-1) dry roots) on H2 and ethanol, i.e. substrates that support CH4 production from CO2. Numbers on acetate (10(5) g(-1) dry roots) and methanol (10(4)g(-1) dry roots) were lower. Methanogenic consortia enriched on H2 and ethanol were characterized phylogenetically by comparative sequence analysis of archaeal small-subunit (SSU) ribosomal RNA-encoding genes (rDNA). These sequences showed a high similarity to SSU rDNA clones that had been obtained previously by direct extraction of total DNA from washed rice roots. The SSU rDNA sequences recovered from the H2/CO2-using consortium either belonged to a novel lineage of methanogens that grouped within the phylogenetic radiation of the Methanosarcinales and Methanomicrobiales or were affiliated with Methanobacterium bryantii. SSU rDNA sequences retrieved from the ethanol-using consortium either grouped within the genus Methanosarcina or belonged to another novel lineage within the phylogenetic radiation of the Methanosarcinales and Methanomicrobiales. Cultured organisms belonging to either of the two novel lineages have not been reported yet.},
}
@article {pmid11175755,
year = {2001},
author = {Horiike, T and Hamada, K and Kanaya, S and Shinozawa, T},
title = {Origin of eukaryotic cell nuclei by symbiosis of Archaea in Bacteria is revealed by homology-hit analysis.},
journal = {Nature cell biology},
volume = {3},
number = {2},
pages = {210-214},
doi = {10.1038/35055129},
pmid = {11175755},
issn = {1465-7392},
mesh = {Archaea/*genetics/physiology ; Bacteria/*genetics ; Bacterial Physiological Phenomena ; Cell Nucleus/*genetics/physiology ; DNA/genetics ; Databases, Factual ; *Evolution, Molecular ; Models, Biological ; Open Reading Frames/*genetics ; Sequence Homology ; *Symbiosis ; Yeasts/*genetics/physiology ; },
abstract = {The origin of eukaryotic cell nuclei by symbiosis of Archaea in Bacteria was proposed on the basis of the phylogenetic topologies of genes. However, it was not possible to conclude whether or not the genes involved were authentic representative genes. Furthermore, using the BLAST and FASTA programs, the similarity of open reading frame (ORF) groups between three domains (Eukarya, Archaea and Bacteria) was estimated at one threshold. Therefore, their similarities at other thresholds could not be clarified. Here we use our newly developed 'homology-hit analysis' method, which uses multiple thresholds, to determine the origin of the nucleus. We removed mitochondria-related ORFs from yeast ORFs, and determined the number of yeast orthologous ORFs in each functional category to the ORFs in six Archaea and nine Bacteria at several thresholds (E-values) using the BLAST. Our results indicate that yeast ORFs related to the nucleus may share their origins with archaeal ORFs, whereas ORFs that are related to the cytoplasm may share their origins with bacterial ORFs. Our results thus strongly support the idea of nucleus symbiosis.},
}
@article {pmid11171552,
year = {2001},
author = {Macario, AJ and Conway De Macario, E},
title = {The molecular chaperone system and other anti-stress mechanisms in archaea.},
journal = {Frontiers in bioscience : a journal and virtual library},
volume = {6},
number = {},
pages = {D262-83},
doi = {10.2741/macario},
pmid = {11171552},
issn = {1093-9946},
mesh = {Acute-Phase Proteins/metabolism ; Adaptation, Physiological ; Animals ; *Antigens, Neoplasm ; Apoptosis/physiology ; Archaea/cytology/*physiology ; *Bacterial Proteins ; Biofilms ; *Biomarkers, Tumor ; Bioreactors ; Carrier Proteins/metabolism ; Cell Differentiation ; DNA-Binding Proteins/metabolism ; Drosophila Proteins ; *Escherichia coli Proteins ; Extracellular Matrix/physiology ; Fungal Proteins/metabolism ; Heat-Shock Proteins/*metabolism ; Janus Kinases ; *Lectins, C-Type ; Molecular Chaperones/*metabolism ; Pancreatitis-Associated Proteins ; Peptidylprolyl Isomerase/metabolism ; Prokaryotic Cells/metabolism ; Protein-Tyrosine Kinases/metabolism ; Stress, Mechanical ; Transcription Factors/metabolism ; },
abstract = {This article presents a brief review of stressors, their cellular and intracellular targets, stress proteins, molecular chaperones, and other anti-stress mechanisms. New data are reported on cochaperones and multicellular structures in archaea. The molecular chaperoning systems of bacteria and eukaryotes have been studied for many years and are relatively well known in terms of their components and mechanisms of action, although many details remain to be elucidated and almost certainly other components will be discovered in the future. By comparison, the molecular chaperoning system of archaea is still unexplored. Since archaea have some molecular genetic and physiologic features similar to those of bacteria and some resembling those of eukaryotes, extrapolation from what is known of organisms from these two phylogenetic domains to archaeal species is unwarranted. For example, the components of the molecular chaperone machine, Hsp70(DnaK), Hsp40(DnaJ), and GrpE, in the archaeal species that have it, are closely related to bacterial counterparts, whereas the archaeal chaperonins are like the eukaryotic equivalents. Furthermore, many archaeal species lack the chaperone machine, in contrast to bacteria and eukaryotes that have it without any known exception. A search for the cochaperones trigger factor, Hop, Hip, BAG-1, and NAC in archaeal genomes demonstrated no conserved equivalents, but two families of archaeal molecules were identified that might be related to NAC and Hop, respectively. Multicellular structures with a single species such as packet and lamina are formed by Methanosarcina species, among which the best studied is M. mazeii. Multispecies multicellular structures are formed by a variety of archaeal organisms, which are either flat (biofilm) or globular (granule) and constitute a functional association or consortium. Details of morphology, formation, and internal organization are described for representative examples of multicellular structures. These may be seen as the result of primitive histogenesis reflecting primeval mechanisms of differentiation-development that might have evolved driven by environmental stressors. Cells in these complex threedimensional arrangements are not only positioned so they can interact with each other for more efficient functioning as in a tissue or organ, but are also protected from stressors. Single cells lacking the protective shield of other cells packed together with intercellular connective material, which is typical of multicellular structures, are directly exposed to environmental stressors and, thus, are at a disadvantage from the evolutionary standpoint. It seems reasonable to argue that differentiation-development leading to histogenesis might have arisen in primeval times as a consequence of the harsh conditions that primitive life forms had to endure, and that the ability to form tissue-like structures was a primary characteristic that ensured positive selection.},
}
@article {pmid11166994,
year = {2001},
author = {Ruppert, C and Schmid, R and Hedderich, R and Müller, V},
title = {Selective extraction of subunit D of the Na(+)-translocating methyltransferase and subunit c of the A(1)A(0) ATPase from the cytoplasmic membrane of methanogenic archaea by chloroform/methanol and characterization of subunit c of Methanothermobacter thermoautotrophicus as a 16-kDa proteolipid.},
journal = {FEMS microbiology letters},
volume = {195},
number = {1},
pages = {47-51},
doi = {10.1111/j.1574-6968.2001.tb10496.x},
pmid = {11166994},
issn = {0378-1097},
mesh = {Adenosine Triphosphatases/*chemistry/isolation &amp; purification ; Amino Acid Sequence ; Archaeal Proteins/chemistry/isolation &amp; purification ; Chloroform ; Membrane Proteins/*chemistry/isolation &amp; purification ; Methanobacteriaceae/chemistry/classification/*enzymology ; Methanol ; Methanosarcina/chemistry/classification/*enzymology ; Methyltransferases/*chemistry/isolation &amp; purification ; Molecular Sequence Data ; Protein Subunits ; Proteolipids/*chemistry ; },
abstract = {Chloroform/methanol was applied to cytoplasmic membranes of the thermophilic methanogens Methanothermobacter thermoautotrophicus and Methanothermobacter marburgensis as well as to the mesophile Methanosarcina mazei Gö1. In any case, the chloroform/methanol extraction yielded only two proteins, subunit D (MtrD) of the Na(+)-translocating methyltetrahydromethanopterin:coenzyme M methyltransferase and the proteolipid of the A(1)A(0) ATPase. Both polypeptides are assumed to be directly involved in ion translocation in their respective enzymes, but have not been studied in detail due to lack of simple isolation procedures. The rapid and selective isolation by chloroform/methanol offers a new way to obtain the large quantities of material required for biochemical analyses. As a first result, molecular and biochemical data suggest that the proteolipid from M. thermoautotrophicus is a duplication of the 8-kDa proteolipid usually present in other archaea, but it retained the conserved glutamate involved in proton translocation in every copy. This is the first 16-kDa proteolipid found in archaea.},
}
@article {pmid11159397,
year = {2001},
author = {Kloda, A and Martinac, B},
title = {Molecular identification of a mechanosensitive channel in archaea.},
journal = {Biophysical journal},
volume = {80},
number = {1},
pages = {229-240},
pmid = {11159397},
issn = {0006-3495},
mesh = {Amino Acid Sequence ; Archaea/*genetics/physiology ; Archaeal Proteins/chemistry/*genetics/physiology ; Bacterial Proteins/chemistry/genetics/physiology ; Biophysical Phenomena ; Biophysics ; Conserved Sequence ; Escherichia coli/genetics/growth &amp; development/physiology ; *Escherichia coli Proteins ; Evolution, Molecular ; Ion Channels/chemistry/*genetics/physiology ; Methanococcus/genetics/physiology ; Molecular Sequence Data ; Phylogeny ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Recombinant Proteins/chemistry/genetics ; Sequence Alignment ; Sequence Homology, Amino Acid ; },
abstract = {The TM1 domain of the large conductance mechanosensitive (MS) channel of Escherichia coli was used as a genetic probe to search the genomic database of the archaeon Methanoccoccus jannashii for MscL homologs. We report that the hypothetical protein MJ0170 of M. jannashii exhibited 38.5% sequence identity with the TM1 domain of Eco-MscL. Moreover, MJ0170 was found to be a conserved homolog of MscS, the second type of E. coli MS channel encoded by the yggB gene. Furthermore, we identified a cluster of charged residues KIKEE in the C-terminus of MJ0170 that strikingly resembled the charged C-terminal amino acid cluster present in Eco-MscL (RKKEE). We cloned and expressed MJ0170 in E. coli, which when reconstituted into liposomes or expressed in the cell membrane of giant E. coli spheroplasts, exhibited similar activity to the bacterial MS channels. Our study suggests that the M. jannashii MS channel and its homologs evolved as a result of gene duplication of the ancestral MscL-like molecule with the TM1 domain remaining the most conserved structural motif among prokaryotic MS channels.},
}
@article {pmid10754577,
year = {2000},
author = {Grogan, DW},
title = {The question of DNA repair in hyperthermophilic archaea.},
journal = {Trends in microbiology},
volume = {8},
number = {4},
pages = {180-185},
doi = {10.1016/s0966-842x(00)01729-7},
pmid = {10754577},
issn = {0966-842X},
mesh = {Archaea/*genetics ; DNA Damage/genetics ; DNA Repair/*genetics ; DNA, Archaeal/genetics ; Genome, Archaeal ; *Hot Temperature ; },
abstract = {Hyperthermophilic archaea grow at temperatures that destabilize the primary structure of DNA and in evolutionary terms they are highly divergent from other well studied microorganisms. These prokaryotes should therefore require DNA damage repair to be unusually effective, and could employ novel mechanisms for this repair. Recent genome sequence analyses and biochemical and genetic assays suggest a distribution of DNA repair strategies that raises intriguing questions for future study.},
}
@article {pmid11155985,
year = {2000},
author = {Arab, H and Völker, H and Thomm, M},
title = {Thermococcus aegaeicus sp. nov. and Staphylothermus hellenicus sp. nov., two novel hyperthermophilic archaea isolated from geothermally heated vents off Palaeochori Bay, Milos, Greece.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {50 Pt 6},
number = {},
pages = {2101-2108},
doi = {10.1099/00207713-50-6-2101},
pmid = {11155985},
issn = {1466-5026},
mesh = {Base Composition ; DNA, Ribosomal/analysis ; Desulfurococcaceae/*classification/genetics/growth &amp; development/isolation &amp; purification ; Greece ; Molecular Sequence Data ; Nucleic Acid Hybridization ; Phenotype ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; Sequence Analysis, DNA ; *Temperature ; Thermococcus/*classification/genetics/growth &amp; development/isolation &amp; purification ; },
abstract = {Two novel, hyperthermophilic, anaerobic, heterotrophic archaea were isolated from shallow hydrothermal vents off Palaeochori Bay, Milos, Greece. Strain P5T (BK17S6-3-b2T) is an irregular coccus, with a single polar flagellum, growing optimally at 90 degrees C, pH 6 and 2% NaCl. The DNA G+C content was 45 mol%. Due to its morphology, phylogenetic analyses based on 16S rRNA gene sequencing, DNA-DNA hybridization experiments, physiological properties and nutritional features, this strain represents a new species within the genus Thermococcus for which the name Thermococcus aegaeicus is proposed. The type strain is P5T (= DSM 12767T = JCM 10828T). Strain p8T (BK20S6-10-b1T) is a coccus that forms aggregates. It grew optimally at 85 degrees C, pH 6 and 3% NaCl. The DNA G+C content was 38 mol%. Physiological properties and sequence analysis of the 165 rRNA gene, as well as DNA-DNA hybridization experiments, indicate that this strain is a new species belonging to the genus Staphylothermus for which the name Staphylothermus hellenicus is proposed. The type strain is P8T (= DSM 12710T = JCM 10830T).},
}
@article {pmid11155984,
year = {2000},
author = {Huber, H and Burggraf, S and Mayer, T and Wyschkony, I and Rachel, R and Stetter, KO},
title = {Ignicoccus gen. nov., a novel genus of hyperthermophilic, chemolithoautotrophic Archaea, represented by two new species, Ignicoccus islandicus sp nov and Ignicoccus pacificus sp nov. and Ignicoccus pacificus sp. nov.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {50 Pt 6},
number = {},
pages = {2093-2100},
doi = {10.1099/00207713-50-6-2093},
pmid = {11155984},
issn = {1466-5026},
mesh = {Base Composition ; Culture Media ; DNA, Ribosomal/analysis ; Desulfurococcaceae/*classification/genetics/*growth &amp; development ; Microscopy, Electron ; Molecular Sequence Data ; Nucleic Acid Hybridization ; Oxidation-Reduction ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; Sequence Analysis, DNA ; Sulfur/*metabolism ; *Temperature ; },
abstract = {Two species of novel, chemolithoautotrophic, sulfidogenic micro-organisms were isolated from submarine hydrothermal systems in the Atlantic (at the Kolbeinsey Ridge north of Iceland) and in the Pacific (at 9 degrees N, 104 degrees W). The coccoid cells grew within a temperature range of 70-98 degrees C (optimum around 90 degrees C). They gained energy by reduction of elemental sulfur using molecular hydrogen as the electron donor. 165 rDNA-based sequence comparisons revealed that the organisms are members of the crenarchaeal branch of the Archaea. They represent a new, deeply branching lineage within the family of the Desulfurococcaceae. In DNA-DNA hybridization experiments both strains exhibited low levels of hybridization to each other and to further representatives of this family. Therefore, they represent a new genus, for which the name Ignicoccus gen. nov. is proposed. At present it consists of two new species, Ignicoccus islandicus sp. nov. (type strain is Kol8T = DSM 13165T = ATCC 700957T) and Ignicoccus pacificus sp. nov. (type strain is LPC33T = DSM 13166T = ATCC 700958T).},
}
@article {pmid11139074,
year = {2000},
author = {Cavicchioli, R and Thomas, T and Curmi, PM},
title = {Cold stress response in Archaea.},
journal = {Extremophiles : life under extreme conditions},
volume = {4},
number = {6},
pages = {321-331},
doi = {10.1007/s007920070001},
pmid = {11139074},
issn = {1431-0651},
mesh = {*Adaptation, Physiological ; Antarctic Regions ; Archaea/genetics/*physiology ; Base Sequence ; *Cold Temperature ; DNA, Archaeal/genetics ; RNA, Archaeal/genetics ; Sequence Homology, Nucleic Acid ; },
abstract = {We live on a cold planet where more than 80% of the biosphere is permanently below 5 degrees C, and yet comparatively little is known about the genetics and physiology of the microorganisms inhabiting these environments. Based on molecular probe and sequencing studies, it is clear that Archaea are numerically abundant in diverse low-temperature environments throughout the globe. In addition, non-low-temperature-adapted Archaea are commonly exposed to sudden decreases in temperature, as are other microorganisms, animals, and plants. Considering their ubiquity in nature, it is perhaps surprising to find that there is such a lack of knowledge regarding low-temperature adaptation mechanisms in Archaea, particularly in comparison to what is known about archaeal thermophiles and hyperthermophiles and responses to heat shock. This review covers what is presently known about adaptation to cold shock and growth at low temperature, with a particular focus on Antarctic Archaea. The review highlights the similarities and differences that exist between Archaea and Bacteria and eukaryotes, and addresses the potentially important role that protein synthesis plays in adaptation to the cold. By reviewing the present state of the field, a number of important areas for future research are identified.},
}
@article {pmid11137601,
year = {2001},
author = {Leclerc, M and Delbes, C and Moletta, R and Godon, J},
title = {Single strand conformation polymorphism monitoring of 16S rDNA Archaea during start-up of an anaerobic digester.},
journal = {FEMS microbiology ecology},
volume = {34},
number = {3},
pages = {213-220},
doi = {10.1111/j.1574-6941.2001.tb00772.x},
pmid = {11137601},
issn = {1574-6941},
abstract = {A laboratory-scale continuously mixed anaerobic digester was inoculated with a mix of anaerobic sludge and fed with glucose. The start-up strategy was progressive and chemical analyses were done to evaluate digester performance from day 1 to day 107. In parallel, Archaeal community dynamics were monitored by SSCP analysis of the V3 region of 16S rDNA genes and further characterized by partial sequencing of 16S rDNA genes. At day 1 the inoculum contained at least five distinct Archaeal peaks close to known methanogenic species. The dominant peak was very close to Methanosaeta concilli, the remaining species being members of the Methanobacteriales and Methanomicrobiales. A rapid shift of the Archaeal population was observed during the experiment. At day 21 Methanobacterium formicicum, which was not detected at day 1, became the dominant methanogenic species in the bioreactor and remained so until the end of the experiment.},
}
@article {pmid11115105,
year = {2000},
author = {Diruggiero, J and Dunn, D and Maeder, DL and Holley-Shanks, R and Chatard, J and Horlacher, R and Robb, FT and Boos, W and Weiss, RB},
title = {Evidence of recent lateral gene transfer among hyperthermophilic archaea.},
journal = {Molecular microbiology},
volume = {38},
number = {4},
pages = {684-693},
doi = {10.1046/j.1365-2958.2000.02161.x},
pmid = {11115105},
issn = {0950-382X},
mesh = {Amino Acid Sequence ; DNA Transposable Elements/genetics ; *Gene Transfer, Horizontal ; *Genes, Archaeal ; Genome, Archaeal ; Molecular Sequence Data ; Pyrococcus furiosus/*genetics ; Sequence Alignment ; Thermococcus/*genetics ; },
abstract = {A total of 153 nucleotide differences were found over a contiguous 16 kb region between two hyperthermophilic Archaea, Pyrococcus furiosus and Thermococcus litoralis. The 16 kb region in P. furiosus is flanked by insertion sequence (IS) elements with inverted and direct repeats. Both IS elements contain a single open reading frame (ORF) encoding a putative protein of 233 amino acids identified as a transposase. This 16 kb region has the features of a typical bacterial composite transposon and represents a possible mechanism for lateral gene transfer between Archaea or possibly between Archaea and Bacteria. A total of 23 homologous IS elements was found in the genome sequence of P. furiosus, whereas no full-length IS elements were identified in the genomes of Pyrococcus abyssi and Pyrococcus horikoshii. Only one IS element was found in T. litoralis. In P. furiosus and T. litoralis, the 16 kb region contains an ABC transport system for maltose and trehalose that was characterized biochemically for T. litoralis. Regulation of expression studies showed that the malE gene, located on the transposon, and the encoded trehalose/maltose-binding protein (TMBP) are induced in the presence of maltose and trehalose in both P. furiosus and T. litoralis. The implications of transposition as a mechanism for lateral gene transfer among Archaea are discussed.},
}
@article {pmid11108017,
year = {2000},
author = {Arahal, DR and Gutiérrez, MC and Volcani, BE and Ventosa, A},
title = {Taxonomic analysis of extremely halophilic archaea isolated from 56-years-old dead sea brine samples.},
journal = {Systematic and applied microbiology},
volume = {23},
number = {3},
pages = {376-385},
doi = {10.1016/S0723-2020(00)80068-5},
pmid = {11108017},
issn = {0723-2020},
mesh = {Archives ; Bacterial Typing Techniques ; Base Composition ; DNA, Bacterial ; Haloarcula/classification ; Halobacteriaceae/*classification ; Halobacterium/classification ; Haloferax/classification ; Nucleic Acid Hybridization ; *Salts ; *Water Microbiology ; },
abstract = {A taxonomic study comprising both phenotypic and genotypic characterization, has been carried out on a total of 158 extremely halophilic aerobic archaeal strains. These strains were isolated from enrichments prepared from Dead Sea water samples dating from 1936 that were collected by B. E. Volcani for the demonstration of microbial life in the Dead Sea. The isolates were examined for 126 morphological, physiological, biochemical and nutritional tests. Numerical analysis of the data, by using the S(J) coefficient and UPGMA clustering method, showed that the isolates clustered into six phenons. Twenty-two out of the 158 strains used in this study were characterized previously (ARAHAL et al., 1996) and were placed into five phenotypic groups. The genotypic study included both the determination of the guanineplus-cytosine content of the DNA and DNA-DNA hybridization studies. For this purpose, representative strains from the six phenons were chosen. These groups were found to represent some members of three different genera - Haloarcula (phenons A, B, and C), Haloferax (phenons D and E) and Halobacterium (phenon F) - of the family Halobacteriaceae, some of them never reported to occur in the Dead Sea, such as Haloarcula hispanica, while Haloferax volcanii (phenons D and E) was described in the Dead Sea by studies carried out several decades later than Volcani's work.},
}
@article {pmid11108007,
year = {2000},
author = {Huber, R and Sacher, M and Vollmann, A and Huber, H and Rose, D},
title = {Respiration of arsenate and selenate by hyperthermophilic archaea.},
journal = {Systematic and applied microbiology},
volume = {23},
number = {3},
pages = {305-314},
doi = {10.1016/S0723-2020(00)80058-2},
pmid = {11108007},
issn = {0723-2020},
mesh = {Anaerobiosis ; Arsenates/*metabolism ; Arsenicals/metabolism ; Base Composition ; DNA, Ribosomal ; Genes, Archaeal ; Geological Phenomena ; Geology ; Hot Temperature ; Molecular Sequence Data ; Oxidation-Reduction ; Phylogeny ; RNA, Ribosomal, 16S ; Selenic Acid ; Selenium Compounds/*metabolism ; Sulfides/metabolism ; Thermoproteaceae/classification/cytology/isolation &amp; purification/*metabolism ; },
abstract = {A novel, strictly anaerobic, hyperthermophilic, facultative organotrophic archaeon was isolated from a hot spring at Pisciarelli Solfatara, Naples, Italy. The rod-shaped cells grew chemolithoautotrophically with carbon dioxide as carbon source, hydrogen as electron donor and arsenate, thiosulfate or elemental sulfur as electron acceptor. H2S was formed from sulfur or thiosulfate, arsenite from arsenate. Organotrophically, the new isolate grew optimally in the presence of an inorganic electron acceptor like sulfur, selenate or arsenate. Cultures, grown on arsenate and thiosulfate or arsenate and L-cysteine, precipitated realgar (As2S2). During growth on selenate, elemental selenium was produced. The G+C content of the DNA was 58.3 mol%. Due to 16S rRNA gene sequence analysis combined with physiological and morphological criteria, the new isolate belongs to the Thermoproteales order. It represents a new species within the genus Pyrobaculum, the type species of which we name Pyrobaculum arsenaticum (type strain PZ6*, DSM 13514, ATCC 700994). Comparative studies with different Pyrobaculum-species showed, that Pyrobaculum aerophilum was also able to grow organotrophically under anaerobic culture conditions in the presence of arsenate, selenate and selenite. During growth on selenite, elemental selenium was formed as final product. In contrast to P. arsenaticum, P. aerophilum could use selenate or arsenate for lithoautotrophic growth with carbon dioxide and hydrogen.},
}
@article {pmid11102688,
year = {2000},
author = {Casamayor, EO and Calderón-Paz, JI and Pedrós-Alió, C},
title = {5S rRNA fingerprints of marine bacteria, halophilic archaea and natural prokaryotic assemblages along a salinity gradient.},
journal = {FEMS microbiology ecology},
volume = {34},
number = {2},
pages = {113-119},
doi = {10.1111/j.1574-6941.2000.tb00760.x},
pmid = {11102688},
issn = {1574-6941},
abstract = {Natural prokaryotic assemblages from two multi-pond solar salterns and pure cultures of both marine bacteria and halophilic archaea were analyzed and compared by electrophoretic analysis of 5S rRNAs. A salinity gradient from seawater (3.7%) to NaCl precipitation (37%) was studied. The culture-independent, PCR-free, fingerprinting analysis covered two objectives: (i) to compare natural assemblages among them and with results previously obtained through a PCR-dependent approach and (ii) to estimate the in situ relevance of those prokaryotic groups obtained with classical culture methodologies. Natural assemblages were analyzed through cluster analysis of quantitative 5S rRNA band patterns. The resulting groups were in accordance with environmental parameters (i.e., NaCl concentration) and with the clustering obtained after a PCR-dependent approach, showing the formation of three salinity-based groups of samples (<10%, 10-25% and >25% salinity). Similarities between the laboratory strains tested and dominant community members were studied by comparing 5S rRNA band patterns. The lack of match obtained after cluster analysis indicated that the prokaryotic populations relevant in the ponds below 25% salinity were neither Flavobacteria nor haloarchaeal strains belonging to the genera Halococcus, Haloarcula and Halobacterium. Members of Proteobacteria and Gram-positive bacteria were found to match bands in these samples. The 5S rRNA fingerprint from the dominant community members in the ponds above 30% salinity did not fit any of the cultured halophilic archaea studied, in agreement with earlier PCR results. This is consistent with a greater bias introduced by culture-dependent methods than by those based on PCR, especially for archaeal populations.},
}
@article {pmid11099387,
year = {2000},
author = {Arnott, MA and Michael, RA and Thompson, CR and Hough, DW and Danson, MJ},
title = {Thermostability and thermoactivity of citrate synthases from the thermophilic and hyperthermophilic archaea, Thermoplasma acidophilum and Pyrococcus furiosus.},
journal = {Journal of molecular biology},
volume = {304},
number = {4},
pages = {657-668},
doi = {10.1006/jmbi.2000.4240},
pmid = {11099387},
issn = {0022-2836},
mesh = {Citrate (si)-Synthase/*chemistry/genetics/isolation &amp; purification/*metabolism ; Enzyme Stability/genetics ; Escherichia coli/genetics ; Kinetics ; Models, Molecular ; Mutation/genetics ; Protein Structure, Quaternary ; Protein Subunits ; Pyrococcus furiosus/*enzymology/genetics ; Recombinant Fusion Proteins/chemistry/genetics/isolation &amp; purification/metabolism ; Static Electricity ; Temperature ; Thermodynamics ; Thermoplasma/*enzymology/genetics ; },
abstract = {Citrate synthases from Thermoplasma acidophilum (optimal growth at 55 degrees C) and Pyrococcus furiosus (100 degrees C) are homo-dimeric enzymes that show a high degree of structural homology with each other, and thermostabilities commensurate with the environmental temperatures in which their host cells are found. A comparison of their atomic structures with citrate synthases from mesophilic and psychrophilic organisms has indicated the potential importance of inter-subunit contacts for thermostability, and here we report the construction and analysis of site-directed mutants of the two citrate synthases to investigate the contribution of these interactions. Three sets of mutants were made: (a) chimeric mutants where the large (inter-subunit contact) and small (catalytic) domains of the T. acidophilum and P. furiosus enzymes were swapped; (b) mutants of the P. furiosus citrate synthase where the inter-subunit ionic network is disrupted; and (c) P. furiosus citrate synthase mutants in which the C-terminal arms that wrap around their partner subunits have been deleted. All three sets of mutant enzymes were expressed as recombinant proteins in Escherichia coli and were found to be catalytically active. Kinetic parameters and the dependence of catalytic activity on temperature were determined, and the stability of each enzyme was analysed by irreversible thermal inactivation experiments. The chimeric mutants indicate that the thermostability of the whole enzyme is largely determined by the origin of the large, inter-subunit domain, whereas the dependence of catalytic activity on temperature is a function of the small domain. Disruption of the inter-subunit ionic network and prevention of the C-terminal interactions both generated enzymes that were substantially less thermostable. Taken together, these data demonstrate the crucial importance of the subunit contacts to the stability of these oligomeric enzymes. Additionally, they also provide a clear distinction between thermostability and thermoactivity, showing that stability is necessary for, but does not guarantee, catalytic activity at elevated temperatures.},
}
@article {pmid11098152,
year = {2000},
author = {Koga, S and Yoshioka, I and Sakuraba, H and Takahashi, M and Sakasegawa, S and Shimizu, S and Ohshima, T},
title = {Biochemical characterization, cloning, and sequencing of ADP-dependent (AMP-forming) glucokinase from two hyperthermophilic archaea, Pyrococcus furiosus and Thermococcus litoralis.},
journal = {Journal of biochemistry},
volume = {128},
number = {6},
pages = {1079-1085},
doi = {10.1093/oxfordjournals.jbchem.a022836},
pmid = {11098152},
issn = {0021-924X},
mesh = {Amino Acid Sequence ; Base Sequence ; Cloning, Molecular ; DNA, Archaeal ; Glucokinase/*genetics/isolation &amp; purification/metabolism ; Molecular Sequence Data ; Pyrococcus furiosus/*enzymology ; Sequence Homology, Amino Acid ; Substrate Specificity ; Thermococcus/*enzymology ; },
abstract = {The ADP-dependent (AMP-forming) glucokinases from the hyperthermophilic archaea Pyrococcus furiosus and Thermococcus litoralis catalyze the phosphorylation of glucose using ADP as the essential phosphoryl group donor. Both enzymes were purified to homogeneity and characterized with regard to each other. The enzymes had similar enzymological properties as to substrate specificity, coenzyme specificity, optimum pH, and thermostability. However, a difference was observed in the subunit composition; while the T. litoralis enzyme is a monomer with a molecular mass of 52 kDa, the P. furiosus enzyme has a molecular mass of about 100 kDa and consists of two subunits with identical molecular masses of 47 kDa. The genes encoding these enzymes were cloned and sequenced. The gene for the P. furiosus enzyme contains an open reading frame for 455 amino acids with a molecular weight of 51,265, and that for the T. litoralis enzyme contains an open reading frame for 467 amino acids with a molecular weight of 53,621. About 59% similarity in amino acid sequence was observed between these two enzymes, whereas they did not show similarity with any ATP-dependent kinases that have been reported so far. In addition, two phosphate binding domains, and adenosine and glucose binding motifs commonly conserved in the eukaryotic hexokinase family were not observed.},
}
@article {pmid11094167,
year = {2000},
author = {Buurman, G and Shima, S and Thauer, RK},
title = {The metal-free hydrogenase from methanogenic archaea: evidence for a bound cofactor.},
journal = {FEBS letters},
volume = {485},
number = {2-3},
pages = {200-204},
doi = {10.1016/s0014-5793(00)02225-0},
pmid = {11094167},
issn = {0014-5793},
mesh = {Chromatography, Gel ; Enzyme Stability ; Escherichia coli/genetics ; Euryarchaeota/*enzymology ; Gene Expression ; Hot Temperature ; Hydrogenase/*chemistry/genetics/metabolism ; Molecular Weight ; Protein Denaturation ; Protein Renaturation ; Ultrafiltration ; Urea ; },
abstract = {The hmd gene, which encodes the metal-free hydrogenase in methanogenic archaea, was heterologously expressed in Escherichia coli. The overproduced enzyme was completely inactive. High activity could, however, be induced by the addition of ultrafiltrate from active enzyme denatured in 8 M urea. The active fraction in the ultrafiltrate was heat-labile and migrated on gel filtration columns with an apparent molecular mass well below 1000 Da.},
}
@article {pmid11084357,
year = {2000},
author = {Kelman, Z},
title = {The replication origin of archaea is finally revealed.},
journal = {Trends in biochemical sciences},
volume = {25},
number = {11},
pages = {521-523},
doi = {10.1016/s0968-0004(00)01687-x},
pmid = {11084357},
issn = {0968-0004},
mesh = {Archaea/*genetics ; Base Sequence ; DNA Replication/genetics ; DNA-Binding Proteins/genetics ; Molecular Sequence Data ; Origin Recognition Complex ; Pyrococcus/genetics ; *Replication Origin ; },
}
@article {pmid11072815,
year = {2000},
author = {Signor, L and Knuppe, C and Hug, R and Schweizer, B and Pfaltz, A and Jaun, B},
title = {Methane formation by reaction of a methyl thioether with a photo-excited nickel thiolate--a process mimicking methanogenesis in archaea.},
journal = {Chemistry (Weinheim an der Bergstrasse, Germany)},
volume = {6},
number = {19},
pages = {3508-3516},
doi = {10.1002/1521-3765(20001002)6:19&lt;3508::aid-chem3508&gt;3.3.co;2-n},
pmid = {11072815},
issn = {0947-6539},
mesh = {Archaea/*metabolism ; Methane/*metabolism ; Nickel/*chemistry ; Sulfhydryl Compounds/*chemistry ; Sulfides/*chemistry ; },
abstract = {The formation of a sulfuranyl radical intermediate followed by methyl transfer to the nickel(I) center of coenzyme F430 and generation of the disulfide has been proposed as a possible mechanism for the formation of methane catalyzed by methyl coenzyme M reductase in methanogenic archaea. In order to test this hypothesis, a sterically shielded, bifunctional model substrate that contained a methyl thioether and a sulfhydryl functional group, which could form a five-membered cyclic sulfuranyl radical according to the postulated mechanism, was synthesized. The corresponding thiolate reacted with Ni(II) salts to give a diamagnetic, square-planar Ni(II) dithiolate complex, which was characterized by X-ray diffraction. Upon irradiation of this complex with light of lambda > 300 nm, methane and the cyclic disulfide were formed, whereas irradiation of the thiolate in the absence of nickel gave only traces of methane and no cyclic disulfide. The observed products are consistent with the postulated mechanism via a sulfuranyl radical, and the role of light is interpreted as the formation of a Ni(I)/thiyl radical pair upon excitation of a charge-transfer band of the Ni(II) dithiolate. In the presence of a large excess of thiolate, the diamagnetic complex was transformed into a paramagnetic, five- or six-coordinate complex that proved to be more active in the generation of both methane and the cyclic disulfide, than the square-planar diamagnetic dithiolate.},
}
@article {pmid11056539,
year = {2000},
author = {Benaroudj, N and Goldberg, AL},
title = {PAN, the proteasome-activating nucleotidase from archaebacteria, is a protein-unfolding molecular chaperone.},
journal = {Nature cell biology},
volume = {2},
number = {11},
pages = {833-839},
doi = {10.1038/35041081},
pmid = {11056539},
issn = {1465-7392},
support = {GM46147/GM/NIGMS NIH HHS/United States ; GM51923/GM/NIGMS NIH HHS/United States ; },
mesh = {Adenosine Diphosphate/metabolism ; Adenosine Monophosphate/metabolism ; Adenosine Triphosphatases/genetics/*metabolism ; Adenosine Triphosphate/metabolism ; Archaeal Proteins ; Endopeptidases/*metabolism ; Enzyme Activation ; Magnesium ; Methanococcus/*enzymology ; Molecular Chaperones/genetics/*metabolism ; Protein Denaturation ; *Protein Folding ; Recombinant Fusion Proteins/genetics/metabolism ; Thermoplasma ; },
abstract = {The proteasome-activating nucleotidase (PAN) from Methanococcus jannaschii is a complex of relative molecular mass 650,000 that is homologous to the ATPases in the eukaryotic 26S proteasome. When mixed with 20S archaeal proteasomes and ATP, PAN stimulates protein degradation. Here we show that PAN reduces aggregation of denatured proteins and enhances their refolding. These processes do not require ATP hydrolysis, although ATP binding enhances the ability of PAN to prevent aggregation. PAN also catalyses the unfolding of the green fluorescent protein with an 11-residue ssrA extension at its carboxy terminus (GFP11). This unfolding requires ATP hydrolysis, and is linked to GFP11 degradation when 20S proteasomes are also present. This unfolding activity seems to be essential for ATP-dependent proteolysis, although PAN may function by itself as a molecular chaperone.},
}
@article {pmid11055931,
year = {2000},
author = {Ouverney, CC and Fuhrman, JA},
title = {Marine planktonic archaea take up amino acids.},
journal = {Applied and environmental microbiology},
volume = {66},
number = {11},
pages = {4829-4833},
pmid = {11055931},
issn = {0099-2240},
mesh = {Amino Acids/*metabolism ; Animals ; Archaea/growth &amp; development/*metabolism ; Autoradiography/methods ; Colony Count, Microbial ; In Situ Hybridization/methods ; Microbiological Techniques/methods ; Plankton/growth &amp; development ; Seawater/*microbiology ; },
abstract = {Archaea are traditionally thought of as "extremophiles," but recent studies have shown that marine planktonic Archaea make up a surprisingly large percentage of ocean midwater microbial communities, up to 60% of the total prokaryotes. However, the basic physiology and contribution of Archaea to community microbial activity remain unknown. We have studied Archaea from 200-m depths of the northwest Mediterranean Sea and the Pacific Ocean near California, measuring the archaeal activity under simulated natural conditions (8 to 17 degrees C, dark and aerobic [corrected]) by means of a method called substrate tracking autoradiography fluorescence in situ hybridization (STARFISH) that simultaneously detects specific cell types by 16S rRNA probe binding and activity by microautoradiography. In the 200-m-deep Mediterranean and Pacific samples, cells binding the archaeal probes made up about 43 and 14% of the total countable cells, respectively. Our results showed that the Archaea are active in the uptake of dissolved amino acids from natural concentrations (nanomolar) with about 60% of the individuals in the archaeal communities showing measurable uptake. Bacteria showed a similar proportion of active cells. We concluded that a portion of these Archaea is heterotrophic and also appears to coexist successfully with Bacteria in the same water.},
}
@article {pmid11053735,
year = {2000},
author = {Jurgens, G and Glöckner, F and Amann, R and Saano, A and Montonen, L and Likolammi, M and Münster, U},
title = {Identification of novel Archaea in bacterioplankton of a boreal forest lake by phylogenetic analysis and fluorescent in situ hybridization(1).},
journal = {FEMS microbiology ecology},
volume = {34},
number = {1},
pages = {45-56},
doi = {10.1111/j.1574-6941.2000.tb00753.x},
pmid = {11053735},
issn = {1574-6941},
abstract = {We report here on novel groups of Archaea in the bacterioplankton of a small boreal forest lake studied by the culture-independent analysis of the 16S rRNA genes amplified directly from lake water in combination with fluorescent in situ hybridization (FISH). Polymerase chain reaction products were cloned and 28 of the 160 Archaea clones with around 900-bp-long 16S rRNA gene inserts, were sequenced. Phylogenetic analysis, including 642 Archaea sequences, confirmed that none of the freshwater clones were closely affiliated with known cultured Archaea. Twelve Archaea sequences from lake Valkea Kotinen (VAL) belonged to Group I of uncultivated Crenarchaeota and affiliated with environmental sequences from freshwater sediments, rice roots and soil as well as with sequences from an anaerobic digestor. Eight of the Crenarchaeota VAL clones formed a tight cluster. Sixteen sequences belonged to Euryarchaeota. Four of these formed a cluster together with environmental sequences from freshwater sediments and peat bogs within the order Methanomicrobiales. Five were affiliated with sequences from marine sediments situated close to marine Group II and three formed a novel cluster VAL III distantly related to the order Thermoplasmales. The remaining four clones formed a distinct clade within a phylogenetic radiation characterized by members of the orders Methanosarcinales and Methanomicrobiales on the same branch as rice cluster I, detected recently on rice roots and in anoxic bulk soil of flooded rice microcosms. FISH with specifically designed rRNA-targeted oligonucleotide probes revealed the presence of Methanomicrobiales in the studied lake. These observations indicate a new ecological niche for many novel 'non-extreme' environmental Archaea in the pelagic water of a boreal forest lake.},
}
@article {pmid11053396,
year = {2000},
author = {Gestwicki, JE and Lamanna, AC and Harshey, RM and McCarter, LL and Kiessling, LL and Adler, J},
title = {Evolutionary conservation of methyl-accepting chemotaxis protein location in Bacteria and Archaea.},
journal = {Journal of bacteriology},
volume = {182},
number = {22},
pages = {6499-6502},
pmid = {11053396},
issn = {0021-9193},
support = {R01 GM055984/GM/NIGMS NIH HHS/United States ; GM52214/GM/NIGMS NIH HHS/United States ; GM55984/GM/NIGMS NIH HHS/United States ; T32 GM008349/GM/NIGMS NIH HHS/United States ; T32GM08349/GM/NIGMS NIH HHS/United States ; },
mesh = {Archaea/*metabolism ; Bacteria/*metabolism ; Bacterial Proteins/isolation &amp; purification ; Biological Evolution ; *Chemotaxis ; *Escherichia coli Proteins ; Membrane Proteins ; Microscopy, Fluorescence ; Type C Phospholipases/*isolation &amp; purification ; },
abstract = {The methyl-accepting chemotaxis proteins (MCPs) are concentrated at the cell poles in an evolutionarily diverse panel of bacteria and an archeon. In elongated cells, the MCPs are located both at the poles and at regions along the length of the cells. Together, these results suggest that MCP location is evolutionarily conserved.},
}
@article {pmid11042147,
year = {2000},
author = {Smit, A and Mushegian, A},
title = {Biosynthesis of isoprenoids via mevalonate in Archaea: the lost pathway.},
journal = {Genome research},
volume = {10},
number = {10},
pages = {1468-1484},
doi = {10.1101/gr.145600},
pmid = {11042147},
issn = {1088-9051},
support = {GM58831/GM/NIGMS NIH HHS/United States ; },
mesh = {Amino Acid Motifs ; Amino Acid Sequence/genetics ; Animals ; Archaea/enzymology/*metabolism ; Archaeal Proteins/chemistry/genetics/metabolism ; Bacterial Proteins/chemistry/genetics ; Conserved Sequence/genetics ; *Evolution, Molecular ; Genetic Linkage ; *Hemiterpenes ; Humans ; Mevalonic Acid/*metabolism ; Molecular Sequence Data ; Organophosphorus Compounds/metabolism ; Pentosephosphates/biosynthesis ; Phylogeny ; Plant Proteins/chemistry/genetics ; Polyisoprenyl Phosphate Sugars/*biosynthesis ; Sequence Alignment ; Sequence Homology, Amino Acid ; },
abstract = {Isoprenoid compounds are ubiquitous in living species and diverse in biological function. Isoprenoid side chains of the membrane lipids are biochemical markers distinguishing archaea from the rest of living forms. The mevalonate pathway of isoprenoid biosynthesis has been defined completely in yeast, while the alternative, deoxy-D-xylulose phosphate synthase pathway is found in many bacteria. In archaea, some enzymes of the mevalonate pathway are found, but the orthologs of three yeast proteins, accounting for the route from phosphomevalonate to geranyl pyrophosphate, are missing, as are the enzymes from the alternative pathway. To understand the evolution of isoprenoid biosynthesis, as well as the mechanism of lipid biosynthesis in archaea, sequence motifs in the known enzymes of the two pathways of isoprenoid biosynthesis were analyzed. New sequence relationships were detected, including similarities between diphosphomevalonate decarboxylase and kinases of the galactokinase superfamily, between the metazoan phosphomevalonate kinase and the nucleoside monophosphate kinase superfamily, and between isopentenyl pyrophosphate isomerases and MutT pyrophosphohydrolases. Based on these findings, orphan members of the galactokinase, nucleoside monophosphate kinase, and pyrophosphohydrolase families in archaeal genomes were evaluated as candidate enzymes for the three missing steps. Alternative methods of finding these missing links were explored, including physical linkage of open reading frames and patterns of ortholog distribution in different species. Combining these approaches resulted in the generation of a short list of 13 candidate genes for the three missing functions in archaea, whose participation in isoprenoid biosynthesis is amenable to biochemical and genetic investigation.},
}
@article {pmid11040282,
year = {2000},
author = {Liao, D},
title = {Gene conversion drives within genic sequences: concerted evolution of ribosomal RNA genes in bacteria and archaea.},
journal = {Journal of molecular evolution},
volume = {51},
number = {4},
pages = {305-317},
doi = {10.1007/s002390010093},
pmid = {11040282},
issn = {0022-2844},
mesh = {Archaea/*genetics ; Bacteria/*genetics ; Base Sequence ; DNA, Intergenic ; *Evolution, Molecular ; *Gene Conversion ; Genetic Heterogeneity ; Molecular Sequence Data ; *RNA, Ribosomal ; },
abstract = {Multiple copies of a given ribosomal RNA gene family undergo concerted evolution such that sequences of all gene copies are virtually identical within a species although they diverge normally between species. In eukaryotes, gene conversion and unequal crossing over are the proposed mechanisms for concerted evolution of tandemly repeated sequences, whereas dispersed genes are homogenized by gene conversion. However, the homogenization mechanisms for multiple-copy, normally dispersed, prokaryotic rRNA genes are not well understood. Here we compared the sequences of multiple paralogous rRNA genes within a genome in 12 prokaryotic organisms that have multiple copies of the rRNA genes. Within a genome, putative sequence conversion tracts were found throughout the entire length of each individual rRNA genes and their immediate flanks. Individual conversion events convert only a short sequence tract, and the conversion partners can be any paralogous genes within the genome. Interestingly, the genic sequences undergo much slower divergence than their flanking sequences. Moreover, genomic context and operon organization do not affect rRNA gene homogenization. Thus, gene conversion underlies concerted evolution of bacterial rRNA genes, which normally occurs within genic sequences, and homogenization of flanking regions may result from co-conversion with the genic sequence.},
}
@article {pmid11031241,
year = {2000},
author = {Spudich, JL and Yang, CS and Jung, KH and Spudich, EN},
title = {Retinylidene proteins: structures and functions from archaea to humans.},
journal = {Annual review of cell and developmental biology},
volume = {16},
number = {},
pages = {365-392},
doi = {10.1146/annurev.cellbio.16.1.365},
pmid = {11031241},
issn = {1081-0706},
mesh = {Amino Acid Sequence ; Animals ; Archaea/*metabolism ; Archaeal Proteins/chemistry/*physiology ; Eukaryotic Cells ; Humans ; Molecular Sequence Data ; *Retinoids/chemistry ; Rhodopsin/chemistry/*physiology ; Structure-Activity Relationship ; },
abstract = {Retinylidene proteins, containing seven membrane-embedded alpha-helices that form an internal pocket in which the chromophore retinal is bound, are ubiquitous in photoreceptor cells in eyes throughout the animal kingdom. They are also present in a diverse range of other organisms and locations, such as archaeal prokaryotes, unicellular eukaryotic microbes, the dermal tissue of frogs, the pineal glands of lizards and birds, the hypothalamus of toads, and the human brain. Their functions include light-driven ion transport and phototaxis signaling in microorganisms, and retinal isomerization and various types of photosignal transduction in higher animals. The aims of this review are to examine this group of photoactive proteins as a whole, to summarize our current understanding of structure/function relationships in the best-studied examples, and to report recent new developments.},
}
@article {pmid11030566,
year = {2000},
author = {Hezayen, FF and Rehm, BH and Eberhardt, R and Steinbüchel, A},
title = {Polymer production by two newly isolated extremely halophilic archaea: application of a novel corrosion-resistant bioreactor.},
journal = {Applied microbiology and biotechnology},
volume = {54},
number = {3},
pages = {319-325},
doi = {10.1007/s002530000394},
pmid = {11030566},
issn = {0175-7598},
mesh = {Archaea/isolation &amp; purification/*metabolism ; Benzophenones ; *Bioreactors ; Ceramics ; Corrosion ; Culture Media ; Cytoplasmic Granules/metabolism ; Egypt ; Fermentation ; Glass ; Hydroxybutyrates/*metabolism ; Ketones ; Polyesters/*metabolism ; Polyethylene Glycols ; Polyglutamic Acid/*biosynthesis ; Polymers ; Sodium Chloride/*pharmacology ; Soil Microbiology ; },
abstract = {A novel corrosion-resistant bioreactor composed of polyetherether ketone (PEEK), tech glass and silicium nitrite ceramics was constructed and applied for the cultivation of two newly isolated, extremely halophilic archaea producing poly(gamma-glutamic acid) (PGA), or poly(beta-hydroxy butyric acid) (PHB), respectively. These bacteria were isolated from hypersaline soil close to Aswan (Egypt). The isolate strain 40, which is related to the genus Natrialba, produced large amounts of PGA when cultivated on solid medium. Culture conditions were optimised applying the corrosion-resistant bioreactor. PGA production was dependent on NaCl concentration and occurred about at 20% (w/v) NaCl in the medium. A maximum cell density of about 1.6 g cell dry matter/l was obtained when the bioreactor was stirred and aerated in a batch fermentation process using proteose-peptone medium. The supernatant was monitored with respect to PGA formation, and after 90 h a maximum of 470 mg/l culture volume was detected by HPLC analysis. Culture conditions were optimized for the isolate 56, which accumulated PHB as intracellular granules. Batch fermentations in the stirred and aerated bioreactor applying acetate and n-butyric acid as carbon sources led to cell density of 2.28 g cell dry matter/l and a maximum PHB accumulation contributing to about 53% of cellular dry weight. About 4.6 g PHB were isolated from 10.6 g dried cells of strain 56, which exhibited a weight average molar mass of 2.3 x 10(5) g mol(-1) and a polydispersity of about 1.4.},
}
@article {pmid11029439,
year = {2000},
author = {Kachlany, SC and Planet, PJ and Bhattacharjee, MK and Kollia, E and DeSalle, R and Fine, DH and Figurski, DH},
title = {Nonspecific adherence by Actinobacillus actinomycetemcomitans requires genes widespread in bacteria and archaea.},
journal = {Journal of bacteriology},
volume = {182},
number = {21},
pages = {6169-6176},
pmid = {11029439},
issn = {0021-9193},
mesh = {Aggregatibacter actinomycetemcomitans/chemistry/*genetics ; Bacterial Adhesion/*genetics ; Bacterial Outer Membrane Proteins/*genetics ; Bacterial Proteins/genetics ; DNA Transposable Elements ; *Genes, Archaeal ; *Genes, Bacterial ; Genetic Vectors ; Humans ; Macromolecular Substances ; Molecular Sequence Data ; Mutagenesis, Insertional ; *Virulence Factors ; },
abstract = {The gram-negative coccobacillus, Actinobacillus actinomycetemcomitans, is the putative agent for localized juvenile periodontitis, a particularly destructive form of periodontal disease in adolescents. This bacterium has also been isolated from a variety of other infections, notably endocarditis. Fresh clinical isolates of A. actinomycetemcomitans form tenacious biofilms, a property likely to be critical for colonization of teeth and other surfaces. Here we report the identification of a locus of seven genes required for nonspecific adherence of A. actinomycetemcomitans to surfaces. The recently developed transposon IS903phikan was used to isolate mutants of the rough clinical isolate CU1000 that are defective in tight adherence to surfaces (Tad(-)). Unlike wild-type cells, Tad(-) mutant cells adhere poorly to surfaces, fail to form large autoaggregates, and lack long, bundled fibrils. Nucleotide sequencing and genetic complementation analysis revealed a 6.7-kb region of the genome with seven adjacent genes (tadABCDEFG) required for tight adherence. The predicted TadA polypeptide is similar to VirB11, an ATPase involved in macromolecular transport. The predicted amino acid sequences of the other Tad polypeptides indicate membrane localization but no obvious functions. We suggest that the tad genes are involved in secretion of factors required for tight adherence of A. actinomycetemcomitans. Remarkably, complete and highly conserved tad gene clusters are present in the genomes of the bubonic plague bacillus Yersinia pestis and the human and animal pathogen Pasteurella multocida. Partial tad loci also occur in strikingly diverse Bacteria and Archaea. Our results show that the tad genes are required for tight adherence of A. actinomycetemcomitans to surfaces and are therefore likely to be essential for colonization and pathogenesis. The occurrence of similar genes in a wide array of microorganisms indicates that they have important functions. We propose that tad-like genes have a significant role in microbial colonization.},
}
@article {pmid11017041,
year = {2000},
author = {Nelson, KE and Paulsen, IT and Heidelberg, JF and Fraser, CM},
title = {Status of genome projects for nonpathogenic bacteria and archaea.},
journal = {Nature biotechnology},
volume = {18},
number = {10},
pages = {1049-1054},
doi = {10.1038/80235},
pmid = {11017041},
issn = {1087-0156},
mesh = {Archaea/genetics ; Bacteria/genetics/pathogenicity ; Biotechnology/methods ; Databases as Topic ; Evolution, Molecular ; *Genome, Archaeal ; *Genome, Bacterial ; Genomics/*methods ; Open Reading Frames/genetics ; Phylogeny ; Reproducibility of Results ; Sequence Analysis, DNA/methods ; },
abstract = {Since the first microbial genome was sequenced in 1995, 30 others have been completed and an additional 99 are known to be in progress. Although the early emphasis of microbial genomics was on human pathogens for obvious reasons, a significant number of sequencing projects have focused on nonpathogenic organisms, beginning with the release of the complete genome sequence of the archaeon Methanococcus jannaschii in 1996. The past 18 months have seen the completion of the genomes of several unusual organisms, including Thermotoga maritima, whose genome reveals extensive potential lateral transfer with archaea; Deinococcus radiodurans, the most radiation-resistant microorganism known; and Aeropyrum pernix, the first Crenarchaeota to be completely sequenced. Although the functional characterization of genomic data is still in its initial stages, it is likely that microbial genomics will have a significant impact on environmental, food, and industrial biotechnology as well as on genomic medicine.},
}
@article {pmid10972193,
year = {2000},
author = {Rothe, O and Thomm, M},
title = {A simplified method for the cultivation of extreme anaerobic Archaea based on the use of sodium sulfite as reducing agent.},
journal = {Extremophiles : life under extreme conditions},
volume = {4},
number = {4},
pages = {247-252},
doi = {10.1007/pl00010716},
pmid = {10972193},
issn = {1431-0651},
mesh = {Anaerobiosis ; Archaea/*growth &amp; development/*metabolism ; Cell Division ; Culture Media/chemistry ; Hydrogen Sulfide/metabolism ; Hydrogen-Ion Concentration ; Methanococcus/growth &amp; development/metabolism ; Reducing Agents/*metabolism ; Sulfites/*metabolism ; Temperature ; },
abstract = {The extreme sensitivity of many Archaea to oxygen is a major obstacle for their cultivation in the laboratory and the development of archaeal genetic exchange systems. The technique of Balch and Wolfe (1976) is suitable for the cultivation of anaerobic Archaea but involves time-consuming procedures such as the use of air locks and glove boxes. We describe here a procedure for the cultivation of anaerobic Archaea that is more convenient and faster and allows the preparation of liquid media without the use of an anaerobic chamber. When the reducing agent sodium sulfide (Na2S) was replaced by sodium sulfite (Na2SO3), anaerobic media could be prepared without protection from oxygen outside an anaerobic chamber. Exchange of the headspace of serum bottles by appropriate gases was sufficient to maintain anaerobic conditions in the culture media. Organisms that were unable to utilize sulfite as a source for cellular sulfur were supplemented with hydrogen sulfide. H2S was simply added to the headspace of serum bottles by a syringe. The use of H2S as a source for sulfur minimized the precipitation of cations by sulfide. Representatives of 12 genera of anaerobic Archaea studied here were able to grow in media prepared by this procedure. For the extremely oxygen-sensitive organism Methanococcus thermolithotrophicus, we show that plates could be prepared outside an anaerobic chamber when sulfite was used as reducing agent. The application of this method may faciliate the cultivation and handling of extreme anaerobic Archaea considerably.},
}
@article {pmid10972190,
year = {2000},
author = {Cambon-Bonavita, MA and Schmitt, P and Zieger, M and Flaman, JM and Lesongeur, F and Raguénès, G and Bindel, D and Frisch, N and Lakkis, Z and Dupret, D and Barbier, G and Quérellou, J},
title = {Cloning, expression, and characterization of DNA polymerase I from the hyperthermophilic archaea Thermococcus fumicolans.},
journal = {Extremophiles : life under extreme conditions},
volume = {4},
number = {4},
pages = {215-225},
doi = {10.1007/pl00010714},
pmid = {10972190},
issn = {1431-0651},
mesh = {Cloning, Molecular ; DNA Polymerase I/*genetics/isolation &amp; purification/metabolism ; Enzyme Stability ; Escherichia coli ; Exonucleases/genetics/isolation &amp; purification/metabolism ; Magnesium/pharmacology ; Polymerase Chain Reaction ; Protein Splicing ; Recombinant Proteins/isolation &amp; purification/metabolism ; Sequence Analysis, DNA ; Temperature ; Thermococcus/*enzymology/genetics ; },
abstract = {The DNA polymerase I gene of a newly described deep-sea hydrothermal vent Archaea species, Thermococcus fumicolans, from IFREMERS's collection of hyperthermophiles has been cloned in Escherichia coli. As in Thermococcus litoralis, the gene is split by two intervening sequences (IVS) encoding inteins inserted in sites A and C of family B DNA polymerases. The entire DNA polymerase gene, containing both inteins, was expressed at 30 degrees C in E. coli strain BL21(DE3)pLysS using the pARHS2 expression vector. The native polypeptide precursor of 170kDa was obtained, and intein splicing as well as ligation of the three exteins was observed in vitro after heat exposure. The recombinant enzyme was purified and some of its activities were characterized: polymerization, thermostability, exonuclease activities, and fidelity.},
}
@article {pmid10966879,
year = {2000},
author = {Scandurra, R and Consalvi, V and Chiaraluce, R and Politi, L and Engel, PC},
title = {Protein stability in extremophilic archaea.},
journal = {Frontiers in bioscience : a journal and virtual library},
volume = {5},
number = {},
pages = {D787-95},
doi = {10.2741/A551},
pmid = {10966879},
issn = {1093-9946},
mesh = {Adaptation, Physiological/genetics ; Archaea/genetics/*physiology ; Archaeal Proteins/genetics/*physiology ; Protein Conformation ; Temperature ; },
abstract = {Extremophilic microorganisms have adapted their molecular machinery to grow and thrive under the most adverse environmental conditions. These microorganisms have found their natural habitat at the boiling and freezing point of water, in high salt concentration and at extreme pH values. The extremophilic proteins, selected by Nature to withstand this evolutionary pressure, represent a wide research field for scientists from different disciplines and the study of the determinants of their stability has been an important task for basic and applied research. A surprising conclusion emerges from these studies: there are no general rules to achieve protein stabilization. Each extremophilic protein adopts various strategies and the outstanding adaptation to extreme temperature and solvent conditions is realized through the same weak electrostatic and hydrophobic interactions among the ordinary amino acid residues which are also responsible for the proper balance between protein stability and flexibility in mesophilic proteins.},
}
@article {pmid10966877,
year = {2000},
author = {Roberts, MF},
title = {Osmoadaptation and osmoregulation in archaea.},
journal = {Frontiers in bioscience : a journal and virtual library},
volume = {5},
number = {},
pages = {D796-812},
doi = {10.2741/roberts},
pmid = {10966877},
issn = {1093-9946},
mesh = {Adaptation, Physiological ; Archaea/*physiology ; Archaeal Proteins/biosynthesis ; Heat-Shock Proteins/biosynthesis ; Methanococcus/physiology ; Sodium Chloride/metabolism ; Solutions ; Water/metabolism ; Water-Electrolyte Balance/physiology ; Yeasts/physiology ; },
abstract = {The response of archaea to changes in external NaCl is reviewed and compared to what is known about osmoadaptation and osmoregulation in bacteria and eukaryotes. Cells placed in altered external NaCl exhibit short term and long term responses. The earliest events are likely to be water movement through aquaporin-like channels (efflux if external NaCl has been increased, influx into the cell if the external NaCl has been decreased) and ion movement (e.g., K+ moving in the direction opposite to water flow) through channels sensitive to osmotic pressure. Accumulation of organic solutes, either by uptake from the medium or de novo synthesis, is triggered after these initial changes. Archaea have some unique organic solutes (osmolytes) that are not used by other organisms. These as well as other more common solutes have a role in stabilizing macromolecules from denaturation. Many osmolytes are distinguished by their stability in the cell and their lack of strong interactions with cellular components. A cell may respond by accumulating one or more temporary osmolytes, then over time readjust the intracellular solute distribution to what is optimal for cell growth under the new conditions. Coupled with the movement and accumulation of solutes is the induction of stress proteins (e.g., chaperonins) and, in some cases, transcriptional regulation of key enzymes. The response to NaCl stress of Methanococcus thermolithotrophicus is presented as an example of how one particular archaeon responds and adapts to altered osmotic pressure. Clearly, the detailed response of other archaea to osmotic stress will be needed in order to identify features (aside from some of the organic osmolytes) unique to the organisms in this kingdom.},
}
@article {pmid10966872,
year = {2000},
author = {Maupin-Furlow, JA and Wilson, HL and Kaczowka, SJ and Ou, MS},
title = {Proteasomes in the archaea: from structure to function.},
journal = {Frontiers in bioscience : a journal and virtual library},
volume = {5},
number = {},
pages = {D837-65},
doi = {10.2741/furlow},
pmid = {10966872},
issn = {1093-9946},
support = {R01GM57498/GM/NIGMS NIH HHS/United States ; },
mesh = {Adenosine Triphosphatases/metabolism ; Amino Acid Sequence ; Archaea/*enzymology/genetics/physiology ; Catalysis ; Cysteine Endopeptidases/chemistry/*physiology ; Genome, Archaeal ; Heat-Shock Response ; Molecular Sequence Data ; Multienzyme Complexes/chemistry/*physiology ; Proteasome Endopeptidase Complex ; Signal Transduction ; Structure-Activity Relationship ; Substrate Specificity ; Ubiquitins/metabolism ; },
abstract = {Survival of cells is critically dependent on their ability to rapidly adapt to changes in the natural environment no matter how 'extreme'the habitat. An interplay between protein folding and hydrolysis is emerging as a central mechanism for stress survival and proper cell function. In eucaryotic cells, most proteins destined for destruction are covalently modified by the ubiquitin-system and then degraded in an energy-dependent mechanism by the 26S proteasome, a multicatalytic protease. The 26S proteasome is composed of a 20S proteolytic core and 19S cap (PA700) regulator which includes six AAA+ ATPase subunits. Related AAA+ proteins and 20S proteasomes are found in the archaea and Gram positive actinomycetes. In general, 20S proteasomes form a barrel-shaped nanocompartment with narrow openings which isolate rather non-specific proteolytic active-sites to the interior of the cylinder and away from interaction with cytosolic proteins. The proteasome-associated AAA+ proteins are predicted to form ring-like structures which unfold substrate proteins for entry into the central proteolytic 20S chamber resulting in an energy-dependent and processive destruction of the protein. Detailed biochemical and biophysical analysis as well as identification of proteasomes in archaea with developed genetic tools are providing a foundation for understanding the biological role of the proteasome in these unusual organisms.},
}
@article {pmid10941105,
year = {2000},
author = {Beifuss, U and Tietze, M and Bäumer, S and Deppenmeier, U},
title = {Methanophenazine: Structure, Total Synthesis, and Function of a New Cofactor from Methanogenic Archaea This work was supported by the Deutsche Forschungsgemeinschaft (Sonderforschungsbereich 416; grants De 488/6-1 and De 488/4-2) and the Fonds der Chemischen Industrie. We are grateful to Drs. J. Paust and H. Jaedicke (BASF AG, Ludwigshafen) and Dr. R. K. Müller (Hoffmann-La Roche Ltd., Basel) for generously providing chemicals.},
journal = {Angewandte Chemie (International ed. in English)},
volume = {39},
number = {14},
pages = {2470-2472},
doi = {10.1002/1521-3773(20000717)39:14&lt;2470::aid-anie2470&gt;3.0.co;2-r},
pmid = {10941105},
issn = {1521-3773},
}
@article {pmid10940377,
year = {2000},
author = {Friedrich, T and Scheide, D},
title = {The respiratory complex I of bacteria, archaea and eukarya and its module common with membrane-bound multisubunit hydrogenases.},
journal = {FEBS letters},
volume = {479},
number = {1-2},
pages = {1-5},
doi = {10.1016/s0014-5793(00)01867-6},
pmid = {10940377},
issn = {0014-5793},
mesh = {Archaea/enzymology/genetics ; Bacteria/enzymology/genetics ; Chloroplasts/enzymology ; Electron Transport ; Electron Transport Complex I ; Eukaryotic Cells ; Evolution, Molecular ; Mitochondria/enzymology ; NADH, NADPH Oxidoreductases/*chemistry/genetics/*metabolism ; Protein Structure, Quaternary ; Protons ; },
abstract = {The proton-pumping NADH:ubiquinone oxidoreductase, also called complex I, is the first of the respiratory complexes providing the proton motive force which is essential for energy consuming processes like the synthesis of ATP. Homologues of this complex exist in bacteria, archaea, in mitochondria of eukaryotes and in chloroplasts of plants. The bacterial and mitochondrial complexes function as NADH dehydrogenase, while the archaeal complex works as F420H2 dehydrogenase. The electron donor of the cyanobacterial and plastidal complex is not yet known. Despite the different electron input sites, 11 polypeptides constitute the structural framework for proton translocation and quinone binding in the complex of all three domains of life. Six of them are also present in a family of membrane-bound multisubunit [NiFe] hydrogenases. It is discussed that they build a module for electron transfer coupled to proton translocation.},
}
@article {pmid10930739,
year = {2000},
author = {Borup, B and Ferry, JG},
title = {Cysteine biosynthesis in the Archaea: Methanosarcina thermophila utilizes O-acetylserine sulfhydrylase.},
journal = {FEMS microbiology letters},
volume = {189},
number = {2},
pages = {205-210},
doi = {10.1111/j.1574-6968.2000.tb09231.x},
pmid = {10930739},
issn = {0378-1097},
mesh = {Amino Acid Sequence ; Carbon-Oxygen Lyases/genetics/*metabolism ; Cysteine/*biosynthesis ; Cysteine Synthase ; Methanosarcina/genetics/*metabolism ; Molecular Sequence Data ; *Multienzyme Complexes ; *Saccharomyces cerevisiae Proteins ; Sequence Alignment ; Sulfur/*metabolism ; },
abstract = {Two pathways for cysteine biosynthesis are known in nature; however, it is not known which, if either, the Archaea utilize. Enzyme activities in extracts of Methanosarcina thermophila grown with combinations of cysteine and sulfide as sulfur sources indicated that this archaeon utilizes the pathway found in the Bacteria domain. The genes encoding serine transacetylase and O-acetylserine sulfhydrylase (cysE and cysK) are adjacent on the chromosome of M. thermophila and possibly form an operon. When M. thermophila is grown with cysteine as the sole sulfur source, O-acetylserine sulfhydrylase activity is maximally expressed suggesting alternative roles for this enzyme apart from cysteine biosynthesis.},
}
@article {pmid10919780,
year = {2000},
author = {Cytryn, E and Minz, D and Oremland, RS and Cohen, Y},
title = {Distribution and diversity of archaea corresponding to the limnological cycle of a hypersaline stratified lake (Solar lake, Sinai, Egypt).},
journal = {Applied and environmental microbiology},
volume = {66},
number = {8},
pages = {3269-3276},
pmid = {10919780},
issn = {0099-2240},
mesh = {Archaea/classification/*genetics/*physiology ; DNA, Archaeal/analysis/genetics ; DNA, Ribosomal/analysis/genetics ; Egypt ; Electrophoresis, Polyacrylamide Gel/methods ; Fresh Water/*microbiology ; *Genetic Variation ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sodium Chloride ; },
abstract = {The vertical and seasonal distribution and diversity of archaeal sequences was investigated in a hypersaline, stratified, monomictic lake, Solar Lake, Sinai, Egypt, during the limnological development of stratification and mixing. Archaeal sequences were studied via phylogenetic analysis of 16S rDNA sequences as well as denaturing gradient gel electrophoresis analysis. The 165 clones studied were grouped into four phylogenetically different clusters. Most of the clones isolated from both the aerobic epilimnion and the sulfide-rich hypolimnion were defined as cluster I, belonging to the Halobacteriaceae family. The three additional clusters were all isolated from the anaerobic hypolimnion. Cluster II is phylogenetically located between the genera Methanobacterium and Methanococcus. Clusters III and IV relate to two previously documented groups of uncultured euryarchaeota, remotely related to the genus Thermoplasma. No crenarchaeota were found in the water column of the Solar Lake. The archaeal community in the Solar Lake under both stratified and mixed conditions was dominated by halobacteria in salinities higher than 10%. During stratification, additional clusters, some of which may possibly relate to uncultured halophilic methanogens, were found in the sulfide- and methane-rich hypolimnion.},
}
@article {pmid10894744,
year = {2000},
author = {Offner, S and Hofacker, A and Wanner, G and Pfeifer, F},
title = {Eight of fourteen gvp genes are sufficient for formation of gas vesicles in halophilic archaea.},
journal = {Journal of bacteriology},
volume = {182},
number = {15},
pages = {4328-4336},
pmid = {10894744},
issn = {0021-9193},
mesh = {*Archaeal Proteins ; Bacterial Proteins/*genetics ; Blotting, Northern ; Genes, Archaeal/*physiology ; Halobacterium/*genetics/ultrastructure ; *Membrane Proteins ; Microscopy, Electron ; *Proteins ; Transcription Factors/*genetics ; },
abstract = {The minimal number of genes required for the formation of gas vesicles in halophilic archaea has been determined. Single genes of the 14 gvp genes present in the p-vac region on plasmid pHH1 of Halobacterium salinarum (p-gvpACNO and p-gvpDEFGHIJKLM) were deleted, and the remaining genes were tested for the formation of gas vesicles in Haloferax volcanii transformants. The deletion of six gvp genes (p-gvpCN, p-gvpDE, and p-gvpHI) still enabled the production of gas vesicles in H. volcanii. The gas vesicles formed in some of these gvp gene deletion transformants were altered in shape (Delta I, Delta C) or strength (Delta H) but still functioned as flotation devices. A minimal p-vac region (minvac) containing the eight remaining genes (gvpFGJKLM-gvpAO) was constructed and tested for gas vesicle formation in H. volcanii. The minvac transformants did not form gas vesicles; however, minvac/gvpJKLM double transformants contained gas vesicles seen as light refractile bodies by phase-contrast microscopy. Transcript analyses demonstrated that minvac transformants synthesized regular amounts of gvpA mRNA, but the transcripts derived from gvpFGJKLM were mainly short and encompassed only gvpFG(J), suggesting that the gvpJKLM genes were not sufficiently expressed. Since gvpAO and gvpFGJKLM are the only gvp genes present in minvac/JKLM transformants containing gas vesicles, these gvp genes represent the minimal set required for gas vesicle formation in halophilic archaea. Homologs of six of these gvp genes are found in Anabaena flos-aquae, and homologs of all eight minimal halobacterial gvp genes are present in Bacillus megaterium and in the genome of Streptomyces coelicolor.},
}
@article {pmid10891279,
year = {2000},
author = {Shima, S and Warkentin, E and Grabarse, W and Sordel, M and Wicke, M and Thauer, RK and Ermler, U},
title = {Structure of coenzyme F(420) dependent methylenetetrahydromethanopterin reductase from two methanogenic archaea.},
journal = {Journal of molecular biology},
volume = {300},
number = {4},
pages = {935-950},
doi = {10.1006/jmbi.2000.3909},
pmid = {10891279},
issn = {0022-2836},
mesh = {Adaptation, Physiological ; Amino Acid Sequence ; Binding Sites ; Crystallography, X-Ray ; Dimerization ; Environment ; Euryarchaeota/*enzymology ; Flavin-Adenine Dinucleotide/chemistry/metabolism ; Flavins/chemistry/metabolism ; Methanobacterium/enzymology ; Models, Molecular ; Molecular Sequence Data ; Oxidoreductases Acting on CH-NH Group Donors/*chemistry/*metabolism ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Riboflavin/*analogs &amp; derivatives/chemistry/*metabolism ; Sequence Alignment ; },
abstract = {Coenzyme F(420)-dependent methylenetetrahydromethanopterin reductase (Mer) is an enzyme of the Cl metabolism in methanogenic and sulfate reducing archaea. It is composed of identical 35-40 kDa subunits and lacks a prosthetic group. The crystal structure of Mer from Methanopyrus kandleri (kMer) revealed in one crystal form a dimeric and in another a tetrameric oligomerisation state and that from Methanobacterium thermoautotrophicum (tMer) a dimeric state. Each monomer is primarily composed of a TIM-barrel fold enlarged by three insertion regions. Insertion regions 1 and 2 contribute to intersubunit interactions. Insertion regions 2 and 3 together with the C-terminal end of the TIM-barrel core form a cleft where the binding sites of coenzyme F(420) and methylene-tetrahydromethanopterin are postulated. Close to the coenzyme F(420)-binding site lies a rarely observed non-prolyl cis-peptide bond. It is surprising that Mer is structurally most similar to a bacterial FMN-dependent luciferase which contains a non-prolyl cis-peptide bond at the equivalent position. The structure of Mer is also related to that of NADP-dependent FAD-harbouring methylenetetrahydrofolate reductase (MetF). However, Mer and MetF do not show sequence similarities although they bind related substrates and catalyze an analogous reaction.},
}
@article {pmid10886656,
year = {2000},
author = {García-Martínez, J and Rodríguez-Valera, F},
title = {Microdiversity of uncultured marine prokaryotes: the SAR11 cluster and the marine Archaea of Group I.},
journal = {Molecular ecology},
volume = {9},
number = {7},
pages = {935-948},
doi = {10.1046/j.1365-294x.2000.00953.x},
pmid = {10886656},
issn = {0962-1083},
mesh = {Antarctic Regions ; Archaea/classification/*genetics ; Base Sequence ; DNA, Archaeal/analysis/genetics ; *Genetic Variation ; Mediterranean Sea ; Molecular Sequence Data ; Multigene Family/*genetics ; Phylogeny ; *Prokaryotic Cells ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; },
abstract = {The SAR11 cluster and the Group I of marine Archaea represent probably the best two examples of uncultured marine prokaryotes of widespread occurrence. To study their microdiversity and distribution, a total of 81 and 48 clones, respectively, were sequenced from Mediterranean and Antarctic waters at different locations and depths. The DNA regions chosen for the analysis were the last third, approximately, of the 16S rRNA gene and the 16S-23S intergenic spacer (also known as internal transcribed spacer [ITS]). There was a high concordance in both, even with the extremely variable ITS, where potential probes have been proposed for the identification and isolation of these micro-organisms. In terms of community structure, our results show that although depth-related factors seem to be predominant in the final associations of the clones, geography also plays a significant role. A major group of surface-associated sequences was found in both SAR11 and marine Archaea. In both cases this group was relatively homogeneous containing little diversity in terms of sequence, while sequences retrieved from deep samples and some surface clones contained much more heterogeneity. As a whole, both groups of prokaryotes seem to fall within the limits of well-defined taxonomic units.},
}
@article {pmid10879986,
year = {2000},
author = {Briones, C and Amils, R},
title = {Nucleotide sequence of the 235 rRNA from Haloferax mediterranei and phylogenetic analysis of halophilic archaea based on LSU rRNA.},
journal = {Systematic and applied microbiology},
volume = {23},
number = {1},
pages = {124-131},
doi = {10.1016/s0723-2020(00)80053-3},
pmid = {10879986},
issn = {0723-2020},
mesh = {Base Sequence ; DNA, Archaeal/genetics ; DNA, Ribosomal Spacer/genetics ; *Genes, rRNA ; Halobacteriales/classification/*genetics ; Haloferax mediterranei/*classification/genetics ; Molecular Sequence Data ; Nucleic Acid Conformation ; Phylogeny ; RNA, Archaeal/chemistry/genetics ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 23S/chemistry/*genetics ; },
abstract = {23S rRNA gene from the halophilic archaeon Haloferax mediterranei (strain ATCC 33500) was cloned and sequenced. Proceeding from the 2,912 nucleotides long sequence, the secondary structure of Haloferax genus large subunit rRNA was proposed. Haloferax mediterranei intergenic spacers 16S/23S and 23S/5S were also sequenced, and found to be 382 and 116 nucleotides long respectively. The 16S/23S spacer showed an Ala-tRNA intervening sequence, which is a common feature in Euryarchaeota. Sequence analysis of 23S rRNA and 16S rRNA was performed for the six organisms from the family Halobacteriaceae with both available gene sequences. Phylogenetic trees with completely different topology were obtained using both molecules.},
}
@article {pmid10871366,
year = {2000},
author = {Watanabe, Y and Gray, MW},
title = {Evolutionary appearance of genes encoding proteins associated with box H/ACA snoRNAs: cbf5p in Euglena gracilis, an early diverging eukaryote, and candidate Gar1p and Nop10p homologs in archaebacteria.},
journal = {Nucleic acids research},
volume = {28},
number = {12},
pages = {2342-2352},
pmid = {10871366},
issn = {1362-4962},
mesh = {Amino Acid Sequence ; Animals ; Archaea/classification/*genetics ; Archaeal Proteins/chemistry/*genetics ; Base Sequence ; Cloning, Molecular ; Euglena gracilis/classification/*genetics ; *Evolution, Molecular ; Fungal Proteins/chemistry/*genetics ; Humans ; *Hydro-Lyases ; Microtubule-Associated Proteins/chemistry/*genetics ; Molecular Sequence Data ; Nuclear Proteins/chemistry/*genetics ; Oligodeoxyribonucleotides ; *Phylogeny ; RNA, Small Nuclear/*genetics ; RNA-Binding Proteins/chemistry/*genetics ; *Ribonucleoproteins, Small Nuclear ; *Ribonucleoproteins, Small Nucleolar ; *Saccharomyces cerevisiae Proteins ; Sequence Alignment ; Sequence Homology, Amino Acid ; },
abstract = {A reverse transcription-polymerase chain reaction (RT-PCR) approach was used to clone a cDNA encoding the Euglena gracilis homolog of yeast Cbf5p, a protein component of the box H/ACA class of snoRNPs that mediate pseudouridine formation in eukaryotic rRNA. Cbf5p is a putative pseudouridine synthase, and the Euglena homolog is the first full-length Cbf5p sequence to be reported for an early diverging unicellular eukaryote (protist). Phylogenetic analysis of putative pseudouridine synthase sequences confirms that archaebacterial and eukaryotic (including Euglena) Cbf5p proteins are specifically related and are distinct from the TruB/Pus4p clade that is responsible for formation of pseudouridine at position 55 in eubacterial (TruB) and eukaryotic (Pus4p) tRNAs. Using a bioinformatics approach, we also identified archaebacterial genes encoding candidate homologs of yeast Gar1p and Nop10p, two additional proteins known to be associated with eukaryotic box H/ACA snoRNPs. These observations raise the possibility that pseudouridine formation in archaebacterial rRNA may be dependent on analogs of the eukaryotic box H/ACA snoRNPs, whose evolutionary origin may therefore predate the split between Archaea (archaebacteria) and Eucarya (eukaryotes). Database searches further revealed, in archaebacterial and some eukaryotic genomes, two previously unrecognized groups of genes (here designated 'PsuX' and 'PsuY') distantly related to the Cbf5p/TruB gene family.},
}
@article {pmid10867921,
year = {2000},
author = {Kiselev, LL and Oparina, NIu and Frolova, LIu},
title = {[Class 1 translation termination factors are structurally and functionally similar to suppressor of tRNA and are related to various structuro-functional families (prokaryotes and mitochondria--eukaryotes and archaebacteria)].},
journal = {Molekuliarnaia biologiia},
volume = {34},
number = {3},
pages = {427-442},
pmid = {10867921},
issn = {0026-8984},
mesh = {Amino Acid Sequence ; Amino Acyl-tRNA Synthetases/metabolism ; Animals ; Archaea/*genetics ; Eukaryotic Cells/*metabolism ; Humans ; Mitochondria/*genetics ; Molecular Sequence Data ; Peptide Termination Factors/*genetics ; Prokaryotic Cells/*metabolism ; Protein Biosynthesis/*genetics ; RNA, Transfer/antagonists &amp; inhibitors/*metabolism ; Sequence Homology, Amino Acid ; Structure-Activity Relationship ; },
}
@article {pmid10866967,
year = {2000},
author = {Bagatolli, L and Gratton, E and Khan, TK and Chong, PL},
title = {Two-photon fluorescence microscopy studies of bipolar tetraether giant liposomes from thermoacidophilic archaebacteria Sulfolobus acidocaldarius.},
journal = {Biophysical journal},
volume = {79},
number = {1},
pages = {416-425},
pmid = {10866967},
issn = {0006-3495},
support = {RR03155/RR/NCRR NIH HHS/United States ; },
mesh = {2-Naphthylamine/*analogs &amp; derivatives/chemistry ; Diglycerides/*chemistry ; Ethers/*chemistry ; Fluorescent Dyes/chemistry ; Hydrogen-Ion Concentration ; Laurates/chemistry ; Liposomes/*chemistry/ultrastructure ; Microscopy, Fluorescence/methods ; Sulfolobus acidocaldarius/*chemistry/ultrastructure ; Temperature ; },
abstract = {The effects of temperature and pH on Laurdan (6-lauroyl-2-(dimethylamino)naphthalene) fluorescence intensity images of giant unilamellar vesicles (GUVs) (approximately 20-150 microm in diameter) composed of the polar lipid fraction E (PLFE) from the thermoacidophilic archaebacteria Sulfolobus acidocaldarius have been studied using two-photon excitation. PLFE GUVs made by the electroformation method were stable and well suited for microscopy studies. The generalized polarization (GP) of Laurdan fluorescence in the center cross section of the vesicles has been determined as a function of temperature at pH 7.23 and pH 2.68. At all of the temperatures and pHs examined, the GP values are low (below or close to 0), and the GP histograms show a broad distribution width (> 0.3). When excited with light polarized in the y direction, Laurdan fluorescence in the center cross section of the PLFE GUVs exhibits a photoselection effect showing much higher intensities in the x direction of the vesicles, a result opposite that previously obtained on monopolar diester phospholipids. This result indicates that the chromophore of Laurdan in PLFE GUVs is aligned parallel to the membrane surface. The x direction photoselection effect and the low GP values lead us to further propose that the Laurdan chromophore resides in the polar headgroup region of the PLFE liposomes, while the lauroyl tail inserts into the hydrocarbon core of the membrane. This unusual L-shaped disposition is presumably caused by the unique lipid structures and by the rigid and tight membrane packing in PLFE liposomes. The GP exhibited, at both pH values, a small but abrupt decrease near 50 degrees C, suggesting a conformational change in the polar headgroups of PLFE. This transition temperature fully agrees with the d-spacing data recently measured by small-angle x-ray diffraction and with the pyrene-labeled phosphatidylcholine and perylene fluorescence data previously obtained from PLFE multilamellar vesicles. Interestingly, the two-photon Laurdan fluorescence images showed snowflake-like lipid domains in PLFE GUVs at pH 7.23 and low temperatures (<20 degrees C in the cooling scan and <24 degrees C in the heating scan). These domains, attributable to lipid lateral separation, were stable and laterally immobile at low temperatures (<23 degrees C), again suggesting tight membrane packing in the PLFE GUVs.},
}
@article {pmid10862614,
year = {2000},
author = {Bai, Y and Fox, DT and Lacy, JA and Van Lanen, SG and Iwata-Reuyl, D},
title = {Hypermodification of tRNA in Thermophilic archaea. Cloning, overexpression, and characterization of tRNA-guanine transglycosylase from Methanococcus jannaschii.},
journal = {The Journal of biological chemistry},
volume = {275},
number = {37},
pages = {28731-28738},
doi = {10.1074/jbc.M002174200},
pmid = {10862614},
issn = {0021-9258},
mesh = {Amino Acid Sequence ; Base Sequence ; Cloning, Molecular ; Codon ; Escherichia coli/genetics ; Methanococcus/*enzymology ; Molecular Sequence Data ; Pentosyltransferases/chemistry/*genetics/isolation &amp; purification ; RNA, Transfer/metabolism ; Recombinant Proteins/isolation &amp; purification ; },
abstract = {tRNA is structurally unique among nucleic acids in harboring an astonishing diversity of modified nucleosides. Two structural variants of the hypermodified nucleoside 7-deazaguanosine have been identified in tRNA: queuosine, which is found at the wobble position of the anticodon in bacterial and eukaryotic tRNA, and archaeosine, which is found at position 15 of the D-loop in archaeal tRNA. From homology searching of the Methanococcus jannaschii genome, a gene coding for an enzyme in the biosynthesis of archaeosine (tgt) was identified and cloned. The tgt gene was overexpressed in an Escherichia coli expression system, and the recombinant tRNA-guanine transglycosylase enzyme was purified and characterized. The enzyme catalyzes a transglycosylation reaction in which guanine is eliminated from position 15 of the tRNA and an archaeosine precursor (preQ(0)) is inserted. The enzyme is able to utilize both guanine and the 7-deazaguanine base preQ(0) as substrates, but not other 7-deazaguanine bases, and is able to modify tRNA from all three phylogenetic domains. The enzyme shows optimal activity at high temperature and acidic pH, consistent with the optimal growth conditions of M. jannaschii. The nature of the temperature dependence is consistent with a requirement for some degree of tRNA tertiary structure in order for recognition by the enzyme to occur.},
}
@article {pmid10846208,
year = {2000},
author = {Sievert, SM and Ziebis, W and Kuever, J and Sahm, K},
title = {Relative abundance of Archaea and Bacteria along a thermal gradient of a shallow-water hydrothermal vent quantified by rRNA slot-blot hybridization.},
journal = {Microbiology (Reading, England)},
volume = {146 (Pt 6)},
number = {},
pages = {1287-1293},
doi = {10.1099/00221287-146-6-1287},
pmid = {10846208},
issn = {1350-0872},
mesh = {Archaea/*genetics/*isolation &amp; purification ; Bacteria/*genetics/*isolation &amp; purification ; Greece ; Hot Temperature ; Nucleic Acid Hybridization ; RNA, Archaeal/analysis/genetics ; RNA, Bacterial/analysis/genetics ; RNA, Ribosomal, 16S/analysis/genetics ; *Water Microbiology ; },
abstract = {Slot-blot hybridization of rRNA with domain-specific oligonucleotide probes targeting the 16S rRNA of Archaea and Bacteria was utilized to assess the relative abundance of these domains along a thermal gradient at a shallow submarine hydrothermal vent near Milos Island (Greece). The highest prokaryotic rRNA concentrations (defined as the sum of bacterial and archaeal rRNA) were found in the uppermost sediment surface (0-20 mm), decreasing strongly with depth. This indicates that the microbial activity was mainly occurring in the surface layer of this hydrothermal vent. Furthermore, rRNA concentrations were higher in regions closer to the vent, suggesting that the hydrothermal activity stimulated microbial activity. Archaea seemed to be a minor component of the microbial community at this vent site, even in the zones with higher temperatures. Bacteria made up at least 78% (mean 95%) of the prokaryotic rRNA. However, along the steepest temperature gradient, the proportion of archaeal rRNA increased. Nevertheless, even in the hottest sediment layer where a quantification was possible (in situ temperature 82 degrees C) archaeal rRNA made up only 11.9% of the prokaryotic rRNA. This suggests that Archaea were generally of minor importance at this vent site and were probably restricted to a narrow niche. The factors that allow Bacteria to dominate in a high temperature environment that was once believed to be the realm of Archaea remain elusive.},
}
@article {pmid10843038,
year = {2000},
author = {Golyshina, OV and Pivovarova, TA and Karavaiko, GI and Kondratéva, TF and Moore, ER and Abraham, WR and Lünsdorf, H and Timmis, KN and Yakimov, MM and Golyshin, PN},
title = {Ferroplasma acidiphilum gen. nov., sp. nov., an acidophilic, autotrophic, ferrous-iron-oxidizing, cell-wall-lacking, mesophilic member of the Ferroplasmaceae fam. nov., comprising a distinct lineage of the Archaea.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {50 Pt 3},
number = {},
pages = {997-1006},
doi = {10.1099/00207713-50-3-997},
pmid = {10843038},
issn = {1466-5026},
mesh = {Aerobiosis ; Cell Wall ; Culture Media ; Ferrous Compounds/*metabolism ; Hydrogen-Ion Concentration ; Iron/*metabolism ; Molecular Sequence Data ; Oxidation-Reduction ; Phenotype ; Phylogeny ; Temperature ; Thermoplasmales/*classification/growth &amp; development/metabolism/ultrastructure ; },
abstract = {An isolate of an acidophilic archaeon, strain YT, was obtained from a bioleaching pilot plant. The organism oxidizes ferrous iron as the sole energy source and fixes inorganic carbon as the sole carbon source. The optimal pH for growth is 1.7, although growth is observed in the range pH 1.3 to 2.2. The cells are pleomorphic and without a cell wall. 16S rRNA gene sequence analysis showed this strain to cluster phylogenetically within the order 'Thermoplasmales' sensu Woese, although with only 89.9 and 87.2% sequence identity, respectively, to its closest relatives, Picrophilus oshimae and Thermoplasma acidophilum. Other principal differences from described species of the 'Thermoplasmales' are autotrophy (strain YT is obligately autotrophic), the absence of lipid components typical of the ' Thermoplasmales' (no detectable tetraethers) and a lower temperature range for growth (growth of strain YT occurs between 15 and 45 degrees C). None of the sugars, amino acids, organic acids or other organic compounds tested was utilized as a carbon source. On the basis of the information described above, the name Ferroplasma acidiphilum gen. nov., sp. nov. is proposed for strain YT within a new family, the Ferroplasmaceae fam. nov. Strain YT is the type and only strain of F. acidiphilum. This is the first report of an autotrophic, ferrous-iron-oxidizing, cell-wall-lacking archaeon.},
}
@article {pmid10839620,
year = {1999},
author = {Tokunaga, H and Hara, S and Arakawa, T and Ishibashi, M and Gupta, RS and Tokunaga, M},
title = {Identification and partial purification of DnaK homologue from extremely halophilic archaebacteria, Halobacterium cutirubrum.},
journal = {Journal of protein chemistry},
volume = {18},
number = {8},
pages = {837-844},
pmid = {10839620},
issn = {0277-8033},
mesh = {Amino Acid Sequence ; Archaeal Proteins/*isolation &amp; purification/metabolism ; Chromatography, Agarose/methods ; Electrophoresis, Polyacrylamide Gel ; Escherichia coli/genetics ; *Escherichia coli Proteins ; HSP70 Heat-Shock Proteins/genetics/*isolation &amp; purification/*metabolism ; Halobacterium/*chemistry/metabolism ; Molecular Sequence Data ; Recombinant Proteins/genetics/metabolism ; Sequence Analysis, Protein ; Sequence Homology, Amino Acid ; Trypsin/metabolism ; },
abstract = {The levels of synthesis of six proteins were increased at elevated growth temperature of the extremely halophilic archaebacterium Halobacterium cutirubrum. One of these proteins, with an apparent molecular mass of 97 kDa on sodium dodecylsulfate-polyacrylamide gel electrophoresis (SDS-PAGE), bound to an ATP-agarose column in the presence of 4 M NaCl, but not in the absence of salt, indicating that this protein retained its ATP-binding activity only at high salt concentration. The NH2-terminal sequence of this protein and the internal sequences of the tryptic peptides covering 1/3 of the total number of residues coincided with that deduced from the nucleotide sequence of the dnaK gene isolated from H. cutirubrum. The results strongly suggest that this apparent 97-kDa protein is the gene product of dnaK, although the molecular mass calculated from the nucleotide sequence is only 68,495, much smaller than the value of this protein determined by SDS-PAGE. Ferguson plot analysis indicated that this protein showed anomalous mobility on SDS-PAGE. We have purified DnaK homologue to greater than 90% homogeneity with stepwise elution from an ATP-agarose column.},
}
@article {pmid10838586,
year = {2000},
author = {Bernander, R},
title = {Chromosome replication, nucleoid segregation and cell division in archaea.},
journal = {Trends in microbiology},
volume = {8},
number = {6},
pages = {278-283},
doi = {10.1016/s0966-842x(00)01760-1},
pmid = {10838586},
issn = {0966-842X},
mesh = {Archaea/cytology/*genetics ; Archaeal Proteins/genetics ; Cell Cycle Proteins/metabolism ; Cell Division ; Cell Nucleus/metabolism ; Chromosome Segregation ; Chromosomes, Archaeal/*metabolism ; DNA Replication ; DNA, Archaeal/chemistry/metabolism ; DNA-Directed DNA Polymerase/physiology ; Proliferating Cell Nuclear Antigen/metabolism ; *Saccharomyces cerevisiae Proteins ; },
abstract = {Recent progress in cell cycle analysis of archaea has included the identification of putative chromosome replication origins, novel DNA polymerases and an unusual mode of cell cycle organization featuring multiple copies of the chromosome and asymmetric cell divisions. Genome sequence data indicate that in crenarchaea, the 'ubiquitous' FtsZ/MinD-based prokaryotic cell division apparatus is absent and division therefore must occur by unique, as-yet-unidentified mechanisms. The evolutionary and functional relationships between the archaeal Cdc6 protein and bacterial and eukaryal replication initiation factors are discussed.},
}
@article {pmid10832633,
year = {2000},
author = {Jolley, KA and Maddocks, DG and Gyles, SL and Mullan, Z and Tang, SL and Dyall-Smith, ML and Hough, DW and Danson, MJ},
title = {2-Oxoacid dehydrogenase multienzyme complexes in the halophilic Archaea? Gene sequences and protein structural predictions.},
journal = {Microbiology (Reading, England)},
volume = {146 (Pt 5)},
number = {},
pages = {1061-1069},
doi = {10.1099/00221287-146-5-1061},
pmid = {10832633},
issn = {1350-0872},
mesh = {3-Methyl-2-Oxobutanoate Dehydrogenase (Lipoamide) ; Amino Acid Sequence ; Archaeal Proteins/chemistry/*genetics ; Base Sequence ; *Genes, Archaeal ; Halobacteriales/enzymology/*genetics ; Ketone Oxidoreductases/chemistry/*genetics ; Molecular Sequence Data ; Molecular Structure ; Multienzyme Complexes/chemistry/*genetics ; Open Reading Frames ; Operon ; Potassium Channels/genetics ; Sequence Alignment ; Shaker Superfamily of Potassium Channels ; },
abstract = {All Archaea catalyse the conversion of pyruvate to acetyl-CoA via a simple pyruvate oxidoreductase. This is in contrast to the Eukarya and most aerobic bacteria, which use the pyruvate dehydrogenase multienzyme complex [PDHC], consisting of multiple copies of three component enzymes: E1 (pyruvate decarboxylase), E2 (lipoate acetyl-transferase) and E3 (dihydrolipoamide dehydrogenase, DHLipDH). Until now no PDHC activity has been found in the Archaea, although DHLipDH has been discovered in the extremely halophilic Archaea and its gene sequence has been determined. In this paper, the discovery and sequencing of an operon containing the DHLipDH gene in the halophilic archaeon Haloferax volcanii are reported. Upstream of the DHLipDH gene are 3 ORFs which show highest sequence identities with the E1alpha, E1beta and E2 genes of the PDHC from gram-positive organisms. Structural predictions of the proposed protein product of the E2 gene show a domain structure characteristic of the E2 component in PDHCs, and catalytically important residues, including the lysine to which the lipoic acid cofactor is covalently bound, are conserved. Northern analyses indicate the transcription of the whole operon, but no PDHC enzymic activity could be detected in cell extracts. The presence in the E2 gene of an insertion (equivalent to approximately 100 aa) not found in bacterial or eukaryal E2 proteins, might be predicted to prevent multienzyme complex assembly. This is the first detailed report of the genes for a putative 2-oxoacid dehydrogenase complex in the Archaea, and the evolutionary and metabolic consequences of these findings are discussed.},
}
@article {pmid10826803,
year = {2000},
author = {Wainø, M and Tindall, BJ and Ingvorsen, K},
title = {Halorhabdus utahensis gen. nov., sp. nov., an aerobic, extremely halophilic member of the Archaea from Great Salt Lake, Utah.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {50 Pt 1},
number = {},
pages = {183-190},
doi = {10.1099/00207713-50-1-183},
pmid = {10826803},
issn = {1466-5026},
mesh = {Base Composition ; Culture Media ; DNA, Archaeal/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Halobacteriaceae/*classification/isolation &amp; purification/physiology/ultrastructure ; Lipids/analysis ; Phylogeny ; Quinones/analysis ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sodium Chloride ; Utah ; *Water Microbiology ; },
abstract = {Strain AX-2T (T = type strain) was isolated from sediment of Great Salt Lake, Utah, USA. Optimal salinity for growth was 27% (w/v) NaCl and only a few carbohydrates supported growth of the strain. Strain AX-2T did not grow on complex substrates such as yeast extract or peptone. 16S rRNA analysis revealed that strain AX-2T was a member of the phyletic group defined by the family Halobacteriaceae, but there was a low degree of similarity to other members of this family. The polar lipid composition comprising phosphatidyl glycerol, the methylated derivative of diphosphatidyl glycerol, triglycosyl diethers and sulfated triglycosyl diethers, but not phosphatidyl glycerosulfate, was not identical to that of any other aerobic, halophilic species. On the basis of the data presented, it is proposed that strain AX-2T should be placed in a new taxon, for which the name Halorhabdus utahensis is appropriate. The type strain is strain AX-2T (= DSM 12940T).},
}
@article {pmid10824097,
year = {2000},
author = {Bartoschek, S and Vorholt, JA and Thauer, RK and Geierstanger, BH and Griesinger, C},
title = {N-carboxymethanofuran (carbamate) formation from methanofuran and CO2 in methanogenic archaea. Thermodynamics and kinetics of the spontaneous reaction.},
journal = {European journal of biochemistry},
volume = {267},
number = {11},
pages = {3130-3138},
doi = {10.1046/j.1432-1327.2000.01331.x},
pmid = {10824097},
issn = {0014-2956},
mesh = {Aldehyde Oxidoreductases/metabolism ; Bacterial Proteins/metabolism ; Carbamates/*metabolism ; Carbon Dioxide/*metabolism ; Furans/*metabolism ; Hydrogen-Ion Concentration ; Kinetics ; Magnetic Resonance Spectroscopy ; Methane/metabolism ; Methanobacterium/*metabolism ; Methanosarcina barkeri/*metabolism ; Thermodynamics ; },
abstract = {N-carboxymethanofuran (carbamate) formation from unprotonated methanofuran (MFR) and CO2 is the first reaction in the reduction of CO2 to methane in methanogenic archaea. The reaction proceeds spontaneously. We address here the question whether the rate of spontaneous carbamate formation is high enough to account for the observed rate of methanogenesis from CO2. The rates of carbamate formation (v1) and cleavage (v2) were determined under equilibrium conditions via 2D proton exchange NMR spectroscopy (EXSY). At pH 7.0 and 300 K the second order rate constant k1* of carbamate formation from 'MFR'(MFR + MFRH+) and 'CO2' (CO2 + H2CO3 + HCO3-+ CO32-) was found to be 7 M-1.s-1 (v1 = k1* ['MFR'] ['CO2']) while the pseudo first order rate constant k2* of carbamate cleavage was 12 s-1 (v2 = k2* [carbamate]). The equilibrium constant K* = k1*/k2* = [carbamate]/['MFR']['CO2'] was 0.6 M-1 at pH 7.0 corresponding to a free energy change DeltaG degrees ' of + 1.3 kJ.mol-1. The pH and temperature dependence of k1*, of k2* and of K* were determined. From the second order rate constant k1* it was calculated that under physiological conditions the rate of spontaneous carbamate formation is of the same order as the maximal rate of methane formation and as the rate of spontaneous CO2 formation from HCO3- in methanogenic archaea, the latter being important as CO2 is mainly present as HCO3- which has to be converted to CO2 before it can react with MFR. An enzyme catalyzed carbamate formation thus appears not to be required for methanogenesis from CO2. Consistent with this conclusion is our finding that the rate of carbamate formation was not enhanced by cell extracts of Methanosarcina barkeri and Methanobacterium thermoautotrophicum or by purified formylmethanofuran dehydrogenase which catalyzes the reduction of N-carboxymethanofuran to N-formylmethanofuran. From the concentrations of 'CO2' and of 'MFR' determined by 1D-NMR spectroscopy and the pKa of H2CO3 and of MFRH+ the concentrations of CO2 and of MFR were obtained, allowing to calculate k1 (v1 = k1 [MFR] [CO2]). The second order rate constant k1 was found to be approximately 1000 M-1 x s-1 at 300 K and pH values between 7.0 and 8. 0 which is in the order of k1 values determined for other carbamate forming reactions by stopped flow.},
}
@article {pmid10802060,
year = {2000},
author = {Fritz, G and Büchert, T and Huber, H and Stetter, KO and Kroneck, PM},
title = {Adenylylsulfate reductases from archaea and bacteria are 1:1 alphabeta-heterodimeric iron-sulfur flavoenzymes--high similarity of molecular properties emphasizes their central role in sulfur metabolism.},
journal = {FEBS letters},
volume = {473},
number = {1},
pages = {63-66},
doi = {10.1016/s0014-5793(00)01500-3},
pmid = {10802060},
issn = {0014-5793},
mesh = {Adenosine Monophosphate/metabolism ; Amino Acid Motifs ; Archaeoglobus fulgidus/*enzymology/genetics/metabolism ; Binding Sites ; Cysteine/genetics/metabolism ; Desulfovibrio/*enzymology/genetics/metabolism ; Desulfovibrio vulgaris/enzymology/genetics/metabolism ; Dimerization ; Electron Spin Resonance Spectroscopy ; Flavin-Adenine Dinucleotide/analysis/metabolism ; Genes, Bacterial/genetics ; Iron/analysis/metabolism ; Iron-Sulfur Proteins/chemistry/genetics/isolation &amp; purification/*metabolism ; Models, Molecular ; Molecular Weight ; Operon/genetics ; Oxidation-Reduction ; Oxidoreductases/chemistry/genetics/*isolation &amp; purification/*metabolism ; *Oxidoreductases Acting on Sulfur Group Donors ; Sequence Homology, Amino Acid ; Spectrophotometry ; Sulfur/analysis/*metabolism ; Sulfur Compounds/metabolism ; },
abstract = {Highly active adenylylsulfate (APS) reductase was isolated under N(2)/H(2) from sulfate-reducing and sulfide-oxidizing bacteria and archaea. It was a 1:1 alphabeta-heterodimer of molecular mass approximately 95 kDa, and two subunits (alpha approximately 75, beta approximately 20 kDa). The specific activity was 11-14 micromol (min mg)(-1); cofactor analysis revealed 0.96+/-0.05 FAD, 7.5+/-0.1 Fe and 7.9+/-0.25 S(2-). The photochemically reduced enzyme had a multiline EPR spectrum resulting from two interacting [4Fe-4S] centers. The properties of the different APS reductases were remarkably similar, although the enzyme is involved in different metabolic pathways and was isolated from phylogenetically far separated organisms. A structural model is proposed, with FAD bound to the alpha-subunit, and two [4Fe-4S] centers located in close proximity on the beta-subunit.},
}
@article {pmid10785368,
year = {2000},
author = {Sauer, K and Thauer, RK},
title = {Methyl-coenzyme M formation in methanogenic archaea. Involvement of zinc in coenzyme M activation.},
journal = {European journal of biochemistry},
volume = {267},
number = {9},
pages = {2498-2504},
doi = {10.1046/j.1432-1327.2000.01245.x},
pmid = {10785368},
issn = {0014-2956},
mesh = {Enzyme Activation ; Mesna/*analogs &amp; derivatives/metabolism ; Methanosarcina barkeri/*enzymology ; Methyltransferases/metabolism ; Protein Binding ; Recombinant Proteins/metabolism ; Zinc/*metabolism ; },
abstract = {Methyl-coenzyme M (2-methylthioethane sulfonate) is the key intermediate of methane formation in methanogenic archaea. It is generated from coenzyme M (2-mercaptoethane sulfonate) in methyl transfer reactions catalyzed by proteins containing zinc. Here, we report that, for methyltransferase MtaA from Methanosarcina barkeri, the zinc is involved in coenzyme M activation. For the experiments an inactive MtaA apoprotein was obtained by heterologous overproduction in Escherichia coli grown in the presence of 2 mM EDTA. The apoprotein was found to react with zinc or cobalt to the fully active holoenzyme. Appoximately 1 mol of transition metal was bound per mol of protein. Upon incubation of the holoenzyme with coenzyme M approximately 1 mol of proton was released per mol of zinc or cobalt. Protons were not released upon incubation of the apoprotein with coenzyme M or of the holoprotein with other thiol compounds or with methyl-coenzyme M. The findings are interpreted as indicating that the role of the transition metal in MtaA is to lower the microscopic pKa of the thiol group of coenzyme M by coordination to the zinc, and thus to increase its nucleophilicity for methyl group attack. The pKZn2+ of MtaA was re-determined and found to be > 15 and not 9.6 as previously reported by us.},
}
@article {pmid10782109,
year = {2000},
author = {Faguy, DM and Doolittle, WF},
title = {Horizontal transfer of catalase-peroxidase genes between archaea and pathogenic bacteria.},
journal = {Trends in genetics : TIG},
volume = {16},
number = {5},
pages = {196-197},
doi = {10.1016/s0168-9525(00)02007-2},
pmid = {10782109},
issn = {0168-9525},
mesh = {Archaea/*genetics ; Bacteria/*genetics/pathogenicity ; Catalase/*genetics ; Escherichia coli/genetics ; *Gene Transfer, Horizontal ; Peroxidases/*genetics ; Phylogeny ; },
}
@article {pmid10775111,
year = {2000},
author = {Omer, AD and Lowe, TM and Russell, AG and Ebhardt, H and Eddy, SR and Dennis, PP},
title = {Homologs of small nucleolar RNAs in Archaea.},
journal = {Science (New York, N.Y.)},
volume = {288},
number = {5465},
pages = {517-522},
doi = {10.1126/science.288.5465.517},
pmid = {10775111},
issn = {0036-8075},
support = {HG01363/HG/NHGRI NIH HHS/United States ; },
mesh = {Archaea/*genetics ; Archaeal Proteins/genetics ; Base Sequence ; Chromosomal Proteins, Non-Histone/genetics ; Cloning, Molecular ; Genome, Archaeal ; Methylation ; Models, Statistical ; Molecular Sequence Data ; Nuclear Proteins/genetics ; RNA Processing, Post-Transcriptional ; RNA, Archaeal/chemistry/*genetics/metabolism ; RNA, Ribosomal/chemistry/genetics/metabolism ; RNA, Small Nucleolar/chemistry/*genetics/metabolism ; Sulfolobus acidocaldarius/*genetics ; RNA, Small Untranslated ; },
abstract = {In eukaryotes, dozens of posttranscriptional modifications are directed to specific nucleotides in ribosomal RNAs (rRNAs) by small nucleolar RNAs (snoRNAs). We identified homologs of snoRNA genes in both branches of the Archaea. Eighteen small sno-like RNAs (sRNAs) were cloned from the archaeon Sulfolobus acidocaldarius by coimmunoprecipitation with archaeal fibrillarin and NOP56, the homologs of eukaryotic snoRNA-associated proteins. We trained a probabilistic model on these sRNAs to search for more sRNAs in archaeal genomic sequences. Over 200 additional sRNAs were identified in seven archaeal genomes representing both the Crenarchaeota and the Euryarchaeota. snoRNA-based rRNA processing was therefore probably present in the last common ancestor of Archaea and Eukarya, predating the evolution of a morphologically distinct nucleolus.},
}
@article {pmid10760181,
year = {2000},
author = {Mojica, FJ and Díez-Villaseñor, C and Soria, E and Juez, G},
title = {Biological significance of a family of regularly spaced repeats in the genomes of Archaea, Bacteria and mitochondria.},
journal = {Molecular microbiology},
volume = {36},
number = {1},
pages = {244-246},
doi = {10.1046/j.1365-2958.2000.01838.x},
pmid = {10760181},
issn = {0950-382X},
mesh = {Archaea/*genetics ; Bacteria/*genetics ; Base Sequence ; Binding Sites ; Conserved Sequence ; DNA-Binding Proteins ; Mitochondria/*genetics ; *Repetitive Sequences, Nucleic Acid ; },
}
@article {pmid10736750,
year = {1999},
author = {Hoppert, M and Mayer, F},
title = {Principles of macromolecular organization and cell function in bacteria and archaea.},
journal = {Cell biochemistry and biophysics},
volume = {31},
number = {3},
pages = {247-284},
doi = {10.1007/BF02738242},
pmid = {10736750},
issn = {1085-9195},
mesh = {Archaea/*cytology/*physiology/ultrastructure ; Bacteria/*cytology/ultrastructure ; *Bacterial Physiological Phenomena ; Cell Membrane/physiology/ultrastructure ; Cytoskeletal Proteins/chemistry/ultrastructure ; Cytoskeleton/physiology/*ultrastructure ; Models, Structural ; Multienzyme Complexes/chemistry/metabolism ; },
abstract = {Structural organization of the cytoplasm by compartmentation is a well established fact for the eukaryotic cell. In prokaryotes, compartmentation is less obvious. Most prokaryotes do not need intracytoplasmic membranes to maintain their vital functions. This review, especially dealing with prokaryotes, will point out that compartmentation in prokaryotes is present, but not only achieved by membranes. Besides membranes, the nucleoid, multienzyme complexes and metabolons, storage granules, and cytoskeletal elements are involved in compartmentation. In this respect, the organization of the cytoplasm of prokaryotes is similar to that in the eukaryotic cell. Compartmentation influences properties of water in cells.},
}
@article {pmid10729828,
year = {2000},
author = {Forterre, P and Bouthier De La Tour, C and Philippe, H and Duguet, M},
title = {Reverse gyrase from hyperthermophiles: probable transfer of a thermoadaptation trait from archaea to bacteria.},
journal = {Trends in genetics : TIG},
volume = {16},
number = {4},
pages = {152-154},
doi = {10.1016/s0168-9525(00)01980-6},
pmid = {10729828},
issn = {0168-9525},
mesh = {Adaptation, Physiological ; Archaea/classification/genetics ; *DNA Topoisomerases, Type I ; DNA Topoisomerases, Type II/classification/*genetics ; *Genes, Archaeal ; *Genes, Bacterial ; Thermotoga maritima/genetics ; },
}
@article {pmid10698781,
year = {2000},
author = {Pancost, RD and Sinninghe Damsté, JS and de Lint, S and van der Maarel, MJ and Gottschal, JC},
title = {Biomarker evidence for widespread anaerobic methane oxidation in Mediterranean sediments by a consortium of methanogenic archaea and bacteria. The Medinaut Shipboard Scientific Party.},
journal = {Applied and environmental microbiology},
volume = {66},
number = {3},
pages = {1126-1132},
pmid = {10698781},
issn = {0099-2240},
mesh = {Anaerobiosis ; Bacteria/chemistry/*metabolism ; Euryarchaeota/chemistry/*metabolism ; Geologic Sediments/chemistry/*microbiology ; Lipids/chemistry ; Marine Biology/instrumentation ; Mediterranean Sea ; Methane/*metabolism ; Oxidation-Reduction ; Seawater/chemistry/*microbiology ; Ships ; Volcanic Eruptions ; },
abstract = {Although abundant geochemical data indicate that anaerobic methane oxidation occurs in marine sediments, the linkage to specific microorganisms remains unclear. In order to examine processes of methane consumption and oxidation, sediment samples from mud volcanoes at two distinct sites on the Mediterranean Ridge were collected via the submersible Nautile. Geochemical data strongly indicate that methane is oxidized under anaerobic conditions, and compound-specific carbon isotope analyses indicate that this reaction is facilitated by a consortium of archaea and bacteria. Specifically, these methane-rich sediments contain high abundances of methanogen-specific biomarkers that are significantly depleted in (13)C (delta(13)C values are as low as -95 per thousand). Biomarkers inferred to derive from sulfate-reducing bacteria and other heterotrophic bacteria are similarly depleted. Consistent with previous work, such depletion can be explained by consumption of (13)C-depleted methane by methanogens operating in reverse and as part a consortium of organisms in which sulfate serves as the terminal electron acceptor. Moreover, our results indicate that this process is widespread in Mediterranean mud volcanoes and in some localized settings is the predominant microbiological process.},
}
@article {pmid10689351,
year = {2000},
author = {Bachhawat, N and Mande, SC},
title = {Complex evolution of the inositol-1-phosphate synthase gene among archaea and eubacteria.},
journal = {Trends in genetics : TIG},
volume = {16},
number = {3},
pages = {111-113},
doi = {10.1016/s0168-9525(99)01966-6},
pmid = {10689351},
issn = {0168-9525},
mesh = {Archaea/*genetics ; Archaeal Proteins/*genetics ; Bacteria/*genetics ; Bacterial Proteins/*genetics ; *Evolution, Molecular ; *Genes ; Genes, Bacterial ; Inositol/metabolism ; Myo-Inositol-1-Phosphate Synthase/*genetics ; Phylogeny ; Species Specificity ; },
}
@article {pmid10681051,
year = {2000},
author = {Laska, S and Kletzin, A},
title = {Improved purification of the membrane-bound hydrogenase-sulfur-reductase complex from thermophilic archaea using epsilon-aminocaproic acid-containing chromatography buffers.},
journal = {Journal of chromatography. B, Biomedical sciences and applications},
volume = {737},
number = {1-2},
pages = {151-160},
doi = {10.1016/s0378-4347(99)00362-x},
pmid = {10681051},
issn = {1387-2273},
mesh = {Aminocaproic Acid/*chemistry ; Archaea/*enzymology ; Buffers ; Chromatography, Ion Exchange/*methods ; Electrophoresis, Polyacrylamide Gel ; Hydrogenase/*isolation &amp; purification/metabolism ; Membrane Proteins/*isolation &amp; purification/metabolism ; Oxidoreductases/*isolation &amp; purification/metabolism ; },
abstract = {A hydrogenase-sulfur reductase (SR) complex was purified from membrane preparations of the extremely thermophilic, acidophilic archaeon Acidianus ambivalens using a combination of sucrose density gradient centrifugation and column chromatography (FPLC). All chromatographic steps were performed in the presence of 0.5% epsilon-aminocaproic acid resulting in the elution of the SR complex as a sharp peak. In contrast, chromatography using buffers without epsilon-aminocaproic acid, or in the presence of detergents, were not successful. The purified A. ambivalens SR complex consisted of at least four subunits with relative molecular masses of 110000, 66000, 39000 and 29000, respectively. A similar procedure was applied to purify the membrane-bound hydrogenase from Thermoproteus neutrophilus, a non-related extremely thermophilic but neutrophilic archaeon, which consisted of only two subunits with relative molecular masses of 66000 and 39000, respectively.},
}
@article {pmid10676961,
year = {2000},
author = {Hou, S and Larsen, RW and Boudko, D and Riley, CW and Karatan, E and Zimmer, M and Ordal, GW and Alam, M},
title = {Myoglobin-like aerotaxis transducers in Archaea and Bacteria.},
journal = {Nature},
volume = {403},
number = {6769},
pages = {540-544},
doi = {10.1038/35000570},
pmid = {10676961},
issn = {0028-0836},
mesh = {Amino Acid Sequence ; Animals ; Archaeal Proteins/genetics/*isolation &amp; purification ; Bacillus subtilis/*chemistry/physiology ; Bacterial Proteins/chemistry/genetics/*isolation &amp; purification ; Chemotaxis ; Escherichia coli/physiology ; Halobacterium salinarum/*chemistry/physiology ; Heme-Binding Proteins ; Hemeproteins/chemistry/genetics/*isolation &amp; purification ; Membrane Proteins/*isolation &amp; purification ; Methyl-Accepting Chemotaxis Proteins ; Molecular Sequence Data ; Oxygen/metabolism ; Recombinant Proteins/chemistry ; Sequence Homology, Amino Acid ; Signal Transduction ; },
abstract = {Haem-containing proteins such as haemoglobin and myoglobin play an essential role in oxygen transport and storage. Comparison of the amino-acid sequences of globins from Bacteria and Eukarya suggests that they share an early common ancestor, even though the proteins perform different functions in these two kingdoms. Until now, no members of the globin family have been found in the third kingdom, Archaea. Recent studies of biological signalling in the Bacteria and Eukarya have revealed a new class of haem-containing proteins that serve as sensors. Until now, no haem-based sensor has been described in the Archaea. Here we report the first myoglobin-like, haem-containing protein in the Archaea, and the first haem-based aerotactic transducer in the Bacteria (termed HemAT-Hs for the archaeon Halobacterium salinarum, and HemAT-Bs for Bacillus subtilis). These proteins exhibit spectral properties similar to those of myoglobin and trigger aerotactic responses.},
}
@article {pmid10675594,
year = {2000},
author = {Galperin, MY and Aravind, L and Koonin, EV},
title = {Aldolases of the DhnA family: a possible solution to the problem of pentose and hexose biosynthesis in archaea.},
journal = {FEMS microbiology letters},
volume = {183},
number = {2},
pages = {259-264},
doi = {10.1111/j.1574-6968.2000.tb08968.x},
pmid = {10675594},
issn = {0378-1097},
mesh = {Amino Acid Sequence ; Archaea/*metabolism ; Fructose-Bisphosphate Aldolase/chemistry/*metabolism ; Hexoses/*biosynthesis ; Molecular Sequence Data ; Pentoses/*biosynthesis ; Protein Folding ; },
abstract = {Sequence analysis of the recently identified class I aldolase of Escherichia coli (dhnA gene product) helped to identify its homologs in Chlamydia trachomatis, Chlamydiophyla pneumoniae and in each of the completely sequenced archaeal genomes. Iterative database searches revealed sequence similarities between the DhnA-family enzymes, deoxyribose phosphate aldolases and bacterial (class II) fructose bisphosphate aldolases and allowed prediction of similar three-dimensional structures (TIM-barrel fold) in all these enzymes. The Schiff base-forming lysyl residues of DhnA and deoxyribose phosphate aldolase are conserved in all members of the DhnA and deoxyribose phosphate aldolase families, indicating that these enzymes share common features with both class I and class II aldolases. The DhnA-family enzymes are predicted to possess an aldolase activity and to play a critical role in sugar biosynthesis in archaea.},
}
@article {pmid10660563,
year = {2000},
author = {Graham, DE and Bock, CL and Schalk-Hihi, C and Lu, ZJ and Markham, GD},
title = {Identification of a highly diverged class of S-adenosylmethionine synthetases in the archaea.},
journal = {The Journal of biological chemistry},
volume = {275},
number = {6},
pages = {4055-4059},
doi = {10.1074/jbc.275.6.4055},
pmid = {10660563},
issn = {0021-9258},
support = {CA06927/CA/NCI NIH HHS/United States ; GM31186/GM/NIGMS NIH HHS/United States ; },
mesh = {Amino Acid Sequence ; Archaeal Proteins/*chemistry ; Cloning, Molecular ; Escherichia coli ; Evolution, Molecular ; Kinetics ; Methanococcus/*enzymology ; Methionine Adenosyltransferase/*chemistry ; Molecular Sequence Data ; Phylogeny ; Recombinant Proteins/chemistry ; Sequence Alignment ; },
abstract = {S-adenosylmethionine is the primary alkylating agent in all known organisms. ATP:L-methionine S-adenosyltransferase (MAT) catalyzes the only known biosynthetic route to this central metabolite. Although the amino acid sequence of MAT is strongly conserved among bacteria and eukarya, no homologs have been recognized in the completed genome sequences of any archaea. In this study, MAT has been purified to homogeneity from the archaeon Methanococcus jannaschii, and the gene encoding it has been identified by mass spectrometry. The peptide mass map identifies the gene encoding MAT as MJ1208, a hypothetical open reading frame. The gene was cloned in Escherichia coli, and expressed enzyme has been purified and characterized. This protein has only 22 and 23% sequence identity to the E. coli and human enzymes, respectively, whereas those are 59% identical to each other. The few identical residues include the majority of those constituting the polar active site residues. Each complete archaeal genome sequence contains a homolog of this archaeal-type MAT. Surprisingly, three bacterial genomes encode both the archaeal and eukaryal/bacterial types of MAT. This identification of a second major class of MAT emphasizes the long evolutionary history of the archaeal lineage and the structural diversity found even in crucial metabolic enzymes.},
}
@article {pmid10648545,
year = {2000},
author = {Jansson, BP and Malandrin, L and Johansson, HE},
title = {Cell cycle arrest in archaea by the hypusination inhibitor N(1)-guanyl-1,7-diaminoheptane.},
journal = {Journal of bacteriology},
volume = {182},
number = {4},
pages = {1158-1161},
pmid = {10648545},
issn = {0021-9193},
mesh = {Cell Cycle/*drug effects ; Enzyme Inhibitors/*pharmacology ; Escherichia coli/drug effects/growth &amp; development ; Flow Cytometry ; Guanine/*analogs &amp; derivatives/pharmacology ; Lysine/analogs &amp; derivatives/metabolism ; Sulfolobus acidocaldarius/cytology/*drug effects/*growth &amp; development ; },
abstract = {Hypusination is an essential posttranslational modification unique to archaeal and eukaryotic protein synthesis initiation factor 5A (aIF5A and eIF5A, respectively). We have investigated the effect of the efficient hypusination inhibitor N(1)-guanyl-1,7-diaminoheptane (GC(7)) on four archaeal and one bacterial species. We found that (i) archaea are sensitive to GC(7), whereas the bacterium Escherichia coli is not, (ii) GC(7) causes rapid and reversible arrest of growth of the archaeon Sulfolobus acidocaldarius, and (iii) the growth arrest is accompanied by a specific reversible arrest of the cell cycle prior to cell division. Our findings establish a link between hypusination and sustained growth of archaea and thereby provide the framework to study molecular details of archaeal cell cycle in connection with in vivo functions of hypusine and of aIF5A and eIF5A.},
}
@article {pmid10637320,
year = {2000},
author = {Gelfand, MS and Koonin, EV and Mironov, AA},
title = {Prediction of transcription regulatory sites in Archaea by a comparative genomic approach.},
journal = {Nucleic acids research},
volume = {28},
number = {3},
pages = {695-705},
pmid = {10637320},
issn = {1362-4962},
mesh = {Archaea/enzymology/genetics ; Base Sequence ; *Computational Biology/methods ; Conserved Sequence/genetics ; Evolution, Molecular ; Genes, Archaeal/*genetics ; *Genome, Archaeal ; Glutamate-Ammonia Ligase/genetics ; Heat-Shock Proteins/genetics ; Histones/genetics ; Molecular Chaperones/genetics ; Molecular Sequence Data ; Nitrogen Fixation/genetics ; Phylogeny ; Promoter Regions, Genetic/genetics ; Purines/metabolism ; Regulon/genetics ; Response Elements/*genetics ; Sequence Alignment ; Transcription, Genetic/*genetics ; Tryptophan/genetics ; },
abstract = {Intragenomic and intergenomic comparisons of upstream nucleotide sequences of archaeal genes were performed with the goal of predicting transcription regulatory sites (operators) and identifying likely regulons. Learning sets for the detection of regulatory sites were constructed using the available experimental data on archaeal transcription regulation or by analogy with known bacterial regulons, and further analysis was performed using iterative profile searches. The information content of the candidate signals detected by this method is insufficient for reliable predictions to be made. Therefore, this approach has to be complemented by examination of evolutionary conservation in different archaeal genomes. This combined strategy resulted in the prediction of a conserved heat shock regulon in all euryarchaea, a nitrogen fixation regulon in the methanogens Methanococcus jannaschii and Methanobacterium thermoautotrophicum and an aromatic amino acid regulon in M.thermoautotrophicum. Unexpectedly, the heat shock regulatory site was detected not only for genes that encode known chaperone proteins but also for archaeal histone genes. This suggests a possible function for archaeal histones in stress-related changes in DNA condensation. In addition, comparative analysis of the genomes of three Pyrococcus species resulted in the prediction of their purine metabolism and transport regulon. The results demonstrate the feasibility of prediction of at least some transcription regulatory sites by comparing poorly characterized prokaryotic genomes, particularly when several closely related genome sequences are available.},
}
@article {pmid10633118,
year = {2000},
author = {Li, WT and Shriver, JW and Reeve, JN},
title = {Mutational analysis of differences in thermostability between histones from mesophilic and hyperthermophilic archaea.},
journal = {Journal of bacteriology},
volume = {182},
number = {3},
pages = {812-817},
pmid = {10633118},
issn = {0021-9193},
support = {R01 GM053185/GM/NIGMS NIH HHS/United States ; GM53185/GM/NIGMS NIH HHS/United States ; },
mesh = {Amino Acid Sequence ; DNA Mutational Analysis ; Dimerization ; Histones/chemistry/*genetics ; Hot Temperature ; Methanobacterium ; Models, Molecular ; Molecular Sequence Data ; Protein Folding ; Protein Structure, Secondary ; },
abstract = {Amino acid residues responsible for the large difference in thermostability between HMfB and HFoB, archaeal histones from the hyperthermophile Methanothermus fervidus and the mesophile Methanobacterium formicicum, respectively, have been identified by site-specific mutagenesis. The thermal denaturation of approximately 70 archaeal histone variants has been monitored by circular dichroism, and the data generated were fit to a two-state unfolding model (dimer-->two random coil monomers) to obtain a standard-state (1M) melting temperature for each variant dimer. The results of single-, double-, and triple-residue substitutions reveal that the much higher stability of rHMfB dimers, relative to rHFoB dimers, is conferred predominantly by improved intermolecular hydrophobic interactions near the center of the histone dimer core and by additional favorable ion pairs on the dimer surface.},
}
@article {pmid10624685,
year = {1999},
author = {Ivanov, VN and Stabnikova, EV},
title = {[Use of the level of G+C n DNA for studying the molecular phylogeny o f methanogenic archaebacteria].},
journal = {Mikrobiologiia},
volume = {68},
number = {5},
pages = {710-715},
pmid = {10624685},
issn = {0026-3656},
mesh = {Adenosine/*analysis ; DNA, Archaeal/*chemistry/genetics ; Euryarchaeota/classification/*genetics ; Guanosine/*analysis ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; },
abstract = {A new method for theoretical analysis of the molecular phylogeny of bacteria, successfully applied earlier to nitrifying bacteria, was used to study the molecular phylogeny of methanogenic archaebacteria. The group studied included Methanococcus igneus, Methanococcus vannielii, Methanothermus fervidus, Methanolobus tindarius, Methanobacterium formicicum, Methanosarcina barkeri, Methanobacterium thermoformicicum, Methanoplanus limicola, Methanospirillum hungatei, and Methanobacterium thermoautotrophicum. Based on the hypothesis that direct linear regression always exists between evolutionary changes in the DNA G + C content and the primary structure of rRNA, the branching order of the phylogenetic tree of methanogenic archaebacteria was determined. For this tree, the values of the evolutionary distance between 16S rRNA primary structures Ei and the values of the G + C evolutionary distance P(i) exhibited a correlation coefficient 0.78. Thus, the DNA G + C content is not only an important taxonomic characteristics but also provides information helpful for the determination of the branching order of phylogenetic trees constructed based on 16S rRNA primary structures.},
}
@article {pmid10591015,
year = {1999},
author = {van de Vossenberg, JL and Driessen, AJ and Grant, WD and Konings, WN},
title = {Lipid membranes from halophilic and alkali-halophilic Archaea have a low H+ and Na+ permeability at high salt concentration.},
journal = {Extremophiles : life under extreme conditions},
volume = {3},
number = {4},
pages = {253-257},
doi = {10.1007/s007920050124},
pmid = {10591015},
issn = {1431-0651},
mesh = {Archaea/*physiology ; Cell Membrane/*physiology ; Cell Membrane Permeability ; Escherichia coli/physiology ; Hot Temperature ; *Hydrogen-Ion Concentration ; Kinetics ; Membrane Lipids/*physiology ; Osmolar Concentration ; Potassium/metabolism ; Protons ; Sodium/*metabolism ; },
abstract = {The influence of pH and the salt concentration on the proton and sodium ion permeability of liposomes formed from lipids of the halophile Halobacterium salinarum and the haloalkaliphile Halorubrum vacuolatum were studied. In contrast with liposomes formed from Escherichia coli lipids, liposomes formed from halophilic lipids remained stable up to 4M of NaCl and KCl. The proton permeability of the liposomes from lipids of halophiles was independent of the salt concentration and was essentially constant between pH 7 and pH 9. The sodium ion permeability increased with the salt concentration but was 10- to 100 fold lower than the proton permeability. It is concluded that the membranes of halophiles are stable over a wide range of salt concentrations and at elevated pH values and are well adapted to the halophilic conditions.},
}
@article {pmid10585970,
year = {1999},
author = {Macario, AJ and Lange, M and Ahring, BK and Conway de Macario, E},
title = {Stress genes and proteins in the archaea.},
journal = {Microbiology and molecular biology reviews : MMBR},
volume = {63},
number = {4},
pages = {923-67, table of contents},
pmid = {10585970},
issn = {1092-2172},
mesh = {Adaptation, Biological/*genetics ; Amino Acid Sequence ; Archaea/classification/*physiology/ultrastructure ; Archaeal Proteins/chemistry/*genetics ; *Genes, Archaeal ; Heat-Shock Proteins/chemistry/classification/genetics ; Heat-Shock Response/*genetics ; Molecular Chaperones/chemistry/classification/genetics ; Molecular Sequence Data ; Phylogeny ; },
abstract = {The field covered in this review is new; the first sequence of a gene encoding the molecular chaperone Hsp70 and the first description of a chaperonin in the archaea were reported in 1991. These findings boosted research in other areas beyond the archaea that were directly relevant to bacteria and eukaryotes, for example, stress gene regulation, the structure-function relationship of the chaperonin complex, protein-based molecular phylogeny of organisms and eukaryotic-cell organelles, molecular biology and biochemistry of life in extreme environments, and stress tolerance at the cellular and molecular levels. In the last 8 years, archaeal stress genes and proteins belonging to the families Hsp70, Hsp60 (chaperonins), Hsp40(DnaJ), and small heat-shock proteins (sHsp) have been studied. The hsp70(dnaK), hsp40(dnaJ), and grpE genes (the chaperone machine) have been sequenced in seven, four, and two species, respectively, but their expression has been examined in detail only in the mesophilic methanogen Methanosarcina mazei S-6. The proteins possess markers typical of bacterial homologs but none of the signatures distinctive of eukaryotes. In contrast, gene expression and transcription initiation signals and factors are of the eucaryal type, which suggests a hybrid archaeal-bacterial complexion for the Hsp70 system. Another remarkable feature is that several archaeal species in different phylogenetic branches do not have the gene hsp70(dnaK), an evolutionary puzzle that raises the important question of what replaces the product of this gene, Hsp70(DnaK), in protein biogenesis and refolding and for stress resistance. Although archaea are prokaryotes like bacteria, their Hsp60 (chaperonin) family is of type (group) II, similar to that of the eukaryotic cytosol; however, unlike the latter, which has several different members, the archaeal chaperonin system usually includes only two (in some species one and in others possibly three) related subunits of approximately 60 kDa. These form, in various combinations depending on the species, a large structure or chaperonin complex sometimes called the thermosome. This multimolecular assembly is similar to the bacterial chaperonin complex GroEL/S, but it is made of only the large, double-ring oligomers each with eight (or nine) subunits instead of seven as in the bacterial complex. Like Hsp70(DnaK), the archaeal chaperonin subunits are remarkable for their evolution, but for a different reason. Ubiquitous among archaea, the chaperonins show a pattern of recurrent gene duplication-hetero-oligomeric chaperonin complexes appear to have evolved several times independently. The stress response and stress tolerance in the archaea involve chaperones, chaperonins, other heat shock (stress) proteins including sHsp, thermoprotectants, the proteasome, as yet incompletely understood thermoresistant features of many molecules, and formation of multicellular structures. The latter structures include single- and mixed-species (bacterial-archaeal) types. Many questions remain unanswered, and the field offers extraordinary opportunities owing to the diversity, genetic makeup, and phylogenetic position of archaea and the variety of ecosystems they inhabit. Specific aspects that deserve investigation are elucidation of the mechanism of action of the chaperonin complex at different temperatures, identification of the partners and substitutes for the Hsp70 chaperone machine, analysis of protein folding and refolding in hyperthermophiles, and determination of the molecular mechanisms involved in stress gene regulation in archaeal species that thrive under widely different conditions (temperature, pH, osmolarity, and barometric pressure). These studies are now possible with uni- and multicellular archaeal models and are relevant to various areas of basic and applied research, including exploration and conquest of ecosystems inhospitable to humans and many mammals and plants.},
}
@article {pmid10584017,
year = {1999},
author = {DeLong, EF and Taylor, LT and Marsh, TL and Preston, CM},
title = {Visualization and enumeration of marine planktonic archaea and bacteria by using polyribonucleotide probes and fluorescent in situ hybridization.},
journal = {Applied and environmental microbiology},
volume = {65},
number = {12},
pages = {5554-5563},
pmid = {10584017},
issn = {0099-2240},
mesh = {Animals ; Archaea/*classification/genetics/isolation &amp; purification ; Bacteria/*classification/genetics/isolation &amp; purification ; Base Sequence ; Biomass ; Cloning, Molecular ; Genes, Archaeal ; Genes, Fungal ; In Situ Hybridization, Fluorescence ; Molecular Sequence Data ; Oligonucleotide Probes ; Operon ; *Phylogeny ; Plankton/*microbiology ; RNA Probes ; RNA, Ribosomal/genetics ; Seawater/*microbiology ; },
abstract = {Fluorescent in situ hybridization (FISH) using rRNA-specific oligonucleotide probes has emerged as a popular technique for identifying individual microbial cells. In natural samples, however, the signal derived from fluor-labeled oligonucleotide probes often is undetectable above background fluorescence in many cells. To circumvent this difficulty, we applied fluorochrome-labeled polyribonucleotide probes to identify and enumerate marine planktonic archaea and bacteria. The approach greatly enhanced the sensitivity and applicability of FISH with seawater samples, allowing confident identification and enumeration of planktonic cells to ocean depths of 3,400 m. Quantitative whole-cell hybridization experiments using these probes accounted for 90 to 100% of the total 4',6-diamidino-2-phenylindole (DAPI)-stained cells in most samples. As predicted in a previous study (R. Massana, A. E. Murray, C. M. Preston, and E. F. DeLong, Appl. Environ. Microbiol. 63:50-56, 1997), group I and II marine archaea predominate in different zones in the water column, with maximal cell densities of 10(5)/ml. The high cell densities of archaea, extending from surface waters to abyssal depths, suggest that they represent a large and significant fraction of the total picoplankton biomass in coastal ocean waters. The data also show that the vast majority of planktonic prokaryotes contain significant numbers of ribosomes, rendering them easily detectable with polyribonucleotide probes. These results imply that the majority of planktonic cells visualized by DAPI do not represent lysed cells or "ghosts," as was suggested in a previous report.},
}
@article {pmid10580099,
year = {1999},
author = {Massenet, S and Ansmant, I and Motorin, Y and Branlant, C},
title = {The first determination of pseudouridine residues in 23S ribosomal RNA from hyperthermophilic Archaea Sulfolobus acidocaldarius.},
journal = {FEBS letters},
volume = {462},
number = {1-2},
pages = {94-100},
doi = {10.1016/s0014-5793(99)01524-0},
pmid = {10580099},
issn = {0014-5793},
mesh = {Base Sequence ; Molecular Sequence Data ; Nucleic Acid Conformation ; Pseudouridine/*analysis ; RNA, Archaeal/*chemistry ; RNA, Ribosomal, 23S/*chemistry ; Sulfolobus acidocaldarius/*chemistry/genetics ; },
abstract = {We describe the first identification of pseudouridine (Psi) residues in ribosomal RNA (23S rRNA) of an hyperthermophilic Archaea Sulfolobus acidocaldarius. In contrast to Eucarya rRNA, only six Psi residues were detected, which is rather close to the situation in Bacteria. However, three modified positions (Psi(2479), Psi(2535) and Psi(2550)) are unique for S. acidocaldarius. Two Psi residues at positions 2060 and 2594 are universally conserved, while one other Psi (position 2066) is also common to Eucarya. Taken together the results argue against the conservation of Psi-synthases between Archaea and Bacteria and provide a basis for the search of snoRNA-like guides for Psi formation in Archaea.},
}
@article {pmid10570986,
year = {1999},
author = {Saito, R and Tomita, M},
title = {Computer analyses of complete genomes suggest that some archaebacteria employ both eukaryotic and eubacterial mechanisms in translation initiation.},
journal = {Gene},
volume = {238},
number = {1},
pages = {79-83},
doi = {10.1016/s0378-1119(99)00254-1},
pmid = {10570986},
issn = {0378-1119},
mesh = {5' Untranslated Regions ; Codon, Initiator ; *Genome, Archaeal ; Phylogeny ; Protein Biosynthesis/*genetics ; RNA, Messenger/genetics ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The translation initiation mechanism of archaebacteria is still not clearly understood. Our previous work showed that ATG triplets before start codons have been strongly depleted in eukaryotic genomes, presumably because ribosome of eukaryotes scans mRNA from the 5' to 3' direction to find proper start codons. Extra ATG triplets before start codons would confuse the process and thus they have been negatively selected in eukaryotic genomes. In eubacterial genomes, on the other hand, ribosome binds to the Shine-Dalgarno (SD) sequence at once without mRNA scanning, and the characteristic patterns of ATG triplet depletion were not observed (Saito, R., Tomita, M., 1999. On negative selection against ATG triplets near start codons in eukaryotic and procaryotic genomes. J. Mol. Evol. 48, 213-217). The ATG triplet analysis on archaebacterial genomes revealed that Methanococcus jannaschii and Pyrococcus horikoshii show patterns similar to eukaryotes, implying that these species employ scanning of mRNA from the 5' to 3' direction in the process of translation initiation. On the other hand, our earlier study found that these archaea have SD-like sequences, which are complementary to the 3' end sequence of 16S rRNA, as in eubacterial translation initiation (Osada, Y., Saito, R., Tomita, M. Analysis of base-pairing potentials between 16S rRNA and 5' UTR for translation initiation in various procaryotes. Bioinformatics, in press). These two results combined lead us to conclude that these archaea probably use a hybrid mechanism; their ribosome scans mRNAs from the 5' to 3' direction and then 16S rRNA binds to the SD-like sequence of the 5' UTR.},
}
@article {pmid10570129,
year = {1999},
author = {Bell, SD and Kosa, PL and Sigler, PB and Jackson, SP},
title = {Orientation of the transcription preinitiation complex in archaea.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {96},
number = {24},
pages = {13662-13667},
pmid = {10570129},
issn = {0027-8424},
support = {//Wellcome Trust/United Kingdom ; GM15225/GM/NIGMS NIH HHS/United States ; },
mesh = {Archaea/*genetics ; *Archaeal Proteins ; *Gene Expression Regulation, Archaeal ; Nuclear Proteins/metabolism ; Peptide Elongation Factor 1/metabolism ; Promoter Regions, Genetic ; *Regulatory Sequences, Nucleic Acid ; TATA Box ; *Transcription Factor TFIIB ; Transcription Factors/metabolism ; Transcription, Genetic ; },
abstract = {The basal transcription machinery of Archaea corresponds to the minimal subset of factors required for RNA polymerase II transcription in eukaryotes. Using just two factors, Archaea recruit the RNA polymerase to promoters and define the direction of transcription. Notably, the principal determinant for the orientation of transcription is not the recognition of the TATA box by the TATA-box-binding protein. Instead, transcriptional polarity is governed by the interaction of the archaeal TFIIB homologue with a conserved motif immediately upstream of the TATA box. This interaction yields an archaeal preinitiation complex with the same orientation as the analogous eukaryal complex.},
}
@article {pmid10561548,
year = {1999},
author = {Nagata, Y and Tanaka, K and Iida, T and Kera, Y and Yamada, R and Nakajima, Y and Fujiwara, T and Fukumori, Y and Yamanaka, T and Koga, Y and Tsuji, S and Kawaguchi-Nagata, K},
title = {Occurrence of D-amino acids in a few archaea and dehydrogenase activities in hyperthermophile Pyrobaculum islandicum.},
journal = {Biochimica et biophysica acta},
volume = {1435},
number = {1-2},
pages = {160-166},
doi = {10.1016/s0167-4838(99)00208-3},
pmid = {10561548},
issn = {0006-3002},
mesh = {Amino Acids/analysis ; Archaea/*chemistry ; Membrane Proteins/chemistry ; Oxidation-Reduction ; Oxidoreductases/analysis ; Thermoproteaceae/*enzymology ; },
abstract = {The contents of D-enantiomers of serine, alanine, proline, glutamate (glutamine) and aspartate (asparagine) were examined in the membrane fractions, soluble proteins and free amino acids from some species of archaea, Pyrobaculum islandicum, Methanosarcina barkeri and Halobacterium salinarium. Around 2% (D/D+L) of D-aspartate was found in the membrane fractions. In the soluble proteins, the D-amino acid content was higher in P. islandicum than that in the other archaeal cells: the concentrations in P. islandicum were 3 and 4% for D-serine and D-aspartate, respectively. High concentrations of free D-amino acids were found in P. islandicum and H. salinarium; the concentrations of D-serine (12-13%), D-aspartate (4-7%) and D-proline (3-4%) were higher than those of D-alanine and D-glutamate. This result showed a resemblance between these archaea and not bacterial, but eukaryotic cells. The presence of D-amino acids was confirmed by their digestion with D-amino acid oxidase and D-aspartate oxidase. The occurrence of D-amino acids was also confirmed by the presence of activities catalyzing catabolism of D-amino acids in the P. islandicum homogenate, as measured by 2-oxo acid formation. The catalytic activities oxidizing D-alanine, D-aspartate and D-serine at 90 degrees C were considerably high. Under anaerobic conditions, dehydrogenase activities of the homogenate were 69, 84 and 30% of the above oxidase activities toward D-alanine, D-aspartate and D-serine, respectively. Comparable or higher dehydrogenase activities were also detected with these D-amino acids as substrate by the reduction of 2, 6-dichlorophenolindophenol. No D-amino acid oxidase activity was detected in the homogenates of M. barkeri and H. salinarium.},
}
@article {pmid10564482,
year = {1999},
author = {Jarrell, KF and Correia, JD and Thomas, NA},
title = {Is the processing and translocation system used by flagellins also used by membrane-anchored secretory proteins in archaea?.},
journal = {Molecular microbiology},
volume = {34},
number = {2},
pages = {395-398},
doi = {10.1046/j.1365-2958.1999.01603.x},
pmid = {10564482},
issn = {0950-382X},
mesh = {Amino Acid Sequence ; Archaea/genetics/*metabolism ; Archaeal Proteins/chemistry/genetics/*metabolism ; Flagellin/genetics/*metabolism ; Membrane Proteins/chemistry/genetics/*metabolism ; Molecular Sequence Data ; Peptide Hydrolases/metabolism ; Protein Precursors/chemistry/genetics/metabolism ; Protein Processing, Post-Translational ; },
}
@article {pmid10556324,
year = {1999},
author = {Aravind, L and Koonin, EV},
title = {DNA-binding proteins and evolution of transcription regulation in the archaea.},
journal = {Nucleic acids research},
volume = {27},
number = {23},
pages = {4658-4670},
doi = {10.1093/nar/27.23.4658},
pmid = {10556324},
issn = {0305-1048},
mesh = {Archaea/*genetics ; DNA-Binding Proteins/chemistry/*genetics ; Databases, Factual ; *Evolution, Molecular ; *Gene Expression Regulation, Archaeal ; Helix-Turn-Helix Motifs ; Protein Conformation ; Transcription, Genetic/*genetics ; },
abstract = {Likely DNA-binding domains in archaeal proteins were analyzed using sequence profile methods and available structural information. It is shown that all archaea encode a large number of proteins containing the helix-turn-helix (HTH) DNA-binding domains whose sequences are much more similar to bacterial HTH domains than to eukaryotic ones, such as the PAIRED, POU and homeodomains. The predominant class of HTH domains in archaea is the winged-HTH domain. The number and diversity of HTH domains in archaea is comparable to that seen in bacteria. The HTH domain in archaea combines with a variety of other domains that include replication system components, such as MCM proteins, translation system components, such as the alpha-subunit of phenyl-alanyl-tRNA synthetase, and several metabolic enzymes. The majority of the archaeal HTH-containing proteins are predicted to be gene/operon-specific transcriptional regulators. This apparent bacterial-type mode of transcription regulation is in sharp contrast to the eukaryote-like layout of the core transcription machinery in the archaea. In addition to the predicted bacterial-type transcriptional regulators, the HTH domain is conserved in archaeal and eukaryotic core transcription factors, such as TFIIB, TFIIE-alpha and MBF1. MBF1 is the only highly conserved, classical HTH domain that is vertically inherited in all archaea and eukaryotes. In contrast, while eukaryotic TFIIB and TFIIE-alpha possess forms of the HTH domain that are divergent in sequence, their archaeal counterparts contain typical HTH domains. It is shown that, besides the HTH domain, archaea encode unexpectedly large numbers of two other predicted DNA-binding domains, namely the Arc/MetJ domain and the Zn-ribbon. The core transcription regulators in archaea and eukaryotes (TFIIB/TFB, TFIIE-alpha and MBF1) and in bacteria (the sigma factors) share no similarity beyond the presence of distinct HTH domains. Thus HTH domains might have been independently recruited for a role in transcription regulation in the bacterial and archaeal/eukaryotic lineages. During subsequent evolution, the similarity between archaeal and bacterial gene/operon transcriptional regulators might have been established and maintained through multiple horizontal gene transfer events.},
}
@article {pmid10548490,
year = {1999},
author = {Yamamoto, T and Shiraki, K and Fujiwara, S and Takagi, M and Fukui, K and Imanaka, T},
title = {In vitro heat effect on functional and conformational changes of cyclodextrin glucanotransferase from hyperthermophilic archaea.},
journal = {Biochemical and biophysical research communications},
volume = {265},
number = {1},
pages = {57-61},
doi = {10.1006/bbrc.1999.1629},
pmid = {10548490},
issn = {0006-291X},
mesh = {Calorimetry, Differential Scanning ; Circular Dichroism ; Cloning, Molecular ; Escherichia coli ; Glucosyltransferases/*chemistry/isolation &amp; purification/*metabolism ; Hot Temperature ; Inclusion Bodies/enzymology ; Kinetics ; Protein Conformation ; Protein Folding ; Recombinant Proteins/chemistry/isolation &amp; purification/metabolism ; Spectrophotometry, Ultraviolet ; Thermococcus/*enzymology ; },
abstract = {The in vitro heat effect on protein characteristics of thermostable enzyme was examined using a cyclodextrin glucanotransferase (CGTase, EC 2.4.1.19) from the hyperthermophilic archaeon Thermococcus sp. B1001 as a model protein. The recombinant form of CGTase was obtained as an inclusion body from Escherichia coli cells harboring a plasmid which carried the B1001 CGTase gene (cgtA). CGTase was solubilized by 6 M urea, refolded, purified to homogeneity, and heat treated at 80 degrees C for 20 min. Enzyme characteristics were examined compared with those of unheated CGTase. Cyclization activity was increased by in vitro heat treatment, while hydrolysis activity was decreased. The heated and unheated CGTases were analyzed for structures by circular dichroism (CD). The near- and far-UV CD spectra indicated that the structure of unheated CGTase with low cyclization activity was different from that of heated CGTase with high activity. Differential scanning calorimetry of unheated CGTase showed two absorption peaks at 87 and 106 degrees C with increasing temperature. After heat treatment, the minor peak at 87 degrees C disappeared, suggesting that heat-dependent structural conversion occurred in CGTase. These results indicate that the thermal environment plays an important role for the protein folding process of thermostable CGTase.},
}
@article {pmid10547803,
year = {1999},
author = {Hartzell, PL and Millstein, J and LaPaglia, C},
title = {Biofilm formation in hyperthermophilic Archaea.},
journal = {Methods in enzymology},
volume = {310},
number = {},
pages = {335-349},
doi = {10.1016/s0076-6879(99)10027-2},
pmid = {10547803},
issn = {0076-6879},
mesh = {Archaea/genetics/*physiology ; Archaeoglobus fulgidus/genetics/physiology ; Biofilms/*growth &amp; development ; Culture Media ; Hot Temperature ; Metals ; Microbiological Techniques/instrumentation ; },
}
@article {pmid10542158,
year = {1999},
author = {Cann, IK and Ishino, S and Hayashi, I and Komori, K and Toh, H and Morikawa, K and Ishino, Y},
title = {Functional interactions of a homolog of proliferating cell nuclear antigen with DNA polymerases in Archaea.},
journal = {Journal of bacteriology},
volume = {181},
number = {21},
pages = {6591-6599},
pmid = {10542158},
issn = {0021-9193},
mesh = {Amino Acid Sequence ; Base Sequence ; Cloning, Molecular ; DNA Polymerase I/metabolism ; DNA Polymerase II/metabolism ; DNA, Archaeal/chemistry/genetics ; DNA-Directed DNA Polymerase/*metabolism ; Eukaryotic Cells/metabolism ; *Genes, Archaeal ; Humans ; Molecular Sequence Data ; Proliferating Cell Nuclear Antigen/chemistry/*genetics/*metabolism ; Pyrococcus furiosus/*genetics/metabolism ; Recombinant Proteins/isolation &amp; purification/metabolism ; Sequence Homology, Amino Acid ; },
abstract = {Proliferating cell nuclear antigen (PCNA) is an essential component of the DNA replication and repair machinery in the domain Eucarya. We cloned the gene encoding a PCNA homolog (PfuPCNA) from an euryarchaeote, Pyrococcus furiosus, expressed it in Escherichia coli, and characterized the biochemical properties of the gene product. The protein PfuPCNA stimulated the in vitro primer extension abilities of polymerase (Pol) I and Pol II, which are the two DNA polymerases identified in this organism to date. An immunological experiment showed that PfuPCNA interacts with both Pol I and Pol II. Pol I is a single polypeptide with a sequence similar to that of family B (alpha-like) DNA polymerases, while Pol II is a heterodimer. PfuPCNA interacted with DP2, the catalytic subunit of the heterodimeric complex. These results strongly support the idea that the PCNA homolog works as a sliding clamp of DNA polymerases in P. furiosus, and the basic mechanism for the processive DNA synthesis is conserved in the domains Bacteria, Eucarya, and Archaea. The stimulatory effect of PfuPCNA on the DNA synthesis was observed by using a circular DNA template without the clamp loader (replication factor C [RFC]) in both Pol I and Pol II reactions in contrast to the case of eukaryotic organisms, which are known to require the RFC to open the ring structure of PCNA prior to loading onto a circular DNA. Because RFC homologs have been found in the archaeal genomes, they may permit more efficient stimulation of DNA synthesis by archaeal DNA polymerases in the presence of PCNA. This is the first stage in elucidating the archaeal DNA replication mechanism.},
}
@article {pmid10527834,
year = {1999},
author = {Sano, K and Taguchi, A and Furumoto, H and Uda, T and Itoh, T},
title = {Cloning, sequencing, and characterization of ribosomal protein and RNA polymerase genes from the region analogous to the alpha-operon of escherichia coli in halophilic archaea, halobacterium halobium.},
journal = {Biochemical and biophysical research communications},
volume = {264},
number = {1},
pages = {24-28},
doi = {10.1006/bbrc.1999.1480},
pmid = {10527834},
issn = {0006-291X},
mesh = {Amino Acid Sequence ; Base Sequence ; Cloning, Molecular ; DNA, Archaeal/analysis/chemistry ; DNA-Directed RNA Polymerases/*genetics ; Escherichia coli/*genetics ; *Genes, Archaeal ; Halobacterium salinarum/*genetics ; Molecular Sequence Data ; Multigene Family ; Nucleic Acid Conformation ; Operon ; Phylogeny ; RNA, Transfer, Arg/genetics ; RNA, Transfer, Ser/genetics ; Ribosomal Proteins/biosynthesis/chemistry/classification/*genetics ; Sequence Homology, Amino Acid ; },
abstract = {A determination was made of the nucleotide sequence of the 3215-bp region of a ribosomal protein gene cluster (HS13, HS4, HS11, and HeL18), RNA polymerase (RNA poly D), and tRNA genes (tRNAser and tRNAarg) of halophilic Archaea Halobacterium halobium, which is analogous to the alpha-operon of Escherichia coli (tRNAser-HS13-HS4-HS11-RNA poly D-tRNAarg-HeL18). The seven-gene string was preceded by a pseudoknot-like structure similar to the proposed S4 ribosomal protein binding site of the alpha-operon mRNA leader in E. coli. Using an inducible expression system H. halobium HS4 was produced in large amounts in E. coli, and immunoblot analysis showed the S4 to constitute a 21-kDa polypeptide component of the ribosome. Analysis of the deduced amino acids sequence revealed that the HS13, HS4, and HS11 sequences including the RNA polymerase subunit are more similar to their eukaryotic than to their bacterial counterparts. HeL18, located downstream of the gene cluster analogous to the E. coli alpha-operon (S13-S11-S4-RNA poly D-L17), was similar to both the eukaryotic (eL18) and eubacterial ribosomal protein L15 located in the spc-operon, but not to L17 positioned as the terminal gene of the bacterial alpha-operon.},
}
@article {pmid10521711,
year = {1999},
author = {Sprott, GD and Brisson, J and Dicaire, CJ and Pelletier, AK and Deschatelets, LA and Krishnan, L and Patel, GB},
title = {A structural comparison of the total polar lipids from the human archaea Methanobrevibacter smithii and Methanosphaera stadtmanae and its relevance to the adjuvant activities of their liposomes.},
journal = {Biochimica et biophysica acta},
volume = {1440},
number = {2-3},
pages = {275-288},
doi = {10.1016/s1388-1981(99)00130-4},
pmid = {10521711},
issn = {0006-3002},
mesh = {Adjuvants, Immunologic/chemistry ; Animals ; Archaea/*chemistry ; Female ; Gas Chromatography-Mass Spectrometry ; Lipids/*chemistry/isolation &amp; purification/pharmacology ; Liposomes/chemistry ; Mice ; Mice, Inbred BALB C ; Molecular Structure ; },
abstract = {Mice were immunized with bovine serum albumin (BSA) entrapped within archaeosomes (i.e. liposomes) composed of the total polar lipids (TPL) from the two methanogenic archaea common to the human digestive tract. Methanobrevibacter smithii archaeosomes boosted serum anti-BSA antibody to titers comparable to those achieved with Freund's adjuvant, whereas Methanosphaera stadtmanae archaeosomes were relatively poor adjuvants. An explanation for this difference was sought by analysis of the polar lipid composition of each archaeobacterium. Fast atom bombardment mass spectrometry and NMR analyses of the purified lipids revealed a remarkable similarity in the ether lipid structures present in each TPL extract. However, the relative amounts of each lipid species varied dramatically. The phospholipid fraction in M. stadtmanae TPL was dominated by archaetidylinositol (50 mol% of TPL) and the glycolipid fraction by beta-Glcp-(1,6)-beta-Glcp-(1,1)-archaeol (36 mol%), whereas in M. smithii extracts, both caldarchaeol and archaeol lipids containing a phosphoserine head group were relatively abundant. Liposomes prepared from purified archaetidylinositol and from M. stadtmanae TPL supplemented with increasing amounts of phosphatidylserine elicited poor humoral responses to encapsulated BSA. A dramatic loss in the adjuvanticity of M. smithii archaeosomes was seen upon incorporation of 36 mol% of the uncharged lipid diglucosyl archaeol and, to a lesser extent, of 50 mol% of archaetidylinositol. Interestingly, the relative rates of uptake of M. smithii and M. stadtmanae archaeosomes by phagocytic cultures in vitro were similar. Thus, the lipid composition may influence archaeosome adjuvanticity, particularly a high diglucosyl archaeol and/or archaetidyl inositol content, resulting in a low adjuvant activity.},
}
@article {pmid10518719,
year = {1999},
author = {Whitehead, TR and Cotta, MA},
title = {Phylogenetic diversity of methanogenic archaea in swine waste storage pits.},
journal = {FEMS microbiology letters},
volume = {179},
number = {2},
pages = {223-226},
doi = {10.1111/j.1574-6968.1999.tb08731.x},
pmid = {10518719},
issn = {0378-1097},
mesh = {Animals ; Euryarchaeota/*classification ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Swine/*microbiology ; },
abstract = {Total DNA was isolated from swine feces and a swine waste storage pit and used as templates for PCR amplification of archaeal 16 rDNA using specific primers. Only the sample from the center of the waste pit produced a PCR product. DNA sequence analyses of random clones demonstrated a variety of methanogenic archaea. Six groups of sequences were identified, including those similar to Methanobrevibacter sp., Methanocorpusculum sp., and Methanoculleus sp. Three groups of sequences represented unidentified organisms. These data suggest that swine waste storage pits may represent an untapped source of novel methanogenic archaea.},
}
@article {pmid10515953,
year = {1999},
author = {Matsumoto, M and Homma, H and Long, Z and Imai, K and Iida, T and Maruyama, T and Aikawa, Y and Endo, I and Yohda, M},
title = {Occurrence of free D-amino acids and aspartate racemases in hyperthermophilic archaea.},
journal = {Journal of bacteriology},
volume = {181},
number = {20},
pages = {6560-6563},
pmid = {10515953},
issn = {0021-9193},
mesh = {Amino Acid Isomerases/genetics/*isolation &amp; purification ; Amino Acids/*chemistry ; *Archaea/chemistry/enzymology/genetics ; Aspartic Acid/*chemistry ; Desulfurococcaceae/chemistry/enzymology/genetics ; Hot Temperature ; Molecular Sequence Data ; Pyrococcus/chemistry/enzymology/genetics ; Stereoisomerism ; Thermococcus/chemistry/enzymology/genetics ; },
abstract = {The occurrence of free D-amino acids and aspartate racemases in several hyperthermophilic archaea was investigated. Aspartic acid in all the hyperthermophilic archaea was highly racemized. The ratio of D-aspartic acid to total aspartic acid was in the range of 43.0 to 49.1%. The crude extracts of the hyperthermophiles exhibited aspartate racemase activity at 70 degrees C, and aspartate racemase homologous genes in them were identified by PCR. D-Enantiomers of other amino acids (alanine, leucine, phenylalanine, and lysine) in Thermococcus strains were also detected. Some of them might be by-products of aspartate racemase. It is proven that D-amino acids are produced in some hyperthermophilic archaea, although their function is unknown.},
}
@article {pmid10508063,
year = {1999},
author = {Vetriani, C and Jannasch, HW and MacGregor, BJ and Stahl, DA and Reysenbach, AL},
title = {Population structure and phylogenetic characterization of marine benthic Archaea in deep-sea sediments.},
journal = {Applied and environmental microbiology},
volume = {65},
number = {10},
pages = {4375-4384},
pmid = {10508063},
issn = {0099-2240},
mesh = {Archaea/*classification/genetics ; Base Sequence ; Ecology ; Electrophoresis ; *Geologic Sediments ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Temperature ; },
abstract = {During the past few years Archaea have been recognized as a widespread and significant component of marine picoplankton assemblages and, more recently, the presence of novel archaeal phylogenetic lineages has been reported in coastal marine benthic environments. We investigated the relative abundance, vertical distribution, phylogenetic composition, and spatial variability of Archaea in deep-sea sediments collected from several stations in the Atlantic Ocean. Quantitative oligonucleotide hybridization experiments indicated that the relative abundance of archaeal 16S rRNA in deep-sea sediments (1500 m deep) ranged from about 2.5 to 8% of the total prokaryotic rRNA. Clone libraries of PCR-amplified archaeal rRNA genes (rDNA) were constructed from 10 depth intervals obtained from sediment cores collected at depths of 1,500, 2,600, and 4,500 m. Phylogenetic analysis of rDNA sequences revealed the presence of a complex archaeal population structure, whose members could be grouped into discrete phylogenetic lineages within the two kingdoms, Crenarchaeota and Euryarchaeota. Comparative denaturing gradient gel electrophoresis profile analysis of archaeal 16S rDNA V3 fragments revealed a significant depth-related variability in the composition of the archaeal population.},
}
@article {pmid10486009,
year = {1999},
author = {Cammarano, P and Creti, R and Sanangelantoni, AM and Palm, P},
title = {The archaea monophyly issue: A phylogeny of translational elongation factor G(2) sequences inferred from an optimized selection of alignment positions.},
journal = {Journal of molecular evolution},
volume = {49},
number = {4},
pages = {524-537},
doi = {10.1007/pl00006574},
pmid = {10486009},
issn = {0022-2844},
mesh = {Amino Acid Sequence ; Animals ; Archaea/*genetics ; Bacteria/genetics ; Databases, Factual ; *Evolution, Molecular ; Molecular Sequence Data ; Peptide Elongation Factor G/*genetics ; *Phylogeny ; Sequence Alignment ; Sequence Homology, Amino Acid ; },
abstract = {A global alignment of EF-G(2) sequences was corrected by reference to protein structure. The selection of characters eligible for construction of phylogenetic trees was optimized by searching for regions arising from the artifactual matching of sequence segments unique to different phylogenetic domains. The spurious matchings were identified by comparing all sections of the global alignment with a comprehensive inventory of significant binary alignments obtained by BLAST probing of the DNA and protein databases with representative EF-G(2) sequences. In three discrete alignment blocks (one in domain II and two in domain IV), the alignment of the bacterial sequences with those of Archaea-Eucarya was not retrieved by database probing with EF-G(2) sequences, and no EF-G homologue of the EF-2 sequence segments was detected by using partial EF-G(2) sequences as probes in BLAST/FASTA searches. The two domain IV regions (one of which comprises the ADP-ribosylatable site of EF-2) are almost certainly due to the artifactual alignment of insertion segments that are unique to Bacteria and to Archaea-Eucarya. Phylogenetic trees have been constructed from the global alignment after deselecting positions encompassing the unretrieved, spuriously aligned regions, as well as positions arising from misalignment of the G' and G" subdomain insertion segments flanking the "fifth" consensus motif of the G domain (AE varsson, 1995). The results show inconsistencies between trees inferred by alternative methods and alternative (DNA and protein) data sets with regard to Archaea being a monophyletic or paraphyletic grouping. Both maximum-likelihood and maximum-parsimony methods do not allow discrimination (by log-likelihood difference and difference in number of inferred substitutions) between the conflicting (monophyletic vs. paraphyletic Archaea) topologies. No specific EF-2 insertions (or terminal accretions) supporting a crenarchaeal-eucaryal clade are detectable in the new EF-G(2) sequence alignment.},
}
@article {pmid10486005,
year = {1999},
author = {DiRuggiero, J and Brown, JR and Bogert, AP and Robb, FT},
title = {DNA repair systems in archaea: mementos from the last universal common ancestor?.},
journal = {Journal of molecular evolution},
volume = {49},
number = {4},
pages = {474-484},
doi = {10.1007/pl00006570},
pmid = {10486005},
issn = {0022-2844},
mesh = {Amino Acid Sequence ; Archaea/*genetics ; *DNA Repair ; DNA-Binding Proteins/genetics ; Databases, Factual ; Endonucleases/genetics ; *Evolution, Molecular ; Models, Genetic ; Molecular Sequence Data ; Phylogeny ; Rad51 Recombinase ; Rec A Recombinases/genetics ; Sequence Homology, Amino Acid ; },
abstract = {DNA repair in the Archaea is relevant to the consideration of genome maintenance and replication fidelity in the last universal common ancestor (LUCA) from two perspectives. First, these prokaryotes embody a mix of bacterial and eukaryal molecular features. Second, DNA repair proteins would have been essential in LUCA to maintain genome integrity, regardless of the environmental temperature. Yet we know very little of the basic molecular mechanisms of DNA damage and repair in the Archaea in general. Many studies on DNA repair in archaea have been conducted with hyperthermophiles because of the additional stress imposed on their macromolecules by high temperatures. In addition, of the six complete archaeal genome sequences published so far, five are thermophilic archaea. We have recently shown that the hyperthermophile Pyrococcus furiosus has an extraordinarily high capacity for repair of radiation-induced double-strand breaks and we have identified and sequenced several genes involved in DNA repair in P. furiosus. At the sequence level, only a few genes share homology with known bacterial repair genes. For instance, our phylogenetic analysis indicates that archaeal recombinases occur in two paralogous gene families, one of which is very deeply branched, and both recombinases are more closely related to the eukaryotic RAD51 and Dmc1 gene families than to the Escherichia coli recA gene. We have also identified a gene encoding a repair endo/exonuclease in the genomes of several Archaea. The archaeal sequences are highly homologous to those of the eukaryotic Rad2 family and they cluster with genes of the FEN-1 subfamily, which are known to be involved in DNA replication and repair in eukaryotes. We argue that there is a commonality of mechanisms and protein sequences, shared between prokaryotes and eukaryotes for several modes of DNA repair, reflecting diversification from a minimal set of genes thought to represent the genome of the LUCA.},
}
@article {pmid10477309,
year = {1999},
author = {Schäfer, G and Engelhard, M and Müller, V},
title = {Bioenergetics of the Archaea.},
journal = {Microbiology and molecular biology reviews : MMBR},
volume = {63},
number = {3},
pages = {570-620},
pmid = {10477309},
issn = {1092-2172},
mesh = {Aerobiosis ; Archaea/*metabolism ; Electron Transport ; *Energy Metabolism ; Euryarchaeota/metabolism ; Light ; Protons ; },
abstract = {In the late 1970s, on the basis of rRNA phylogeny, Archaea (archaebacteria) was identified as a distinct domain of life besides Bacteria (eubacteria) and Eucarya. Though forming a separate domain, Archaea display an enormous diversity of lifestyles and metabolic capabilities. Many archaeal species are adapted to extreme environments with respect to salinity, temperatures around the boiling point of water, and/or extremely alkaline or acidic pH. This has posed the challenge of studying the molecular and mechanistic bases on which these organisms can cope with such adverse conditions. This review considers our cumulative knowledge on archaeal mechanisms of primary energy conservation, in relationship to those of bacteria and eucarya. Although the universal principle of chemiosmotic energy conservation also holds for Archaea, distinct features have been discovered with respect to novel ion-transducing, membrane-residing protein complexes and the use of novel cofactors in bioenergetics of methanogenesis. From aerobically respiring Archaea, unusual electron-transporting supercomplexes could be isolated and functionally resolved, and a proposal on the organization of archaeal electron transport chains has been presented. The unique functions of archaeal rhodopsins as sensory systems and as proton or chloride pumps have been elucidated on the basis of recent structural information on the atomic scale. Whereas components of methanogenesis and of phototrophic energy transduction in halobacteria appear to be unique to Archaea, respiratory complexes and the ATP synthase exhibit some chimeric features with respect to their evolutionary origin. Nevertheless, archaeal ATP synthases are to be considered distinct members of this family of secondary energy transducers. A major challenge to future investigations is the development of archaeal genetic transformation systems, in order to gain access to the regulation of bioenergetic systems and to overproducers of archaeal membrane proteins as a prerequisite for their crystallization.},
}
@article {pmid16535669,
year = {1997},
author = {Hoefs, M and Schouten, S and De Leeuw, JW and King, LL and Wakeham, SG and Damste, J},
title = {Ether lipids of planktonic archaea in the marine water column.},
journal = {Applied and environmental microbiology},
volume = {63},
number = {8},
pages = {3090-3095},
pmid = {16535669},
issn = {0099-2240},
abstract = {Acyclic and cyclic biphytanes derived from the membrane ether lipids of archaea were found in water column particulate and sedimentary organic matter from several oxic and anoxic marine environments. Compound-specific isotope analyses of the carbon skeletons suggest that planktonic archaea utilize an isotopically heavy carbon source such as algal carbohydrates and proteins or dissolved bicarbonate. Due to their high preservation potential, these lipids provide a fossil record of planktonic archaea and suggest that they have thrived in marine environments for more than 50 million years.},
}
@article {pmid16535556,
year = {1997},
author = {Martins, LO and Huber, R and Huber, H and Stetter, KO and Da Costa, MS and Santos, H},
title = {Organic solutes in hyperthermophilic archaea.},
journal = {Applied and environmental microbiology},
volume = {63},
number = {3},
pages = {896-902},
pmid = {16535556},
issn = {0099-2240},
abstract = {We examined the accumulation of organic solutes under optimum growth conditions in 12 species of thermophilic and hyperthermophilic Archaea belonging to the Crenarchaeota and Euryarchaeota. Pyrobaculum aerophilum, Thermoproteus tenax, Thermoplasma acidophilum, and members of the order Sulfolobales accumulated trehalose. Pyrococcus furiosus accumulated di-myo-inositol-1,1(prm1)(3,3(prm1))-phosphate and (beta)-mannosylglycerate, Methanothermus fervidus accumulated cyclic-2,3-bisphosphoglycerate and (beta)-mannosylglycerate, while the only solute detected in Pyrodictium occultum was di-myo-inositol-1,1(prm1)(3,3(prm1))-phosphate. Methanopyrus kandleri accumulated large concentrations of cyclic-2,3-bisphosphoglycerate. On the other hand, Archaeoglobus fulgidus accumulated three phosphorylated solutes; prominent among them was a compound identified as di-glycerol-phosphate. This solute increased in concentration as the salinity of the medium and the growth temperature were raised, suggesting that this compound serves as a general stress solute. Di-myo-inositol-1,1(prm1)(3,3(prm1))-phosphate accumulated at supraoptimal temperature only. The relationship between the accumulation of unusual solutes and high temperatures is also discussed.},
}
@article {pmid11370026,
year = {1997},
author = {Kääriäinen, L},
title = {[Archaea a third basic form of life found at the bottom of the sea].},
journal = {Duodecim; laaketieteellinen aikakauskirja},
volume = {113},
number = {3},
pages = {179-180},
pmid = {11370026},
issn = {0012-7183},
mesh = {Animals ; Archaea/*classification ; Archaeal Proteins/*isolation &amp; purification ; Environment ; Oceans and Seas ; Sensitivity and Specificity ; },
}
@article {pmid16349019,
year = {1993},
author = {Brown, SH and Kelly, RM},
title = {Characterization of Amylolytic Enzymes, Having Both alpha-1,4 and alpha-1,6 Hydrolytic Activity, from the Thermophilic Archaea Pyrococcus furiosus and Thermococcus litoralis.},
journal = {Applied and environmental microbiology},
volume = {59},
number = {8},
pages = {2614-2621},
pmid = {16349019},
issn = {0099-2240},
abstract = {Extracellular pullulanases were purified from cell-free culture supernatants of the marine thermophilic archaea Thermococcus litoralis (optimal growth temperature, 90 degrees C) and Pyrococcus furiosus (optimal growth temperature, 98 degrees C). The molecular mass of the T. litoralis enzyme was estimated at 119,000 Da by electrophoresis, while the P. furiosus enzyme exhibited a molecular mass of 110,000 Da under the same conditions. Both enzymes tested positive for bound sugar by the periodic acid-Schiff technique and are therefore glycoproteins. The thermoactivity and thermostability of both enzymes were enhanced in the presence of 5 mM Ca, and under these conditions, enzyme activity could be measured at temperatures of up to 130 to 140 degrees C. The addition of Ca also affected substrate binding, as evidenced by a decrease in K(m) for both enzymes when assayed in the presence of this metal. Each of these enzymes was able to hydrolyze, in addition to the alpha-1,6 linkages in pullulan, alpha-1,4 linkages in amylose and soluble starch. Neither enzyme possessed activity against maltohexaose or other smaller alpha-1,4-linked oligosaccharides. The enzymes from T. litoralis and P. furiosus appear to represent highly thermostable amylopullulanases, versions of which have been isolated from less-thermophilic organisms. The identification of these enzymes further defines the saccharide-metabolizing systems possessed by these two organisms.},
}
@article {pmid16348799,
year = {1992},
author = {Jannasch, HW and Wirsen, CO and Molyneaux, SJ and Langworthy, TA},
title = {Comparative Physiological Studies on Hyperthermophilic Archaea Isolated from Deep-Sea Hot Vents with Emphasis on Pyrococcus Strain GB-D.},
journal = {Applied and environmental microbiology},
volume = {58},
number = {11},
pages = {3472-3481},
pmid = {16348799},
issn = {0099-2240},
abstract = {Three new sulfur- or non-sulfur-dependent archaeal isolates, including a Pyrococcus strain, from Guaymas Basin hydrothermal vents (Gulf of California; depth, 2,010 m) were characterized and physiologically compared with four known hyperthermophiles, previously isolated from other vent sites, with an emphasis on growth and survival under the conditions particular to the natural habitat. Incubation under in situ pressure (200 atm [1 atm = 101.29 kPa]) did not increase the maximum growth temperature by more than 1 degrees C for any of the organisms but did result in increases in growth rates of up to 15% at optimum growth temperatures. At in situ pressure, temperatures considerably higher than those limiting growth (i.e., > 105 degrees C) were survived best by isolates with the highest maximum growth temperatures, but none of the organisms survived at temperatures of 150 degrees C or higher for 5 min. Free oxygen was toxic to all isolates at growth range temperatures, but at ambient deep-sea temperature (3 to 4 degrees C), the effect varied in different isolates, the non-sulfur-dependent isolate being the most oxygen tolerant. Hyperthermophiles could be isolated from refrigerated and oxygenated samples after 5 years of storage. Cu, Zn, and Pb ions were found to be toxic under nongrowth conditions (absence of organic substrate), with the non-sulfur-dependent isolate again being the most tolerant.},
}
@article {pmid16348469,
year = {1991},
author = {Reysenbach, AL and Deming, JW},
title = {Effects of hydrostatic pressure on growth of hyperthermophilic archaebacteria from the juan de fuca ridge.},
journal = {Applied and environmental microbiology},
volume = {57},
number = {4},
pages = {1271-1274},
pmid = {16348469},
issn = {0099-2240},
abstract = {Two new strains (AL1 and AL2) of hyperthermophilic, sulfur-reducing, heterotrophic archaebacteria from high-temperature (350 degrees C) vents on the Juan de Fuca Ridge were highly barotolerant at their optimal growth temperatures (90 and 100 degrees C, respectively). A trend towards barophily at pressures greater than those encountered in situ at the sea floor was demonstrated for the more extremely thermophilic strain (AL2), implying an ability to thrive in (unexplored) habitats well below accessible vent formations.},
}
@article {pmid11540071,
year = {1991},
author = {Winker, S and Woese, CR},
title = {A definition of the domains Archaea, Bacteria and Eucarya in terms of small subunit ribosomal RNA characteristics.},
journal = {Systematic and applied microbiology},
volume = {14},
number = {4},
pages = {305-310},
doi = {10.1016/S0723-2020(11)80303-6},
pmid = {11540071},
issn = {0723-2020},
support = {NSG-7044/NS/NINDS NIH HHS/United States ; },
mesh = {Archaea/*classification/genetics ; Bacteria/*classification/genetics ; Base Sequence ; Biological Evolution ; Eukaryotic Cells/classification ; Molecular Sequence Data ; Nucleotides ; Phylogeny ; RNA, Bacterial/chemistry/classification/*genetics ; RNA, Ribosomal, 16S/chemistry/classification/*genetics ; *Sequence Homology, Nucleic Acid ; },
abstract = {The number of small subunit rRNA sequences is now great enough that the three domains Archaea, Bacteria and Eucarya (Woese et al., 1990) can be reliably defined in terms of their sequence "signatures". Approximately 50 homologous positions (or nucleotide pairs) in the small subunit rRNA characterize and distinguish among the three. In addition, the three can be recognized by a variety of nonhomologous rRNA characters, either individual positions and/or higher-order structural features. The Crenarchaeota and the Euryarchaeota, the two archaeal kingdoms, can also be defined and distinguished by their characteristic compositions at approximately fifteen positions in the small subunit rRNA molecule.},
}
@article {pmid11607093,
year = {1990},
author = {Ladapo, J and Whitman, WB},
title = {Method for isolation of auxotrophs in the methanogenic archaebacteria: role of the acetyl-CoA pathway of autotrophic CO2 fixation in Methanococcus maripaludis.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {87},
number = {15},
pages = {5598-5602},
pmid = {11607093},
issn = {0027-8424},
abstract = {A procedure was developed for the enrichment of auxotrophs in the antibiotic-insensitive archaebacterium Methanococcus. After mutagenesis with ethyl methanesulfonate, growing cells were selectively killed upon exposure to the base analogs 6-azauracil and 8-azahypoxanthine for 48 hr. Using this method, eight independent acetate autotrophs of Methanococcus maripaludis were isolated. Six of the auxotrophs had an absolute growth requirement for acetate and contained 1-16% of the wild-type levels of CO dehydrogenase. Three of these six also contained 14-29% of the wild-type levels of pyruvate oxidoreductase and 12-30% of the wild-type levels of pyruvate synthase. Two spontaneous revertants of these latter auxotrophs regained the ability to grow normally in the absence of acetate and wild-type levels of CO dehydrogenase, acetyl-CoA synthase, pyruvate oxidoreductase, and pyruvate synthase. Likewise, a spontaneous revertant of an auxotroph with reduced levels of CO dehydrogenase and wild-type levels of pyruvate oxidoreductase regained the ability to grow normally in the absence of acetate and wild-type levels of CO dehydrogenase and acetyl-CoA synthase. Two additional auxotrophs grew poorly in the absence of acetate but contained wild-type levels of CO dehydrogenase and pyruvate oxidoreductase. These results provide direct genetic evidence for the Ljungdahl-Wood pathway [Ljungdahl, L. G. (1986) Annu. Rev. Microbiol. 40, 415-450; Wood, H. G., Ragsdale, S. W. &amp; Pezacka, E. (1986) Trends Biochem. Sci. 11, 14-18] of autotrophic acetyl-CoA biosynthesis in the methanogenic archaebacteria. Moreover, it suggests that the acetyl-CoA and pyruvate synthases may share a common protein or coenzyme component, be linked genetically, or be regulated by a common system.},
}
@article {pmid16347998,
year = {1989},
author = {Brown, SH and Kelly, RM},
title = {Cultivation Techniques for Hyperthermophilic Archaebacteria: Continuous Culture of Pyrococcus furiosus at Temperatures near 100 degrees C.},
journal = {Applied and environmental microbiology},
volume = {55},
number = {8},
pages = {2086-2088},
pmid = {16347998},
issn = {1098-5336},
abstract = {A system which allows continuous cultivation of hyperthermophilic archaebacteria at temperatures approaching 100 degrees C has been developed. Continuous cultivation of the hyperthermophile Pyrococcus furiosus was carried out with this system; the resulting dilution rate and gas production profiles are discussed.},
}
@article {pmid16347631,
year = {1988},
author = {Jannasch, HW and Wirsen, CO and Molyneaux, SJ and Langworthy, TA},
title = {Extremely thermophilic fermentative archaebacteria of the genus desulfurococcus from deep-sea hydrothermal vents.},
journal = {Applied and environmental microbiology},
volume = {54},
number = {5},
pages = {1203-1209},
pmid = {16347631},
issn = {0099-2240},
abstract = {Two strains of extremely thermophilic, anaerobic bacteria are described that are representative of isolates obtained from a variety of oceanic hydrothermal vent sites at depths from 2,000 to 3,700 m. The isolates were similar in their requirements for complex organic media, elemental sulfur, and seawater-range salinities (optimum, 2.1 to 2.4%); their high tolerance for sulfide (100 mM) and oxic conditions below growth-range temperatures (50 to 95 degrees C); and their archaebacterial characteristics: absence of murein, presence of certain diand tetraethers, and response to specific antibiotics. The two strains (S and SY, respectively) differed slightly in their optimum growth temperatures (85 and 90 degrees C, optimum pHs for growth (7.5 and 7.0), and DNA base compositions (52.01 and 52.42 G+C mol%). At their in situ pressure of about 250 atm (25,313 kPa), growth rates at 80 and 90 degrees C were about 40% lower than those at 1 atm (101.29 kPa), and no growth occurred at 100 and 110 degrees C, respectively, at either pressure. In yeast extract medium, only 2% of the organic carbon was used and appeared to stem largely from the proteinaceous constituents. According to physiological criteria, the isolates belong to the genus Desulfurococcus.},
}
@article {pmid11542149,
year = {1988},
author = {Achenbach-Richter, L and Woese, CR},
title = {The ribosomal gene spacer region in archaebacteria.},
journal = {Systematic and applied microbiology},
volume = {10},
number = {},
pages = {211-214},
doi = {10.1016/s0723-2020(88)80002-x},
pmid = {11542149},
issn = {0723-2020},
mesh = {Alanine/genetics ; Archaea/classification/*genetics ; Archaeoglobus/classification/*genetics ; Biological Evolution ; Phylogeny ; RNA, Archaeal ; RNA, Ribosomal, 16S/*genetics ; RNA, Ribosomal, 23S/*genetics ; RNA, Transfer, Ala/*genetics ; Sequence Analysis, RNA ; Thermococcus/classification/*genetics ; },
abstract = {Sequences for the spacer regions that separate the 16S and 23S ribosomal RNA genes have been determined for four more (strategically placed) archaebacteria. These confirm the general rule that methanogens and extreme halophiles have spacers that contain a single tRNAala gene, while tRNA genes are not found in the spacer region of the true extreme thermophiles. The present study also shows that the spacer regions from the sulfate reducing Archaeglobus and the extreme thermophile Thermococcus (both of which cluster phylogenetically with the methanogens and extreme halophiles) contain each a tRNAala gene. Thus, not only all methanogens and extreme halophiles show this characteristic, but all organisms on the "methanogen branch" of the archaebacterial tree appear to do so. The finding of a tRNA gene in the spacer region of the extreme thermophile Thermococcus celer is the first known phenotypic property that links this organism with its phylogenetic counterparts, the methanogens, rather than with its phenotypic counterparts, the sulfur-dependent extreme thermophiles.},
}
@article {pmid17191342,
year = {1987},
author = {Reiter, WD and Palm, P and Yeats, S and Zillig, W},
title = {Gene expression in archaebacteria: physical mapping of constitutive and UV-inducible transcripts from the Sulfolobus virus-like particle SSV1.},
journal = {Molecular &amp; general genetics : MGG},
volume = {209},
number = {2},
pages = {270-275},
pmid = {17191342},
issn = {0026-8925},
mesh = {Base Sequence ; Blotting, Northern ; Chromosome Mapping ; Fuselloviridae/*genetics ; Gene Expression Regulation, Archaeal/*genetics ; Molecular Sequence Data ; Sulfolobus/*genetics ; Ultraviolet Rays ; },
abstract = {The transcription of the genome of the UV-inducible Sulfolobus virus-like particle SSV1 was studied. Eight different transcripts could be distinguished by Northern analysis that were present in uninduced cells and the coordinately increased in amount after UV induction of SSV1. Using single-stranded DNA probes from different parts of the genome, the approximate map positions of these RNAs and the directions of transcription were determined. In two cases, terminator read-through resulted in the formation of more than one RNA species from a single 5' end and therefore the eight different RNAs corresponded to only five different transcriptional starts. Two RNAs sharing a common 5' end encode SSV1 structural proteins. The 5' end of these transcripts was determined by S1 nuclease analysis. About 20 nucleotides upstream of the transcriptional start of these RNAs, there is an AT-rich region resembling putative promoter sequences which have been found at a similar distance 5' to the genes encoding stable RNAs in Thermoproteus. In addition to the eight constitutive transcripts, a UV-inducible RNA of 0.3 kb was mapped on the SSV1 genome. In contrast to all other RNAs, it was not detectable in uninduced cells and it is expressed shortly before the amplification and packaging of the SSV1 genome commences.},
}
@article {pmid11540893,
year = {1987},
author = {Achenbach-Richter, L and Stetter, KO and Woese, CR},
title = {A possible biochemical missing link among archaebacteria.},
journal = {Nature},
volume = {327},
number = {6120},
pages = {348-349},
doi = {10.1038/327348a0},
pmid = {11540893},
issn = {0028-0836},
mesh = {Archaea/*classification/genetics/metabolism ; Archaeoglobus/*classification/genetics/metabolism ; Base Sequence ; Biological Evolution ; Methane/metabolism ; Methanococcus ; Molecular Sequence Data ; Phenotype ; *Phylogeny ; *RNA, Archaeal ; RNA, Ribosomal, 16S/*analysis ; Sequence Analysis, RNA ; *Sequence Homology, Nucleic Acid ; Sulfolobus ; Sulfur/metabolism ; Thermococcus ; },
abstract = {Until recently all archaebacteria isolated conformed to one of three basic phenotypes: they were either methanogens, extreme halophiles, or ('sulphur-dependent') extreme thermophiles. However, a novel phenotype, that fits none of these categories, has recently been described. The organism, strain VC-16 (tentatively called "Archaeoglobus fulgidus") reduces sulphate--the only archaebacterium so far known to do so--and makes very small quantities of methane, although it lacks some of the cofactors normally associated with methanogenesis. These characteristics suggest that strain VC-16 might represent a transition form between an anaerobic thermophilic sulfur-based type of metabolism (which seems to be the ancestral metabolism for archaebacteria and methanogenesis (which somehow then derives from it). We here show that the lineage represented by strain VC-16 arises from the archaebacterial tree precisely where such an interpretation would predict that it would, between the Methanococcus lineage (which is the deepest of the methanogen branchings) and that of Thermococcus (the deepest of all branchings on the methanogen side of the tree).},
}
@article {pmid17777850,
year = {1987},
author = {Stetter, KO and Lauerer, G and Thomm, M and Neuner, A},
title = {Isolation of extremely thermophilic sulfate reducers: evidence for a novel branch of archaebacteria.},
journal = {Science (New York, N.Y.)},
volume = {236},
number = {4803},
pages = {822-824},
doi = {10.1126/science.236.4803.822},
pmid = {17777850},
issn = {0036-8075},
abstract = {Extremely thermophilic archaebacteria are known to be metabolizers of elemental sulfur and the methanogens. A novel group of extremely thermophilic archaebacteria is described, which consists of sulfate-respiring organisms that contain pure factor 420 and that have been isolated from marine hydrothermal systems in Italy. They possess a third type of archaebacterial RNA polymerase structure previously unknown, indicating an exceptional phylogenetic position. Most likely, this group represents a third major branch within the archaebacteria. The existence of sulfate reducers at extremely high temperatures could explain hydrogen sulfide formation in hot sulfate-containing environments, such as submarine hydrothermal systems and deep oil wells.},
}
@article {pmid15957218,
year = {1986},
author = {Chant, J and Dennis, P},
title = {Archaebacteria: transcription and processing of ribosomal RNA sequences in Halobacterium cutirubrum.},
journal = {The EMBO journal},
volume = {5},
number = {5},
pages = {1091-1097},
pmid = {15957218},
issn = {0261-4189},
mesh = {Base Sequence ; DNA, Intergenic/genetics ; Genes, Bacterial/genetics ; Halobacterium/*genetics ; Molecular Sequence Data ; RNA Precursors/genetics ; RNA, Ribosomal/*genetics ; Transcription, Genetic/*genetics ; },
abstract = {The chromosome of Halobacterium cutirubrum contains a single ribosomal RNA gene cluster. The 5' to 3' organization of genes within this 6-kpb region is: 16S, alanine tRNA, 23S, 5S, cysteine tRNA. The entire gene cluster is transcribed as a single long primary transcript; processing of mature RNA sequences from the 5' region of the transcript begins prior to the completion of synthesis at the 3' end. There are five conserved octanucleotide direct repeats (TGCGAACG) in the 900-bp 5'-flanking sequence in front of the 16S gene. The positions of these repeat sequences correspond to the different 5' ends of the primary transcript and probably represent the RNA polymerase start sites. The 16S and 23S rRNA genes are surrounded by long nearly perfect inverted repeat sequences. These sequences probably form duplex structures in the primary transcript and are recognized by an RNaseIII-like endonuclease activity that carries out the initial excision of the precursor 16S and 23S rRNA sequences. These precursors are rapidly trimmed tot he mature 16S and 23S molecules and assembled into ribosomal particles. The processing sites for 5S rRNA appear to be at or very near to the mature ends of the 5S molecule. The tRNA sequences are processed with reduced efficiency from the primary transcript. Nuclease cuts have been detected at the ends as well as in the middle of the cysteine tRNA sequence suggesting that there may be alternative processing pathways, one resulting in proper excision of the mature tRNA sequence and the other resulting in improper excision and degradation of the tRNA sequence. The transcription termination sequence is believed to be at or beyond an AT-rich sequence preceded by a GC-rich sequence located distal to the cysteine tRNA gene.},
}
@article {pmid11540841,
year = {1985},
author = {Luehrsen, KR and Nicholson, DE and Fox, GE},
title = {Widespread distribution of a 7S RNA in archaebacteria.},
journal = {Current microbiology},
volume = {12},
number = {},
pages = {69-72},
pmid = {11540841},
issn = {0343-8651},
support = {NSG-7440/NS/NINDS NIH HHS/United States ; PCM-82158876/PC/NCI NIH HHS/United States ; },
mesh = {Archaea/classification/*genetics ; Base Sequence ; Biological Evolution ; Oligonucleotides/*analysis ; RNA, Archaeal/*analysis/genetics/isolation &amp; purification ; RNA, Small Nuclear/*analysis/genetics/isolation &amp; purification ; Sequence Homology, Nucleic Acid ; },
abstract = {An RNA of nonribosomal origin was found in the extreme halophilic bacteria. This novel small RNA was found to be a homogeneous species by RNA fingerprinting. Analysis of the ribonuclease T1 oligonucleotides gave no evidence of the presence of posttranscriptional modifications. Comparisons of electrophoretic mobility with other RNAs of known size suggest that this is a 7S RNA containing 325-375 nucleotides. An RNA of similar mobility was found in all major divisions of the archaebacteria. Insufficient sequence information is available to determine whether these RNAs are homologs of any other known small RNA.},
}
@article {pmid11541975,
year = {1984},
author = {Woese, CR and Gupta, R and Hahn, CM and Zillig, W and Tu, J},
title = {The phylogenetic relationships of three sulfur dependent archaebacteria.},
journal = {Systematic and applied microbiology},
volume = {5},
number = {},
pages = {97-105},
doi = {10.1016/s0723-2020(84)80054-5},
pmid = {11541975},
issn = {0723-2020},
support = {NSG-7044/NS/NINDS NIH HHS/United States ; },
mesh = {Archaea/*classification/*genetics ; Base Sequence ; Biological Evolution ; Oligonucleotides ; *Phylogeny ; RNA, Archaeal ; RNA, Ribosomal, 16S/*genetics ; Sulfolobus/*classification/genetics ; Thermoproteaceae/*classification/genetics ; },
abstract = {Oligonucleotide catalogs have been determined for the 16S ribosomal RNAs of three sulfur dependent (i.e. "thermoacidophilic") archaebacteria--Sulfolobus acidocaldarius, S. solfataricus, and Thermoproteus tenax. The three form a group specifically related to one another, but are only distantly related to the other archaebacteria--i.e. the group comprising the methanogens, extreme halophiles, and (peripherially) the genus Thermoplasma. The three catalogs exhibit two features unique among bacteria: (1) an unusually high number of long pyrimidine runs, and (2) a remarkably high number of (post-transcriptionally) modified nucleotides.},
}
@article {pmid10872322,
year = {1983},
author = {Huet, J and Schnabel, R and Sentenac, A and Zillig, W},
title = {Archaebacteria and eukaryotes possess DNA-dependent RNA polymerases of a common type.},
journal = {The EMBO journal},
volume = {2},
number = {8},
pages = {1291-1294},
pmid = {10872322},
issn = {0261-4189},
mesh = {Archaea/*enzymology ; DNA-Directed RNA Polymerases/*analysis/immunology ; Eukaryotic Cells/enzymology ; },
abstract = {DNA-dependent RNA polymerases of archaebacteria not only resemble the nuclear RNA polymerases of eukaryotes rather than the eubacterial enzymes in their complex component patterns but also show striking immunochemical, i.e., structural, homology with the eukaryotic polymerases at the level of single components. Thus, eukaryotic and archaebacterial RNA polymerases are indeed of the same type, distinct from the eubacterial enzymes, which, however, are also derived from a common ancestral structure.},
}
@article {pmid17739984,
year = {1982},
author = {Chappe, B and Albrecht, P and Michaelis, W},
title = {Polar lipids of archaebacteria in sediments and petroleums.},
journal = {Science (New York, N.Y.)},
volume = {217},
number = {4554},
pages = {65-66},
doi = {10.1126/science.217.4554.65},
pmid = {17739984},
issn = {0036-8075},
abstract = {Glycerol tetraethers with head-to-head isoprenoid 40-carbon chains that are typical of archaebacteria, in particular of methanogens, were identified in the polar lipids of sediments and petroleums. These structures are at least partially preserved in the subsurface beyond the stage of petroleum formation. Their identification provides further evidence that a significant part of geological organic matter derives from the lipids of membranes of microorganisms.},
}
@article {pmid11968208,
year = {1980},
author = {Tornabene, TG and Lloyd, RE and Holzer, G and Oro, J},
title = {Lipids as a principle for the identification of archaebacteria.},
journal = {Life sciences and space research},
volume = {18},
number = {},
pages = {109-121},
doi = {10.1016/b978-0-08-024436-5.50016-0},
pmid = {11968208},
issn = {0075-9422},
mesh = {Archaea/classification/genetics/*physiology ; *Biological Evolution ; DNA, Archaeal ; DNA, Bacterial ; Euryarchaeota/classification/*genetics ; Lipid Metabolism ; Lipids/*analysis ; Phylogeny ; },
abstract = {The 'Archaebacteria' consist of several distinct subgroups including methanogens, extreme halophiles and specific thermoacidophiles. These bacteria are distinct from other bacteria with respect to their characteristic RNA compositions, the absence of muramic acid in the cell walls and the predominance of nonsaponifiable [correction of nonsaponifable] lipids. The lipid composition of the archaebacteria consists of isoprenoid and hydroisoprenoid hydrocarbons and isopranyl glycerol ether lipids. The pathways for the biosynthesis of the lipid components are those shared by most microorganisms and demonstrate a close relationship; however, an independent line of descent is indicated by the formation of the isopranyl glycerol ether lipids. This discontinuity formulates a point for delineating the early stages of biological evolution and for dividing bacteria into two subgroups.},
}
@article {pmid10471795,
year = {1999},
author = {Deppenmeier, U and Lienard, T and Gottschalk, G},
title = {Novel reactions involved in energy conservation by methanogenic archaea.},
journal = {FEBS letters},
volume = {457},
number = {3},
pages = {291-297},
doi = {10.1016/s0014-5793(99)01026-1},
pmid = {10471795},
issn = {0014-5793},
mesh = {Cytochromes/metabolism ; Energy Metabolism ; Euryarchaeota/chemistry/classification/*metabolism ; Methyltransferases/chemistry/*metabolism ; Oxidation-Reduction ; Oxidoreductases/chemistry/*metabolism ; Phenazines/chemistry/*metabolism ; },
abstract = {Methanogenic archaea of the order Methanosarcinales which utilize C(1) compounds such as methanol, methylamines or H(2)+CO(2), employ two novel membrane-bound electron transport systems generating an electrochemical proton gradient: the H(2):heterodisulfide oxidoreductase and the F(420)H(2):heterodisulfide oxidoreductase. The systems are composed of the heterodisulfide reductase and either a membrane-bound hydrogenase or a F(420)H(2) dehydrogenase which is functionally homologous to the proton-translocating NADH dehydrogenase. Cytochromes and the novel electron carrier methanophenazine are also involved. In addition, the methyl-H(4)MPT:HS-CoM methyltransferase is bioenergetically relevant. The enzyme couples methyl group transfer with the translocation of sodium ions and seems to be present in all methanogens. The proton-translocating systems with the participation of cytochromes and methanophenazine have been found so far only in the Methanosarcinales.},
}
@article {pmid10461202,
year = {1999},
author = {Shutov, AD and Blattner, FR and Bäumlein, H},
title = {Evolution of a conserved protein module from Archaea to plants.},
journal = {Trends in genetics : TIG},
volume = {15},
number = {9},
pages = {348-349},
doi = {10.1016/s0168-9525(99)01813-2},
pmid = {10461202},
issn = {0168-9525},
mesh = {Amino Acid Sequence ; Archaeal Proteins/*genetics ; Bacterial Proteins/genetics ; Conserved Sequence ; Evolution, Molecular ; Molecular Sequence Data ; Plant Proteins/*genetics ; Sequence Homology, Amino Acid ; },
}
@article {pmid10447886,
year = {1999},
author = {López-García, P and Forterre, P},
title = {Control of DNA topology during thermal stress in hyperthermophilic archaea: DNA topoisomerase levels, activities and induced thermotolerance during heat and cold shock in Sulfolobus.},
journal = {Molecular microbiology},
volume = {33},
number = {4},
pages = {766-777},
doi = {10.1046/j.1365-2958.1999.01524.x},
pmid = {10447886},
issn = {0950-382X},
mesh = {Archaeal Proteins/metabolism ; Cold Temperature ; DNA Topoisomerases, Type I/*metabolism ; *DNA Topoisomerases, Type II/metabolism ; DNA, Archaeal/*chemistry ; DNA, Superhelical/chemistry ; Hot Temperature ; Nucleic Acid Conformation ; Plasmids/chemistry ; Protein Biosynthesis ; Puromycin ; Sulfolobus/*genetics/metabolism ; Temperature ; },
abstract = {Plasmid topology varies transiently in hyperthermophilic archaea during thermal stress. As in mesophilic bacteria, DNA linking number (Lk) increases during heat shock and decreases during cold shock. Despite this correspondence, plasmid DNA topology and proteins presumably involved in DNA topological control in each case are different. Plasmid DNA in hyperthermophilic archaea is found in a topological form from relaxed to positively supercoiled in contrast to the negatively supercoiled state typical of bacteria, eukaryotes and mesophilic archaea. We have analysed the regulation of DNA topological changes during thermal stress in Sulfolobus islandicus (kingdom Crenarchaeota), which harbours two plasmids, pRN1 and pRN2. In parallel with plasmid topological variations, we analysed levels of reverse gyrase, topoisomerase VI (Topo VI) and the small DNA-binding protein Sis7, as well as topoisomerase activities in crude extracts during heat shock from 80 degrees C to 85-87 degrees C, and cold shock from 80 degrees C to 65 degrees C. Quantitative changes in reverse gyrase, Topo VI and Sis7 were not significant. In support of this, inhibition of protein synthesis in S. islandicus during shocks did not alter plasmid topological dynamics, suggesting that an increase in topoisomerase levels is not needed for control of DNA topology during thermal stress. A reverse gyrase activity was detected in crude extracts, which was strongly dependent on the assay temperature. It was inhibited at 65 degrees C, but was greatly enhanced at 85 degrees C. However, the intrinsic reverse gyrase activity did not vary with heat or cold shock. These results suggest that the control of DNA topology during stress in Sulfolobus relies primarily on the physical effect of temperature on topoisomerase activities and on the geometry of DNA itself. Additionally, we have detected an enhanced thermoresistance of reverse gyrase activities in cultures subject to prolonged heat shock (but not cold shock). This acquired thermotolerance at the enzymatic level is abolished when cultures are treated with puromycin, suggesting a requirement for protein synthesis.},
}
@article {pmid10430863,
year = {1999},
author = {Komori, K and Sakae, S and Shinagawa, H and Morikawa, K and Ishino, Y},
title = {A Holliday junction resolvase from Pyrococcus furiosus: functional similarity to Escherichia coli RuvC provides evidence for conserved mechanism of homologous recombination in Bacteria, Eukarya, and Archaea.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {96},
number = {16},
pages = {8873-8878},
pmid = {10430863},
issn = {0027-8424},
mesh = {Amino Acid Sequence ; Animals ; Archaea/*genetics ; Bacteria/*genetics ; Bacterial Proteins/*chemistry/genetics/metabolism ; Base Sequence ; Cloning, Molecular ; Conserved Sequence ; DNA/chemistry/metabolism ; Endodeoxyribonucleases/*chemistry/genetics/metabolism ; Escherichia coli/enzymology/*genetics ; *Escherichia coli Proteins ; *Holliday Junction Resolvases ; Mammals ; Molecular Sequence Data ; Nucleic Acid Conformation ; Pyrococcus furiosus/enzymology/*genetics ; Recombinant Proteins/chemistry/metabolism ; Recombinases ; Restriction Mapping ; Saccharomyces cerevisiae/genetics ; Sequence Alignment ; Sequence Homology, Amino Acid ; Transposases/*chemistry/genetics/metabolism ; },
abstract = {The Holliday junction is an essential intermediate of homologous recombination. RecA of Bacteria, Rad51 of Eukarya, and RadA of Archaea are structural and functional homologs. These proteins play a pivotal role in the formation of Holliday junctions from two homologous DNA duplexes. RuvC is a specific endonuclease that resolves Holliday junctions in Bacteria. A Holliday junction-resolving activity has been found in both yeast and mammalian cells. To examine whether the paradigm of homologous recombination apply to Archaea, we assayed and found the activity to resolve a synthetic Holliday junction in crude extract of Pyrococcus furiosus cells. The gene, hjc (Holliday junction cleavage), encodes a protein composed of 123 amino acids, whose sequence is not similar to that of any proteins with known function. However, all four archaea, whose total genome sequences have been published, have the homologous genes. The purified Hjc protein cleaved the recombination intermediates formed by RecA in vitro. These results support the notion that the formation and resolution of Holliday junction is the common mechanism of homologous recombination in the three domains of life.},
}
@article {pmid10430567,
year = {1999},
author = {Kraft, A and Lutz, C and Lingenhel, A and Gröbner, P and Piendl, W},
title = {Control of ribosomal protein L1 synthesis in mesophilic and thermophilic archaea.},
journal = {Genetics},
volume = {152},
number = {4},
pages = {1363-1372},
pmid = {10430567},
issn = {0016-6731},
mesh = {Amino Acid Sequence ; Archaea/*genetics/metabolism ; Archaeal Proteins/*genetics/metabolism ; Base Sequence ; Codon/genetics ; Genes ; *Genes, Archaeal ; Methanococcus/genetics/metabolism ; Molecular Sequence Data ; Nucleic Acid Conformation ; RNA, Archaeal/genetics ; RNA, Messenger/genetics ; Recombinant Fusion Proteins/biosynthesis/chemistry ; Ribosomal Proteins/*biosynthesis/genetics ; Sequence Homology, Amino Acid ; Sulfolobus/genetics/metabolism ; Transcription, Genetic ; },
abstract = {The mechanisms for the control of ribosomal protein synthesis have been characterized in detail in Eukarya and in Bacteria. In Archaea, only the regulation of the MvaL1 operon (encoding ribosomal proteins MvaL1, MvaL10, and MvaL12) of the mesophilic Methanococcus vannielii has been extensively investigated. As in Bacteria, regulation takes place at the level of translation. The regulator protein MvaL1 binds preferentially to its binding site on the 23S rRNA, and, when in excess, binds to the regulatory target site on its mRNA and thus inhibits translation of all three cistrons of the operon. The regulatory binding site on the mRNA, a structural mimic of the respective binding site on the 23S rRNA, is located within the structural gene about 30 nucleotides downstream of the ATG start codon. MvaL1 blocks a step before or at the formation of the first peptide bond of MvaL1. Here we demonstrate that a similar regulatory mechanism exists in the thermophilic M. thermolithotrophicus and M. jannaschii. The L1 gene is cotranscribed together with the L10 and L11 gene, in all genera of the Euryarchaeota branch of the Archaea studied so far. A potential regulatory L1 binding site located within the structural gene, as in Methanococcus, was found in Methanobacterium thermoautotrophicum and in Pyrococcus horikoshii. In contrast, in Archaeoglobus fulgidus a typical L1 binding site is located in the untranslated leader of the L1 gene as described for the halophilic Archaea. In Sulfolobus, a member of the Crenarchaeota, the L1 gene is part of a long transcript (encoding SecE, NusG, L11, L1, L10, L12). A previously suggested regulatory L1 target site located within the L11 structural gene could not be confirmed as an L1 binding site.},
}
@article {pmid10430561,
year = {1999},
author = {Kletzin, A and Lieke, A and Urich, T and Charlebois, RL and Sensen, CW},
title = {Molecular analysis of pDL10 from Acidianus ambivalens reveals a family of related plasmids from extremely thermophilic and acidophilic archaea.},
journal = {Genetics},
volume = {152},
number = {4},
pages = {1307-1314},
pmid = {10430561},
issn = {0016-6731},
mesh = {Acids ; Amino Acid Sequence ; Anaerobiosis ; Archaea/*genetics/physiology ; Archaeal Proteins/genetics ; Cloning, Molecular ; DNA Replication ; DNA, Archaeal/genetics ; DNA, Single-Stranded/genetics ; Hot Temperature ; Hydrogen-Ion Concentration ; Molecular Sequence Data ; Nucleic Acid Conformation ; Plasmids/*genetics ; Sequence Alignment ; Sequence Homology, Amino Acid ; Sequence Homology, Nucleic Acid ; Transcription, Genetic ; },
abstract = {The 7598-bp plasmid pDL10 from the extremely thermophilic, acidophilic, and chemolithoautotrophic Archaeon Acidianus ambivalens was sequenced. It contains 10 open reading frames (ORFs) organized in five putative operons. The deduced amino acid sequence of the largest ORF (909 aa) showed similarity to bacterial Rep proteins known from phages and plasmids with rolling-circle (RC) replication. From the comparison of the amino acid sequences, a novel family of RC Rep proteins was defined. The pDL10 Rep protein shared 45-80% identical residues with homologous protein genes encoded by the Sulfolobus islandicus plasmids pRN1 and pRN2. Two DNA regions capable of forming extended stem-loop structures were also conserved in the three plasmids (48-69% sequence identity). In addition, a putative plasmid regulatory protein gene (plrA) was found, which was conserved among the three plasmids and the conjugative Sulfolobus plasmid pNOB8. A homolog of this gene was also found in the chromosome of S. solfataricus. Single-stranded DNA of both pDL10 strands was detected with a mung bean nuclease protection assay using PCR detection of protected fragments, giving additional evidence for an RC mechanism of replication.},
}
@article {pmid10430560,
year = {1999},
author = {Maeder, DL and Weiss, RB and Dunn, DM and Cherry, JL and González, JM and DiRuggiero, J and Robb, FT},
title = {Divergence of the hyperthermophilic archaea Pyrococcus furiosus and P. horikoshii inferred from complete genomic sequences.},
journal = {Genetics},
volume = {152},
number = {4},
pages = {1299-1305},
pmid = {10430560},
issn = {0016-6731},
mesh = {Archaeal Proteins/genetics ; DNA, Archaeal/*genetics ; Evolution, Molecular ; *Genes, Archaeal ; Genome ; Hot Temperature ; Pyrococcus/*genetics ; Pyrococcus furiosus/*genetics ; Sequence Homology, Nucleic Acid ; Species Specificity ; },
abstract = {Divergence of the hyperthermophilic Archaea, Pyrococcus furiosus and Pyrococcus horikoshii, was assessed by analysis of complete genomic sequences of both species. The average nucleotide identity between the genomic sequences is 70-75% within ORFs. The P. furiosus genome (1.908 mbp) is 170 kbp larger than the P. horikoshii genome (1.738 mbp) and the latter displays significant deletions in coding regions, including the trp, his, aro, leu-ile-val, arg, pro, cys, thr, and mal operons. P. horikoshii is auxotrophic for tryptophan and histidine and is unable to utilize maltose, unlike P. furiosus. In addition, the genomes differ considerably in gene order, displaying displacements and inversions. Six allelic intein sites are common to both Pyrococcus genomes, and two intein insertions occur in each species and not the other. The bacteria-like methylated chemotaxis proteins form a functional group in P. horikoshii, but are absent in P. furiosus. Two paralogous families of ferredoxin oxidoreductases provide evidence of gene duplication preceding the divergence of the Pyrococcus species.},
}
@article {pmid10430559,
year = {1999},
author = {Takai, K and Horikoshi, K},
title = {Genetic diversity of archaea in deep-sea hydrothermal vent environments.},
journal = {Genetics},
volume = {152},
number = {4},
pages = {1285-1297},
pmid = {10430559},
issn = {0016-6731},
mesh = {Adaptation, Physiological ; Archaea/*genetics ; DNA, Archaeal/genetics ; DNA, Ribosomal/genetics ; Genetic Variation ; Hot Temperature ; Marine Biology ; Nucleic Acid Hybridization ; Phylogeny ; RNA, Archaeal/genetics ; RNA, Ribosomal/genetics ; Sequence Homology, Nucleic Acid ; Water Microbiology ; },
abstract = {Molecular phylogenetic analysis of naturally occurring archaeal communities in deep-sea hydrothermal vent environments was carried out by PCR-mediated small subunit rRNA gene (SSU rDNA) sequencing. As determined through partial sequencing of rDNA clones amplified with archaea-specific primers, the archaeal populations in deep-sea hydrothermal vent environments showed a great genetic diversity, and most members of these populations appeared to be uncultivated and unidentified organisms. In the phylogenetic analysis, a number of rDNA sequences obtained from deep-sea hydrothermal vents were placed in deep lineages of the crenarchaeotic phylum prior to the divergence of cultivated thermophilic members of the crenarchaeota or between thermophilic members of the euryarchaeota and members of the methanogen-halophile clade. Whole cell in situ hybridization analysis suggested that some microorganisms of novel phylotypes predicted by molecular phylogenetic analysis were likely present in deep-sea hydrothermal vent environments. These findings expand our view of the genetic diversity of archaea in deep-sea hydrothermal vent environments and of the phylogenetic organization of archaea.},
}
@article {pmid10430555,
year = {1999},
author = {Whitman, WB and Pfeifer, F and Blum, P and Klein, A},
title = {What archaea have to tell biologists.},
journal = {Genetics},
volume = {152},
number = {4},
pages = {1245-1248},
pmid = {10430555},
issn = {0016-6731},
mesh = {*Archaea/classification/physiology ; Biological Evolution ; Environment ; Origin of Life ; Phylogeny ; },
}
@article {pmid10427009,
year = {1999},
author = {Sandaa, RA and Enger, O and Torsvik, V},
title = {Abundance and diversity of Archaea in heavy-metal-contaminated soils.},
journal = {Applied and environmental microbiology},
volume = {65},
number = {8},
pages = {3293-3297},
pmid = {10427009},
issn = {0099-2240},
mesh = {Archaea/*drug effects/genetics/*isolation &amp; purification ; Base Sequence ; DNA Primers/genetics ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Ecosystem ; Metals, Heavy/*toxicity ; Phylogeny ; *Soil Microbiology ; Soil Pollutants/*toxicity ; },
abstract = {The impact of heavy-metal contamination on archaean communities was studied in soils amended with sewage sludge contaminated with heavy metals to varying extents. Fluorescent in situ hybridization showed a decrease in the percentage of Archaea from 1.3% +/- 0.3% of 4', 6-diamidino-2-phenylindole-stained cells in untreated soil to below the detection limit in soils amended with heavy metals. A comparison of the archaean communities of the different plots by denaturing gradient gel electrophoresis revealed differences in the structure of the archaean communities in soils with increasing heavy-metal contamination. Analysis of cloned 16S ribosomal DNA showed close similarities to a unique and globally distributed lineage of the kingdom Crenarchaeota that is phylogenetically distinct from currently characterized crenarchaeotal species.},
}
@article {pmid10426953,
year = {1999},
author = {Xu, H and Aurora, R and Rose, GD and White, RH},
title = {Identifying two ancient enzymes in Archaea using predicted secondary structure alignment.},
journal = {Nature structural biology},
volume = {6},
number = {8},
pages = {750-754},
doi = {10.1038/11525},
pmid = {10426953},
issn = {1072-8368},
mesh = {Archaea/*enzymology ; Base Sequence ; DNA Primers ; Dihydropteroate Synthase/*chemistry ; Hydrogen Bonding ; Protein Structure, Secondary ; Thymidylate Synthase/*chemistry ; },
abstract = {It is now possible to compare life forms at high levels of detail and completeness due to the increasing availability of whole genomes from all three domains. However, exploration of interesting hypotheses requires the ability to recognize a correspondence between proteins that may since have diverged beyond the threshold of detection by sequence-based methods. Since protein structure is far better conserved than protein sequence, structural information can enhance detection sensitivity, and this is the basis for the field of structural genomics. Demonstrating the effectiveness of this approach, we identify two important but previously elusive Archaeal enzymes: a homolog of dihydropteroate synthase and a thymidylate synthase. The former is especially noteworthy in that no Archaeal homolog of a bacterial folate biosynthetic enzyme has been found to date. Experimental confirmation of the deduced activity of both enzymes is described. Identification of two different proteins was attempted deliberately to help allay concern that predictive success is merely a lucky accident.},
}
@article {pmid10419407,
year = {1999},
author = {Eisen, JA},
title = {Going to extremes. Archaea: bridging the gap between bacteria and eukarya (A Keystone Symposia), Taos, NM, USA, 9-14 January 1999.},
journal = {Trends in genetics : TIG},
volume = {15},
number = {6},
pages = {218-219},
doi = {10.1016/s0168-9525(99)01739-4},
pmid = {10419407},
issn = {0168-9525},
mesh = {Archaea/classification/*genetics ; Bacteria/classification/genetics ; *Biological Evolution ; Eukaryotic Cells ; },
}
@article {pmid10413400,
year = {1999},
author = {Makarova, KS and Aravind, L and Galperin, MY and Grishin, NV and Tatusov, RL and Wolf, YI and Koonin, EV},
title = {Comparative genomics of the Archaea (Euryarchaeota): evolution of conserved protein families, the stable core, and the variable shell.},
journal = {Genome research},
volume = {9},
number = {7},
pages = {608-628},
pmid = {10413400},
issn = {1088-9051},
mesh = {Amino Acid Sequence ; Archaeal Proteins/genetics ; Bacterial Proteins/genetics ; Conserved Sequence ; Eukaryotic Cells/metabolism ; Euryarchaeota/*genetics ; Evolution, Molecular ; Genes, Archaeal/genetics ; Genetic Variation ; *Genome ; Phylogeny ; Sequence Alignment ; Sequence Homology, Amino Acid ; },
abstract = {Comparative analysis of the protein sequences encoded in the four euryarchaeal species whose genomes have been sequenced completely (Methanococcus jannaschii, Methanobacterium thermoautotrophicum, Archaeoglobus fulgidus, and Pyrococcus horikoshii) revealed 1326 orthologous sets, of which 543 are represented in all four species. The proteins that belong to these conserved euryarchaeal families comprise 31%-35% of the gene complement and may be considered the evolutionarily stable core of the archaeal genomes. The core gene set includes the great majority of genes coding for proteins involved in genome replication and expression, but only a relatively small subset of metabolic functions. For many gene families that are conserved in all euryarchaea, previously undetected orthologs in bacteria and eukaryotes were identified. A number of euryarchaeal synapomorphies (unique shared characters) were identified; these are protein families that possess sequence signatures or domain architectures that are conserved in all euryarchaea but are not found in bacteria or eukaryotes. In addition, euryarchaea-specific expansions of several protein and domain families were detected. In terms of their apparent phylogenetic affinities, the archaeal protein families split into bacterial and eukaryotic families. The majority of the proteins that have only eukaryotic orthologs or show the greatest similarity to their eukaryotic counterparts belong to the core set. The families of euryarchaeal genes that are conserved in only two or three species constitute a relatively mobile component of the genomes whose evolution should have involved multiple events of lineage-specific gene loss and horizontal gene transfer. Frequently these proteins have detectable orthologs only in bacteria or show the greatest similarity to the bacterial homologs, which might suggest a significant role of horizontal gene transfer from bacteria in the evolution of the euryarchaeota.},
}
@article {pmid10411912,
year = {1999},
author = {Kyrpides, NC and Ouzounis, CA},
title = {Transcription in archaea.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {96},
number = {15},
pages = {8545-8550},
pmid = {10411912},
issn = {0027-8424},
mesh = {Archaea/classification/*genetics ; Archaeoglobus/genetics ; Bacteria/genetics/metabolism ; Databases, Factual ; Eukaryotic Cells/metabolism ; Evolution, Molecular ; Genes, Archaeal/genetics ; Genome ; Methanobacterium/genetics ; Methanococcus/genetics ; Pyrococcus/genetics ; Sequence Homology, Nucleic Acid ; Transcription Factors/genetics ; Transcription, Genetic/*genetics ; },
abstract = {Using the sequences of all the known transcription-associated proteins from Bacteria and Eucarya (a total of 4,147), we have identified their homologous counterparts in the four complete archaeal genomes. Through extensive sequence comparisons, we establish the presence of 280 predicted transcription factors or transcription-associated proteins in the four archaeal genomes, of which 168 have homologs only in Bacteria, 51 have homologs only in Eucarya, and the remaining 61 have homologs in both phylogenetic domains. Although bacterial and eukaryotic transcription have very few factors in common, each exclusively shares a significantly greater number with the Archaea, especially the Bacteria. This last fact contrasts with the obvious close relationship between the archaeal and eukaryotic transcription mechanisms per se, and in particular, basic transcription initiation. We interpret these results to mean that the archaeal transcription system has retained more ancestral characteristics than have the transcription mechanisms in either of the other two domains.},
}
@article {pmid10411718,
year = {1999},
author = {Tumbula, DL and Whitman, WB},
title = {Genetics of Methanococcus: possibilities for functional genomics in Archaea.},
journal = {Molecular microbiology},
volume = {33},
number = {1},
pages = {1-7},
doi = {10.1046/j.1365-2958.1999.01463.x},
pmid = {10411718},
issn = {0950-382X},
mesh = {Anaerobiosis ; Archaea/*genetics ; Bacterial Proteins/genetics ; DNA, Bacterial/genetics ; Drug Resistance, Microbial ; Flagella/metabolism ; Forecasting ; Genes, Bacterial ; Genes, Reporter ; Genetic Vectors/genetics ; Genetics, Microbial/methods ; *Genome, Bacterial ; Methanococcus/*genetics ; Nitrogen Fixation/genetics ; Selection, Genetic ; Sequence Analysis, DNA ; },
abstract = {Although the genomic sequences of a number of Archaea have been completed in the last three years, genetic systems in the sequenced organisms are absent. In contrast, genetic studies of the mesophiles in the archaeal genus Methanococcus have become commonplace following the recent developments of antibiotic resistance markers, DNA transformation methods, reporter genes, shuttle vectors and expression vectors. These developments have led to investigations of the transcription of the genes for hydrogen metabolism, nitrogen fixation and flagellin assembly. These genetic systems can potentially be used to analyse the genomic sequence of the hyperthermophile Methanococcus jannaschii, addressing questions of its physiology and the function of its many uncharacterized open reading frames. Thus, the sequence of M. jannaschii can serve as a starting point for gene isolation, while in vivo genetics in the mesophilic methanococci can provide the experimental systems to test the predictions from genomics.},
}
@article {pmid10398835,
year = {1999},
author = {Slobodkin, AI and Jeanthon, C and L'Haridon, S and Nazina, T and Miroshnichenko, M and Bonch-Osmolovskaya, E},
title = {Dissimilatory reduction of Fe(III) by thermophilic bacteria and archaea in deep subsurface petroleum reservoirs of western siberia.},
journal = {Current microbiology},
volume = {39},
number = {2},
pages = {99-102},
doi = {10.1007/s002849900426},
pmid = {10398835},
issn = {1432-0991},
abstract = {Twenty-five samples of stratal fluids obtained from a high-temperature (60-84 degrees C) deep subsurface (1700-2500 m) petroleum reservoir of Western Siberia were investigated for the presence of dissimilatory Fe(III)-reducing microorganisms. Of the samples, 44% and 76% were positive for Fe(III) reduction with peptone and H2 respectively as electron donors. In most of these samples, the numbers of culturable thermophilic H2-utilizing iron reducers were in the order of 10-100 cells/ml. Nine strains of thermophilic anaerobic bacteria and archaea isolated from petroleum reservoirs were tested for their ability to reduce Fe(III). Eight strains belonging to the genera Thermoanaerobacter, Thermotoga, and Thermococcus were found capable of dissimilatory Fe(III) reduction, with peptone or H2 as electron donor and amorphous Fe(III) oxide as electron acceptor. These results demonstrated that Fe(III) reduction may be a common feature shared by a wide range of anaerobic thermophiles and hyperthermophiles in deep subsurface petroleum reservoirs.http://link.springer-ny. com/link/service/journals/00284/bibs/39n2p99.html},
}
@article {pmid10397337,
year = {1998},
author = {Filipowicz, W and Billy, E and Drabikowski, K and Genschik, P},
title = {Cyclases of the 3'-terminal phosphate in RNA: a new family of RNA processing enzymes conserved in eucarya, bacteria and archaea.},
journal = {Acta biochimica Polonica},
volume = {45},
number = {4},
pages = {895-906},
pmid = {10397337},
issn = {0001-527X},
mesh = {Archaea/*enzymology ; Bacteria/*enzymology ; Base Sequence ; Conserved Sequence ; DNA, Complementary/analysis ; Dose-Response Relationship, Drug ; Escherichia coli/enzymology ; HeLa Cells ; Humans ; Kinetics ; Ligases/*chemistry/isolation &amp; purification/*metabolism/*physiology ; Models, Chemical ; Models, Genetic ; Molecular Sequence Data ; Substrate Specificity ; },
abstract = {The 2',3'-cyclic phosphate termini are produced, as either intermediates or final products, during RNA cleavage by many different endoribonucleases. Likewise, ribozymes such as hammerheads, hairpins, or the hepatitis delta ribozyme, generate 2',3'-cyclic phosphate ends. Discovery of the RNA 3'-terminal phosphate cyclase has indicated that cyclic phosphate termini in RNA can also be produced by an entirely different mechanism. The RNA 3'-phosphate cyclase converts the 3'-terminal phosphate in RNA into the 2',3'-cyclic phosphodiester in the ATP-dependent reaction which involves formation of the covalent cyclase-AMP and the RNA-N3' pp5' A intermediates. The findings that several eukaryotic and prokaryotic RNA ligases require the 2',3'-cyclic phosphate for the ligation of RNA molecules raised a possibility that the RNA 3'-phosphate cyclase may have an anabolic function in RNA metabolism by generating terminal cyclic groups required for ligation. Recent cloning of a cDNA encoding the human cyclase indicated that genes encoding cyclase-like proteins are conserved among Eucarya, Bacteria, and Archaea. The protein encoded by the Escherichia coli gene was overexpressed and shown to have the RNA 3'-phosphate cyclase activity. This article reviews properties of the human and bacterial cyclases, their mechanism of action and substrate specificity. Possible biological functions of the enzymes are also discussed.},
}
@article {pmid10393902,
year = {1999},
author = {Pannucci, JA and Haas, ES and Hall, TA and Harris, JK and Brown, JW},
title = {RNase P RNAs from some Archaea are catalytically active.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {96},
number = {14},
pages = {7803-7808},
pmid = {10393902},
issn = {0027-8424},
support = {GM52894/GM/NIGMS NIH HHS/United States ; },
mesh = {Archaea/*enzymology/genetics ; Bacillus/enzymology/*genetics ; Base Sequence ; Conserved Sequence ; Endoribonucleases/chemistry/genetics/*metabolism ; Kinetics ; Methanobacterium/*enzymology/*genetics ; Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; Phylogeny ; RNA, Archaeal/chemistry/genetics/*metabolism ; RNA, Bacterial/metabolism ; RNA, Catalytic/chemistry/genetics/*metabolism ; Ribonuclease P ; },
abstract = {The RNA subunits of RNase Ps of Archaea and eukaryotes have been thought to depend fundamentally on protein for activity, unlike those of Bacteria that are capable of efficient catalysis in the absence of protein. Although the eukaryotic RNase P RNAs are quite different than those of Bacteria in both sequence and structure, the archaeal RNAs generally contain the sequences and structures of the bacterial, phylogenetically conserved catalytic core. A spectrum of archaeal RNase P RNAs were therefore tested for activity in a wide range of conditions. Many remain inactive in ionically extreme conditions, but catalytic activity could be detected from those of the methanobacteria, thermococci, and halobacteria. Chimeric holoenzymes, reconstituted from the Methanobacterium RNase P RNA and the Bacillus subtilis RNase P protein subunits, were functional at low ionic strength. The properties of the archaeal RNase P RNAs (high ionic-strength requirement, low affinity for substrate, and catalytic reconstitution by bacterial RNase P protein) are similar to synthetic RNase P RNAs that contain all of the catalytic core of the bacterial RNA but lack phylogenetically variable, stabilizing elements.},
}
@article {pmid10384269,
year = {1998},
author = {Bell, SD and Jackson, SP},
title = {Transcription in Archaea.},
journal = {Cold Spring Harbor symposia on quantitative biology},
volume = {63},
number = {},
pages = {41-51},
doi = {10.1101/sqb.1998.63.41},
pmid = {10384269},
issn = {0091-7451},
support = {//Wellcome Trust/United Kingdom ; },
mesh = {Amino Acid Sequence ; Archaea/classification/*genetics ; Archaeal Proteins/chemistry/metabolism ; Bacteria/genetics ; Humans ; Molecular Sequence Data ; Nuclear Proteins/chemistry/*metabolism ; Sequence Alignment ; Sequence Homology, Amino Acid ; Transcription Factor TFIIB ; Transcription Factors/chemistry/*metabolism ; *Transcription, Genetic ; },
}
@article {pmid10369758,
year = {1999},
author = {Ponting, CP and Aravind, L and Schultz, J and Bork, P and Koonin, EV},
title = {Eukaryotic signalling domain homologues in archaea and bacteria. Ancient ancestry and horizontal gene transfer.},
journal = {Journal of molecular biology},
volume = {289},
number = {4},
pages = {729-745},
doi = {10.1006/jmbi.1999.2827},
pmid = {10369758},
issn = {0022-2836},
mesh = {Amino Acid Sequence ; Animals ; Binding Sites ; Caenorhabditis elegans/*genetics ; Enzymes/genetics ; Eukaryotic Cells ; *Evolution, Molecular ; *Genes, Archaeal ; *Genes, Bacterial ; Molecular Sequence Data ; Phylogeny ; Recombination, Genetic ; Saccharomyces cerevisiae/*genetics ; Sequence Homology, Amino Acid ; *Signal Transduction ; src Homology Domains ; },
abstract = {Phyletic distributions of eukaryotic signalling domains were studied using recently developed sensitive methods for protein sequence analysis, with an emphasis on the detection and accurate enumeration of homologues in bacteria and archaea. A major difference was found between the distributions of enzyme families that are typically found in all three divisions of cellular life and non-enzymatic domain families that are usually eukaryote-specific. Previously undetected bacterial homologues were identified for# plant pathogenesis-related proteins, Pad1, von Willebrand factor type A, src homology 3 and YWTD repeat-containing domains. Comparisons of the domain distributions in eukaryotes and prokaryotes enabled distinctions to be made between the domains originating prior to the last common ancestor of all known life forms and those apparently originating as consequences of horizontal gene transfer events. A number of transfers of signalling domains from eukaryotes to bacteria were confidently identified, in contrast to only a single case of apparent transfer from eukaryotes to archaea.},
}
@article {pmid10368959,
year = {1999},
author = {Brinkmann, H and Philippe, H},
title = {Archaea sister group of Bacteria? Indications from tree reconstruction artifacts in ancient phylogenies.},
journal = {Molecular biology and evolution},
volume = {16},
number = {6},
pages = {817-825},
doi = {10.1093/oxfordjournals.molbev.a026166},
pmid = {10368959},
issn = {0737-4038},
mesh = {Archaea/*genetics ; Archaeal Proteins/genetics ; Bacteria/*genetics ; Bacterial Proteins/genetics ; Evolution, Molecular ; GTP Phosphohydrolases/genetics ; Genes, Archaeal ; Genes, Bacterial ; *Phylogeny ; Receptors, Cytoplasmic and Nuclear/genetics ; Receptors, Peptide/genetics ; Signal Recognition Particle/genetics ; Time Factors ; },
abstract = {The 54-kDa signal recognition particle and the receptor SR alpha, two proteins involved in the cotranslational translocation of proteins, are paralogs. They originate from a gene duplication that occurred prior to the last universal common ancestor, allowing one to root the universal tree of life. Phylogenetic analysis using standard methods supports the generally accepted cluster of Archaea and Eucarya. However, a new method increasing the signal-to-noise ratio strongly suggests that this result is due to a long-branch attraction artifact, with the Bacteria evolving fastest. In fact, the Archaea/Eucarya sisterhood is recovered only by the fast-evolving positions. In contrast, the most slowly evolving positions, which are the most likely to retain the ancient phylogenetic signal, support the monophyly of prokaryotes. Such a eukaryotic rooting provides a simple explanation for the high similarity of Archaea and Bacteria observed in complete-genome analysis, and should prompt a reconsideration of current views on the origin of eukaryotes.},
}
@article {pmid10368132,
year = {1999},
author = {Reeve, JN},
title = {Archaebacteria then ... Archaes now (are there really no archaeal pathogens?).},
journal = {Journal of bacteriology},
volume = {181},
number = {12},
pages = {3613-3617},
pmid = {10368132},
issn = {0021-9193},
mesh = {Archaea/*classification/genetics/pathogenicity ; RNA, Archaeal/genetics ; },
}
@article {pmid10361290,
year = {1999},
author = {Lopez, P and Philippe, H and Myllykallio, H and Forterre, P},
title = {Identification of putative chromosomal origins of replication in Archaea.},
journal = {Molecular microbiology},
volume = {32},
number = {4},
pages = {883-886},
doi = {10.1046/j.1365-2958.1999.01370.x},
pmid = {10361290},
issn = {0950-382X},
mesh = {Archaea/*genetics ; Chromosomes/*genetics ; Codon ; DNA Replication/*genetics ; DNA-Binding Proteins ; Methanobacterium/genetics ; Origin Recognition Complex ; Physical Chromosome Mapping ; Pyrococcus/genetics ; Repetitive Sequences, Nucleic Acid ; Sequence Alignment ; Viral Proteins ; },
}
@article {pmid10360571,
year = {1999},
author = {Nelson, KE and Clayton, RA and Gill, SR and Gwinn, ML and Dodson, RJ and Haft, DH and Hickey, EK and Peterson, JD and Nelson, WC and Ketchum, KA and McDonald, L and Utterback, TR and Malek, JA and Linher, KD and Garrett, MM and Stewart, AM and Cotton, MD and Pratt, MS and Phillips, CA and Richardson, D and Heidelberg, J and Sutton, GG and Fleischmann, RD and Eisen, JA and White, O and Salzberg, SL and Smith, HO and Venter, JC and Fraser, CM},
title = {Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima.},
journal = {Nature},
volume = {399},
number = {6734},
pages = {323-329},
doi = {10.1038/20601},
pmid = {10360571},
issn = {0028-0836},
mesh = {Archaea/*genetics ; Bacterial Proteins/metabolism ; DNA, Bacterial ; Genes, Archaeal ; *Genome, Bacterial ; Molecular Sequence Data ; Multigene Family ; Open Reading Frames ; Phylogeny ; Protein Biosynthesis ; *Recombination, Genetic ; Sequence Analysis, DNA ; Thermotoga maritima/classification/*genetics/physiology ; Transcription, Genetic ; Transformation, Bacterial ; },
abstract = {The 1,860,725-base-pair genome of Thermotoga maritima MSB8 contains 1,877 predicted coding regions, 1,014 (54%) of which have functional assignments and 863 (46%) of which are of unknown function. Genome analysis reveals numerous pathways involved in degradation of sugars and plant polysaccharides, and 108 genes that have orthologues only in the genomes of other thermophilic Eubacteria and Archaea. Of the Eubacteria sequenced to date, T. maritima has the highest percentage (24%) of genes that are most similar to archaeal genes. Eighty-one archaeal-like genes are clustered in 15 regions of the T. maritima genome that range in size from 4 to 20 kilobases. Conservation of gene order between T. maritima and Archaea in many of the clustered regions suggests that lateral gene transfer may have occurred between thermophilic Eubacteria and Archaea.},
}
@article {pmid10354597,
year = {1999},
author = {Sowers, KR and Schreier, HJ},
title = {Gene transfer systems for the Archaea.},
journal = {Trends in microbiology},
volume = {7},
number = {5},
pages = {212-219},
doi = {10.1016/s0966-842x(99)01492-4},
pmid = {10354597},
issn = {0966-842X},
mesh = {Adaptation, Physiological/genetics ; Archaea/classification/*genetics/growth &amp; development ; Biomarkers ; Culture Media ; *Gene Transfer Techniques ; Genetic Vectors/genetics ; Phenotype ; Temperature ; Transduction, Genetic ; Transformation, Genetic ; },
abstract = {The recent focus on exobiology and the potential for life in extreme environments has generated a great deal of interest in the Archaea because of their adaptation to extremes of temperature, salinity and anaerobicity. Recent advances in the development of genetic transfer systems for the Archaea provide the first glimpse of their genetic mechanisms and have the potential to serve as powerful tools for studying their unique adaptive strategies.},
}
@article {pmid10340845,
year = {1999},
author = {Müller, V and Ruppert, C and Lemker, T},
title = {Structure and function of the A1A0-ATPases from methanogenic Archaea.},
journal = {Journal of bioenergetics and biomembranes},
volume = {31},
number = {1},
pages = {15-27},
doi = {10.1023/a:1005451311009},
pmid = {10340845},
issn = {0145-479X},
mesh = {Amino Acid Sequence ; Archaeal Proteins ; Catalysis ; Euryarchaeota/*enzymology ; Molecular Sequence Data ; Molecular Weight ; Protein Structure, Secondary ; Proton-Translocating ATPases/chemistry/genetics/*metabolism ; Structure-Activity Relationship ; },
abstract = {Recent molecular studies revealed nine to ten gene products involved in function/assembly of the methanoarchaeal ATPase and unravel a close relationship of the A1A0-ATPase and the V1V0-ATPase with respect to subunit composition and the structure of individual subunits. Most interestingly, there is an astonishing variability in the size of the proteolipids in methanoarchaeal A1A0-ATPases with six, four, or two transmembrane helices and a variable number of conserved protonizable groups per monomer. Despite the structural similarities the A1A0-ATPase differs fundamentally from the V1V0-ATPase by its ability to synthesize ATP, a feature shared with F1F0-ATPases. The discovery of duplicated and triplicated versions of the proteolipid in A1A0-ATP synthases questions older views of the structural requirements for ATP synthases versus ATP hydrolases and sheds new light on the evolution of these secondary energy converters.},
}
@article {pmid10338124,
year = {1999},
author = {Hippler, B and Thauer, RK},
title = {The energy conserving methyltetrahydromethanopterin:coenzyme M methyltransferase complex from methanogenic archaea: function of the subunit MtrH.},
journal = {FEBS letters},
volume = {449},
number = {2-3},
pages = {165-168},
doi = {10.1016/s0014-5793(99)00429-9},
pmid = {10338124},
issn = {0014-5793},
mesh = {Amino Acid Sequence ; Bacterial Proteins/metabolism ; Energy Metabolism ; Iron-Sulfur Proteins/metabolism ; Methanobacterium/*enzymology ; Methyltransferases/chemistry/genetics/*metabolism ; Molecular Sequence Data ; Pterins/metabolism ; Sequence Homology, Amino Acid ; Tetrahydrofolates/metabolism ; Vitamin B 12/analogs &amp; derivatives/metabolism ; },
abstract = {In methanogenic archaea the transfer of the methyl group of N5-methyltetrahydromethanopterin to coenzyme M is coupled with energy conservation. The reaction is catalyzed by a membrane associated multienzyme complex composed of eight different subunits MtrA-H. The 23 kDa subunit MtrA harbors a corrinoid prosthetic group which is methylated and demethylated in the catalytic cycle. We report here that the 34 kDa subunit MtrH catalyzes the methylation reaction. MtrH was purified and shown to exhibit methyltetrahydromethanopterin:cob(I)alamin methyltransferase activity. Sequence comparison revealed similarity of MtrH with MetH from Escherichia coli and AcsE from Clostridium thermoaceticum: both enzymes exhibit methyltetrahydrofolate:cob(I)alamin methyltransferase activity.},
}
@article {pmid10333564,
year = {1998},
author = {Ishino, Y and Cann, IK},
title = {The euryarchaeotes, a subdomain of Archaea, survive on a single DNA polymerase: fact or farce?.},
journal = {Genes &amp; genetic systems},
volume = {73},
number = {6},
pages = {323-336},
doi = {10.1266/ggs.73.323},
pmid = {10333564},
issn = {1341-7568},
mesh = {Amino Acid Sequence ; Animals ; Archaea/enzymology/genetics ; DNA Replication ; DNA, Archaeal ; DNA-Directed DNA Polymerase/genetics/*metabolism ; Euryarchaeota/*enzymology/genetics ; Molecular Sequence Data ; },
abstract = {Archaea is now recognized as the third domain of life. Since their discovery, much effort has been directed towards understanding the molecular biology and biochemistry of Archaea. The objective is to comprehend the complete structure and the depth of the phylogenetic tree of life. DNA replication is one of the most important events in living organisms and DNA polymerase is the key enzyme in the molecular machinery which drives the process. All archaeal DNA polymerases were thought to belong to family B. This was because all of the products of pol genes that had been cloned showed amino acid sequence similarities to those of this family, which includes three eukaryal DNA replicases and Escherichia coli DNA polymerase II. Recently, we found a new heterodimeric DNA polymerase from the hyperthermophilic archaeon, Pyrococcus furiosus. The genes coding for the subunits of this DNA polymerase are conserved in the euryarchaeotes whose genomes have been completely sequenced. The biochemical characteristics of the novel DNA polymerase family suggest that its members play an important role in DNA replication within euryarchaeal cells. We review here our current knowledge on DNA polymerases in Archaea with emphasis on the novel DNA polymerase discovered in Euryarchaeota.},
}
@article {pmid10322164,
year = {1999},
author = {Leigh, JA},
title = {Transcriptional regulation in Archaea.},
journal = {Current opinion in microbiology},
volume = {2},
number = {2},
pages = {131-134},
doi = {10.1016/S1369-5274(99)80023-X},
pmid = {10322164},
issn = {1369-5274},
mesh = {Eukaryotic Cells ; *Gene Expression Regulation, Archaeal ; Models, Genetic ; Trans-Activators/*metabolism ; *Transcription, Genetic ; },
abstract = {Information regarding transcriptional regulation in Archaea has begun to emerge from in vivo genetic studies. Evidence to date suggests a varied repertoire of regulatory mechanisms in Archaea that invokes both bacterial and eukaryal paradigms, as well as some novel features. Overall simplicity of mechanisms may reflect the prokaryotic lifestyle. Sequencing projects suggest the existence of certain classes of regulators, but experimental verification is needed.},
}
@article {pmid10235261,
year = {1999},
author = {Hinrichs, KU and Hayes, JM and Sylva, SP and Brewer, PG and DeLong, EF},
title = {Methane-consuming archaebacteria in marine sediments.},
journal = {Nature},
volume = {398},
number = {6730},
pages = {802-805},
doi = {10.1038/19751},
pmid = {10235261},
issn = {0028-0836},
mesh = {Archaea/classification/genetics/isolation &amp; purification/*metabolism ; California ; Euryarchaeota/classification ; Geologic Sediments ; Lipid Metabolism ; Methane/*metabolism ; Phylogeny ; RNA, Ribosomal, 16S/analysis ; *Water Microbiology ; },
abstract = {Large amounts of methane are produced in marine sediments but are then consumed before contacting aerobic waters or the atmosphere. Although no organism that can consume methane anaerobically has ever been isolated, biogeochemical evidence indicates that the overall process involves a transfer of electrons from methane to sulphate and is probably mediated by several organisms, including a methanogen (operating in reverse) and a sulphate-reducer (using an unknown intermediate substrate). Here we describe studies of sediments related to a decomposing methane hydrate. These provide strong evidence that methane is being consumed by archaebacteria that are phylogenetically distinct from known methanogens. Specifically, lipid biomarkers that are commonly characteristic of archaea are so strongly depleted in carbon-13 that methane must be the carbon source, rather than the metabolic product, for the organisms that have produced them. Parallel gene surveys of small-subunit ribosomal RNA (16S rRNA) indicate the predominance of a new archael group which is peripherally related to the methanogenic orders Methanomicrobiales and Methanosarcinales.},
}
@article {pmid10203795,
year = {1999},
author = {Vothknecht, UC and Tumbula, DL},
title = {Archaea: from genomics to physiology and the origin of life.},
journal = {Trends in cell biology},
volume = {9},
number = {4},
pages = {159-161},
doi = {10.1016/s0962-8924(99)01522-6},
pmid = {10203795},
issn = {0962-8924},
mesh = {Anaerobiosis ; *Archaea/genetics/physiology ; Bacterial Proteins/genetics/physiology ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Genetic Vectors ; Genome, Bacterial ; Glycerophosphates/metabolism ; Hot Temperature ; Lipid Metabolism ; Lipids/classification ; Origin of Life ; Phylogeny ; Soil Microbiology ; Water Microbiology ; },
}
@article {pmid10223964,
year = {1999},
author = {Martin, DD and Ciulla, RA and Roberts, MF},
title = {Osmoadaptation in archaea.},
journal = {Applied and environmental microbiology},
volume = {65},
number = {5},
pages = {1815-1825},
pmid = {10223964},
issn = {1098-5336},
}
@article {pmid10220894,
year = {1999},
author = {van der Maarel, MJ and Sprenger, W and Haanstra, R and Forney, LJ},
title = {Detection of methanogenic archaea in seawater particles and the digestive tract of a marine fish species.},
journal = {FEMS microbiology letters},
volume = {173},
number = {1},
pages = {189-194},
doi = {10.1111/j.1574-6968.1999.tb13501.x},
pmid = {10220894},
issn = {0378-1097},
mesh = {Animals ; DNA, Archaeal/analysis ; DNA, Ribosomal/analysis ; Euryarchaeota/genetics/*isolation &amp; purification ; Feces/microbiology ; Flounder/*microbiology ; Intestines/*microbiology ; Methanosarcinaceae/genetics ; Phylogeny ; Polymerase Chain Reaction/methods ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; *Water Microbiology ; },
abstract = {A methanogen-specific nested PCR approach was used to detect methanogenic archaea in seawater particles of the North Sea and the feces and the digestive tract of flounder (Platichthys flesus), a fish found in the North Sea. A number of 16S rDNA sequences with 97.6-99.5% similarity to Methanococcoides methylutens were found in the seawater particles as well as the digestive tract and fecal samples.},
}
@article {pmid10207917,
year = {1999},
author = {Schäfer, G},
title = {How can archaea cope with extreme acidity?.},
journal = {Novartis Foundation symposium},
volume = {221},
number = {},
pages = {131-44; discussion 145-51},
pmid = {10207917},
issn = {1528-2511},
mesh = {Acids ; Adaptation, Biological ; Archaea/*physiology ; Hydrogen-Ion Concentration ; Oxidation-Reduction ; },
abstract = {Archaea are the most extremophilic of the acidophilic microbes, combining, in many cases, acidophilicity with hyperthermophilicity. They form one of the three branches of the phylogenetic tree, and they are specifically found within the so-called crenarchaeota, typical members of which thrive at pH 1-3 and at temperatures of 75 degrees C to nearly 100 degrees C. Despite this, these cells can maintain a near neutral cytosol, and they use H+ for chemiosmotic coupling of ADP phosphorylation. These phenomena require efficient exclusion and disposal of protons. This is achieved by multiple synergistic mechanisms that act in parallel. One strategy is to use bipolar tetraether lipids as a matrix of their plasma membranes, providing low ion permeabilities, even at high temperatures. Additionally, an inverted membrane potential can help to balance a large pH gradient of up to 4 at a proton motive force of delta p = 140-180 mV. This is not a general rule, because in several species the membrane potential contributes only minimally. Also, local buffering capacity and charge profiles across the membrane may significantly influence adaptation to bulk phase acidity. Neither complex I nor complex III electron transport-coupled proton pump equivalents have been found in aerobic archaea. Only terminal oxidases seem to provide either H+ pumping or the generation of a proton gradient by chemical charge separation. Organization, redox centres and primary structures of some archaeal terminal quinol oxidase complexes are known and will be discussed. Much less is known about anaerobic sulfur reducers. For those a possible mechanism for proton exclusion is proposed.},
}
@article {pmid10200977,
year = {1999},
author = {Albers, SV and Konings, WN and Driessen, AJ},
title = {A unique short signal sequence in membrane-anchored proteins of Archaea.},
journal = {Molecular microbiology},
volume = {31},
number = {5},
pages = {1595-1596},
doi = {10.1046/j.1365-2958.1999.01286.x},
pmid = {10200977},
issn = {0950-382X},
mesh = {Archaea/*genetics ; Carrier Proteins/genetics ; Databases, Factual ; Flagellin/metabolism ; Glucose/metabolism ; Membrane Proteins/*genetics ; Models, Biological ; Molecular Sequence Data ; Protein Processing, Post-Translational ; Protein Sorting Signals/genetics ; Sequence Homology, Amino Acid ; },
}
@article {pmid10200952,
year = {1999},
author = {Soppa, J},
title = {Transcription initiation in Archaea: facts, factors and future aspects.},
journal = {Molecular microbiology},
volume = {31},
number = {5},
pages = {1295-1305},
doi = {10.1046/j.1365-2958.1999.01273.x},
pmid = {10200952},
issn = {0950-382X},
mesh = {Archaea/*genetics/*physiology ; *Archaeal Proteins ; Bacteria/genetics ; DNA-Directed RNA Polymerases/physiology ; Eukaryotic Cells ; Genes, Regulator/physiology ; Models, Genetic ; Nuclear Proteins/physiology ; Promoter Regions, Genetic ; TATA Box/physiology ; *Transcription Factor TFIIB ; Transcription Factors/physiology ; Transcription, Genetic/*physiology ; },
abstract = {The basal apparatus for transcription initiation in Archaea is more closely related to the eukaryal than to the bacterial counterpart. The understanding of archaeal transcription initiation has been deepened by recent advances, which include genome sequencing, biochemical approaches and the structure determination of a protein DNA complex. Archaeal promoter elements, transcription factors, RNA polymerase and their interactions are discussed and compared with the eukaryal situation. It is emerging that transcription initiation is not uniform in Archaea. A minimal set of promoter elements and transcription factors is conserved, but the relative importance for transcription initiation can vary. Furthermore, additional basal transcription factors and promoter elements seem to be crucial in subgroups of Archaea. Finally, some aspects of global as well as gene-specific transcriptional regulation are discussed.},
}
@article {pmid10198128,
year = {1999},
author = {Stravopodis, DJ and Kyrpides, NC},
title = {Identification of protein-tyrosine phosphatases in Archaea.},
journal = {Journal of molecular evolution},
volume = {48},
number = {5},
pages = {625-627},
doi = {10.1007/pl00013155},
pmid = {10198128},
issn = {0022-2844},
mesh = {Amino Acid Sequence ; Archaea/*enzymology/*genetics ; Archaeoglobus fulgidus/enzymology/genetics ; Conserved Sequence ; Evolution, Molecular ; Genome ; Methanobacterium/enzymology/genetics ; Methanococcus/enzymology/genetics ; Molecular Sequence Data ; Protein Tyrosine Phosphatases/*genetics ; Pyrococcus/enzymology/genetics ; Sequence Homology, Amino Acid ; },
abstract = {Protein-tyrosine dephosphorylation is a major mechanism in cellular regulation. A large number of protein-tyrosine phosphatases is known from Eukarya, and more recently bacterial homologues have also been identified. By employing conserved sequence patterns from both eukaryotic and bacterial protein-tyrosine phosphatases, we have identified three homologous sequences in two of the four complete archaeal genomes. Two hypothetical open reading frames in the genome of Methanococcus jannaschii (MJ0215 and MJECL20) and one in the genome of Pyrococcus horikoshii (PH1732) clearly bear all the conserved residues of this family. No homologues were found in the genomes of Archaeoglobus fulgidus and Methanobacterium thermoautotrophicum. This is the first report of protein-tyrosine phosphatase sequences in Archaea.},
}
@article {pmid10191143,
year = {1999},
author = {Thiru, A and Hodach, M and Eloranta, JJ and Kostourou, V and Weinzierl, RO and Matthews, S},
title = {RNA polymerase subunit H features a beta-ribbon motif within a novel fold that is present in archaea and eukaryotes.},
journal = {Journal of molecular biology},
volume = {287},
number = {4},
pages = {753-760},
doi = {10.1006/jmbi.1999.2638},
pmid = {10191143},
issn = {0022-2836},
support = {B08519/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; B13343/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; },
mesh = {Amino Acid Sequence ; Base Sequence ; Crystallography, X-Ray ; DNA Primers ; DNA-Directed RNA Polymerases/*chemistry ; Enzyme Stability ; Eukaryotic Cells/enzymology ; Humans ; Magnetic Resonance Spectroscopy ; Methanococcus/*enzymology ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Protein Folding ; Recombinant Proteins/chemistry ; Sequence Homology, Amino Acid ; },
abstract = {The archaeal H and eukaryotic RPB5 RNA polymerase subunits are highly homologous and are likely to play a fundamental role in transcription that extends from archaea to humans. We report the structure of subunit H, in solution, from the archaeon Methanococcus jannaschii using multidimensional nuclear magnetic resonance. The structure reveals a novel fold containing a four-stranded mixed beta sheet that is flanked on one side by three short helices. The dominant feature is beta-ribbon motif, which presents a hydrophobic, basic surface, and defines a general RNA polymerase architectural scaffold.},
}
@article {pmid10086840,
year = {1999},
author = {Schreier, HJ and Robinson-Bidle, KA and Romashko, AM and Patel, GV},
title = {Heterologous expression in the Archaea: transcription from Pyrococcus furiosus gdh and mlrA promoters in Haloferax volcanii.},
journal = {Extremophiles : life under extreme conditions},
volume = {3},
number = {1},
pages = {11-19},
doi = {10.1007/s007920050094},
pmid = {10086840},
issn = {1431-0651},
mesh = {Archaeal Proteins/*genetics ; Base Sequence ; DNA, Archaeal ; Haloferax volcanii/*genetics ; Hydro-Lyases/*genetics ; Molecular Sequence Data ; Plasmids ; *Promoter Regions, Genetic ; Pyrococcus/*genetics ; Sequence Homology, Nucleic Acid ; *Transcription, Genetic ; },
abstract = {Multicopy plasmids containing the promoter regions for gdh and mlrA genes from Pyrococcus furiosus were propagated in Haloferax volcanii. High-level expression was detected from gdh promoter sequences, with transcription initiating at the same start-site as that found in P. furiosus. For mlrA, several transcripts were detected, with one initiating at the P. furiosus start-site; removal or disruption of the likely P. furiosus boxA element resulted in the disappearance of this transcript, indicating that these sequences were utilized by the H. volcanii RNA polymerase for initiation. This is the first demonstration of the utilization of promoters from a hyperthermophilic archaeon in a mesophilic haloarchaeon and provides further evidence for the unity of transcription processes in the domain Archaea.},
}
@article {pmid10079280,
year = {1999},
author = {Janecek, S and Lévêque, E and Belarbi, A and Haye, B},
title = {Close evolutionary relatedness of alpha-amylases from Archaea and plants.},
journal = {Journal of molecular evolution},
volume = {48},
number = {4},
pages = {421-426},
doi = {10.1007/pl00006486},
pmid = {10079280},
issn = {0022-2844},
mesh = {Amino Acid Sequence ; Archaea/*enzymology/genetics ; *Evolution, Molecular ; Molecular Sequence Data ; Plants/*enzymology/genetics ; Sequence Homology, Amino Acid ; alpha-Amylases/chemistry/*genetics ; },
abstract = {The amino acid sequences of 22 alpha-amylases from family 13 of glycosyl hydrolases were analyzed with the aim of revealing the evolutionary relationships between the archaeal alpha-amylases and their eubacterial and eukaryotic counterparts. Two evolutionary distance trees were constructed: (i) the first one based on the alignment of extracted best-conserved sequence regions (58 residues) comprising beta2, beta3, beta4, beta5, beta7, and beta8 strand segments of the catalytic (alpha/beta)8-barrel and a short conserved stretch in domain B protruding out of the barrel in the beta3 --> alpha3 loop, and (ii) the second one based on the alignment of the substantial continuous part of the (alpha/beta)8-barrel involving the entire domain B (consensus length: 386 residues). With regard to archaeal alpha-amylases, both trees compared brought, in fact, the same results; i.e., all family 13 alpha-amylases from domain Archaea were clustered with barley pI isozymes, which represent all plant alpha-amylases. The enzymes from Bacillus licheniformis and Escherichia coli, representing liquefying and cytoplasmic alpha-amylases, respectively, seem to be the further closest relatives to archaeal alpha-amylases. This evolutionary relatedness clearly reflects the discussed similarities in the amino acid sequences of these alpha-amylases, especially in the best-conserved sequence regions. Since the results for alpha-amylases belonging to all three domains (Eucarya, Eubacteria, Archaea) offered by both evolutionary trees are very similar, it is proposed that the investigated conserved sequence regions may indeed constitute the "sequence fingerprints" of a given alpha-amylase.},
}
@article {pmid10049390,
year = {1999},
author = {Watson, GM and Yu, JP and Tabita, FR},
title = {Unusual ribulose 1,5-bisphosphate carboxylase/oxygenase of anoxic Archaea.},
journal = {Journal of bacteriology},
volume = {181},
number = {5},
pages = {1569-1575},
pmid = {10049390},
issn = {0021-9193},
support = {R01 GM024497/GM/NIGMS NIH HHS/United States ; GM24497/GM/NIGMS NIH HHS/United States ; },
mesh = {Amino Acid Sequence ; Anaerobiosis ; Archaea/classification/*enzymology ; Cyanobacteria/enzymology ; Evolution, Molecular ; Macromolecular Substances ; Methanococcus/enzymology ; Models, Molecular ; Molecular Sequence Data ; *Phylogeny ; Protein Structure, Tertiary ; Ribulose-Bisphosphate Carboxylase/*chemistry/genetics/*metabolism ; Sequence Alignment ; Sequence Homology, Amino Acid ; },
abstract = {The predominant pool of organic matter on earth is derived from the biological reduction and assimilation of carbon dioxide gas, catalyzed primarily by the enzyme ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO). By virtue of its capacity to use molecular oxygen as an alternative and competing gaseous substrate, the catalytic efficiency of RubisCO and the enzyme's ability to assimilate CO2 may be severely limited, with consequent environmental and agricultural effects. Recent genomic sequencing projects, however, have identified putative RubisCO genes from anoxic Archaea. In the present study, these potential RubisCO sequences, from Methanococcus jannaschii and Archaeoglobus fulgidus, were analyzed in order to ascertain whether such sequences might encode functional proteins. We also report the isolation and properties of recombinant RubisCO using sequences obtained from the obligately anaerobic hyperthermophilic methanogen M. jannaschii. This is the first description of an archaeal RubisCO sequence; this study also represents the initial characterization of a RubisCO molecule that has evolved in the absence of molecular oxygen. The enzyme was shown to be a homodimer whose deduced sequence, along with other recently obtained archaeal RubisCO sequences, differs substantially from those of known RubisCO molecules. The recombinant M. jannaschii enzyme has a somewhat low, but reasonable kcat, however, unlike previously isolated RubisCO molecules, this enzyme is very oxygen sensitive yet it is stable to hyperthermal temperatures and catalyzes the formation of the expected carboxylation product. Despite inhibition by oxygen, this unusual RubisCO still catalyzes a weak yet demonstrable oxygenase activity, with perhaps the lowest capacity for CO2/O2 discrimination ever encountered for any RubisCO.},
}
@article {pmid10028271,
year = {1999},
author = {Xu, Y and Zhou, P and Tian, X},
title = {Characterization of two novel haloalkaliphilic archaea Natronorubrum bangense gen. nov., sp. nov. and Natronorubrum tibetense gen. nov., sp. nov.},
journal = {International journal of systematic bacteriology},
volume = {49 Pt 1},
number = {},
pages = {261-266},
doi = {10.1099/00207713-49-1-261},
pmid = {10028271},
issn = {0020-7713},
mesh = {Archaea/chemistry/*classification ; Base Sequence ; Lipids/analysis ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Two haloalkaliphilic archaea were isolated from a soda lake in Tibet. The two strains, designated A33T and GA33T, were Gram-negative, pleomorphic, flat, non-motile and strictly aerobic. Growth required at least 12% NaCl. Growth was between pH 8.0 and pH 11 with an optimum at pH 9.0-9.5. Cells were chemo-organotrophic. Polar lipids were C20-C25 derivatives of phosphatidylglycerol and phosphatidylglycerol phosphate. The nucleotide sequences of the 16S rRNA genes from the two strains were obtained by the analysis of the cloned rDNAs. On 16S rRNA phylogenetic trees, the two strains formed a monophyletic cluster. They differed from their closet neighbours, Halobacterium trapanicum and Natrialba asiatica, in polar lipid composition, as well as physiological and phenotypic characteristics. DNA-DNA hybridization indicated that the two strains belonged to different species of the same genus. The results indicated that the strains A33T and GA33T should be classified in a new genus Natronorubrum gen. nov. as Natronorubrum bangense sp. nov. (strain A33T) and Natronorubrum tibetense sp. nov. (strain GA33T).},
}
@article {pmid9973362,
year = {1999},
author = {Nishihara, M and Yamazaki, T and Oshima, T and Koga, Y},
title = {sn-glycerol-1-phosphate-forming activities in Archaea: separation of archaeal phospholipid biosynthesis and glycerol catabolism by glycerophosphate enantiomers.},
journal = {Journal of bacteriology},
volume = {181},
number = {4},
pages = {1330-1333},
pmid = {9973362},
issn = {0021-9193},
mesh = {Dihydroxyacetone Phosphate/*metabolism ; Euryarchaeota/*metabolism ; Glyceraldehyde-3-Phosphate Dehydrogenases/analysis ; Glycerol/*metabolism ; Glycerol Kinase/analysis ; Glycerophosphates/biosynthesis/*metabolism ; Models, Biological ; Peptide Fragments/analysis ; Phospholipids/*biosynthesis ; Stereoisomerism ; },
abstract = {In Methanobacterium thermoautotrophicum, sn-glycerol-1-phosphate (G-1-P) dehydrogenase is responsible for the formation of the Archaea-specific backbone of phospholipids, G-1-P, from dihydroxyacetonephosphate (DHAP). The possible G-1-P-forming activities were surveyed in cell-free extracts of six species of Archaea. All the archaeal cell-free homogenates tested revealed the ability to form G-1-P from DHAP. In addition, activities of G-3-P-forming glycerol kinase and G-3-P dehydrogenase were also detected in four heterotrophic archaea, while glycerol kinase activity was not detected in two autotrophic methanogens. These results show that G-1-P is produced from DHAP by G-1-P dehydrogenase in a wide variety of archaea while exogenous glycerol is catabolized via G-3-P.},
}
@article {pmid9922255,
year = {1999},
author = {Sandler, SJ and Hugenholtz, P and Schleper, C and DeLong, EF and Pace, NR and Clark, AJ},
title = {Diversity of radA genes from cultured and uncultured archaea: comparative analysis of putative RadA proteins and their use as a phylogenetic marker.},
journal = {Journal of bacteriology},
volume = {181},
number = {3},
pages = {907-915},
pmid = {9922255},
issn = {0021-9193},
support = {AI05371/AI/NIAID NIH HHS/United States ; },
mesh = {Amino Acid Sequence ; Archaea/*classification/*genetics ; *Archaeal Proteins ; Bacteria/classification/genetics ; *Bacterial Proteins ; Cloning, Molecular ; DNA Primers ; DNA Repair ; DNA-Binding Proteins/chemistry/*genetics ; *Evolution, Molecular ; Humans ; Molecular Sequence Data ; *Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Recombinant Proteins/chemistry ; Saccharomyces cerevisiae/classification/genetics ; Sequence Alignment ; },
abstract = {Archaea-specific radA primers were used with PCR to amplify fragments of radA genes from 11 cultivated archaeal species and one marine sponge tissue sample that contained essentially an archaeal monoculture. The amino acid sequences encoded by the PCR fragments, three RadA protein sequences previously published (21), and two new complete RadA sequences were aligned with representative bacterial RecA proteins and eucaryal Rad51 and Dmc1 proteins. The alignment supported the existence of four insertions and one deletion in the archaeal and eucaryal sequences relative to the bacterial sequences. The sizes of three of the insertions were found to have taxonomic and phylogenetic significance. Comparative analysis of the RadA sequences, omitting amino acids in the insertions and deletions, shows a cladal distribution of species which mimics to a large extent that obtained by a similar analysis of archaeal 16S rRNA sequences. The PCR technique also was used to amplify fragments of 15 radA genes from uncultured natural sources. Phylogenetic analysis of the amino acid sequences encoded by these fragments reveals several clades with affinity, sometimes only distant, to the putative RadA proteins of several species of Crenarcheota. The two most deeply branching archaeal radA genes found had some amino acid deletion and insertion patterns characteristic of bacterial recA genes. Possible explanations are discussed. Finally, signature codons are presented to distinguish among RecA protein family members.},
}
@article {pmid9914525,
year = {1999},
author = {Moll, R and Schmidtke, S and Schäfer, G},
title = {Domain structure, GTP-hydrolyzing activity and 7S RNA binding of Acidianus ambivalens ffh-homologous protein suggest an SRP-like complex in archaea.},
journal = {European journal of biochemistry},
volume = {259},
number = {1-2},
pages = {441-448},
doi = {10.1046/j.1432-1327.1999.00065.x},
pmid = {9914525},
issn = {0014-2956},
mesh = {Amino Acid Sequence ; Archaeal Proteins/*genetics/metabolism ; Cloning, Molecular ; Escherichia coli/genetics ; *Escherichia coli Proteins ; GTP Phosphohydrolases/*metabolism ; *Genes, Archaeal ; Hot Temperature ; Molecular Sequence Data ; Protein Binding ; Protein Denaturation ; RNA, Archaeal/genetics ; RNA, Small Nuclear/*metabolism ; RNA-Binding Proteins/*genetics/metabolism ; Recombinant Fusion Proteins/metabolism ; Sequence Homology, Amino Acid ; Signal Recognition Particle/*genetics/metabolism ; Sulfolobaceae/*genetics ; },
abstract = {In this study we provide, for the first time, experimental evidence that a protein homologous to bacterial Ffh is part of an SRP-like ribonucleoprotein complex in hyperthermophilic archaea. The gene encoding the Ffh homologue in the hyperthermophilic archaeote Acidianus ambivalens has been cloned and sequenced. Recombinant Ffh protein was expressed in E. coli and subjected to biochemical and functional studies. A. ambivalens Ffh encodes a 50.4-kDa protein that is structured by three distinct regions: the N-terminal hydrophilic N-region (N), the GTP/GDP-binding domain (G) and a C-terminal located C-domain (C). The A. ambivalens Ffh sequence shares 44-46% sequence similarity with Ffh of methanogenic archaea, 34-36% similarity with eukaryal SRP54 and 30-34% similarity with bacterial Ffh. A polyclonal antiserum raised against the first two domains of A. ambivalens Ffh reacts specifically with a single protein (apparent molecular mass: 46 kDa, termed p46) present in cytosolic and in plasmamembrane cell fractions of A. ambivalens. Recombinant Ffh has a melting point of tm = 89 degreesC. Its intrinsic GTPase activity obviously depends on neutral pH and low ionic strength with a preference for chloride and acetate salts. Highest rates of GTP hydrolysis have been achieved at 81 degreesC in presence of 0.1-1 mm Mg2+. GTP hydrolysis is significantly inhibited by high glycerol concentrations, and the GTP hydrolysis rate also markedly decreases by addition of detergents. The Km for GTP is 13.7 microm at 70 degreesC and GTP hydrolysis is strongly inhibited by GDP (Ki = 8 microm). A. ambivalens Ffh, which includes an RNA-binding motif in the C-terminal domain, is shown to bind specifically to 7S RNA of the related crenarchaeote Sulfolobus solfataricus. Comparative sequence analysis reveals the presence of typical signal sequences in plasma membrane as well as extracellular proteins of hyperthermophilic crenarchaea which strongly supposes recognition events by an Ffh containing SRP-like particle in these organisms.},
}
@article {pmid9914204,
year = {1998},
author = {DeLong, EF},
title = {Everything in moderation: archaea as 'non-extremophiles'.},
journal = {Current opinion in genetics &amp; development},
volume = {8},
number = {6},
pages = {649-654},
doi = {10.1016/s0959-437x(98)80032-4},
pmid = {9914204},
issn = {0959-437X},
mesh = {*Archaea/classification/physiology ; Genes, Archaeal ; Phylogeny ; },
abstract = {Well characterized and cultivated archaea are prokaryotic specialists that thrive in habitats of elevated temperature, low pH, high salinity, or strict anoxia. Recently, however, new groups of abundant, uncultivated archaea have been found to be widespread in more pedestrian biotopes, including marine plankton, terrestrial soils, lakes, marine and freshwater sediments, and in association with metazoa. Research efforts are presently focused on characterizing the physiology, biochemistry and genetics of these abundant and cosmopolitan but poorly understood archaea.},
}
@article {pmid9889977,
year = {1998},
author = {Saier, MH},
title = {Molecular phylogeny as a basis for the classification of transport proteins from bacteria, archaea and eukarya.},
journal = {Advances in microbial physiology},
volume = {40},
number = {},
pages = {81-136},
doi = {10.1016/s0065-2911(08)60130-7},
pmid = {9889977},
issn = {0065-2911},
mesh = {Archaea/*enzymology ; Bacteria/*enzymology ; Biological Evolution ; Biological Transport ; Energy Transfer ; Eukaryotic Cells/*enzymology ; Membrane Transport Proteins/*classification/genetics ; Multigene Family ; *Phylogeny ; Substrate Specificity ; },
abstract = {Although enzymes catalyzing chemical reactions have long been classified according to the system developed by the Enzyme Commission (EC), no comparable system has been developed or proposed for transport proteins catalyzing transmembrane vectorial reactions. We here propose a comprehensive system, designated the Transport Commission (TC) system, based both on function and phylogeny. The TC system initially categorizes permeases according to mode of transport and energy coupling mechanism, and each category is assigned a one-component TC number (W). The secondary level of classification corresponds to the phylogenetic family (or superfamily) to which a particular permease is assigned, and each family is assigned a two-component TC number (W.X). The third level of classification refers to the phylogenetic cluster within a family (or the family within a superfamily) to which the permease belongs, and each cluster receives a three-component TC number (W.X.Y). Finally, the last level of categorization is based on substrate specificity and polarity of transport, and each entry is assigned a four component TC number (W.X.Y.Z). This system is based on the observation that mode of transport and energy coupling mechanism are fundamental properties of transport systems that very seldom transcend familial lines, but substrate specificity, being readily alterable by point mutations, is a superficial characteristic that often transcends familial lines. The proposed system has the potential to include all known permeases for which sequence data are available and has the flexibility to accommodate the multitude of permeases likely to be revealed by future genome sequencing and biochemical analysis. Major conclusions resulting from our classification efforts are described. The classification system, which will be continuously updated, is available on our World Wide Web site (http:/(/)www-biology.ucsd.edu/ approximately msaier/transport/titlepage.html).},
}
@article {pmid9882656,
year = {1999},
author = {Gribaldo, S and Lumia, V and Creti, R and Conway de Macario, E and Sanangelantoni, A and Cammarano, P},
title = {Discontinuous occurrence of the hsp70 (dnaK) gene among Archaea and sequence features of HSP70 suggest a novel outlook on phylogenies inferred from this protein.},
journal = {Journal of bacteriology},
volume = {181},
number = {2},
pages = {434-443},
pmid = {9882656},
issn = {0021-9193},
mesh = {Amino Acid Sequence ; Animals ; Archaea/*classification/*genetics ; Bacteria/classification/*genetics ; *Escherichia coli Proteins ; *Evolution, Molecular ; Gram-Positive Bacteria/classification/genetics ; HSP70 Heat-Shock Proteins/*chemistry/*genetics ; Likelihood Functions ; Molecular Chaperones/genetics ; Molecular Sequence Data ; *Phylogeny ; Sequence Alignment ; Sequence Homology, Amino Acid ; },
abstract = {Occurrence of the hsp70 (dnaK) gene was investigated in various members of the domain Archaea comprising both euryarchaeotes and crenarchaeotes and in the hyperthermophilic bacteria Aquifex pyrophilus and Thermotoga maritima representing the deepest offshoots in phylogenetic trees of bacterial 16S rRNA sequences. The gene was not detected in 8 of 10 archaea examined but was found in A. pyrophilus and T. maritima, from which it was cloned and sequenced. Comparative analyses of the HSP70 amino acid sequences encoded in these genes, and others in the databases, showed that (i) in accordance with the vicinities seen in rRNA-based trees, the proteins from A. pyrophilus and T. maritima form a thermophilic cluster with that from the green nonsulfur bacterium Thermomicrobium roseum and are unrelated to their counterparts from gram-positive bacteria, proteobacteria/mitochondria, chlamydiae/spirochetes, deinococci, and cyanobacteria/chloroplasts; (ii) the T. maritima HSP70 clusters with the homologues from the archaea Methanobacterium thermoautotrophicum and Thermoplasma acidophilum, in contrast to the postulated unique kinship between archaea and gram-positive bacteria; and (iii) there are exceptions to the reported association between an insert in HSP70 and gram negativity, or vice versa, absence of insert and gram positivity. Notably, the HSP70 from T. maritima lacks the insert, although T. maritima is phylogenetically unrelated to the gram-positive bacteria. These results, along with the absence of hsp70 (dnaK) in various archaea and its presence in others, suggest that (i) different taxa retained either one or the other of two hsp70 (dnaK) versions (with or without insert), regardless of phylogenetic position; and (ii) archaea are aboriginally devoid of hsp70 (dnaK), and those that have it must have received it from phylogenetically diverse bacteria via lateral gene transfer events that did not involve replacement of an endogenous hsp70 (dnaK) gene.},
}
@article {pmid9864346,
year = {1999},
author = {Howell, DM and Xu, H and White, RH},
title = {(R)-citramalate synthase in methanogenic archaea.},
journal = {Journal of bacteriology},
volume = {181},
number = {1},
pages = {331-333},
pmid = {9864346},
issn = {0021-9193},
mesh = {Acetyltransferases ; Acyltransferases ; Base Sequence ; Cloning, Molecular ; DNA Primers/genetics ; Escherichia coli/genetics ; Gene Expression ; Genes, Archaeal ; Kinetics ; Malates/*metabolism ; Methanococcus/*enzymology/*genetics ; Oxo-Acid-Lyases/*genetics/isolation &amp; purification/*metabolism ; Recombinant Proteins/genetics/isolation &amp; purification/metabolism ; Substrate Specificity ; },
abstract = {The Methanococcus jannaschii gene MJ1392 was cloned, and its protein product was hyperexpressed in Escherichia coli. The resulting protein was purified and shown to catalyze the condensation of pyruvate and acetyl coenzyme A, with the formation of (R)-citramalate. Thus, this gene (cimA) encodes an (R)-citramalate synthase (CimA). This is the first identification of this enzyme, which is likely involved in the biosynthesis of isoleucine.},
}
@article {pmid9851985,
year = {1998},
author = {Kim, HS and Vothknecht, UC and Hedderich, R and Celic, I and Söll, D},
title = {Sequence divergence of seryl-tRNA synthetases in archaea.},
journal = {Journal of bacteriology},
volume = {180},
number = {24},
pages = {6446-6449},
pmid = {9851985},
issn = {0021-9193},
support = {GM22864/GM/NIGMS NIH HHS/United States ; GM55674/GM/NIGMS NIH HHS/United States ; },
mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Cloning, Molecular ; DNA, Archaeal ; Gene Expression ; Humans ; Methanobacterium/*enzymology/genetics ; Methanococcus/*enzymology/genetics ; Molecular Sequence Data ; RNA, Archaeal/metabolism ; RNA, Transfer/metabolism ; Sequence Homology, Amino Acid ; Serine-tRNA Ligase/*genetics/isolation &amp; purification/metabolism ; },
abstract = {The genomic sequences of Methanococcus jannaschii and Methanobacterium thermoautotrophicum contain a structurally uncommon seryl-tRNA synthetase (SerRS) sequence and lack an open reading frame (ORF) for the canonical cysteinyl-tRNA synthetase (CysRS). Therefore, it is not clear if Cys-tRNACys is formed by direct aminoacylation or by a transformation of serine misacylated to tRNACys. To address this question, we prepared SerRS from two methanogenic archaea and measured the enzymatic properties of these proteins. SerRS was purified from M. thermoautotrophicum; its N-terminal peptide sequence matched the sequence deduced from the relevant ORF in the genomic data of M. thermoautotrophicum and M. jannaschii. In addition, SerRS was expressed from a cloned Methanococcus maripaludis serS gene. The two enzymes charged serine to their homologous tRNAs and also accepted Escherichia coli tRNA as substrate for aminoacylation. Gel shift experiments showed that M. thermoautotrophicum SerRS did not mischarge tRNACys with serine. This indicates that Cys-tRNACys is formed by direct acylation in these organisms.},
}
@article {pmid9841678,
year = {1998},
author = {Gupta, RS},
title = {Protein phylogenies and signature sequences: A reappraisal of evolutionary relationships among archaebacteria, eubacteria, and eukaryotes.},
journal = {Microbiology and molecular biology reviews : MMBR},
volume = {62},
number = {4},
pages = {1435-1491},
pmid = {9841678},
issn = {1092-2172},
mesh = {Amino Acid Sequence ; *Archaea/genetics ; Archaeal Proteins/chemistry/genetics ; *Bacteria/genetics ; Bacterial Proteins/chemistry/genetics ; *Eukaryotic Cells ; *Evolution, Molecular ; HSP70 Heat-Shock Proteins/chemistry/genetics ; Molecular Sequence Data ; *Phylogeny ; Proteins/chemistry/*genetics ; Sequence Alignment ; },
abstract = {The presence of shared conserved insertion or deletions (indels) in protein sequences is a special type of signature sequence that shows considerable promise for phylogenetic inference. An alternative model of microbial evolution based on the use of indels of conserved proteins and the morphological features of prokaryotic organisms is proposed. In this model, extant archaebacteria and gram-positive bacteria, which have a simple, single-layered cell wall structure, are termed monoderm prokaryotes. They are believed to be descended from the most primitive organisms. Evidence from indels supports the view that the archaebacteria probably evolved from gram-positive bacteria, and I suggest that this evolution occurred in response to antibiotic selection pressures. Evidence is presented that diderm prokaryotes (i.e., gram-negative bacteria), which have a bilayered cell wall, are derived from monoderm prokaryotes. Signature sequences in different proteins provide a means to define a number of different taxa within prokaryotes (namely, low G+C and high G+C gram-positive, Deinococcus-Thermus, cyanobacteria, chlamydia-cytophaga related, and two different groups of Proteobacteria) and to indicate how they evolved from a common ancestor. Based on phylogenetic information from indels in different protein sequences, it is hypothesized that all eukaryotes, including amitochondriate and aplastidic organisms, received major gene contributions from both an archaebacterium and a gram-negative eubacterium. In this model, the ancestral eukaryotic cell is a chimera that resulted from a unique fusion event between the two separate groups of prokaryotes followed by integration of their genomes.},
}
@article {pmid9833672,
year = {1998},
author = {Herzel, H and Weiss, O and Trifonov, EN},
title = {Sequence periodicity in complete genomes of archaea suggests positive supercoiling.},
journal = {Journal of biomolecular structure &amp; dynamics},
volume = {16},
number = {2},
pages = {341-345},
doi = {10.1080/07391102.1998.10508251},
pmid = {9833672},
issn = {0739-1102},
mesh = {DNA, Archaeal/*chemistry ; DNA, Superhelical/*chemistry ; *Nucleic Acid Conformation ; },
abstract = {The topological state of genomic DNA is of importance for its replication, recombination and transcription. The wrapping of the DNA around nucleosomes is associated with sequence periodicities (Trifonov and Sussman, Proc. Natl. Acad. Sci. USA, 77, pp. 3816-20). Recently, also the negative supercoiling of eubacterial DNA was related to 11 base pair (bp) periodicity (Herzel et al. Physica A, 249, pp. 449-59). Archaeal plasmids and a virus-like particle from Sulfolobus are positively supercoiled, but the superhelical conformation of archaeal genomic DNA is still uncertain. The problem of superhelicity can now be addressed via a comparative statistical analysis of the available complete genomes. For this purpose one has to look for periodicities which are in phase with the helical repeat of 10-11 bp. Similar periodicities are induced, however, by the amphipatic character of alpha-helices of encoded proteins (Zhurkin, Nucl. Acids Res., 9, pp. 1963-71). We show that these protein-induced periodicities are extended over a few periods only. The periods of additional long-ranging oscillations deviate significantly from the value for free DNA. A period of 11 bp in Eubacteria reflects negative supercoiling, whereas the significantly different period of thermophilic Archaea close to 10 bp suggests positive supercoiling of archaeal genomes.},
}
@article {pmid9828419,
year = {1998},
author = {Canganella, F and Jones, WJ and Gambacorta, A and Antranikian, G},
title = {Thermococcus guaymasensis sp. nov. and Thermococcus aggregans sp. nov., two novel thermophilic archaea isolated from the Guaymas Basin hydrothermal vent site.},
journal = {International journal of systematic bacteriology},
volume = {48 Pt 4},
number = {},
pages = {1181-1185},
doi = {10.1099/00207713-48-4-1181},
pmid = {9828419},
issn = {0020-7713},
mesh = {DNA, Archaeal/chemistry ; DNA, Ribosomal/chemistry ; Molecular Sequence Data ; Nucleic Acid Hybridization ; Pacific Ocean ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Species Specificity ; Terminology as Topic ; Thermococcus/*classification/cytology/isolation &amp; purification/physiology ; *Water Microbiology ; },
abstract = {Thermococcus strains TYST and TYT isolated from the Guaymas Basin hydrothermal vent site and previously described were compared by DNA-DNA hybridization analysis with the closest Thermococcus species in terms of physiology and nutritional aspects. On the basis of the new data and taking into consideration the molecular, physiological and morphological traits published previously, it is proposed that strains TYT and TYST should be classified as new species named Thermococcus aggregans sp. nov. and Thermococcus guaymasensis sp. nov., respectively. The type strain of T. aggregans is strain TYT (= DSM 10597T) and the type strain of T. guaymasensis is strain TYST (= DSM 11113T).},
}
@article {pmid9813164,
year = {1998},
author = {McLean, MA and Maves, SA and Weiss, KE and Krepich, S and Sligar, SG},
title = {Characterization of a cytochrome P450 from the acidothermophilic archaea Sulfolobus solfataricus.},
journal = {Biochemical and biophysical research communications},
volume = {252},
number = {1},
pages = {166-172},
doi = {10.1006/bbrc.1998.9584},
pmid = {9813164},
issn = {0006-291X},
support = {GM 31756/GM/NIGMS NIH HHS/United States ; GM 33775/GM/NIGMS NIH HHS/United States ; },
mesh = {Amino Acid Sequence ; Archaeal Proteins ; Base Sequence ; Calorimetry, Differential Scanning ; Carbon Dioxide/metabolism ; Cloning, Organism ; Cytochrome P-450 Enzyme System/*chemistry/genetics/*metabolism ; DNA Primers ; Escherichia coli ; Kinetics ; Models, Molecular ; Molecular Sequence Data ; Oxidation-Reduction ; Oxygenases/*chemistry/genetics/*metabolism ; Photolysis ; Polymerase Chain Reaction ; Protein Conformation ; Recombinant Proteins/biosynthesis/chemistry/metabolism ; Spectrophotometry ; Sulfolobus/*enzymology/genetics ; },
abstract = {We report the cloning, expression, purification, and molecular characterization of a cytochrome P450 (CYP119) from the thermophilic archaea Sulfolobus solfataricus. This protein displays an absorption spectra in the reduced, oxidized, and carbonyl adduct analogous to those of other P450 enzymes. We demonstrate that P450 (CYP119) exhibits remarkable thermo- and pressure stability, with a melting temperature 40 degrees higher than that of the extensively studied cytochrome P450cam (CYP101) and an optical spectra completely resistant to the formation of the inactive P420 by hydrostatic pressure up to 2 kbar. CO flash photolysis experiments, as well as construction of a CYP119 homology model, suggest an open active site with greater solvent access than P450 (CYP101) and similar to that of P450 (CYP102). This communication represents the first molecular characterization of an extremophilic cytochrome P450.},
}
@article {pmid9806856,
year = {1998},
author = {Prangishvili, D and Albers, SV and Holz, I and Arnold, HP and Stedman, K and Klein, T and Singh, H and Hiort, J and Schweier, A and Kristjansson, JK and Zillig, W},
title = {Conjugation in archaea: frequent occurrence of conjugative plasmids in Sulfolobus.},
journal = {Plasmid},
volume = {40},
number = {3},
pages = {190-202},
doi = {10.1006/plas.1998.1363},
pmid = {9806856},
issn = {0147-619X},
mesh = {Bacteriological Techniques ; Clone Cells ; *Conjugation, Genetic ; DNA, Bacterial/genetics ; Plasmids/classification/genetics/*isolation &amp; purification/physiology ; Sequence Deletion ; Sulfolobus/*cytology/genetics ; },
abstract = {We describe five novel conjugative plasmids (CPs) and two subfamilies, each comprising several closely related variants of CPs isolated from colony-cloned strains of the extremely thermophilic, heterotrophic archaeon Sulfolobus islandicus, which were obtained by plating of samples from Icelandic solfataras after liquid enrichment. They are related to each other and to the previously described CP pNOB8 from a Japanese Sulfolobus strain in that they share essential functions and limited similarity of genomes as demonstrated by DNA cross-hybridization and sequences. All these plasmids thus form a family of highly efficient self-spreading elements directly transferred from donor into recipient cells. Conjugation is initiated by pair formation, followed by selective transfer of the plasmids into the recipient and expression of transfer functions. Some of these CPs exclude superconjugation of the transcipients with closely related CPs. The novel CPs are stable upon conjugative transfer, but vary upon growth of transcipients. The stability of the CPs is higher in their original hosts or in related S. islandicus strains, than in Sulfolobus solfataricus strain PH1 as recipient. The deletion variant pING3 has lost the ability to transfer itself but is still subject to being transferred by the transfer apparatus of its complete relative, pING6. The dissection of genes and functions has been initiated by characterizing this incomplete variant.},
}
@article {pmid9799791,
year = {1998},
author = {Leonard, CJ and Aravind, L and Koonin, EV},
title = {Novel families of putative protein kinases in bacteria and archaea: evolution of the "eukaryotic" protein kinase superfamily.},
journal = {Genome research},
volume = {8},
number = {10},
pages = {1038-1047},
doi = {10.1101/gr.8.10.1038},
pmid = {9799791},
issn = {1088-9051},
mesh = {Amino Acid Sequence ; Animals ; Archaea/*enzymology/genetics ; Bacteria/*enzymology/genetics ; Conserved Sequence ; Eukaryotic Cells/*enzymology ; *Evolution, Molecular ; Humans ; Molecular Sequence Data ; Multigene Family ; Phylogeny ; Protein Kinases/chemistry/genetics/*physiology ; Protein Serine-Threonine Kinases/chemistry/genetics/physiology ; Protein-Tyrosine Kinases/chemistry/genetics/physiology ; },
abstract = {The central role of serine/threonine and tyrosine protein kinases in signal transduction and cellular regulation in eukaryotes is well established and widely documented. Considerably less is known about the prevalence and role of these protein kinases in bacteria and archaea. In order to examine the evolutionary origins of the eukaryotic-type protein kinase (ePK) superfamily, we conducted an extensive analysis of the proteins encoded by the completely sequenced bacterial and archaeal genomes. We detected five distinct families of known and predicted putative protein kinases with representatives in bacteria and archaea that share a common ancestry with the eukaryotic protein kinases. Four of these protein families have not been identified previously as protein kinases. From the phylogenetic distribution of these families, we infer the existence of an ancestral protein kinase(s) prior to the divergence of eukaryotes, bacteria, and archaea.},
}
@article {pmid9797402,
year = {1998},
author = {Moreira, D and Lopez-Garcia, P},
title = {Symbiosis between methanogenic archaea and delta-proteobacteria as the origin of eukaryotes: the syntrophic hypothesis.},
journal = {Journal of molecular evolution},
volume = {47},
number = {5},
pages = {517-530},
doi = {10.1007/pl00006408},
pmid = {9797402},
issn = {1432-1432},
abstract = {We present a novel hypothesis for the origin of the eukaryotic cell, or eukaryogenesis, based on a metabolic symbiosis (syntrophy) between a methanogenic archaeon (methanobacterial-like) and a delta-proteobacterium (an ancestral sulfate-reducing myxobacterium). This syntrophic symbiosis was originally mediated by interspecies H2 transfer in anaerobic, possibly moderately thermophilic, environments. During eukaryogenesis, progressive cellular and genomic cointegration of both types of prokaryotic partners occurred. Initially, the establishment of permanent consortia, accompanied by extensive membrane development and close cell-cell interactions, led to a highly evolved symbiotic structure already endowed with some primitive eukaryotic features, such as a complex membrane system defining a protonuclear space (corresponding to the archaeal cytoplasm), and a protoplasmic region (derived from fusion of the surrounding bacterial cells). Simultaneously, bacterial-to-archaeal preferential gene transfer and eventual replacement took place. Bacterial genome extinction was thus accomplished by gradual transfer to the archaeal host, where genes adapted to a new genetic environment. Emerging eukaryotes would have inherited archaeal genome organization and dynamics and, consequently, most DNA-processing information systems. Conversely, primordial genes for social and developmental behavior would have been provided by the ancient myxobacterial symbiont. Metabolism would have been issued mainly from the versatile bacterial organotrophy, and progressively, methanogenesis was lost.},
}
@article {pmid9797280,
year = {1998},
author = {Pernthaler, J and Glockner, FO and Unterholzner, S and Alfreider, A and Psenner, R and Amann, R},
title = {Seasonal community and population dynamics of pelagic bacteria and archaea in a high mountain lake.},
journal = {Applied and environmental microbiology},
volume = {64},
number = {11},
pages = {4299-4306},
pmid = {9797280},
issn = {1098-5336},
abstract = {The seasonal variations in community structure and cell morphology of pelagic procaryotes from a high mountain lake (Gossenkollesee, Austria) were studied by in situ hybridization with rRNA-targeted fluorescently labeled oligonucleotide probes (FISH) and image-analyzed microscopy. Compositional changes and biomass fluctuations within the assemblage were observed both in summer and beneath the winter ice cover and are discussed in the context of physicochemical and biotic parameters. Proteobacteria of the beta subclass (beta-proteobacteria) formed a dominant fraction of the bacterioplankton (annual mean, 24% of the total counts), whereas alpha-proteobacteria were of similar relative importance only during spring (mean, 11%). Bacteria of the Cytophaga-Flavobacterium cluster, although less abundant, constituted the largest fraction of the filamentous morphotypes during most of the year, thus contributing significantly to the total microbial biomass. Successive peaks of threadlike and rod-shaped archaea were observed during autumn thermal mixing and the period of ice cover formation, respectively. A set of oligonucleotide probes targeted to single phylotypes was constructed from 16S rRNA-encoding gene clone sequences. Three distinct populations of uncultivated microbes, affiliated with the alpha- and beta-proteobacteria, were subsequently monitored by FISH. About one-quarter of all of the beta-proteobacteria (range, 6 to 53%) could be assigned to only two phylotypes. The bacterial populations studied were annually recurrent, seasonally variable, and vertically stratified, except during the periods of lake overturn. Their variability clearly exceeded the fluctuations of the total microbial assemblage, suggesting that the apparent stability of total bacterioplankton abundances may mask highly dynamic community fluctuations.},
}
@article {pmid9783158,
year = {1998},
author = {Pereira, SL and Reeve, JN},
title = {Histones and nucleosomes in Archaea and Eukarya: a comparative analysis.},
journal = {Extremophiles : life under extreme conditions},
volume = {2},
number = {3},
pages = {141-148},
doi = {10.1007/s007920050053},
pmid = {9783158},
issn = {1431-0651},
support = {GM53185/GM/NIGMS NIH HHS/United States ; },
mesh = {Amino Acid Sequence ; Animals ; Archaea/*chemistry/*genetics ; DNA, Archaeal/chemistry ; Dimerization ; Eukaryotic Cells ; Evolution, Molecular ; Histones/*chemistry/*genetics ; Models, Molecular ; Molecular Sequence Data ; Nucleosomes/chemistry ; Protein Conformation ; Protein Folding ; Sequence Homology, Amino Acid ; Transcription, Genetic ; },
abstract = {Archaeal histones from mesophilic, thermophilic, and hyperthermophilic members of the Euryarchaeota have primary sequences, the histone fold, tertiary structures, and dimer formation in common with the eukaryal nucleosome core histones H2A, H2B, H3, and H4. Archaeal histones form nucleoprotein complexes in vitro and in vivo, designated archaeal nucleosomes, that contain histone tetramers and protect approximately 60 base pairs of DNA from nuclease digestion. Based on the sequence and structural homologies and experimental data reviewed here, archaeal nucleosomes appear similar, and may be homologous in evolutionary terms and function, to the structure at the center of the eukaryal nucleosome formed by the histone (H3 + H4)2 tetramer.},
}
@article {pmid9767564,
year = {1998},
author = {Bernander, R},
title = {Archaea and the cell cycle.},
journal = {Molecular microbiology},
volume = {29},
number = {4},
pages = {955-961},
doi = {10.1046/j.1365-2958.1998.00956.x},
pmid = {9767564},
issn = {0950-382X},
mesh = {Archaea/*cytology/*genetics/metabolism ; Archaeal Proteins/genetics ; Bacteria/cytology/genetics/metabolism ; *Cell Cycle/genetics/physiology ; Cell Division ; DNA Replication/genetics ; Genes, Archaeal ; Mitosis ; },
abstract = {Sequence similarity data suggest that archaeal chromosome replication is eukaryotic in character. Putative nucleoid-processing proteins display similarities to both eukaryotic and bacterial counterparts, whereas cell division may occur through a predominantly bacterial mechanism. Insights into the organization of the archaeal cell cycle are therefore of interest, not only for understanding archaeal biology, but also for investigating how components from the other two domains interact and work in concert within the same cell; in addition, archaea may have the potential to provide insights into eukaryotic initiation of chromosome replication.},
}
@article {pmid9765860,
year = {1997},
author = {Benbouzid-Rollet, N and López-García, P and Watrin, L and Erauso, G and Prieur, D and Forterre, P},
title = {Isolation of new plasmids from hyperthermophilic Archaea of the order Thermococcales.},
journal = {Research in microbiology},
volume = {148},
number = {9},
pages = {767-775},
doi = {10.1016/s0923-2508(97)82452-7},
pmid = {9765860},
issn = {0923-2508},
mesh = {Blotting, Southern ; DNA, Bacterial/*isolation &amp; purification ; Electrophoresis, Gel, Pulsed-Field ; Hot Temperature ; Pacific Ocean ; Plasmids/*isolation &amp; purification ; Polymorphism, Restriction Fragment Length ; Pyrococcus/chemistry/*genetics ; Restriction Mapping ; Seawater ; Thermococcus/chemistry/*genetics ; },
abstract = {A collection of 57 strains of hyperthermophilic Archaea from the order Thermococcales was screened for the presence of plasmids; 9 plasmids present in six of these strains were isolated and characterized in terms of size and cross-hybridization. The Notl macrorestriction patterns of genomic DNA of strains harbouring these plasmids were obtained. Pyrococcus abyssi strains GE27 and GE23 as well as Thermococcus sp. GE31 contained a single plasmid of 3.5 kb (pGN27), 16.8 kb (pGN23) and 5.3 kb (pGN31), respectively, whilst the three strains I559, I560 and I690 all contained two plasmids of 3.5 kb (pSN559, pSN560, pSN690) and 24 kb (pLN559, pLN560, pLN690), respectively. Plasmid pGN27 strongly cross-hybridized with the previously described plasmid pGT5 from P. abyssi strain GE5, whilst plasmids pGN23 and pGN31 did not cross-hybridize with each other, nor with any other plasmid. The three small plasmids of strains I559, I560 and I690 cross-hybridized, as well as their three large plasmids. Macrorestriction pattern analysis and the results of plasmid cross-hybridization experiments indicated that these three strains were different but closely related, and likely belonged to the genus Thermococcus. This study shows that plasmids are widespread in hyperthermophilic archaea, and significantly increases the number and diversity of plasmids available for laboratory work.},
}
@article {pmid9757822,
year = {1998},
author = {Chédin, F and Seitz, EM and Kowalczykowski, SC},
title = {Novel homologs of replication protein A in archaea: implications for the evolution of ssDNA-binding proteins.},
journal = {Trends in biochemical sciences},
volume = {23},
number = {8},
pages = {273-277},
doi = {10.1016/s0968-0004(98)01243-2},
pmid = {9757822},
issn = {0968-0004},
mesh = {Amino Acid Sequence ; Archaeal Proteins/*physiology ; Binding Sites ; Conserved Sequence ; DNA, Single-Stranded/*metabolism ; DNA-Binding Proteins/genetics/metabolism/*physiology ; Evolution, Molecular ; Methanococcus/genetics/metabolism ; Models, Biological ; Molecular Sequence Data ; Replication Protein A ; Sequence Alignment ; Sequence Homology, Amino Acid ; },
abstract = {In Bacteria and Eukarya, ssDNA-binding proteins are central to most aspects of DNA metabolism. Until recently, however, no counterpart of an ssDNA-binding protein had been identified in the third domain of life, Archaea. Here, we report the discovery of a novel type of ssDNA-binding protein in the genomes of several archaeons. These proteins, in contrast to all known members of this protein family, possess four conserved DNA-binding sites within a single polypeptide or, in one case, two polypeptides. This peculiar structural organization allows us to propose a model for the evolution of this class of proteins.},
}
@article {pmid9746940,
year = {1998},
author = {Danson, MJ and Hough, DW},
title = {Structure, function and stability of enzymes from the Archaea.},
journal = {Trends in microbiology},
volume = {6},
number = {8},
pages = {307-314},
doi = {10.1016/s0966-842x(98)01316-x},
pmid = {9746940},
issn = {0966-842X},
mesh = {Archaea/*enzymology ; Archaeal Proteins/*chemistry/metabolism ; Atmospheric Pressure ; Hydrogen-Ion Concentration ; Protein Conformation ; },
abstract = {The Archaea include microorganisms growing in some of the most extreme environments on earth. Consequently, their cellular components are remarkably stable entities and have considerable potential in the biotechnology industry. Here, we review the structure of archaeal enzymes in the context of their ability to function at extremes of temperature, salinity, pH and pressure.},
}
@article {pmid9746351,
year = {1998},
author = {Köhrer, C and Mayer, C and Neumair, O and Gröbner, P and Piendl, W},
title = {Interaction of ribosomal L1 proteins from mesophilic and thermophilic Archaea and Bacteria with specific L1-binding sites on 23S rRNA and mRNA.},
journal = {European journal of biochemistry},
volume = {256},
number = {1},
pages = {97-105},
doi = {10.1046/j.1432-1327.1998.2560097.x},
pmid = {9746351},
issn = {0014-2956},
mesh = {*Archaea ; Binding Sites ; Escherichia coli ; *Gram-Negative Aerobic Rods and Cocci ; Methanococcus ; Molecular Sequence Data ; Protein Binding/drug effects ; RNA, Messenger/*metabolism ; RNA, Ribosomal, 23S/*metabolism ; Ribosomal Proteins/*metabolism ; Salts/pharmacology ; Sulfolobus ; Thermus thermophilus ; },
abstract = {In Bacteria and Archaea (formerly Archaebacteria) ribosomal protein L1 has a dual function, as a primary rRNA-binding protein and as a translational repressor which binds to its own mRNA. The L1-binding site on the mRNA exhibits high similarity in both sequence and secondary structure to the binding site for L1 on the 23 S rRNA. A sensitive membrane-filter-binding assay has been used to examine the interactions between ribosomal L1 proteins from different archaeal and bacterial species, and 23S rRNA and mRNA fragments from Methanococcus vannielii containing the MvaL1-binding site. Under standard conditions (0 degrees C, pH 7.5, 20 mM Mg2+, 500 mM KCl), the apparent dissociation constant Kd of the homologous MvaL1-23S rRNA complex is 5 nM, the apparent dissociation constant Kd of the MvaL1-mRNA complex is 0.15 degrees M. L1 proteins from Escherichia coli (EcoL1) and from the thermophilic Bacterium Thermus thermophilus (TthL1), and from the thermophilic Archaea Methanococcus thermolithotrophicus (MthL1), Methanococcus jannaschii (MjaL1), and Sulfolobus solfataricus (SsoL1) were tested for their affinity to the specific L1-binding sites on the 23 S rRNA and mRNA. In general, the affinity of L1 proteins from thermophilic species to the binding sites on both 23 S rRNA and mRNA is about one order of magnitude higher than that of their mesophilic counterparts. This stronger protein-RNA interaction might make a substantial contribution to the thermal tolerance of ribosomes in thermophilic organisms.},
}
@article {pmid9746349,
year = {1998},
author = {Siatecka, M and Rozek, M and Barciszewski, J and Mirande, M},
title = {Modular evolution of the Glx-tRNA synthetase family--rooting of the evolutionary tree between the bacteria and archaea/eukarya branches.},
journal = {European journal of biochemistry},
volume = {256},
number = {1},
pages = {80-87},
doi = {10.1046/j.1432-1327.1998.2560080.x},
pmid = {9746349},
issn = {0014-2956},
mesh = {Amino Acid Sequence ; Amino Acyl-tRNA Synthetases/classification/*genetics ; Anticodon ; Archaea/enzymology/genetics ; Bacteria/enzymology/genetics ; Binding Sites ; DNA, Complementary/genetics ; *Evolution, Molecular ; Fabaceae/enzymology/*genetics ; Glutamate-tRNA Ligase/classification/*genetics ; Molecular Sequence Data ; Phylogeny ; *Plants, Medicinal ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; },
abstract = {The accuracy of protein biosynthesis generally rests on a family of 20 aminoacyl-tRNA synthetases, one for each amino acid. In bacteria, archaea and eukaryotic organelles, the formation of Gln-tRNA(Gln) is prevalently accomplished by a transamidation pathway, aminoacylation of tRNA(Gln) with Glu by glutamyl-tRNA synthetase (GluRS) followed by a tRNA-dependent transamidation of Glu from Glu-tRNA(Gln). A few bacterial species, such as Escherichia coli, possess a glutaminyl-tRNA synthetase (GlnRS), responsible for Gln-tRNA(Gln) formation. Phylogenetic analysis of the GluRS or GlnRS families (GlxRS) suggested that GlnRS has a eukaryotic origin and was horizontally transferred to a restricted set of bacteria. We have now isolated an additional GlnRS gene from the plant Lupinus luteus and analyzed in more details the modular architecture of the paralogous enzymes GluRS and GlnRS, starting from a large data set of 33 GlxRS sequences. Our analysis suggests that the ancestral GluRS-like enzyme was solely composed of the catalytic domain bearing the class-defining motifs of aminoacyl-tRNA synthetases, and that the anticodon-binding domain of GlxRSs was independently acquired in the bacteria and archaea branches of the universal tree of life, the eukarya sub-branch arising as a sister group of archaea. The transient capture of UAA and UAG codons could have favored the emergence of a GlnRS in early eukaryotes.},
}
@article {pmid9738442,
year = {1998},
author = {Serrano, JA and Camacho, M and Bonete, MJ},
title = {Operation of glyoxylate cycle in halophilic archaea: presence of malate synthase and isocitrate lyase in Haloferax volcanii.},
journal = {FEBS letters},
volume = {434},
number = {1-2},
pages = {13-16},
doi = {10.1016/s0014-5793(98)00911-9},
pmid = {9738442},
issn = {0014-5793},
mesh = {Glyoxylates/*metabolism ; Haloferax volcanii/*enzymology ; Isocitrate Lyase/*metabolism ; Malate Synthase/*metabolism ; },
abstract = {The occurrence of the glyoxylate cycle has not previously been demonstrated in any of the Archaea. In halophilic archaea, only isocitrate lyase activity has been detected. The halophilic archaeon Haloferax volcanii was tested for the presence of the other key enzyme of this pathway, malate synthase. High activities of this enzyme were detected when the carbon source was acetate. Both glyoxylate cycle key enzymes, isocitrate lyase and malate synthase, from Hf. volcanii were purified and characterized.},
}
@article {pmid9733652,
year = {1998},
author = {Gupta, RS},
title = {Life's third domain (Archaea): an established fact or an endangered paradigm?.},
journal = {Theoretical population biology},
volume = {54},
number = {2},
pages = {91-104},
doi = {10.1006/tpbi.1998.1376},
pmid = {9733652},
issn = {0040-5809},
mesh = {Amino Acid Sequence ; Archaea/*classification/genetics ; Bacteria/*classification/genetics ; Biological Evolution ; Classification ; Eukaryotic Cells/classification ; Molecular Sequence Data ; Prokaryotic Cells/classification ; },
abstract = {The three-domain proposal of Woese et al. (Proc. Natl. Acad. Sci. USA 87, 4576 (1990)) divides all living organisms into three primary groups or domains named Archaea (or archaebacteria), Bacteria (or eubacteria), and Eucarya (or eukaryotes), with Eucarya being relatives (or descendants) of Archaea. Although this proposal is currently widely accepted, sequence features and phylogenies derived from many highly conserved proteins are inconsistent with it and point to a close and specific relationship between archaebacteria and gram-positive bacteria, whereas gram-negative bacteria are indicated to be phylogenetically distinct. A closer relationship of archaebacteria to gram-positive bacteria in comparison to gram-negative bacteria is generally seen for the majority of the available gene/protein sequences. To account for these results, and the fact that both archaebacteria and gram-positive bacteria are prokaryotes surrounded by a single cell membrane, I propose that the primary division within prokaryotes is between Monoderm prokaryotes (surrounded by a single membrane) and Diderm prokaryotes (i.e., all true gram-negative bacteria containing both an inner cytoplasmic membrane and an outer membrane). This proposal is consistent with both cell morphology and signature sequences in different proteins. Protein phylogenies and signature sequences also show that all eukaryotic cells have received significant gene contributions from both an archaebacterium and a gram- negative eubacterium. Thus, the hypothesis that archaebacteria and eukaryotes shared a common ancestor exclusive of eubacteria, or that the ancestral eukaryotic cell directly descended from an archaea, is erroneous. These results call into question the validity of the currently popular three-domain proposal and the assignment of a domain status to archaebacteria. A new classifica- tion of organisms consistent with phenotype and macromolecular sequence data is proposed.},
}
@article {pmid9729742,
year = {1998},
author = {Oesterhelt, D},
title = {The structure and mechanism of the family of retinal proteins from halophilic archaea.},
journal = {Current opinion in structural biology},
volume = {8},
number = {4},
pages = {489-500},
doi = {10.1016/s0959-440x(98)80128-0},
pmid = {9729742},
issn = {0959-440X},
mesh = {Archaeal Proteins/chemistry/*metabolism ; Bacteriorhodopsins/chemistry/*metabolism ; Binding Sites ; *Carotenoids ; Halorhodopsins ; Models, Molecular ; Protein Conformation ; Retinaldehyde/*chemistry/metabolism ; *Sensory Rhodopsins ; },
abstract = {Retinal proteins from halophilic archaea provide a unique opportunity to analyze vectorial ion translocation. Studies on its structure, conformational changes, proton conduction and electrogenic steps have helped to elucidate the catalytic cycle of bacteriorhodopsin in increasing detail. Experimental modulation of the vectoriality and ion specificity by altering the substrate availability, point mutations and light conditions for the different retinal proteins allows the proposal of a general model of ion transport for this protein family.},
}
@article {pmid9723910,
year = {1998},
author = {Gupta, RS},
title = {What are archaebacteria: life's third domain or monoderm prokaryotes related to gram-positive bacteria? A new proposal for the classification of prokaryotic organisms.},
journal = {Molecular microbiology},
volume = {29},
number = {3},
pages = {695-707},
doi = {10.1046/j.1365-2958.1998.00978.x},
pmid = {9723910},
issn = {0950-382X},
mesh = {Amino Acid Sequence ; Archaea/*classification/genetics ; Biological Evolution ; Eukaryotic Cells/classification ; Gram-Positive Bacteria/*classification/genetics ; Molecular Sequence Data ; Prokaryotic Cells/classification ; },
abstract = {The evolutionary relationship within prokaryotes is examined based on signature sequences (defined as conserved inserts or deletions shared by specific taxa) and phylogenies derived from different proteins. Archaebacteria are indicated as being monophyletic by a number of proteins related to the information transfer processes. In contrast, for several other highly conserved proteins, common signature sequences are present in archaebacteria and Gram-positive bacteria, whereas Gram-negative bacteria are indicated as being distinct. For these proteins, archaebacteria do not form a phylogenetically distinct clade but show polyphyletic branching within Gram-positive bacteria. A closer relationship of archaebacteria to Gram-positive bacteria in comparison with Gram-negative bacteria is generally seen for the majority of the available gene/ protein sequences. To account for these results and the fact that both archaebacteria and Gram-positive bacteria are prokaryotes surrounded by a single cell membrane, I propose that the primary division within prokaryotes is between monoderm prokaryotes (surrounded by a single membrane) and diderm prokaryotes (i.e. all true Gram-negative bacteria containing both an inner cytoplasmic membrane and an outer membrane). This proposal is consistent with both cell morphology and signature sequences in different proteins. The monophyletic nature of archaebacteria for some genes, and their polyphyletic branching within Gram-positive bacteria as suggested by others, is critically examined, and several explanations, including derivation of archaebacteria from Gram-positive bacteria in response to antibiotic selection pressure, are proposed. Signature sequences in proteins also indicate that the low-G+C Gram-positive bacteria are phylogenetically distinct from the high-G+C Gram-positive group and that the diderm prokaryotes (i.e. Gram-negative bacteria) appear to have evolved from the latter group. Protein phylogenies and signature sequences also show that all eukaryotic cells have received significant gene contributions from both an archaebacterium and a Gram-negative eubacterium. Thus, the hypothesis that archaebacteria and eukaryotes shared a common ancestor exclusive of eubacteria is not supported. These observations provide evidence for an alternate view of the evolutionary relationship among living organisms that is different from the currently popular three-domain proposal.},
}
@article {pmid9720046,
year = {1998},
author = {Baensch, M and Frank, R and Khl, J},
title = {Conservation of the amino-terminal epitope of elongation factor Tu in eubacteria and Archaea.},
journal = {Microbiology (Reading, England)},
volume = {144 (Pt 8)},
number = {},
pages = {2241-2246},
doi = {10.1099/00221287-144-8-2241},
pmid = {9720046},
issn = {1350-0872},
mesh = {Amino Acid Sequence ; Antibodies, Monoclonal/metabolism ; Archaea/*chemistry/immunology ; Bacteria/*chemistry/immunology ; Binding Sites, Antibody ; *Conserved Sequence ; Epitope Mapping ; Epitopes/*chemistry/immunology ; Molecular Sequence Data ; Mutagenesis, Site-Directed/immunology ; Mycoplasma hominis/immunology ; Peptide Elongation Factor Tu/*chemistry/immunology ; Peptide Fragments/*chemistry/immunology ; Protein Structure, Tertiary ; },
abstract = {An epitope of elongation factor Tu (EF-Tu), which is found in organisms in both the bacterial and archaeal domains, was recently defined by mAb 900. To localize the conserved epitope within the EF-Tu molecule and to determine its sequence, SPOTScan analysis of synthetic peptides, Western blot analysis of purified EF-Tu domains and site-directed mutagenesis studies were used. Analysis of mAb 900 binding to overlapping 15-mer peptides encompassing the complete sequence of EF-Tu of Escherichia coli was inconclusive, suggesting three distinct regions may be epitopes. Western blot analysis of EF-Tu domains 1-3 of Thermus thermophilus suggested that the epitope was located at the N terminus. This was confirmed by site-directed mutagenesis of EF-Tu domain 1 of Mycoplasma hominis. By C-terminal truncation of the N-terminal 15-mer peptide the epitope was mapped to EF-Tu residues 1-6. Replacement of each of the residues in the epitope peptide demonstrated that only positions 5 and 6 were indispensable for antibody binding. These data provide evidence that the highly conserved epitope recognized by mAb 900 in the bacterial and archaeal domains is located at the very end of the N terminus of the EF-Tu molecule.},
}
@article {pmid9708919,
year = {1998},
author = {Dib, R and Chobert, JM and Dalgalarrondo, M and Barbier, G and Haertlé, T},
title = {Purification, molecular properties and specificity of a thermoactive and thermostable proteinase from Pyrococcus abyssi, strain st 549, hyperthermophilic archaea from deep-sea hydrothermal ecosystem.},
journal = {FEBS letters},
volume = {431},
number = {2},
pages = {279-284},
doi = {10.1016/s0014-5793(98)00782-0},
pmid = {9708919},
issn = {0014-5793},
mesh = {Amino Acid Sequence ; Amino Acids/analysis ; Archaeal Proteins/genetics/*isolation &amp; purification/metabolism ; Ecosystem ; Electrophoresis, Polyacrylamide Gel/methods ; Endopeptidases/genetics/*isolation &amp; purification/metabolism ; Enzyme Repression ; Hydrogen-Ion Concentration ; Insulin/metabolism ; Marine Biology ; Molecular Sequence Data ; Pyrococcus/*enzymology/genetics ; Serine Endopeptidases/metabolism ; Substrate Specificity ; Temperature ; Water Microbiology ; },
abstract = {A protease was isolated and purified from the supernatant of a culture of hyperthermophilic archaebacteria: Pyrococcus abyssi strain st 549. Purification consisted of three chromatographic steps. The enzyme purification yield was 4% and the purification factor 890. This protease is a seryl-protease hydrolyzing proteins and peptides with a preference for cleavage at the aromatic and hydrophobic residues in P1 and P'1 positions. Its activity is optimal at 95 degrees C and at pH 9. The electrophoretic mobility of the protease observed by zymogram suggests that it can adopt several oligomer forms. Three of them predominate displaying apparent molecular masses of 150, 105 and 60 kDa. Interdependence of the observed bands was revealed by changing the denaturation conditions of the samples (temperature, SDS concentration) before electrophoresis.},
}
@article {pmid9687447,
year = {1998},
author = {van der Maarel, MJ and Artz, RR and Haanstra, R and Forney, LJ},
title = {Association of marine archaea with the digestive tracts of two marine fish species.},
journal = {Applied and environmental microbiology},
volume = {64},
number = {8},
pages = {2894-2898},
pmid = {9687447},
issn = {0099-2240},
mesh = {Animals ; Archaea/classification/genetics/*isolation &amp; purification ; Base Sequence ; DNA Fingerprinting ; DNA, Archaeal/analysis ; DNA, Ribosomal/analysis ; Digestive System/*microbiology ; Feces/microbiology ; Flounder/*microbiology ; Molecular Sequence Data ; Netherlands ; North Sea ; Nucleic Acid Hybridization ; Perciformes/*microbiology ; Phylogeny ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; Water Microbiology ; },
abstract = {Recent studies have shown that archaea which were always thought to live under strict anoxic or extreme environmental conditions are also present in cold, oxygenated seawater, soils, the digestive tract of a holothurian deep-sea-deposit feeder, and a marine sponge. In this study, we show, by using PCR-mediated screening in other marine eukaryotes, that marine archaea are also present in the digestive tracts of flounder and grey mullet, two fish species common in the North Sea, in fecal samples of flounder, and in suspended particulate matter of the North Sea water column. No marine archaea could be detected in the digestive tracts of mussels or the fecal pellets of a copepod species. The archaeal 16S ribosomal DNA clone libraries of feces of flounder and the contents of the digestive tracts of grey mullet and flounder were dominated by group II marine archaea. The marine archaeal clones derived from flounder and grey mullet digestive tracts and feces formed a distinct cluster within the group II marine archaea, with 76.7 to 89. 8% similarity to previously described group II clones. Fingerprinting of the archaeal community of flounder digestive tract contents and feces by terminal restriction fragment length polymorphism of archaeal 16S rRNA genes after restriction with HhaI showed a dominant fragment at 249 bp, which is likely to be derived from group II marine archaea. Clones of marine archaea that were closely related to the fish-associated marine archaea clones were obtained from suspended particulate matter of the water column at two stations in the North Sea. Terminal restriction fragment length polymorphism fingerprinting of the archaeal community present in suspended particulate matter showed the same fragment pattern as was found for the archaeal community of the flounder digestive tract contents and feces. These data demonstrate that marine archaea are present in the digestive tracts and feces of very common marine fish. It is possible that the marine archaea associated with the digestive tracts of marine fish are liberated into the water column through the feces and subsequently contribute to the marine archaeal community of suspended particulate matter.},
}
@article {pmid9683472,
year = {1998},
author = {Chen, L and Spiliotis, ET and Roberts, MF},
title = {Biosynthesis of Di-myo-inositol-1,1'-phosphate, a novel osmolyte in hyperthermophilic archaea.},
journal = {Journal of bacteriology},
volume = {180},
number = {15},
pages = {3785-3792},
pmid = {9683472},
issn = {0021-9193},
mesh = {Cell-Free System/metabolism ; Cytidine Triphosphate/metabolism ; Hot Temperature ; Inositol/metabolism ; Inositol Phosphates/*biosynthesis/metabolism ; Methanococcus/*metabolism ; Molecular Structure ; Nuclear Magnetic Resonance, Biomolecular ; Stereoisomerism ; },
abstract = {Biosynthesis of di-myo-inositol-1,1'-phosphate (DIP) is proposed to occur with myo-inositol and myo-inositol 1-phosphate (I-1-P) used as precursors. Activation of the I-1-P with CTP and condensation of the resultant CDP-inositol (CDP-I) with myo-inositol then generates DIP. The sole known biosynthetic pathway of inositol in all organisms is the conversion of D-glucose-6-phosphate to myo-inositol. This conversion requires two key enzymes: L-I-1-P synthase and I-1-P phosphatase. Enzymatic assays using 31P nuclear magnetic resonance spectroscopy as well as a colorimetric assay for inorganic phosphate have confirmed the occurrence of L-I-1-P synthase and a moderately specific I-1-P phosphatase. The enzymatic reaction that couples CDP-I with myo-inositol to generate DIP has also been detected in Methanococcus igneus. 13C labeling studies with [2,3-13C]pyruvate and [3-13C]pyruvate were used to examine this pathway in M. igneus. Label distribution in DIP was consistent with inositol units formed from glucose-6-phosphate, but the label in the glucose moiety was scrambled via transketolase and transaldolase activities of the pentose phosphate pathway.},
}
@article {pmid9680299,
year = {1997},
author = {Aravalli, RN and Garrett, RA},
title = {Shuttle vectors for hyperthermophilic archaea.},
journal = {Extremophiles : life under extreme conditions},
volume = {1},
number = {4},
pages = {183-191},
doi = {10.1007/s007920050032},
pmid = {9680299},
issn = {1431-0651},
mesh = {Alcohol Dehydrogenase/genetics ; Base Sequence ; Escherichia coli/genetics ; Genetic Markers ; *Genetic Vectors ; Pyrococcus/*genetics ; Sulfolobus acidocaldarius/enzymology/*genetics ; },
abstract = {Progress in understanding the basic molecular, biochemical, and physiological characteristics of archaeal hyperthermophiles has been limited by the lack of suitable expression vectors. Here, we report the construction of versatile shuttle vectors that can be maintained, and selected for, in both archaea and bacteria. The primary construct, pAG1, was produced by ligating portions of the archaeal cryptic plasmid pGT5 and the bacterial plasmid pUC19, both of which exhibit high copy numbers. A second vector construct, pAG2, was generated, with a reduced copy number in Escherichia coli, by introducing the Rom/Rop gene from pBR322 into pAG1. After transformation, both pAG1 and pAG2 were stably maintained and propagated in the euryarchaeote Pyrococcus furiosus, the crenarchaeote Sulfolobus acidocaldarius, and in Escherichia coli. An archaeal selective marker, the alcohol dehydrogenase gene from Sulfolobus solfataricus, was isolated by polymerase chain reaction (PCR) amplification and cloned into the two constructs. They were stably maintained and expressed in the two archaea and conferred resistance to butanol and benzyl alcohol. However, the vector pAG21, deriving from pAG2, proved the more stable in E. coli probably due to its lower copy number in the bacterium. Conditions are presented for the use of the vectors which, potentially, can be used for other hyperthermophilic archaea.},
}
@article {pmid9675798,
year = {1998},
author = {Bell, SD and Jackson, SP},
title = {Transcription and translation in Archaea: a mosaic of eukaryal and bacterial features.},
journal = {Trends in microbiology},
volume = {6},
number = {6},
pages = {222-228},
doi = {10.1016/s0966-842x(98)01281-5},
pmid = {9675798},
issn = {0966-842X},
mesh = {Archaea/*genetics ; Evolution, Molecular ; Gene Expression Regulation, Archaeal ; Genes, Archaeal/genetics ; *Protein Biosynthesis ; *Transcription, Genetic ; },
abstract = {The principal components involved in the processes of transcription and translation in Archaea have been identified by a combination of biochemistry and genome sequencing. In many cases, these factors are closely related to previously characterized proteins from Eukarya and Bacteria. Elucidating the function of these proteins will shed considerable light on the evolution of gene regulatory processes.},
}
@article {pmid9670799,
year = {1998},
author = {da Costa, MS and Santos, H and Galinski, EA},
title = {An overview of the role and diversity of compatible solutes in Bacteria and Archaea.},
journal = {Advances in biochemical engineering/biotechnology},
volume = {61},
number = {},
pages = {117-153},
doi = {10.1007/BFb0102291},
pmid = {9670799},
issn = {0724-6145},
mesh = {Archaea/chemistry/*metabolism ; Bacteria/chemistry/*metabolism ; *Bacterial Physiological Phenomena ; Carbohydrates/chemistry ; Euryarchaeota/metabolism ; Glutamates/chemistry ; Osmolar Concentration ; Potassium/chemistry ; *Temperature ; *Water Microbiology ; },
abstract = {The accumulation of compatible solutes is a prerequisite for the adaptation of microorganisms to osmotic stress imposed by salt or organic solutes. Two types of strategies exist to cope with high external solute concentrations; one strategy is found in the extremely halophilic Archaea of the family Halobacteriaceae and the Bacteria of the order Haloanaerobiales involving the accumulation of inorganic ions. The other strategy of osmoadaptation involves the accumulation of specific organic solutes and is found in the vast majority of microorganisms. The organic osmolytes range from sugars, polyols, amino acids and their respective derivatives, ectoines and betaines. The diversity of these organic solutes has increased in the past few years as more organisms, especially thermophilic and hyperthermophilic Bacteria and Archaea, have been examined. The term compatible solute can also be applied to solutes that protect macromolecules and cells against stresses such as high temperature, desiccation and freezing. The mechanisms by which compatible solutes protect enzymes, cell components and cells are still a long way from being thoroughly elucidated, but there is a growing interest in the utilization of these solutes to protect macromolecules and cells from heating, freezing and desiccation.},
}
@article {pmid9670798,
year = {1998},
author = {van der Oost, J and Ciaramella, M and Moracci, M and Pisani, FM and Rossi, M and de Vos, WM},
title = {Molecular biology of hyperthermophilic Archaea.},
journal = {Advances in biochemical engineering/biotechnology},
volume = {61},
number = {},
pages = {87-115},
doi = {10.1007/BFb0102290},
pmid = {9670798},
issn = {0724-6145},
mesh = {Archaea/chemistry/*genetics/metabolism ; Bacterial Proteins/chemistry/genetics ; Base Sequence ; Cloning, Molecular ; DNA Replication ; Gene Expression Regulation, Bacterial/*genetics ; Genotype ; Molecular Sequence Data ; Multigene Family ; Promoter Regions, Genetic/genetics ; Protein Biosynthesis ; Thermus/chemistry/*genetics/metabolism ; Transcription Factors/chemistry ; Transcription, Genetic ; },
abstract = {The sequences of a number of archaeal genomes have recently been completed, and many more are expected shortly. Consequently, the research of Archaea in general and hyperthermophiles in particular has entered a new phase, with many exciting discoveries to be expected. The wealth of sequence information has already led, and will continue to lead to the identification of many enzymes with unique properties, some of which have potential for industrial applications. Subsequent functional genomics will help reveal fundamental matters such as details concerning the genetic, biochemical and physiological adaptation of extremophiles, and hence give insight into their genomic evolution, polypeptide structure-function relations, and metabolic regulation. In order to optimally exploit many unique features that are now emerging, the development of genetic systems for hyperthermophilic Archaea is an absolute requirement. Such systems would allow the application of this class of Archaea as so-called "cell factories": (i) expression of certain archaeal enzymes for which no suitable conventional (mesophilic bacterial or eukaryal) systems are available, (ii) selection for thermostable variants of potentially interesting enzymes from mesophilic origin, and (iii) the development of in vivo production systems by metabolic engineering. An overview is given of recent insight in the molecular biology of hyperthermophilic Archaea, as well as of a number of promising developments that should result in the generation of suitable genetic systems in the near future.},
}
@article {pmid9665716,
year = {1998},
author = {Howell, DM and Harich, K and Xu, H and White, RH},
title = {Alpha-keto acid chain elongation reactions involved in the biosynthesis of coenzyme B (7-mercaptoheptanoyl threonine phosphate) in methanogenic Archaea.},
journal = {Biochemistry},
volume = {37},
number = {28},
pages = {10108-10117},
doi = {10.1021/bi980662p},
pmid = {9665716},
issn = {0006-2960},
mesh = {Acetyl Coenzyme A/metabolism ; Adipates/metabolism ; Cloning, Molecular ; Coenzymes/*biosynthesis/genetics ; Dicarboxylic Acids/metabolism ; Isocitrate Dehydrogenase/metabolism ; Keto Acids/*metabolism ; Ketoglutaric Acids/metabolism ; Methanosarcina/*enzymology/*metabolism ; Phosphothreonine/*analogs &amp; derivatives/metabolism ; Pimelic Acids/metabolism ; Substrate Specificity ; Tricarboxylic Acids/metabolism ; },
abstract = {The biochemistry of the 13 steps involved in the conversion of alpha-ketoglutarate and acetylCoA to alpha-ketosuberate, a precursor to the coenzymes coenzyme B (7-mercapto heptanoylthreonine phosphate) and biotin, has been established in Methanosarcina thermophila. These series of reactions begin with the condensation of alpha-ketoglutarate and acetylCoA to form trans-homoaconitate. The trans-homoaconitate is then hydrated and dehydrated to cis-homoaconitate with (S)-homocitrate serving as an intermediate. Rehydration of the cis-homoaconitate produces (-)-threo-isohomocitrate [(2R,3S)-1-hydroxy-1,2, 4-butanetricarboxylic acid], which undergoes a NADP+-dependent oxidative decarboxylation to produce alpha-ketoadipate. The resulting alpha-ketoadipate then undergoes two consecutive sets of alpha-ketoacid chain elongation reactions to produce alpha-ketosuberate. In each of these sets of reactions, it has been shown that the homologues of cis-homoaconitate, homocitrate, and (-)-threo-isohomocitrate serve as intermediates. The protein product of the Methanococcus jannaschii MJ0503 gene aksA (AksA) was found to catalyze the condensation of alpha-ketoglutarate and acetylCoA to form trans-homoaconitate. This gene product also catalyzed the condensation of alpha-ketoadipate or alpha-ketopimelate with acetylCoA to form, respectively, the (R)-homocitrate homologues of (R)-2-hydroxy-1,2,5-pentanetricarboxylic acid and (R)-2-hydroxy-1,2, 6-hexanetricarboxylic acid. The alpha-ketosuberate resulting from this series of reactions then undergoes a nonoxidative decarboxylation to form 7-oxoheptanoic acid, a precursor to coenzyme B, and an oxidative decarboxylation to form pimelate, the precursor to biotin. Of the 13 intermediates in this pathway, eight have not previously been reported as occurring in biological systems.},
}
@article {pmid9660187,
year = {1998},
author = {Wasserfallen, A and Ragettli, S and Jouanneau, Y and Leisinger, T},
title = {A family of flavoproteins in the domains Archaea and Bacteria.},
journal = {European journal of biochemistry},
volume = {254},
number = {2},
pages = {325-332},
doi = {10.1046/j.1432-1327.1998.2540325.x},
pmid = {9660187},
issn = {0014-2956},
mesh = {Amino Acid Sequence ; Archaeal Proteins/chemistry/classification/*genetics ; Bacterial Proteins/chemistry/classification/*genetics ; Base Sequence ; Cloning, Molecular ; Cyanobacteria/genetics ; DNA Primers/genetics ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; Desulfovibrio/genetics ; Escherichia coli/genetics ; Flavoproteins/chemistry/classification/*genetics ; Mixed Function Oxygenases/chemistry/genetics ; Molecular Sequence Data ; Recombinant Proteins/chemistry/genetics ; Rhodobacter capsulatus/genetics ; Rubredoxins/chemistry/genetics ; Sequence Homology, Amino Acid ; },
abstract = {A family of flavoproteins, called A-type flavoproteins, is described. It consists of 14 protein sequences of 385-597 amino acids in length, 7 from methanogens (domain: Archaea), 5 from phototrophic prokaryotes, one from Escherichia coli, and a partial sequence from the sulfate reducer Desulfovibrio gigas (domain: Bacteria). No similar sequence could be found in the domain Eucarya. All sequences show significant similarity over a 385-400 amino acid portion overlapping a recognizable flavodoxin signature starting at positions 245-285 of the common core sequence. Cofactor analysis and, to some extent, analysis of the primary structure of six A-type flavoproteins, three of which are structurally characterized here, support the existence of four sub-families: (a) simple flavoproteins binding only FMN; (b) diflavin flavoproteins binding FMN and FAD; (c) a flavorubredoxin binding FMN and iron; (d) a hemoflavoprotein. The possible involvement of A-type flavoproteins in the metabolism of oxygen, as suggested for D. gigas hemoflavoprotein [Gomes, C. M., Silva, G., Oliveira, S., LeGall, J., Liu, M.-Y., Xavier, A. V., Rodrigues-Pousada, C. &amp; Teixeira, M. (1997) J. Biol. Chem. 272, 22502-22508], is discussed.},
}
@article {pmid9651254,
year = {1998},
author = {Chistoserdova, L and Vorholt, JA and Thauer, RK and Lidstrom, ME},
title = {C1 transfer enzymes and coenzymes linking methylotrophic bacteria and methanogenic Archaea.},
journal = {Science (New York, N.Y.)},
volume = {281},
number = {5373},
pages = {99-102},
doi = {10.1126/science.281.5373.99},
pmid = {9651254},
issn = {0036-8075},
support = {GM36296/GM/NIGMS NIH HHS/United States ; },
mesh = {Amino Acid Sequence ; Aminohydrolases/chemistry/genetics/isolation &amp; purification/*metabolism ; Biological Evolution ; Escherichia coli/enzymology/genetics ; Euryarchaeota/*enzymology/genetics ; Genes, Archaeal ; Genes, Bacterial ; Gram-Negative Aerobic Rods and Cocci/*enzymology/genetics ; Hydroxymethyl and Formyl Transferases/chemistry/genetics/isolation &amp; purification/*metabolism ; Methanol/metabolism ; Molecular Sequence Data ; Mutation ; NAD/metabolism ; NADP/metabolism ; Oxidation-Reduction ; Pterins/chemistry/isolation &amp; purification/*metabolism ; Sequence Alignment ; Succinic Acid/metabolism ; Transformation, Bacterial ; },
abstract = {Methanogenic and sulfate-reducing Archaea are considered to have an energy metabolism involving C1 transfer coenzymes and enzymes unique for this group of strictly anaerobic microorganisms. An aerobic methylotrophic bacterium, Methylobacterium extorquens AM1, was found to contain a cluster of genes that are predicted to encode some of these enzymes and was shown to contain two of the enzyme activities and one of the methanogenic coenzymes. Insertion mutants were all unable to grow on C1 compounds, suggesting that the archaeal enzymes function in aerobic C1 metabolism. Thus, methylotrophy and methanogenesis involve common genes that cross the bacterial/archaeal boundaries.},
}
@article {pmid9642185,
year = {1998},
author = {Sismeiro, O and Trotot, P and Biville, F and Vivares, C and Danchin, A},
title = {Aeromonas hydrophila adenylyl cyclase 2: a new class of adenylyl cyclases with thermophilic properties and sequence similarities to proteins from hyperthermophilic archaebacteria.},
journal = {Journal of bacteriology},
volume = {180},
number = {13},
pages = {3339-3344},
pmid = {9642185},
issn = {0021-9193},
mesh = {Adenylyl Cyclases/chemistry/*genetics/*metabolism ; Aeromonas hydrophila/*enzymology/genetics ; Amino Acid Sequence ; Base Sequence ; *Chromosome Mapping ; Chromosomes, Bacterial ; Cloning, Molecular ; Consensus Sequence ; Enzyme Stability ; Escherichia coli/genetics ; Genetic Complementation Test ; Hot Temperature ; Kinetics ; Molecular Sequence Data ; Plasmids ; Sequence Alignment ; Sequence Homology, Amino Acid ; Thermodynamics ; },
abstract = {Complementation of an Escherichia coli cya mutant with a genomic library from Aeromonas hydrophila allowed isolation of clones containing two different cya genes. Whereas one of these genes (cyaA) coded for an adenylyl cyclase (AC1) belonging to the previously described class I adenylyl cyclases (ACs), the second one (cyaB) coded for a protein (AC2) that did not match any previously characterized protein when compared to protein sequence databases. In particular, it did not align with any of members of the three known classes of ACs. The purified AC2 enzyme exhibited remarkable biochemical characteristics, namely, an optimum activity at a high temperature (65 degrees C) and at an alkalinic pH (9.5). In order to investigate the functions of both cyclases in A. hydrophila, each gene was inactivated in the chromosome and the resulting mutant strains were examined for physiological alterations. It was shown that, in contrast to cyaA, the cyaB gene was not expressed under usual laboratory growth conditions. However, introduction of a plasmid harboring the cyaB gene in a cyaA mutant, as well as in a cyaA cyaB mutant, allowed cyclic AMP production. AC2 is the first member of a new class of previously unrecognized ACs, and to date, no functional counterpart has been demonstrated in other organisms. However, scanning databases revealed a significant similarity between AC2 and the gene product of three hyperthermophilic archaebacteria: Methanobacterium thermoautotrophicum, Archaeglobus fulgidus, and Methanococcus jannaschii. The possibility of a gene transfer between such phylogenetically divergent bacteria is discussed.},
}
@article {pmid9631551,
year = {1998},
author = {Gilboa-Garber, N and Mymon, H and Oren, A},
title = {Typing of halophilic Archaea and characterization of their cell surface carbohydrates by use of lectins.},
journal = {FEMS microbiology letters},
volume = {163},
number = {1},
pages = {91-97},
doi = {10.1111/j.1574-6968.1998.tb13031.x},
pmid = {9631551},
issn = {0378-1097},
mesh = {*Bacterial Typing Techniques ; Carbohydrate Sequence ; Carbohydrates/*analysis ; Halobacteriaceae/chemistry/*classification ; Hemagglutination Inhibition Tests ; *Lectins ; Molecular Sequence Data ; Sodium Chloride/pharmacology ; },
abstract = {Lectins are important tools for cell typing and for the study of cell surface components. They have been widely used for the analysis of carbohydrates on the surface of many eukaryotic and prokaryotic cells, but they have not yet been exploited in the study of the halophilic Archaea (family Halobacteriaceae), because of the high salinity required for the structural integrity of these microorganisms. We have defined the salt concentration threshold high enough for survival of the Archaea, but sufficiently low for lectins to bind to them. Under these conditions we studied the interactions of a series of lectins, exhibiting different sugar specificities, with diverse halophilic Archaea. Concanavalin A was the most reactive by virtue of its glucose (and mannose) binding. The other lectins varied in their interactions. The results indicate that lectins might be useful probes for both archaeal typing and analysis of their cell surface carbohydrates.},
}
@article {pmid9622563,
year = {1998},
author = {Chandler, DP and Brockman, FJ and Bailey, TJ and Fredrickson, JK},
title = {Phylogenetic Diversity of Archaea and Bacteria in a Deep Subsurface Paleosol.},
journal = {Microbial ecology},
volume = {36},
number = {1},
pages = {37-50},
doi = {10.1007/s002489900091},
pmid = {9622563},
issn = {1432-184X},
}
@article {pmid9614965,
year = {1998},
author = {Kandler, O and König, H},
title = {Cell wall polymers in Archaea (Archaebacteria).},
journal = {Cellular and molecular life sciences : CMLS},
volume = {54},
number = {4},
pages = {305-308},
doi = {10.1007/s000180050156},
pmid = {9614965},
issn = {1420-682X},
mesh = {Archaea/*chemistry/cytology ; Biopolymers/*chemistry ; Carbohydrate Sequence ; Cell Wall/*chemistry ; Molecular Sequence Data ; },
abstract = {The distribution of the various cell wall and cell envelope (S-layer) polymers among the main lineages of the domain Archaea (Archaebacteria) and the chemical composition and primary structure of polymers forming rigid cell wall sacculi is described. Differences between bacteria and archaea in their sensitivity to antibiotics which inhibit cell wall synthesis in bacteria are discussed.},
}
@article {pmid9612080,
year = {1998},
author = {Shen, B and Qiu, J and Hosfield, D and Tainer, JA},
title = {Flap endonuclease homologs in archaebacteria exist as independent proteins.},
journal = {Trends in biochemical sciences},
volume = {23},
number = {5},
pages = {171-173},
doi = {10.1016/s0968-0004(98)01199-2},
pmid = {9612080},
issn = {0968-0004},
mesh = {Amino Acid Sequence ; Archaeal Proteins/*genetics ; *DNA Repair ; Endodeoxyribonucleases/*genetics ; Flap Endonucleases ; Molecular Sequence Data ; Sequence Homology, Amino Acid ; },
}
@article {pmid9542073,
year = {1998},
author = {Huber, R and Dyba, D and Huber, H and Burggraf, S and Rachel, R},
title = {Sulfur-inhibited Thermosphaera aggregans sp. nov., a new genus of hyperthermophilic archaea isolated after its prediction from environmentally derived 16S rRNA sequences.},
journal = {International journal of systematic bacteriology},
volume = {48 Pt 1},
number = {},
pages = {31-38},
doi = {10.1099/00207713-48-1-31},
pmid = {9542073},
issn = {0020-7713},
mesh = {Bacteriological Techniques ; Cell Membrane/chemistry/ultrastructure ; DNA, Archaeal/analysis ; Desulfurococcaceae/*classification/genetics/metabolism ; Freeze Fracturing ; Lipids/analysis ; Molecular Sequence Data ; Nucleic Acid Hybridization ; Phylogeny ; RNA, Archaeal/analysis ; RNA, Ribosomal, 16S/*analysis ; Sulfur/*metabolism ; Temperature ; },
abstract = {Recently, a new procedure was developed which allowed for the first time the isolation of a hyperthermophilic archaeum tracked by 165 rRNA analysis from a terrestrial hot solfataric spring ('Obsidian Pool', Yellowstone National Park, WY, USA). This novel isolate is characterized here. Cells are round cocci with a diameter of 0.2-0.8 micron, occurring singly, in pairs, short chains and in grape-like aggregates. The aggregates exhibit a weak bluish-green fluorescence under UV radiation at 420 nm. The new isolate is an anaerobic obligate heterotroph, using preferentially yeast extract for growth. The metabolic products include CO2, H2, acetate and isovalerate. Growth is observed between 65 and 90 degrees C (optimum: 85 degrees C), from pH 5.0 to 7.0 (optimum: 6.5) and up to 0.7% NaCl. The apparent activation energy for growth is about 149 kJ mol-1. Elemental sulfur or hydrogen inhibits growth. The core lipids consist mainly of acyclic and cyclic glycerol diphytanyl tetraethers. The cell envelope contains a cytoplasmic membrane covered by an amorphous layer of unknown composition; there is no evidence for a regularly arrayed surface-layer protein. The G + C content is 46 mol%. On the basis of 165 rRNA sequence comparisons in combination with morphological, physiological and biochemical properties, the isolate represents a new genus within the Desulfurococcaceae, which has been named Thermosphaera. The type species is Thermosphaera aggregans, the type strain is isolate M11TLT (= DSM 11486T).},
}
@article {pmid9542072,
year = {1998},
author = {Miroshnichenko, ML and Gongadze, GM and Rainey, FA and Kostyukova, AS and Lysenko, AM and Chernyh, NA and Bonch-Osmolovskaya, EA},
title = {Thermococcus gorgonarius sp. nov. and Thermococcus pacificus sp. nov.: heterotrophic extremely thermophilic archaea from New Zealand submarine hot vents.},
journal = {International journal of systematic bacteriology},
volume = {48 Pt 1},
number = {},
pages = {23-29},
doi = {10.1099/00207713-48-1-23},
pmid = {9542072},
issn = {0020-7713},
mesh = {Cell Membrane/chemistry ; DNA, Archaeal/analysis ; Hot Temperature ; Microscopy, Electron ; Molecular Sequence Data ; New Zealand ; RNA, Archaeal/analysis ; RNA, Ribosomal, 16S/analysis ; Seawater/*microbiology ; Thermococcus/*classification/genetics/ultrastructure ; },
abstract = {Two extremely thermophilic archaea, designated W-12 and P-4, were isolated from a geothermal vent in the tidal zone of Whale Island, New Zealand, and from geothermally heated bottom deposits of the Bay of Plenty, New Zealand, respectively. Cells of isolate W-12 are irregular cocci, 0.3-1.2 microns in diameter, motile with polar flagella. The cell envelope consists of one layer of subunits with a major protein of M(r) 75,000. Cells produce protrusions of different kinds: prostheca-like, chains of bubbles, or network of fimbriae. Cells of isolate P-4 are regular cocci, 0.7-1.0 micron in diameter, motile with polar flagella. The cell envelope consists of two layers of subunits; its major protein has an M(r) of 56,000. Both organisms are obligate anaerobes, fermenting peptides in the case of strain W-12, or peptides and starch in the case of P-4. Elemental sulfur is required for growth and is reduced to hydrogen sulfide. The optimal growth temperature of the new isolates is in the range 80-88 degrees C. The optimal growth pH is 6.5-7.2. The G + C content of the DNA of strain W-12 is 50.6 mol%, and of strain P-4 is 53.3 mol%. Based on physiological characteristics, 165 rDNA sequence comparison and DNA base composition, the new isolates were considered to be members of the genus Thermococcus. The low level of DNA-DNA hybridization with the type strains of other Thermococcus species confirms the novel species status of the new isolates. The new isolates are described as Thermococcus gorgonarius sp. nov., with type strain W-12 (= DSM 10395T), and Thermococcus pacificus sp. nov., with type strain P-4 (= DSM 10394T).},
}
@article {pmid9560807,
year = {1998},
author = {Lattuati, A and Guezennec, J and Metzger, P and Largeau, C},
title = {Lipids of Thermococcus hydrothermalis, an archaea isolated from a deep-sea hydrothermal vent.},
journal = {Lipids},
volume = {33},
number = {3},
pages = {319-326},
pmid = {9560807},
issn = {0024-4201},
mesh = {Archaea/chemistry ; Chromatography, Gas ; Glyceryl Ethers/chemistry ; Mass Spectrometry ; Membrane Lipids/*chemistry ; Molecular Structure ; Pacific Ocean ; Phytanic Acid/analogs &amp; derivatives ; Terpenes/chemistry ; Thermococcus/*chemistry ; },
abstract = {The membrane lipids of a deep-sea hydrothermal vent archaea, Thermococcus hydrothermalis, were isolated, purified, and structurally characterized. On the basis of acid methanolysis and spectroscopic studies, the polar lipids, amounting to 4.5% (w/w) of the dry cells, comprised diphytanyl glycerol diethers and dibiphytanyldiglycerol tetraethers, in a 45:55 ratio. No cyclopentane ring was present in the tetraethers. From the neutral lipids, accounting for 0.4% (w/w) of the dry cells, besides low amounts of di- and tetraethers occurring in a free form, four acyclic tetraterpenoid hydrocarbons, di- and tri-unsaturated were identified. All were structurally related to lycopane. The presence of these hydrocarbons provides some evidence that lycopane, widely distributed in oceans, could be derived, at least partially, from the hydrocarbons synthesized by some thermophilic Archaea. Finally, analysis of the uninoculated culture medium indicates that fatty acid derivatives and some steroid and triterpenoid compounds identified in the lipidic extract of the archaea originated from the culture medium.},
}
@article {pmid9555910,
year = {1998},
author = {Ishino, Y and Komori, K and Cann, IK and Koga, Y},
title = {A novel DNA polymerase family found in Archaea.},
journal = {Journal of bacteriology},
volume = {180},
number = {8},
pages = {2232-2236},
pmid = {9555910},
issn = {0021-9193},
mesh = {Amino Acid Sequence ; Archaea/*enzymology/genetics ; DNA Polymerase II/chemistry/genetics/*metabolism ; Escherichia coli/enzymology ; Kinetics ; Methanococcus/*enzymology/genetics ; Molecular Sequence Data ; Open Reading Frames ; Pyrococcus/*enzymology/genetics ; Sequence Alignment ; Sequence Homology, Amino Acid ; Substrate Specificity ; },
abstract = {One of the most puzzling results from the complete genome sequence of the methanogenic archaeon Methanococcus jannaschii was that the organism may have only one DNA polymerase gene. This is because no other DNA polymerase-like open reading frames (ORFs) were found besides one ORF having the typical alpha-like DNA polymerase (family B). Recently, we identified the genes of DNA polymerase II (the second DNA polymerase) from the hyperthermophilic archaeon Pyrococcus furiosus, which has also at least one alpha-like DNA polymerase (T. Uemori, Y. Sato, I. Kato, H. Doi, and Y. Ishino, Genes Cells 2:499-512, 1997). The genes in M. jannaschii encoding the proteins that are homologous to the DNA polymerase II of P. furiosus have been located and cloned. The gene products of M. jannaschii expressed in Escherichia coli had both DNA polymerizing and 3'-->5' exonuclease activities. We propose here a novel DNA polymerase family which is entirely different from other hitherto-described DNA polymerases.},
}
@article {pmid9546662,
year = {1998},
author = {Künkel, A and Vorholt, JA and Thauer, RK and Hedderich, R},
title = {An Escherichia coli hydrogenase-3-type hydrogenase in methanogenic archaea.},
journal = {European journal of biochemistry},
volume = {252},
number = {3},
pages = {467-476},
doi = {10.1046/j.1432-1327.1998.2520467.x},
pmid = {9546662},
issn = {0014-2956},
mesh = {Amino Acid Sequence ; Cell Membrane/enzymology ; Conserved Sequence ; Escherichia coli/*enzymology/genetics ; Hydrogenase/*chemistry/genetics/isolation &amp; purification ; Macromolecular Substances ; Methanobacterium/*enzymology/genetics ; Methanosarcina barkeri/*enzymology/genetics ; Molecular Sequence Data ; Operon ; Peptide Fragments/chemistry ; Polymerase Chain Reaction ; Protein Structure, Secondary ; Sequence Alignment ; Sequence Homology, Amino Acid ; Species Specificity ; },
abstract = {Methanogenic archaea are known to contain two types of [NiFe] hydrogenases designated F420-reducing hydrogenase and F420-non-reducing hydrogenase. We report here that they additionally contain Escherichia coli hydrogenase-3-type [NiFe] hydrogenases. The evidence is based on biochemical studies and analysis of the subunit primary structure of this hydrogenase (designated Ech) purified from membranes of acetate-grown cells of Methanosarcina barkeri. The subunits EchE and EchC of the EchABCDEF complex showed 34% and 45% sequence identity to the nickel-containing large subunit HycE and to the iron-sulfur cluster containing small subunit HycG, respectively, of the hydrogenase in the formate hydrogen lyase complex from E. coli. Analysis of the totally sequenced genomes of Methanococcus jannaschii and Methanobacterium thermoautotrophicum strain deltaH revealed that these organisms contain similar open reading frames, indicating the presence of an E. coli hydrogenase-3-type hydrogenase also in these methanogenic archaea.},
}
@article {pmid9546660,
year = {1998},
author = {Talfournier, F and Colloc'h, N and Mornon, JP and Branlant, G},
title = {Comparative study of the catalytic domain of phosphorylating glyceraldehyde-3-phosphate dehydrogenases from bacteria and archaea via essential cysteine probes and site-directed mutagenesis.},
journal = {European journal of biochemistry},
volume = {252},
number = {3},
pages = {447-457},
doi = {10.1046/j.1432-1327.1998.2520447.x},
pmid = {9546660},
issn = {0014-2956},
mesh = {Amino Acid Sequence ; Amino Acid Substitution ; Apoenzymes/chemistry/metabolism ; Archaea/*enzymology ; Binding Sites ; *Cysteine ; Escherichia coli/*enzymology ; Geobacillus stearothermophilus/*enzymology ; Glyceraldehyde-3-Phosphate Dehydrogenases/*chemistry/isolation &amp; purification/*metabolism ; Kinetics ; Molecular Sequence Data ; Mutagenesis, Site-Directed ; Recombinant Proteins/chemistry/isolation &amp; purification/metabolism ; Sequence Alignment ; Sequence Homology, Amino Acid ; Substrate Specificity ; },
abstract = {Phosphorylating glyceraldehyde-3-phosphate dehydrogenase (GraP-DH) catalyzes the oxidative phosphorylation of D-glyceraldehyde-3-phosphate to form 1.3-diphosphoglycerate. The currently accepted mechanism involves an oxidoreduction step followed by a phosphorylation. Two essential aminoacids, Cys149 and His176 are involved in the chemical mechanism of bacterial and eukaryotic GraP-DHs. Roles have been assigned to the His176 as (a) a chemical activator for enhancing the reactivity of Cys149, (b) a stabilizator of the tetrahedral transition states, and (c) a base catalyst facilitating hydride transfer towards NAD. In a previous study carried out on Escherichia coli GraP-DH [Soukri, A., Mougin, A., Corbier, C., Wonacott, A. J., Branlant, C. &amp; Branlant, G. (1989) Biochemistry, 28, 2586-2592], the role of His176 as an activator of the reactivity of Cys149 was studied. Here, we further investigated the role of the His residue in the chemical mechanism of phosphorylating GraP-DH from E. coli and Bacillus stearothermophilus. The chemical reactivity of Cys149 in the His176Asn mutant was reinvestigated. At neutral pH, its reactivity was shown to be at least as high as that observed in the Cys-/His+ ion pair present in the wild type. No pre-steady state burst of NADH was found with the His176Asn mutant in contrast to what is observed for the wild type, and a primary isotope effect was observed when D-[1-2H]glyceraldehyde-3-phosphate was used as the substrate. Therefore, the major role of the His176 in the catalytic mechanism under physiological conditions is not to activate the nucleophilicity of Cys149 but first to facilitate the hydride transfer. These results hypothesized that a phosphorylating GraP-DH possessing a different protein environment competent to increase the nucleophilic character of the essential Cys residue and to favor the hydride transfer in place of His, could be enzymically efficient. This is most likely the case for archaeal Methanothermus fervidus GraP-DH which shares less than 15% amino-acid identity with the bacterial or eukaryotic counterparts. No Cys-/His+ ion pair was detectable. Only one thiolate entity was observed with an apparent pKa of 6.2. This result was confirmed by the fact that none of the mutations of the five invariant His changed the catalytic efficiency.},
}
@article {pmid9512414,
year = {1998},
author = {Doolittle, WF and Logsdon, JM},
title = {Archaeal genomics: do archaea have a mixed heritage?.},
journal = {Current biology : CB},
volume = {8},
number = {6},
pages = {R209-11},
doi = {10.1016/s0960-9822(98)70127-7},
pmid = {9512414},
issn = {0960-9822},
mesh = {Archaea/chemistry/*genetics ; *Genes, Archaeal ; },
abstract = {A third complete archaeal genome sequence, replete with eukaryote-like genes for replication, transcription and translation, has appeared. The sequence also shows bacteria-like features. It is time to come to grips with this evidence for a mixed heritage.},
}
@article {pmid9503984,
year = {1998},
author = {Kirino-Kagawa, H and Yaoi, T and Trent, JD},
title = {[Is chaperonin from archaea, Sulfolobus shibatae, cytoskeleton?].},
journal = {Seikagaku. The Journal of Japanese Biochemical Society},
volume = {70},
number = {1},
pages = {31-36},
pmid = {9503984},
issn = {0037-1017},
mesh = {Chaperonin 60/*metabolism ; Cytoskeleton/*metabolism ; Sulfolobus/*cytology ; },
}
@article {pmid9480823,
year = {1998},
author = {Gomes, CM and Teixeira, M},
title = {The NADH oxidase from the thermoacidophilic archaea Acidianus ambivalens: isolation and physicochemical characterisation.},
journal = {Biochemical and biophysical research communications},
volume = {243},
number = {2},
pages = {412-415},
doi = {10.1006/bbrc.1998.8111},
pmid = {9480823},
issn = {0006-291X},
mesh = {Flavoproteins/chemistry ; Hydrogen Peroxide/metabolism ; Hydrogen-Ion Concentration ; Molecular Weight ; Multienzyme Complexes/*chemistry ; NADH, NADPH Oxidoreductases/*chemistry ; Oxidoreductases/metabolism ; Oxygen/metabolism ; Sulfolobaceae/*enzymology ; Temperature ; },
abstract = {A flavoprotein with NADH oxidising activity (NADH: acceptor oxidoreductase) was isolated from the soluble fraction of the thermoacidophilic archaea Acidianus ambivalens. The protein is a monomer with a molecular mass of 70 kDa and contains FAD as single cofactor. Its activity as NADH:O2 oxidoreductase is FAD, but not FMN, dependent and yields hydrogen peroxide as the reaction product. The activity decreases with pH in the range 4.5 to 9.8, and increases with the temperature, as tested from 30 degrees to 60 degrees C. As elicited by EPR, the purified enzyme also acts as an NADH:ferredoxin oxidoreductase. These features are discussed in light of the possible involvement of this protein in the metabolism of this archaea.},
}
@article {pmid9468785,
year = {1997},
author = {Forterre, P},
title = {Archaea: what can we learn from their sequences?.},
journal = {Current opinion in genetics &amp; development},
volume = {7},
number = {6},
pages = {764-770},
doi = {10.1016/s0959-437x(97)80038-x},
pmid = {9468785},
issn = {0959-437X},
mesh = {Archaea/classification/*genetics ; Base Sequence ; DNA, Archaeal ; Evolution, Molecular ; },
abstract = {Gene-by-gene and traditional biochemical approaches continue to reveal surprising molecular features in the archaeal domain. In addition, the complete sequencing of several archaeal genomes has further confirmed the phenotypic coherence of these micro-organisms at the molecular level. Nevertheless, the phylogeny of Archaea and the nature of the last universal common ancestor are still matters for debate.},
}
@article {pmid9468335,
year = {1998},
author = {Nagata, Y and Fujiwara, T and Kawaguchi-Nagata, K and Fukumori, Y and Yamanaka, T},
title = {Occurrence of peptidyl D-amino acids in soluble fractions of several eubacteria, archaea and eukaryotes.},
journal = {Biochimica et biophysica acta},
volume = {1379},
number = {1},
pages = {76-82},
doi = {10.1016/s0304-4165(97)00084-6},
pmid = {9468335},
issn = {0006-3002},
mesh = {Amino Acids/analysis/*chemistry ; Archaea/*chemistry ; Bacteria/*chemistry ; Chromatography, High Pressure Liquid ; Eukaryotic Cells/*chemistry ; Gram-Negative Bacteria/chemistry ; Gram-Positive Bacteria/chemistry ; Peptides/analysis/*chemistry ; *Stereoisomerism ; },
abstract = {The occurrence of peptidyl D-amino acids in the aqueous soluble fractions was investigated in various eubacteria, some archaea and some eukaryotes. The contents of the D-enantiomers of serine, alanine, proline, glutamate (glutamine), aspartate (asparagine) and phenylalanine were determined with cell- and tissue-extracts, by means of acid hydrolysis and high-performance liquid chromatography. The rate of D-enantiomer (%, the ratio in molar concentration of a D-amino acid to the total of the D-amino acid and the corresponding L-amino acid) of alanine and glutamate were high in some Gram-positive eubacteria: 11.7% in Staphylococcus epidermidis and 10.3% in Streptococcus pyogenes for alanine, and 22.3% for glutamate in Bacillus YN-1. The D-glutamate content was also high (8.0%) in the Gram-negative eubacterium, Thiobacillus ferrooxidans. D-Aspartate was common, as was D-glutamate: the highest D-aspartate content was detected in an archaeum, Pyrobaculum islandicum (4.0%). However, the content of D-aspartate was low, 0.2-1.8% in most other bacteria. The presence of D-serine was shown in some organisms, but that of D-proline was scarce. The D-enantiomer of phenylalanine was not detected in any of the organisms examined. These results indicate that of the bacteria examined herein most Gram-negative and some Gram-positive eubacteria, as well as archaea contain only low levels of D-amino acids in the soluble peptidyl fraction, and the levels were comparable to those in eukaryotes examined. To our knowledge, the general presence of peptidyl D-amino acids in these organisms, especially archaea and eukaryotic cells including those from rat liver tissues, has been shown here for the first time.},
}
@article {pmid9457844,
year = {1998},
author = {Stuer-Lauridsen, B and Nygaard, P},
title = {Purine salvage in two halophilic archaea: characterization of salvage pathways and isolation of mutants resistant to purine analogs.},
journal = {Journal of bacteriology},
volume = {180},
number = {3},
pages = {457-463},
pmid = {9457844},
issn = {0021-9193},
mesh = {Carbon Radioisotopes ; Drug Resistance, Microbial ; Halobacterium salinarum/drug effects/enzymology/growth &amp; development/*metabolism ; Haloferax volcanii/drug effects/enzymology/growth &amp; development/*metabolism ; Mutation ; Nucleotides/metabolism ; Pentosyltransferases/genetics/metabolism ; Purine Nucleosides/metabolism ; Purines/biosynthesis/*metabolism/*pharmacology ; },
abstract = {In exponentially growing cultures of the extreme halophile Halobacterium halobium and the moderate halophile Haloferax volcanii, growth characteristics including intracellular protein levels, RNA content, and nucleotide pool sizes were analyzed. This is the first report on pool sizes of nucleoside triphosphates, NAD, and PRPP (5-phosphoribosyl-alpha-1-pyrophosphate) in archaea. The presence of a number of salvage and interconversion enzymes was determined by enzymatic assays. The levels varied significantly between the two organisms. The most significant difference was the absence of GMP reductase activity in H. halobium. The metabolism of exogenous purines was investigated in growing cultures. Both purine bases and nucleosides were readily taken up and were incorporated into nucleic acids. Growth of both organisms was affected by a number of inhibitors of nucleotide synthesis. H. volcanii was more sensitive than H. halobium, and purine base analogs were more toxic than nucleoside analogs. Growth of H. volcanii was inhibited by trimethoprim and sulfathiazole, while these compounds had no effect on the growth of H. halobium. Spontaneous mutants resistant to purine analogs were isolated. The most frequent cause of resistance was a defect in purine phosphoribosyltransferase activity coupled with reduced purine uptake. A single phosphoribosyltransferase seemed to convert guanine as well as hypoxanthine to nucleoside monophosphates, and another phosphoribosyltransferase had specificity towards adenine. The differences in the metabolism of purine bases and nucleosides and the sensitivity to purine analogs between the two halobacteria were reflected in differences in purine enzyme levels. Based on our results, we conclude that purine salvage and interconversion pathways differ just as much between the two archaeal species as among archaea, bacteria, and eukarya.},
}
@article {pmid9454075,
year = {1997},
author = {Nevskaia, NA and Fomenkova, NP and Nikonov, SV},
title = {[Common and distinctive traits of the spatial structure of ribosomal proteins L1 from bacteria and archaea].},
journal = {Molekuliarnaia biologiia},
volume = {31},
number = {5},
pages = {888-893},
pmid = {9454075},
issn = {0026-8984},
mesh = {Amino Acid Sequence ; Archaeal Proteins/*chemistry ; Bacterial Proteins/*chemistry ; Conserved Sequence ; Molecular Sequence Data ; Protein Conformation ; Ribosomal Proteins/*chemistry ; Sequence Homology, Amino Acid ; },
}
@article {pmid9409149,
year = {1997},
author = {Brown, JR and Doolittle, WF},
title = {Archaea and the prokaryote-to-eukaryote transition.},
journal = {Microbiology and molecular biology reviews : MMBR},
volume = {61},
number = {4},
pages = {456-502},
pmid = {9409149},
issn = {1092-2172},
mesh = {Archaea/enzymology/*genetics ; Bacteria/genetics ; *Biological Evolution ; Eukaryotic Cells ; *Phylogeny ; },
abstract = {Since the late 1970s, determining the phylogenetic relationships among the contemporary domains of life, the Archaea (archaebacteria), Bacteria (eubacteria), and Eucarya (eukaryotes), has been central to the study of early cellular evolution. The two salient issues surrounding the universal tree of life are whether all three domains are monophyletic (i.e., all equivalent in taxanomic rank) and where the root of the universal tree lies. Evaluation of the status of the Archaea has become key to answering these questions. This review considers our cumulative knowledge about the Archaea in relationship to the Bacteria and Eucarya. Particular attention is paid to the recent use of molecular phylogenetic approaches to reconstructing the tree of life. In this regard, the phylogenetic analyses of more than 60 proteins are reviewed and presented in the context of their participation in major biochemical pathways. Although many gene trees are incongruent, the majority do suggest a sisterhood between Archaea and Eucarya. Altering this general pattern of gene evolution are two kinds of potential interdomain gene transferrals. One horizontal gene exchange might have involved the gram-positive Bacteria and the Archaea, while the other might have occurred between proteobacteria and eukaryotes and might have been mediated by endosymbiosis.},
}
@article {pmid9406392,
year = {1997},
author = {Munson, MA and Nedwell, DB and Embley, TM},
title = {Phylogenetic diversity of Archaea in sediment samples from a coastal salt marsh.},
journal = {Applied and environmental microbiology},
volume = {63},
number = {12},
pages = {4729-4733},
pmid = {9406392},
issn = {0099-2240},
mesh = {Archaea/classification/*genetics/isolation &amp; purification ; Base Sequence ; Cloning, Molecular ; DNA Primers/genetics ; DNA, Ribosomal/genetics ; Gene Library ; Phylogeny ; Polymerase Chain Reaction ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; *Water Microbiology ; },
abstract = {The Archaea present in salt marsh sediment samples from a tidal creek and from an adjacent area of vegetative marshland, both of which showed active methanogenesis and sulfate reduction, were sampled by using 16S rRNA gene libraries created with Archaea-specific primers. None of the sequences were the same as reference sequences from cultured taxa, although some were closely related to sequences from methanogens previously isolated from marine sediments. A wide range of Euryarchaeota sequences were recovered, but no sequences from Methanococcus, Methanobacterium, or the Crenarchaeota were recovered. Clusters of closely related sequences were common and generally contained sequences from both sites, suggesting that some related organisms were present in both samples. Recovery of sequences closely related to those of methanogens such as Methanococcoides and Methanolobus, which can use substrates other than hydrogen, provides support for published hypotheses that such methanogens are probably important in sulfate-rich sediments and identifies some likely candidates. Sequences closely related to those of methanogens such as Methanoculleus and Methanogenium, which are capable of using hydrogen, were also discovered, in agreement with previous inhibitor and process measurements suggesting that these taxa are present at low levels of activity. More surprisingly, we recovered a variety of sequences closely related to those from different halophilic Archaea and a cluster of divergent sequences specifically related to the marine group II archaeal sequences recently shown by PCR and probing to have a cosmopolitan distribution in marine samples.},
}
@article {pmid9401030,
year = {1997},
author = {Raffaelli, N and Pisani, FM and Lorenzi, T and Emanuelli, M and Amici, A and Ruggieri, S and Magni, G},
title = {Characterization of nicotinamide mononucleotide adenylyltransferase from thermophilic archaea.},
journal = {Journal of bacteriology},
volume = {179},
number = {24},
pages = {7718-7723},
pmid = {9401030},
issn = {0021-9193},
mesh = {Amino Acid Sequence ; Amino Acids/analysis ; Archaeal Proteins/genetics/*isolation &amp; purification ; Cloning, Molecular ; Enzyme Stability ; Escherichia coli/genetics ; Hot Temperature ; Methanococcus/*enzymology/genetics ; Molecular Sequence Data ; Nicotinamide-Nucleotide Adenylyltransferase/genetics/*isolation &amp; purification ; Recombinant Proteins/isolation &amp; purification ; Sequence Analysis ; Sequence Homology, Amino Acid ; Sulfolobus/*enzymology ; },
abstract = {The enzyme nicotinamide mononucleotide (NMN) adenylyltransferase (EC 2.7.7.1) catalyzes the synthesis of NAD+ and nicotinic acid adenine dinucleotide. It has been purified to homogeneity from cellular extracts of the thermophilic archaeon Sulfolobus solfataricus. Through a database search, a highly significant match was found between its N-terminal sequence and a hypothetical protein coded by the thermophilic archaeon Methanococcus jannaschii MJ0541 open reading frame (GenBank accession no. U67503). The MJ0541 gene was isolated, cloned into a T7-based vector, and expressed in Escherichia coli cells, yielding a high level of thermophilic NMN adenylyltransferase activity. The expressed protein was purified to homogeneity by a single-step chromatographic procedure. Both the subunit molecular mass and the N-terminal sequence of the pure recombinant protein were as expected from the deduced amino acid sequence of the MJ0541 open reading frame-encoded protein. Molecular and kinetic properties of the enzymes from both archaea are reported and compared with those already known for the mesophilic eukaryotic NMN adenylyltransferase.},
}
@article {pmid9401018,
year = {1997},
author = {Popławski, A and Bernander, R},
title = {Nucleoid structure and distribution in thermophilic Archaea.},
journal = {Journal of bacteriology},
volume = {179},
number = {24},
pages = {7625-7630},
pmid = {9401018},
issn = {0021-9193},
mesh = {Cell Cycle ; Chromosomes, Bacterial/*ultrastructure ; DNA, Bacterial/isolation &amp; purification ; Microscopy, Fluorescence ; Sulfolobus/*growth &amp; development/*ultrastructure ; Sulfolobus acidocaldarius/growth &amp; development/ultrastructure ; },
abstract = {Nucleoid structure and distribution in thermophilic organisms from the Archaea domain were studied. Combined phase-contrast and fluorescence microscopy of DAPI (4',6-diamidino-2-phenylindole)-stained Sulfolobus acidocaldarius and Sulfolobus solfataricus cells revealed that the nucleoids were highly structured. Different nucleoid distribution within the cells, representing different partition stages, was observed. The conformation of the nucleoids differed between exponentially growing and stationary-phase cells. Also, the stationary-phase cells contained two chromosomes, and the nucleoids occupied a larger part of the interior of the cells than in the exponentially growing cells. The part of the cell cycle during which fully separated nucleoids could be detected was short. Since the postreplication period is long in these organisms, there was a considerable time interval between termination of chromosome replication and completion of nucleoid separation, similar to the G2 phase in eukaryotic cells. The length of the visible cell constriction period was found to be in the same range as that of eubacteria. Finally, cell-cell connections were observed under certain conditions. Possible eubacterial, eukaryotic, and unique features of nucleoid processing and cell division in thermophilic archaea are discussed.},
}
@article {pmid9348086,
year = {1997},
author = {Nishihara, M and Koga, Y},
title = {Purification and properties of sn-glycerol-1-phosphate dehydrogenase from Methanobacterium thermoautotrophicum: characterization of the biosynthetic enzyme for the enantiomeric glycerophosphate backbone of ether polar lipids of Archaea.},
journal = {Journal of biochemistry},
volume = {122},
number = {3},
pages = {572-576},
doi = {10.1093/oxfordjournals.jbchem.a021791},
pmid = {9348086},
issn = {0021-924X},
mesh = {Amino Acid Sequence ; Archaea/*enzymology ; Bacterial Proteins/*isolation &amp; purification/*metabolism ; Glycerolphosphate Dehydrogenase/*isolation &amp; purification/*metabolism ; Glycerophosphates/biosynthesis ; Kinetics ; Methanobacterium/*enzymology/metabolism ; Molecular Sequence Data ; Phospholipid Ethers/*metabolism ; Stereoisomerism ; Substrate Specificity ; },
abstract = {The enzyme which seems to be responsible for the formation of the enantiomeric configuration of the glycerophosphate backbone (sn-glycerol-1-phosphate) of archaeal ether lipids was purified from a methanogenic archaeon, Methanobacterium thermoautotrophicum, and characterized. The enzyme, sn-glycerol-1-phosphate: NAD(P)+ oxidoreductase (sn-glycerol-1-phosphate dehydrogenase), was purified 7,600-fold from a cell free extract by ammonium sulfate fractionation and seven steps of chromatography. The final preparation exhibited a specific activity of 617 micromol/min/mg (Vmax) and gave a single band corresponding to 38 kDa on polyacrylamide gel electrophoresis in the presence of sodium dodecyl sulfate. The native enzyme showed an apparent molecular mass of 302 kDa on gel-filtration chromatography, indicating it is present as a homooctamer. Maximum activity was observed at 75 degrees C at near neutral pH. The activity was stimulated by potassium ions. The Km for dihydroxyacetone phosphate was 7.5 times smaller than that for sn-glycerol-1-phosphate, suggesting that the formation of sn-glycerol-1-phosphate is the natural direction in the cell. Under the assay conditions used, no product inhibition was observed. The N-terminal amino acid sequence was determined.},
}
@article {pmid9325428,
year = {1997},
author = {Berk, H and Thauer, RK},
title = {Function of coenzyme F420-dependent NADP reductase in methanogenic archaea containing an NADP-dependent alcohol dehydrogenase.},
journal = {Archives of microbiology},
volume = {168},
number = {5},
pages = {396-402},
doi = {10.1007/s002030050514},
pmid = {9325428},
issn = {0302-8933},
mesh = {Alcohol Oxidoreductases/*metabolism ; Amino Acid Sequence ; Euryarchaeota/*enzymology ; Hydrogen-Ion Concentration ; Kinetics ; Models, Chemical ; Molecular Sequence Data ; Molecular Weight ; NADH, NADPH Oxidoreductases/chemistry/isolation &amp; purification/*metabolism ; NADP/metabolism ; Oxidoreductases Acting on CH-NH Group Donors/metabolism ; Pterins/metabolism ; Riboflavin/*analogs &amp; derivatives/metabolism ; Sequence Analysis ; },
abstract = {Methanogenic archaea growing on ethanol or isopropanol as the electron donor for CO2 reduction to CH4 contain either an NADP-dependent or a coenzyme F420-dependent alcohol dehydrogenase. We report here that in both groups of methanogens, the N5, N10-methylenetetrahydromethanopterin dehydrogenase and the N5, N10-methylenetetrahydromethanopterin reductase, two enzymes involved in CO2 reduction to CH4, are specific for F420. This raised the question how F420H2 is regenerated in the methanogens with an NADP-dependent alcohol dehydrogenase. We found that these organisms contain catabolic activities of an enzyme catalyzing the reduction of F420 with NADPH. The F420-dependent NADP reductase from Methanogenium organophilum was purified and characterized. The N-terminal amino acid sequence showed 42% sequence identity to a putative gene product in Methanococcus jannaschii, the total genome of which has recently been sequenced.},
}
@article {pmid9342247,
year = {1997},
author = {Vorholt, JA and Thauer, RK},
title = {The active species of 'CO2' utilized by formylmethanofuran dehydrogenase from methanogenic Archaea.},
journal = {European journal of biochemistry},
volume = {248},
number = {3},
pages = {919-924},
doi = {10.1111/j.1432-1033.1997.00919.x},
pmid = {9342247},
issn = {0014-2956},
mesh = {Aldehyde Oxidoreductases/*metabolism ; Bicarbonates/metabolism ; Carbon Dioxide/*metabolism ; Carbon Radioisotopes ; Furans/metabolism ; Kinetics ; Methanosarcina barkeri/*enzymology/metabolism ; Molecular Structure ; Temperature ; },
abstract = {Formylmethanofuran dehydrogenase from methanogenic Archaea catalyzes the reversible conversion of CO2 and methanofuran to formylmethanofuran, which is an intermediate in methanogenesis from CO2, a biological process yielding approximately 0.3 billion tons of CH4 per year. With the enzyme from Methanosarcina barkeri, it is shown that CO2 rather than HCO3- is the active species of 'CO2' utilized by the dehydrogenase. Evidence is also presented that the enzyme catalyzes a methanofuran-dependent exchange between CO2 and the formyl group of formylmethanofuran. The results are consistent with N-carboxymethanofuran being an intermediate in CO2 reduction to formylmethanofuran.},
}
@article {pmid9335278,
year = {1997},
author = {Kuo, YP and Thompson, DK and St Jean, A and Charlebois, RL and Daniels, CJ},
title = {Characterization of two heat shock genes from Haloferax volcanii: a model system for transcription regulation in the Archaea.},
journal = {Journal of bacteriology},
volume = {179},
number = {20},
pages = {6318-6324},
pmid = {9335278},
issn = {0021-9193},
mesh = {Amino Acid Sequence ; *Archaeal Proteins ; Base Sequence ; Chaperonin Containing TCP-1 ; Chaperonins/chemistry/genetics ; Cloning, Molecular ; Conserved Sequence ; *Gene Expression Regulation, Archaeal ; Genes, Archaeal ; Genes, Reporter ; Haloferax/chemistry/*genetics ; Heat-Shock Proteins/chemistry/*genetics ; Hot Temperature ; Humans ; Molecular Chaperones/chemistry/*genetics ; Molecular Sequence Data ; Promoter Regions, Genetic ; TATA Box ; *Transcription, Genetic ; },
abstract = {The expression of two heat-responsive cct (chaperonin-containing Tcp-1) genes from the archaeon Haloferax volcanii was investigated at the transcription level. The cct1 and cct2 genes, which encode proteins of 560 and 557 amino acids, respectively, were identified on cosmid clones of an H. volcanii genomic library and subsequently sequenced. The deduced amino acid sequences of these genes exhibited a high degree of similarity to other archaeal and eucaryal cct family members. Expression of the cct genes was characterized in detail for the purpose of developing a model for studying transcription regulation in the domain Archaea. Northern (RNA) analysis demonstrated that the cct mRNAs were maximally induced after heat shock from 37 to 55 degrees C and showed significant heat inducibility after 30 min at 60 degrees C. Transcription of cct mRNAs was also stimulated in response to dilute salt concentrations. Transcriptional analysis of cct promoter regions coupled to a yeast tRNA reporter gene demonstrated that 5' flanking sequences up to position -233 (cct1) and position -170 (cct2) were sufficient for promoting heat-induced transcription. Transcript analysis indicated that both basal transcription and stress-induced transcription of the H. volcanii cct genes were directed by a conserved archaeal consensus TATA motif (5'-TTTATA-3') centered at -25 relative to the mapped initiation site. Comparison of the cct promoter regions also revealed a striking degree of sequence conservation immediately 5' and 3' of the TATA element.},
}
@article {pmid9301332,
year = {1997},
author = {Zhulin, IB and Taylor, BL and Dixon, R},
title = {PAS domain S-boxes in Archaea, Bacteria and sensors for oxygen and redox.},
journal = {Trends in biochemical sciences},
volume = {22},
number = {9},
pages = {331-333},
doi = {10.1016/s0968-0004(97)01110-9},
pmid = {9301332},
issn = {0968-0004},
mesh = {Amino Acid Sequence ; Animals ; Archaea/*genetics/metabolism ; Bacteria/*genetics/metabolism ; Bacterial Proteins/*genetics/metabolism ; Humans ; Molecular Sequence Data ; Oxidation-Reduction ; Oxygen/metabolism ; Proteins/genetics/metabolism ; Sequence Homology, Amino Acid ; },
}
@article {pmid9297234,
year = {1997},
author = {Russell, AG and de Sa, MM and Dennis, PP},
title = {A U3-like small nucleolar RNA in Archaea.},
journal = {Science (New York, N.Y.)},
volume = {277},
number = {5330},
pages = {1189},
doi = {10.1126/science.277.5330.1185d},
pmid = {9297234},
issn = {0036-8075},
}
@article {pmid9415440,
year = {1997},
author = {Voorhorst, WG and Warner, A and de Vos, WM and Siezen, RJ},
title = {Homology modelling of two subtilisin-like proteases from the hyperthermophilic archaea Pyrococcus furiosus and Thermococcus stetteri.},
journal = {Protein engineering},
volume = {10},
number = {8},
pages = {905-914},
doi = {10.1093/protein/10.8.905},
pmid = {9415440},
issn = {0269-2139},
mesh = {Amino Acid Sequence ; Amino Acids/analysis/chemistry ; *Archaeal Proteins ; Binding Sites ; Cloning, Molecular ; Enzyme Stability ; Models, Molecular ; Molecular Sequence Data ; *Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Pyrococcus/*enzymology/genetics ; Sequence Alignment ; Sequence Analysis ; Serine Endopeptidases/*chemistry/genetics/metabolism ; Substrate Specificity ; Subtilisins/chemistry ; Thermococcus/*enzymology/genetics ; },
abstract = {The hyperthermophilic archaeon Pyrococcus furiosus produces an extracellular, glycosylated hyperthermostable subtilisin-like serine protease, termed pyrolysin (Voorhorst,W.G.B., Eggen,R.I.L., Geerling,A.C.M., Platteeuw,C., Siezen,R.J. and de Vos,W.M. (1996) J. Biol. Chem., 271, 20426-20431). Based on the pyrolysin coding sequence, a pyrolysin-like gene fragment was cloned and characterized from the extreme thermophilic archaeon Thermococcus stetteri. Like pyrolysin, the deduced sequence of this serine protease, designated stetterlysin, contains a catalytic domain with high homology with other subtilases, allowing homology modelling starting from known crystal structures. Comparison of the predicted three-dimensional models of the catalytic domain of stetterlysin and pyrolysin with the crystal structure of subtilases from mesophilic and thermophilic origin, i.e. subtilisin BPN' and thermitase, and the homology model of subtilisin S41 from psychrophilic origin, led to the identification of features that could be related to protein stabilization. Higher thermostability was found to be correlated with an increased number of residues involved in pairs and networks of charge-charge and aromatic-aromatic interactions. These highly thermostable proteases have several extra surface loops and inserts with a relatively high frequency of aromatic residues and Asn residues. The latter are often present in putative N-glycosylation sites. Results from modelling of known substrates in the substrate-binding region support the broad substrate range and the autocatalytic activation previously suggested for pyrolysin.},
}
@article {pmid9379893,
year = {1997},
author = {Koonin, EV and Mushegian, AR and Galperin, MY and Walker, DR},
title = {Comparison of archaeal and bacterial genomes: computer analysis of protein sequences predicts novel functions and suggests a chimeric origin for the archaea.},
journal = {Molecular microbiology},
volume = {25},
number = {4},
pages = {619-637},
doi = {10.1046/j.1365-2958.1997.4821861.x},
pmid = {9379893},
issn = {0950-382X},
mesh = {Algorithms ; Amino Acid Sequence ; Archaea/*genetics ; Archaeal Proteins/chemistry/genetics ; Bacterial Proteins/chemistry/genetics ; Chaperonins/chemistry/genetics ; Chimera/genetics ; Conserved Sequence/genetics ; Databases as Topic ; Evolution, Molecular ; *Genome, Bacterial ; Methanococcus/chemistry/genetics ; Molecular Sequence Data ; Mycoplasma/chemistry/genetics ; Sequence Homology, Amino Acid ; Software ; },
abstract = {Protein sequences encoded in three complete bacterial genomes, those of Haemophilus influenzae, Mycoplasma genitalium and Synechocystis sp., and the first available archaeal genome sequence, that of Methanococcus jannaschii, were analysed using the BLAST2 algorithm and methods for amino acid motif detection. Between 75% and 90% of the predicted proteins encoded in each of the bacterial genomes and 73% of the M. jannaschii proteins showed significant sequence similarity to proteins from other species. The fraction of bacterial and archaeal proteins containing regions conserved over long phylogenetic distances is nearly the same and close to 70%. Functions of 70-85% of the bacterial proteins and about 70% of the archaeal proteins were predicted with varying precision. This contrasts with the previous report that more than half of the archaeal proteins have no homologues and shows that, with more sensitive methods and detailed analysis of conserved motifs, archaeal genomes become as amenable to meaningful interpretation by computer as bacterial genomes. The analysis of conserved motifs resulted in the prediction of a number of previously undetected functions of bacterial and archaeal proteins and in the identification of novel protein families. In spite of the generally high conservation of protein sequences, orthologues of 25% or less of the M. jannaschii genes were detected in each individual completely sequenced genome, supporting the uniqueness of archaea as a distinct domain of life. About 53% of the M. jannaschii proteins belong to families of paralogues, a fraction similar to that in bacteria with larger genomes, such as Synechocystis sp. and Escherichia coli, but higher than that in H. influenzae, which has approximately the same number of genes as M. jannaschii. Certain groups of proteins, e.g. molecular chaperones and DNA repair enzymes, thought to be ubiquitous and represented in the minimal gene set derived by bacterial genome comparison, are missing in M. jannaschii, indicating massive non-orthologous displacement of genes responsible for essential functions. An unexpectedly large fraction of the M. jannaschii gene products, 44%, shows significantly higher similarity to bacterial than to eukaryotic proteins, compared with 13% that have eukaryotic proteins as their closest homologues (the rest of the proteins show approximately the same level of similarity to bacterial and eukaryotic homologues or have no homologues). Proteins involved in translation, transcription, replication and protein secretion are most closely related to eukaryotic proteins, whereas metabolic enzymes, metabolite uptake systems, enzymes for cell wall biosynthesis and many uncharacterized proteins appear to be 'bacterial'. A similar prevalence of proteins of apparent bacterial origin was observed among the currently available sequences from the distantly related archaeal genus, Sulfolobus. It is likely that the evolution of archaea included at least one major merger between ancestral cells from the bacterial lineage and the lineage leading to the eukaryotic nucleocytoplasm.},
}
@article {pmid9260960,
year = {1997},
author = {Howell, DM and White, RH},
title = {D-erythro-neopterin biosynthesis in the methanogenic archaea Methanococcus thermophila and Methanobacterium thermoautotrophicum deltaH.},
journal = {Journal of bacteriology},
volume = {179},
number = {16},
pages = {5165-5170},
pmid = {9260960},
issn = {0021-9193},
mesh = {Biopterins/*analogs &amp; derivatives/biosynthesis ; Chromatography, Thin Layer ; GTP Cyclohydrolase/metabolism ; Guanosine Triphosphate/metabolism ; Methanobacterium/enzymology/*metabolism ; Methanococcus/enzymology/*metabolism ; Neopterin ; Pteridines/metabolism ; },
abstract = {The steps in the biosynthetic transformation of GTP to 7,8-dihydro-D-erythro-neopterin (H2neopterin), the precursor to the modified folates found in the methanogenic archaea, has been elucidated for the first time in two members of the domain Archaea. In Methanococcus thermophila and Methanobacterium thermoautotrophicum deltaH, it has been demonstrated that H2neopterin 2':3'-cyclic phosphate is an intermediate in this conversion. In addition, the formation of the pterin ring of the H2neopterin 2':3'-cyclic phosphate is catalyzed not by a single enzyme, as is known to occur with GTP cyclohydrolase I in the Eucarya and Bacteria, but rather by two or more enzymes. A 2,4,5-triamino-4(3H)-pyrimidinone-containing molecule, most likely 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-triphosphate, has been identified as an intermediate in the formation of the H2neopterin 2':3'-cyclic phosphate. Synthetic H2neopterin 2':3'-cyclic phosphate was found to be readily hydrolyzed by cell extracts of M. thermophila via the H2neopterin 3'-phosphate to H2neopterin, a known precursor to the pterin portion of methanopterin.},
}
@article {pmid9260934,
year = {1997},
author = {Bernander, R and Poplawski, A},
title = {Cell cycle characteristics of thermophilic archaea.},
journal = {Journal of bacteriology},
volume = {179},
number = {16},
pages = {4963-4969},
pmid = {9260934},
issn = {0021-9193},
mesh = {Cell Cycle ; Chromosomes, Bacterial/metabolism ; DNA Replication ; DNA, Bacterial/metabolism ; Deoxyribonuclease I/metabolism ; Endopeptidase K/metabolism ; Flow Cytometry ; Genome, Bacterial ; Light ; Ribonuclease, Pancreatic/metabolism ; Scattering, Radiation ; Sulfolobus/cytology/genetics/*growth &amp; development ; Sulfolobus acidocaldarius/cytology/genetics/*growth &amp; development ; },
abstract = {We have performed a cell cycle analysis of organisms from the Archaea domain. Exponentially growing cells of the thermophilic archaea Sulfolobus solfataricus and Sulfolobus acidocaldarius were analyzed by flow cytometry, and several unusual cell cycle characteristics were found. The cells initiated chromosome replication shortly after cell division such that the proportion of cells with a single chromosome equivalent was low in the population. The postreplication period was found to be long; i.e., there was a considerable time interval from termination of chromosome replication until cell division. A further unusual feature was that cells in stationary phase contained two genome equivalents, showing that they entered the resting stage during the postreplication period. Also, a reduction in cellular light scatter was observed during entry into stationary phase, which appeared to reflect changes not only in cell size but also in morphology and/or composition. Finally, the in vivo organization of the chromosome DNA appeared to be different from that of eubacteria, as revealed by variation in the relative binding efficiency of different DNA stains.},
}
@article {pmid9238098,
year = {1997},
author = {Noll, KM and Vargas, M},
title = {Recent advances in genetic analyses of hyperthermophilic archaea and bacteria.},
journal = {Archives of microbiology},
volume = {168},
number = {2},
pages = {73-80},
doi = {10.1007/s002030050472},
pmid = {9238098},
issn = {0302-8933},
mesh = {Archaea/*genetics/growth &amp; development ; Gene Transfer Techniques ; Genetic Markers ; Genetic Vectors ; Gram-Negative Anaerobic Bacteria/*genetics/growth &amp; development ; Hot Temperature ; Methanococcus/genetics ; Sulfolobus/genetics ; },
abstract = {Hyperthermophilic Archaea and Bacteria are an extraordinarily important class of organisms for which genetic tools remain to be developed. Unique technological obstacles to this goal are posed by the thermophilic and, in some cases, strictly anaerobic nature of these organisms. However, recent advances in the cultivation of hyperthermophiles, in the discovery of genetic elements for vector development, and in the construction of genetic markers point toward the achievement of this goal in the near future. Transformation protocols have already been reported for Sulfolobus and Pyrococcus, and plasmid-mediated conjugation was recently found in Sulfolobus. Plasmids are available for Sulfolobus, Pyrococcus, and the bacterial hyperthermophile Thermotoga, and these provide the bases for vector construction in these hosts. A Desulfurococcus mobile intron may provide a novel means to introduce genes into a variety of archaeal hosts. With full genome sequences of several hyperthermophiles available soon, genetic tools will allow full exploitation of this information to study these organisms in depth and to utilize their unique properties in biotechnological applications.},
}
@article {pmid9215623,
year = {1997},
author = {Dennis, PP},
title = {Ancient ciphers: translation in Archaea.},
journal = {Cell},
volume = {89},
number = {7},
pages = {1007-1010},
doi = {10.1016/s0092-8674(00)80288-3},
pmid = {9215623},
issn = {0092-8674},
mesh = {Archaea/*genetics ; Base Sequence ; Consensus Sequence ; Protein Biosynthesis/*genetics ; RNA, Bacterial/genetics ; },
}
@article {pmid9215622,
year = {1997},
author = {Belfort, M and Weiner, A},
title = {Another bridge between kingdoms: tRNA splicing in archaea and eukaryotes.},
journal = {Cell},
volume = {89},
number = {7},
pages = {1003-1006},
doi = {10.1016/s0092-8674(00)80287-1},
pmid = {9215622},
issn = {0092-8674},
mesh = {Archaea/*genetics ; Eukaryotic Cells/*physiology ; RNA Splicing/*physiology ; RNA, Transfer/*genetics ; Species Specificity ; },
}
@article {pmid9215620,
year = {1997},
author = {Edgell, DR and Doolittle, WF},
title = {Archaea and the origin(s) of DNA replication proteins.},
journal = {Cell},
volume = {89},
number = {7},
pages = {995-998},
doi = {10.1016/s0092-8674(00)80285-8},
pmid = {9215620},
issn = {0092-8674},
mesh = {Archaea/*chemistry/*genetics ; Bacterial Proteins/genetics ; DNA Replication/*genetics ; DNA, Bacterial/*genetics ; Replication Origin/*genetics ; },
}
@article {pmid9184239,
year = {1997},
author = {Genschik, P and Billy, E and Swianiewicz, M and Filipowicz, W},
title = {The human RNA 3'-terminal phosphate cyclase is a member of a new family of proteins conserved in Eucarya, Bacteria and Archaea.},
journal = {The EMBO journal},
volume = {16},
number = {10},
pages = {2955-2967},
pmid = {9184239},
issn = {0261-4189},
mesh = {Amino Acid Sequence ; Animals ; Archaea/enzymology/genetics ; Bacteria/enzymology/genetics ; Base Sequence ; Cell Compartmentation ; Cell Nucleus/chemistry ; Cloning, Molecular ; Conserved Sequence ; Escherichia coli/enzymology/genetics ; Eukaryotic Cells ; Fluorescent Antibody Technique ; Humans ; Ligases/*genetics/metabolism ; Mice ; Molecular Sequence Data ; Nuclear Proteins/*genetics/metabolism ; Prokaryotic Cells ; RNA/*metabolism ; Rats ; Recombinant Proteins/metabolism ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Species Specificity ; Substrate Specificity ; Tissue Distribution ; },
abstract = {RNA 3'-terminal phosphate cyclase catalyses the ATP-dependent conversion of the 3'-phosphate to a 2',3'-cyclic phosphodiester at the end of RNA. The physiological function of the cyclase is not known, but the enzyme could be involved in the maintenance of cyclic ends in tRNA splicing intermediates or in the cyclization of the 3' end of U6 snRNA. In this work, we describe cloning of the human cyclase cDNA. The purified bacterially overexpressed protein underwent adenylylation in the presence of [alpha-32P]ATP and catalysed cyclization of the 3'-terminal phosphate in different RNA substrates, consistent with previous findings. Comparison of oligoribonucleotides and oligodeoxyribonucleotides of identical sequence demonstrated that the latter are approximately 500-fold poorer substrates for the enzyme. In Northern analysis, the cyclase was expressed in all analysed mammalian tissues and cell lines. Indirect immunofluorescence, performed with different transfected mammalian cell lines, showed that this protein is nuclear, with a diffuse nucleoplasmic localization. The sequence of the human cyclase has no apparent motifs in common with any proteins of known function. However, inspection of the databases identified proteins showing strong similarity to the enzyme, originating from as evolutionarily distant organisms as yeast, plants, the bacterium Escherichia coli and the archaeon Methanococcus jannaschii. The overexpressed E. coli protein has cyclase activity similar to that of the human enzyme. The conservation of the RNA 3'-terminal phosphate cyclase among Eucarya, Bacteria and Archaea argues that the enzyme performs an important function in RNA metabolism.},
}
@article {pmid9178572,
year = {1997},
author = {Kudo, Y and Shibata, S and Miyaki, T and Aono, T and Oyaizu, H},
title = {Peculiar archaea found in Japanese paddy soils.},
journal = {Bioscience, biotechnology, and biochemistry},
volume = {61},
number = {5},
pages = {917-920},
pmid = {9178572},
issn = {0916-8451},
mesh = {Archaea/*isolation &amp; purification ; Cloning, Molecular ; Ecosystem ; Euryarchaeota/isolation &amp; purification ; Molecular Sequence Data ; Oryza ; *Phylogeny ; *Soil Microbiology ; Species Specificity ; },
abstract = {Archaeal 16S rDNA clones retrieved from paddy soil DNA were sequenced. Among 100 clones, 88 clones were assigned to methanogens and nine clones were assigned to crenarchaeota. However, three of the nine clones were phylogenetically far from the cultured crenarchaeota and closely related to marine planktonic archaea. The other three clones showed extremely novel 16S rDNA sequences and were phylogenetically far from both Crenarchaeola and Euryarchaeota. This paper reports the ubiquitous presence of crenarchaeotal and extremely novel clones in paddy soils.},
}
@article {pmid9150241,
year = {1997},
author = {White, RH},
title = {Purine biosynthesis in the domain Archaea without folates or modified folates.},
journal = {Journal of bacteriology},
volume = {179},
number = {10},
pages = {3374-3377},
pmid = {9150241},
issn = {0021-9193},
mesh = {Aminoimidazole Carboxamide/analogs &amp; derivatives/metabolism ; Archaea/*metabolism ; Folic Acid/*metabolism ; Formaldehyde/metabolism ; Inosine Monophosphate/metabolism ; Methanobacterium/metabolism ; Pterins/metabolism ; Purines/*biosynthesis ; Ribonucleotides/metabolism ; },
abstract = {The established pathway for the last two steps in purine biosynthesis, the conversion of 5-aminoimidazole-4-carboxamide ribonucleotide (ZMP) to IMP, is known to utilize 10-formyl-tetrahydrofolate as the required C1 donor cofactor. The biosynthetic conversion of ZMP to IMP in three members of the domain Archaea, Methanobacterium thermoautotrophicum deltaH, M. thermoautotrophicum Marburg, and Sulfolobus solfataricus, however, has been demonstrated to occur with only formate and ATP serving as cofactors. Thus, in these archaea, which use methanopterin (MPT) or another modified folate in place of folate as the C1 carrier coenzyme, neither folate nor a modified folate serves as a cofactor for this biosynthetic transformation. It is concluded that archaea, which function with modified folates such as MPT, are able to carry out purine biosynthesis without the involvement of folates or modified folates.},
}
@article {pmid9150208,
year = {1997},
author = {Desmarais, D and Jablonski, PE and Fedarko, NS and Roberts, MF},
title = {2-Sulfotrehalose, a novel osmolyte in haloalkaliphilic archaea.},
journal = {Journal of bacteriology},
volume = {179},
number = {10},
pages = {3146-3153},
pmid = {9150208},
issn = {0021-9193},
support = {AR42358/AR/NIAMS NIH HHS/United States ; },
mesh = {Disaccharides/*chemistry/metabolism ; Halobacteriaceae/*chemistry/growth &amp; development ; Intracellular Fluid/chemistry/drug effects/metabolism ; Magnetic Resonance Spectroscopy ; Osmolar Concentration ; Sodium Chloride/pharmacology ; Solutions ; Trehalose/*analogs &amp; derivatives/chemistry/metabolism ; },
abstract = {A novel 1-->1 alpha-linked glucose disaccharide with sulfate at C-2 of one of the glucose moieties, 1-(2-O-sulfo-alpha-D-glucopyranosyl)-alpha-D-glycopyranose, was found to be the major organic solute accumulated by a Natronococcus sp. and several Natronobacterium species. The concentration of this novel disaccharide, termed sulfotrehalose, increased with increasing concentrations of external NaCl, behavior consistent with its identity as an osmolyte. A variety of noncharged disaccharides (trehalose, sucrose, cellobiose, and maltose) were added to the growth medium to see if they could suppress synthesis and accumulation of sulfotrehalose. Sucrose was the most effective in suppressing biosynthesis and accumulation of sulfotrehalose, with levels as low as 0.1 mM being able to significantly replace the novel charged osmolyte. Other common osmolytes (glycine betaine, glutamate, and proline) were not accumulated or used for osmotic balance in place of the sulfotrehalose by the halophilic archaeons.},
}
@article {pmid9108153,
year = {1997},
author = {Harrod, R and Lovett, PS},
title = {Leader peptides of inducible chloramphenicol resistance genes from gram-positive and gram-negative bacteria bind to yeast and Archaea large subunit rRNA.},
journal = {Nucleic acids research},
volume = {25},
number = {9},
pages = {1720-1726},
pmid = {9108153},
issn = {0305-1048},
support = {GM-42925/GM/NIGMS NIH HHS/United States ; },
mesh = {Base Sequence ; Chloramphenicol Resistance/*genetics ; DNA Footprinting ; Gram-Negative Bacteria/*genetics ; Gram-Positive Bacteria/*genetics ; Halobacterium/genetics ; Molecular Sequence Data ; Nucleic Acid Conformation ; Protein Binding ; Protein Sorting Signals/*metabolism ; RNA, Bacterial/chemistry/metabolism ; RNA, Fungal/chemistry/metabolism ; RNA, Ribosomal/chemistry/*metabolism ; RNA-Binding Proteins/metabolism ; Saccharomyces cerevisiae/genetics ; },
abstract = {catA86 is the second gene in a constitutively transcribed, two-gene operon cloned from Bacillus pumilus . The region that intervenes between the upstream gene, termed the leader, and the catA86 coding sequence contains a pair of inverted repeat sequences which cause sequestration of the catA86 ribosome binding site in mRNA secondary structure. As a consequence, the catA86 coding sequence is untranslatable in the absence of inducer. Translation of the catA86 coding sequence is induced by chloramphenicol in Gram-positives and induction requires a function of the leader coding sequence. The leader-encoded peptide has been proposed to instruct its translating ribosome to pause at leader codon 6, enabling chloramphenicol to stall the ribosome at that site. Ribosome stalling causes destabilization of the RNA secondary structure, exposing the catA86 ribosome binding site, allowing activation of its translation. A comparable mechanism of induction by chloramphenicol has been proposed for the regulated cmlA gene from Gram-negative bacteria. The catA86 and cmlA leader-encoded peptides are in vitro inhibitors of peptidyl transferase, which is thought to be the basis for selection of the site of ribosome stalling. Both leader-encoded peptides have been shown to alter the secondary structure of Escherichia coli 23S rRNA in vitro. All peptide-induced changes in rRNA conformation are within domains IV and V, which contains the peptidyl transferase center. Here we demonstrate that the leader peptides alter the conformation of domains IV and V of large subunit rRNA from yeast and a representative of the Archaea. The rRNA target for binding the leader peptides is therefore conserved across kingdoms.},
}
@article {pmid9094221,
year = {1997},
author = {Pfeifer, F and Krüger, K and Röder, R and Mayr, A and Ziesche, S and Offner, S},
title = {Gas vesicle formation in halophilic Archaea.},
journal = {Archives of microbiology},
volume = {167},
number = {5},
pages = {259-268},
doi = {10.1007/s002030050441},
pmid = {9094221},
issn = {0302-8933},
mesh = {*Archaeal Proteins ; Bacterial Outer Membrane Proteins/genetics/metabolism ; Base Sequence ; Consensus Sequence ; DNA, Bacterial/genetics ; Gases/*metabolism ; Genes, Bacterial ; Halobacteriales/*genetics/*metabolism ; Halobacterium/genetics/metabolism ; *Membrane Proteins ; Molecular Sequence Data ; Multigene Family ; Promoter Regions, Genetic ; *Proteins ; Trans-Activators/genetics/metabolism ; Transformation, Genetic ; },
abstract = {Gas vesicles are intracellular, microbial flotation devices that consist of mainly one protein, GvpA. The formation of halobacterial gas vesicles occurs along a complex pathway involving 14 different gvp genes that are clustered in a genomic region termed the "vac region". Various vac regions found in Halobacterium salinarum (p-vac and c-vac), Haloferax mediterranei (mc-vac), and Natronobacterium vacuolatum (nv-vac) have been investigated. Except for the latter vac region, the arrangement of the gvp genes is identical. Single gvp genes have been mutated to study the effect on gas vesicle synthesis in transformants and to determine their possible function. Each vac region exhibits a characteristic transcription pattern, and regulatory steps have been observed at the DNA, RNA, and protein level, indicating a complex regulatory network acting during gas vesicle gene expression.},
}
@article {pmid9079930,
year = {1997},
author = {Smith, SC and Kennelly, PJ and Potts, M},
title = {Protein-tyrosine phosphorylation in the Archaea.},
journal = {Journal of bacteriology},
volume = {179},
number = {7},
pages = {2418-2420},
pmid = {9079930},
issn = {0021-9193},
support = {GM45368/GM/NIGMS NIH HHS/United States ; },
mesh = {Archaea/*metabolism ; Bacterial Proteins/*metabolism ; Methanosarcina/*metabolism ; Molecular Weight ; Phosphoproteins/*metabolism ; Phosphotyrosine/*metabolism ; Sulfolobus/*metabolism ; },
abstract = {Sulfolobus sulfataricus ATCC 35091, Haloferax volcanii, and Methanosarcina thermophila TM-1, representing the Euryarchaeota and Crenarchaeota subdomains of the Archaea, contain proteins which are phosphorylated on tyrosine. These data raise fundamental questions as to the origin and evolution of tyrosine phosphorylation, a protein modification that is of pivotal importance in the regulation of the physiology of eukaryotic cells.},
}
@article {pmid9075622,
year = {1997},
author = {Selig, M and Xavier, KB and Santos, H and Schönheit, P},
title = {Comparative analysis of Embden-Meyerhof and Entner-Doudoroff glycolytic pathways in hyperthermophilic archaea and the bacterium Thermotoga.},
journal = {Archives of microbiology},
volume = {167},
number = {4},
pages = {217-232},
doi = {10.1007/BF03356097},
pmid = {9075622},
issn = {0302-8933},
mesh = {Archaea/*metabolism ; Glucose/metabolism ; *Glycolysis ; Gram-Negative Anaerobic Bacteria/*metabolism ; Magnetic Resonance Spectroscopy ; Oxidation-Reduction ; Pyruvic Acid/metabolism ; },
abstract = {The Embden-Meyerhof (EM) or Entner-Doudoroff (ED) pathways of sugar degradation were analyzed in representative species of the hyperthermophilic archaeal genera Thermococcus, Desulfurococcus, Thermoproteus, and Sulfolobus, and in the hyperthermophilic (eu)bacterial genus Thermotoga. The analyses included (1) determination of 13C-labeling patterns by 1H- and 13C-NMR spectroscopy of fermentation products derived from pyruvate after fermentation of specifically 13C-labeled glucose by cell suspensions, (2) identification of intermediates of sugar degradation after conversion of 14C-labeled glucose by cell extracts, and (3) measurements of enzyme activities in cell extracts. Thermococcus celer and Thermococcus litoralis fermented 13C-glucose to acetate and alanine via a modified EM pathway (100%). This modification involves ADP-dependent hexokinase, 6-phosphofructokinase, and glyceraldehyde-3-phosphate:ferredoxin oxidoreductase (GAP:FdOR). Desulfurococcus amylolyticus fermented 13C-glucose to acetate via a modified EM pathway in which GAP:FdOR replaces GAP-DH/phosphoglycerate kinase. Thermoproteus tenax fermented 13C-glucose to low amounts of acetate and alanine via simultaneous operation of the EM pathway (85%) and the ED pathway (15%). Aerobic Sulfolobus acidocaldarius fermented 13C-labeled glucose to low amounts of acetate and alanine exclusively via the ED pathway. The anaerobic (eu)bacterium Thermotoga maritima fermented 13C-glucose to acetate and lactate via the EM pathway (85%) and the ED pathway (15%). Cell extracts contained glucose-6-phosphate dehydrogenase and 2-keto-3-deoxy-6-phosphogluconate aldolase, key enzymes of the conventional phosphorylated ED pathway, and, as reported previously, all enzymes of the conventional EM pathway. In conclusion, glucose was degraded by hyperthermophilic archaea to pyruvate either via modified EM pathways with different types of hexose kinases and GAP-oxidizing enzymes, by the nonphosphorylated ED pathway, or by a combination of both pathways. In contrast, glucose catabolism in the hyperthermophilic (eu)bacterium Thermotoga involves the conventional forms of the EM and ED pathways. The data are in accordance with various previous reports.},
}
@article {pmid9121560,
year = {1997},
author = {Bergerat, A and de Massy, B and Gadelle, D and Varoutas, PC and Nicolas, A and Forterre, P},
title = {An atypical topoisomerase II from Archaea with implications for meiotic recombination.},
journal = {Nature},
volume = {386},
number = {6623},
pages = {414-417},
doi = {10.1038/386414a0},
pmid = {9121560},
issn = {0028-0836},
mesh = {Amino Acid Sequence ; Archaeal Proteins ; Cloning, Molecular ; Conserved Sequence ; DNA/metabolism ; *DNA Topoisomerases, Type II/chemistry/genetics/*metabolism ; Fungal Proteins/chemistry/metabolism ; Meiosis ; Molecular Sequence Data ; Mutagenesis, Site-Directed ; Recombination, Genetic ; Saccharomyces cerevisiae ; Sequence Homology, Amino Acid ; Sulfolobus/*enzymology ; },
abstract = {Type II topoisomerases help regulate DNA topology during transcription, replication and recombination by catalysing DNA strand transfer through transient double-stranded breaks. All type II topoisomerases described so far are members of a single protein family. We have cloned and sequenced the genes encoding the A and B subunits of topoisomerase II from the archaeon Sulfolobus shibatae. This enzyme is the first of a new family. It has no similarity with other type II topoisomerases, except for three motifs in the B subunit probably involved in ATP binding and hydrolysis. We also found these motifs in proteins of the Hsp90 and MutL families. The A subunit has similarities with four proteins of unknown function. One of them, the Saccharomyces cerevisiae Spo11 protein, is required for the initiation of meiotic recombination. Mutagenesis, performed on SPO11, of the single tyrosine conserved between the five homologues shows that this amino acid is essential for Spo11 activity. By analogy with the mechanism of action of known type II topoisomerases, we suggest that Spo11 catalyses the formation of double-strand breaks that initiate meiotic recombination in S. cerevisiae.},
}
@article {pmid9122246,
year = {1997},
author = {Metcalf, WW and Zhang, JK and Apolinario, E and Sowers, KR and Wolfe, RS},
title = {A genetic system for Archaea of the genus Methanosarcina: liposome-mediated transformation and construction of shuttle vectors.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {94},
number = {6},
pages = {2626-2631},
pmid = {9122246},
issn = {0027-8424},
support = {F32 GM016504/GM/NIGMS NIH HHS/United States ; 1 F GM16504-)1A1/GM/NIGMS NIH HHS/United States ; GM51334/GM/NIGMS NIH HHS/United States ; },
mesh = {Amino Acid Sequence ; Base Sequence ; Cloning, Molecular/methods ; DNA Primers ; *DNA Replication ; Drug Carriers ; Escherichia coli ; Liposomes ; Methanosarcina/*genetics ; Molecular Sequence Data ; Plasmids/*administration &amp; dosage/genetics ; Polymerase Chain Reaction ; Restriction Mapping ; },
abstract = {New methods that allow, for the first time, genetic analysis in Archaea of the genus Methanosarcina are presented. First, several autonomously replicating plasmid shuttle vectors have been constructed based on the naturally occurring plasmid pC2A from Methanosarcina acetivorans. These vectors replicate in 9 of 11 Methanosarcina strains tested and in Escherichia coli. Second, a highly efficient transformation system based upon introduction of DNA by liposomes has been developed. This method allows transformation frequencies of as high as 2 x 10(8) transformants per microgram of DNA per 10(9) cells or approximately 20% of the recipient population. During the course of this work, the complete 5467-bp DNA sequence of pC2A was determined. The implications of these findings for the future of methanoarchaeal research are also discussed.},
}
@article {pmid9102456,
year = {1997},
author = {Wilting, R and Schorling, S and Persson, BC and Böck, A},
title = {Selenoprotein synthesis in archaea: identification of an mRNA element of Methanococcus jannaschii probably directing selenocysteine insertion.},
journal = {Journal of molecular biology},
volume = {266},
number = {4},
pages = {637-641},
doi = {10.1006/jmbi.1996.0812},
pmid = {9102456},
issn = {0022-2836},
mesh = {Amino Acid Sequence ; Archaea/chemistry/genetics/metabolism ; Bacterial Proteins/biosynthesis/chemistry/genetics ; Base Sequence ; Codon/genetics ; Electrophoresis, Polyacrylamide Gel ; Methanococcus/chemistry/genetics/*metabolism ; Molecular Sequence Data ; Molecular Weight ; Nucleic Acid Conformation ; Open Reading Frames/genetics ; *Protein Biosynthesis ; Proteins/chemistry/genetics ; RNA, Bacterial/chemistry/genetics ; RNA, Messenger/chemistry/*genetics ; Selenocysteine/*metabolism ; Selenoproteins ; Sequence Alignment ; },
abstract = {Selenocysteine is encoded by a UGA codon in all organisms that synthesise selenoproteins. This codon is specified as a selenocysteine codon by an mRNA secondary structure, which is located immediately 3' of the UGA in the reading frame of selenoprotein genes in Gram-negative bacteria, whereas it is located in the 3' untranslated region of eukaryal selenoprotein genes. The location and the structure of a similar mRNA signal in archaea has so far not been determined. Seven selenoproteins were identified for the archaeon Methanococcus jannaschii by labelling with 75Se and by SDS/polyacrylamide electrophoresis. Their size could be correlated with open reading frames possessing internal UGA codons from the total genomic sequence. One of the open reading frames, that of the VhuD subunit of a hydrogenase, possesses two UGA codons and appears to code for a selenoprotein with two selenocysteine residues. A strongly conserved mRNA element was identified that is exclusively linked to selenoprotein genes. It is located in the 3' untranslated region in six of the mRNAs and in the 5' untranslated region of the fdhA mRNA. This element, which is present in the 3' non-translated region of two selenoprotein mRNAs from Methanococcus voltae, is proposed to act in decoding of the UGA with selenocysteine.},
}
@article {pmid9106366,
year = {1997},
author = {Dennis, PP and Shimmin, LC},
title = {Evolutionary divergence and salinity-mediated selection in halophilic archaea.},
journal = {Microbiology and molecular biology reviews : MMBR},
volume = {61},
number = {1},
pages = {90-104},
pmid = {9106366},
issn = {1092-2172},
mesh = {Archaea/*genetics/*physiology ; Base Sequence ; *Biological Evolution ; Codon ; *Genetic Variation ; Hot Temperature ; Molecular Sequence Data ; Osmolar Concentration ; Phylogeny ; Polymorphism, Genetic ; RNA, Ribosomal, 16S/genetics ; *Selection, Genetic ; Sequence Homology, Nucleic Acid ; Serine ; Sodium Chloride ; },
abstract = {Halophilic (literally salt-loving) archaea are a highly evolved group of organisms that are uniquely able to survive in and exploit hypersaline environments. In this review, we examine the potential interplay between fluctuations in environmental salinity and the primary sequence and tertiary structure of halophilic proteins. The proteins of halophilic archaea are highly adapted and magnificently engineered to function in an intracellular milieu that is in ionic balance with an external environment containing between 2 and 5 M inorganic salt. To understand the nature of halophilic adaptation and to visualize this interplay, the sequences of genes encoding the L11, L1, L10, and L12 proteins of the large ribosome subunit and Mn/Fe superoxide dismutase proteins from three genera of halophilic archaea have been aligned and analyzed for the presence of synonymous and nonsynonymous nucleotide substitutions. Compared to homologous eubacterial genes, these halophilic genes exhibit an inordinately high proportion of nonsynonymous nucleotide substitutions that result in amino acid replacement in the encoded proteins. More than one-third of the replacements involve acidic amino acid residues. We suggest that fluctuations in environmental salinity provide the driving force for fixation of the excessive number of nonsynonymous substitutions. Tinkering with the number, location, and arrangement of acidic and other amino acid residues influences the fitness (i.e., hydrophobicity, surface hydration, and structural stability) of the halophilic protein. Tinkering is also evident at halophilic protein positions monomorphic or polymorphic for serine; more than one-third of these positions use both the TCN and the AGY serine codons, indicating that there have been multiple nonsynonymous substitutions at these positions. Our model suggests that fluctuating environmental salinity prevents optimization of fitness for many halophilic proteins and helps to explain the unusual evolutionary divergence of their encoding genes.},
}
@article {pmid9106217,
year = {1997},
author = {López-García, P and Forterre, P},
title = {DNA topology in hyperthermophilic archaea: reference states and their variation with growth phase, growth temperature, and temperature stresses.},
journal = {Molecular microbiology},
volume = {23},
number = {6},
pages = {1267-1279},
doi = {10.1046/j.1365-2958.1997.3051668.x},
pmid = {9106217},
issn = {0950-382X},
mesh = {Archaea/growth &amp; development/*metabolism ; Cold Temperature/adverse effects ; DNA, Bacterial/*chemistry ; DNA, Superhelical/chemistry ; Hot Temperature/adverse effects ; Plasmids/physiology ; Sulfolobales/genetics/physiology ; },
abstract = {In order to address the dynamics of DNA topology in hyperthermophilic archaea, we analysed the topological state of several plasmids recently discovered in Thermococcales and Sulfolobales. All of these plasmids were from relaxed to highly positively supercoiled in vitro, i.e. they exhibited a significant linking excess compared to the negatively supercoiled plasmids from mesophilic organisms (both Archaea and Bacteria). In the two archaeal orders, plasmid linking number (Lk) decreased as growth temperature was lowered from its optimal value, i.e. positively supercoiled plasmids were relaxed whereas relaxed plasmids became negatively supercoiled. Growth temperatures above the optimum correlated with higher positive supercoiling in Sulfolobales (Lk increase) but with relaxation of positive supercoils in Thermococcus sp. GE31. The topological variation of plasmid DNA isolated from cells at different growth phases were found to be species specific in both archaeal orders. In contrast, the direction of topological variation under temperature stress was the same, i.e. a heat shock correlated with an increase in plasmid positive supercoiling, whilst a cold shock induced negative supercoiling. The kinetics of these effects were analysed in Sulfolobales. In both temperature upshift (from 80 to 85 degrees C) and downshift (from 80 to 65 degrees C), a transient sharp variation of Lk occurred first, and then DNA supercoiling progressively reached levels typical of steady-state growth at the final temperature. These results indicate that DNA topology can change with physiological states and environmental modifications in hyperthermophilic archaea.},
}
@article {pmid9039908,
year = {1997},
author = {Burggraf, S and Heyder, P and Eis, N},
title = {A pivotal Archaea group.},
journal = {Nature},
volume = {385},
number = {6619},
pages = {780},
doi = {10.1038/385780a0},
pmid = {9039908},
issn = {0028-0836},
mesh = {Archaea/classification/genetics/growth &amp; development/*isolation &amp; purification ; Culture Media ; Molecular Sequence Data ; Oligonucleotide Probes ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; },
}
@article {pmid9047361,
year = {1997},
author = {Ofengand, J and Bakin, A},
title = {Mapping to nucleotide resolution of pseudouridine residues in large subunit ribosomal RNAs from representative eukaryotes, prokaryotes, archaebacteria, mitochondria and chloroplasts.},
journal = {Journal of molecular biology},
volume = {266},
number = {2},
pages = {246-268},
doi = {10.1006/jmbi.1996.0737},
pmid = {9047361},
issn = {0022-2836},
mesh = {Animals ; Bacillus subtilis/genetics ; Base Sequence ; Binding Sites ; Chloroplasts/*genetics ; Drosophila melanogaster/genetics ; Halobacterium salinarum/*genetics ; Humans ; Mice ; Mitochondria/*genetics ; Molecular Sequence Data ; Nucleic Acid Conformation ; Nucleosides/chemistry/genetics ; Peptidyl Transferases/genetics ; Pseudouridine/*analysis/chemistry/genetics ; RNA, Ribosomal/*chemistry ; RNA-Directed DNA Polymerase/genetics/metabolism ; Trypanosoma brucei brucei/genetics ; Zea mays/genetics ; },
abstract = {The pseudouridine (psi) residues present in the high molecular mass RNA from the large ribosomal subunit (LSU) have been sequenced from representative species of the eukaryotes, prokaryotes and archaebacteria, and from mitochondrial and chloroplast organelles. Ribosomes from Bacillus subtilis, Halobacter halobium, Drosphilia melanogaster, Mus musculus, Homo sapiens, mitochondria of M. musculus, H. sapiens and Trypanosoma brucei, and Zea mays chloroplasts were examined, resulting in the exact localization of 190 psi residues. The number of psi residues per RNA varied from one in the mitochondrial RNAs to 57 in the cytoplasmic LSU RNA of D. melanogaster and M. musculus. Despite this, all of the psi residues were found in three domains, II, IV and V. All three are at or have been linked to the peptidyl transferase center according to the literature. Comparison of the sites for psi among the species examined revealed four conserved or semi-conserved segments. One is the region 1911 to 1917, which contains three psi or modified psi in almost all species examined. This site is also juxtaposed to the decoding site of the 30 S subunit in the 70 S ribosome and has been implicated in the fidelity of codon recognition. Three additional sites were at the peptidyl transferase center itself. The juxtaposition of the conserved sites for psi with the two important functions of the ribosome, codon recognition and peptide bond formation, implies an important role for psi in ribosome function. We report some new putative modified nucleosides in LSU RNAs as detected by reverse transcription, correct a segment of the sequence of Z. mays chloroplasts and D. melanogaster LSU RNA, correlate the secondary structural context for all known psi residues in ribosomal RNA, and compare the sites for psi with those known for methylated nucleosides in H. sapiens.},
}
@article {pmid9037050,
year = {1997},
author = {Cohen-Kupiec, R and Blank, C and Leigh, JA},
title = {Transcriptional regulation in Archaea: in vivo demonstration of a repressor binding site in a methanogen.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {94},
number = {4},
pages = {1316-1320},
pmid = {9037050},
issn = {0027-8424},
mesh = {Base Sequence ; Binding Sites ; *Gene Expression Regulation, Bacterial ; Genes, Reporter ; Methanococcus/*genetics ; Molecular Sequence Data ; Mutagenesis, Site-Directed ; Nitrogen Fixation/*genetics ; Nitrogenase/biosynthesis/genetics ; *Oxidoreductases ; Plasmids ; *Promoter Regions, Genetic ; Protein Binding ; Repressor Proteins/*metabolism ; Transcription, Genetic ; Transformation, Genetic ; },
abstract = {The status of the Archaea as one of the three primary Domains emphasizes the importance of understanding their molecular fundamentals. Basic transcription in the Archaea resembles eucaryal transcription. However, little is known about transcriptional regulation. We have taken an in vivo approach, using genetics to address transcriptional regulation in the methanogenic Archaeon Methanococcus maripaludis. We identified a repressor binding site that regulates nif (nitrogen fixation) gene expression. The repressor binding site was palindromic (an inverted repeat) and was located just after the transcription start site of nifH. Mutations that changed the sequence of the palindrome resulted in marked decreases in repression by ammonia, even when the palindromic nature of the site was retained. The same mutations greatly decreased binding to the site by components of cell extract. These results provide the first partial description of a transcriptional regulatory mechanism in the methanogenic Archaea. This work also illustrates the utility of genetic approaches in Methanococcus that have not been widely used in the methanogens: directed mutagenesis and reporter gene fusions with lacZ.},
}
@article {pmid9082070,
year = {1997},
author = {Hatzoglou, E and Sekeris, CE},
title = {The detection of nucleotide sequences with strong similarity to hormone responsive elements in the genome of eubacteria and archaebacteria and their possible relation to similar sequences present in the mitochondrial genome.},
journal = {Journal of theoretical biology},
volume = {184},
number = {3},
pages = {339-344},
doi = {10.1006/jtbi.1996.0285},
pmid = {9082070},
issn = {0022-5193},
mesh = {Animals ; Archaea/*genetics ; Base Sequence ; DNA ; *DNA, Mitochondrial ; *Genome, Bacterial ; Humans ; Mice ; Molecular Sequence Data ; Rats ; Receptors, Cell Surface/*genetics ; Symbiosis ; },
abstract = {To account for the presence of nucleotide sequences in mitochondria with similarity to the Hormone Response Elements (HREs) of the nuclear genomes of man, rat and mouse, the genomes of several procaryotes have been screened for the presence of the sequences AGAACA NNN TGTTCT and GGTACA NNN TGTTCT, which represent perfect palindromic and consensus class I HREs, respectively, and for the sequence AGGTCA NNN TGACCT, which represents class II HRE. In many of the examined procaryotes, eubacteria and archaebacteria, almost perfect palindromic class I HREs and perfect or almost perfect class II half palindromic HREs have been detected in various genes, some of which encode proteins involved in energy metabolism, in replication and in transcription control. These findings support the hypothesis that the similar sequences found in mitochondria, potentially involved in hormonal regulation of respiratory enzyme biosynthesis, were introduced into eucaryotic cell by the procaryotic endosymbionts.},
}
@article {pmid9013590,
year = {1997},
author = {Iwasaki, T and Suzuki, T and Kon, T and Imai, T and Urushiyama, A and Ohmori, D and Oshima, T},
title = {Novel zinc-containing ferredoxin family in thermoacidophilic archaea.},
journal = {The Journal of biological chemistry},
volume = {272},
number = {6},
pages = {3453-3458},
doi = {10.1074/jbc.272.6.3453},
pmid = {9013590},
issn = {0021-9258},
mesh = {Amino Acid Sequence ; Crystallography, X-Ray ; Electron Spin Resonance Spectroscopy ; Ferredoxins/*chemistry ; Models, Molecular ; Molecular Sequence Data ; Sequence Alignment ; Sulfolobus/*chemistry ; Thermoplasma/*chemistry ; *Zinc ; },
abstract = {The dicluster-type ferredoxins from the thermoacidophilic archaea such as Thermoplasma acidophilum and Sulfolobus sp. are known to contain an unusually long extension of unknown function in the N-terminal region. Recent x-ray structural analysis of the Sulfolobus ferredoxin has revealed the presence of a novel zinc center, which is coordinated by three histidine ligand residues in the N-terminal region and one aspartate in the ferredoxin core domain. We report here the quantitative metal analyses together with electron paramagnetic resonance and resonance Raman spectra of T. acidophilum ferredoxin, demonstrating the presence of a novel zinc center in addition to one [3Fe-4S] and one [4Fe-4S] cluster (Fe/Zn = 6.8 mol/mol). A phylogenetic tree constructed for several archaeal monocluster and dicluster type ferredoxins suggests that the zinc-containing ferredoxins of T. acidophilum and Sulfolobus sp. form an independent subgroup, which is more distantly related to the ferredoxins from the hyperthermophiles than those from the methanogenic archaea, indicating the existence of a novel group of ferredoxins, namely, a "zinc-containing ferredoxin family" in the thermoacidophilic archaea. Inspection of the N-terminal extension regions of the archaeal zinc-containing ferredoxins suggested strict conservation of three histidine and one aspartate residues as possible ligands to the novel zinc center.},
}
@article {pmid9680332,
year = {1997},
author = {Blöchl, E and Rachel, R and Burggraf, S and Hafenbradl, D and Jannasch, HW and Stetter, KO},
title = {Pyrolobus fumarii, gen. and sp. nov., represents a novel group of archaea, extending the upper temperature limit for life to 113 degrees C.},
journal = {Extremophiles : life under extreme conditions},
volume = {1},
number = {1},
pages = {14-21},
doi = {10.1007/s007920050010},
pmid = {9680332},
issn = {1431-0651},
mesh = {Ammonia/metabolism ; Archaea/*classification/genetics/metabolism/ultrastructure ; Base Composition ; DNA, Archaeal ; Heat-Shock Proteins/analysis ; Hydrogen/metabolism ; Hydrogenase/metabolism ; Nitrates/metabolism ; Nucleic Acid Hybridization ; Oxidation-Reduction ; Pressure ; Temperature ; Thiosulfates/metabolism ; },
abstract = {A novel, irregular, coccoid-shaped archaeum was isolated from a hydrothermally heated black smoker wall at the TAG site at the Mid Atlantic Ridge (depth 3650 meters). It grew at between 90 degrees C and 113 degrees C (optimum 106 degrees C) and pH 4.0-6.5 (optimum 5.5) and 1%-4% salt (optimum 1.7%). The organism was a facultatively aerobic obligate chemolithoautotroph gaining energy by H2-oxidation. Nitrate, S2O3(2-), and low concentrations of O2 (up to 0.3% v/v) served as electron acceptors, yielding NH4+, H2S, and H2O as end products, respectively. Growth was inhibited by acetate, pyruvate, glucose, starch, or sulfur. The new isolate was able to form colonies on plates (at 102 degrees C) and to grow at a pressure of 25000 kPa (250 bar). Exponentially growing cultures survived a one-hour autoclaving at 121 degrees C. The GC content was 53 mol%. The core lipids consisted of glycerol-dialkyl glycerol tetraethers and traces of 2,3-di-O-phytanyl-sn-glycerol. The cell wall was composed of a surface layer of tetrameric protein complexes arranged on a p4-lattice (center-to-center distance 18.5 nm). By its 16S rRNA sequence, the new isolate belonged to the Pyrodictiaceae. Based on its GC-content, DNA homology, S-layer composition, and metabolism, we describe here a new genus, which we name Pyrolobus (the "fire lobe"). The type species is Pyrolobus fumarii (type strain 1A; DSM 11204).},
}
@article {pmid9023200,
year = {1997},
author = {Franzetti, B and Sohlberg, B and Zaccai, G and von Gabain, A},
title = {Biochemical and serological evidence for an RNase E-like activity in halophilic Archaea.},
journal = {Journal of bacteriology},
volume = {179},
number = {4},
pages = {1180-1185},
pmid = {9023200},
issn = {0021-9193},
mesh = {Antibodies, Monoclonal ; Blotting, Western ; Cross Reactions ; Endoribonucleases/chemistry/immunology/isolation &amp; purification/*metabolism ; Enzyme Stability ; Escherichia coli/enzymology ; Halobacteriaceae/*enzymology ; Molecular Weight ; Polyribosomes/enzymology ; Potassium Chloride/pharmacology ; RNA, Bacterial/*metabolism ; RNA, Messenger/*metabolism ; Substrate Specificity ; },
abstract = {Endoribonuclease RNase E appears to control the rate-limiting step that mediates the degradation of many mRNA species in bacteria. In this work, an RNase E-like activity in Archaea is described. An endoribonucleolytic activity from the extreme halophile Haloarcula marismortui showed the same RNA substrate specificity as the Escherichia coli RNase E and cross-reacted with a monoclonal antibody raised against E. coli RNase E. The archaeal RNase E activity was partially purified from the extreme halophilic cells and shown, contrary to the E. coli enzyme, to require a high salt concentration for cleavage specificity and stability. These data indicate that a halophilic RNA processing enzyme can specifically recognize and cleave mRNA from E. coli in an extremely salty environment (3 M KCI). Having recently been shown in mammalian cells (A. Wennborg, B. Sohlberg, D. Angerer, G. Klein, and A. von Gabain, Proc. Natl. Acad. Sci. USA 92:7322-7326, 1995), RNase E-like activity has now been identified in all three evolutionary domains: Archaea, Bacteria, and Eukarya. This strongly suggests that mRNA decay mechanisms are highly conserved despite quite different environmental conditions.},
}
@article {pmid8990199,
year = {1997},
author = {Bintrim, SB and Donohue, TJ and Handelsman, J and Roberts, GP and Goodman, RM},
title = {Molecular phylogeny of Archaea from soil.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {94},
number = {1},
pages = {277-282},
pmid = {8990199},
issn = {0027-8424},
mesh = {Archaea/*classification/*genetics ; Bacterial Typing Techniques ; Cell Lineage ; Cloning, Molecular ; DNA, Bacterial/isolation &amp; purification ; DNA, Ribosomal/*genetics ; *Evolution, Molecular ; Gene Amplification ; Genes, Bacterial ; Molecular Sequence Data ; Sequence Analysis, DNA ; *Soil Microbiology ; },
abstract = {Cultivation methods have contributed to our present knowledge about the presence and diversity of microbes in naturally occurring communities. However, it is well established that only a small fraction of prokaryotes have been cultivated by standard methods and, therefore, the prokaryotes that are cultivated may not reflect the composition and diversity within those communities. Of the two prokaryotic phylogenetic domains, Bacteria and Archaea, members of the former have been shown to be ubiquitous in nature, with ample evidence of vast assemblages of uncultured organisms. There is also now increasingly compelling evidence that the Archaea, which were once thought to occupy a limited number of environments, are also globally widespread. Here we report the use of molecular phylogenetic techniques, which are independent of microbial cultivation, to conduct an assessment of Archaea in a soil microbial community. Small subunit ribosomal RNA genes of Archaea were amplified from soil and cloned. Phylogenetic and nucleotide signature analyses of these cloned small subunit ribosomal RNA gene sequences revealed a cluster of Archaea from a soil microbial community that diverge deeply from the crenarchaeotal line of descent and has the closest affiliation to the lineage of planktonic Archaea. The identification and phylogenetic classification of this archaeal lineage from soil contributes to our understanding of the ecological significance of Archaea as a component of microbial communities in non-extreme environments.},
}
@article {pmid9586121,
year = {1997},
author = {Ibba, M and Celic, I and Curnow, A and Kim, H and Pelaschier, J and Tumbula, D and Vothknecht, U and Woese, C and Söll, D},
title = {Aminoacyl-tRNA synthesis in Archaea.},
journal = {Nucleic acids symposium series},
volume = {},
number = {37},
pages = {305-306},
pmid = {9586121},
issn = {0261-3166},
mesh = {Amino Acyl-tRNA Synthetases/genetics/*metabolism ; Haloferax volcanii/genetics/*metabolism ; Lysine-tRNA Ligase/genetics/*metabolism ; RNA, Transfer, Amino Acyl/*biosynthesis/metabolism ; },
abstract = {The mechanism of aminoacyl-tRNA synthesis differs substantially between Archaea, Bacteria and Eukarya. Sequencing of archaeal genomes has suggested that the asparaginyl-, cysteinyl-, glutaminyl- and lysyl-tRNA synthetases are absent from a number of organisms in this kingdom. The absence of the asparaginyl- and glutaminyl-tRNA synthetases is in agreement with the observation that Asn-tRNA and Gln-tRNA are synthesized by tRNA-dependent transamidation of Asp-tRNA and Glu-tRNA respectively in the archaeon Haloferax volcanii. Biochemical and genetic studies have now shown that while the cysteinyl- and lysyl-tRNA synthetases are present, the enzymes responsible for these activities are unique to Archaea.},
}
@article {pmid9254012,
year = {1997},
author = {Jovell, RJ and Macario, AJ and Conway de Macario, E},
title = {An ABC-transporter system homolog in an organism of the phylogenetic domain Archaea.},
journal = {DNA sequence : the journal of DNA sequencing and mapping},
volume = {7},
number = {3-4},
pages = {193-197},
doi = {10.3109/10425179709034034},
pmid = {9254012},
issn = {1042-5179},
mesh = {*ATP-Binding Cassette Transporters ; Amino Acid Sequence ; Archaea/*genetics ; *Archaeal Proteins ; Bacterial Proteins/*genetics ; Base Sequence ; Cloning, Molecular ; Cyclins/genetics ; *Endoribonucleases ; *Escherichia coli Proteins ; Methanosarcina/*genetics/metabolism ; Molecular Sequence Data ; Multigene Family ; Phylogeny ; Plant Proteins/*genetics ; Sequence Homology, Amino Acid ; },
abstract = {A cluster of genes was identified in an archaeal organism, the methanogen Methanosarcina mazei S-6, that was a homolog of the ABC-transporter system loci of several organisms belonging to the phylogenetic domain Bacteria. The gene number, size, and organization were also similar. The proteins encoded by these genes were similar in structure, hydrophilicity-hydrophobicity profiles, and motifs to the equivalent components of homolog systems in bacteria and eucarya.},
}
@article {pmid9251004,
year = {1997},
author = {White, RH},
title = {Structural characterization of modified folates in Archaea.},
journal = {Methods in enzymology},
volume = {281},
number = {},
pages = {391-401},
doi = {10.1016/s0076-6879(97)81046-4},
pmid = {9251004},
issn = {0076-6879},
mesh = {Amines/analysis/metabolism ; Archaea/*chemistry/metabolism ; Azo Compounds/analysis/chemistry/metabolism ; Chitinases/metabolism ; Chromatography, High Pressure Liquid ; Chromatography, Thin Layer ; Folic Acid/*analogs &amp; derivatives/*chemistry/isolation &amp; purification/metabolism ; Gas Chromatography-Mass Spectrometry ; Molecular Structure ; Phosphodiesterase I ; Phosphoric Diester Hydrolases/metabolism ; Phosphoric Monoester Hydrolases/metabolism ; Pterins/analysis/chemistry/metabolism ; },
}
@article {pmid9020585,
year = {1997},
author = {Bateman, A},
title = {The structure of a domain common to archaebacteria and the homocystinuria disease protein.},
journal = {Trends in biochemical sciences},
volume = {22},
number = {1},
pages = {12-13},
doi = {10.1016/s0968-0004(96)30046-7},
pmid = {9020585},
issn = {0968-0004},
mesh = {Amino Acid Sequence ; Animals ; Bacterial Proteins/*chemistry ; Homocystinuria/*metabolism ; Humans ; Methanococcus/*chemistry ; Molecular Sequence Data ; *Protein Structure, Tertiary ; },
}
@article {pmid8997717,
year = {1997},
author = {Purwantini, E and Gillis, TP and Daniels, L},
title = {Presence of F420-dependent glucose-6-phosphate dehydrogenase in Mycobacterium and Nocardia species, but absence from Streptomyces and Corynebacterium species and methanogenic Archaea.},
journal = {FEMS microbiology letters},
volume = {146},
number = {1},
pages = {129-134},
doi = {10.1111/j.1574-6968.1997.tb10182.x},
pmid = {8997717},
issn = {0378-1097},
mesh = {Corynebacterium/enzymology ; Euryarchaeota/enzymology ; Glucosephosphate Dehydrogenase/*metabolism ; Kinetics ; Mycobacterium/*enzymology ; Mycobacterium leprae/enzymology ; Mycobacterium tuberculosis/enzymology ; NAD/metabolism ; NADP/metabolism ; Nocardia/*enzymology ; Riboflavin/*analogs &amp; derivatives/metabolism ; Species Specificity ; Streptomyces/enzymology ; },
abstract = {A range of organisms known to contain F420 or to be relatives of mycobacteria were examined for F420-dependent glucose-6-phosphate dehydrogenase (FGD) and NADP-dependent glucose-6-phosphate dehydrogenase (NADP-G6PD) activities. All free-growing Mycobacterium species examined (including a virulent Mycobacterium tuberculosis strain) had FGD activities of 0.014-0.418 mumol min-1 mg protein-1, and NADP-G6PD activities of 0.013-0.636 mumol min-1 mg-1. Armadillo-grown Mycobacterium leprae had FGD activity of 0.008 mumol min-1 mg-1, but no detectable NADP-G6PD activity. Nocardia species also had FGD activity (0.088-0.154 mumol min-1 mg-1). Streptomyces and Corynebacterium species had no FGD, but had NADP-G6PD. Methanogenic Archaea had neither activity.},
}
@article {pmid8995805,
year = {1997},
author = {Ihara, K and Watanabe, S and Tamura, T},
title = {Haloarcula argentinensis sp. nov. and Haloarcula mukohataei sp. nov., two new extremely halophilic archaea collected in Argentina.},
journal = {International journal of systematic bacteriology},
volume = {47},
number = {1},
pages = {73-77},
doi = {10.1099/00207713-47-1-73},
pmid = {8995805},
issn = {0020-7713},
mesh = {Argentina ; Bacteriological Techniques ; Base Composition ; Culture Media/metabolism ; DNA, Bacterial/*analysis ; Glycolipids/analysis ; Halobacteriaceae/*classification/*genetics/isolation &amp; purification ; Molecular Sequence Data ; Nucleic Acid Hybridization ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/*genetics ; },
abstract = {Strains arg-1T (T = type strain) and arg-2T, two new strains of extremely halophilic archaea, were isolated from the soils of the Argentine salt flats. The taxonomic features of arg-1T were similar to, but distinct from, those of the type strain of Haloarcula vallismortis and other Haloarcula species. On the 16S rRNA phylogenetic tree, strain arg-1T formed a cluster together with Haloarcula species. Strain arg-2T differed in its glycolipid composition but still was more closely related to the genus Haloarcula than to other established genera. We propose that strain arg-1T be classified as a member of a new species, Haloarcula argentinensis, and that strain arg-2T be classified as a member of Haloarcula mukohataei sp. nov., although arg-2T may belong to a new genus or a subgenus of the genus Haloarcula. The type strain of H. argentinensis is strain arg-1 (= JCM 9737), and the type strain of H. mukohataei is strain arg-2 (= JCM 9738).},
}
@article {pmid8979338,
year = {1997},
author = {Massana, R and Murray, AE and Preston, CM and DeLong, EF},
title = {Vertical distribution and phylogenetic characterization of marine planktonic Archaea in the Santa Barbara Channel.},
journal = {Applied and environmental microbiology},
volume = {63},
number = {1},
pages = {50-56},
pmid = {8979338},
issn = {0099-2240},
mesh = {Animals ; Archaea/classification/*genetics/*isolation &amp; purification ; Base Sequence ; California ; DNA Primers/genetics ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Molecular Sequence Data ; Phylogeny ; Plankton/classification/*genetics/*isolation &amp; purification ; Seawater/microbiology ; },
abstract = {Newly described phylogenetic lineages within the domain Archaea have recently been found to be significant components of marine picoplankton assemblages. To better understand the ecology of these microorganisms, we investigated the relative abundance, distribution, and phylogenetic composition of Archaea in the Santa Barbara Channel. Significant amounts of archaeal rRNA and rDNA (genes coding for rRNA) were detected in all samples analyzed. The relative abundance of archaeal rRNA as measured by quantitative oligonucleotide hybridization experiments was low in surface waters but reached higher values (20 to 30% of prokaryotic rRNA) at depths below 100 m. Probes were developed for the two major groups of marine Archaea detected. rRNA originating from the euryarchaeal group (group II) was most abundant in surface waters, whereas rRNA from the crenarchaeal group (group I) dominated at depth. Clone libraries of PCR-amplified archaeal rRNA genes were constructed with samples from 0 and 200 m deep. Screening of libraries by hybridization with specific oligonucleotide probes, as well as subsequent sequencing of the cloned genes, indicated that virtually all archaeal rDNA clones recovered belonged to one of the two groups. The recovery of cloned rDNA sequence types in depth profiles exhibited the same trends as were observed in quantitative rRNA hybridization experiments. One representative of each of 18 distinct restriction fragment length polymorphism types was partially sequenced. Recovered sequences spanned most of the previously reported phylogenetic diversity detected in planktonic crenarchaeal and euryarchaeal groups. Several rDNA sequences appeared to be harbored in archaeal types which are widely distributed in marine coastal waters. In total, data suggest that marine planktonic crenarchaea and euryarchaea of temperate coastal habitats thrive in different zones of the water column. The relative rRNA abundance of the crenarchaeal group suggests that its members constitute a significant fraction of the prokaryotic biomass in subsurface coastal waters.},
}
@article {pmid8986768,
year = {1996},
author = {Guimarães, MJ and Peterson, D and Vicari, A and Cocks, BG and Copeland, NG and Gilbert, DJ and Jenkins, NA and Ferrick, DA and Kastelein, RA and Bazan, JF and Zlotnik, A},
title = {Identification of a novel selD homolog from eukaryotes, bacteria, and archaea: is there an autoregulatory mechanism in selenocysteine metabolism?.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {93},
number = {26},
pages = {15086-15091},
pmid = {8986768},
issn = {0027-8424},
mesh = {Amino Acid Sequence ; Animals ; Archaea/genetics/*metabolism ; Bacterial Proteins/chemistry/*genetics/*metabolism ; Base Sequence ; COS Cells ; Chromosome Mapping ; Cloning, Molecular ; *Drosophila Proteins ; Escherichia coli/genetics/*metabolism ; Female ; Genetic Markers ; Humans ; Mice ; Mice, Inbred BALB C ; Molecular Sequence Data ; *Phosphotransferases ; Phylogeny ; Polymerase Chain Reaction ; Selenium/metabolism ; Selenocysteine/*metabolism ; Sequence Homology, Amino Acid ; Transfection ; },
abstract = {Escherichia coli selenophosphate synthetase (SPS, the selD gene product) catalyzes the production of monoselenophosphate, the selenium donor compound required for synthesis of selenocysteine (Sec) and seleno-tRNAs. We report the molecular cloning of human and mouse homologs of the selD gene, designated Sps2, which contains an in-frame TGA codon at a site corresponding to the enzyme's putative active site. These sequences allow the identification of selD gene homologs in the genomes of the bacterium Haemophilus influenzae and the archaeon Methanococcus jannaschii, which had been previously misinterpreted due to their in-frame TGA codon. Sps2 mRNA levels are elevated in organs previously implicated in the synthesis of selenoproteins and in active sites of blood cell development. In addition, we show that Sps2 mRNA is up-regulated upon activation of T lymphocytes and have mapped the Sps2 gene to mouse chromosome 7. Using the mouse gene isolated from the hematopoietic cell line FDCPmixA4, we devised a construct for protein expression that results in the insertion of a FLAG tag sequence at the N terminus of the SPS2 protein. This strategy allowed us to document the readthrough of the in-frame TGA codon and the incorporation of 75Se into SPS2. These results suggest the existence of an autoregulatory mechanism involving the incorporation of Sec into SPS2 that might be relevant to blood cell biology. This mechanism is likely to have been present in ancient life forms and conserved in a variety of living organisms from all domains of life.},
}
@article {pmid8994805,
year = {1996},
author = {Harris, R},
title = {Archaea make it big.},
journal = {Current biology : CB},
volume = {6},
number = {12},
pages = {1540},
doi = {10.1016/s0960-9822(02)70761-6},
pmid = {8994805},
issn = {0960-9822},
mesh = {Archaea/genetics ; Methanococcus/*genetics ; },
}
@article {pmid8987902,
year = {1996},
author = {Newbold, CJ and Ushida, K and Morvan, B and Fonty, G and Jouany, JP},
title = {The role of ciliate protozoa in the lysis of methanogenic archaea in rumen fluid.},
journal = {Letters in applied microbiology},
volume = {23},
number = {6},
pages = {421-425},
doi = {10.1111/j.1472-765x.1996.tb01350.x},
pmid = {8987902},
issn = {0266-8254},
mesh = {Animals ; Bacteriophages/physiology ; *Colony Count, Microbial ; Eukaryota/*metabolism ; Euryarchaeota/*physiology/virology ; Proteins/metabolism ; Rumen/*microbiology/*parasitology ; Sheep ; },
abstract = {Predation by ciliate protozoa can account for 90% of the eubacterial protein turnover in the rumen. However, little is known about the factors affecting the lysis of archaea in rumen fluid. Bacterial lysis was followed from the release of acid-soluble 14C from 14C leucine-labelled bacteria. The rumen methanogen Methanobrevibacter MF1 was broken down more rapidly than other non-ruminal archaea in rumen fluid withdrawn from sheep harbouring either a mixed protozoa population or monofaunated with Polyplastron multivesiculatum or Entodinium spp. The removal of protozoa from the rumen fluid had little effect on the breakdown of Methanobrevibacter, while lysis of the non-methanogenic ruminal bacterium Selenomonas ruminantium decreased by over 70%. Substantial lysis of Methanobrevibacter occurred in cell-free rumen fluid and this effect could be abolished by autoclaving. In view of the high number of bacteriophages in rumen fluid and susceptibility of ruminal bacteria to phage-induced lysis it is tempting to suggest that phages have a role in the lysis of archaea in rumen fluid.},
}
@article {pmid8900104,
year = {1996},
author = {Watrin, L and Prieur, D},
title = {UV and ethyl methanesulfonate effects in hyperthermophilic archaea and isolation of auxotrophic mutants of Pyrococcus strains.},
journal = {Current microbiology},
volume = {33},
number = {6},
pages = {377-382},
doi = {10.1007/s002849900131},
pmid = {8900104},
issn = {0343-8651},
mesh = {Archaea/drug effects/*genetics/radiation effects ; Mesylates ; *Mutation ; Ultraviolet Rays ; Uracil/metabolism ; },
abstract = {The lethal and mutagenic effects of ethyl methanesulfonate (EMS) and UV on nine archaeal strains belonging to each of the two described genera of Thermococcales, Pyrococcus and Thermococcus, were investigated. To test the efficiency of the EMS and UV mutagenesis under a variety of experimental conditions, we chose Pyrococcus abyssi strain GE5 as a model strain. We observed a strong induced mutagenicity in both cases, since the spontaneous mutation frequency (expressed as the frequency of resistance to 5-fluoroorotic acid) increased up to 150-fold with EMS and 400-fold with UV, after mutagen exposure. Although a heterogeneous response to the induced effects caused after EMS and UV exposures was detected for all the other sulfothermophilic archaea tested, an efficient mutagenicity of Pyrococcus-like isolates GE27, GE23, and GE9 was observed. Optimal procedures described for UV mutagenesis yielded a number of useful uracil auxotrophic mutant strains of Pyrococcus abyssi.},
}
@article {pmid8955643,
year = {1996},
author = {Fujiwara, S and Okuyama, S and Imanaka, T},
title = {The world of archaea: genome analysis, evolution and thermostable enzymes.},
journal = {Gene},
volume = {179},
number = {1},
pages = {165-170},
doi = {10.1016/s0378-1119(96)00428-3},
pmid = {8955643},
issn = {0378-1119},
mesh = {Archaea/*enzymology/*genetics ; *Biological Evolution ; Enzyme Stability ; Genes, Bacterial ; *Genome, Bacterial ; Hot Temperature ; Restriction Mapping ; },
abstract = {Pyrococcus sp. KOD1 is a newly isolated hyperthermophilic archaeon from a solfatara at a wharf on Kodakara Island, Kagoshima, Japan. A physical map of the KOD1 chromosome was constructed using pulsed-field gel electrophoresis of restriction fragments generated by AscI, PacI and PmeI. The order of the AscI fragments was deduced from Southern hybridization using the AscI, PmeI and PacI fragments as a probe. The derived physical map indicates that KOD1 possesses a circular-form genome and its size was estimated to be 2036 kb. Several cloned genes were hybridized to restriction fragments to locate their positions on the physical map. Some genes involved in the central dogma were located on the restricted segment of the genome. Novel characteristics of KOD1 enzymes are also introduced in this article.},
}
@article {pmid8918227,
year = {1996},
author = {De Vendittis, E and Bocchini, V},
title = {Protein-encoding genes in the sulfothermophilic archaea Sulfolobus and Pyrococcus.},
journal = {Gene},
volume = {176},
number = {1-2},
pages = {27-33},
doi = {10.1016/0378-1119(96)00203-x},
pmid = {8918227},
issn = {0378-1119},
mesh = {Animals ; Archaea/*genetics/metabolism ; Bacterial Proteins/*genetics ; Base Composition ; Base Sequence ; Cattle ; Codon ; DNA, Bacterial ; Humans ; Molecular Sequence Data ; Sulfolobus/*genetics/metabolism ; },
abstract = {A number of unrelated protein-encoding genes from sulfothermophilic archaea, Sulfolobus acidocaldarius, Sulfolobus solfataricus, Pyrococcus furiosus and Pyrococcus woesei, has been analyzed. In the Sulfolobus genus, the content of A + T is significantly higher than that of C + G and the base usage follows the order, A > T > G > C. In Pyrococcus, the A + T content is also higher than that of C + G, but with lower values; in the order of base usage, G precedes T. The codon usage of these sulfothermophiles has been determined; alternative start codons are frequently used in both genera; codon preferences reflect the rich A + T composition of the corresponding genomes; for both genera the codon bias is particularly evident within the different arginine triplets, where AGA and AGG are predominant. From the similarities in the codon usage, close taxonomic relationships become evident within the Sulfolobus or the Pyrococcus genus; a lower, but significant similarity is also clear between these genera. The synonymous codon usage of these sulfothermophiles shows similarities with that of Saccharomyces cerevisiae and bovine mitochondria, whereas clear divergences are observed with the halophilic archaeal genus, Halobacterium, or the eubacterium, Escherichia coli. The unrelated proteins of the considered sulfothermophiles have been analyzed for the content of hydrophobic residues; the comparison with mesophiles reveals a significant increase in the average hydrophobicity of amino acid residues. This finding could indicate a mechanism of adaptation of proteins in organisms living under extreme environments. It is noteworthy that an opposite trend, i.e. a decreased average hydrophobicity, occurs in unrelated halophilic proteins.},
}
@article {pmid8890747,
year = {1996},
author = {Jovell, RJ and Macario, AJ and Conway de Macario, E},
title = {ABC transporters in Archaea: two genes encoding homologs of the nucleotide-binding components in the methanogen Methanosarcina mazei S-6.},
journal = {Gene},
volume = {174},
number = {2},
pages = {281-284},
doi = {10.1016/0378-1119(96)00249-1},
pmid = {8890747},
issn = {0378-1119},
mesh = {ATP-Binding Cassette Transporters/*genetics ; Amino Acid Sequence ; *Archaeal Proteins ; Bacterial Proteins/*genetics ; Cloning, Molecular ; Codon, Initiator ; Cyclins/*genetics ; *Endoribonucleases ; Genes, Bacterial ; Methanosarcina/*genetics ; Molecular Sequence Data ; Phylogeny ; Protein Biosynthesis ; },
abstract = {Two genes, 5'-orfD-orfF-3', were found in the genome of the archaeon Methanosarcina mazei S-6 that encode the deduced proteins, OrfD and OrfF, with structural motifs typical of the nucleotide-binding components of the ABC-transporter systems of Bacteria and Eukarya. These motifs, and other similarities of OrfD and OrfF with bacterial and eukaryal counterparts, indicate that the two archaeal molecules belong to the ATP-binding cassette (ABC)-transporter family.},
}
@article {pmid8865818,
year = {1996},
author = {Seki, SI and Sasabe, H and Tomioka, H},
title = {Voltage-dependent absorbance change of carotenoids in halophilic archaebacteria.},
journal = {Biochimica et biophysica acta},
volume = {1284},
number = {1},
pages = {79-85},
doi = {10.1016/0005-2736(96)00114-9},
pmid = {8865818},
issn = {0006-3002},
mesh = {Carotenoids/*chemistry ; Halobacterium/*chemistry/genetics ; Hydrogen-Ion Concentration ; Light ; Membrane Potentials ; Mutation ; },
abstract = {Membrane vesicles of wild-type Halobacterium sp. mex strain show a wavy absorbance change which has not been so far reported in halophilic archaebacteria. A white mutant strain lacking carotenoids did not show the wavy absorbance change. The wavy absorbance change in the range of 440-590 nm was induced by a red flash (600-640 nm), which photoexcited electrogenic ion pumps, mex bacteriorhodopsin and mex halorhodopsin but not carotenoids. The wavy change was also caused by K+ diffusion potentials without light. These results suggest that the wavy absorbance change in the membrane vesicles is the voltage-dependent absorbance change of the carotenoids.},
}
@article {pmid8987674,
year = {1996},
author = {Kobayashi, K and Kato, M and Miura, Y and Kettoku, M and Komeda, T and Iwamatsu, A},
title = {Gene analysis of trehalose-producing enzymes from hyperthermophilic archaea in Sulfolobales.},
journal = {Bioscience, biotechnology, and biochemistry},
volume = {60},
number = {10},
pages = {1720-1723},
doi = {10.1271/bbb.60.1720},
pmid = {8987674},
issn = {0916-8451},
mesh = {Amino Acid Sequence ; Cloning, Molecular ; *Genes, Bacterial ; Genetic Code ; Glycosyltransferases/*genetics ; *Hot Temperature ; Molecular Sequence Data ; Sequence Homology, Amino Acid ; Sulfolobales/enzymology/*genetics ; Trehalose/*biosynthesis ; alpha-Amylases/*genetics ; },
abstract = {The genes encoding new trehalose-producing enzymes from S. acidocaldarius ATCC33909 were cloned to analyze the distribution of these genes in Sulfolobales. Comparison of the amino acid sequences with S. solfataricus KM1 showed approximately 50% similarity. Southern analysis suggest that homologues of the trehalose-producing enzyme genes exist widely in sulfolobales and strains in Sulfolobales were classified into three kinds of genotypes.},
}
@article {pmid8885405,
year = {1996},
author = {Beveridge, TJ and Schultze-Lam, S},
title = {The response of selected members of the archaea to the gram stain.},
journal = {Microbiology (Reading, England)},
volume = {142 (Pt 10)},
number = {},
pages = {2887-2895},
doi = {10.1099/13500872-142-10-2887},
pmid = {8885405},
issn = {1350-0872},
mesh = {Archaea/*cytology/ultrastructure ; Cell Membrane/ultrastructure ; Cell Wall/ultrastructure ; Coloring Agents ; *Gentian Violet ; Glyceryl Ethers ; Gram-Negative Bacteria/*cytology/ultrastructure ; Gram-Positive Bacteria/cytology/ultrastructure ; Organoplatinum Compounds ; *Phenazines ; Rosaniline Dyes ; Spectrometry, X-Ray Emission ; Staining and Labeling/*methods ; },
abstract = {Archaea possess a broader range of cell envelope structural formats than eubacteria and their cell walls do not contain peptidoglycan. Some archaea have only a single S-layer as their cell wall (e.g. Methanococcus jannaschii and Sulfolobus acidocaldarius), whereas others have multiple layers (e.g. Methanospirillum hungatei). Sometimes there can also be a high proportion of tetraether lipids in membranes to make the envelope more resilient to environmental stress (e.g. Methanococcus jannaschii and Sulfolobus acidocaldarius grown at 70 degrees C). Since the Gram reaction depends on both the structural format and the chemical composition of the cell envelope of eubacteria, it was important to determine if the same is true for archaea. Methanospirillum hungatei, Methanosarcina mazei, Methanobacterium formicicum, Methanococcus jannaschii and Sulfolobus acidocaldarius, chosen because of their different envelope formats and chemistries, were subjected to a Gram stain that can be used for transmission electron microscopy. In this staining regimen, the iodine is replaced by potassium trichloro(eta 2-ethylene)platinate(II) as the mordant, and the platinum of the new compound is the electron-scattering agent for electron microscopy. Of all these archaea, only Methanobacterium formicicum stained Gram-positive since its pseudomurein wall remained intact; the platinum compound formed large electron-dense aggregates with the crystal violet that were located in the vicinity of the cell wall and the plasma membrane. All but the terminal filament cells of Methanospirillum hungatei stained Gram-negative because the limiting porosity of its external sheath was so small that the Gram reagents could not enter the cells. The terminal cells of filaments stained Gram-positive because the staining reagents gained entry through the terminal plugs. All other archaea stained Gram-negative because their cell walls were so disrupted during staining that the crystal violet-platinum complex could not be retained by the cells. Methanococcus jannaschii was grown at both 50 degrees C and 70 degrees C so that the tetraether lipids in its plasma membrane could be increased from 20% (50 degrees C) to 45% (70 degrees C) of the total lipids; in both cases the cells stained Gram-negative.},
}
@article {pmid8837434,
year = {1996},
author = {Arahal, DR and Dewhirst, FE and Paster, BJ and Volcani, BE and Ventosa, A},
title = {Phylogenetic analyses of some extremely halophilic archaea isolated from Dead Sea water, determined on the basis of their 16S rRNA sequences.},
journal = {Applied and environmental microbiology},
volume = {62},
number = {10},
pages = {3779-3786},
pmid = {8837434},
issn = {0099-2240},
support = {DE-08303/DE/NIDCR NIH HHS/United States ; DE-10374/DE/NIDCR NIH HHS/United States ; },
mesh = {Archaea/*genetics/growth &amp; development/metabolism ; DNA, Bacterial/analysis ; Genes, Bacterial/genetics ; Israel ; Molecular Sequence Data ; Phenotype ; *Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; *Water Microbiology ; },
abstract = {Twenty-two extremely halophilic aerobic archaeal strains were isolated from enrichments prepared from Dead Sea water samples collected 57 years ago. The isolates were phenotypically clustered into five different groups, and a representative from each group was chosen for further study. Almost the entire sequences of the 16S rRNA genes of these representatives, and of Haloarcula hispanica ATCC 33960, were determined to establish their phylogenetic positions. The sequences of these strains were compared to previously published sequences of 27 reference halophilic archaea (members of the family Halobacteriaceae) and two other archaea, Methanobacterium formicicum DSM 1312 and Methanospirillum hungatei DSM 864. Phylogenetic analysis using approximately 1,400 base comparisons of 16S rRNA-encoding gene sequences demonstrated that the five isolates clustered closely to species belonging to three different genera--Haloferax, Halobacterium, and Haloarcula. Strains E1 and E8 were closely related and identified as members of the species Haloferax volcanii, and strain E12 was closely related and identified as a member of the species Halobacterium salinarum. However, strains E2 and E11 clustered in the Haloarcula branch with Haloarcula hispanica as the closest relative at 98.9 and 98.8% similarity, respectively. Strains E2 and E11 could represent two new species of the genus Haloarcula. However, because strains of these two new species were isolated from a single source, they will not be named until additional strains are isolated from other sources and fully characterized.},
}
@article {pmid8814335,
year = {1996},
author = {McCready, S},
title = {The repair of ultraviolet light-induced DNA damage in the halophilic archaebacteria, Halobacterium cutirubrum, Halobacterium halobium and Haloferax volcanii.},
journal = {Mutation research},
volume = {364},
number = {1},
pages = {25-32},
doi = {10.1016/0921-8777(96)00018-3},
pmid = {8814335},
issn = {0027-5107},
support = {//Wellcome Trust/United Kingdom ; },
mesh = {*DNA Damage ; *DNA Repair ; DNA, Bacterial/genetics/*radiation effects ; Darkness ; Halobacteriales/genetics/metabolism/*radiation effects ; Halobacterium/genetics/metabolism/radiation effects ; Halobacterium salinarum/genetics/metabolism/radiation effects ; Kinetics ; Pyrimidine Dimers/analysis ; Saccharomyces cerevisiae/genetics/radiation effects ; Time Factors ; *Ultraviolet Rays ; },
abstract = {Extremely halophilic archaebacteria have been reported to have no capacity for dark repair (excision repair) of ultraviolet damage and to rely on very efficient photoreactivation for recovery after UVC irradiation. Post-UV incubation in the light restores 100% survival in these organisms. This has been taken to indicate that cyclobutane dimers are the only significant UV-induced lesions and that they are completely repaired by photoreactivation. However, in all organisms studied to date, pyrimidine (6-4) pyrimidone photoproducts are a significant cytotoxic and mutagenic lesion and constitute 10-30% of UV photoproducts. The question arises, therefore--are 6-4 photoproducts induced in the halophilic archaebacteria and, if they are, how are they repaired? This paper shows that both cyclobutane dimers and 6-4 photoproducts are induced in the extremely halophilic archaebacteria, Halobacterium cutirubrum, Halobacterium halobium and Haloferax volcanii, at similar levels as in other organisms. Furthermore, contrary to previous reports, there is dark repair of both lesions. As in other organisms, 6-4 photoproducts are removed more efficiently than cyclobutane dimers in the dark. In the light, cyclobutane dimers are repaired very rapidly and there is also photoenhanced repair of 6-4 photoproducts. This work confirms that organisms such as Halobacterium and Haloferax which live in conditions of high exposure to sunlight have very efficient rates of repair of UV lesions in the light.},
}
@article {pmid8799104,
year = {1996},
author = {Doolittle, WF},
title = {At the core of the Archaea.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {93},
number = {17},
pages = {8797-8799},
pmid = {8799104},
issn = {0027-8424},
mesh = {Archaea/*classification/*genetics ; *Biological Evolution ; Eukaryotic Cells ; Prokaryotic Cells ; },
}
@article {pmid8755911,
year = {1996},
author = {Shimmin, LC and Dennis, PP},
title = {Conserved sequence elements involved in regulation of ribosomal protein gene expression in halophilic archaea.},
journal = {Journal of bacteriology},
volume = {178},
number = {15},
pages = {4737-4741},
pmid = {8755911},
issn = {0021-9193},
mesh = {Archaea/*genetics ; Bacterial Proteins/*genetics ; Base Sequence ; Chromosome Mapping ; Conserved Sequence ; DNA Primers/genetics ; DNA, Bacterial/genetics ; Gene Expression Regulation, Bacterial ; *Genes, Bacterial ; Molecular Sequence Data ; Nucleic Acid Conformation ; RNA, Fungal/chemistry/genetics ; Ribosomal Proteins/*genetics ; },
abstract = {A region of the Haloferax volcanii genome encoding ribosomal proteins L11e, L1e, L10e, and L12e was cloned and sequenced, and the transcripts derived from the cluster were characterized. Flanking and noncoding regions of the sequence were analyzed phylogenetically by comparison with the homologous sequences from two other halophilic archaea, i.e., Halobacterium cutirubrum and Haloarcula marismortui. Motifs, identified by high-level sequence conservation, include both transcriptional and translational regulatory elements and other elements of unknown function.},
}
@article {pmid8688447,
year = {1996},
author = {Schäfer, G and Purschke, WG and Gleissner, M and Schmidt, CL},
title = {Respiratory chains of archaea and extremophiles.},
journal = {Biochimica et biophysica acta},
volume = {1275},
number = {1-2},
pages = {16-20},
doi = {10.1016/0005-2728(96)00043-6},
pmid = {8688447},
issn = {0006-3002},
mesh = {Amino Acid Sequence ; Archaea/*metabolism ; Cytochromes/metabolism ; *Electron Transport ; Iron-Sulfur Proteins/metabolism ; Molecular Sequence Data ; Oxidoreductases/metabolism ; Phylogeny ; },
abstract = {Extremophilic organisms are adapted to harsh environmental conditions like high temperature, extremely acidic or alkaline pH, high salt, or a combination of those. With a few exceptions extremophilic bacteria are colonizing only moderately hot biotopes, whereas hyperthermophiles are found specifically among archaea (formerly 'archaebacteria') which can thrive at temperatures close to or even above the boiling point of water. It has been a challenging question whether the special properties of their proteins and membranes have been acquired by adaptation, or whether they might reflect early evolutionary states as suggested by their phylogenetic position at the lowest branches of the universal tree of life.},
}
@article {pmid9158771,
year = {1996},
author = {Martin, HH and König, H},
title = {beta-Lactamases are absent from Archaea (archaebacteria).},
journal = {Microbial drug resistance (Larchmont, N.Y.)},
volume = {2},
number = {2},
pages = {269-272},
doi = {10.1089/mdr.1996.2.269},
pmid = {9158771},
issn = {1076-6294},
mesh = {Archaea/*enzymology/genetics/ultrastructure ; Bacteria/metabolism ; Cell Membrane/chemistry/metabolism ; Cell Wall/metabolism ; Cephalosporins/metabolism ; Culture Media ; beta-Lactamases/*metabolism ; },
abstract = {beta-Lactamases, enzymes that hydrolyze and inactive beta-lactam antibiotics, are of widespread occurrence in Bacteria and are related to the metabolism of bacterial cell wall murein. So far, no information exists on beta-lactamases in Archaea, a separate domain of prokaryotes with diverse types of unique cell wall polymers. Different mesophilic methanogenic and extremely halophilic Archaea containing methanochondroitin, pseudomurein, or S-layer protein or glycoprotein cell walls, were tested for beta-lactamase activity with the chromogenic beta-lactam nitrocefin as substrate. Also tested were representative microbial Eucarya from algae, yeasts, and protozoa. No beta-lactamase activity was detected in any of the archaeal and eukaryotic organisms. This supports the view that beta-lactamases are restricted to the domain of Bacteria.},
}
@article {pmid8858586,
year = {1996},
author = {Wang, X and Lutkenhaus, J},
title = {FtsZ ring: the eubacterial division apparatus conserved in archaebacteria.},
journal = {Molecular microbiology},
volume = {21},
number = {2},
pages = {313-319},
doi = {10.1046/j.1365-2958.1996.6421360.x},
pmid = {8858586},
issn = {0950-382X},
support = {GM29764/GM/NIGMS NIH HHS/United States ; },
mesh = {Amino Acid Sequence ; Archaea/cytology/*genetics/*physiology ; Bacterial Proteins/*genetics/*physiology ; Base Sequence ; Cell Division/genetics/physiology ; Conserved Sequence ; *Cytoskeletal Proteins ; DNA, Bacterial/genetics ; Escherichia coli/genetics ; GTP Phosphohydrolases/genetics/physiology ; Halobacteriaceae/cytology/genetics/physiology ; Methanobacterium/cytology/genetics/physiology ; Molecular Sequence Data ; Sequence Homology, Amino Acid ; Species Specificity ; Tubulin/genetics/physiology ; },
abstract = {FtsZ is a tubulin-like protein that is essential for cell division in eubacteria. It functions by forming a ring at the division site that directs septation. The archaebacteria constitute a kingdom of life separate from eubacteria and eukaryotes. Like eubacteria, archaebacteria are prokaryotes, although they are phylogenetically closer to eukaryotes. Here it is shown that archaebacteria also possess FtsZ and that it is biochemically similar to eubacterial FtsZs. Significantly, FtsZ from the archaebacterium Haloferax volcanii is a GTPase that is localized to a ring that coincides with the division constriction. These results indicate that the FtsZ ring was part of the division apparatus of a common prokaryotic ancestor that was retained by both eubacteria and archaebacteria.},
}
@article {pmid8779604,
year = {1996},
author = {Ravot, G and Ollivier, B and Fardeau, ML and Patel, BK and Andrews, KT and Magot, M and Garcia, JL},
title = {L-alanine production from glucose fermentation by hyperthermophilic members of the domains bacteria and Archaea: a remnant of an ancestral metabolism?.},
journal = {Applied and environmental microbiology},
volume = {62},
number = {7},
pages = {2657-2659},
pmid = {8779604},
issn = {0099-2240},
mesh = {Alanine/*biosynthesis ; Archaea/classification/genetics/*metabolism ; Bacteria/classification/genetics/*metabolism ; Ecosystem ; Glucose/*metabolism ; Hot Temperature ; Molecular Sequence Data ; Phylogeny ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; },
abstract = {New members of the order Thermotogales were isolated from nonvolcanically heated geothermal environments, including oil fields and waters of the Great Artesian Basin of Australia, thereby extending their known habitats, previously recognized primarily as volcanic. The hyperthermophilic and thermophilic members of Thermotogales of volcanic origin, together with the recently described nonvolcanic species of this order and three new isolates described in this paper, were all found to produce L-alanine from glucose fermentation, in addition to acetate, lactate, CO2 and H2. L-alanine production from glucose is a trait in common with Pyrococcus furiosus and Thermococcus profundus. We propose that L-alanine production from sugar fermentation be regarded as an ancestral metabolic characteristic.},
}
@article {pmid8655531,
year = {1996},
author = {Ruggero, D and Londei, P},
title = {Differential antibiotic sensitivity determined by the large ribosomal subunit in thermophilic archaea.},
journal = {Journal of bacteriology},
volume = {178},
number = {11},
pages = {3396-3398},
pmid = {8655531},
issn = {0021-9193},
mesh = {Anti-Bacterial Agents/*pharmacology ; Archaea/*drug effects ; *Endoribonucleases ; Fungal Proteins/*pharmacology ; Paromomycin/*pharmacology ; Ribosomes/*drug effects ; Sulfolobus/drug effects ; },
abstract = {Hybrid ribosomes obtained by mixing the ribosomal subunits of the extremely thermophilic archaea Sulfolobus solfataricus and Desulfurococcus mobilis were tested for their sensitivity to selected antibiotics. It is shown that structural differences in the large ribosomal subunits determine qualitatively and quantitatively the patterns of response to alpha-sarcin and paromomycin in these species.},
}
@article {pmid8643567,
year = {1996},
author = {Southworth, MW and Kong, H and Kucera, RB and Ware, J and Jannasch, HW and Perler, FB},
title = {Cloning of thermostable DNA polymerases from hyperthermophilic marine Archaea with emphasis on Thermococcus sp. 9 degrees N-7 and mutations affecting 3'-5' exonuclease activity.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {93},
number = {11},
pages = {5281-5285},
pmid = {8643567},
issn = {0027-8424},
mesh = {Amino Acid Sequence ; Archaea/*enzymology ; Base Sequence ; Cloning, Molecular ; DNA-Directed DNA Polymerase/biosynthesis/isolation &amp; purification/*metabolism ; Enzyme Stability ; Escherichia coli ; Exodeoxyribonuclease V ; Exodeoxyribonucleases/biosynthesis/isolation &amp; purification/*metabolism ; Hot Temperature ; Kinetics ; Molecular Sequence Data ; Mutagenesis, Site-Directed ; Oligodeoxyribonucleotides ; Recombinant Proteins/biosynthesis/isolation &amp; purification/metabolism ; },
abstract = {Five extremely thermophilic Archaea from hydrothermal vents were isolated, and their DNA polymerases were cloned and expressed in Escherichia coli. Protein splicing elements (inteins) are present in many archaeal DNA polymerases, but only the DNA polymerase from strain GB-C contained an intein. Of the five cloned DNA polymerases, the Thermococcus sp. 9 degrees N-7 DNA polymerase was chosen for biochemical characterization. Thermococcus sp. 9 degrees N-7 DNA polymerase exhibited temperature-sensitive strand displacement activity and apparent Km values for DNA and dNTP similar to those of Thermococcus litoralis DNA polymerase. Six substitutions in the 3'-5' exonuclease motif I were constructed in an attempt to reduce the 3'-5' exonuclease activity of Thermococcus sp. 9 degrees N-7 DNA polymerase. Five mutants resulted in no detectable 3'-5' exonuclease activity, while one mutant (Glul43Asp) had <1% of wild-type activity.},
}
@article {pmid8639331,
year = {1996},
author = {Forterre, P and Bergerat, A and Lopez-Garcia, P},
title = {The unique DNA topology and DNA topoisomerases of hyperthermophilic archaea.},
journal = {FEMS microbiology reviews},
volume = {18},
number = {2-3},
pages = {237-248},
doi = {10.1111/j.1574-6976.1996.tb00240.x},
pmid = {8639331},
issn = {0168-6445},
mesh = {Archaea/enzymology/*genetics ; DNA Topoisomerases, Type I/*metabolism ; DNA Topoisomerases, Type II/*metabolism ; DNA, Bacterial/*analysis ; },
abstract = {Hyperthermophilic archaea exhibit a unique pattern of DNA topoisomerase activities. They have a peculiar enzyme, reverse gyrase, which introduces positive superturns into DNA at the expense of ATP. This enzyme has been found in all hyperthermophiles tested so far (including Bacteria) but never in mesophiles. Reverse gyrases are formed by the association of a helicase-like domain and a 5'-type 1 DNA topoisomerase. These two domains might be located on the same polypeptide. However, in the methanogenic archaeon Methanopyrus kandleri, the topoisomerase domain is divided between two subunits. Besides reverse gyrase, Archaea contain other type 1 DNA topoisomerases; in particular, M. kandleri harbors the only known procaryotic 3'-type 1 DNA topoisomerase (Topo V). Hyperthermophilic archaea also exhibit specific type II DNA topoisomerases (Topo II), i.e. whereas mesophilic Bacteria have a Topo II that produces negative supercoiling (DNA gyrase), the Topo II from Sulfolobus and Pyrococcus lack gyrase activity and are the smallest enzymes of this type known so far. This peculiar pattern of DNA topoisomerases in hyperthermophilic archaea is paralleled by a unique DNA topology, i.e. whereas DNA isolated from Bacteria and Eucarya is negatively supercoiled, plasmidic DNA from hyperthermophilic archaea are from relaxed to positively supercoiled. The possible evolutionary implications of these findings are discussed in this review. We speculate that gyrase activity in mesophiles and reverse gyrase activity in hyperthermophiles might have originated in the course of procaryote evolution to balance the effect of temperature changes on DNA structure.},
}
@article {pmid8639330,
year = {1996},
author = {Zillig, W and Prangishvilli, D and Schleper, C and Elferink, M and Holz, I and Albers, S and Janekovic, D and Götz, D},
title = {Viruses, plasmids and other genetic elements of thermophilic and hyperthermophilic Archaea.},
journal = {FEMS microbiology reviews},
volume = {18},
number = {2-3},
pages = {225-236},
doi = {10.1111/j.1574-6976.1996.tb00239.x},
pmid = {8639330},
issn = {0168-6445},
mesh = {Archaea/*genetics/*virology ; Genetic Vectors ; Phylogeny ; *Plasmids ; Viral Plaque Assay ; },
abstract = {We review and update the work on genetic elements, e.g., viruses and plasmids (exluding IS elements and transposons) in the kingdom Crenarchaeota (Thermoproteales and Sulfolobales) and the orders Thermococcales and Thermoplasmales in the kingdom Euryarchaeota of the archael domain, including unpublished data from our laboratory. The viruses of Crenarchaeota represent four novel virus families. The Fuselloviridae represented by SSVI of S. shibatae and relatives in other Sulfolobus strains have the form of a tailed spindle. The envelope is highly hydrophobic. The DNA is double-stranded and circular. Members of this group have also been found in Methanococcus and Haloarcula. The Lipothrivciridae (e.g., T TV1 to 3) have the form of flexible filaments. They have a core containing linear double-stranded DNA and DNA-binding proteins which is wrapped into a lipid membrane. The "Bacilloviridae" (e.g., TTV4 and SIRV) are stiff rods lacking this membrane, but also featuring linear double-stranded DNA and DNA-binding proteins. Both virus types carry on both ends structures involved in the attachment to receptors. Both types are represented in Thermoproteus and Sulfolobus. The droplet-formed novel Sulfolobus virus SNDV represents the "Guttaviridae" containing circular double-stranded DNA. Though head and tail viruses distantly resembling T phages or lambdoid phages were seen electronmicroscopically in solfataric water samples, no such virus has so far been isolated. SSV1 is temperate, TTV1 causes lysis after induction, the other viruses found so far exist in carrier states. The hosts of all but TTV1 survive virus production. We discuss the implications of the nature of these viruses for understanding virus evolution. The plasmids found so far range in size from 4.5 kb to about 40 kb. Most of them occur in high copy number, probably due to the way of their detection. Most are cryptic, pNOB8 is conjugative, the widespread pDL10 alleviates in an unknown way autotrophic growth of its host Desulfurolobus by sulfur reduction. The plasmid pTIK4 appears to encode a killer function. pNOB8 has been used as a vector for the transfer of the lac S (beta-galactosidase) gene into a mutant of S. solfataricus.},
}
@article {pmid8639328,
year = {1996},
author = {Grayling, RA and Sandman, K and Reeve, JN},
title = {Histones and chromatin structure in hyperthermophilic Archaea.},
journal = {FEMS microbiology reviews},
volume = {18},
number = {2-3},
pages = {203-213},
doi = {10.1111/j.1574-6976.1996.tb00237.x},
pmid = {8639328},
issn = {0168-6445},
support = {1RO1GM53185/GM/NIGMS NIH HHS/United States ; },
mesh = {Amino Acid Sequence ; Archaea/growth &amp; development/*metabolism ; Chromatin/*chemistry ; DNA/metabolism ; Histones/biosynthesis/*chemistry ; Molecular Sequence Data ; Structure-Activity Relationship ; },
abstract = {HMf is a histone from the hyperthermophile Methanothermus fervidus. It is the archetype and most studied member of a family of archaeal histones that have primary sequences and three-dimensional structures in common with the eukaryal nucleosome core histones and that bind and compact DNA molecules into nucleosome-like structures (NLS). HMf preparations are mixtures of two similar, small (approximately 7.5 kDa) polypeptides designated HMfA and HMfB that in vivo form both homodimers and heterodimers. HMfA synthesis predominates during exponential growth but the relative amount of HMfB increases as M. fervidus cells enter the stationary growth phase. Analyses of homogeneous preparations of recombinant (r) (HMfA)2 and (rHMfB)2 have demonstrated that these proteins have different DNA-binding and compaction properties in vitro, consistent with different roles in vivo for the (HMfA)2, (HMfB)2 and HMfA. HmfB dimers, and for the NLS that they form, in regulating gene expression and in genome compaction and stability.},
}
@article {pmid8639327,
year = {1996},
author = {Schäfer, G and Purschke, W and Schmidt, CL},
title = {On the origin of respiration: electron transport proteins from archaea to man.},
journal = {FEMS microbiology reviews},
volume = {18},
number = {2-3},
pages = {173-188},
doi = {10.1111/j.1574-6976.1996.tb00235.x},
pmid = {8639327},
issn = {0168-6445},
mesh = {Amino Acid Sequence ; Archaea/*metabolism ; Bacterial Proteins/*physiology ; Cytochrome a Group/physiology ; Electron Transport ; *Electron Transport Complex III ; Electron Transport Complex IV/physiology ; Humans ; Iron-Sulfur Proteins/physiology ; Molecular Sequence Data ; Structure-Activity Relationship ; },
abstract = {All aerobic organisms use the exergonic reduction of molecular oxygen to water as primary source of metabolic energy. This reaction is catalyzed by membrane residing terminal heme/Cu-oxidases which belong to a superfamily of widely varying structural complexity between mitochondrial and bacterial members of this family. Over the last few years, considerable information from this and other laboratories accumulated also on archaeal respiratory chains and their terminal oxidases. In the following, the molecular and catalytic properties of the latter are discussed and compared to those from bacteria and eucarya under the aspect of their energy conserving capabilities and their phylogenetic relations. The Rieske iron-sulfur proteins being important functional constituents of energy transducing respiratory complexes are included in this study. A number of essential conclusions can be drawn. (1) Like bacteria, archaea can also contain split respiratory chains with parallel expression of separate terminal oxidases. (2) The functional core of all oxidases is the highly conserved topological motif of subunit I consisting of at least 12 membrane spanning helices with the 6 histidine residues of the heme/Cu-binding centers in identical locations. (3) Some archaeal oxidases are organized in unusual supercomplexes with other cytochromes and Rieske [2Fe2S] proteins. These complexes are likely to function as proton pumps, whereas on a structural basis several subunit I equivalents alone are postulated to be unable to pump protons. (4) The genes of two archaeal Rieske proteins have been cloned from Sulfolobus; phylogenetically they are forming a separate archaeal branch and suggest the existence of an evolutionary ancestor preceding the split into the three urkingdoms. (5) Archaeal oxidase complexes may combine features of electron transport systems occurring exclusively as separate respiratory complexes in bacteria and eucarya. (6) As far back as the deepest branches of the phylogentic tree, terminal oxidases reveal a degree of complexity comparable to that found in higher organisms. (7) Sequence analysis suggests a monophyletic origin of terminal oxidases with an early split into two types found in archaea as well as bacteria. This view implies an origin of terminal oxidases prior to oxygenic photosynthesis in contrast to the widely accepted inverse hypothesis.},
}
@article {pmid8925906,
year = {1996},
author = {Kohlhoff, M and Dahm, A and Hensel, R},
title = {Tetrameric triosephosphate isomerase from hyperthermophilic Archaea.},
journal = {FEBS letters},
volume = {383},
number = {3},
pages = {245-250},
doi = {10.1016/0014-5793(96)00249-9},
pmid = {8925906},
issn = {0014-5793},
mesh = {Amino Acid Sequence ; Animals ; Archaea/*enzymology ; Base Sequence ; Chickens ; Chromatography ; Chromatography, Gel ; Chromatography, Ion Exchange ; Cloning, Molecular ; Durapatite ; Euryarchaeota/enzymology ; Genes, Bacterial ; Macromolecular Substances ; Methanobacterium/enzymology ; Models, Structural ; Molecular Sequence Data ; Molecular Weight ; Protein Structure, Secondary ; Recombinant Proteins/chemistry/isolation &amp; purification/metabolism ; Sequence Homology, Amino Acid ; Species Specificity ; Triose-Phosphate Isomerase/*chemistry/isolation &amp; purification/*metabolism ; Trypanosoma/enzymology ; Zea mays/enzymology ; },
abstract = {Triosephosphate isomerase (TIM) of the hyperthermophilic Archaea Pyrococcus woesei and Methanothermus fervidus have been purified to homogeneity. The enzymes from the two hyperthermophiles represent homo-tetramers of 100 kDa, contrary to all known bacterial and eukaryotic TIMs, which are dimers of 48-60 kDa. Molecular size determination of the TIM from the mesophilic methanogen Methanobacterium bryantii yielded the usual molecular mass of only 57 kDa, indicating that the tetrameric aggregation state does not represent an archaeal feature but rather correlates with thermoadaptation. A similar preference for higher protein aggregates in hyperthermophilic Archaea has previously been demonstrated for 3-phosphoglycerate kinases. The gene of the P. woesei TIM was cloned and sequenced. The archaeal TIM proved to be homologous to its bacterial and eukaryotic pendants. Most strikingly, the deduced protein sequence comprises only 224 residues and thus represents the shortest TIM sequence known as yet. Taking the three-dimensional structure of the eucaryal TIM as a basis, from the shortenings of the chain considerable rearrangements at the bottom of the alpha/beta barrel and at its functionally inactive flank are expected, which are interpreted in terms of the formation of new subunit contacts.},
}
@article {pmid8614627,
year = {1996},
author = {Haas, ES and Armbruster, DW and Vucson, BM and Daniels, CJ and Brown, JW},
title = {Comparative analysis of ribonuclease P RNA structure in Archaea.},
journal = {Nucleic acids research},
volume = {24},
number = {7},
pages = {1252-1259},
pmid = {8614627},
issn = {0305-1048},
support = {1-R29-GM52894-01/GM/NIGMS NIH HHS/United States ; R01-GM48665-03/GM/NIGMS NIH HHS/United States ; },
mesh = {Archaea/*genetics ; Base Sequence ; Cloning, Molecular ; Endoribonucleases/*genetics ; Molecular Sequence Data ; Nucleic Acid Conformation ; Phylogeny ; RNA, Bacterial/*genetics ; RNA, Catalytic/*genetics ; Ribonuclease P ; Sequence Homology, Nucleic Acid ; },
abstract = {Although the structure of the catalytic RNA component of ribonuclease P has been well characterized in Bacteria, it has been little studied in other organisms, such as the Archaea. We have determined the sequences encoding RNase P RNA in eight euryarchaeal species: Halococcus morrhuae, Natronobacterium gregoryi, Halobacterium cutirubrum, Halobacteriurn trapanicum, Methanobacterium thermoautotrophicum strains deltaH and Marburg, Methanothermus fervidus and Thermococcus celer strain AL-1. On the basis of these and previously available sequences from Sulfolobus acidocaldarius, Haloferax volcanii and Methanosarcina barkeri the secondary structure of RNase P RNA in Archaea has been analyzed by phylogenetic comparative analysis. The archaeal RNAs are similar in both primary and secondary structure to bacterial RNase P RNAs, but unlike their bacterial counterparts these archaeal RNase P RNAs are not by themselves catalytically proficient in vitro.},
}
@article {pmid8626418,
year = {1996},
author = {O'Connor, KA and McBride, MJ and West, M and Yu, H and Trinh, L and Yuan, K and Lee, T and Zusman, DR},
title = {Photolyase of Myxococcus xanthus, a Gram-negative eubacterium, is more similar to photolyases found in Archaea and "higher" eukaryotes than to photolyases of other eubacteria.},
journal = {The Journal of biological chemistry},
volume = {271},
number = {11},
pages = {6252-6259},
doi = {10.1074/jbc.271.11.6252},
pmid = {8626418},
issn = {0021-9258},
support = {GM20509/GM/NIGMS NIH HHS/United States ; },
mesh = {Amino Acid Sequence ; Animals ; Archaea/enzymology/genetics ; Base Sequence ; Cloning, Molecular ; DNA Primers/genetics ; DNA, Bacterial/genetics ; Deoxyribodipyrimidine Photo-Lyase/*genetics ; Eukaryotic Cells/enzymology ; Genes, Bacterial ; Molecular Sequence Data ; Myxococcus xanthus/*enzymology/*genetics ; Open Reading Frames ; Plasmids/genetics ; Prokaryotic Cells/enzymology ; Sequence Homology, Amino Acid ; Sequence Homology, Nucleic Acid ; },
abstract = {We report the identification of the gene encoding a DNA photolyase (phrA) from the Gram-negative eubacterium Myxococcus xanthus. The deduced amino acid sequence of M. xanthus photolyase indicates that the protein contains 401 amino acids (Mr 45,071). By comparison of the amino acid and DNA sequences with those of other known photolyases, it has been found that it is more similar to the deduced amino acid sequences of the photolyases of "higher" eukaryotes than to the photolyases of other eubacteria. Recombinant plasmids carrying M. xanthus phrA rescue the photoreactivation activity of an irradiated strain of Escherichia coli with a deletion in phrA. This rescue is light-dependent.},
}
@article {pmid8704656,
year = {1996},
author = {Morvan, B and Bonnemoy, F and Fonty, G and Gouet, P},
title = {Quantitative determination of H2-utilizing acetogenic and sulfate-reducing bacteria and methanogenic archaea from digestive tract of different mammals.},
journal = {Current microbiology},
volume = {32},
number = {3},
pages = {129-133},
doi = {10.1007/s002849900023},
pmid = {8704656},
issn = {0343-8651},
mesh = {Acetates/*metabolism ; Animals ; Bacteria/*isolation &amp; purification/metabolism ; Cattle ; Cellulose/metabolism ; Euryarchaeota/*isolation &amp; purification/metabolism ; Horses/microbiology ; Hydrogen/*metabolism ; Intestines/*microbiology ; Sheep/microbiology ; Sulfates/*metabolism ; },
abstract = {Total number of bacteria, cellulolytic bacteria, and H2-utilizing microbial populations (methanogenic archaea, acetogenic and sulfate-reducing bacteria) were enumerated in fresh rumen samples from sheep, cattle, buffaloes, deer, llamas, and caecal samples from horses. Methanogens and sulfate reducers were found in all samples, whereas acetogenes were not detected in some samples of each animal. Archaea methanogens were the largest H2-utilizing populations in all animals, and a correlation was observed between the numbers of methanogens and those of cellulolytic microorganisms. Higher counts of acetogens were found in horses and llamas (1 x 10(4) and 4 x 10(4) cells ml-1 respectively).},
}
@article {pmid8626070,
year = {1996},
author = {Yang, Y and Fox, GE},
title = {An Archaea 5S rRNA analog is stably expressed in Escherichia coli.},
journal = {Gene},
volume = {168},
number = {1},
pages = {81-85},
doi = {10.1016/0378-1119(95)00683-4},
pmid = {8626070},
issn = {0378-1119},
mesh = {Base Sequence ; Blotting, Northern ; DNA Probes/chemistry ; Electrophoresis, Polyacrylamide Gel ; Environmental Monitoring/methods ; Escherichia coli/*genetics ; Gene Expression Regulation, Bacterial/genetics ; Genetic Engineering ; Genetic Vectors/genetics ; Halobacteriaceae/chemistry/*genetics ; Molecular Sequence Data ; Mutagenesis, Site-Directed/genetics ; Nucleic Acid Conformation ; Phylogeny ; RNA Probes/genetics ; RNA, Bacterial/biosynthesis/*genetics ; RNA, Ribosomal, 5S/biosynthesis/*genetics ; Ribosomes/metabolism ; Transformation, Genetic/genetics ; },
abstract = {Mini-genes for 5S-like rRNA were constructed. These genes had a sequence which largely resembles that of the naturally occurring 5S rRNA of a bacterium, Halococcus morrhuae, which phylogenetically belongs to the Archaea. Plasmids carrying the mini-genes were transformed into Escherichia coli (Ec). Ribosomal incorporation was not a prerequisite for stable accumulation of the RNA product. However, only those constructs with a well-base-paired helix I accumulated RNA product. This result strongly implies that this aspect of the structure is likely to be an important condition for stabilizing 5S rRNA-like products. The results are consistent with our current understanding of 5S rRNA processing in Ec. When used in conjunction with rRNA probe technology, the resulting chimeric RNA may be useful as a monitoring tool for genetically engineered microorganisms or naturally occurring organisms that are released into the environment.},
}
@article {pmid8919875,
year = {1996},
author = {Ouzounis, CA and Kyrpides, NC},
title = {Parallel origins of the nucleosome core and eukaryotic transcription from Archaea.},
journal = {Journal of molecular evolution},
volume = {42},
number = {2},
pages = {234-239},
pmid = {8919875},
issn = {0022-2844},
mesh = {Amino Acid Sequence ; Animals ; Archaea/*genetics ; Eukaryotic Cells ; Evolution, Molecular ; Histones/*genetics ; Humans ; Molecular Sequence Data ; Nucleosomes/*genetics ; Sequence Homology, Amino Acid ; Transcription, Genetic ; },
abstract = {Computational sequence analysis of 10 available archaean histone-like proteins has shown that this family is not only divergently related to the eukaryotic core histones H2A/B, H3, and H4, but also to the central domain of subunits A and C of the CCAAT-binding factor (CBF), a transcription factor associated with eukaryotic promoters. Despite the low sequence identity, it is unambiguously shown that the core histone fold shares a common evolutionary history. Archaean histones and the two CBF families show a remarkable variability in contrast to eukaryotic core histones. Conserved residues shared between families are identified, possibly being responsible for the functional versatility of the core histone fold. The H4 subfamily is most similar to archaean proteins and may be the progenitor of the other core histones in eukaryotes. While it is not clear whether archaean histones are more actively involved in transcription regulation, the present observations link two processes, nucleosomal packing and transcription in a unique way. Both these processes, evidently hybrid in Archaea, have originated before the ermergence of the eukaryotic cell.},
}
@article {pmid8867896,
year = {1996},
author = {Masullo, M and Raimo, G and Dello Russo, A and Bocchini, V and Bannister, JV},
title = {Purification and characterization of NADH oxidase from the archaea Sulfolobus acidocaldarius and Sulfolobus solfataricus.},
journal = {Biotechnology and applied biochemistry},
volume = {23},
number = {1},
pages = {47-54},
pmid = {8867896},
issn = {0885-4513},
mesh = {Amino Acid Sequence ; Enzyme Stability ; Guanidine ; Guanidines ; Hot Temperature ; Kinetics ; Molecular Sequence Data ; Molecular Weight ; Multienzyme Complexes/chemistry/*isolation &amp; purification ; NADH, NADPH Oxidoreductases/chemistry/*isolation &amp; purification ; Protein Denaturation ; Solvents ; Spectrophotometry ; Sulfolobus/*enzymology ; Sulfolobus acidocaldarius/*enzymology ; Urea ; },
abstract = {The enzyme NADH oxidase (EC 1.6.99.3) has been isolated from the two thermoacidophilic archaea Sulfolobus acidocaldarius and Sulfolobus solfataricus and characterized. In both organisms the enzyme oxidizes specifically beta-NADH in the presence of molecular oxygen and requires the presence of a flavin cofactor, showing a high specificity for FAD. A stoicheiometric amount of hydrogen peroxide to NADH is formed as the end product of the reaction, indicating that both enzymes are two-electron donors. The purified enzymes exhibit quite different molecular properties. S. acidocaldarius NADH oxidase is a monomeric protein with an estimated molecular mass of about 27 kDa, whereas S. solfataricus NADH oxidase is a dimeric protein with a molecular mass of 35 kDa per subunit; S. solfataricus NADH oxidase is purified as an FAD-containing protein, whereas S. acidocaldarius NADH oxidase does not contain a flavin molecule. Furthermore, a comparison of the N-terminal amino acid sequence shows no similarities either between the two proteins or to any other NADH oxidases. Both enzymes are essentially thermophilic. In the temperature range 20-80 degrees C, the energy of activation is almost the same for both activities, suggesting that similar energetic parameters are required. Also both oxidases display a great stability to heat. The half-life of heat inactivation is about 180 min at 90 degrees C for S. acidocaldarius NADH oxidase and 77 min at 98 degrees C for the S. solfataricus enzyme. The activity of the two enzymes is inhibited by urea and guanidine and are regulated very differently by several organic solvents.},
}
@article {pmid8550533,
year = {1996},
author = {Nyce, GW and White, RH},
title = {dTMP biosynthesis in Archaea.},
journal = {Journal of bacteriology},
volume = {178},
number = {3},
pages = {914-916},
pmid = {8550533},
issn = {0021-9193},
mesh = {Deoxyuracil Nucleotides/metabolism ; Methanosarcina/*metabolism ; Sulfolobus/*metabolism ; Thymidine Monophosphate/*biosynthesis ; },
abstract = {The biosynthesis of dTMP has been studied in cell extracts of two different members of the domain Archaea, Methanosarcina thermophila and Sulfolobus solfataricus. In M. thermophila, the dTMP was formed from dUMP and [methylene-2H2]-5,10-methylenetetrahydrosarcinapterin generated in situ from added [methylene-2H2] formaldehyde and the tetrahydrosarcinapterin present in the cell extract. In S. solfataricus, the 5,10-methyl-enetetrahydro derivative of a synthetic fragment of sulfopterin, the modified folate present in these cells, served as the C1 donor. These data indicate that the Archaea thymidylate synthases carry out the same basic reaction which occurs in other organisms but use the 5,10-methylenetetrahydro derivatives of modified folates as C1 donors.},
}
@article {pmid8550530,
year = {1996},
author = {Faguy, DM and Bayley, DP and Kostyukova, AS and Thomas, NA and Jarrell, KF},
title = {Isolation and characterization of flagella and flagellin proteins from the Thermoacidophilic archaea Thermoplasma volcanium and Sulfolobus shibatae.},
journal = {Journal of bacteriology},
volume = {178},
number = {3},
pages = {902-905},
pmid = {8550530},
issn = {0021-9193},
mesh = {Amino Acid Sequence ; Flagella/*chemistry ; Flagellin/chemistry/*isolation &amp; purification ; Molecular Sequence Data ; Sulfolobus/*chemistry ; Thermoplasma/*chemistry ; },
abstract = {Isolated flagellar filaments of Sulfolobus shibatae were 15 nm in diameter, and they were composed of two major flagellins which have M(r)s of 31,000 and 33,000 and which stained positively for glycoprotein. The flagellar filaments of Thermoplasma volcanium were 12 nm in diameter and were composed of one major flagellin which has an M(r) of 41,000 and which also stained positively for glycoprotein. N-terminal amino acid sequencing indicated that 18 of the N-terminal 20 amino acid positions of the 41-kDa flagellin of T. volcanium were identical to those of the Methanococcus voltae 31-kDa flagellin. Both flagellins of S. shibatae had identical amino acid sequences for at least 23 of the N-terminal positions. This sequence was least similar to any of the available archaeal flagellin sequences, consistent with the phylogenetic distance of S. shibatae from the other archaea studied.},
}
@article {pmid8550513,
year = {1996},
author = {Heider, J and Mai, X and Adams, MW},
title = {Characterization of 2-ketoisovalerate ferredoxin oxidoreductase, a new and reversible coenzyme A-dependent enzyme involved in peptide fermentation by hyperthermophilic archaea.},
journal = {Journal of bacteriology},
volume = {178},
number = {3},
pages = {780-787},
pmid = {8550513},
issn = {0021-9193},
mesh = {Amino Acid Sequence ; Archaea/*metabolism ; Coenzyme A/*physiology ; Electron Spin Resonance Spectroscopy ; *Fermentation ; Hemiterpenes ; Keto Acids/*metabolism ; Molecular Sequence Data ; Oxidoreductases/chemistry/isolation &amp; purification/*metabolism ; Peptides/*metabolism ; },
abstract = {Cell extracts of the proteolytic and hyperthermophilic archaea Thermococcus litoralis, Thermococcus sp. strain ES-1, Pyrococcus furiosus, and Pyrococcus sp. strain ES-4 contain an enzyme which catalyzes the coenzyme A-dependent oxidation of branched-chain 2-ketoacids coupled to the reduction of viologen dyes or ferredoxin. This enzyme, termed VOR (for keto-valine-ferredoxin oxidoreductase), has been purified from all four organisms. All four VORs comprise four different subunits and show amino-terminal sequence homology. T. litoralis VOR has an M(r) of ca. 230,000, with subunit M(r) values of 47,000 (alpha), 34,000 (beta), 23,000 (gamma), and 13,000 (delta). It contains about 11 iron and 12 acid-labile sulfide atoms and 13 cysteine residues per heterotetramer (alpha beta gamma delta), but thiamine pyrophosphate, which is required for catalytic activity, was lost during purification. The most efficient substrates (kcat/Km > 1.0 microM-1 s-1; Km < 100 microM) for the enzyme were the 2-ketoacid derivatives of valine, leucine, isoleucine, and methionine, while pyruvate and aryl pyruvates were very poor substrates (kcat/Km < 0.2 microM-1 s-1) and 2-ketoglutarate was not utilized. T. litoralis VOR also functioned as a 2-ketoisovalerate synthase at 85 degrees C, producing 2-ketoisovalerate and coenzyme A from isobutyryl-coenzyme A (apparent Km, 250 microM) and CO2 (apparent Km, 48 mM) with reduced viologen as the electron donor. The rate of 2-ketoisovalerate synthesis was about 5% of the rate of 2-ketoisovalerate oxidation. The optimum pH for both reactions was 7.0. A mechanism for 2-ketoisovalerate oxidation based on data from substrate-induced electron paramagnetic resonance spectra is proposed, and the physiological role of VOR is discussed.},
}
@article {pmid8547344,
year = {1996},
author = {Piller, K and Daniel, RM and Petach, HH},
title = {Properties and stabilization of an extracellular alpha-glucosidase from the extremely thermophilic archaebacteria Thermococcus strain AN1: enzyme activity at 130 degrees C.},
journal = {Biochimica et biophysica acta},
volume = {1292},
number = {1},
pages = {197-205},
doi = {10.1016/0167-4838(95)00203-0},
pmid = {8547344},
issn = {0006-3002},
mesh = {Archaea/*enzymology ; Carbohydrate Metabolism ; Carbohydrate Sequence ; Dithiothreitol/pharmacology ; Enzyme Activation ; Enzyme Inhibitors/pharmacology ; Enzyme Stability ; Hot Temperature ; Hydrogen-Ion Concentration ; Kinetics ; Metals/pharmacology ; Molecular Sequence Data ; Molecular Weight ; Protein Conformation ; Protein Denaturation ; Sodium Dodecyl Sulfate/pharmacology ; Sorbitol/pharmacology ; Substrate Specificity ; Urea/pharmacology ; alpha-Glucosidases/chemistry/isolation &amp; purification/*metabolism ; },
abstract = {An extracellular alpha-glucosidase from the thermophilic archaebacterium Thermococcus strain AN1 was purified 875-fold in five steps (Hiload Q-Sepharose, phenyl Sepharose, HPHT-hydroxyapatite, gel filtration and Mono Q chromatography) with a yield of 4%. It is a monomer with a molecular mass of about 60 kDa and a pI around 5. At 98 degrees C, the purified enzyme in buffer has a half-life around 35 min, which is increased to around 215 min in presence of 1% (w/v) dithiothreitol and 1% (w/v) BSA. Dithiothreitol (1%, w/v) and BSA (0.4%, w/v) also substantially increase the enzyme activity. The Km at 75 degrees C is 0.41 mM with pNP-alpha-D-glucopyranoside as substrate. The substrate preference of the enzyme is: pNP-alpha-D-glucoside > nigerose > panose > palatinose > isomaltose > maltose and turanose. No activity was found against starch, pullulan, amylose, maltotriose, maltotetraose, isomaltotriose, cellobiose and beta-gentiobiose. A variety of techniques including immobolization (e.g., on epoxy and glass beads), chemical modification (cross- and cocross-linking) and the use of additives (including polyhydroxylic molecules, BSA, salts, etc.) were applied to enhance stability at temperatures above 100 degrees C. The half-life could be increased from about 4 min at 100 degrees C to 30-60 min at 130 degrees C in presence of 90% (w/v) sorbitol, 1% (w/v) dithiothreitol and 1% (w/v) BSA, and by cross-linking with BSA in the presence of 90% (w/v) sorbitol. The stabilized enzyme showed good activity at 130 degrees C.},
}
@article {pmid8791625,
year = {1996},
author = {Adams, MW and Kletzin, A},
title = {Oxidoreductase-type enzymes and redox proteins involved in fermentative metabolisms of hyperthermophilic Archaea.},
journal = {Advances in protein chemistry},
volume = {48},
number = {},
pages = {101-180},
doi = {10.1016/s0065-3233(08)60362-9},
pmid = {8791625},
issn = {0065-3233},
mesh = {Amino Acid Sequence ; Archaea/*enzymology ; Bacterial Proteins/chemistry/genetics/*metabolism ; *Fermentation ; Hot Temperature ; Molecular Sequence Data ; Oxidoreductases/chemistry/genetics/*metabolism ; Phylogeny ; },
}
@article {pmid8637606,
year = {1996},
author = {Mayer, F and Hoppert, M},
title = {Functional compartmentalization in bacteria and archaea. A hypothetical interface between cytoplasmic membrane and cytoplasm.},
journal = {Die Naturwissenschaften},
volume = {83},
number = {1},
pages = {36-39},
pmid = {8637606},
issn = {0028-1042},
mesh = {Archaea/*physiology/*ultrastructure ; Bacteria/*ultrastructure ; *Bacterial Physiological Phenomena ; Bacterial Proteins/metabolism ; Cell Membrane/physiology/ultrastructure ; Cytoplasm/physiology/ultrastructure ; Micelles ; Models, Biological ; Species Specificity ; Water ; },
}
@article {pmid8825096,
year = {1995},
author = {van de Vossenberg, JL and Ubbink-Kok, T and Elferink, MG and Driessen, AJ and Konings, WN},
title = {Ion permeability of the cytoplasmic membrane limits the maximum growth temperature of bacteria and archaea.},
journal = {Molecular microbiology},
volume = {18},
number = {5},
pages = {925-932},
doi = {10.1111/j.1365-2958.1995.18050925.x},
pmid = {8825096},
issn = {0950-382X},
mesh = {Archaea/*growth &amp; development/metabolism ; Bacteria/*growth &amp; development/metabolism ; *Cell Membrane Permeability ; Cytoplasm/*metabolism ; Ion Transport ; Liposomes ; Membrane Lipids/metabolism ; Protons ; Sodium/metabolism ; Temperature ; },
abstract = {Protons and sodium ions are the most commonly used coupling ions in energy transduction in bacteria and archaea. At their growth temperature, the permeability of the cytoplasmic membrane of thermophilic bacteria to protons is high compared with that of sodium ions. In some thermophiles, sodium is the sole energy-coupling ion. To test whether sodium is the preferred coupling ion at high temperatures, the proton- and sodium permeability was determined in liposomes prepared from lipids isolated from various bacterial and archaeal species that differ in their optimal growth temperature. The proton permeability increased with the temperature and was comparable for most species at their respective growth temperatures. Liposomes of thermophilic bacteria are an exception in the sense that the proton permeability is already high at the growth temperature. In all liposomes, the sodium permeability was lower than the proton permeability and increased with the temperature. The results suggest that the proton permeability of the cytoplasmic membrane is an important parameter in determining the maximum growth temperature.},
}
@article {pmid8522509,
year = {1995},
author = {Schleper, C and Puehler, G and Holz, I and Gambacorta, A and Janekovic, D and Santarius, U and Klenk, HP and Zillig, W},
title = {Picrophilus gen. nov., fam. nov.: a novel aerobic, heterotrophic, thermoacidophilic genus and family comprising archaea capable of growth around pH 0.},
journal = {Journal of bacteriology},
volume = {177},
number = {24},
pages = {7050-7059},
pmid = {8522509},
issn = {0021-9193},
mesh = {Archaea/*classification/genetics/growth &amp; development/isolation &amp; purification ; Base Sequence ; Hydrogen-Ion Concentration ; Japan ; Molecular Sequence Data ; Phylogeny ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Two species belonging to a novel genus of archaea, designated Picrophilus oshimae and Picrophilus torridus, have been isolated from two different solfataric locations in northern Japan. One habitat harboring both organisms was a dry, extremely acidic soil (pH < 0.5) that was heated by solfataric gases to about 55 degrees C. In the laboratory both species grew heterotrophically on yeast extract and poorly on tryptone under aerobic conditions at temperatures between 45 and 65 degrees C; they grew optimally at 60 degrees C. The pH optimum was 0.7, but growth occurred even around pH 0. Under optimal conditions, the generation time was about 6 h, yielding densities of up to 10(10) cells per ml. The cells were surrounded by a highly filigreed regular tetragonal S-layer, and the core lipids of the membrane were mainly bis-phytanyltetraethers. The 16S rRNA sequences of the two species were about 3% different. The complete 16S rRNA sequence of P. oshimae was 9.3% different from that of the closest relative, Thermoplasma acidophilum. The morphology and physiological properties of the two species characterize Picrophilus as a novel genus that is a member of a novel family within the order Thermoplasmales.},
}
@article {pmid7489922,
year = {1995},
author = {Mayerhofer, LE and Conway de Macario, E and Macario, AJ},
title = {Conservation and variability in Archaea: protein antigens with tandem repeats encoded by a cluster of genes with common motifs in Methanosarcina mazei S-6.},
journal = {Gene},
volume = {165},
number = {1},
pages = {87-91},
doi = {10.1016/0378-1119(95)00524-a},
pmid = {7489922},
issn = {0378-1119},
mesh = {Amino Acid Sequence ; Antigens, Bacterial/*genetics ; Base Sequence ; Conserved Sequence ; Methanosarcina/*genetics/metabolism ; Molecular Sequence Data ; Multigene Family ; Open Reading Frames/*genetics ; Repetitive Sequences, Nucleic Acid ; Sequence Alignment ; },
abstract = {Three open reading frames, orf492, orf375 and orf783, were identified in a 5.9-kb DNA fragment from the genome of Methanosarcina mazei S-6 that code for proteins recognized by antibodies against cell-surface antigens. The deduced amino-acid (aa) sequences of orfs492 and 375, i.e., ORF492 and ORF375, contain seven and four copies of an approx. 42-aa repeat, respectively. The aa sequence of ORF783 contains nine copies of an approx. 85-aa repeat, one of which is also present once in each of the first two ORFs. The organization of the repeats is similar to that of some Gram+ cell-wall-associated proteins. Comparative analyses of aa sequences, compositions and hydropathy profiles of the archaeal ORFs showed similarity with surface (S-) layer and outer-membrane proteins of Bacteria and Archaea.},
}
@article {pmid8721997,
year = {1995},
author = {Potter, S and Durovic, P and Russell, A and Wang, X and de Jong-Wong, D and Dennis, PP},
title = {Preribosomal RNA processing in archaea: characterization of the RNP endonuclease mediated processing of precursor 16S rRNA in the thermoacidophile Sulfolobus acidocaldarius.},
journal = {Biochemistry and cell biology = Biochimie et biologie cellulaire},
volume = {73},
number = {11-12},
pages = {813-823},
doi = {10.1139/o95-089},
pmid = {8721997},
issn = {0829-8211},
mesh = {Base Sequence ; Endonucleases/*metabolism ; Molecular Sequence Data ; RNA Precursors/*genetics ; *RNA Processing, Post-Transcriptional ; RNA, Bacterial/*genetics ; RNA, Ribosomal, 16S/*genetics ; Ribonucleoproteins/*metabolism ; Sulfolobus acidocaldarius/*genetics ; },
abstract = {The hyperthermophilic archaeon Sulfolobus acidocaldarius uses a novel RNA-containing endonuclease to excise and mature 16S rRNA from the precursor (pre) rRNA transcript. A cell-free processing system has been developed using an in vitro transcribed RNA substrate containing the entire 144 nucleotide 5' external transcribed spacer (5'ETS) and the first 72 nucleotides of 16S rRNA. The cell-free extract cleaves in the 5'ETS at positions -99, -31, and +1 (i.e., the 5'ETS-16S junction). These positions are at or near the positions cleaved in vivo during processing of the pre rRNA transcript. The processing activity has been purified between 100 and 200-fold and appears to contain five or six polypeptide components and perhaps as many as 10 different small RNA components. Using combined reverse transcription-PCR amplification, full or partial cDNA copies of two of the RNA components have been obtained. One of the RNAs exhibits sequence and structural similarities to eukaryotic U3 snoRNA. The processing activity has been shown to be inactivated by micrococcal nuclease. It can be reactivated by reconstituting using bulk RNA from S.acidocaldarius but not bulk RNA from distantly related organisms. The activity is also abolished by RNase H digestion in the presence of oligonucleotides complementary to the U3-like RNA. These results demonstrate that the U3-like RNA is an essential component of the pre rRNA processing RNP endonuclease. Furthermore, this RNP endonuclease is not a derived eukaryotic feature, instead its existence predates the divergence of archaea and eukaryotes.},
}
@article {pmid7479025,
year = {1995},
author = {Gohl, HP and Gröndahl, B and Thomm, M},
title = {Promoter recognition in archaea is mediated by transcription factors: identification of transcription factor aTFB from Methanococcus thermolithotrophicus as archaeal TATA-binding protein.},
journal = {Nucleic acids research},
volume = {23},
number = {19},
pages = {3837-3841},
pmid = {7479025},
issn = {0305-1048},
mesh = {Adenoviridae/genetics ; *Archaeal Proteins ; Base Sequence ; Binding Sites ; DNA-Binding Proteins/*metabolism ; Methanococcus/*chemistry ; Molecular Sequence Data ; *Promoter Regions, Genetic ; RNA, Transfer, Val/genetics ; *TATA Box ; TATA-Box Binding Protein ; Templates, Genetic ; Transcription Factors/*metabolism ; },
abstract = {At least two transcription factors, aTFB and aTFA, are required for accurate and faithful in vitro transcription of homologous templates in cell-free extracts from the methanogenic Archaeon Methanococcus thermolithotrophicus. We have recently shown that the function of aTFB can be replaced by eucaryal TATA-binding proteins. Here we demonstrate using template commitment experiments that promoter recognition in an Archaeon is mediated by transcription factors. The archaeal TATA box was identified as recognition site for binding of aTFB by gel shift analyses. aTFB binds also to the TATA box of adenovirus 2 major late promoter suggesting homology of eucaryal and archaeal TATA boxes. Our analyses provide evidence for a common molecular mechanism of transcription initiation by eucaryal RNA polymerases and archaeal RNA polymerase. They indicate also an evolutionary homology for aTFB and TBP.},
}
@article {pmid7588769,
year = {1995},
author = {Klein, AR and Hartmann, GC and Thauer, RK},
title = {Hydrogen isotope effects in the reactions catalyzed by H2-forming N5,N10-methylenetetrahydromethanopterin dehydrogenase from methanogenic Archaea.},
journal = {European journal of biochemistry},
volume = {233},
number = {1},
pages = {372-376},
doi = {10.1111/j.1432-1033.1995.372_1.x},
pmid = {7588769},
issn = {0014-2956},
mesh = {Deuterium ; Euryarchaeota/*enzymology ; Hydrogen ; Hydrogen-Ion Concentration ; Kinetics ; Methanobacterium/enzymology ; Methanococcus/enzymology ; Oxidoreductases Acting on CH-NH Group Donors/*metabolism ; Protons ; Pterins/chemistry/metabolism ; },
abstract = {H2-forming N5,N10-methylenetetrahydromethanopterin dehydrogenase from methanogenic Archaea, which is a novel hydrogenase containing neither nickel nor iron-sulfur clusters, catalyzes the reversible reduction of N5,N10-methenyltetrahydomethanopterin (CH identical to H4MPT+) with H2 to N5,N10-methylenetetrahydromethanopterin (CH2 = H4MPT) and a proton (delta G degree' = -5.5 kJ/mol). The enzyme also catalyzes a CH identical to H4MPT(+)-dependent H2/H+ exchange. We report here on kinetic deuterium isotope effects in these reactions. When CH identical to H4MPT+ reduction was performed with D2 instead of H2, Vmax and the Km did not change. A primary isotope effect of 1 was found at all pH and temperatures tested and independent of whether H2O or D2O was the solvent. The findings indicate that a step other than the activation of H2 was rate-determining in CH identical to H4MPT+ reduction with H2. This was substantiated by the observation that also the CH identical to H4MPT(+)-dependent H2/H+ exchange reaction did not exhibit an appreciable deuterium isotope effect. Vmax for CH2 = H4MPT dehydrogenation to CH identical to H4MPT+ and H2 was only 2-3 times higher than for CD2 = H4MPT dehydrogenation to CD identical to H4MPT+ and HD. Such a small primary isotope effect indicates that the breakage of the C-H bond in the methylene group of CH2 = H4MPT was only rate-limiting when hydrogen was substituted by a deuterium.},
}
@article {pmid7588750,
year = {1995},
author = {Hess, D and Krüger, K and Knappik, A and Palm, P and Hensel, R},
title = {Dimeric 3-phosphoglycerate kinases from hyperthermophilic Archaea. Cloning, sequencing and expression of the 3-phosphoglycerate kinase gene of Pyrococcus woesei in Escherichia coli and characterization of the protein. Structural and functional comparison with the 3-phosphoglycerate kinase of Methanothermus fervidus.},
journal = {European journal of biochemistry},
volume = {233},
number = {1},
pages = {227-237},
doi = {10.1111/j.1432-1033.1995.227_1.x},
pmid = {7588750},
issn = {0014-2956},
mesh = {Amino Acid Sequence ; Archaea/*enzymology/*genetics ; Base Sequence ; Binding Sites ; Cloning, Molecular ; DNA Primers/genetics ; DNA, Bacterial/genetics ; Escherichia coli/genetics ; Euryarchaeota/*enzymology/*genetics ; Gene Expression ; *Genes, Bacterial ; Kinetics ; Molecular Sequence Data ; Molecular Structure ; Molecular Weight ; Phosphoglycerate Kinase/chemistry/*genetics/metabolism ; Phylogeny ; Protein Conformation ; Restriction Mapping ; Sequence Homology, Amino Acid ; },
abstract = {The gene coding for the 3-phosphoglycerate kinase (EC 2.7.2.3) of Pyrococcus woesei was cloned and sequenced. The gene sequence comprises 1230 bp coding for a polypeptide with the theoretical M(r) of 46,195. The deduced protein sequence exhibits a high similarity (46.1% and 46.6% identity) to the other known archaeal 3-phosphoglycerate kinases of Methanobacterium bryantii and Methanothermus fervidus [Fabry, S., Heppner, P., Dietmaier, W. &amp; Hensel, R. (1990) Gene 91, 19-25]. By comparing the 3-phosphoglycerate kinase sequences of the mesophilic and the two thermophilic Archaea, trends in thermoadaptation were confirmed that could be deduced from comparisons of glyceraldehyde-3-phosphate dehydrogenase sequences from the same organisms [Zwickl, P., Fabry, S., Bogedain, C., Haas, A. &amp; Hensel, R. (1990) J. Bacteriol. 172, 4329-4338]. With increasing temperature the average hydrophobicity and the portion of aromatic residues increases, whereas the chain flexibility as well as the content in chemically labile residues (Asn, Cys) decreases. To study the phenotypic properties of the 3-phosphoglycerate kinases from thermophilic Archaea in more detail, the 3-phosphoglycerate kinase genes from P. woesei and M. fervidus were expressed in Escherichia coli. Comparisons of kinetic and molecular properties of the enzymes from the original organisms and from E. coli indicate that the proteins expressed in the mesophilic host are folded correctly. Besides their higher thermostability according to their origin from hyperthermophilic organisms, both enzymes differ from their bacterial and eucaryotic homologues mainly in two respects. (a) The 3-phosphoglycerate kinases from P. woesei and M. fervidus are homomeric dimers in their native state contrary to all other known 3-phosphoglycerate kinases, which are monomers including the enzyme from the mesophilic Archaeum M. bryantii. (b) Monovalent cations are essential for the activity of both archaeal enzymes with K+ being significantly more efficient than Na+. For the P. woesei enzyme, non-cooperative K+ binding with an apparent Kd (K+) of 88 mM could be determined by kinetic analysis, whereas for the M. fervidus 3-phosphoglycerate kinase the K+ binding is rather complex: from the fitting of the saturation data, non-cooperative binding sites with low selectivity for K+ and Na+ (apparent Kd = 270 mM) and at least three cooperative and highly specific K+ binding sites/subunit are deduced. At the optimum growth temperature of P. woesei (100 degrees C) and M. fervidus (83 degrees C), the 3-phosphoglycerate kinases show half-lives of inactivation of only 28 min and 44 min, respectively.(ABSTRACT TRUNCATED AT 400 WORDS)},
}
@article {pmid7574654,
year = {1995},
author = {Chaucheyras, F and Fonty, G and Bertin, G and Gouet, P},
title = {In vitro H2 utilization by a ruminal acetogenic bacterium cultivated alone or in association with an archaea methanogen is stimulated by a probiotic strain of Saccharomyces cerevisiae.},
journal = {Applied and environmental microbiology},
volume = {61},
number = {9},
pages = {3466-3467},
pmid = {7574654},
issn = {0099-2240},
mesh = {Acetates/metabolism ; Acetic Acid ; Animals ; Bacteria/growth &amp; development/isolation &amp; purification/*metabolism ; Euryarchaeota/growth &amp; development/*metabolism ; Hydrogen/*metabolism ; Methane/metabolism ; Rumen/*microbiology ; Saccharomyces cerevisiae/growth &amp; development/*metabolism ; Sheep ; },
abstract = {The effects of a live strain of Saccharomyces cerevisiae on hydrogen utilization and acetate and methane production by two hydrogenotrophic ruminal microorganisms, an acetogenic bacterial strain and an archaea methanogen, were investigated. The addition of yeast cells enhanced by more than fivefold the hydrogenotrophic metabolism of the acetogenic strain and its acetate production. In the absence of yeasts, and in a coculture of the acetogen and the methanogen, hydrogen was principally used for methane synthesis, but the presence of live yeast cells stimulated the utilization of hydrogen by the acetogenic strain and enhanced acetogenesis.},
}
@article {pmid9383453,
year = {1995},
author = {Goldberg, AL and Stein, R and Adams, J},
title = {New insights into proteasome function: from archaebacteria to drug development.},
journal = {Chemistry &amp; biology},
volume = {2},
number = {8},
pages = {503-508},
doi = {10.1016/1074-5521(95)90182-5},
pmid = {9383453},
issn = {1074-5521},
support = {R01 GM 46147/GM/NIGMS NIH HHS/United States ; },
mesh = {Archaea/*enzymology/metabolism/ultrastructure ; Drug Design ; Endopeptidases/drug effects/metabolism/*physiology ; Ubiquitins/antagonists &amp; inhibitors/metabolism ; },
abstract = {The proteasome is not simply a 'garbage disposal unit' but also has functions in the control of the cell cycle and immune responses. The structure of an archaebacterial proteasome has recently been determined to high resolution, and provides insight into the unusual mechanism of proteolytic cleavage by the proteasome.},
}
@article {pmid7578579,
year = {1995},
author = {Serganova, IS and Polosina, IuIu and Kostiukova, AS and Metlina, AL and Piatibratov, MG and Fedorov, OV},
title = {[Halophilic archaea flagella: biochemical and genetic analysis].},
journal = {Biokhimiia (Moscow, Russia)},
volume = {60},
number = {8},
pages = {1261-1267},
pmid = {7578579},
issn = {0320-9725},
mesh = {Archaea/genetics/*metabolism/ultrastructure ; Base Sequence ; Blotting, Southern ; DNA Primers ; DNA Probes ; DNA, Bacterial ; Flagella/genetics/*metabolism ; Flagellin/genetics/metabolism ; Microscopy, Electron ; Molecular Sequence Data ; },
abstract = {The protein compositions of archaebacteria (Halobacterium salinarium, Halobacterium volcanii, Halobacterium saccharovorum and Natronobacterium pharaonis 12) flagella have been studied. It was found that flagella of these archaebacterial species are made up of flagellins. The flagellins of H. salinarium, H. volcanii and H. saccharovorum are glycosylated. Based on the known primary sequences of Halobacterium halobium R1M1 flagellin genes, oligonucleotides to the 5'- and 3'-ends of locus A containing two out of five such genes have been synthesized. The amplified by primers fragment of chromosomal DNA coding for H. halobium flagellins A1 and A2 was used as a probe for detecting homologous sites in archaebacterial DNA. Southern blotting hybridization revealed that the DNA of all archaebacterial species tested in this study contains sequences that are homologous to genes flg A1 and flg A2 of H. halobium.},
}
@article {pmid7482778,
year = {1995},
author = {Baumann, P and Qureshi, SA and Jackson, SP},
title = {Transcription: new insights from studies on Archaea.},
journal = {Trends in genetics : TIG},
volume = {11},
number = {7},
pages = {279-283},
doi = {10.1016/s0168-9525(00)89075-7},
pmid = {7482778},
issn = {0168-9525},
support = {//Wellcome Trust/United Kingdom ; },
mesh = {Archaea/*genetics ; Evolution, Molecular ; Gene Expression Regulation, Bacterial ; Genes, Bacterial ; Transcription Factors/chemistry ; *Transcription, Genetic ; },
abstract = {Molecular-genetic analyses have revealed that the Archaea (archaebacteria) are phylogenetically distinct from both eukaryotes and eubacteria. Archaea lack nuclei and resemble eubacteria in morphology and genomic organization, but their molecular design shares many features with eukaryotes. Here, we review recent work that indicates that the archaeal transcriptional machinery is strikingly similar to the RNA polymerase I, II, and III systems of eukaryotic cell nuclei. These findings provide important insights into the evolution of the transcriptional apparatus.},
}
@article {pmid7476211,
year = {1995},
author = {Mojica, FJ and Ferrer, C and Juez, G and Rodríguez-Valera, F},
title = {Long stretches of short tandem repeats are present in the largest replicons of the Archaea Haloferax mediterranei and Haloferax volcanii and could be involved in replicon partitioning.},
journal = {Molecular microbiology},
volume = {17},
number = {1},
pages = {85-93},
doi = {10.1111/j.1365-2958.1995.mmi_17010085.x},
pmid = {7476211},
issn = {0950-382X},
mesh = {Base Sequence ; DNA, Bacterial/genetics ; Halobacteriaceae/*genetics/growth &amp; development ; Molecular Sequence Data ; Plasmids/genetics ; Repetitive Sequences, Nucleic Acid/*genetics/physiology ; Replicon/*genetics ; Restriction Mapping ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; Transformation, Bacterial ; },
abstract = {We report the presence of long stretches of tandem repeats in the genome of the halophilic Archaea Haloferax mediterranei and Haloferax volcanii. A 30 bp sequence with dyad symmetry (including 5 bp inverted repeats) was repeated in tandem, interspersed with 33-39 bp unique sequences. This structure extends for long stretches--1.4 kb at one location in H. mediterranei chromosome and about 3 kb in the H. volcanii chromosome. The tandem repeats (designated TREPs) show a similar distribution in both organisms, appearing once or twice in the H. volcanii and H. mediterranei chromosomes, and once in the largest, probably essential megaplasmid of each organism but not in the smaller replicons. Sequencing of the structures in both H. volcanii replicons revealed an extremely high sequence conservation in both replicons within the species, as well as in the different organisms. Homologous sequences have also been found in other more distantly related halophilic members of the Archaea. Transformation of H. volcanii with a recombinant plasmid containing a 1.1 kb fragment of the TREPs produced significant alterations in the host cells, particularly in terms of cell viability. The introduction of extra copies of TREPs within the vector significantly alters the distribution of the genome among the daughter cells, as observed by DAPI staining. Although the precise biological role cannot be completely ascertained, all the data conform with the tandem repeats being involved in replicon partitioning in halobacteria.},
}
@article {pmid7597027,
year = {1995},
author = {Langer, D and Hain, J and Thuriaux, P and Zillig, W},
title = {Transcription in archaea: similarity to that in eucarya.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {92},
number = {13},
pages = {5768-5772},
pmid = {7597027},
issn = {0027-8424},
mesh = {Amino Acid Sequence ; Animals ; Archaea/genetics/*metabolism ; DNA-Directed RNA Polymerases/*genetics ; Escherichia coli/enzymology/genetics ; Eukaryotic Cells/metabolism ; Genes, Bacterial ; Macromolecular Substances ; Molecular Sequence Data ; Multigene Family ; Operon ; Saccharomyces cerevisiae/genetics/*metabolism ; Sequence Homology, Amino Acid ; Sulfolobus acidocaldarius/genetics/*metabolism ; Transcription Factors/*genetics ; },
abstract = {We present homologies between archaeal and eucaryal DNA-dependent RNA polymerase (RNAP) subunits and transcription factors. The sequences of the Sulfolobus acidocaldarius subunits D, E, and N and alignments with eucaryal homologs are presented here. The similarities between archaeal transcription factors and their eucaryal homologs TFIIB and TBP have been established in other laboratories. The archaeal RNAP subunits H, K, and N, respectively, show high sequence similarity to ABC27, ABC23, and ABC10 beta (found in all three eucaryal RNAPs); subunit D, to AC40 (common to polymerase II and polymerase III) and B44 (polymerase II); and subunit L, to AC19 and B12.5. The similarity of subunit D and its eucaryal homologs to bacterial alpha is limited to the "alpha-motif," which is also present in subunit L and its eucaryal homologs. Genes encoding homologs of the related eucaryal RNAP subunits A12.2/B12.6 and also homologs of eucaryal transcription elongation factors of the TFIIS family have been detected in Sulfolobus acidocaldarius and Thermococcus celer. In archaea, the protein is not an RNAP subunit. Together with the sequence similarities between archaeal box A-containing and eucaryal TATA box-containing promoters, this shows that the archaeal and eucaryal transcription systems are truly homologous and that they differ structurally and functionally from the bacterial transcription machinery. In contrast, however, a number of genes for the archaeal transcription apparatus are organized in clusters resembling the clusters of transcription-associated genes in Bacteria.},
}
@article {pmid7597025,
year = {1995},
author = {Keeling, PJ and Doolittle, WF},
title = {Archaea: narrowing the gap between prokaryotes and eukaryotes.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {92},
number = {13},
pages = {5761-5764},
pmid = {7597025},
issn = {0027-8424},
mesh = {Archaea/*classification/genetics/*metabolism ; Eukaryotic Cells/metabolism ; *Phylogeny ; Prokaryotic Cells/metabolism ; Protein Biosynthesis ; Species Specificity ; Sulfolobus/metabolism ; Transcription Factors/metabolism ; Transcription, Genetic ; },
}
@article {pmid7773330,
year = {1995},
author = {DiRuggiero, J and Tuttle, JH and Robb, FT},
title = {Rapid differentiation of hyperthermophilic Archaea by restriction mapping of the intergenic spacer regions of the ribosomal RNA operons.},
journal = {Molecular marine biology and biotechnology},
volume = {4},
number = {2},
pages = {123-127},
pmid = {7773330},
issn = {1053-6426},
mesh = {Archaea/*classification ; Base Sequence ; DNA, Ribosomal/*genetics ; Hot Temperature ; Molecular Sequence Data ; Operon/genetics ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal/*genetics ; *Restriction Mapping ; Sequence Analysis ; Time Factors ; },
abstract = {We report a sensitive and convenient method for rapid differentiation of new isolates of hyperthermophilic Archaea. Polymerase chain reaction (PCR) was used to amplify the intergenic spacer regions of the ribosomal RNA operons of eight Archaea. Spacer regions from one Euryarcheote, Pyrococcus furiosus, and one Crenarcheote, Pyrodictium brockii, were sequenced completely. Restriction fragment length polymorphism (RFLP) analyses were performed on the spacer regions from eight hyperthermophilic Archaea, and the restriction patterns were used as fingerprints for six known strains and two isolates. The PCR-RFLP method used in this study allowed the differentiation of seven of the eight strains tested and could be generally applicable to all the Archaea.},
}
@article {pmid7768791,
year = {1995},
author = {Rusnak, P and Haney, P and Konisky, J},
title = {The adenylate kinases from a mesophilic and three thermophilic methanogenic members of the Archaea.},
journal = {Journal of bacteriology},
volume = {177},
number = {11},
pages = {2977-2981},
pmid = {7768791},
issn = {0021-9193},
support = {GM41587/GM/NIGMS NIH HHS/United States ; },
mesh = {Adenylate Kinase/antagonists &amp; inhibitors/genetics/*metabolism ; Amino Acid Sequence ; Hot Temperature ; Methanobacterium/*enzymology/genetics ; Molecular Sequence Data ; Potassium Chloride/pharmacology ; Sequence Alignment ; Sequence Homology, Amino Acid ; },
abstract = {Adenylate kinase has been isolated from four related methanogenic members of the Archaea. For each, the optimum temperature for enzyme activity was similar to the temperature for optimal microbial growth and was approximately 30 degrees C for Methanococcus voltae, 70 degrees C for Methanococcus thermolithotrophicus, 80 degrees C for Methanococcus igneus, and 80 to 90 degrees C for Methanococcus jannaschii. The enzymes were sensitive to the adenylate kinase inhibitor P1, P5-di(adenosine-5')pentaphosphate, a property that was exploited to purify the enzymes by CIBACRON Blue affinity chromatography. The enzymes had an estimated molecular mass (approximately 23 to 25 kDa) in the range common for adenylate kinases. Each of the enzymes had a region of amino acid sequence close to its N terminus that was similar to the canonical P-loop sequence reported for all adenylate kinases. However, the methanogen sequences lacked a lysine residue that has previously been found to be invariant in adenylate kinases, including an enzyme isolated from the archaeon Sulfolobus acidocaldarius. If verified as a nucleotide-binding domain, the methanogen sequence would represent a novel nucleotide-binding motif. There was no correlation between amino acid abundance and the optimal temperature for enzyme activity.},
}
@article {pmid8586635,
year = {1995},
author = {Nishihara, M and Koga, Y},
title = {sn-glycerol-1-phosphate dehydrogenase in Methanobacterium thermoautotrophicum: key enzyme in biosynthesis of the enantiomeric glycerophosphate backbone of ether phospholipids of archaebacteria.},
journal = {Journal of biochemistry},
volume = {117},
number = {5},
pages = {933-935},
doi = {10.1093/oxfordjournals.jbchem.a124822},
pmid = {8586635},
issn = {0021-924X},
mesh = {Animals ; Archaea/chemistry/metabolism ; Chemical Fractionation ; Chromatography ; Dihydroxyacetone Phosphate/metabolism ; Glycerolphosphate Dehydrogenase/isolation &amp; purification/*metabolism ; Glycerophosphates/*biosynthesis ; Methanobacterium/*enzymology ; NADP/metabolism ; Oxidoreductases/chemistry/*isolation &amp; purification/*metabolism ; Phospholipid Ethers/chemistry/metabolism ; Rabbits ; Stereoisomerism ; Triose-Phosphate Isomerase/metabolism ; },
abstract = {One of the most characteristic features of archaebacterial ether phospholipids is the enantiomeric configuration of their glycerophosphate backbone (sn-glycerol-1-phosphate), that is the mirror image of the structure of the eubacterial or eukaryotic counterpart. The enzyme that forms glycerophosphate of this configuration was found for the first time in a cell-free extract of the methanogen, Methanobacterium thermoautotrophicum, and was identified as sn-glycerol-1-phosphate:NAD+ oxidoreductase (sn-glycerol-1-phosphate dehydrogenase) after partial purification. Because sn-glycerol-1-phosphate has been found to be a precursor of ether lipids of this organism, sn-glycerol-1-phosphate dehydrogenase is a key enzyme in the biosynthesis of the enantiomeric ether lipids of methanogens.},
}
@article {pmid7736359,
year = {1995},
author = {Oren, A and Gurevich, P},
title = {Diversity of lactate metabolism in halophilic archaea.},
journal = {Canadian journal of microbiology},
volume = {41},
number = {3},
pages = {302-307},
doi = {10.1139/m95-042},
pmid = {7736359},
issn = {0008-4166},
mesh = {Halobacteriaceae/enzymology/*metabolism ; L-Lactate Dehydrogenase/classification/*metabolism ; Lactates/*metabolism ; Lactic Acid ; NAD ; },
abstract = {D-Lactate is readily used as a substrate for the growth of species of halophilic archaea belonging to the genera Haloferax and Haloarcula. L-Lactate was used by Haloferax species (Haloferax volcanii, Haloferax mediterranei) only when a substantial concentration of the D-isomer was also present in the medium. On the enzymatic level, considerable diversity was found in the lactate metabolism of the different representatives of the Halobacteriaceae. At least three types of lactate dehydrogenases were detected in halophilic archaea. A high level of activity of an NAD-linked enzyme was present constitutively in Haloarcula species, and a low level of activity was also detected in Haloferax mediterranei. NAD-independent lactate dehydrogenases, oxidizing L-lactate and D-lactate with 2,6-dichlorophenol-indophenol as electron acceptor, were detected in all nine species tested, but L-lactate dehydrogenase activity in Halobacterium species was very low, and Haloarcula species, which possess a high level of activity of NAD-linked lactate dehydrogenase, showed very low activities of both NAD-independent D- and L-lactate dehydrogenase. An inducible lactate racemase, displaying an unusually high pH optimum, was found in Haloferax volcanii. Lactate racemase activity was found constitutively in Haloarcula species, but no activity was detected in Halobacterium species and in Haloferax mediterranei.},
}
@article {pmid7827120,
year = {1995},
author = {Nishihara, M and Koga, Y},
title = {Two new phospholipids, hydroxyarchaetidylglycerol and hydroxyarchaetidylethanolamine, from the Archaea Methanosarcina barkeri.},
journal = {Biochimica et biophysica acta},
volume = {1254},
number = {2},
pages = {155-160},
doi = {10.1016/0005-2760(94)00178-2},
pmid = {7827120},
issn = {0006-3002},
mesh = {Chromatography, Gas ; Chromatography, Thin Layer ; Methanosarcina barkeri/*chemistry ; Molecular Conformation ; Molecular Structure ; Phospholipid Ethers/*analysis/chemistry ; Spectrometry, Mass, Fast Atom Bombardment ; },
abstract = {The structures of two new ether phospholipids of the methanogenic Archaea, Methanosarcina barkeri, were determined as hydroxyarchaetidylglycerol and hydroxyarchaetidylethanolamine by means of chemical, chromatographic and enzymatic analyses, and fast atom bombardment-mass spectrometry. These lipids are hydroxy diether analogs of phosphatidylglycerol and phosphatidylethanolamine, respectively, with beta-hydroxyarachaeol (2-O-(3'-hydroxy)phytanyl-3-O-phytanyl-sn-glycerol) as a core lipid. In addition, two other ether phospholipids, usual archaetidylglycerol and archaetidylethanolamine, were also identified in the organism. The stereochemical structure of the unalkylated glycerophosphate of hydroxyarchaetidylglycerol and archaetidylglycerol was determined as sn-glycerol-3-phosphate by use of sn-glycerol-3-phosphate dehydrogenase. The stereochemical configuration of the glycerophosphoglycerol backbone of these lipids was a mirror image of that of diacylphosphatidylglycerol from the organisms of the domains Bacteria and Eucarya, and it was shared with extremely halophilic Archaea. These four phospholipids, in addition to five lipids that had already been reported, accounted for 88% of the total polar lipids of this organism.},
}
@article {pmid7851382,
year = {1995},
author = {Klein, AR and Thauer, RK},
title = {Re-face specificity at C14a of methylenetetrahydromethanopterin and Si-face specificity at C5 of coenzyme F420 for coenzyme F420-dependent methylenetetrahydromethanopterin dehydrogenase from methanogenic Archaea.},
journal = {European journal of biochemistry},
volume = {227},
number = {1-2},
pages = {169-174},
doi = {10.1111/j.1432-1033.1995.tb20373.x},
pmid = {7851382},
issn = {0014-2956},
mesh = {Archaea/*enzymology ; Carbon/*metabolism ; Oxidoreductases Acting on CH-NH Group Donors/*metabolism ; Pterins/*metabolism ; Riboflavin/*analogs &amp; derivatives/metabolism ; Structure-Activity Relationship ; Substrate Specificity ; },
abstract = {Coenzyme F420-dependent methylenetetrahydromethanopterin dehydrogenase from methanogenic Archaea catalyzes the reversible transfer of a hydride ion from C14a of N5,N10-methylenetetrahydromethanopterin to C5 of coenzyme F420. In this study, we report that this hydride transfer proceeds stereospecifically from the Re face at C14a to the Si face at C5. The results were obtained by using chirally 3H-labelled N5,N10-methylenetetrahydromethanopterin generated via Re-face-specific H2-forming N5,N10-methylenetetrahydromethanopterin dehydrogenase and by analyzing reduced coenzyme F420 via Si-face-specific F420-reducing hydrogenase.},
}
@article {pmid8901499,
year = {1995},
author = {Brown, JW and Haas, ES},
title = {Ribonuclease P structure and function in Archaea.},
journal = {Molecular biology reports},
volume = {22},
number = {2-3},
pages = {131-134},
pmid = {8901499},
issn = {0301-4851},
support = {1-R29-GM52894-01/GM/NIGMS NIH HHS/United States ; },
mesh = {Archaea/classification/*enzymology ; Base Sequence ; Endoribonucleases/*chemistry/*metabolism ; Evolution, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; RNA, Bacterial/chemistry/metabolism ; RNA, Catalytic/*chemistry/*metabolism ; Ribonuclease P ; Sequence Homology, Nucleic Acid ; },
abstract = {An important approach to understanding RNA-based catalytic function by ribonuclease P is the investigation of its evolutionary diversity in structure and function. Because RNase P enzymes from all organisms are thought to share common ancestry, the fundamental features of structure and biochemistry should be conserved in all of its modern forms. In contrast to the bacterial enzyme, the RNase P enzymes from Eucarya, organelles, and Archaea are poorly understood. This review describes our nascent understanding of the structure and function of RNase P in Archaea, and how this enzyme compares to its homologs in the other evolutionary Domains.},
}
@article {pmid7773169,
year = {1995},
author = {Smith, RF and King, KY},
title = {Identification of a eukaryotic-like protein kinase gene in Archaebacteria.},
journal = {Protein science : a publication of the Protein Society},
volume = {4},
number = {1},
pages = {126-129},
pmid = {7773169},
issn = {0961-8368},
support = {1R01-HG00973-01/HG/NHGRI NIH HHS/United States ; P30-HG00210/HG/NHGRI NIH HHS/United States ; },
mesh = {Amino Acid Sequence ; Conserved Sequence ; Eukaryotic Cells ; *Genes, Bacterial ; Methanococcus/enzymology/*genetics ; Molecular Sequence Data ; Open Reading Frames/genetics ; Protein Kinases/chemistry/*genetics ; Sequence Alignment ; },
abstract = {Primary sequence patterns based on known conserved sites in eukaryotic protein kinases were used to search for eukaryotic-like protein kinase sequences in a six-frame translation of the bacterial subsection of GenBank. This search identified a previously unrecognized eukaryotic-like protein kinase gene in three related methanogenic archaebacteria, Methanococcus vannielii, M. voltae, and M. thermolithotrophicus. The proposed coding sequences are located in orthologous open reading frames (ORFs): ORF547, ORF294, and ORF114, respectively. The C-terminus of the ORFs contains 9 of the 11 subdomains characteristically conserved within the eukaryotic protein kinase catalytic domain. The N-terminus of the ORFs is similar to a putative glycoprotease in Pasteurella haemolytica and its homologue in Escherichia coli, the orfX gene. This is the first report of a eukaryotic-like protein kinase sequence observed in Archaebacteria.},
}
@article {pmid7715485,
year = {1995},
author = {Zviagintseva, IS and Beliaev, SS and Borzenkov, IA and Kostrikina, NA and Milekhina, EI and Ivanov, MV},
title = {[Halophilic archaebacteria from the Kalamkass oilfield].},
journal = {Mikrobiologiia},
volume = {64},
number = {1},
pages = {83-87},
pmid = {7715485},
issn = {0026-3656},
mesh = {Archaea/genetics/*isolation &amp; purification/metabolism ; Base Sequence ; Chemical Industry ; DNA, Bacterial/genetics ; Molecular Sequence Data ; Petroleum ; RNA, Ribosomal, 16S/genetics ; Sequence Homology, Nucleic Acid ; Species Specificity ; },
abstract = {Two strains of halophilic archebacteria, growing in the range from 10 to 25% NaCl, were obtained from the brines of the Kalamkass (Mangyshlak) oilfield. Both strains are extremely halophilic archaebacteria according to their total phenotypic properties. Strain M-11 was identified as Haloferax mediterranei on the basis of the composition of polar lipids and DNA-DNA homology. The composition of polar lipids and 16S rRNA sequences of M-18 strain permitted to include it in Haloferax genus. This strain differs from the affirmed species of Haloferax genus--H. volcanii and H. mediterranei. However, the additional investigations are necessary for its relation to new species.},
}
@article {pmid7988679,
year = {1994},
author = {Raffaelli, N and Amici, A and Emanuelli, M and Ruggieri, S and Magni, G},
title = {Pyridine dinucleotide biosynthesis in archaebacteria: presence of NMN adenylyltransferase in Sulfolobus solfataricus.},
journal = {FEBS letters},
volume = {355},
number = {3},
pages = {233-236},
doi = {10.1016/0014-5793(94)01195-8},
pmid = {7988679},
issn = {0014-5793},
mesh = {Adenosine Triphosphate/metabolism ; Hot Temperature ; Isoelectric Point ; Kinetics ; Molecular Weight ; NAD/*biosynthesis ; Nicotinamide Mononucleotide/metabolism ; Nicotinamide-Nucleotide Adenylyltransferase/isolation &amp; purification/*metabolism ; Subcellular Fractions/enzymology ; Sulfolobus/*enzymology ; },
abstract = {The enzyme NMN adenylyltransferase, leading to NAD synthesis, has been observed for the first time in soluble extracts from the extreme acidothermophilic archaeon Sulfolobus solfataricus. Comparison of its molecular and kinetic properties with those of the enzyme isolated from prokaryotes and eukaryotes revealed significant differences, knowledge of which may contribute to the understanding of metabolic evolutionary mechanisms. The thermophilic enzyme shows a molecular mass of about 66,000 and an isoelectric point of 5.4. The Km values for ATP, NMN and nicotinic acid mononucleotide are 0.08 microM, 1.4 microM and 17 microM, respectively. The enzyme shows a remarkable degree of thermophilicity, with an activation energy of 95 kJ/mol.},
}
@article {pmid7884279,
year = {1994},
author = {Yamagishi, A},
title = {[Archaebacteria and evolution of life: recent progress in the research].},
journal = {Seikagaku. The Journal of Japanese Biochemical Society},
volume = {66},
number = {12},
pages = {1528-1533},
pmid = {7884279},
issn = {0037-1017},
mesh = {*Archaea/genetics/metabolism ; *Biological Evolution ; },
}
@article {pmid7765648,
year = {1994},
author = {Conway de Macario, E and Macario, AJ},
title = {Heat-shock response in Archaea.},
journal = {Trends in biotechnology},
volume = {12},
number = {12},
pages = {512-518},
doi = {10.1016/0167-7799(94)90059-0},
pmid = {7765648},
issn = {0167-7799},
mesh = {Archaea/genetics/*physiology ; Heat-Shock Proteins/*biosynthesis/genetics ; },
abstract = {The Archaea are one of the three phylogenetic domains into which all organisms have been classified, and include extreme halophiles, extreme thermophiles and methanogens. Some of these organisms inhabit inhospitable environments on Earth, and thus have evolved stress responses to cope with the extremes of heat, pH and salinity that they encounter. Although the archaeal stress or heat-shock response bears some similarity to the heat-shock responses of other organisms, it possesses some unique features. A better understanding of this response would facilitate its exploitation in the biotechnological industries; for example, in engineering cells that exhibit an improved ability to withstand, or recover from, stress.},
}
@article {pmid7986808,
year = {1994},
author = {Pugh, EL and Kates, M},
title = {Acylation of proteins of the archaebacteria Halobacterium cutirubrum and Methanobacterium thermoautotrophicum.},
journal = {Biochimica et biophysica acta},
volume = {1196},
number = {1},
pages = {38-44},
doi = {10.1016/0005-2736(94)90292-5},
pmid = {7986808},
issn = {0006-3002},
mesh = {Acylation ; Bacterial Proteins/*metabolism ; Fatty Acid Synthases/metabolism ; Fatty Acids/analysis ; Halobacterium/*metabolism ; Membrane Lipids/chemistry ; Membrane Proteins/chemistry ; Methanobacterium/*metabolism ; },
abstract = {Although the membrane lipids of extremely halophilic archaebacteria are exclusively derived from diphytanylglycerol diether, which is non-acylated, small amounts of fatty acids have been detected in these organisms. These fatty acids are formed by the action of a fatty acid synthase (FAS), shown to be present in the extreme halophile Halobacterium cutirubrum, despite the fact that only a fraction of the activity of FAS remains at the high salt concentration (> 4 M) present in the cytoplasm. It has now been demonstrated that fatty acids do not occur in lipid-bound form but largely in the form of acylated proteins in the red membrane of H. cutirubrum. In contrast, the bacteriorhodopsin of the purple membrane of this extreme halophile does not appear to be acylated. The thermophilic methanogen, Methanobacterium thermoautotrophicum had a much higher fatty acid synthase activity than the extreme halophile, and the synthase activity of the methanogen was optimal under its normal (anaerobic) growth conditions. The methanogen also utilized the resulting fatty acids to acylate its membrane proteins. The major fatty acids in both organisms were palmitic and stearic acids with small amounts of myristic and 18:1 acids, and these were bound to protein through both ester and amide linkages.},
}
@article {pmid7963587,
year = {1994},
author = {Tomioka, K and Kii, F and Fukuda, H and Katoh, S},
title = {Homogeneous immunoassay of antibody by use of liposomes made of a model lipid of archaebacteria.},
journal = {Journal of immunological methods},
volume = {176},
number = {1},
pages = {1-7},
doi = {10.1016/0022-1759(94)90345-x},
pmid = {7963587},
issn = {0022-1759},
mesh = {Animals ; Archaea/*immunology ; Chymotrypsinogen/*immunology ; Immunoassay/methods ; Immunoglobulin G/*analysis ; Liposomes ; Membrane Lipids/*immunology ; Models, Biological ; Phosphatidylcholines/*immunology ; Rabbits ; },
abstract = {Liposomes made of 1,2-di(3RS,7R,11R-phytanyl)-sn-glycero-3-phosphocholine (DPhyPC), which was synthesized as one of the model lipids existing in archaebacterial halophiles, showed excellent stability. Because of this high stability, DPhyPC liposomes could be constituted high ratios (50%) of N-[4-(p-maleimidophenyl) butyryl] dipalmitoyl phosphatidylethanolamine (MPB-DPPE), and consequently could bind large amounts of antigen (alpha-chymotrypsinogen A) on the liposome surface in comparison with those made of ordinary lipids, such as dipalmitoylphosphatidylcholine (DPPC). Though the characteristics of the DPhyPC liposomal membranes in lysis by the classical complement pathway were similar to those of DPPC liposomes, a high sensitivity and a low detection limit in the liposome immune lysis assay (LILA) of antibodies were attained by binding large amounts of the antigen. Further, by coupling sufficient amounts of antigen, almost all the DPhyPC liposome surface was covered with the antigen, and such liposomes showed higher resistance against non-specific lysis caused by complement activity in serum samples, which may be effective in reducing positive-false errors in LILA.},
}
@article {pmid7807543,
year = {1994},
author = {Gupta, RS and Golding, GB and Singh, B},
title = {HSP70 phylogeny and the relationship between archaebacteria, eubacteria, and eukaryotes.},
journal = {Journal of molecular evolution},
volume = {39},
number = {5},
pages = {537-540},
pmid = {7807543},
issn = {0022-2844},
mesh = {Algorithms ; Amino Acid Sequence ; Archaea/*classification/genetics ; Bacteria/*classification/genetics ; Conserved Sequence ; Eukaryotic Cells/*classification ; HSP70 Heat-Shock Proteins/*classification/*genetics ; Phylogeny ; Sequence Homology, Amino Acid ; },
}
@article {pmid7804904,
year = {1994},
author = {Dyall-Smith, ML and Doolittle, WF},
title = {Construction of composite transposons for halophilic Archaea.},
journal = {Canadian journal of microbiology},
volume = {40},
number = {11},
pages = {922-929},
doi = {10.1139/m94-148},
pmid = {7804904},
issn = {0008-4166},
mesh = {Base Sequence ; Blotting, Southern ; DNA Transposable Elements/*genetics ; DNA, Bacterial/analysis ; DNA, Recombinant/*genetics ; Drug Resistance, Microbial ; Genes, Bacterial/*genetics ; Genetic Markers ; Halobacteriaceae/drug effects/*genetics ; Hydroxymethylglutaryl CoA Reductases/genetics ; Lovastatin/pharmacology ; Molecular Sequence Data ; Plasmids/analysis ; Transformation, Bacterial ; },
abstract = {Transposons with selectable marker genes (e.g., antibiotic resistance) have been extremely useful tools in bacterial genetics but have not been found naturally in Archaea. We constructed synthetic transposons consisting of halobacterial ISH elements (ISH2, ISH26, or ISH28) flanking a mevinolin resistance determinant. Introduction of these constructs into Haloferax volcanii cells can produce drug-resistant transformants through homologous recombination between the plasmid hmgA gene and the chromosomal hmgA locus. This problem was overcome by using another host, Haloarcula hispanica, the hmgA gene of which shares little homology with that from Haloferax volcanii. Introduction of an ISH28-based transposon (ThD28) into Haloarcula hispanica cells produced numerous transformants. Each of these was shown to contain an ISH-flanked mevinolin resistance determinant integrated into the cellular DNA. Integration was not obviously site specific. Transposon ThD26 (based on ISH26a), was less mobile, relative to ThD28, and the ISH2-based construct (ThD22) did not transpose at all in these cells. The further development of halobacterial transposons may provide useful genetic tools allowing rapid isolation and analysis of halobacterial genes, particularly those with no selectable phenotype.},
}
@article {pmid7935813,
year = {1994},
author = {DeLong, EF and Wu, KY and Prézelin, BB and Jovine, RV},
title = {High abundance of Archaea in Antarctic marine picoplankton.},
journal = {Nature},
volume = {371},
number = {6499},
pages = {695-697},
doi = {10.1038/371695a0},
pmid = {7935813},
issn = {0028-0836},
mesh = {Animals ; Archaea/classification/*isolation &amp; purification ; Arctic Regions ; Base Sequence ; Biomass ; DNA, Ribosomal/analysis ; Molecular Sequence Data ; Phylogeny ; *Plankton ; RNA, Ribosomal/analysis ; },
abstract = {Archaea (archaebacteria) constitute one of the three major evolutionary lineages of life on Earth. Previously these prokaryotes were thought to predominate in only a few unusual and disparate niches, characterized by hypersaline, extremely hot, or strictly anoxic conditions. Recently, novel (uncultivated) phylotypes of Archaea have been detected in coastal and subsurface marine waters, but their abundance, distribution, physiology and ecology remain largely undescribed. Here we report exceptionally high archaeal abundance in frigid marine surface waters of Antarctica. Pelagic Archaea constituted up to 34% of the prokaryotic biomass in coastal Antarctic surface waters, and they were also abundant in a variety of other cold, pelagic marine environments. Because they can make up a significant fraction of picoplankton biomass in the vast habitats encompassed by cold and deep marine waters, these pelagic Archaea represent an unexpectedly abundant component of the Earth's biota.},
}
@article {pmid7935810,
year = {1994},
author = {Olsen, GJ},
title = {Microbial ecology. Archaea, Archaea, everywhere.},
journal = {Nature},
volume = {371},
number = {6499},
pages = {657-658},
doi = {10.1038/371657a0},
pmid = {7935810},
issn = {0028-0836},
mesh = {Animals ; Archaea/classification/*isolation &amp; purification ; Phylogeny ; Plankton ; },
}
@article {pmid7988884,
year = {1994},
author = {Gadelle, D and Forterre, P},
title = {DNA intercalating drugs inhibit positive supercoiling induced by novobiocin in halophilic archaea.},
journal = {FEMS microbiology letters},
volume = {123},
number = {1-2},
pages = {161-166},
doi = {10.1111/j.1574-6968.1994.tb07216.x},
pmid = {7988884},
issn = {0378-1097},
mesh = {DNA-Binding Proteins ; Dactinomycin/pharmacology ; Ellipticines/pharmacology ; Halobacterium/*drug effects/genetics ; Indoles/pharmacology ; Intercalating Agents/*pharmacology ; Novobiocin/*antagonists &amp; inhibitors ; Plasmids/drug effects ; Topoisomerase I Inhibitors ; },
abstract = {The two DNA intercalators, actinomycin D and 2-methyl-9-hydroxy-ellipticine, and the DNA minor groove ligant DAPI inhibited the growth of the haloarchaeon Halobacterium sp. GRB and bind to its plasmid pGRB-1. In contrast to specific DNA topoisomerase II inhibitors, they produced neither double-stranded breaks nor relaxation of plasmidic DNA. The two DNA intercalators inhibited positive supercoiling induced by novobiocin, suggesting that positive supercoiling in haloarchaea is due to transcription, as in the domain Bacteria. Plasmids from haloarchaea could thus be used to prescreen for DNA intercalators and to discriminate between different drug families via their mode of action.},
}
@article {pmid7850430,
year = {1994},
author = {Klenk, HP and Doolittle, WF},
title = {Evolution. Archaea and eukaryotes versus bacteria?.},
journal = {Current biology : CB},
volume = {4},
number = {10},
pages = {920-922},
doi = {10.1016/s0960-9822(00)00206-2},
pmid = {7850430},
issn = {0960-9822},
mesh = {Archaea/*classification/genetics ; DNA-Binding Proteins/*chemistry/physiology ; Phylogeny ; TATA-Box Binding Protein ; Transcription Factors/*chemistry/physiology ; Transcription, Genetic ; },
abstract = {The recent discovery of homologs of the eukaryotic transcription factor TATA-binding protein in archaea has been taken as support for the view that archaea and eukaryotes have a close phylogenetic relationship.},
}
@article {pmid7833831,
year = {1994},
author = {Ravi, K and Suryanarayana, T},
title = {Ribosomal protein S1 in archaea.},
journal = {Biochemistry and molecular biology international},
volume = {34},
number = {3},
pages = {543-552},
pmid = {7833831},
issn = {1039-9712},
mesh = {Archaea/*chemistry ; Cross Reactions ; Halobacterium salinarum/chemistry ; Immunoblotting ; Molecular Weight ; Ribosomal Proteins/*analysis/genetics/immunology ; },
abstract = {Cell extracts and ribosomes of thermoacidophilic and halophilic archaebacteria were analysed by immunoblotting to detect ribosomal protein S1 homologues. Antisera to E. coli S1, the N-terminal ribosome binding domain (F2a) and the central and COOH-terminal nucleic acid binding domain (S1F1) of the protein were used. The results show that the thermoacidophilic archaebacterium sulfolobus acidocaldarius contains a protein with molecular weight of 66,000 that cross-reacts with anti-S1F1. However, the halophilic archaebacteria Halobacterium halobium, H. cutirubrum and H. salinarum contain a protein of molecular weight of about 100,000 that cross-reacts only with anti-F2a. The results indicate a differential conservation of the structural and functional domains of protein S1 in archaebacteria.},
}
@article {pmid7873098,
year = {1994},
author = {Oren, A},
title = {Enzyme diversity in halophilic archaea.},
journal = {Microbiologia (Madrid, Spain)},
volume = {10},
number = {3},
pages = {217-228},
pmid = {7873098},
issn = {0213-4101},
mesh = {*Bacterial Proteins/analysis ; Bacteriorhodopsins/metabolism ; Classification ; Electron Transport ; Energy Metabolism ; Fermentation ; Halobacteriaceae/classification/*enzymology ; Halobacterium/enzymology ; Pigments, Biological/metabolism ; Species Specificity ; Substrate Specificity ; },
abstract = {The halophilic archaea display a considerable extent of enzyme diversity. The presence or absence of certain enzymatic activities is closely linked with the taxonomic status of the strains investigated. Thus, Halobacterium species such as Hb. salinarium, Hb. halobium, and Hb. cutirubrum differ from most other Halobacteriaceae tested by the possession of an NAD(+)-dependent glycerol dehydrogenase, by the absence of methylglyoxal synthase activity, and the ability of fermentative growth on arginine. Species such as Hb. saccharovorum and Hb. sodomense, which are still classified within the genus Halobacterium, have an enzymatic machinery greatly different from that of the Hb. salinarium-Hb. halobium group, confirming the need for a taxonomic reappraisal of these species. The presence of NAD(+)-dependent D-lactate dehydrogenase is characteristic of representatives of the genus Haloarcula, which possess only low activities of NAD(+)-independent L- and D-lactate dehydrogenases, if at all. Other enzymes which show considerable diversity are fructose 1,6-bisphosphate aldolase, of which two classes exist, and ribulose 1,6-bisphosphate carboxylase, which is present in a limited number of species.},
}
@article {pmid7524440,
year = {1994},
author = {Burggraf, S and Mayer, T and Amann, R and Schadhauser, S and Woese, CR and Stetter, KO},
title = {Identifying members of the domain Archaea with rRNA-targeted oligonucleotide probes.},
journal = {Applied and environmental microbiology},
volume = {60},
number = {9},
pages = {3112-3119},
pmid = {7524440},
issn = {0099-2240},
mesh = {Archaea/classification/*genetics/isolation &amp; purification ; Base Sequence ; DNA Probes/genetics ; Ecosystem ; Hot Temperature ; Molecular Sequence Data ; Nucleic Acid Hybridization ; Phylogeny ; RNA, Bacterial/*genetics ; RNA, Ribosomal, 16S/*genetics ; Sequence Homology, Nucleic Acid ; Species Specificity ; Water Microbiology ; },
abstract = {Two 16S rRNA-targeted oligonucleotide probes were designed for the archaeal kingdoms Euryachaeota and Crenarchaeota. Probe specificities were evaluated by nonradioactive dot blot hybridization against selected reference organisms. The successful application of fluorescent-probe derivatives for whole-cell hybridization required organism-specific optimizations of fixation and hybridization conditions to assure probe penetration and morphological integrity of the cells. The probes allowed preliminary grouping of three new hyperthermophilic isolates. Together with other group-specific rRNA-targeted oligonucleotide probes, these probes will facilitate rapid in situ monitoring of the populations present in hydrothermal systems and support cultivation attempts.},
}
@article {pmid8063781,
year = {1994},
author = {Lübben, M and Morand, K},
title = {Novel prenylated hemes as cofactors of cytochrome oxidases. Archaea have modified hemes A and O.},
journal = {The Journal of biological chemistry},
volume = {269},
number = {34},
pages = {21473-21479},
pmid = {8063781},
issn = {0021-9258},
mesh = {Archaea/*chemistry/enzymology ; Bacteria/chemistry ; Chromatography, High Pressure Liquid ; Diterpenes/chemistry ; Electron Transport Complex IV/*chemistry ; Farnesol/analogs &amp; derivatives ; Heme/*analogs &amp; derivatives/chemistry ; Mass Spectrometry ; Membranes/chemistry ; Spectrophotometry ; Sulfolobus acidocaldarius/chemistry/enzymology ; Terpenes/*chemistry ; Thermoplasma/chemistry/enzymology ; },
abstract = {A series of novel hemes with modifications of the isoprenyl side chain has been detected in archaea. Heme A(S) was isolated from cytochrome oxidases of the thermoacidophilic archaeon, Sulfolobus acidocaldarius. Heme A(S) has the same spectroscopic features as heme A but has a hydroxyethylgeranylgeranyl side chain instead of the hydroxyethylfarnesyl group. This variant is also present in other archaeal oxidases as well as in the cytochrome oxidases of a thermophilic eubacterium. Other archaea (Thermoplasma, Pyrobaculum) were also shown to have cytochrome oxidases. From these organisms, three novel prenylated heme variants (called OT, OP1, and OP2) were isolated. They are structurally related to heme O; OP2 has a hydroxyethylgeranylgeranyl instead of the hydroxyethylfarnesyl side chain. In OP1 and OT, the hydroxyethylprenyl group is altered to ethenylprenyl by elimination of a water molecule. Most probably, the novel hemes are cofactors binding to the binuclear reaction centers of archaeal cytochrome oxidases.},
}
@article {pmid8085828,
year = {1994},
author = {Hoaki, T and Nishijima, M and Kato, M and Adachi, K and Mizobuchi, S and Hanzawa, N and Maruyama, T},
title = {Growth requirements of hyperthermophilic sulfur-dependent heterotrophic archaea isolated from a shallow submarine geothermal system with reference to their essential amino acids.},
journal = {Applied and environmental microbiology},
volume = {60},
number = {8},
pages = {2898-2904},
pmid = {8085828},
issn = {0099-2240},
mesh = {Amino Acids, Essential/*metabolism ; Anaerobiosis ; Archaea/genetics/*growth &amp; development/physiology/ultrastructure ; Base Composition ; Base Sequence ; Culture Media ; DNA, Ribosomal/analysis ; Hot Temperature ; Molecular Sequence Data ; RNA, Ribosomal, 16S/genetics ; Seawater ; Sequence Analysis, DNA ; *Soil Microbiology ; },
abstract = {Three hyperthermophilic sulfur-dependent heterotrophs were isolated from a shallow submarine hydrothermal system at an inlet of Kodakara-jima island, Kagoshima, Japan. The isolates grew at 60 to 97 degrees C, with the optimum temperatures at 85 to 90 degrees C. Sensitivity to rifampin and the existence of ether lipids indicated that the isolates are hyperthermophilic archaea. Partial sequencing of the genes coding for 16S rRNA showed that the three isolates are closely related to the genus Thermococcus. They grew on proteinaceous mixtures, such as yeast extract, Casamino Acids, and purified proteins (e.g., casein and gelatin), but not on carbohydrates or organic acids as sole carbon and energy sources. Nine amino acids were essential for growth of isolate KS-1 (Thr, Leu, Ile, Val, Met, Phe, His, Tyr, and Arg). Isolate KS-2 required Lys in addition to the nine amino acids, and KS-8 required Lys instead of Tyr. In comparative studies, it was shown that Thermococcus celer DSM 2476 required 10 amino acids (Thr, Leu, Ile, Val, Met, Phe, Tyr, Trp, Lys, and Arg) while Pyrococcus furiosus DSM 3638 required only Ile and Val. The hyperthermophilic fermentative eubacterium Thermotoga neapolitana DSM 4359 did not require any amino acids for growth.},
}
@article {pmid7858973,
year = {1994},
author = {Adams, MW and Kelly, RM},
title = {Thermostability and thermoactivity of enzymes from hyperthermophilic Archaea.},
journal = {Bioorganic &amp; medicinal chemistry},
volume = {2},
number = {7},
pages = {659-667},
doi = {10.1016/0968-0896(94)85015-1},
pmid = {7858973},
issn = {0968-0896},
mesh = {Archaea/*classification/*enzymology/genetics ; DNA-Directed DNA Polymerase/chemistry/isolation &amp; purification/*metabolism ; Enzyme Stability ; Hot Temperature ; Hydrolases/chemistry/isolation &amp; purification/*metabolism ; Kinetics ; Oxidoreductases/chemistry/isolation &amp; purification/*metabolism ; Phylogeny ; Thermodynamics ; },
abstract = {Enzymes from hyperthermophilic microorganisms are characteristically thermostable and thermoactive at extremely high temperatures. Information about the basis for the structure and function of these novel proteins is beginning to emerge. However, there are very few generalizations that can be drawn at this point that can be derived from the limited number of studies that have focused on biocatalysis and thermostability at extremely high temperatures.},
}
@article {pmid8191287,
year = {1994},
author = {Rowlands, T and Baumann, P and Jackson, SP},
title = {The TATA-binding protein: a general transcription factor in eukaryotes and archaebacteria.},
journal = {Science (New York, N.Y.)},
volume = {264},
number = {5163},
pages = {1326-1329},
doi = {10.1126/science.8191287},
pmid = {8191287},
issn = {0036-8075},
support = {//Wellcome Trust/United Kingdom ; },
mesh = {Adenovirus E1A Proteins/genetics ; Amino Acid Sequence ; Arabidopsis/genetics ; Archaea/chemistry/*genetics/metabolism ; Base Sequence ; *Biological Evolution ; Cloning, Molecular ; DNA-Binding Proteins/chemistry/*genetics/metabolism ; Eukaryotic Cells/*metabolism ; Genes, Bacterial ; Molecular Sequence Data ; Polymerase Chain Reaction ; Recombinant Fusion Proteins ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae Proteins ; *TATA Box ; TATA-Box Binding Protein ; Transcription Factor TFIIB ; *Transcription Factor TFIIIB ; Transcription Factors/chemistry/*genetics/metabolism ; Transcription, Genetic ; Tumor Suppressor Protein p53/genetics ; },
abstract = {The TATA-binding protein TBP appears to be essential for all transcription in eukaryotic cell nuclei, which suggests that its function was established early in evolution. Archaebacteria constitute a kingdom of organisms distinct from eukaryotes and eubacteria. Archaebacterial gene regulatory sequences often map to TATA box-like motifs. Here it is shown that the archaebacterium Pyrococcus woesei expresses a protein with structural and functional similarity to eukaryotic TBP molecules. This suggests that TBP's role in transcription was established before the archaebacterial and eukaryotic lineages diverged and that the transcription systems of archaebacteria and eukaryotes are fundamentally homologous.},
}
@article {pmid8191278,
year = {1994},
author = {Barinaga, M},
title = {Molecular evolution. Archaea and eukaryotes grow closer.},
journal = {Science (New York, N.Y.)},
volume = {264},
number = {5163},
pages = {1251},
doi = {10.1126/science.8191278},
pmid = {8191278},
issn = {0036-8075},
mesh = {Archaea/*genetics ; *Biological Evolution ; DNA-Binding Proteins/*metabolism ; *Eukaryotic Cells/metabolism ; *TATA Box ; TATA-Box Binding Protein ; Transcription Factors/*metabolism ; Transcription, Genetic ; },
}
@article {pmid8183889,
year = {1994},
author = {Marsh, TL and Reich, CI and Whitelock, RB and Olsen, GJ},
title = {Transcription factor IID in the Archaea: sequences in the Thermococcus celer genome would encode a product closely related to the TATA-binding protein of eukaryotes.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {91},
number = {10},
pages = {4180-4184},
pmid = {8183889},
issn = {0027-8424},
mesh = {Amino Acid Sequence ; Animals ; Archaea/*genetics/metabolism ; *Biological Evolution ; Cloning, Molecular ; *Conserved Sequence ; DNA, Bacterial/genetics/metabolism ; *Genome, Bacterial ; Humans ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; Probability ; Restriction Mapping ; Sequence Homology, Amino Acid ; Transcription Factor TFIID ; Transcription Factors/biosynthesis/chemistry/*genetics ; },
abstract = {The first step in transcription initiation in eukaryotes is mediated by the TATA-binding protein, a subunit of the transcription factor IID complex. We have cloned and sequenced the gene for a presumptive homolog of this eukaryotic protein from Thermococcus celer, a member of the Archaea (formerly archaebacteria). The protein encoded by the archaeal gene is a tandem repeat of a conserved domain, corresponding to the repeated domain in its eukaryotic counterparts. Molecular phylogenetic analyses of the two halves of the repeat are consistent with the duplication occurring before the divergence of the archael and eukaryotic domains. In conjunction with previous observations of similarity in RNA polymerase subunit composition and sequences and the finding of a transcription factor IIB-like sequence in Pyrococcus woesei (a relative of T. celer) it appears that major features of the eukaryotic transcription apparatus were well-established before the origin of eukaryotic cellular organization. The divergence between the two halves of the archael protein is less than that between the halves of the individual eukaryotic sequences, indicating that the average rate of sequence change in the archael protein has been less than in its eukaryotic counterparts. To the extent that this lower rate applies to the genome as a whole, a clearer picture of the early genes (and gene families) that gave rise to present-day genomes is more apt to emerge from the study of sequences from the Archaea than from the corresponding sequences from eukaryotes.},
}
@article {pmid8174557,
year = {1994},
author = {McDougall, J and Wittmann-Liebold, B},
title = {Comparative analysis of the protein components from 5S rRNA.protein complexes of halophilic archaebacteria.},
journal = {European journal of biochemistry},
volume = {221},
number = {2},
pages = {779-785},
doi = {10.1111/j.1432-1033.1994.tb18791.x},
pmid = {8174557},
issn = {0014-2956},
mesh = {Amino Acid Sequence ; Bacterial Proteins/*chemistry/isolation &amp; purification ; Electrophoresis, Polyacrylamide Gel ; Halobacteriaceae/*chemistry ; Molecular Sequence Data ; RNA, Ribosomal, 5S/*chemistry/isolation &amp; purification ; Ribonucleoproteins/*chemistry/isolation &amp; purification ; Ribosomal Proteins/*chemistry/isolation &amp; purification ; Sequence Alignment ; Sequence Homology, Amino Acid ; Terminology as Topic ; },
abstract = {The 5S RNA.protein complexes have been isolated from the 50S subunit of the halophilic archaebacteria Halobacterium cutirubrum, Halobacterium halobium, Halobacterium salinarium, Haloferax mediterranei, Haloferax volcanii and Haloarcula marismortui. The 50S subunits from most of the halophiles released a multiprotein ribonucleoprotein particle similar to that previously observed with the H. cutirubrum 5S RNA.protein complex, which contained proteins from the L5 and L18 ribosomal protein families. Ribosomes from H. marismortui, however, released an RNA.protein complex containing a single protein (L18) that is homologous to the single protein found in the eukaryotic 5S ribonucleoprotein complexes. N-terminal sequence analyses of the halophilic 5S RNA-binding proteins suggest that the L18 protein primary structure is highly conserved, with only the H. marismortui protein having a sequence difference in at least the first twenty amino acids. Although the L5 group of ribosomal proteins also shows a high conservation, it appears that the proteins may have had more freedom to diverge throughout evolution.},
}
@article {pmid8144483,
year = {1994},
author = {Amiri, KA},
title = {Fibrillarin-like proteins occur in the domain Archaea.},
journal = {Journal of bacteriology},
volume = {176},
number = {7},
pages = {2124-2127},
pmid = {8144483},
issn = {0021-9193},
mesh = {Amino Acid Sequence ; Chromosomal Proteins, Non-Histone/*genetics ; Cloning, Molecular ; Genes, Bacterial/*genetics ; Methanococcus/*genetics ; Molecular Sequence Data ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; },
abstract = {Fibrillarin is found in the nucleolus of Eucarya and associated with small nucleolar RNAs. It is involved in the processing of precursor rRNA. Two genes, encoding fibrillarin-like proteins from Methanococcus voltae and Methanococcus vannielii, have been isolated. The genes were named flpA (fibrillarin-like protein).},
}
@article {pmid8125106,
year = {1994},
author = {Bertram, PA and Karrasch, M and Schmitz, RA and Böcher, R and Albracht, SP and Thauer, RK},
title = {Formylmethanofuran dehydrogenases from methanogenic Archaea. Substrate specificity, EPR properties and reversible inactivation by cyanide of the molybdenum or tungsten iron-sulfur proteins.},
journal = {European journal of biochemistry},
volume = {220},
number = {2},
pages = {477-484},
doi = {10.1111/j.1432-1033.1994.tb18646.x},
pmid = {8125106},
issn = {0014-2956},
mesh = {Aldehyde Oxidoreductases/antagonists &amp; inhibitors/chemistry/*metabolism ; Cyanides/pharmacology ; Electron Spin Resonance Spectroscopy ; Iron-Sulfur Proteins/antagonists &amp; inhibitors/chemistry/*metabolism ; Kinetics ; Methanobacterium/*enzymology ; Methanosarcina barkeri/*enzymology ; Molybdenum/metabolism ; Protein Conformation ; Substrate Specificity ; Tungsten/metabolism ; },
abstract = {Formylmethanofuran dehydrogenases, which are found in methanogenic Archaea, are molybdenum or tungsten iron-sulfur proteins containing a pterin cofactor. We report here on differences in substrate specificity, EPR properties and susceptibility towards cyanide inactivation of the enzymes from Methanosarcina barkeri, Methanobacterium thermoautotrophicum and Methanobacterium wolfei. The molybdenum enzyme from M. barkeri (relative activity with N-formylmethanofuran = 100%) was found to catalyze, albeit at considerably reduced apparent Vmax, the dehydrogenation of N-furfurylformamide (11%), N-methylformamide (0.2%), formamide (0.1%) and formate (1%). The molybdenum enzyme from M. wolfei could only use N-furfurylformamide (1%) and formate (3%) as pseudosubstrates. The molybdenum enzyme from M. thermoautotrophicum and the tungsten enzymes from M. thermoautotrophicum and M. wolfei were specific for N-formylmethanofuran. The molybdenum formylmethanofuran dehydrogenases exhibited at 77 K two rhombic EPR signals, designated FMDred and FMDox, both derived from Mo as shown by isotopic substitution with 97Mo. The FMDred signal was only displayed by the active enzyme in the reduced form and was lost upon enzyme oxidation; the FMDox signal was displayed by an inactive form and was not quenched by O2. The tungsten isoenzymes were EPR silent. The molybdenum formylmethanofuran dehydrogenases were found to be inactivated by cyanide whereas the tungsten isoenzymes, under the same conditions, were not inactivated. Inactivation was associated with a characteristic change in the molybdenum-derived EPR signal. Reactivation was possible in the presence of sulfide.},
}
@article {pmid8113163,
year = {1994},
author = {Charbonnier, F and Forterre, P},
title = {Comparison of plasmid DNA topology among mesophilic and thermophilic eubacteria and archaebacteria.},
journal = {Journal of bacteriology},
volume = {176},
number = {5},
pages = {1251-1259},
pmid = {8113163},
issn = {0021-9193},
mesh = {Archaea/*chemistry/genetics/metabolism ; DNA Topoisomerases, Type II/metabolism ; DNA, Bacterial/*chemistry ; Escherichia coli/*chemistry/genetics/metabolism ; Hot Temperature ; Methanobacterium/chemistry/genetics/metabolism ; Phylogeny ; Plasmids/*chemistry/isolation &amp; purification ; Species Specificity ; },
abstract = {Several plasmid DNAs have been isolated from mesophilic and thermophilic archaebacteria. Their superhelical densities were estimated at their host strain's optimal growth temperature, and in some representative strains, the presence of reverse gyrase activity (positive DNA supercoiling) was investigated. We show here that these plasmids can be grouped in two clusters with respect to their topological state. The group I plasmids have a highly negatively supercoiled DNA and belong to the mesophilic archaebacteria and all types of eubacteria. The group II plasmids have DNA which is close to the relaxed state and belong exclusively to the thermophilic archaebacteria. All archaebacteria containing a relaxed plasmid, with the exception of the moderately thermophilic methanogen Methanobacterium thermoautotrophicum Marburg, also exhibit reverse gyrase activity. These findings show that extrachromosomal DNAs with very different topological states coexist in the archaebacterial domain.},
}
@article {pmid7968661,
year = {1994},
author = {Hamana, K and Hamana, H and Niitsu, M and Samejima, K and Sakane, T and Yokota, A},
title = {Occurrence of tertiary and quaternary branched polyamines in thermophilic archaebacteria.},
journal = {Microbios},
volume = {79},
number = {319},
pages = {109-119},
pmid = {7968661},
issn = {0026-2633},
mesh = {Archaea/*chemistry ; Biogenic Amines/chemistry/*isolation &amp; purification ; Chromatography, High Pressure Liquid ; Molecular Structure ; Polyamines/chemistry/*isolation &amp; purification ; Species Specificity ; Sulfolobus/chemistry ; Thermoplasma/chemistry ; },
abstract = {Polyamines of thermophilic archaebacteria were analysed by high-performance liquid chromatography and gas chromatography. Thermoplasma acidophilum and Thermoplasma volcanium ubiquitously contained spermidine and spermine. Four species of Sulfolobus, S. acidocaldarius, S. solfataricus, S. metallicus and S. shibatae, two species of Acidianus, A. brierleyi and A. infernus, and Metallosphaera sedula, contained norspermidine and norspermine in addition to spermidine and spermine, but quantitative distribution profiles were species-specific. A tertiary tetra-amine, N4-aminopropylspermidine, and a quaternary penta-amine, N4-bis(aminopropyl)spermidine, were detected as a major polyamine in three species of Thermococcus, T. celer, T. litoralis and T. stetteri, and two Pyrococcus species, P. furiosus and P. woesei. This is the first report on the occurrence of branched polyamines in archaebacteria.},
}
@article {pmid7872839,
year = {1994},
author = {Hartmann, E and König, H},
title = {A novel pathway of peptide biosynthesis found in methanogenic Archaea.},
journal = {Archives of microbiology},
volume = {162},
number = {6},
pages = {430-432},
pmid = {7872839},
issn = {0302-8933},
mesh = {Cell Wall/metabolism ; Glutamic Acid/metabolism ; Methanobacterium/*metabolism ; Peptidoglycan/*biosynthesis/chemistry ; },
abstract = {The peptide subunits of the pseudomurein, the cell-wall peptidoglycan of some methanogens, are usually composed of glutamic acid, alanine and lysine. In order to get a more detailed picture of the biosynthetic pathway of the peptide subunit, we performed in vitro assays. Starting from glutamic acid a pentapeptide was obtained in seven steps: [formula: see text] The pentapeptide structure was identical to that of the peptide subunit of the intact pseudomurein except one additional alanine residue, which is split off during further processing. The pentapeptide synthesis starts with glutamic acid, which is phosphorylated at the N alpha-amino group. N alpha-phosphoryl-glutamic acid is transferred to a nucleotide-carrier, forming N alpha-UDP-glutamic acid. The further pentapeptide biosynthesis is achieved via a di-, tri- and tetrapeptide by stepwise addition of the corresponding amino acids.},
}
@article {pmid8253663,
year = {1993},
author = {Spudich, JL},
title = {Color sensing in the Archaea: a eukaryotic-like receptor coupled to a prokaryotic transducer.},
journal = {Journal of bacteriology},
volume = {175},
number = {24},
pages = {7755-7761},
pmid = {8253663},
issn = {0021-9193},
support = {GM-27750/GM/NIGMS NIH HHS/United States ; },
mesh = {Amino Acid Sequence ; Archaea/*physiology ; Bacteriorhodopsins/chemistry/metabolism/*physiology ; *Color ; *Halorhodopsins ; Models, Structural ; Molecular Sequence Data ; Photoreceptor Cells/*physiology ; Protein Folding ; Protein Structure, Secondary ; *Sensory Rhodopsins ; Signal Transduction ; },
}
@article {pmid8249290,
year = {1993},
author = {Nuttall, SD and Dyall-Smith, ML},
title = {HF1 and HF2: novel bacteriophages of halophilic archaea.},
journal = {Virology},
volume = {197},
number = {2},
pages = {678-684},
doi = {10.1006/viro.1993.1643},
pmid = {8249290},
issn = {0042-6822},
mesh = {Bacteriophages/drug effects/genetics/*isolation &amp; purification/ultrastructure ; Chloroform/pharmacology ; DNA, Viral/analysis/metabolism ; Deoxyribonucleases, Type II Site-Specific/metabolism ; Genome, Viral ; *Halobacteriales ; Sodium/pharmacology ; Species Specificity ; Viral Proteins/analysis ; },
abstract = {Two novel halophilic archaebacterial bacteriophages, HF1 and HF2, were isolated from an Australian solar saltern. They were morphologically identical with icosahedral-shaped heads (diameter 58 nm) and contractile tails (length 94 nm). Other similarities included sensitivity to reduced ionic conditions, similar protein profiles by SDS-PAGE, and dsDNA genomes of identical size (73.5 kbp) with analogous restriction patterns. DNA-DNA hybridization data showed the two phages to be closely related. HF1 has a broad host-range, infecting members of three halobacterial genera including Halobacterium salinarium and the genetically well-characterized strain Haloferax volcanii WFD11. Mutants showing increased plating efficiency on alternative hosts were readily selectable. By contrast, HF2 showed a limited host range, confined to the closely related dam-methylated strains Ch2 and H. saccharovorum.},
}
@article {pmid8114110,
year = {1993},
author = {Gupta, RS and Golding, GB},
title = {Evolution of HSP70 gene and its implications regarding relationships between archaebacteria, eubacteria, and eukaryotes.},
journal = {Journal of molecular evolution},
volume = {37},
number = {6},
pages = {573-582},
pmid = {8114110},
issn = {0022-2844},
mesh = {Amino Acid Sequence ; Animals ; Archaea/*genetics ; Bacteria/*genetics ; *Biological Evolution ; Eukaryotic Cells ; Heat-Shock Proteins/chemistry/*genetics ; Humans ; Molecular Sequence Data ; Phylogeny ; Protein Conformation ; Sequence Homology, Amino Acid ; },
abstract = {The 70-kDa heat-shock protein (HSP70) constitutes the most conserved protein present in all organisms that is known to date. Based on global alignment of HSP70 sequences from organisms representing all three domains, numerous sequence signatures that are specific for prokaryotic and eukaryotic homologs have been identified. HSP70s from the two archaebacterial species examined (viz., Halobacterium marismortui and Methanosarcina mazei) have been found to contain all eubacterial but no eukaryotic signature sequences. Based on several novel features of the HSP70 family of proteins (viz., presence of tandem repeats of a 9-amino-acid [a.a.] polypeptide sequence and structural similarity between the first and second quadrants of HSP70, homology of the N-terminal half of HSP70 to the bacterial MreB protein, presence of a conserved insert of 23-27 a.a. in all HSP70s except those from archaebacteria and gram-positive eubacteria) a model for the evolution of HSP70 gene from an early stage is proposed. The HSP70 homologs from archaebacteria and gram-positive bacteria lacking the insert in the N-terminal quadrants are indicated to be the ancestral form of the protein. Detailed phylogenetic analyses of HSP70 sequence data (viz., by bootstrap analyses, maximum parsimony, and maximum likelihood methods) provide evidence that archaebacteria are not monophyletic and show a close evolutionary linkage with the gram-positive eubacteria. These results do not support the traditional archaebacterial tree, where a close relationship between archaebacterial and eukaryotic homologs is observed. To explain the phylogenies based on HSP70 and other gene sequences, a model for the origin of eukaryotic cells involving fusion between archaebacteria and gram-negative eubacteria is proposed.},
}
@article {pmid8366053,
year = {1993},
author = {Chen, W and Konisky, J},
title = {Characterization of a membrane-associated ATPase from Methanococcus voltae, a methanogenic member of the Archaea.},
journal = {Journal of bacteriology},
volume = {175},
number = {17},
pages = {5677-5682},
pmid = {8366053},
issn = {0021-9193},
support = {GM41587/GM/NIGMS NIH HHS/United States ; },
mesh = {Adenosine Triphosphatases/antagonists &amp; inhibitors/*metabolism ; Amino Acid Sequence ; Anti-Bacterial Agents/pharmacology ; Cell Membrane/enzymology ; Dicyclohexylcarbodiimide/pharmacology ; Electrophoresis, Polyacrylamide Gel ; Hydrogen-Ion Concentration ; *Macrolides ; Membrane Proteins/*metabolism ; Methanococcus/*enzymology/ultrastructure ; Molecular Sequence Data ; Nitrates/pharmacology ; Sequence Homology, Amino Acid ; },
abstract = {A membrane-associated ATPase with an M(r) of approximately 510,000 and containing subunits with M(r)s of 80,000 (alpha), 55,000 (beta), and 25,000 (gamma) was isolated from the methanogen Methanococcus voltae. Enzymatic activity was not affected by vanadate or azide, inhibitors of P- and F1-ATPase, respectively, but was inhibited by nitrate and bafilomycin A1, inhibitors of V1-type ATPases. Since dicyclohexylcarbodiimide inhibited the enzyme when it was present in membranes but not after the ATPase was solubilized, we suggest the presence of membrane-associated component analogous to the F0 and V0 components of both F-type and V-type ATPases. N-terminal amino acid sequence analysis of the alpha subunit showed a higher similarity to ATPases of the V-type family than to those of the F-type family.},
}
@article {pmid8372232,
year = {1993},
author = {Koga, Y},
title = {[Characteristics of ether lipids specific to Archaea].},
journal = {Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme},
volume = {38},
number = {10},
pages = {1566-1574},
pmid = {8372232},
issn = {0039-9450},
mesh = {Archaea/genetics/*metabolism ; Ethers/chemistry/*metabolism ; Membrane Lipids/chemistry/*metabolism ; Molecular Conformation ; Phylogeny ; Species Specificity ; },
}
@article {pmid8372231,
year = {1993},
author = {Yamagishi, A},
title = {[Genetic structure and engineering of Archaebacteria].},
journal = {Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme},
volume = {38},
number = {10},
pages = {1556-1565},
pmid = {8372231},
issn = {0039-9450},
mesh = {Adenosine Triphosphatases ; Archaea/enzymology/*genetics ; Chromosomes, Bacterial ; DNA, Bacterial ; DNA-Directed DNA Polymerase ; *Genetic Engineering ; Histones ; Introns ; Phylogeny ; RNA Splicing ; rRNA Operon ; },
}
@article {pmid8372230,
year = {1993},
author = {Hasegawa, M},
title = {[Phylogenetic place of Archaebacteria and the origin of eukaryotes].},
journal = {Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme},
volume = {38},
number = {10},
pages = {1546-1555},
pmid = {8372230},
issn = {0039-9450},
mesh = {Animals ; Archaea/*genetics ; *Genes, Overlapping ; Peptide Elongation Factor 1 ; Peptide Elongation Factor 2 ; Peptide Elongation Factor G ; Peptide Elongation Factor Tu ; Peptide Elongation Factors ; *Phylogeny ; RNA, Ribosomal, 5S ; },
}
@article {pmid8335078,
year = {1993},
author = {Kamekura, M and Seno, Y},
title = {Partial sequence of the gene for a serine protease from a halophilic archaeum Haloferax mediterranei R4, and nucleotide sequences of 16S rRNA encoding genes from several halophilic archaea.},
journal = {Experientia},
volume = {49},
number = {6-7},
pages = {503-513},
pmid = {8335078},
issn = {0014-4754},
mesh = {Amino Acid Sequence ; Base Sequence ; *Genes, Bacterial ; Halobacteriaceae/*enzymology/*genetics ; Halobacterium/enzymology/genetics ; Molecular Sequence Data ; Oligodeoxyribonucleotides ; Oligopeptides/metabolism ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Sequence Homology, Nucleic Acid ; Serine Endopeptidases/*genetics/isolation &amp; purification/metabolism ; Substrate Specificity ; },
abstract = {A part of the gene coding for a halophilic serine protease from a halophilic archaeum Haloferax mediterranei R4 was amplified by PCR and its 672 nucleotide sequence was determined. Tentative translation to the amino acid sequence suggested that the enzyme was quite similar to halolysin produced by another halophilic archaeum strain 172P1. Nucleotide sequences of 16S rRNA encoding genes from 9 halophilic archaea were determined. Alignment of 19 sequences known so far showed that there are more than 20 positions carrying bases or deletions specific for each halobacterial genus: Halobacterium, Haloarcula, Haloferax, and Halococcus.},
}
@article {pmid8332479,
year = {1993},
author = {Macario, AJ and Dugan, CB and Clarens, M and Conway de Macario, E},
title = {dnaJ in Archaea.},
journal = {Nucleic acids research},
volume = {21},
number = {11},
pages = {2773},
pmid = {8332479},
issn = {0305-1048},
mesh = {Amino Acid Sequence ; Archaea/*genetics ; Bacterial Proteins/*genetics ; Base Sequence ; Conserved Sequence ; *Genes, Bacterial ; HSP40 Heat-Shock Proteins ; Heat-Shock Proteins/*genetics ; Humans ; Methanosarcina/*genetics ; Molecular Sequence Data ; Sequence Homology, Amino Acid ; },
}
@article {pmid7763882,
year = {1993},
author = {Ohshima, T and Nishida, N},
title = {Purification and properties of extremely thermostable glutamate dehydrogenases from two hyperthermophilic archaebacteria, Pyrococcus woesei and Pyrococcus furiosus.},
journal = {Bioscience, biotechnology, and biochemistry},
volume = {57},
number = {6},
pages = {945-951},
doi = {10.1271/bbb.57.945},
pmid = {7763882},
issn = {0916-8451},
mesh = {Amino Acid Sequence ; Amino Acids/metabolism ; Archaea/*enzymology ; Electrophoresis, Polyacrylamide Gel ; Enzyme Stability ; Glutamate Dehydrogenase/chemistry/*isolation &amp; purification/metabolism ; Hydrogen-Ion Concentration ; Keto Acids/metabolism ; Kinetics ; Molecular Sequence Data ; Molecular Weight ; NAD/metabolism ; NADP/metabolism ; Substrate Specificity ; Temperature ; },
abstract = {Glutamate dehydrogenase (L-glutamate: NADP oxidoreductase, deaminating, EC 1.4.1.4) from the hyperthermophilic archaebacteria Pyrococcus woesei and P. furiosus were purified to homogeneity from crude extracts. The enzymes had similar enzymological properties: molecular mass, subunit structure, optimum pHs for the oxidative deamination and reductive amination, substrate specificity and coenzyme specificity as well as thermostability; the activity was not lost after incubation at 105 degrees C for 30 min. However, some differences were detected in resistance to urea denaturation and effects of salts on their activity and stability. The N-terminal 20 amino acid sequences of the two enzymes were identical.},
}
@article {pmid8316235,
year = {1993},
author = {Derkacheva, NI and Kagramanova, VK and Man'kin, AS},
title = {[Instability of the halophilic archaebacteria genome].},
journal = {Molekuliarnaia biologiia},
volume = {27},
number = {3},
pages = {485-499},
pmid = {8316235},
issn = {0026-8984},
mesh = {Base Sequence ; DNA, Bacterial ; *Genome, Bacterial ; Halobacterium/*genetics ; Molecular Sequence Data ; Mutation ; Plasmids ; Recombination, Genetic ; Sequence Deletion ; },
abstract = {The phenomenon of high genetic variability in the extremely halophilic archaebacterium Hb. salinarium is reviewed. The role of IS elements and homologous recombination in frequent genetic rearrangements in this organism is discussed. A possible cause of high genetic variability of Hb. salinarium is considered.},
}
@article {pmid8315654,
year = {1993},
author = {Benachenhou-Lahfa, N and Forterre, P and Labedan, B},
title = {Evolution of glutamate dehydrogenase genes: evidence for two paralogous protein families and unusual branching patterns of the archaebacteria in the universal tree of life.},
journal = {Journal of molecular evolution},
volume = {36},
number = {4},
pages = {335-346},
pmid = {8315654},
issn = {0022-2844},
mesh = {Algorithms ; Amino Acid Sequence ; Animals ; Archaea/*genetics ; Bacteria/genetics ; Bacterial Proteins/*genetics ; Consensus Sequence ; Genes ; *Genes, Bacterial ; Glutamate Dehydrogenase/*genetics ; Molecular Sequence Data ; *Phylogeny ; Sequence Alignment ; Sequence Homology, Amino Acid ; Species Specificity ; Vertebrates/genetics ; },
abstract = {The existence of two families of genes coding for hexameric glutamate dehydrogenases has been deduced from the alignment of 21 primary sequences and the determination of the percentages of similarity between each pair of proteins. Each family could also be characterized by specific motifs. One family (Family I) was composed of gdh genes from six eubacteria and six lower eukaryotes (the primitive protozoan Giardia lamblia, the green alga Chlorella sorokiniana, and several fungi and yeasts). The other one (Family II) was composed of gdh genes from two eubacteria, two archaebacteria, and five higher eukaryotes (vertebrates). Reconstruction of phylogenetic trees using several parsimony and distance methods confirmed the existence of these two families. Therefore, these results reinforced our previously proposed hypothesis that two close but already different gdh genes were present in the last common ancestor to the three Ur-kingdoms (eubacteria, archaebacteria, and eukaryotes). The branching order of the different species of Family I was found to be the same whatever the method of tree reconstruction although it varied slightly according the region analyzed. Similarly, the topological positions of eubacteria and eukaryotes of Family II were independent of the method used. However, the branching of the two archaebacteria in Family II appeared to be unexpected: (1) the thermoacidophilic Sulfolobus solfataricus was found clustered with the two eubacteria of this family both in parsimony and distance trees, a situation not predicted by either one of the contradictory trees recently proposed; and (2) the branching of the halophilic Halobacterium salinarium varied according to the method of tree construction: it was closer to the eubacteria in the maximum parsimony tree and to eukaryotes in distance trees. Therefore, whatever the actual position of the halophilic species, archaebacteria did not appear to be monophyletic in these gdh gene trees. This result questions the firmness of the presently accepted interpretation of previous protein trees which were supposed to root unambiguously the universal tree of life and place the archaebacteria in this tree.},
}
@article {pmid8444863,
year = {1993},
author = {Johnson, JL and Rajagopalan, KV and Mukund, S and Adams, MW},
title = {Identification of molybdopterin as the organic component of the tungsten cofactor in four enzymes from hyperthermophilic Archaea.},
journal = {The Journal of biological chemistry},
volume = {268},
number = {7},
pages = {4848-4852},
pmid = {8444863},
issn = {0021-9258},
support = {GM00091/GM/NIGMS NIH HHS/United States ; },
mesh = {Aldehyde Oxidoreductases/*chemistry/isolation &amp; purification ; Archaea/*enzymology ; Chromatography, High Pressure Liquid ; *Coenzymes ; Metalloproteins/*analysis ; Molecular Structure ; Molybdenum Cofactors ; Organometallic Compounds/*chemistry ; Protein Conformation ; Pteridines/*analysis ; Pterins/*chemistry ; Spectrometry, Fluorescence ; Spectrophotometry, Ultraviolet ; },
abstract = {The hyperthermophilic Archaea represent some of the most ancient organisms on earth. A study of enzymatic cofactors in these organisms could provide basic information on the origins of related cofactors in man and other more recently evolved organisms. To this end, the nature of the tungsten cofactor in aldehyde ferredoxin oxidoreductases from Pyrococcus furiosus and ES-4 and in formaldehyde ferredoxin oxidoreductases from P. furiosus and Thermococcus litoralis has been investigated. All four proteins contain molybdopterin, previously characterized as the organic component of the molybdenum cofactor in a large number of molybdoenzymes. Molybdopterin was identified by conversion to the dicarboxamidomethyl derivative by alkylation of the vicinal sulfhydryl groups on the pterin side chain and by conversion to the oxidized fluorescent derivative, Form A. The pterin of the tungsten cofactor in the four enzymes was examined for the presence of appended GMP, CMP, AMP, or IMP previously observed in molybdenum cofactors of some molybdoenzymes. No evidence for the presence of a molybdopterin dinucleotide or other modified form of molybdopterin was obtained. These results further document the essential nature of molybdopterin for the function of molybdenum and tungsten enzymes in diverse life forms.},
}
@article {pmid8449866,
year = {1993},
author = {Joshi, P and Dennis, PP},
title = {Structure, function, and evolution of the family of superoxide dismutase proteins from halophilic archaebacteria.},
journal = {Journal of bacteriology},
volume = {175},
number = {6},
pages = {1572-1579},
pmid = {8449866},
issn = {0021-9193},
mesh = {Amino Acid Sequence ; Archaea/classification/*enzymology/genetics ; *Biological Evolution ; Genetic Variation ; Halobacterium/enzymology/genetics ; Molecular Sequence Data ; Phylogeny ; Sequence Homology, Amino Acid ; Superoxide Dismutase/chemistry/*genetics/metabolism ; },
abstract = {The protein sequences of seven members of the superoxide dismutase (SOD) family from halophilic archaebacteria have been aligned and compared with each other and with the homologous Mn and Fe SOD sequences from eubacteria and the methanogenic archaebacterium Methanobacterium thermoautotrophicum. Of 199 common residues in the SOD proteins from halophilic archaebacteria, 125 are conserved in all seven sequences, and 64 of these are encoded by single unique triplets. The 74 remaining positions exhibit a high degree of variability, and for almost half of these, the encoding triplets are connected by at least two nonsynonymous nucleotide substitutions. The majority of nucleotide substitutions within the seven genes are nonsynonymous and result in amino acid replacement in the respective protein; silent third-codon-position (synonymous) substitutions are unexpectedly rare. Halophilic SODs contain 30 specific residues that are not found at the corresponding positions of the methanogenic or eubacterial SOD proteins. Seven of these are replacements of highly conserved amino acids in eubacterial SODs that are believed to play an important role in the three-dimensional structure of the protein. Residues implicated in formation of the active site, catalysis, and metal ion binding are conserved in all Mn and Fe SODs. Molecular phylogenies based on parsimony and neighbor-joining methods coherently group the halophile sequences but surprisingly fail to distinguish between the Mn SOD of Escherichia coli and the Fe SOD of M. thermoautotrophicum as the outgroup. These comparisons indicate that as a group, the SODs of halophilic archaebacteria have many unique and characteristic features. At the same time, the patterns of nucleotide substitution and amino acid replacement indicate that these genes and the proteins that they encode continue to be subject to strong and changing selection. This selection may be related to the presence of oxygen radicals and the inter- and intracellular composition and concentration of metal cations.},
}
@article {pmid8449865,
year = {1993},
author = {Joshi, P and Dennis, PP},
title = {Characterization of paralogous and orthologous members of the superoxide dismutase gene family from genera of the halophilic archaebacteria.},
journal = {Journal of bacteriology},
volume = {175},
number = {6},
pages = {1561-1571},
pmid = {8449865},
issn = {0021-9193},
mesh = {Amino Acid Sequence ; Archaea/enzymology/*genetics ; Base Sequence ; Blotting, Southern ; DNA, Bacterial ; Gene Expression Regulation, Bacterial/drug effects ; Halobacterium/enzymology/genetics ; Molecular Sequence Data ; *Multigene Family ; Paraquat/pharmacology ; Protein Biosynthesis/drug effects ; Regulatory Sequences, Nucleic Acid ; Sequence Homology, Nucleic Acid ; Superoxide Dismutase/*genetics/metabolism ; Transcription, Genetic/drug effects ; },
abstract = {Four species representing three genera of halophilic archaebacteria were examined for the presence of genomic sequences that encode proteins of the superoxide dismutase family. Three species, Halobacterium cutirubrum, Halobacterium sp. strain GRB, and Haloferax volcanii, contain duplicated (paralogous) genes of the sod family; a fourth species, Haloarcula marismortui, contains only a single gene. These seven genes were cloned and sequenced, and their transcripts were characterized by Northern (RNA) hybridization, S1 nuclease protection, and primer extension. The expression of one of the two genes in H. cutirubrum, Halobacterium sp. strain GRB, and Haloferax volcanii was shown to be elevated in the presence of paraquat, a generator of superoxide radicals. The other genes, including the single gene from Haloarcula marismortui, exhibited no elevated expression in the presence of paraquat. The 5' and 3' flanking regions of all the genes contain recognizable promoter and terminator elements that are appropriately positioned relative to the 5' and 3' transcript end sites. Between genera, the orthologous paraquat-responsive genes exhibit no sequence similarity in either their 5' or 3' flanking regions, whereas the orthologous nonresponsive genes exhibit limited sequence similarity but only in the 5' flanking region. Within the coding region, the two paralogous genes of Haloferax volcanii are virtually identical (99.5%) despite the absence of similarity in the flanking regions. In contrast, the paralogous genes of H. cutirubrum and Halobacterium sp. strain GRB are only about 87% identical. In the alignment of all seven sequences, there are nine codon positions where both the TCN and AGY serine codons are utilized; some or all of these may well be examples of convergent evolution.},
}
@article {pmid8094388,
year = {1993},
author = {Akhmanova, AS and Kagramanova, VK and Mankin, AS},
title = {Heterogeneity of small plasmids from halophilic archaea.},
journal = {Journal of bacteriology},
volume = {175},
number = {4},
pages = {1081-1086},
pmid = {8094388},
issn = {0021-9193},
mesh = {Amino Acid Sequence ; Base Sequence ; DNA, Bacterial/*genetics ; Halobacterium/*genetics ; Molecular Sequence Data ; Open Reading Frames ; *Plasmids ; Polymorphism, Restriction Fragment Length ; Sequence Alignment ; Species Specificity ; },
abstract = {Small multicopy plasmids in three strains of halophilic archaea, SB3, GRB, and GN101, were found to be present in a cell as a population of related but not identical sequences. Two types of heterogeneity were observed: macroheterogeneity, represented by two major plasmid sequence versions homologous to each other by 80%, and microheterogeneity, in which individual plasmids differ by one or a few nucleotide substitutions.},
}
@article {pmid8422380,
year = {1993},
author = {White, RH},
title = {Structures of the modified folates in the thermophilic archaebacteria Pyrococcus furiosus.},
journal = {Biochemistry},
volume = {32},
number = {3},
pages = {745-753},
doi = {10.1021/bi00054a003},
pmid = {8422380},
issn = {0006-2960},
mesh = {Acetylglucosamine/analysis ; Archaea/*chemistry ; Carbohydrate Sequence ; Folic Acid/*analogs &amp; derivatives/chemistry ; Molecular Sequence Data ; Pentanols/isolation &amp; purification ; Pterins/chemistry ; Ribitol/analogs &amp; derivatives/chemistry ; Ribose/analysis ; Stereoisomerism ; },
abstract = {The structures of the modified folates present in Pyrococcus furiosus have been determined. This was accomplished largely by the characterization of the arylamines resulting from the air oxidative cleavage of the reduced modified folates present in these cells, using both chemical and enzymatic methods. Cell extracts separated on DEAE-Sephadex columns showed one major peak containing the arylamines derived from the modified folates. These arylamines were not retained on the DEAE-Sephadex columns, indicating that they contained no net negative charge. Purification of the azo dye derivatives of these arylamines on a Bio-Gel P-6 column showed the presence of three different compounds (compounds 1, 2, and 3) in an average amount of 4.1, 7.6, and 22 nmol/g dry weight of cells, respectively. Each of these compounds readily underwent mild acid hydrolysis (0.1 M HCl, 110 degrees C, 1 min) to produce the azo dye derivative of 5-(p-aminophenyl)-1,2,3,4-tetrahydroxypentane (pAPT). The structure and stereochemistry (ribo) of the pAPT was the same as the pAPT present in methanopterin. In addition, compounds 1, 2, and 3 were each shown to contain 1 mol equiv of ribose and 1, 2, and 3 mol equiv of N-acetylglucosamine (gluNAc), respectively, and were designated as the azo dye derivatives of pAPT-ribose-gluNAc, pAPT-ribose-(gluNAc)2, and pAPT-ribose-(gluNAc)3. Each of these compounds was readily cleaved to the azo dye derivative of pAPT-ribose by the enzymatic action of beta-N-acetylglucosaminidase, indicating that all the gluNAc residues were beta-linked.(ABSTRACT TRUNCATED AT 250 WORDS)},
}
@article {pmid8420970,
year = {1993},
author = {Kong, H and Kucera, RB and Jack, WE},
title = {Characterization of a DNA polymerase from the hyperthermophile archaea Thermococcus litoralis. Vent DNA polymerase, steady state kinetics, thermal stability, processivity, strand displacement, and exonuclease activities.},
journal = {The Journal of biological chemistry},
volume = {268},
number = {3},
pages = {1965-1975},
pmid = {8420970},
issn = {0021-9258},
mesh = {Archaea/*enzymology ; Base Sequence ; DNA-Directed DNA Polymerase/genetics/isolation &amp; purification/*metabolism ; Enzyme Stability ; Escherichia coli/genetics ; *Hot Temperature ; Kinetics ; Molecular Sequence Data ; Mutagenesis ; Recombinant Proteins/isolation &amp; purification/metabolism ; },
abstract = {We have isolated, cloned, and characterized a DNA polymerase from the hyperthermophile archaea Thermococcus litoralis, the Tli DNA polymerase (also referred to as Vent DNA polymerase). The enzyme is extremely thermostable, having a half-life of 8 h at 95 degrees C and about 2 h at 100 degrees C. Pseudo-first-order kinetics at 70 degrees C reveal an extremely low Km for a primed M13mp18 substrate (0.1 nM), coupled with a relatively high Km for dNTPs (50 microM). Accompanying extension rates are on the order of 1000 nucleotides/min. Synthesis by the polymerase is largely distributive, adding an average of 7 nucleotides/initiation event. This distributive synthesis can generate products of at least 10,000 bases. Tli DNA polymerase contains a 3'-->5' exonuclease activity that enhances the fidelity of replication by the enzyme (Mattila, P., Korpela, J., Tenkanen, T. and Pitkanen, K. (1991) Nucleic Acids Res. 19, 4967-4973). A 2-amino acid substitution within the conserved exonuclease domain abolishes both double and single strand-dependent exonuclease activity, without altering kinetic parameters for polymerization on a primed single-stranded template. Strand displacement activity by the mutated and unmutated forms increases with increasing temperature and is enhanced in the exonuclease-deficient form of the enzyme.},
}
@article {pmid7680117,
year = {1993},
author = {Kurosawa, N and Itoh, YH},
title = {Nucleotide sequence of the 16S rRNA gene from thermoacidophilic archaea Sulfolobus acidocaldarius ATCC33909.},
journal = {Nucleic acids research},
volume = {21},
number = {2},
pages = {357},
pmid = {7680117},
issn = {0305-1048},
mesh = {Base Sequence ; RNA, Bacterial ; RNA, Ribosomal, 16S/*genetics ; Sequence Homology, Nucleic Acid ; Sulfolobus acidocaldarius/*genetics ; },
}
@article {pmid8481089,
year = {1993},
author = {Schwörer, B and Breitung, J and Klein, AR and Stetter, KO and Thauer, RK},
title = {Formylmethanofuran: tetrahydromethanopterin formyltransferase and N5,N10-methylenetetrahydromethanopterin dehydrogenase from the sulfate-reducing Archaeoglobus fulgidus: similarities with the enzymes from methanogenic Archaea.},
journal = {Archives of microbiology},
volume = {159},
number = {3},
pages = {225-232},
pmid = {8481089},
issn = {0302-8933},
mesh = {Amino Acid Sequence ; Archaea/*enzymology/genetics ; Enzyme Stability ; Euryarchaeota/enzymology/genetics ; Hydrogen-Ion Concentration ; *Hydroxymethyl and Formyl Transferases ; Kinetics ; Molecular Sequence Data ; Molecular Weight ; Oxidoreductases Acting on CH-NH Group Donors/chemistry/genetics/*metabolism ; Species Specificity ; Transferases/chemistry/genetics/*metabolism ; },
abstract = {The sulfate-reducing Archaeoglobus fulgidus contains a number of enzymes previously thought to be unique for methanogenic Archaea. The purification and properties of two of these enzymes, of formylmethanofuran: tetrahydromethanopterin formyltransferase and of N5,N10-methylenetetrahydromethanopterin dehydrogenase (coenzyme F420 dependent) are described here. A comparison of the N-terminal amino acid sequences and of other molecular properties with those of the respective enzymes from three methanogenic Archaea revealed a high degree of similarity.},
}
@article {pmid8422966,
year = {1993},
author = {Bruenger, E and Kowalak, JA and Kuchino, Y and McCloskey, JA and Mizushima, H and Stetter, KO and Crain, PF},
title = {5S rRNA modification in the hyperthermophilic archaea Sulfolobus solfataricus and Pyrodictium occultum.},
journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology},
volume = {7},
number = {1},
pages = {196-200},
doi = {10.1096/fasebj.7.1.8422966},
pmid = {8422966},
issn = {0892-6638},
support = {GM 29812/GM/NIGMS NIH HHS/United States ; },
mesh = {Archaea/*chemistry ; Base Sequence ; Cytidine/*analogs &amp; derivatives/analysis ; Hot Temperature ; Molecular Sequence Data ; Nucleic Acid Conformation ; Nucleic Acid Denaturation ; Nucleosides/*analysis ; RNA, Ribosomal, 5S/*chemistry/drug effects ; Ribonuclease T1/pharmacology ; Sulfolobus ; },
abstract = {The 5S rRNAs from Sulfolobus solfataricus and Pyrodictium occultum were digested to nucleosides and analyzed using directly-combined HPLC/mass spectrometry. P. occultum 5S rRNA contains two modified nucleoside species, N4-acetylcytidine (ac4C) and N4-acetyl-2'-O-methylcytidine (ac4Cm). Oligonucleotides were generated from P. occultum 5S rRNA by RNase T1 hydrolysis, and their molecular weights were determined using electrospray mass spectrometry and compared with those predicted from the P. occultum 5S RNA gene sequence. Deviation in mass between expected and observed molecular weights permitted ac4Cm to be located at position 35, in the nonanucleotide CAA-CACC[ac4Cm]G, and the ac4C in one or both of two (C,U)G trinucleotides. 2'-O-Methylcytidine is unambiguously characterized in S. solfataricus 5S rRNA, confirming earlier tentative assignments at the analogous sequence position (Stahl, D.A., Luehrsen, K.R., Woese, C.R., and Pace, N.R. (1981) Nucleic Acids Res., Vol. 9, pp. 6129-6137; Dams, E., Londei, P., Cammarano, P., Vandenberghe, A., and De Wachter, R. (1983) Nucleic Acids Res. Vol. 11, pp. 4667-4676). Potential effects of the presence of ac4C and ac4Cm on thermal stabilization of 5S rRNA in thermophiles are discussed.},
}
@article {pmid1475179,
year = {1992},
author = {Hodges, RA and Perler, FB and Noren, CJ and Jack, WE},
title = {Protein splicing removes intervening sequences in an archaea DNA polymerase.},
journal = {Nucleic acids research},
volume = {20},
number = {23},
pages = {6153-6157},
pmid = {1475179},
issn = {0305-1048},
mesh = {Amino Acid Sequence ; Archaea/*enzymology/metabolism ; Base Sequence ; DNA, Bacterial ; DNA-Directed DNA Polymerase/genetics/*metabolism ; Molecular Sequence Data ; *Protein Processing, Post-Translational ; RNA Splicing ; Sequence Homology, Amino Acid ; },
abstract = {The Vent DNA polymerase gene from Thermococcus litoralis contains two in-frame insertions that must be spliced out to form the mature polymerase. Primer extension and cDNA PCR revealed no evidence of spliced RNA to account for this editing. In contrast, pulse-chase analysis indicated that expression constructs lacking the first insertion produced a protein precursor in Escherichia coli that was processed post-translationally to form polymerase and I-TliI, the endonuclease protein that is the product of the second insertion. At least one intermediate, which migrated more slowly than the precursor and may be branched, was also detected. Amino acid substitutions at the splice junction slowed or blocked the protein splicing reaction. Processing occurs in several heterologous systems, indicating either self-splicing or ubiquitous splicing factors. Processing occurs in a mutant lacking I-TliI endonuclease activity, establishing the independence of splicing and endonuclease activities.},
}
@article {pmid1459989,
year = {1992},
author = {Pfeifer, F and Englert, C},
title = {Function and biosynthesis of gas vesicles in halophilic Archaea.},
journal = {Journal of bioenergetics and biomembranes},
volume = {24},
number = {6},
pages = {577-585},
pmid = {1459989},
issn = {0145-479X},
mesh = {Amino Acid Sequence ; Bacterial Proteins/genetics/metabolism ; Base Sequence ; DNA, Bacterial ; Genome, Bacterial ; Halobacterium/genetics/growth &amp; development/*metabolism/ultrastructure ; Molecular Sequence Data ; Mutation ; Organelles/*metabolism ; Promoter Regions, Genetic ; *Proteins ; Sequence Homology, Amino Acid ; Sequence Homology, Nucleic Acid ; Transcription, Genetic ; Transformation, Bacterial ; },
abstract = {The proteinaceous gas vesicles produced by various microorganisms including halophilic Archaea are hollow, gas-filled structures with a hydrophobic inner and a hydrophilic outer surface. The structural components of gas vesicles and their biosynthesis are still under investigation; an 8-kDa polypeptide appears to be the major constituent of the gas-vesicle envelope. Genetic analysis of the halobacterial gas-vesicle synthesis revealed an unexpected complexity: about 14 genes organized in three transcription units are involved in gas-vesicle structure, assembly, and gene regulation. Here we describe the comparison of three different genomic regions encoding gas vesicles in Halobacterium salinarium (p-vac and c-vac regions) and Haloferax mediterranei (mc-vac region) and speculate on the function of the gene products involved in gas-vesicle synthesis.},
}
@article {pmid1288326,
year = {1992},
author = {Schäfer, G and Meyering-Vos, M},
title = {The plasma membrane ATPase of archaebacteria. A chimeric energy converter.},
journal = {Annals of the New York Academy of Sciences},
volume = {671},
number = {},
pages = {293-309},
doi = {10.1111/j.1749-6632.1992.tb43804.x},
pmid = {1288326},
issn = {0077-8923},
mesh = {Adenosine Triphosphatases/chemistry/genetics/*metabolism ; Amino Acid Sequence ; Animals ; Archaea/*enzymology/genetics ; Cattle ; Cell Membrane/*enzymology ; Kinetics ; Macromolecular Substances ; Molecular Sequence Data ; Protein Structure, Secondary ; Sequence Homology, Amino Acid ; Sulfolobus/*enzymology/genetics ; },
}
@article {pmid1280806,
year = {1992},
author = {Reddy, DM and Crain, PF and Edmonds, CG and Gupta, R and Hashizume, T and Stetter, KO and Widdel, F and McCloskey, JA},
title = {Structure determination of two new amino acid-containing derivatives of adenosine from tRNA of thermophilic bacteria and archaea.},
journal = {Nucleic acids research},
volume = {20},
number = {21},
pages = {5607-5615},
pmid = {1280806},
issn = {0305-1048},
support = {AI 12277/AI/NIAID NIH HHS/United States ; GM 21584/GM/NIGMS NIH HHS/United States ; GM 36042/GM/NIGMS NIH HHS/United States ; },
mesh = {Adenosine/*chemistry ; Archaea/*genetics ; Bacteria/*genetics ; Chromatography, High Pressure Liquid ; Gram-Negative Anaerobic Bacteria/genetics ; Mass Spectrometry ; Molecular Structure ; Molecular Weight ; *Nucleic Acid Conformation ; Nucleosides/chemistry ; RNA, Bacterial/chemistry ; RNA, Transfer/*chemistry ; },
abstract = {Two new nucleosides have been identified in unfractionated transfer RNA of two thermophilic bacteria, Thermodesulfobacterium commune, and Thermotoga maritima, six hyperthermophilic archaea, including Pyrobaculum islandicum, Pyrococcus furiosus and Thermococcus sp. and two mesophilic archaea, Methanococcus vannielii and Methanolobus tindarius. Structures were determined primarily by mass spectrometry, as 3-hydroxy-N-[[(9-beta-D-ribofuranosyl-9H-purin-6- yl)amino]carbonyl]norvaline, (hn6A), structure 1, and 3-hydroxy-N-[[(9-beta-D-ribofuranosyl-9H-2-methylthiopurin-6- yl)amino]carbonyl]norvaline (ms2hn6A), 2. The amino acid side chain was characterized as 3-hydroxynorvaline (3) by gas chromatography-mass spectrometry of the trimethylsilyl derivative after cleavage from 1 and 2 by alkaline hydrolysis. Evidence for the amino acid-purine carbamoyl linkage was obtained from the collision-induced dissociation mass spectrum of trimethylsilylated 1, and the total structure was confirmed by chemical synthesis of 1.},
}
@article {pmid1426243,
year = {1992},
author = {Siegmund, KD and Klink, F},
title = {Production of an antiserum specific to the ADP-ribosylated form of elongation factor 2 from archaebacteria and eukaryotes.},
journal = {FEBS letters},
volume = {312},
number = {2-3},
pages = {139-142},
doi = {10.1016/0014-5793(92)80921-3},
pmid = {1426243},
issn = {0014-5793},
mesh = {Adenosine Diphosphate/metabolism ; Animals ; Antibodies, Bacterial/*immunology ; Antibody Specificity ; Cloning, Molecular ; Cross Reactions ; Enzyme-Linked Immunosorbent Assay ; Immune Sera/*immunology ; Immunization ; Isoelectric Focusing ; Peptide Elongation Factor 2 ; Peptide Elongation Factors/*immunology/metabolism ; Rabbits ; Rats ; Ribose/metabolism ; Sulfolobus acidocaldarius/*immunology ; },
abstract = {An antiserum to ADP-ribosylated elongation factor 2 (ADPR-EF-2) from S. acidocaldarius was raised in rabbits using stained, homogenized, ADPR-EF-2-containing slices from SDS-gels as a source of antigen. Elongation factor 2 (EF-2) from S. acidocaldarius was cloned in E. coli and the expressed gene product was used in order to adsorb all anti-EF-2 antibodies which do not contain the ADP-ribosyl group within their epitopes, as E. coli is unable to synthesize the ADP-ribosyl acceptor diphthamide. The remaining antibodies were specific to ADP-ribosylated EF-2 from Thermoplasma acidophilum, S. acidocaldarius and Desulfurococcus mucosus. ADP-ribosylated EF-2 from eukaryotic sources also reacted with the adsorbed antiserum as shown for EF-2 isolated from the killi-fish Cynolebias whitei, the mouse species BALB/c and Han/Wistar rats. The adsorbed antiserum did not cross-react with ADP-ribosylated actin or rho protein or with FAD-containing D-amino acid oxidase.},
}
@article {pmid1459413,
year = {1992},
author = {Pochart, P and Doré, J and Lémann, F and Goderel, I and Rambaud, JC},
title = {Interrelations between populations of methanogenic archaea and sulfate-reducing bacteria in the human colon.},
journal = {FEMS microbiology letters},
volume = {77},
number = {1-3},
pages = {225-228},
doi = {10.1016/0378-1097(92)90160-p},
pmid = {1459413},
issn = {0378-1097},
mesh = {Adolescent ; Adult ; Bacteria/metabolism ; Colon/metabolism/*microbiology ; Euryarchaeota/*isolation &amp; purification ; Female ; Humans ; Male ; Middle Aged ; Oxidation-Reduction ; Sulfates/*metabolism ; },
abstract = {In humans, CH4 is produced in the colon by methanogenic archaea and is detected in breath samples from approximately 50% of healthy adults, identified as CH4-excretors. Methanogenesis and sulfate reduction have been described as two mutually exclusive processes, potentially regulated by sulfate availability. To determine whether microbial population balances reflected these apparently co-regulated activities, we compared sulfate-reducing bacteria, methanogenic archaea, sulfate and sulfide concentrations in faeces of 10 CH4-excretors (CH4+) and 9 non-CH4-excretors (CH4-). The mean +/- SE of the logarithm of methanogenic archaea per gram wet weight were 9.0 +/- 0.2 and 4.0 +/- 0.7 for CH4+ and CH4-, respectively (P < 0.001). Sulfate-reducing bacterial counts were 6.5 +/- 0.1 and 7.3 +/- 0.2, respectively (P < 0.001). Fecal sulfate and sulfide concentrations did not differ between groups. These results suggest that a competitive interrelation between methanogenic archaea and sulfate-reducing bacteria occurs in the human colon. However, it does not lead to a complete exclusion of the two populations.},
}
@article {pmid1423586,
year = {1992},
author = {Ouzounis, C and Sander, C},
title = {TFIIB, an evolutionary link between the transcription machineries of archaebacteria and eukaryotes.},
journal = {Cell},
volume = {71},
number = {2},
pages = {189-190},
doi = {10.1016/0092-8674(92)90347-f},
pmid = {1423586},
issn = {0092-8674},
mesh = {Amino Acid Sequence ; Animals ; Archaea/*genetics ; Conserved Sequence ; *Eukaryotic Cells ; Humans ; Molecular Sequence Data ; Sequence Homology, Amino Acid ; Sulfur-Reducing Bacteria/classification ; Transcription Factor TFIIB ; Transcription Factors/*genetics ; Transcription, Genetic ; },
}
@article {pmid1356441,
year = {1992},
author = {Miyauchi, S and Komatsubara, M and Kamo, N},
title = {In archaebacteria, there is a doxorubicin efflux pump similar to mammalian P-glycoprotein.},
journal = {Biochimica et biophysica acta},
volume = {1110},
number = {2},
pages = {144-150},
doi = {10.1016/0005-2736(92)90351-l},
pmid = {1356441},
issn = {0006-3002},
mesh = {ATP Binding Cassette Transporter, Subfamily B, Member 1 ; Animals ; Archaea/drug effects/*metabolism ; Bacillus subtilis/drug effects/metabolism ; Biological Transport, Active/drug effects ; Carbonyl Cyanide p-Trifluoromethoxyphenylhydrazone/pharmacology ; Cell Division/drug effects ; Diltiazem/pharmacology ; Doxorubicin/*metabolism/pharmacology ; Drug Resistance, Microbial ; Drug Synergism ; Flow Cytometry ; Fluorescent Dyes ; Mammals ; Membrane Glycoproteins/*metabolism ; Nifedipine/pharmacology ; Rhodamine 123 ; Rhodamines/metabolism ; Tumor Cells, Cultured ; Verapamil/pharmacology ; },
abstract = {We selected for study an anthracycline-resistant mutant from the archaebacteria Haloferax volcanii. This resistance was reversed by a Ca(2+)-channel antagonist, nifedipine (NDP). This resistance and its reversal by NDP suggest P-glycoprotein (Pgp) to be responsible for maintaining an anticancer drug concentration below the cytotoxic level. Using rhodamine 123 (RH123) as a substrate for Pgp, we then examined whether the resistance to anthracyclines in this bacteria might involve a Pgp-like anthracycline efflux pump. RH123 accumulation by the bacteria was determined with flow cytometry. A steady-state RH123 accumulation by the resistant cells revealed approx. one-fifteenth of that by the wild-type cells, which could be remarkably enhanced by NDP. The other modulators of Pgp, diltiazem and verapamil, also enhanced RH123 accumulation in resistant cells. The uncoupler FCCP completely restored RH123 accumulation in resistant cells to the wild-type cell level. RH123 unidirectional efflux from resistant cells after its preloading revealed much greater than that from wild-type cells, which was remarkably inhibited by FCCP. These confirmed that RH123 low accumulation involves its active efflux mechanism. Taken together, the present study indicated that lower evolutionary archaebacteria might also express a Pgp-like protein very similar to mammalian Pgp.},
}
@article {pmid1404376,
year = {1992},
author = {Englert, C and Krüger, K and Offner, S and Pfeifer, F},
title = {Three different but related gene clusters encoding gas vesicles in halophilic archaea.},
journal = {Journal of molecular biology},
volume = {227},
number = {2},
pages = {586-592},
doi = {10.1016/0022-2836(92)90914-6},
pmid = {1404376},
issn = {0022-2836},
mesh = {*Archaeal Proteins ; Bacterial Outer Membrane Proteins/*genetics ; Base Sequence ; Blotting, Northern ; DNA, Bacterial ; *Genes, Bacterial ; Halobacteriaceae/*genetics ; Halobacterium/*genetics ; *Membrane Proteins ; Molecular Sequence Data ; *Multigene Family ; Open Reading Frames ; *Proteins ; Restriction Mapping ; Vacuoles/*metabolism ; },
abstract = {We present an analysis of the chromosomal region comprising the gene cluster involved in gas vesicle (Vac) synthesis in Haloferax mediterranei (mc-vac-region) and Halobacterium salinarium (c-vac-region) and compare both of them to the plasmid located p-vac-region of H. salinarium. The p-vac-region of 9000 base-pairs (9 kb) is more related to mc-vac (9.4 kb) of Hf. mediterranei than it is to the c-vac-region (8.3 kb) present in the same cell. The Vac- species Hf. volcanii becomes Vac+ following transformation with a fragment containing the entire mc-vac-region. Also the p-vac-region transforms Hf. volcanii to a Vac+ phenotype, indicating that this gene cluster is sufficient for gas vesicle synthesis and does not depend on products of the c-vac-region. Each of these vac-regions contains, in addition to gvpA encoding the major gas vesicle protein, 13 open reading frames named gvpC through gvpO. Ten of these, gvpD through gvpM, are located upstream from gvpA in opposite orientation, while gvpC, gvpN and gvpO are found 3' to gvpA. The absolute requirement of gvpO for gas vesicle synthesis was demonstrated by transformation experiments. Northern analyses with RNA samples isolated during the growth cycle of Hf. mediterranei or of H. salinarium PHH4 revealed that the mc-gvpD or c-gvpD mRNAs occur similar to the respective gvpA mRNA in stationary growth phase, while gvpF-gvpM are transcribed mainly during logarithmic growth. S1-nuclease mapping was performed to determine the transcriptional start site of the gvpD mRNA. The distance between the two divergent start sites of gvpA and gvpD mRNA is 109 base-pairs in mc-vac and p-vac, while in the case of c-vac this distance is 22 base-pairs larger. The conservation of the various gvp products, characteristic features and their possible functions in gas vesicle synthesis are discussed.},
}
@article {pmid1521540,
year = {1992},
author = {Zirngibl, C and Van Dongen, W and Schwörer, B and Von Bünau, R and Richter, M and Klein, A and Thauer, RK},
title = {H2-forming methylenetetrahydromethanopterin dehydrogenase, a novel type of hydrogenase without iron-sulfur clusters in methanogenic archaea.},
journal = {European journal of biochemistry},
volume = {208},
number = {2},
pages = {511-520},
doi = {10.1111/j.1432-1033.1992.tb17215.x},
pmid = {1521540},
issn = {0014-2956},
mesh = {Amino Acid Sequence ; Base Sequence ; Catalysis ; Cyanides/pharmacology ; Cysteine/analysis ; Flavins/analysis ; Hydrogen/*metabolism ; Iron-Sulfur Proteins/analysis ; Methanobacterium/*enzymology ; Molecular Sequence Data ; Nickel/analysis ; Oxidation-Reduction ; Oxidoreductases Acting on CH-NH Group Donors/chemistry/genetics/*metabolism ; Oxygen/pharmacology ; Sequence Homology, Nucleic Acid ; Spectrophotometry ; },
abstract = {A novel hydrogenase has recently been found in methanogenic archaea. It catalyzes the reversible dehydrogenation of methylenetetrahydromethanopterin (CH2 = H4MPT) to methenyltetrahydromethanopterin (CH identical to H4MPT+) and H2 and was therefore named H2-forming methylenetetrahydromethanopterin dehydrogenase. The hydrogenase, which is composed of only one polypeptide with an apparent molecular mass of 43 kDa, does not mediate the reduction of viologen dyes with either H2 or CH2 = H4MPT. We report here that the purified enzyme from Methanobacterium thermoautotrophicum exhibits the following other unique properties: (a) the colorless protein with a specific activity of 2000 U/mg (Vmax) did not contain iron-sulfur clusters, nickel, or flavins; (b) the activity was not inhibited by carbon monoxide, acetylene, nitrite, cyanide, or azide; (c) the enzyme did not catalyze an isotopic exchange between 3H2 and 1H+; (d) the enzyme catalyzed the reduction of CH identical to H4MPT+ with 3H2 generating [methylene-3H]CH2 = H4MPT; and (e) the primary structure contained at most four conserved cysteines as revealed by a comparison of the DNA-deduced amino acid sequence of the proteins from M. thermoautotrophicum and Methanopyrus kandleri. None of the four cysteines were closely spaced as would be indicative for a (NiFe) hydrogenase or a ferredoxin-type iron-sulfur protein. Properties of the H2-forming methylenetetrahydromethanopterin dehydrogenase from Methanobacterium wolfei are also described indicating that the enzyme from this methanogenic archaeon is very similar to the enzyme from M. thermoautotrophicum with respect both to molecular and catalytic properties.},
}
@article {pmid1369088,
year = {1992},
author = {Cowan, DA},
title = {Biotechnology of the Archaea.},
journal = {Trends in biotechnology},
volume = {10},
number = {9},
pages = {315-323},
doi = {10.1016/0167-7799(92)90257-v},
pmid = {1369088},
issn = {0167-7799},
mesh = {*Archaea/classification/genetics/metabolism ; Biotechnology ; Ecology ; Enzyme Stability ; Euryarchaeota/metabolism ; Phylogeny ; },
abstract = {The Archaea, designated since 1979 as a separate Super-Kingdom (the highest taxonomic order), are a highly novel group of microorganisms which look much like bacteria but have many molecular and genetic characteristics that are more typical of eukaryotes. These unusual organisms can be conveniently divided according to their 'extreme' environmental niche, into three broad phenotypes: the thermophiles, methanogens and extreme halophiles. Each group has unique biochemical features which can be exploited for use in the biotechnological industries. The extreme molecular stability of thermophile enzymes, the novel C1 pathways of the methanogens and the synthesis of organic polymers by some halophiles are all currently or potentially valuable examples of the biotechnology of the Archaea.},
}
@article {pmid1630899,
year = {1992},
author = {Ilyina, TV and Koonin, EV},
title = {Conserved sequence motifs in the initiator proteins for rolling circle DNA replication encoded by diverse replicons from eubacteria, eucaryotes and archaebacteria.},
journal = {Nucleic acids research},
volume = {20},
number = {13},
pages = {3279-3285},
pmid = {1630899},
issn = {0305-1048},
mesh = {Amino Acid Sequence ; Bacteria/genetics ; Bacterial Proteins/*chemistry ; Bacteriophages/genetics ; Consensus Sequence ; DNA Replication/*physiology ; DNA, Bacterial/genetics ; DNA, Circular/*genetics ; DNA, Single-Stranded/genetics ; DNA, Viral/genetics ; DNA-Binding Proteins/*chemistry ; Eukaryotic Cells ; Molecular Sequence Data ; Plasmids/genetics ; Viral Proteins/*chemistry ; },
abstract = {An amino acid motif was identified that consists of the sequence HisHydrHisHydrHydrHydr (Hydr--bulky hydrophobic residue) and is conserved in two vast classes of proteins, one of which is involved in initiation and termination of rolling circle DNA replication, or RCR (Rep proteins), and the other in mobilization (conjugal transfer) of plasmid DNA (Mob proteins). Based on analogies with metalloenzymes, it is hypothesized that the two conserved His residues in this motif may be involved in metal ion coordination required for the activity of the Rep and Mob proteins. Rep proteins contained two additional conserved motifs, one of which was located upstream, and the other downstream from the 'two His' motif. The C-terminal motif encompassed the Tyr residue(s) forming the covalent link with nicked DNA. Mob proteins were characterized by the opposite orientation of the conserved motifs, with the (putative) DNA-linking Tyr being located near their N-termini. Both Rep and Mob protein classes further split into several distinct families. Although it was not possible to find a motif or pattern that would be unique for the entire Rep or Mob class, unique patterns were derived for large subsets of the proteins of each class. These observations allowed the prediction of the amino acid residues involved in DNA nicking, which is required for the initiation of RCR or conjugal transfer of single-stranded (ss) DNA, in Rep and Mob proteins encoded by a number of replicons of highly diverse size, structure and origin. It is conjectured that recombination has played a major part in the dissemination of genes encoding related Rep or Mob proteins among the replicons exploiting RCR. It is speculated that the eucaryotic small ssDNA replicons encoding proteins with the conserved RCR motifs and replicating via RCR-related mechanisms, such as geminiviruses and parvoviruses, may have evolved from eubacterial replicons.},
}
@article {pmid1378590,
year = {1992},
author = {Kamekura, M and Seno, Y},
title = {Nucleotide sequences of 16S rRNA encoding genes from halophilic archaea Halococcus morrhuae NRC16008 and Haloferax mediterranei ATCC33500.},
journal = {Nucleic acids research},
volume = {20},
number = {13},
pages = {3517},
pmid = {1378590},
issn = {0305-1048},
mesh = {Base Sequence ; Genes, Bacterial/genetics ; Halobacteriaceae/*genetics ; Molecular Sequence Data ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/*genetics ; },
}
@article {pmid1535621,
year = {1992},
author = {Nishihara, M and Utagawa, M and Akutsu, H and Koga, Y},
title = {Archaea contain a novel diether phosphoglycolipid with a polar head group identical to the conserved core of eucaryal glycosyl phosphatidylinositol.},
journal = {The Journal of biological chemistry},
volume = {267},
number = {18},
pages = {12432-12435},
pmid = {1535621},
issn = {0021-9258},
mesh = {Carbohydrate Sequence ; Glycolipids/*analysis/chemistry ; Glycosylphosphatidylinositols ; Magnetic Resonance Spectroscopy ; Methanosarcina barkeri/*chemistry ; Molecular Sequence Data ; Molecular Structure ; Phosphatidylinositols/*analysis/chemistry ; },
abstract = {The structure of a major ether polar lipid of the methanogenic archaeon Methanosarcina barkeri was identified as glucosaminyl archaetidylinositol. This lipid had archaeol (2,3-di-O-phytanyl-sn-glycerol) as a core lipid portion, and the polar head group consisted of 1 mol each of phosphate, myo-inositol and D-GlcN. The polar head group was identified by means of chemical degradations, phosphatidylinositol-specific phospholipase C treatment, permethylation analysis, and fast atom bombardment-mass spectrometry as glucosaminylinositol phosphate, which was linked to the glycerol backbone via a phosphodiester bond. The stereochemical configuration of the phospho-myo-inositol residue of glucosaminyl archaetidylinositol was determined to be 1-D-myo-inositol 1-phosphate by measuring optical rotation of phospho-myo-inositol prepared by nitrous acid deamination and alkaline hydrolysis from the lipid. 1H NMR of the intact lipid showed that GlcN was linked to C-6 position of myo-inositol as an alpha-anomer. It is, finally, concluded that the complete structure of this lipid is 2,3-di-O-phytanyl-sn-glycero-1-phospho- 1'[6'-O-(2"-amino-2"-deoxy-alpha-D-glucopyranosyl)]-1'-D-myo-inositol. This lipid has a hybrid nature of an archaeal feature in alkyl glycerol diether core portion and an eucaryal feature in the polar head group identical to the conserved core structure (GlcNp(alpha 1-6)-myo-inositol 1-phosphate) of glycosylated phosphatidylinositol which serves as a membrane protein anchor in eucaryal cells.},
}
@article {pmid1608980,
year = {1992},
author = {DeLong, EF},
title = {Archaea in coastal marine environments.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {89},
number = {12},
pages = {5685-5689},
pmid = {1608980},
issn = {0027-8424},
mesh = {Animals ; Archaea/*genetics ; Base Sequence ; DNA, Bacterial/*genetics/isolation &amp; purification ; Molecular Sequence Data ; Nucleic Acid Conformation ; Oligodeoxyribonucleotides ; *Phylogeny ; Plankton/genetics ; Polymerase Chain Reaction/methods ; RNA, Ribosomal/genetics ; Seawater ; Sequence Homology, Nucleic Acid ; Water Microbiology ; },
abstract = {Archaea (archaebacteria) are a phenotypically diverse group of microorganisms that share a common evolutionary history. There are four general phenotypic groups of archaea: the methanogens, the extreme halophiles, the sulfate-reducing archaea, and the extreme thermophiles. In the marine environment, archaeal habitats are generally limited to shallow or deep-sea anaerobic sediments (free-living and endosymbiotic methanogens), hot springs or deep-sea hydrothermal vents (methanogens, sulfate reducers, and extreme thermophiles), and highly saline land-locked seas (halophiles). This report provides evidence for the widespread occurrence of unusual archaea in oxygenated coastal surface waters of North America. Quantitative estimates indicated that up to 2% of the total ribosomal RNA extracted from coastal bacterioplankton assemblages was archaeal. Archaeal small-subunit ribosomal RNA-encoding DNAs (rDNAs) were cloned from mixed bacterioplankton populations collected at geographically distant sampling sites. Phylogenetic and nucleotide signature analyses of these cloned rDNAs revealed the presence of two lineages of archaea, each sharing the diagnostic signatures and structural features previously established for the domain Archaea. Both of these lineages were found in bacterioplankton populations collected off the east and west coasts of North America. The abundance and distribution of these archaea in oxic coastal surface waters suggests that these microorganisms represent undescribed physiological types of archaea, which reside and compete with aerobic, mesophilic eubacteria in marine coastal environments.},
}
@article {pmid1608969,
year = {1992},
author = {Perler, FB and Comb, DG and Jack, WE and Moran, LS and Qiang, B and Kucera, RB and Benner, J and Slatko, BE and Nwankwo, DO and Hempstead, SK},
title = {Intervening sequences in an Archaea DNA polymerase gene.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {89},
number = {12},
pages = {5577-5581},
pmid = {1608969},
issn = {0027-8424},
mesh = {Amino Acid Sequence ; Archaea/enzymology/*genetics ; Base Sequence ; Chromosome Deletion ; DNA-Directed DNA Polymerase/*genetics/metabolism ; Escherichia coli/genetics ; Exons ; *Genes, Bacterial ; Humans ; *Introns ; Molecular Sequence Data ; Oligodeoxyribonucleotides ; Open Reading Frames ; Plasmids ; Recombinant Proteins/metabolism ; Restriction Mapping ; Saccharomyces cerevisiae/enzymology/genetics ; Sequence Homology, Nucleic Acid ; Viruses/enzymology/genetics ; },
abstract = {The DNA polymerase gene from the Archaea Thermococcus litoralis has been cloned and expressed in Escherichia coli. It is split by two intervening sequences (IVSs) that form one continuous open reading frame with the three polymerase exons. To our knowledge, neither IVS is similar to previously described introns. However, the deduced amino acid sequences of both IVSs are similar to open reading frames present in mobile group I introns. The second IVS (IVS2) encodes an endonuclease, I-Tli I, that cleaves at the exon 2-exon 3 junction after IVS2 has been deleted. IVS2 self-splices in E. coli to yield active polymerase, but processing is abolished if the IVS2 reading frame is disrupted. Silent changes in the DNA sequence at the exon 2-IVS2 junction that maintain the original protein sequence do not inhibit splicing. These data suggest that protein rather than mRNA splicing may be responsible for production of the mature polymerase.},
}
@article {pmid1579479,
year = {1992},
author = {Forterre, P},
title = {The DNA polymerase from the archaebacterium Pyrococcus furiosus does not testify for a specific relationship between archaebacteria and eukaryotes.},
journal = {Nucleic acids research},
volume = {20},
number = {7},
pages = {1811},
pmid = {1579479},
issn = {0305-1048},
mesh = {Amino Acid Sequence ; Archaea/classification/*enzymology ; Bacterial Proteins/chemistry/*classification ; DNA-Directed DNA Polymerase/chemistry/*classification ; Escherichia coli/classification/enzymology ; Humans ; Molecular Sequence Data ; Sequence Alignment ; Yeasts/classification/enzymology ; },
}
@article {pmid1311844,
year = {1992},
author = {Cohen, A and Lam, WL and Charlebois, RL and Doolittle, WF and Schalkwyk, LC},
title = {Localizing genes on the map of the genome of Haloferax volcanii, one of the Archaea.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {89},
number = {5},
pages = {1602-1606},
pmid = {1311844},
issn = {0027-8424},
mesh = {Archaea/*genetics ; Chromosome Mapping ; Chromosomes, Bacterial/*ultrastructure ; Cosmids ; DNA Transposable Elements ; DNA, Bacterial/*genetics ; *Genes, Bacterial ; Mutagenesis ; Nucleic Acid Hybridization ; RNA, Transfer/genetics ; Transformation, Genetic ; },
abstract = {We have assigned genetic markers to locations on the physical map of the genome of the archaeon Haloferax volcanii, using both a physical method (hybridization) and a more specific genetic technique (transformation with cosmids). Hybridizations were against restriction digests of each of 151 cosmids making up a minimally overlapping set and covering 96% of the genome. Results with a cloned insertion sequence and a tRNA probe indicated that transposable elements are concentrated on two of the four plasmids of this species, whereas regions complementary to tRNA are largely chromosomal. For a genetic analysis of genes involved in the biosynthesis of amino acids, purines, and pyrimidines, we used cosmid transformation to assign 139 of 243 ethyl methanesulfonate-induced auxotrophic mutations, generated and characterized for this study, to single cosmids or pairs of cosmids from the minimal set. Mutations affecting the biosynthesis of uracil, adenine, guanine, and 14 amino acids have been mapped in this way. All mutations mapped to the 2920-kilobase-pair chromosome of Hf. volcanii and seemed uniformly distributed around this circular replicon. In some cases, many mutations affecting a single pathway map to the same or overlapping cosmids, as would be expected were genes for the pathway linked. For other biosynthetic pathways, several unlinked genetic loci can be identified.},
}
@article {pmid1732209,
year = {1992},
author = {Kamekura, M and Seno, Y and Holmes, ML and Dyall-Smith, ML},
title = {Molecular cloning and sequencing of the gene for a halophilic alkaline serine protease (halolysin) from an unidentified halophilic archaea strain (172P1) and expression of the gene in Haloferax volcanii.},
journal = {Journal of bacteriology},
volume = {174},
number = {3},
pages = {736-742},
pmid = {1732209},
issn = {0021-9193},
mesh = {Amino Acid Sequence ; Base Sequence ; *Cloning, Molecular ; *Gene Expression ; Halobacteriales/*genetics ; Molecular Sequence Data ; Osmolar Concentration ; Restriction Mapping ; Sequence Homology, Nucleic Acid ; Serine Endopeptidases/*genetics ; Subtilisins/genetics ; Transformation, Genetic ; },
abstract = {The gene of a halophilic alkaline serine protease, halolysin, from an unidentified halophilic archaea (archaebacterium) was cloned and its nucleotide sequence was determined. The deduced amino acid sequence showed that halolysin consists of 411 amino acids, with a molecular weight of 41,963. The highest homology was found with thermitase from Thermoactinomyces vulgaris. Halolysin has a long C-terminal extension of approximately 120 amino acids which has not been found in other extracellular subtilisin type serine proteases. The gene, hly, was expressed in another halophilic archaea, Haloferax volcanii, in a medium containing 18% salts by using a plasmid shuttle vector which has a novobiocin resistance determinant as a selectable marker.},
}
@article {pmid1730657,
year = {1992},
author = {Köpke, AK and Leggatt, PA and Matheson, AT},
title = {Structure function relationships in the ribosomal stalk proteins of archaebacteria.},
journal = {The Journal of biological chemistry},
volume = {267},
number = {2},
pages = {1382-1390},
pmid = {1730657},
issn = {0021-9258},
mesh = {Amino Acid Sequence ; Base Sequence ; Cloning, Molecular ; Electrophoresis, Agar Gel ; Electrophoresis, Gel, Two-Dimensional ; Molecular Sequence Data ; Mutation ; Poly U/genetics ; Protein Biosynthesis ; Ribosomal Proteins/*genetics/metabolism ; Ribosomes/metabolism ; Structure-Activity Relationship ; Sulfolobus/*metabolism ; Ultracentrifugation ; },
abstract = {The ribosomal L12 protein gene of Sulfolobus solfataricus (SsoL12) has been subcloned and overexpressed in Escherichia coli. Five protein L12 mutants were designed: two NH2-terminal and two COOH-terminal truncated mutants and one mutant lacking the highly charged part of the COOH-terminal region. The mutant protein genes were overexpressed in E. coli and the products purified. The amino acid composition was verified and the NH2 terminally truncated mutants were subjected to Edman degradation. The SsoL12 protein was selectively removed from entire S. solfataricus ribosomes by an ethanol wash. The remaining ribosomal core particles showed a substantial decrease in the in vitro translational activity. S. solfataricus L12 protein overexpressed in E. coli (SsoL12e) was incorporated into these ribosomal cores and restored their translational activity. Mutants lacking any part of the COOH-terminal region could be incorporated into these cores, as proven by two-dimensional polyacrylamide gels of the reconstituted particles. Mutant SsoL12 MC2 (residue 1-70) was sufficient for dimerization and incorporation into ribosomes. In contrast to the COOH terminally truncated mutants, L12 proteins lacking the 12 highly conserved NH2-terminal residues or the entire NH2-terminal region (44 amino acids) are unable to bind to ribosomes, suggesting that the SsoL12 protein binds with its NH2-terminal portion to the ribosome. None of the mutants could significantly increase the translational activity of the core particles suggesting that every deleted part of the protein was needed directly or indirectly for translational activity. Our results suggest that the COOH terminally truncated mutants were bound to ribosomes but not functional for translation. Cores preincubated with these COOH terminally truncated mutants regained activity when a second incubation with the entire overexpressed SsoL12e protein followed. This finding suggests that archaebacterial L12 proteins are freely exchanged on the ribosome.},
}
@article {pmid1729711,
year = {1992},
author = {Klenk, HP and Palm, P and Lottspeich, F and Zillig, W},
title = {Component H of the DNA-dependent RNA polymerases of Archaea is homologous to a subunit shared by the three eucaryal nuclear RNA polymerases.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {89},
number = {1},
pages = {407-410},
pmid = {1729711},
issn = {0027-8424},
mesh = {Amino Acid Sequence ; Archaea/*enzymology/genetics ; Base Sequence ; Biological Evolution ; DNA-Directed RNA Polymerases/*chemistry/genetics ; *Genes, Bacterial ; Molecular Sequence Data ; Saccharomyces cerevisiae/enzymology/genetics ; Sequence Alignment ; },
abstract = {The gene encoding component H of the DNA-dependent RNA polymerase (RNAP, EC 2.7.7.6) of Sulfolobus acidocaldarius has been identified by comparison of the amino acid sequence with the derived amino acid sequence of an open reading frame (ORF88) in the RNAP operon. Corresponding genes were identified in Halobacterium halobium and were cloned and sequenced from Thermococcus celer and Methanococcus vannielii. All these rpoH genes are situated between the promoters of the RNAP operons and the corresponding rpoB and rpoB2 genes. The archaeal H subunits show high sequence similarity to each other and to the C-terminal portions of the largest of four subunits shared by all three specialized nuclear RNAPs. These correlations are further evidence for the striking similarity between archaeal and eucaryal RNAP structures and transcription systems.},
}
@article {pmid1508173,
year = {1992},
author = {Popenko, VI and Cherin, NE and Ivanova, IuL and Beresten', SF and Filonenko, VV},
title = {[Immunoelectron-microscopic determination of the localization of tryptophanyl-tRNA synthetase in eubacterial cells of Escherichia coli and Methanococcus halophilus archaebacteria].},
journal = {Molekuliarnaia biologiia},
volume = {26},
number = {1},
pages = {83-92},
pmid = {1508173},
issn = {0026-8984},
mesh = {Antibodies, Monoclonal ; Escherichia coli/*enzymology ; Immunohistochemistry ; Methanococcus/*enzymology ; Microscopy, Immunoelectron ; Tryptophan-tRNA Ligase/*ultrastructure ; },
abstract = {Localization of tryptophanyl-tRNA-synthetase (TRS) was studied in halophilic archaebacterium Methanococcus halophilus and eubacterium E. coli. Ultrathin sections of the cells, fixed with glutaraldehyde and embedded in "Lowicryl K4M" at -35 degrees C, were treated with colloidal gold complexes containing monoclonal antibodies Aml against TRS. The latter bind specifically to TRS isolated both from eucaryotes, archae- and eubacteria. According to the label distribution three zones in M. halophilus and E. coli can be distinguished: (i) about 75% of the whole amount of gold particles are localized in the cytoplasm, the distribution of label being more or less homogeneous; (ii) cytoplasmic regions, adjacent to nucleoid, are intensively labelled (about 20% of the whole amount of label); (iii) very few gold particles (not more than 10% of the whole amount) are present in the nucleoid. The data obtained show, that the distribution of TRS in the nucleoid and cytoplasm of archaebacterium M. halophilus is close to the distribution of TRS, found in E. coli. It supports our previous conclusion that the structural organization of transcription-translation apparatus in methanogen and halophilic archaebacteria is similar to that in eubacteria.},
}
@article {pmid1445415,
year = {1992},
author = {Forterre, P and Charbonnier, F and Marguet, E and Harper, F and Henckes, G},
title = {Chromosome structure and DNA topology in extremely thermophilic archaebacteria.},
journal = {Biochemical Society symposium},
volume = {58},
number = {},
pages = {99-112},
pmid = {1445415},
issn = {0067-8694},
mesh = {Archaea/*chemistry/ultrastructure ; Chromosomes, Bacterial/*chemistry/ultrastructure ; DNA, Bacterial/*chemistry/ultrastructure ; Hot Temperature ; *Nucleic Acid Conformation ; },
}
@article {pmid1445413,
year = {1992},
author = {Zillig, W and Palm, P and Langer, D and Klenk, HP and Lanzendörfer, M and Hüdepohl, U and Hain, J},
title = {RNA polymerases and transcription in archaebacteria.},
journal = {Biochemical Society symposium},
volume = {58},
number = {},
pages = {79-88},
pmid = {1445413},
issn = {0067-8694},
mesh = {Archaea/*enzymology/*genetics ; Base Sequence ; DNA-Directed RNA Polymerases/*genetics ; Molecular Sequence Data ; *Transcription, Genetic ; },
}
@article {pmid1445408,
year = {1992},
author = {Fuchs, G and Ecker, A and Strauss, G},
title = {Bioenergetics and autotrophic carbon metabolism of chemolithotrophic archaebacteria.},
journal = {Biochemical Society symposium},
volume = {58},
number = {},
pages = {23-39},
pmid = {1445408},
issn = {0067-8694},
mesh = {Archaea/*metabolism ; Carbon/*metabolism ; Energy Metabolism ; },
}
@article {pmid1445407,
year = {1992},
author = {Kandler, O},
title = {Where next with the archaebacteria?.},
journal = {Biochemical Society symposium},
volume = {58},
number = {},
pages = {195-207},
pmid = {1445407},
issn = {0067-8694},
mesh = {Archaea/*chemistry/*classification ; Microbiology/trends ; },
}
@article {pmid1445405,
year = {1992},
author = {Norris, PR},
title = {Thermoacidophilic archaebacteria: potential applications.},
journal = {Biochemical Society symposium},
volume = {58},
number = {},
pages = {171-180},
pmid = {1445405},
issn = {0067-8694},
mesh = {Archaea/*chemistry ; *Hot Temperature ; *Industrial Microbiology ; Sulfolobus/chemistry ; },
}
@article {pmid1445404,
year = {1992},
author = {Cowan, DA},
title = {Enzymes from thermophilic archaebacteria: current and future applications in biotechnology.},
journal = {Biochemical Society symposium},
volume = {58},
number = {},
pages = {149-169},
pmid = {1445404},
issn = {0067-8694},
mesh = {Archaea/*enzymology/genetics ; Industrial Microbiology/*trends ; },
abstract = {The one guaranteed property of enzymes isolated from extremely thermophilic micro-organisms is their thermostability. Most significantly, almost any such enzyme will be more thermostable than the functionally similar enzyme from a lower temperature source. Thermostability is not an isolated property: resistance to heat denaturation imparts stability to a number of other denaturing influences (detergents, organic solvents, etc). These characteristics of hyperthermophilic enzymes are the most likely basis for the development of new biotechnological applications. A limited number of hyperthermophilic enzymes have found application in specialist biotechnological applications; others have visible potential in growing areas of biotechnology. Existing and potential applications are discussed using DNA manipulation enzymes, dehydrogenases, and esterases as examples.},
}
@article {pmid1445402,
year = {1992},
author = {Hensel, R and Jakob, I and Scheer, H and Lottspeich, F},
title = {Proteins from hyperthermophilic archaea: stability towards covalent modification of the peptide chain.},
journal = {Biochemical Society symposium},
volume = {58},
number = {},
pages = {127-133},
pmid = {1445402},
issn = {0067-8694},
mesh = {Amino Acid Sequence ; Archaea/*chemistry ; Bacterial Proteins/*chemistry ; *Hot Temperature ; Molecular Sequence Data ; Peptides/*chemistry ; Protein Conformation ; },
}
@article {pmid1445400,
year = {1992},
author = {Doolittle, WF},
title = {What are the archaebacteria and why are they important?.},
journal = {Biochemical Society symposium},
volume = {58},
number = {},
pages = {1-6},
pmid = {1445400},
issn = {0067-8694},
mesh = {*Archaea ; },
}
@article {pmid1445399,
year = {1992},
author = {},
title = {The Archaebacteria: biochemistry and biotechnology.},
journal = {Biochemical Society symposium},
volume = {58},
number = {},
pages = {1-207},
pmid = {1445399},
issn = {0067-8694},
mesh = {*Archaea ; },
}
@article {pmid1444718,
year = {1992},
author = {Fischer, R and Gärtner, P and Yeliseev, A and Thauer, RK},
title = {N5-methyltetrahydromethanopterin: coenzyme M methyltransferase in methanogenic archaebacteria is a membrane protein.},
journal = {Archives of microbiology},
volume = {158},
number = {3},
pages = {208-217},
pmid = {1444718},
issn = {0302-8933},
mesh = {Euryarchaeota/*enzymology ; Membrane Proteins/biosynthesis/*isolation &amp; purification ; Mesna/*metabolism ; Methyltransferases/*analysis/metabolism ; Pterins/*metabolism ; },
abstract = {An assay is described that allows the direct measurement of the enzyme activity catalyzing the transfer of the methyl group from N5-methyltetrahydromethanopterin (CH3-H4MPT) to coenzyme M (H-S-CoM) in methanogenic archaebacteria. With this method the topology, the partial purification, and the catalytic properties of the methyltransferase in methanol- and acetate-grown Methanosarcina barkeri and in H2/CO(2)-grown Methanobacterium thermoautotrophicum were studied. The enzyme activity was found to be associated almost completely with the membrane fraction and to require detergents for solubilization. The transferase activity in methanol-grown M. barkeri was studied in detail. The membrane fraction exhibited a specific activity of CH3-S-CoM formation from CH3-H4MPT (apparent Km = 50 microM) and H-S-CoM (apparent Km = 250 microM) of approximately 0.6 mumol.min-1.mg protein-1. For activity the presence of Ti(III) citrate (apparent Km = 15 microM) and of ATP (apparent Km = 30 microM) were required in catalytic amounts. Ti(III) could be substituted by reduced ferredoxin. ATP could not be substituted by AMP, CTP, GTP, S-adenosylmethionine, or by ATP analogues. The membrane fraction was methylated by CH3-H4MPT in the absence of H-S-CoM. This methylation was dependent on Ti(III) and ATP. The methylated membrane fraction catalyzed the methyltransfer from CH3-H4MPT to H-S-CoM in the absence of ATP and Ti(III). Demethylation in the presence of H-S-CoM also did not require Ti(III) or ATP. Based on these findings a mechanism for the methyltransfer reaction and for the activation of the enzyme is proposed.},
}
@article {pmid1316221,
year = {1992},
author = {Jarrell, KF and Faguy, D and Hebert, AM and Kalmokoff, ML},
title = {A general method of isolating high molecular weight DNA from methanogenic archaea (archaebacteria).},
journal = {Canadian journal of microbiology},
volume = {38},
number = {1},
pages = {65-68},
doi = {10.1139/m92-010},
pmid = {1316221},
issn = {0008-4166},
mesh = {Archaea/chemistry ; Bacteriological Techniques ; DNA Restriction Enzymes ; DNA, Bacterial/chemistry/*isolation &amp; purification ; Euryarchaeota/*chemistry ; Molecular Weight ; },
abstract = {High molecular weight DNA was readily isolated from all methanogens treated, as well as from thermophilic anaerobic eubacteria, by grinding cells frozen in liquid N2, prior to lysis with SDS. DNA can subsequently be purified by the usual phenol-chloroform extractions. The procedure yields DNA readily cut by restriction enzymes and suitable for oligonucleotide probing, as well as for mole percent G + C content determination by thermal denaturation. The method routinely yields DNA of high molecular weight and is an improvement over DNA isolation methods for many methanogens, which often involve an initial breakage of the cells in a French pressure cell.},
}
@article {pmid1822288,
year = {1991},
author = {Zillig, W},
title = {Comparative biochemistry of Archaea and Bacteria.},
journal = {Current opinion in genetics &amp; development},
volume = {1},
number = {4},
pages = {544-551},
doi = {10.1016/s0959-437x(05)80206-0},
pmid = {1822288},
issn = {0959-437X},
mesh = {Archaea/classification/*genetics/metabolism ; Bacteria/classification/*genetics/metabolism ; Bacterial Proteins/genetics ; DNA, Bacterial/genetics ; Electron Transport ; Energy Metabolism ; Eukaryotic Cells ; Lipid Metabolism ; *Phylogeny ; },
abstract = {This review compares exemplary molecular and metabolic features of Archaea and Bacteria in terms of phylogenetic aspects. The results of the comparison confirm the coherence of the Archaea as postulated by Woese. Archaea and Bacteria share many basic features of their genetic machinery and their central metabolism. Similarities and distinctions allow projections regarding the nature of the common ancestor and the process of lineage diversification.},
}
@article {pmid1725258,
year = {1991},
author = {Londei, P and Altamura, S and Caprini, E and Martayan, A},
title = {Translation and ribosome assembly in extremely thermophilic archaebacteria.},
journal = {Biochimie},
volume = {73},
number = {12},
pages = {1465-1472},
doi = {10.1016/0300-9084(91)90179-5},
pmid = {1725258},
issn = {0300-9084},
mesh = {Hot Temperature ; Hydrogen-Ion Concentration ; *Protein Biosynthesis ; RNA, Bacterial/metabolism ; RNA, Ribosomal/*metabolism ; Ribosomes/*metabolism ; Sulfolobus/*genetics ; Yeasts/metabolism ; },
abstract = {Several features of translation and ribosome structure in extremely thermophilic, sulfur-dependent archaebacteria are described, including: i) a peculiar mechanism of transfer RNA-mediated 70S ribosome formation from free subunits; ii) poly(U)translation by hybrid ribosomes composed by one archaebacterial and one eucaryotic subunit; iii) ribosome assembly and homologous and heterologous RNA/protein recognition.},
}
@article {pmid1804250,
year = {1991},
author = {Rinker, AG and Evans, DR},
title = {Isolation of chromosomal DNA from a methanogenic archaebacteria using a French pressure cell press.},
journal = {BioTechniques},
volume = {11},
number = {5},
pages = {612-613},
pmid = {1804250},
issn = {0736-6205},
mesh = {DNA, Bacterial/*isolation &amp; purification ; Methanosarcina barkeri/*genetics ; },
}
@article {pmid1909323,
year = {1991},
author = {Alam, M and Hazelbauer, GL},
title = {Structural features of methyl-accepting taxis proteins conserved between archaebacteria and eubacteria revealed by antigenic cross-reaction.},
journal = {Journal of bacteriology},
volume = {173},
number = {18},
pages = {5837-5842},
pmid = {1909323},
issn = {0021-9193},
support = {GM29963/GM/NIGMS NIH HHS/United States ; },
mesh = {Archaea/immunology/*physiology ; Bacteria/immunology ; *Bacterial Physiological Phenomena ; Bacterial Proteins/chemistry/immunology/ultrastructure ; *Chemotaxis ; Cross Reactions ; Halobacterium/immunology/physiology ; Membrane Proteins/chemistry/immunology/*ultrastructure ; Methyl-Accepting Chemotaxis Proteins ; Methylation ; Molecular Weight ; Mutation ; Signal Transduction ; },
abstract = {A number of eubacterial species contain methyl-accepting taxis proteins that are antigenically and thus structurally related to the well-characterized methyl-accepting chemotaxis proteins of Escherichia coli. Recent studies of the archaebacterium Halobacterium halobium have characterized methyl-accepting taxis proteins that in some ways resemble and in other ways differ from the analogous eubacterial proteins. We used immunoblotting with antisera raised to E. coli transducers to probe shared structural features of methyl-accepting proteins from archaebacteria and eubacteria and found substantial antigenic relationships. This implies that the genes for the contemporary methyl-accepting proteins are related through an ancestral gene that existed before the divergence of arachaebacteria and eubacteria. Analysis by immunoblot of mutants of H. halobium defective in taxis revealed that some strains were deficient in covalent modification of methyl-accepting proteins although the proteins themselves were present, while other strains appeared to be missing specific methyl-accepting proteins.},
}
@article {pmid1909318,
year = {1991},
author = {Lai, MC and Sowers, KR and Robertson, DE and Roberts, MF and Gunsalus, RP},
title = {Distribution of compatible solutes in the halophilic methanogenic archaebacteria.},
journal = {Journal of bacteriology},
volume = {173},
number = {17},
pages = {5352-5358},
pmid = {1909318},
issn = {0021-9193},
support = {GM 33463/GM/NIGMS NIH HHS/United States ; },
mesh = {Amino Acids/*metabolism ; Archaea/growth &amp; development/*metabolism ; Biological Transport ; Chromatography, High Pressure Liquid ; Chromatography, Ion Exchange ; Euryarchaeota/growth &amp; development/*metabolism ; Magnetic Resonance Spectroscopy ; *Osmosis ; Potassium/metabolism ; Sodium Chloride/metabolism ; },
abstract = {Accumulation of compatible solutes, by uptake or de novo synthesis, enables bacteria to reduce the difference between osmotic potentials of the cell cytoplasm and the extracellular environment. To examine this process in the halophilic and halotolerant methanogenic archaebacteria, 14 strains were tested for the accumulation of compatible solutes in response to growth in various extracellular concentrations of NaCl. In external NaCl concentrations of 0.7 to 3.4 M, the halophilic methanogens accumulated K+ ion and low-molecular-weight organic compounds. beta-Glutamate was detected in two halotolerant strains that grew below 1.5 M NaCl. Two unusual beta-amino acids, N epsilon-acetyl-beta-lysine and beta-glutamine (3-aminoglutaramic acid), as well as L-alpha-glutamate were compatible solutes among all of these strains. De novo synthesis of glycine betaine was also detected in several strains of moderately and extremely halophilic methanogens. The zwitterionic compounds (beta-glutamine, N epsilon-acetyl-beta-lysine, and glycine betaine) and potassium were the predominant compatible solutes among the moderately and extremely halophilic methanogens. This is the first report of beta-glutamine as a compatible solute and de novo biosynthesis of glycine betaine in the methanogenic archaebacteria.},
}
@article {pmid1768142,
year = {1991},
author = {Olson, KD and McMahon, CW and Wolfe, RS},
title = {Light sensitivity of methanogenic archaebacteria.},
journal = {Applied and environmental microbiology},
volume = {57},
number = {9},
pages = {2683-2686},
pmid = {1768142},
issn = {0099-2240},
support = {AI 12277/AI/NIAID NIH HHS/United States ; },
mesh = {Euryarchaeota/growth &amp; development/*radiation effects ; *Light/adverse effects ; Microscopy, Fluorescence ; Ultraviolet Rays ; },
abstract = {Representatives of four families of methanogenic archaebacteria (archaea), Methanobacterium thermoautotrophicum delta H, Methanobacterium thermoautotrophicum Marburg, Methanosarcina acetivorans, Methanococcus voltae, and Methanomicrobium mobile, were found to be light sensitive. The facultative anaerobic eubacteria Escherichia coli and Salmonella typhimurium, however, were tolerant of light when grown anaerobically under identical light conditions. Interference filters were used to show that growth of the methanogens is inhibited by light in the blue end of the visible spectrum (370 to 430 nm).},
}
@article {pmid1648092,
year = {1991},
author = {Slesarev, AI and Zaitzev, DA and Kopylov, VM and Stetter, KO and Kozyavkin, SA},
title = {DNA topoisomerase III from extremely thermophilic archaebacteria. ATP-independent type I topoisomerase from Desulfurococcus amylolyticus drives extensive unwinding of closed circular DNA at high temperature.},
journal = {The Journal of biological chemistry},
volume = {266},
number = {19},
pages = {12321-12328},
pmid = {1648092},
issn = {0021-9258},
mesh = {Adenosine Triphosphate/*metabolism ; Archaea/*enzymology ; DNA Topoisomerases, Type I/*metabolism ; DNA Topoisomerases, Type II/metabolism ; DNA, Bacterial/*chemistry ; DNA, Circular/*chemistry ; DNA, Superhelical/chemistry ; Electrophoresis, Agar Gel ; Electrophoresis, Gel, Two-Dimensional ; Electrophoresis, Polyacrylamide Gel ; Nucleic Acid Conformation ; Potassium/metabolism ; Sodium/metabolism ; Temperature ; },
abstract = {A second type I topoisomerase was purified from the extremely thermophilic archaebacterium Desulfurococcus amylolyticus. In contrast to the previously described reverse gyrase from this organism, the novel enzyme designated as Dam topoisomerase III is an ATP-independent relaxing topoisomerase. It is a monomer with Mr 108,000, as determined by electrophoresis under denaturing conditions and by size exclusion chromatography. Dam topoisomerase III, like other bacterial type I topoisomerases, absolutely requires Mg2+ for activity and is specific for single-stranded DNA. At 60-80 degrees C, it relaxes negatively but not positively supercoiled DNA and is inhibited by single-stranded M13 DNA. At 95 degrees C, the enzyme unwinds both positively and negatively supercoiled substrates and produces extensively unwound form I* and I** DNA. The peculiarities of DNA topoisomerization at high temperatures are discussed.},
}
@article {pmid1828761,
year = {1991},
author = {Phipps, BM and Hoffmann, A and Stetter, KO and Baumeister, W},
title = {A novel ATPase complex selectively accumulated upon heat shock is a major cellular component of thermophilic archaebacteria.},
journal = {The EMBO journal},
volume = {10},
number = {7},
pages = {1711-1722},
pmid = {1828761},
issn = {0261-4189},
mesh = {Adenosine Triphosphatases/*isolation &amp; purification/ultrastructure ; Archaea/*enzymology/ultrastructure ; Chromatography, DEAE-Cellulose ; Cytoplasm/ultrastructure ; Electrophoresis, Polyacrylamide Gel ; Enzyme Stability ; Heat-Shock Proteins/*isolation &amp; purification/ultrastructure ; Image Processing, Computer-Assisted ; Immunoblotting ; Models, Molecular ; Phylogeny ; Protein Conformation ; },
abstract = {We have discovered a large cylindrical protein complex which is an abundant component of the cytoplasm of extremely thermophilic archaebacteria. Structural analysis by image processing of electron micrographs suggests that the complex is composed of two stacked rings of eight subunits each; the rings enclose a central channel. The complex purified from the hyperthermophile Pyrodictium occultum is composed of equal quantities of two polypeptides of Mr 56,000 and 59,000. It exhibits an extremely thermostable ATPase activity with a temperature optimum of 100 degrees C. The basal level of the ATPase complex in the cell is high, and it becomes highly enriched as a result of heat shock (shift from 102 degrees C to 108 degrees C) or balanced growth at temperatures near the physiological upper limit. Immunoblotting results indicate that a related protein is present in most thermophilic archaebacteria and in Escherichia coli. This protein complex may play an important role in the adaptation of thermophilic archaebacteria to life at high temperature.},
}
@article {pmid1764524,
year = {1991},
author = {Stöffler-Meilicke, M and Stöffler, G},
title = {The binding site of ribosomal protein L10 in eubacteria and archaebacteria is conserved: reconstitution of chimeric 50S subunits.},
journal = {Biochimie},
volume = {73},
number = {6},
pages = {797-804},
doi = {10.1016/0300-9084(91)90059-a},
pmid = {1764524},
issn = {0300-9084},
mesh = {Archaea/*chemistry ; Binding Sites ; Electrophoresis, Gel, Two-Dimensional ; Escherichia coli/*chemistry ; Escherichia coli Proteins ; Macromolecular Substances ; Methanococcus/chemistry ; Microscopy, Electron ; Ribosomal Protein L10 ; Ribosomal Proteins/*chemistry ; Ribosomes/*chemistry/ultrastructure ; Sulfolobus/chemistry ; },
abstract = {It has been shown by electron microscopy that the selective removal of the stalk from 50S ribosomal subunits of two representative archaebacteria, namely Methanococcus vaniellii and Sulfolobus solfataricus, is accompanied by loss of the archaebacterial L10 and L12 proteins. The stalk was reformed if archaebacterial core particles were reconstituted with their corresponding split proteins. Next, structurally intact chimeric 50S subunits have been reconstituted in vitro by addition of Escherichia coli ribosomal proteins L10 and L7/L12 to 50S core particles from M vaniellii or S solfataricus, respectively. In the reverse experiment, using core particles from E coli and split proteins from M vaniellii, stalk-bearing 50S particles were also obtained. Analysis of the reconstituted 50S subunits by immunoblotting revealed that E coli L10 was incorporated into archaebacterial core particles in both presence or absence of E coli L7/L12. In contrast, incorporation of E coli L7/L12 into archaebacterial cores was only possible in the presence of E coli L10. Our results suggest that in archaebacteria - as in E coli - the stalk is formed by archaebacterial L12 proteins that bind to the ribosome via L10. The structural equivalence of eubacterial and archaebacterial L10 and L12 proteins has thus for the first time been established. The chimeric reconstitution experiments provide evidence that the domain of protein L10 that interacts with the ribosomal particle is highly conserved between eubacteria and archaebacteria.},
}
@article {pmid1764512,
year = {1991},
author = {Köpke, AK and Hannemann, F and Boeckh, T},
title = {Genetic engineering and overexpression of ribosomal L12 protein genes from three different archaebacteria in E coli.},
journal = {Biochimie},
volume = {73},
number = {6},
pages = {647-655},
doi = {10.1016/0300-9084(91)90044-2},
pmid = {1764512},
issn = {0300-9084},
mesh = {Amino Acids/analysis ; Archaea/*genetics ; Base Sequence ; Chromatography, Ion Exchange ; Escherichia coli/*genetics ; *Gene Expression Regulation, Bacterial ; Genetic Engineering ; Genetic Vectors ; Molecular Sequence Data ; Mutagenesis, Site-Directed ; Oligonucleotides/chemical synthesis ; Ribosomal Proteins/biosynthesis/*genetics/isolation &amp; purification ; },
abstract = {Genes coding for ribosomal protein L12 from Methanococcus vannielii (Mva), Halobacterium halobium (Hha) and Sulfolobus solfataricus (Sso) have been subcloned in the polylinker region of pUC19. An efficient Shine-Dalgarno sequence has been attached to the 5' end of the genes, and two ochre stop codons have been created at their 3' ends, where necessary. In addition, mutants of the MvaL12 and HhaL12 genes were constructed, which coded for a cysteine residue at the C-terminus of the protein. The constructs were transferred together with the pUC19 polylinker as gene cartridges into different expression vectors. These constructed plasmids were transformed in the appropriate E coli hosts and tested for expression. Two systems were found to work efficiently for overexpression, namely the pKK223-3 vector featuring a tac promoter, and the pT7-5 vector featuring a T7-promoter. The over-expressed proteins were purified to homogeneity; their purity was investigated by one and two-dimensional gel systems, amino acid analysis and N-terminal protein sequencing for 10 steps or more. The amount of protein purified from E coli test cultures bearing the expression plasmids was always more than 2.5 mg/l of medium used.},
}
@article {pmid1956294,
year = {1991},
author = {Horne, M and Englert, C and Wimmer, C and Pfeifer, F},
title = {A DNA region of 9 kbp contains all genes necessary for gas vesicle synthesis in halophilic archaebacteria.},
journal = {Molecular microbiology},
volume = {5},
number = {5},
pages = {1159-1174},
doi = {10.1111/j.1365-2958.1991.tb01889.x},
pmid = {1956294},
issn = {0950-382X},
mesh = {Amino Acid Sequence ; Archaea/*genetics/metabolism/ultrastructure ; *Archaeal Proteins ; Bacterial Proteins/*genetics/metabolism ; Base Sequence ; DNA, Bacterial/*genetics ; *Genes, Bacterial ; Halobacterium/*genetics/metabolism/ultrastructure ; *Membrane Proteins ; Molecular Sequence Data ; Mutagenesis, Insertional ; Open Reading Frames ; Organelles ; *Proteins ; Recombinant Fusion Proteins/metabolism ; Sequence Homology, Nucleic Acid ; Transcription Factors/genetics/metabolism ; Transcription, Genetic ; Transformation, Bacterial ; },
abstract = {We determined the minimal size of the genomic region necessary for gas vesicle synthesis in halophilic archaebacteria by transformation experiments, comparative DNA sequence analysis and investigation of gas vesicle (Vac) mutants. The comparison of the three genomic regions encoding gas vesicles in Halobacterium halobium (p-vac- and c-vac-region) and Haloferax mediterranei (mc-vac-region) indicates high DNA sequence similarity throughout a contiguous sequence of 9 kbp. In each case, this area encompassed at least 13 open reading frames (ORFs). Ten of these ORFs (gvpD to gvpM) were located 5' to the vac gene encoding the major gas vesicle protein, but were transcribed from the opposite strand. At least two ORFs (gvpC, and gvpN) were located 3' to each vac gene and transcribed from the same strand as the respective vac gene. In the p-vac-region present on plasmid pHH1 these ORFs were transcribed as at least three units, one transcript encompassing gvpD-gvpE, the second encompassing ORFs gvpF to gvpM, and the third unit comprising the ORFs located 3' to the p-vac gene. In H. halobium Vac mutants copies of the insertion elements ISH2, ISH23, ISH26 or ISH27 were found to be integrated throughout the p-vac-region. The de novo synthesis of gas vesicles was tested by transformation of the Vac-negative species, Haloferax volcanii, with various subfragments of the mc-vac- or p-vac-region cloned into vector plasmids. In contrast to a fragment containing the entire 9 kbp region, none of the subfragments tested was sufficient to promote gas vesicle synthesis. However, gas vesicle synthesis could be restored in each Vac mutant containing an ISH element when the entire transcription unit encompassing the mutated gene on pHH1 was present in the wild-type form on the vector construct.},
}
@article {pmid1913880,
year = {1991},
author = {Madsen, LH and Kreiberg, JD and Gausing, K},
title = {A small gene family in barley encodes ribosomal proteins homologous to yeast YL17 and L22 from archaebacteria, eubacteria, and chloroplasts.},
journal = {Current genetics},
volume = {19},
number = {5},
pages = {417-422},
pmid = {1913880},
issn = {0172-8083},
mesh = {Amino Acid Sequence ; Archaea/*genetics ; Base Sequence ; Blotting, Southern ; *Chloroplasts ; DNA/genetics ; *Fungal Proteins ; Genes, Bacterial ; Genes, Fungal ; Hordeum/*genetics ; Molecular Sequence Data ; *Multigene Family ; *RNA-Binding Proteins ; Restriction Mapping ; Ribosomal Proteins/*genetics ; Sequence Alignment ; Sequence Homology, Nucleic Acid ; Yeasts/*genetics ; },
abstract = {The amino acid sequences of two barley ribosomal proteins, termed HvL17-1 and HvL17-2, were decoded from green leaf cDNA clones. The N-terminal sequences of the derived barley proteins are 48% identical to the N-terminal amino acid sequence of protein YL17 from the large subunit of yeast cytoplasmic ribosomes. Via archaebacterial ribosomal proteins this homology extends to ribosomal protein L22 from eubacteria and chloroplast. Barley L17, and ribosomal proteins L22 and L23 from the archaebacteria Halobacterium halobium and H. marismortui, are 25-33% identical. Interestingly, the barley and archaebacterial proteins share a long, central stretch of amino acids, which is absent in the corresponding proteins from eubacteria and chloroplasts. Barley L17 proteins are encoded by a small gene family with probably only two members, represented by the cDNA clones encoding HvL17-1 and HvL17-2. Both these genes are active in green leaf cells. The expression of the L17 genes in different parts of the 7-day old barley seedlings was analyzed by semiquantitative hybridization. The level of L17 mRNA is high in meristematic and young cells found in the leaf base and root tip. In the leaf, the L17 mRNA level rapidly decreases with increasing cell age, and in older root cells this mRNA is undetectable.},
}
@article {pmid1902467,
year = {1991},
author = {Zhou, D and White, RH},
title = {Transsulfuration in archaebacteria.},
journal = {Journal of bacteriology},
volume = {173},
number = {10},
pages = {3250-3251},
pmid = {1902467},
issn = {0021-9193},
mesh = {Archaea/*metabolism ; Cysteine/metabolism ; Halobacterium/*metabolism ; Methionine/metabolism ; Sulfur/*metabolism ; },
abstract = {The transfer of sulfur from methionine to cysteine in the archaebacteria Sulfolobus acidocaldarius and Halobacterium marismortui was studied by feeding 34S-labeled methionine to cells and measuring the incorporation of 34S into protein-bound cellular cysteine and methionine by mass spectrometry. It was found that, as are eucaryotes, both of these archaebacteria were able to convert the sulfur of methionine to cysteine.},
}
@article {pmid1708763,
year = {1991},
author = {Edmonds, CG and Crain, PF and Gupta, R and Hashizume, T and Hocart, CH and Kowalak, JA and Pomerantz, SC and Stetter, KO and McCloskey, JA},
title = {Posttranscriptional modification of tRNA in thermophilic archaea (Archaebacteria).},
journal = {Journal of bacteriology},
volume = {173},
number = {10},
pages = {3138-3148},
pmid = {1708763},
issn = {0021-9193},
support = {GM 21584/GM/NIGMS NIH HHS/United States ; GM 36042/GM/NIGMS NIH HHS/United States ; GM29812/GM/NIGMS NIH HHS/United States ; },
mesh = {Adenosine/analogs &amp; derivatives/metabolism ; Archaea/*metabolism ; Gram-Negative Anaerobic Bacteria/metabolism ; Guanosine/analogs &amp; derivatives/metabolism ; Phylogeny ; Pseudouridine/metabolism ; *RNA Processing, Post-Transcriptional ; RNA, Bacterial/metabolism ; RNA, Transfer/chemistry/*metabolism ; Ribonucleosides/chemistry ; Thymidine/analogs &amp; derivatives/metabolism ; },
abstract = {Nucleoside modification has been studied in unfractionated tRNA from 11 thermophilic archaea (archaebacteria), including phylogenetically diverse representatives of thermophilic methanogens and sulfur-metabolizing hyperthermophiles which grow optimally in the temperature range of 56 (Thermoplasma acidophilum) to 105 degrees C (Pyrodictium occultum), and for comparison from the most thermophilic bacterium (eubacterium) known, Thermotoga maritima (80 degrees C). Nine nucleosides are found to be unique to the archaea, six of which are structurally novel in being modified both in the base and by methylation in ribose and occur primarily in tRNA from the extreme thermophiles in the Crenarchaeota of the archaeal phylogenetic tree. 2-Thiothymine occurs in tRNA from Thermococcus sp., and constitutes the only known occurrence of the thymine moiety in archaeal RNA, in contrast to its near-ubiquitous presence in tRNA from bacteria and eukarya. A total of 33 modified nucleosides are rigorously characterized in archaeal tRNA in the present study, demonstrating that the structural range of posttranscriptional modifications in archaeal tRNA is more extensive than previously known. From a phylogenetic standpoint, certain tRNA modifications occur in the archaea which are otherwise unique to either the bacterial or eukaryal domain, although the overall patterns of modification are more typical of eukaryotes than bacteria.},
}
@article {pmid1899138,
year = {1991},
author = {Kjems, J and Garrett, RA},
title = {Ribosomal RNA introns in archaea and evidence for RNA conformational changes associated with splicing.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {88},
number = {2},
pages = {439-443},
pmid = {1899138},
issn = {0027-8424},
mesh = {Archaea/*genetics ; Base Sequence ; DNA-Directed RNA Polymerases/metabolism ; Escherichia coli/enzymology ; *Introns ; Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; Oligonucleotide Probes ; *RNA Splicing ; RNA, Ribosomal, 23S/chemistry/*genetics ; RNA, Transfer/*genetics ; Sequence Homology, Nucleic Acid ; T-Phages/enzymology ; Transcription, Genetic ; },
abstract = {The single 23S rRNA gene of the archaeon Staphylothermus marinus exhibits two introns which, at the RNA level, are located in highly conserved regions of domains IV and V. The RNA introns, which are 56 and 54 nucleotides long, respectively, can form single hairpin structures. In vivo, RNA splicing occurs efficiently, whereas in vitro pre-rRNA transcripts containing each intron were cleaved efficiently when incubated with archaeal cell extracts but were poorly ligated. The introns are cleaved by a mechanism which differs from the mechanisms of eukaryotic rRNA introns but resembles those of the rRNA intron of Desulfurococcus mobilis and the archaeal tRNA introns. The cleavage enzyme recognizes and cuts a putative bulge-helix-bulge structure that can form at the archaeal exon-intron junctions. Using a phylogenetic sequence comparison approach, we define the parts of this structural feature that are essential for cleavage. We also provide evidence for conformational changes occurring in the S. marinus 23S RNA, after cleavage, at both exon-exon junctions, which may account for the low yields of ligation observed in vitro.},
}
@article {pmid1902842,
year = {1991},
author = {Klöppel, KD and Fredrickson, HL},
title = {Fast atom bombardment mass spectrometry as a rapid means of screening mixtures of ether-linked polar lipids from extremely halophilic archaebacteria for the presence of novel chemical structures.},
journal = {Journal of chromatography},
volume = {562},
number = {1-2},
pages = {369-376},
doi = {10.1016/0378-4347(91)80592-z},
pmid = {1902842},
mesh = {Archaea/*analysis/metabolism ; Chromatography, Thin Layer ; Glycolipids/analysis ; Halobacterium/analysis/metabolism ; Lipids/*analysis/chemistry ; Spectrometry, Mass, Fast Atom Bombardment ; },
abstract = {Fast atom bombardment mass spectrometry was used to analyse intact polar ether lipids present at microgram levels in crude lipid mixtures extracted from Halobacterium halobium, Natronococcus occultus and Halobacterium marismortui. Negative-ion spectra showed the intact deprotonated lipid molecules and in some instances their sodium salts. The simplicity of the mass spectra permits the rapid screening of polar lipid mixtures for the presence of novel lipids. Additional structural information of ions with selected masses was obtained after collisionally induced decomposition.},
}
@article {pmid1906756,
year = {1991},
author = {Searcy, DG and Hixon, WG},
title = {Cytoskeletal origins in sulfur-metabolizing archaebacteria.},
journal = {Bio Systems},
volume = {25},
number = {1-2},
pages = {1-11},
doi = {10.1016/0303-2647(91)90008-9},
pmid = {1906756},
issn = {0303-2647},
mesh = {Archaea/*physiology ; Biological Evolution ; Cytoskeleton/*physiology ; Eukaryotic Cells/physiology ; Sulfur/*metabolism ; },
abstract = {Several of the thermophilic acidopholic sulfur-metabolizing archaebacteria lack rigid cell walls. Their irregular shapes were maintained by an internal mechanism, presumably a cytoskeleton. Apparently this is an adaptation for respiration upon elemental sulfur, which requires cell contact since sulfur is insoluble in water. Also, we speculate that there could be additional functions of the cytoskeleton, such as prevention of osmotic cell lysis, thermal stabilization of enzymes, and improvements in metabolic efficiency through specific enzyme positioning. Such a well-developed cytoskeleton, evolving first in thermophilic archaebacteria, could have been a preadaptation for the evolution of eukaryotic cells.},
}
@article {pmid1905546,
year = {1991},
author = {Robertson, DE and Roberts, MF},
title = {Organic osmolytes in methanogenic archaebacteria.},
journal = {BioFactors (Oxford, England)},
volume = {3},
number = {1},
pages = {1-9},
pmid = {1905546},
issn = {0951-6433},
support = {GM33463/GM/NIGMS NIH HHS/United States ; },
mesh = {Amino Acids/biosynthesis ; Archaea/*physiology ; Euryarchaeota/*physiology ; Molecular Structure ; Water-Electrolyte Balance/*physiology ; },
abstract = {Methanogenic archaebacteria have developed unique ways of dealing with osmotic stress. While several of them have transport systems capable of internalizing betaine, an osmolyte in many eubacteria, in general they have developed de novo synthesis of a novel series of beta-amino acids as compatible solutes. 13C-NMR spectroscopy has been the key tool in elucidating both the identity of these organic osmolytes and in investigating their dynamics.},
}
@article {pmid1901370,
year = {1991},
author = {Iwabe, N and Kuma, K and Kishino, H and Hasegawa, M and Miyata, T},
title = {Evolution of RNA polymerases and branching patterns of the three major groups of Archaebacteria.},
journal = {Journal of molecular evolution},
volume = {32},
number = {1},
pages = {70-78},
pmid = {1901370},
issn = {0022-2844},
mesh = {Amino Acid Sequence ; Animals ; Archaea/enzymology/*genetics ; *Biological Evolution ; DNA-Directed RNA Polymerases/*genetics ; Mice ; Molecular Sequence Data ; Phylogeny ; Sequence Homology, Nucleic Acid ; },
abstract = {The amino acid sequences of the largest subunits of the RNA polymerases I, II, and III from eukaryotes were compared with those of archaebacterial and eubacterial homologs, and their evolutionary relationships were analyzed in detail by a recently developed tree-making method, the likelihood method of protein phylogeny, as well as by the neighbor-joining method and the parsimony method, together with bootstrap analyses. It was shown that the best tree topologies predicted by the first two methods are identical, whereas the last one predicts a distinct tree. The maximum likelihood tree revealed that, after the separation from archaebacteria, the three eukaryotic RNA polymerases diverged from an ancestral precursor in the eukaryotic lineage. This result is contrasted with the published result showing multiple origins for the three eukaryotic polymerases. It was shown that eukaryotic RNA polymerase I evolved much more rapidly than RNA polymerases II and III: The N-terminal half of RNA polymerase I shows an extraordinarily high evolutionary rate, possibly due to relaxed functional constraints. In contrast the evolutionary rate of archaebacterial RNA polymerase is remarkably limited. In addition, including the second largest subunit of the RNA polymerase, a detailed analysis for the branching pattern of the three major groups of archaebacteria was carried out by the maximum likelihood method. It was shown that the three major groups of archaebacteria are likely to form a single cluster; that is, archaebacteria are likely to be monophyletic as originally proposed by Woese and his colleagues.},
}
@article {pmid1846146,
year = {1991},
author = {Holmes, ML and Dyall-Smith, ML},
title = {Mutations in DNA gyrase result in novobiocin resistance in halophilic archaebacteria.},
journal = {Journal of bacteriology},
volume = {173},
number = {2},
pages = {642-648},
pmid = {1846146},
issn = {0021-9193},
mesh = {Amino Acid Sequence ; Archaea/drug effects/enzymology/*genetics ; Bacillus subtilis/enzymology/genetics ; Base Sequence ; DNA Topoisomerases, Type II/*genetics ; Drug Resistance, Microbial/*genetics ; Genes, Bacterial ; Molecular Sequence Data ; *Mutation ; Novobiocin/*pharmacology ; Plasmids ; RNA, Messenger/analysis/genetics ; Restriction Mapping ; Sequence Homology, Nucleic Acid ; },
abstract = {We have developed a cloning vector for use in halophilic archaebacteria which has a novobiocin resistance determinant as a selectable marker. The resistance determinant, which was derived from the genome of a resistant mutant strain, was mapped to a site within a 6.7-kb DNA clone by using a recombination assay and was sequenced. An open reading frame of 1.920 nucleotides (640 amino acids) was identified, with the predicted protein being highly homologous to the DNA gyrase B subunit (i.e., GyrB) of eubacteria. Three mutations were identified in the GyrB protein of the resistant mutant compared with the wild type (at amino acids 82, 122, and 137) which together enable Haloferax cells to grow in concentrations of novobiocin some 1,000 times higher than that possible for cells carrying only the wild-type enzyme. One base beyond the stop codon of gyrB was the start of gyrA, coding for the gyrase A subunit.},
}
@article {pmid1703956,
year = {1991},
author = {Ben-Mahrez, K and Sorokine, I and Nakayama, M and Kohiyama, M},
title = {Reverse transcriptase in archaebacteria. Purification and characterization of a primase-reverse-transcriptase complex from Halobacterium halobium.},
journal = {European journal of biochemistry},
volume = {195},
number = {1},
pages = {157-162},
doi = {10.1111/j.1432-1033.1991.tb15689.x},
pmid = {1703956},
issn = {0014-2956},
mesh = {Chromatography ; Chromatography, Ion Exchange ; DNA Primase ; DNA Replication ; DNA-Directed DNA Polymerase/*isolation &amp; purification/metabolism ; Durapatite ; Electrophoresis, Polyacrylamide Gel ; Endoribonucleases/*isolation &amp; purification/metabolism ; Halobacterium/*enzymology ; Hydroxyapatites ; Kinetics ; Molecular Weight ; Multienzyme Complexes/*isolation &amp; purification/metabolism ; RNA Nucleotidyltransferases/*isolation &amp; purification/metabolism ; RNA-Directed DNA Polymerase/*isolation &amp; purification/metabolism ; Ribonuclease H ; },
abstract = {A primase-reverse-transcriptase of Halobacterium halobium was purified by column chromatography on DEAE-cellulose, hydroxyapatite and carboxymethyl-cellulose, followed by sedimentation on a glycerol gradient. The enzyme is a multifunctional enzyme containing reverse transcriptase. DNA polymerase and RNase H activities and does not require a performed primer to initiate DNA synthesis. Using a single-stranded DNA as template, this enzyme synthesizes oligonucleotides (8-12 bases) that can be used a primer by Escherichia coli DNA nucleotidyltransferase I (DNA polymerase I, Klenow fragment). Two polypeptides of 67 and 57 kDa were found after 14750-fold purification of the enzyme.},
}
@article {pmid2174859,
year = {1990},
author = {Bouthier de la Tour, C and Portemer, C and Nadal, M and Stetter, KO and Forterre, P and Duguet, M},
title = {Reverse gyrase, a hallmark of the hyperthermophilic archaebacteria.},
journal = {Journal of bacteriology},
volume = {172},
number = {12},
pages = {6803-6808},
pmid = {2174859},
issn = {0021-9193},
mesh = {Adenosine Triphosphate/metabolism ; Archaea/classification/*enzymology ; Blotting, Western ; Cross Reactions ; *DNA Topoisomerases, Type I ; DNA Topoisomerases, Type II/immunology/*metabolism ; DNA, Superhelical/metabolism ; Electrophoresis, Gel, Two-Dimensional ; },
abstract = {Investigation of the presence of a reverse gyrase-like activity in archaebacteria revealed wide distribution of this activity in hyperthermophilic species, including methanogens and sulfur-dependent organisms. In contrast, no reverse gyrase activity was detected in mesophilic and moderately thermophilic organisms, which exhibited only an ATP-independent activity of DNA relaxation. These results suggest that the presence of reverse gyrase in archaebacteria is tightly linked to the high growth temperatures of these organisms. With respect to antigenic properties, the enzyme appeared similar among members of the genus Sulfolobus. In contrast, no close antigenic relatedness was found between the reverse gyrase of members of the order Sulfolobales and that of the other hyperthermophilic organisms.},
}
@article {pmid2123548,
year = {1990},
author = {Sowers, KR and Robertson, DE and Noll, D and Gunsalus, RP and Roberts, MF},
title = {N epsilon-acetyl-beta-lysine: an osmolyte synthesized by methanogenic archaebacteria.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {87},
number = {23},
pages = {9083-9087},
pmid = {2123548},
issn = {0027-8424},
support = {GM 33643/GM/NIGMS NIH HHS/United States ; },
mesh = {Aspartic Acid/metabolism ; Chromatography, High Pressure Liquid ; Chromatography, Ion Exchange ; Euryarchaeota/*metabolism ; Glutamates/metabolism ; Lysine/*analogs &amp; derivatives/biosynthesis/isolation &amp; purification ; Magnetic Resonance Spectroscopy ; },
abstract = {Methanosarcina thermophila, a nonmarine methanogenic archaebacterium, can grow in a range of saline concentrations. At less than 0.4 M NaCl, Ms. thermophila accumulated glutamate in response to increasing osmotic stress. At greater than 0.4 M NaCl, this organism synthesized a modified beta-amino acid that was identified as N epsilon-acetyl-beta-lysine by NMR spectroscopy and ion-exchange HPLC. This beta-amino acid derivative accumulated to high intracellular concentrations (up to 0.6 M) in Ms. thermophila and in another methanogen examined--Methanogenium cariaci, a marine species. The compound has features that are characteristic of a compatible solute: it is neutrally charged at physiological pH and it is highly soluble. When the cells were grown in the presence of exogenous glycine betaine, a physiological compatible solute, N epsilon-acetyl-beta-lysine synthesis was repressed and glycine betaine was accumulated. N epsilon-acetyl-beta-lysine was synthesized by species from three phylogenetic families when grown in high solute concentrations, suggesting that it may be ubiquitous among the methanogens. The ability to control the biosynthesis of N epsilon-acetyl-beta-lysine in response to extracellular solute concentration indicates that the methanogenic archaebacteria have a unique beta-amino acid biosynthetic pathway that is osmotically regulated.},
}
@article {pmid2123815,
year = {1990},
author = {Van Vliet, F and Crabeel, M and Boyen, A and Tricot, C and Stalon, V and Falmagne, P and Nakamura, Y and Baumberg, S and Glansdorff, N},
title = {Sequences of the genes encoding argininosuccinate synthetase in Escherichia coli and Saccharomyces cerevisiae: comparison with methanogenic archaebacteria and mammals.},
journal = {Gene},
volume = {95},
number = {1},
pages = {99-104},
doi = {10.1016/0378-1119(90)90419-r},
pmid = {2123815},
issn = {0378-1119},
mesh = {Amino Acid Sequence ; Animals ; Archaea/genetics ; Argininosuccinate Synthase/*genetics ; Base Sequence ; Cloning, Molecular ; Escherichia coli/*genetics ; *Genes, Bacterial ; *Genes, Fungal ; Mammals/genetics ; Molecular Sequence Data ; Saccharomyces cerevisiae/*genetics ; },
abstract = {The nucleotide (nt) sequences of the genes encoding argininosuccinate synthetase from Escherichia coli K-12 (argG) and Saccharomyces cerevisiae (ARG1) were determined. The deduced amino-acid sequences were compared to each other and to their counterparts in two methanogens and in mammals. Three regions are highly conserved. Two of them appear to contain possible Walker-type nt-binding sites [Walker et al., EMBO J. 1 (1982) 945-951] and are therefore candidates for ATP-binding sites. The third region shows some similarity to a short portion of the N-proximal part of the PurA enzyme which catalyses an analogous reaction.},
}
@article {pmid1697068,
year = {1990},
author = {Holmes, ML and Olsen, GJ and Dyall-Smith, ML},
title = {The halophilic archaebacteria Hb. lacusprofundi and Hb. saccharovorum are closely related: 16S rRNA sequence comparison.},
journal = {Nucleic acids research},
volume = {18},
number = {15},
pages = {4607},
pmid = {1697068},
issn = {0305-1048},
mesh = {Base Sequence ; Biological Evolution ; Halobacterium/*genetics ; Molecular Sequence Data ; RNA, Bacterial/genetics ; RNA, Ribosomal/*genetics ; RNA, Ribosomal, 16S/*genetics ; Sequence Homology, Nucleic Acid ; },
}
@article {pmid1696321,
year = {1990},
author = {Kjems, J and Garrett, RA},
title = {Secondary structural elements exclusive to the sequences flanking ribosomal RNAs lend support to the monophyletic nature of the archaebacteria.},
journal = {Journal of molecular evolution},
volume = {31},
number = {1},
pages = {25-32},
pmid = {1696321},
issn = {0022-2844},
mesh = {Archaea/*genetics ; Bacteria/*genetics ; Base Sequence ; *Biological Evolution ; DNA, Ribosomal/genetics ; Molecular Sequence Data ; Nucleic Acid Conformation ; RNA, Bacterial/genetics ; RNA, Messenger/genetics ; RNA, Ribosomal/*genetics ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 23S/genetics ; RNA, Ribosomal, 5S/genetics ; Sequence Homology, Nucleic Acid ; Transcription, Genetic ; },
abstract = {Several sequences flanking the large rRNA genes of several transcripts from extreme thermophiles, extreme halophiles, and methanogens were aligned and analyzed for the presence of common primary and secondary structural features, which would bear on the concept of monophyletic archaebacteria. Few sequences were common to all the archaebacterial transcripts, and these were confined to short regions generally flanking putative double helices. At a secondary structural level, however, in addition to the previously characterized processing stems of the 16S and 23S RNAs, four helices were detected that were common to the archaebacterial transcripts: two in the 16S RNA leader sequence and two in the 16S-23S RNA spacer. Although all of these helices vary in size and form from organism to organism, three of them contain double helical segments that are strongly supported by compensating base changes among the three archaebacterial groups. Three extreme halophiles exhibited two additional helices in their relatively large spacers and a further helix preceding the 5S RNA, which are also supported by compensating base changes. Ribosomal RNA transcripts from eubacteria/chloroplasts and eukaryotes were also examined for secondary structural features with locations and forms corresponding to those of the archaebacteria, but none were detected. The analysis provides support for the monophyletic nature of the archaebacteria and reinforces their differences from eubacteria/chloroplasts and eukaryotes.},
}
@article {pmid2112744,
year = {1990},
author = {Woese, CR and Kandler, O and Wheelis, ML},
title = {Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {87},
number = {12},
pages = {4576-4579},
pmid = {2112744},
issn = {0027-8424},
mesh = {Archaea/*genetics ; Bacteria/*genetics ; *Biological Evolution ; *Cells ; *Eukaryotic Cells ; Phylogeny ; },
abstract = {Molecular structures and sequences are generally more revealing of evolutionary relationships than are classical phenotypes (particularly so among microorganisms). Consequently, the basis for the definition of taxa has progressively shifted from the organismal to the cellular to the molecular level. Molecular comparisons show that life on this planet divides into three primary groupings, commonly known as the eubacteria, the archaebacteria, and the eukaryotes. The three are very dissimilar, the differences that separate them being of a more profound nature than the differences that separate typical kingdoms, such as animals and plants. Unfortunately, neither of the conventionally accepted views of the natural relationships among living systems--i.e., the five-kingdom taxonomy or the eukaryote-prokaryote dichotomy--reflects this primary tripartite division of the living world. To remedy this situation we propose that a formal system of organisms be established in which above the level of kingdom there exists a new taxon called a "domain." Life on this planet would then be seen as comprising three domains, the Bacteria, the Archaea, and the Eucarya, each containing two or more kingdoms. (The Eucarya, for example, contain Animalia, Plantae, Fungi, and a number of others yet to be defined). Although taxonomic structure within the Bacteria and Eucarya is not treated herein, Archaea is formally subdivided into the two kingdoms Euryarchaeota (encompassing the methanogens and their phenotypically diverse relatives) and Crenarchaeota (comprising the relatively tight clustering of extremely thermophilic archaebacteria, whose general phenotype appears to resemble most the ancestral phenotype of the Archaea.},
}
@article {pmid2107795,
year = {1990},
author = {Larsson, L and Olsson, G and Holst, O and Karlsson, HT},
title = {Pyrite oxidation by thermophilic archaebacteria.},
journal = {Applied and environmental microbiology},
volume = {56},
number = {3},
pages = {697-701},
pmid = {2107795},
issn = {0099-2240},
mesh = {Archaea/*metabolism ; Bacteria/*metabolism ; Iron/*metabolism ; Oxidation-Reduction ; Species Specificity ; Sulfides/*metabolism ; },
abstract = {Three species of thermophilic archaebacteria of the genera Sulfolobus (Sulfolobus acidocaldarius and S. solfataricus) and Acidianus (Acidianus brierleyi) were tested for their ability to oxidize pyrite and to grow autotrophically on pyrite, to explore their potential for use in coal desulfurization. Only A. brierleyi was able to oxidize and grow autotrophically on pyrite. Jarosite was formed during the pyrite oxidation, resulting in the precipitation of sulfate and iron. The medium composition affected the extent of jarosite formation.},
}
@article {pmid2106880,
year = {1990},
author = {Kalmokoff, ML and Karnauchow, TM and Jarrell, KF},
title = {Conserved N-terminal sequences in the flagellins of archaebacteria.},
journal = {Biochemical and biophysical research communications},
volume = {167},
number = {1},
pages = {154-160},
doi = {10.1016/0006-291x(90)91744-d},
pmid = {2106880},
issn = {0006-291X},
mesh = {Amino Acid Sequence ; Amino Acids/analysis ; Archaea/*genetics ; Bacteria/*genetics ; Bacterial Proteins/*genetics ; Electrophoresis, Polyacrylamide Gel ; Flagellin/*genetics ; Molecular Sequence Data ; Peptide Mapping ; Sequence Homology, Nucleic Acid ; },
abstract = {Methanococcus voltae produces two flagellins of molecular weight 31,000 and 33,000. Amino acid analysis as well as peptide mapping with cyanogen bromide, chymotrypsin and Staphylococcus aureus V-8 protease indicates that the two flagellins are distinct. N-terminal sequencing of the 31,000 Mc. voltae flagellin as well as the 24,000 and 25,000 molecular weight flagellins of Methanospirillum hungatei GP1 shows an extensive homology with the reported N-terminus of the flagellins from Halobacterium halobium, deduced from the nucleotide sequence of the cloned genes. However, the N-termini of all three sequenced methanogen flagellins lack a terminal methionine and start at position 13 from the N-terminus of H. halobium flagellins. This initial 12 amino acid stretch may be a leader peptide which is subsequently cleaved to generate the mature flagellin, which could suggest flagellar assembly in archaebacteria occurs by a mechanism distinct from that in eubacteria. The high degree of conservation of the N-terminus of the flagellins from Mc. voltae, Msp. hungatei and H. halobium suggests an important role for this sequence, and that the archaebacteria share a common mechanism for flagellar biosynthesis.},
}
@article {pmid2155623,
year = {1990},
author = {Slesarev, AI and Kozyavkin, SA},
title = {DNA substrate specificity of reverse gyrase from extremely thermophilic archaebacteria.},
journal = {Journal of biomolecular structure &amp; dynamics},
volume = {7},
number = {4},
pages = {935-942},
doi = {10.1080/07391102.1990.10508533},
pmid = {2155623},
issn = {0739-1102},
mesh = {Archaea/*enzymology ; Bacteria/*enzymology ; *DNA Topoisomerases, Type I ; DNA Topoisomerases, Type II/*metabolism ; DNA, Single-Stranded/metabolism/pharmacology ; Hot Temperature ; Nucleic Acid Denaturation ; Substrate Specificity ; Topoisomerase II Inhibitors ; },
abstract = {It has been shown earlier that eukaryotic type I DNA topoisomerases act on duplex DNA regions, while eubacterial type I topoisomerases require single-stranded regions. The present paper demonstrates that the type I topoisomerase from extremely thermophilic archaebacteria, reverse gyrase, winds DNA by binding to single-stranded DNA regions. Thus, type I topoisomerases, both relaxing one in eubacteria and reverse gyrase in extremely thermophilic archaebacteria share a substrate specificity to melted DNA regions. The important consequence of this specificity is that the cellular DNA superhelical stress actively controlled by bacterial topoisomerases is confined to a narrow range characterized by a low stability of the double helix. Hence we suppose that bacterial topoisomerase systems control duplex stability near its minimum, for which purpose they create an appropriate negative superhelicity at moderate temperatures or a positive one at extremely high temperatures, the feedback being ensured by the aforesaid specificity of type I bacterial topoisomerases.},
}
@article {pmid2105303,
year = {1990},
author = {Holmes, ML and Dyall-Smith, ML},
title = {A plasmid vector with a selectable marker for halophilic archaebacteria.},
journal = {Journal of bacteriology},
volume = {172},
number = {2},
pages = {756-761},
pmid = {2105303},
issn = {0021-9193},
mesh = {Archaea/drug effects/*genetics ; Bacteria/*genetics ; Base Sequence ; DNA, Bacterial/genetics ; Drug Resistance, Microbial/genetics ; Escherichia coli/genetics ; *Genetic Vectors ; Halobacterium/*genetics ; Molecular Sequence Data ; Novobiocin/pharmacology ; *Plasmids ; RNA, Ribosomal/genetics/isolation &amp; purification ; Restriction Mapping ; Transformation, Bacterial ; },
abstract = {A mutant resistant to the gyrase inhibitor novobiocin was selected from a halophilic archaebacterium belonging to the genus Haloferax. Chromosomal DNA from this mutant was able to transform wild-type cells to novobiocin resistance, and these transformants formed visible colonies in 3 to 4 days on selective plates. The resistance gene was isolated on a 6.7-kilobase DNA KpnI fragment, which was inserted into a cryptic multicopy plasmid (pHK2) derived from the same host strain. The recombinant plasmid transformed wild-type cells at a high efficiency (greater than 10(6)/micrograms), was stably maintained, and could readily be reisolated from transformants. It could also transform Halobacterium volcanii and appears to be a useful system for genetic analysis in halophilic archaebacteria.},
}
@article {pmid2531898,
year = {1989},
author = {Iwabe, N and Kuma, K and Hasegawa, M and Osawa, S and Miyata, T},
title = {Evolutionary relationship of archaebacteria, eubacteria, and eukaryotes inferred from phylogenetic trees of duplicated genes.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {86},
number = {23},
pages = {9355-9359},
pmid = {2531898},
issn = {0027-8424},
mesh = {Adenosine Triphosphatases/genetics ; Amino Acid Sequence ; Animals ; Archaea/*genetics ; Bacteria/*genetics ; *Biological Evolution ; Eubacterium/*genetics ; *Genes ; Genes, Bacterial ; Humans ; Macromolecular Substances ; Molecular Sequence Data ; *Multigene Family ; Peptide Elongation Factor G ; Peptide Elongation Factor Tu/genetics ; Peptide Elongation Factors/genetics ; *Phylogeny ; Sequence Homology, Nucleic Acid ; },
abstract = {All extant organisms are though to be classified into three primary kingdoms, eubacteria, eukaryotes, and archaebacteria. The molecular evolutionary studies on the origin and evolution of archaebacteria to date have been carried out by inferring a molecular phylogenetic tree of the primary kingdoms based on comparison of a single molecule from a variety of extant species. From such comparison, it was not possible to derive the exact evolutionary relationship among the primary kingdoms, because the root of the tree could not be determined uniquely. To overcome this difficulty, we compared a pair of duplicated genes, elongation factors Tu and G, and the alpha and beta subunits of ATPase, which are thought to have diverged by gene duplication before divergence of the primary kingdoms. Using each protein pair, we inferred a composite phylogenetic tree with two clusters corresponding to different proteins, from which the evolutionary relationship of the primary kingdoms is determined uniquely. The inferred composite trees reveal that archaebacteria are more closely related to eukaryotes than to eubacteria for all the cases. By bootstrap resamplings, this relationship is reproduced with probabilities of 0.96, 0.79, 1.0, and 1.0 for elongation factors Tu and G and for ATPase subunits alpha and beta, respectively. There are also several lines of evidence for the close sequence similarity between archaebacteria and eukaryotes. Thus we propose that this tree topology represents the general evolutionary relationship among the three primary kingdoms.},
}
@article {pmid2515294,
year = {1989},
author = {Shimmin, LC and Ramirez, C and Matheson, AT and Dennis, PP},
title = {Sequence alignment and evolutionary comparison of the L10 equivalent and L12 equivalent ribosomal proteins from archaebacteria, eubacteria, and eucaryotes.},
journal = {Journal of molecular evolution},
volume = {29},
number = {5},
pages = {448-462},
pmid = {2515294},
issn = {0022-2844},
mesh = {Amino Acid Sequence ; Archaea/*genetics ; Bacteria/*genetics ; *Biological Evolution ; Escherichia coli/*genetics ; *Escherichia coli Proteins ; Eubacterium/*genetics ; Micrococcus/*genetics ; Molecular Sequence Data ; Phosphoproteins/analysis/*genetics ; Ribosomal Proteins/*analysis/*genetics ; },
abstract = {The genes corresponding to the L10 and L12 equivalent ribosomal proteins (L10e and L12e) of Escherichia coli have been cloned and sequenced from two widely divergent species of archaebacteria, Halobacterium cutirubrum and Sulfolobus solfataricus. The deduced amino acid sequences of the L10e and L12e proteins have been compared to each other and to available eubacterial and eucaryotic sequences. We have identified the human P0 protein as the eucaryotic L10e. The L10e proteins from the three kingdoms were found to be colinear. The eubacterial L10e protein is much shorter than the archaebacterial-eucaryotic proteins because of two large deletions, one internal and one at the carboxy terminus. The archaebacterial and eucaryotic L12e proteins were also colinear; the eubacterial protein is homologous to the archaebacterial and eucaryotic L12e proteins, but has suffered rearrangement through what appear to be gene fusion events. Intraspecies comparisons between L10e and L12e sequences indicate the archaebacterial and eucaryotic L10e proteins contain a partial copy of the L12e protein fused to their carboxy terminus. In the eubacteria most of this fusion has been removed by the carboxy terminal deletion. Within the L12e-derived region, a 26-amino acid-long internal modular sequence reiterated thrice in the archaebacterial L10e, twice in the eucaryotic L10e, and once in the eubacterial L10e was discovered. This modular sequence also appears to be present as a single copy in all L12e proteins and may play a role in L12e dimerization, L10e-L12e complex formation, and the function of L10e-L12e complex in translation.(ABSTRACT TRUNCATED AT 250 WORDS)},
}
@article {pmid2507788,
year = {1989},
author = {Stezowski, JJ and Englmaier, R and Galdiga, C and Hartl, T and Rommel, I and Dauter, Z and Görisch, H and Grossebüter, W and Wilson, K and Musil, D},
title = {Preliminary X-ray crystallographic study of malate dehydrogenases from the thermoacidophilic Archaebacteria Thermoplasma acidophilum and Sulfolobus acidocaldarius.},
journal = {Journal of molecular biology},
volume = {208},
number = {3},
pages = {507-508},
doi = {10.1016/0022-2836(89)90514-7},
pmid = {2507788},
issn = {0022-2836},
mesh = {Archaea/*enzymology ; Bacteria/*enzymology ; *Malate Dehydrogenase ; X-Ray Diffraction ; },
abstract = {Malate dehydrogenases from the thermoacidophilic Archaebacteria Thermoplasma acidophilum and Sulfolobus acidocaldarius have been crystallized and characterized by X-ray diffraction measurements. Crystals of the enzyme from T. acidophilum display space-group symmetry P2(1), a = 63 A, b = 135 A, c = 83 A and beta = 105 degrees; they scattered to approximately 4 A resolution. Two crystal modifications of malate dehydrogenase from S. acidocaldarius were characterized; one displayed trigonal symmetry corresponding to space groups P321, P3(1)21 or P3(2)21 with lattice parameters a = 151 A and c = 248 A and with resolution approximately to 5 A, whereas the other modification displayed space group symmetry I23 or I2(1)3 with lattice parameters a = 129 A and approximately 4.5 A resolution.},
}
@article {pmid2527371,
year = {1989},
author = {Südhof, TC and Fried, VA and Stone, DK and Johnston, PA and Xie, XS},
title = {Human endomembrane H+ pump strongly resembles the ATP-synthetase of Archaebacteria.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {86},
number = {16},
pages = {6067-6071},
pmid = {2527371},
issn = {0027-8424},
support = {CA21765/CA/NCI NIH HHS/United States ; DK33627/DK/NIDDK NIH HHS/United States ; HL39644/HL/NHLBI NIH HHS/United States ; },
mesh = {Amino Acid Sequence ; Archaea/enzymology/*genetics ; Bacteria/*genetics ; Base Sequence ; Biological Evolution ; Humans ; Macromolecular Substances ; Molecular Sequence Data ; Molecular Weight ; Proton-Translocating ATPases/*genetics ; Sequence Homology, Nucleic Acid ; },
abstract = {Preparations of mammalian H+ pumps that acidify intracellular vesicles contain eight or nine polypeptides, ranging in size from 116 to 17 kDa. Biochemical analysis indicates that the 70- and 58-kDa polypeptides are subunits critical for ATP hydrolysis. The amino acid sequences of the major catalytic subunits (58 and 70 kDa) of the endomembrane H+ pump are unknown from animal cells. We report here the complete sequence of the 58-kDa subunit derived from a human kidney cDNA clone and partial sequences of the 70- and 58-kDa subunits purified from clathrin-coated vesicles of bovine brain. The amino acid sequences of both proteins strongly resemble the sequences of the corresponding subunits of the vacuolar H+ pumps of Archaebacteria, plants, and fungi. The archaebacterial enzyme is believed to use a H+ gradient to synthesize ATP. Thus, a common ancestral protein has given rise to a H+ pump that synthesizes ATP in one organism and hydrolyzes it in another and is highly conserved from prokaryotes to humans. The same pump appears to mediate the acidification of intracellular organelles, including coated vesicles, lysosomes, and secretory granules, as well as extracellular fluids such as urine.},
}
@article {pmid2502434,
year = {1989},
author = {Dahlmann, B and Kopp, F and Kuehn, L and Niedel, B and Pfeifer, G and Hegerl, R and Baumeister, W},
title = {The multicatalytic proteinase (prosome) is ubiquitous from eukaryotes to archaebacteria.},
journal = {FEBS letters},
volume = {251},
number = {1-2},
pages = {125-131},
doi = {10.1016/0014-5793(89)81441-3},
pmid = {2502434},
issn = {0014-5793},
mesh = {Animals ; Archaea/*enzymology ; Bacteria/*enzymology ; Biological Evolution ; Calcium Chloride/pharmacology ; Chromatography ; Cysteine Endopeptidases/*isolation &amp; purification/metabolism ; Electrophoresis, Polyacrylamide Gel ; Macromolecular Substances ; Microscopy, Electron ; Molecular Weight ; Multienzyme Complexes/*isolation &amp; purification/metabolism ; Muscles/enzymology ; Peptide Fragments ; Proteasome Endopeptidase Complex ; Rats ; Substrate Specificity ; },
abstract = {From the thermoacidophilic archaebacterium, Thermoplasma acidophilum, a proteolytically active particle has been isolated which is almost identical in size and shape with the multicatalytic proteinase (prosome) from rat. This result indicates that prosomes have been developed early in evolution and that they possibly serve functions common to all living cells.},
}
@article {pmid2504703,
year = {1989},
author = {Friedman, SM and Oshima, T},
title = {Polyamines of sulfur-dependent archaebacteria and their role in protein synthesis.},
journal = {Journal of biochemistry},
volume = {105},
number = {6},
pages = {1030-1033},
doi = {10.1093/oxfordjournals.jbchem.a122761},
pmid = {2504703},
issn = {0021-924X},
mesh = {Amino Acids/metabolism ; Archaea/*metabolism ; Bacteria/*metabolism ; Bacterial Proteins/*biosynthesis ; Biogenic Polyamines/*metabolism ; Phenylalanine/metabolism ; Poly U/metabolism ; Putrescine/pharmacology ; RNA, Transfer, Phe/biosynthesis ; Ribosomes/metabolism ; Sulfur/*metabolism ; Temperature ; },
abstract = {Several strains of the sulfur-dependent archaebacterium, Sulfolobus, were analyzed for their polyamine content. Caldine (norspermidine), spermidine, and thermine were found to be major components in all of the cells tested. The most abundant polyamine in all cultures examined was spermidine. The Langworthy strain had the highest spermine content, whereas S. acidocaldarius strain no. 7 was devoid of this polyamine. Cultures of strain no. 7 grown at 70 degrees C were rich in spermidine and caldine (triamines) and the thermine: spermidine ratio was much lower than that of cultures grown at 78 degrees C. Equal amounts of thermine and spermidine were present in strain DSM 1616. Preincubation of Langworthy strain extracts at 10 degrees C did not overcome the requirement for polyamines in protein synthesis. Putrescine exerted a concentration-dependent inhibition of the spermine-induced stimulation of protein synthesis at 70 degrees C. Increasing concentrations (6 and 9 mM) of spermine and thermine progressively inhibited poly(U)-dependent phenylalanine incorporation at 45 degrees C to about the same extent, whereas the same concentrations of these polyamines had little effect on the reaction at 70 degrees C. Although 3 mM spermine had only a slight stimulatory effect on the attachment of phenylalanine to tRNA at 65 degrees C, this polyamine had a pronounced effect on the formation of 70S ribosomes in a standard buffer containing 10 mM Mg2+. Increasing the Mg2+ concentration to 30 mM in the absence of spermine was even more effective in causing the reassociation of subunits to form 70S particles.},
}
@article {pmid2497779,
year = {1989},
author = {Bukhrashvili, IS and Chinchaladze, DZ and Lavrik, OI and Levina, AS and Nevinsky, GA and Prangishvili, DA},
title = {Comparison of initiating abilities of primers of different length in polymerization reactions catalyzed by DNA polymerases from thermoacidophilic archaebacteria.},
journal = {Biochimica et biophysica acta},
volume = {1008},
number = {1},
pages = {102-107},
doi = {10.1016/0167-4781(89)90175-9},
pmid = {2497779},
issn = {0006-3002},
mesh = {Archaea/*enzymology ; Bacteria/*enzymology ; DNA-Directed DNA Polymerase/*metabolism ; Kinetics ; Poly A ; Poly T ; Poly dA-dT ; Structure-Activity Relationship ; Templates, Genetic ; },
abstract = {Optimal conditions for polymerization reaction catalyzed on poly(dA) and poly(dT) templates by DNA polymerases from thermoacidophilic archaebacteria--DNA polymerase A from Sulfolobus acidocaldarius and DNA polymerase B from Thermoplasma acidophilum--have been established. Values of Km and Vmax (60 degrees C) for a set of primers d(pA)n and d(pT)n have been estimated. Minimal primers for both enzymes are dNMP. Lengthening of primers by each mononucleotide increases their affinity about 2.16-fold. Linear dependence of log Km and of log vmax on the number of mononucleotide links in primers (n) has breaking point at n = 10. The value of Vmax is about 20% of that for decanucleotide. The affinity of the primer d(pA)9p(rib*) with a deoxyribosylurea residue at the 3'-end does not differ essentially from that of d(pA)9. Substitution of the 3'-terminal nucleotide of a complementary primer for a noncomplementary nucleotide, e.g., substitution of 3'-terminal A for C in d(pA)10 in the reaction catalyzed on poly(dT), decreases the affinity of a primer by one order of magnitude.},
}
@article {pmid2497352,
year = {1989},
author = {Cavalier-Smith, T},
title = {Molecular phylogeny. Archaebacteria and Archezoa.},
journal = {Nature},
volume = {339},
number = {6220},
pages = {l00-1},
doi = {10.1038/339100a0},
pmid = {2497352},
issn = {0028-0836},
mesh = {Animals ; Archaea/*classification ; Bacteria/*classification ; Base Sequence ; *DNA ; Humans ; *Phylogeny ; RNA, Ribosomal ; },
}
@article {pmid2495771,
year = {1989},
author = {White, RH},
title = {A novel biosynthesis of medium chain length alpha-ketodicarboxylic acids in methanogenic archaebacteria.},
journal = {Archives of biochemistry and biophysics},
volume = {270},
number = {2},
pages = {691-697},
doi = {10.1016/0003-9861(89)90552-3},
pmid = {2495771},
issn = {0003-9861},
mesh = {Adipates/biosynthesis ; Archaea/*metabolism ; Bacteria/*metabolism ; *Caprylates ; Dicarboxylic Acids/*biosynthesis ; Euryarchaeota/*metabolism ; Gas Chromatography-Mass Spectrometry ; Keto Acids/*biosynthesis ; Ketoglutaric Acids/biosynthesis ; Pimelic Acids/biosynthesis ; },
abstract = {Gas chromatographic-mass spectrometric analysis on the distribution of alpha-ketodicarboxylic acids in various bacteria determined that alpha-ketoglutarate and alpha-ketoadipate are widely distributed in all the bacteria examined, whereas alpha-ketopimelate and alpha-ketosuberate are found only in the methanogenic archaebacteria. Labeling experiments with stable isotopes indicated that each of these acids arises from alpha-ketoglutarate by repeated alpha-ketoacid chain elongation. The final product in this series of reactions, alpha-ketosuberate, serves in the methanogenic bacteria as the biosynthetic precursor to the 7-mercaptoheptanoic acid portion of 7-mercaptoheptanoylthreonine phosphate, a methanogenic coenzyme.},
}
@article {pmid2492940,
year = {1989},
author = {Fabry, S and Lang, J and Niermann, T and Vingron, M and Hensel, R},
title = {Nucleotide sequence of the glyceraldehyde-3-phosphate dehydrogenase gene from the mesophilic methanogenic archaebacteria Methanobacterium bryantii and Methanobacterium formicicum. Comparison with the respective gene structure of the closely related extreme thermophile Methanothermus fervidus.},
journal = {European journal of biochemistry},
volume = {179},
number = {2},
pages = {405-413},
doi = {10.1111/j.1432-1033.1989.tb14568.x},
pmid = {2492940},
issn = {0014-2956},
mesh = {Amino Acids/analysis ; Archaea/enzymology/*genetics ; Bacteria/*genetics ; Base Sequence ; Chemical Phenomena ; Chemistry ; Computers ; Euryarchaeota/enzymology/*genetics ; Genes ; *Genes, Bacterial ; Genetic Vectors ; Glyceraldehyde-3-Phosphate Dehydrogenases/*genetics/isolation &amp; purification ; Molecular Sequence Data ; Plasmids ; Sequence Homology, Nucleic Acid ; },
abstract = {The genes for glyceraldehyde-3-phosphate dehydrogenase (gap genes) from the mesophilic methanogenic archaebacteria Methanobacterium formicicum and Methanobacterium bryantii were cloned and sequenced. The deduced amino acid sequences show 95% identity to each other and about 70% identity to the glyceraldehyde-3-phosphate dehydrogenase from the thermophilic methanogenic archaebacterium Methanothermus fervidus. Although the sequence similarity between the archaebacterial glyceraldehyde-3-phosphate dehydrogenase and the homologous enzyme of eubacteria and eukaryotes is low, an equivalent secondary-structural arrangement can be deduced from the profiles of the physical parameters hydropathy, chain flexibility and amphipathy. In order to find possible thermophile-specific structural features of the enzyme from M. fervidus, a comparative primary-sequence analysis was performed. Amino acid exchanges leading, to a stabilization of the main-chain conformation, could be found throughout the sequence of the thermophile enzyme. Striking features of the thermophile sequence are the preference for isoleucine, especially in beta-sheets, and a low arginine/lysine ratio of 0.54.},
}
@article {pmid2472901,
year = {1989},
author = {Itaya, T and Mizutani, A and Takeda, M and Shioyama, C},
title = {Studies towards the synthesis of the fluorescent bases of phenylalanine transfer ribonucleic acids: synthesis of 7-methylwye isolated from extremely thermophilic archaebacteria.},
journal = {Chemical &amp; pharmaceutical bulletin},
volume = {37},
number = {2},
pages = {284-291},
doi = {10.1248/cpb.37.284},
pmid = {2472901},
issn = {0009-2363},
mesh = {Archaea/*metabolism ; Bacteria/*metabolism ; Fluorescent Dyes/*chemical synthesis ; Guanine/*analogs &amp; derivatives/chemical synthesis ; Phenylalanine/*metabolism ; RNA, Bacterial/*chemical synthesis ; RNA, Transfer, Amino Acid-Specific/*chemical synthesis ; RNA, Transfer, Phe/*chemical synthesis ; },
abstract = {Acid- or base-catalyzed acylation of 1-benzylwye (7) provided the 7-substituted derivatives 9, 10, and 11 in poor yields. Although the reactions of lithiated 7 with electrophiles gave the 2-substituted derivatives 14, 15, 17, 20, 21, and 22, lithiation of 1-benzyl-7-bromo-2-chlorowye (23) followed by treatment with Me2CHCH2CHO (13) successfully introduced a side chain at the 7-position to afford 1-benzyl-2-chloro-7-(1-hydroxy-3-methylbutyl)wye (24). Cyclization of 1-benzyl-3-methylguanine (5) with 3-bromo-2-butanone followed by catalytic hydrogenolysis afforded 7-methylwye (2b), the hypermodified base isolated from archaebacterial transfer ribonucleic acids. A more efficient route for the synthesis of 2b has been developed via a series of reactions: the Vilsmeier-Haack reaction of 7, reduction with NaBH4, and catalytic hydrogenolysis over Pd-C.},
}
@article {pmid2541879,
year = {1989},
author = {Zillig, W and Klenk, HP and Palm, P and Pühler, G and Gropp, F and Garrett, RA and Leffers, H},
title = {The phylogenetic relations of DNA-dependent RNA polymerases of archaebacteria, eukaryotes, and eubacteria.},
journal = {Canadian journal of microbiology},
volume = {35},
number = {1},
pages = {73-80},
doi = {10.1139/m89-011},
pmid = {2541879},
issn = {0008-4166},
mesh = {Amino Acid Sequence ; Animals ; Archaea/enzymology/*genetics ; Bacteria/*genetics ; Cells/*enzymology ; Chromosome Deletion ; DNA Transposable Elements ; DNA-Directed RNA Polymerases/*genetics ; Eubacterium/enzymology/*genetics ; Eukaryotic Cells/*enzymology ; Molecular Sequence Data ; Phylogeny ; Species Specificity ; },
abstract = {Unrooted phylogenetic dendrograms were calculated by two independent methods, parsimony and distance matrix analysis, from an alignment of the derived amino acid sequences of the A and C subunits of the DNA-dependent RNA polymerases of the archaebacteria Sulfolobus acidocaldarius and Halobacterium halobium with 12 corresponding sequences including a further set of archaebacterial A+C subunits, eukaryotic nuclear RNA polymerases, pol I, pol II, and pol III, eubacterial beta' and chloroplast beta' and beta" subunits. They show the archaebacteria as a coherent group in close neighborhood of and sharing a bifurcation with eukaryotic pol II and (or) pol IIIA components. The most probable trees show pol IA branching off from the tree separately at a bifurcation with the eubacterial beta' lineage. The implications of these results, especially for understanding the possibly chimeric origin of the eukaryotic nuclear genome, are discussed.},
}
@article {pmid2541877,
year = {1989},
author = {Forterre, P and Elie, C and Sioud, M and Hamal, A},
title = {Studies on DNA polymerases and topoisomerases in archaebacteria.},
journal = {Canadian journal of microbiology},
volume = {35},
number = {1},
pages = {228-233},
doi = {10.1139/m89-035},
pmid = {2541877},
issn = {0008-4166},
mesh = {Archaea/*enzymology ; Bacteria/*enzymology ; Biological Evolution ; DNA Topoisomerases, Type I/*metabolism ; DNA Topoisomerases, Type II/metabolism ; DNA, Bacterial/metabolism ; DNA, Superhelical/metabolism ; DNA-Directed DNA Polymerase/*metabolism ; Molecular Weight ; Plasmids ; Prokaryotic Cells/enzymology ; },
abstract = {We have isolated DNA polymerases and topoisomerases from two thermoacidophilic archaebacteria: Sulfolobus acidocaldarius and Thermoplasma acidophilum. The DNA polymerases are composed of a single polypeptide with molecular masses of 100 and 85 kDa, respectively. Antibodies against Sulfolobus DNA polymerase did not cross react with Thermoplasma DNA polymerase. Whereas the major DNA topoisomerase activity in S. acidocaldarius is an ATP-dependent type I DNA topoisomerase with a reverse gyrase activity, the major DNA topoisomerase activity in T. acidophilum is a ATP-independent relaxing activity. Both enzymes resemble more the eubacterial than the eukaryotic type I DNA topoisomerase. We have found that small plasmids from halobacteria are negatively supercoiled and that DNA topoisomerase II inhibitors modify their topology. This suggests the existence of an archaebacterial type II DNA topoisomerase related to its eubacterial and eukaryotic counterparts. As in eubacteria, novobiocin induces positive supercoiling of halobacterial plasmids, indicating the absence of a eukaryotic-like type I DNA topoisomerase that relaxes positive superturns.},
}
@article {pmid2535117,
year = {1989},
author = {Stan-Lotter, H and Lang, FJ and Hochstein, LI},
title = {Electrophoresis and isoelectric focusing of whole cell and membrane proteins from the extremely halophilic archaebacteria.},
journal = {Applied and theoretical electrophoresis : the official journal of the International Electrophoresis Society},
volume = {1},
number = {3},
pages = {147-153},
pmid = {2535117},
issn = {0954-6642},
mesh = {Adenosine Triphosphatases/analysis ; Archaea/*analysis ; Cell Membrane/chemistry/enzymology ; Cytoplasm/chemistry ; *Electrophoresis, Polyacrylamide Gel ; Halobacterium/*analysis ; *Isoelectric Focusing ; Isoelectric Point ; Membrane Proteins/*analysis ; Nitrate Reductase ; Nitrate Reductases/analysis ; },
abstract = {The isoelectric points of most proteins from the extremely halophilic archaebacteria are between 4.0 and 4.65 which agrees with the generally high content of glutamic and aspartic acid in proteins from halobacteria. The subunits from two purified halobacterial membrane enzymes (ATPase and nitrate reductase) behaved differently with respect to isoelectric focusing, silver staining and interaction with ampholytes. Differential behavior was also observed in whole cell proteins from Halobacterium saccharovorum regarding resolution in two-dimensional gels and silver staining. We propose that these differences reflect the existence of two classes of halobacterial proteins, one resembling non-halophilic proteins, and the other possessing unique properties that may be related to salt dependence.},
}
@article {pmid2497944,
year = {1989},
author = {Danson, MJ},
title = {Central metabolism of the archaebacteria: an overview.},
journal = {Canadian journal of microbiology},
volume = {35},
number = {1},
pages = {58-64},
doi = {10.1139/m89-009},
pmid = {2497944},
issn = {0008-4166},
mesh = {Archaea/*metabolism ; Bacteria/*metabolism ; Citric Acid Cycle ; Eubacterium/metabolism ; Eukaryotic Cells/metabolism ; Hexoses/metabolism ; Oxidation-Reduction ; Pyruvates/metabolism ; Pyruvic Acid ; },
}
@article {pmid2497943,
year = {1989},
author = {Allmansberger, R and Bokranz, M and Kröckel, L and Schallenberg, J and Klein, A},
title = {Conserved gene structures and expression signals in methanogenic archaebacteria.},
journal = {Canadian journal of microbiology},
volume = {35},
number = {1},
pages = {52-57},
doi = {10.1139/m89-008},
pmid = {2497943},
issn = {0008-4166},
mesh = {Amino Acid Sequence ; Archaea/*genetics ; Bacteria/*genetics ; Binding Sites ; Biological Evolution ; DNA-Directed RNA Polymerases/genetics/metabolism ; Euryarchaeota/*genetics/metabolism ; Gene Expression Regulation ; *Genes, Bacterial ; Molecular Sequence Data ; Multigene Family ; Signal Transduction ; Transcription, Genetic ; },
abstract = {A comparative analysis of cotranscribed gene clusters comprising the structural genes mcrA, mcrB, mcrC, mcrD, and mcrG was carried out in three species of methanogens. mcrA, mcrB, and mcrG are the structural genes for the three subunits of methyl coenzyme M reductase, while the two other genes encode polypeptides of unknown functions. The degree of conservation of the mcr gene products among different species of methanogens varies. No correlation was found between the conservation of the G+C contents of the homologous genes and of the amino acid sequences of their products among the different bacteria. The comparison of RNA polymerase core subunit genes of Methanobacterium thermoautotrophicum as evolutionary markers with their equivalents in Escherichia coli, Saccharomyces cerevisiae, and Drosophila melanogaster showed that homologous polypeptide domains are encoded by different numbers of genes suggesting gene fusion of adjacent genes in the course of evolution. The archaebacterial subunits exhibit much stronger homology with their eukaryotic than with their eubacterial equivalents on the polypeptide sequence level. All the analyzed genes are preceded by ribosome binding sites of eubacterial type. In addition to known putative promoter sequences, conserved structural elements of the DNA were detected surrounding the transcription initiation sites of the mcr genes.},
}
@article {pmid2497941,
year = {1989},
author = {Ramirez, C and Shimmin, LC and Newton, CH and Matheson, AT and Dennis, PP},
title = {Structure and evolution of the L11, L1, L10, and L12 equivalent ribosomal proteins in eubacteria, archaebacteria, and eucaryotes.},
journal = {Canadian journal of microbiology},
volume = {35},
number = {1},
pages = {234-244},
doi = {10.1139/m89-036},
pmid = {2497941},
issn = {0008-4166},
mesh = {Amino Acid Sequence ; Archaea/*genetics ; Bacteria/*genetics ; Biological Evolution ; Cells/*metabolism ; Eubacterium/*genetics ; Eukaryotic Cells/*metabolism ; Genes ; Molecular Sequence Data ; Molecular Structure ; Ribosomal Proteins/*genetics ; Species Specificity ; },
abstract = {The genes corresponding to the L11, L1, L10, and L12 equivalent ribosomal proteins (L11e, L1e, L10e, and L12e) of Escherichia coli have been cloned and sequenced from two widely divergent species of archaebacteria, Halobacterium cutirubrum and Sulfolobus solfataricus, and the L10 and four different L12 genes have been cloned and sequenced from the eucaryote Saccharomyces cerevisiae. Alignments between the deduced amino acid sequences of these proteins and to other available homologous proteins of eubacteria and eucaryotes have been made. The data suggest that the archaebacteria are a distinct coherent phylogenetic group. Alignment of the proline-rich L11e proteins reveals that the N-terminal region, believed to be responsible for interaction with release factor 1, is the most highly conserved region and that there is specific conservation of most of the proline residues, which may be important in maintaining the highly elongated structure of the molecule. Although L11 is the most highly methylated protein in the E. coli ribosome, the sites of methylation are not conserved in the archaebacterial L11e proteins. The L1e proteins of eubacteria and archaebacteria show two regions of very high similarity near the center and the carboxy termini of the proteins. The L10e proteins of all kingdoms are colinear and contain approximately three fourths of an L12e protein fused to their carboxy terminus, although much of this fusion has been lost in the truncated eubacterial protein. The archaebacterial and eucaryotic L12e proteins are colinear, whereas the eubacterial protein has suffered a rearrangement through what appear to be gene fusion events. Within the L12e derived region of the L10e proteins there exists a repeated module of 26 amino acids, present in two copies in eucaryotes, three in archaebacteria, and one in eubacteria. This modular sequence is apparently also present in the L12e proteins of all kingdoms and may play a role in L12e dimerization, L10e-L12e complex formation, and the function of the L10e-L12e complex in translation.},
}
@article {pmid2497939,
year = {1989},
author = {Shimmin, LC and Newton, CH and Ramirez, C and Yee, J and Downing, WL and Louie, A and Matheson, AT and Dennis, PP},
title = {Organization of genes encoding the L11, L1, L10, and L12 equivalent ribosomal proteins in eubacteria, archaebacteria, and eucaryotes.},
journal = {Canadian journal of microbiology},
volume = {35},
number = {1},
pages = {164-170},
doi = {10.1139/m89-025},
pmid = {2497939},
issn = {0008-4166},
mesh = {Amino Acid Sequence ; Archaea/*genetics ; Bacteria/*genetics ; Base Sequence ; Biological Evolution ; Cells/*metabolism ; Cloning, Molecular ; DNA/genetics ; Eubacterium/*genetics ; Eukaryotic Cells/*metabolism ; Genes ; Molecular Sequence Data ; Ribosomal Proteins/*genetics ; },
abstract = {Archaebacterial and eucaryotic cytoplasmic ribosomes contain proteins equivalent to the L11, L1, L10, and L12 proteins of the eubacterium Escherichia coli. In E. coli the genes encoding these ribosomal proteins are clustered, cotranscribed, and autogenously regulated at the level of mRNA translation. Genomic restriction fragments encoding the L11e, L1e, L10e, and L12e (equivalent) proteins from two divergent archaebacteria. Halobacterium cutirubrum and Sulfolobus solfataricus, and the L10e and L12e proteins from the eucaryote Saccharomyces cerevisiae have been cloned, sequenced, and analyzed. In the archaebacteria, as in eubacteria, the four genes are clustered and the L11e, L1e, L10e, and L12e order is maintained. The transcription pattern of the H. cutirubrum cluster is different from the E. coli pattern and the flanking genes on either side of the tetragenic clusters in E. coli, H. cutirubrum, and Sulfolobus solfataricus are all unrelated to each other. In the eucaryote Saccharomyces cerevisiae there is a single L10e gene and four separate L12e genes that are designated L12eIA, L12eIB, L12eIIA, and L12eIIB. These five genes are not closely linked and each is transcribed as a monocistronic mRNA; the L10e, L12eIA, L12eIB, and the L12eIIA genes are contiguous and uninterrupted, whereas the L12eIIB gene is interrupted by a 301 nucleotide long intron located between codons 38 and 39.},
}
@article {pmid2497937,
year = {1989},
author = {Cline, SW and Lam, WL and Charlebois, RL and Schalkwyk, LC and Doolittle, WF},
title = {Transformation methods for halophilic archaebacteria.},
journal = {Canadian journal of microbiology},
volume = {35},
number = {1},
pages = {148-152},
doi = {10.1139/m89-022},
pmid = {2497937},
issn = {0008-4166},
mesh = {Archaea/genetics ; Bacteriophages/genetics ; DNA, Bacterial/genetics ; DNA, Viral/genetics ; Genetic Techniques ; Halobacterium/*genetics ; Plasmids ; Polyethylene Glycols ; Spheroplasts ; Transfection ; *Transformation, Genetic ; },
abstract = {We present a practical description of polyethylene glycol mediated spheroplast transformation of Halobacterium halobium and Halobacterium volcanii. This method has been applied to phage DNA transfection, plasmid DNA transformation, and transformation with linear fragments of high molecular weight genomic DNA. Efficient spheroplast regeneration allows uncomplicated recovery of transformed progeny. Transformations can be performed equally well using fresh or frozen cell preparations. These methods should find application in molecular cloning, genetic fine mapping, and strain construction.},
}
@article {pmid2497934,
year = {1989},
author = {},
title = {Molecular biology of the archaebacteria. 31 July-5 August, 1988, Victoria, British Columbia, Canada. Meeting proceedings.},
journal = {Canadian journal of microbiology},
volume = {35},
number = {1},
pages = {1-244},
pmid = {2497934},
issn = {0008-4166},
mesh = {Archaea/*genetics ; Bacteria/*genetics ; Molecular Biology ; },
}
@article {pmid2470486,
year = {1989},
author = {Thompson, LD and Brandon, LD and Nieuwlandt, DT and Daniels, CJ},
title = {Transfer RNA intron processing in the halophilic archaebacteria.},
journal = {Canadian journal of microbiology},
volume = {35},
number = {1},
pages = {36-42},
doi = {10.1139/m89-006},
pmid = {2470486},
issn = {0008-4166},
mesh = {Base Sequence ; Endoribonucleases/metabolism ; Genes, Bacterial ; Halobacterium/genetics/*metabolism ; Introns ; Molecular Sequence Data ; Nucleic Acid Conformation ; RNA Precursors/genetics/metabolism ; *RNA Processing, Post-Transcriptional ; RNA, Bacterial/genetics/*metabolism ; RNA, Transfer/genetics/*metabolism ; Substrate Specificity ; },
abstract = {An in vitro assay system has been developed for the Halobacterium volcanii tRNA intron endonuclease using in vitro generated precursor RNAs. A partially purified enzyme preparation is capable of precise and accurate excision of the intron from the halobacterial tRNA(Trp) precursor. The cleavage reaction produces products having 5' hydroxyl and 2',3' cyclic phosphate termini. Processing of precursor molecules containing deletions within the exon regions indicates that the halobacterial endonuclease does not require intact mature tRNA structure in the substrate; this is in contrast to the eukaryotic endonuclease enzyme that has an absolute requirement for these structures. The large halobacterial tRNA(Trp) intron does not appear to be a primary site for recognition by the endonuclease, however, its removal affects cleavage efficiency. Through a comparison of the structural and sequence features of the halobacterial substrates and the precursors of other archaebacterial intron-containing precursors, a common element is proposed for the recognition of substrates by intron endonuclease.},
}
@article {pmid2467783,
year = {1989},
author = {Brown, JW and Daniels, CJ and Reeve, JN},
title = {Gene structure, organization, and expression in archaebacteria.},
journal = {Critical reviews in microbiology},
volume = {16},
number = {4},
pages = {287-338},
doi = {10.3109/10408418909105479},
pmid = {2467783},
issn = {1040-841X},
mesh = {Archaea/*genetics ; Bacteria/*genetics ; Base Sequence ; Codon/genetics ; DNA, Bacterial/*genetics ; *Gene Expression Regulation ; *Genes, Bacterial ; Molecular Sequence Data ; Promoter Regions, Genetic ; RNA Processing, Post-Transcriptional ; RNA, Bacterial/genetics ; RNA, Messenger/genetics ; Transcription, Genetic ; },
abstract = {Major advances have recently been made in understanding the molecular biology of the archaebacteria. In this review, we compare the structure of protein and stable RNA-encoding genes cloned and sequenced from each of the major classes of archaebacteria: the methanogens, extreme halophiles, and acid thermophiles. Protein-encoding genes, including some encoding proteins directly involved in methanogenesis and photoautotrophy, are analyzed on the basis of gene organization and structure, transcriptional control signals, codon usage, and evolutionary conservation. Stable RNA-encoding genes are compared for gene organization and structure, transcriptional signals, and processing events involved in RNA maturation, including intron removal. Comparisons of archaebacterial structures and regulatory systems are made with their eubacterial and eukaryotic homologs.},
}
@article {pmid3255682,
year = {1988},
author = {Rawal, N and Kelkar, SM and Altekar, W},
title = {Alternative routes of carbohydrate metabolism in halophilic archaebacteria.},
journal = {Indian journal of biochemistry &amp; biophysics},
volume = {25},
number = {6},
pages = {674-686},
pmid = {3255682},
issn = {0301-1208},
mesh = {*Carbohydrate Metabolism ; Glucose/metabolism ; Glycerol/metabolism ; Halobacterium/*metabolism ; Hexoses/metabolism ; Pyruvates/metabolism ; Pyruvic Acid ; },
}
@article {pmid3150881,
year = {1988},
author = {Eisenberg, H},
title = {Archaebacteria coming of age.},
journal = {Trends in biochemical sciences},
volume = {13},
number = {11},
pages = {416-417},
doi = {10.1016/0968-0004(88)90207-1},
pmid = {3150881},
issn = {0968-0004},
mesh = {Archaea/*genetics ; Bacteria/*genetics ; },
}
@article {pmid3139633,
year = {1988},
author = {White, RH},
title = {Analysis and characterization of the folates in the nonmethanogenic archaebacteria.},
journal = {Journal of bacteriology},
volume = {170},
number = {10},
pages = {4608-4612},
pmid = {3139633},
issn = {0021-9193},
mesh = {Archaea/*analysis ; Bacteria/*analysis ; Chromatography ; Folic Acid/*analysis ; Halobacterium/*analysis ; },
abstract = {A detailed analysis of the folate coenzymes in the nonmethanogenic archaebacteria has been performed. By using the Lactobacillus casei microbiological assay for folates, the levels of folates in Sulfolobus solfataricus and Sulfolobus acidocaldarius were found to be 3.7 and 8.3 ng/g (dry weight) of cells, respectively, compared with 88,000 and 28,000 ng/g (dry weight) of cells in Halobacterium halobium and Halobacterium strain GN-1, respectively. The levels of folates found in the Sulfolobus spp. were approximately 100 times less than those found in the typical eubacterium, whereas the levels in the halobacteria were approximately 10 times higher. The folate in Sulfolobus solfataricus was shown to consist of only 5-formyltetrahydropteroylglutamate, and the folate in Halobacterium strain GN-1 was shown to consist of only pteroyldiglutamate. The low folate levels in the Sulfolobus spp. are the same as those found in the methanogenic bacteria, suggesting that another C1 carrier may function in these cells.},
}
@article {pmid3137217,
year = {1988},
author = {Worrell, VE and Nagle, DP},
title = {Folic acid and pteroylpolyglutamate contents of archaebacteria.},
journal = {Journal of bacteriology},
volume = {170},
number = {9},
pages = {4420-4423},
pmid = {3137217},
issn = {0021-9193},
mesh = {Archaea/*analysis ; Bacteria/*analysis ; Biological Assay ; Euryarchaeota/*analysis ; Folic Acid/*analogs &amp; derivatives/*analysis ; Halobacterium/*analysis ; Pteroylpolyglutamic Acids/*analysis ; },
abstract = {Cell extracts of methanogens and the thermoacidophile Sulfolobus solfataricus contained little or no folic acid (pteroylglutamate) or pteroylpolyglutamate activity (less than 0.1 nmol/g [dry weight]). However, the halophile Halobacterium salinarum contained pteroylmono- or pteroyldiglutamates, and Halobacterium volcanii and Halobacterium halobium contained pteroyltriglutamates at levels equivalent to those in eubacteria (greater than 1 nmol/g [dry weight]).},
}
@article {pmid3137215,
year = {1988},
author = {Noll, KM and Barber, TS},
title = {Vitamin contents of archaebacteria.},
journal = {Journal of bacteriology},
volume = {170},
number = {9},
pages = {4315-4321},
pmid = {3137215},
issn = {0021-9193},
support = {AI 12277/AI/NIAID NIH HHS/United States ; GM 07283-11/GM/NIGMS NIH HHS/United States ; },
mesh = {Archaea ; Bacteria ; Biological Assay ; Biotin/analysis ; Coenzymes/analysis ; Escherichia coli ; Lacticaseibacillus casei/growth &amp; development ; Niacin/analysis ; Pantothenic Acid/analysis ; Pyridoxine/analysis ; Riboflavin/analysis ; Thioctic Acid/analysis ; Vitamins/*analysis ; },
abstract = {The levels of six water-soluble vitamins of seven archaebacterial species were determined and compared with the levels found in a eubacterium, Escherichia coli. Biotin, riboflavin, pantothenic acid, nicotinic acid, pyridoxine, and lipoic acid contents of Halobacterium volcanii, Methanobacterium thermoautotrophicum delta H, "Archaeoglobus fulgidus" VC-16, Thermococcus celer, Pyrodictium occultum, Thermoproteus tenax, and Sulfolobus solfataricus were measured by using bioassays. The archaebacteria examined were found to contain these vitamins at levels similar to or significantly below the levels found in in E. coli. Riboflavin was found at levels comparable to those in E. coli. Pyridoxine was as abundant among the archaebacteria of the methanogenhalophile branch as in E. coli. It was only one-half as abundant in the sulfur-metabolizing branch. "A. fulgidus," however, contained only 4% as much pyridoxine as E. coli. Nicotinic and pantothenic acids were approximately 10-fold less abundant (except for a 200-fold-lower nicotinic acid level in "A. fulgidus"). Nicotinic acid may be replaced by an 8-hydroxy-5-deazaflavin coenzyme (factor F420) in some archaebacteria (such as "A. fulgidus"). Compared with the level in E. coli, biotin was equally as abundant in Thermococcus celer and Methanobacterium thermoautotrophicum, about one-fourth less abundant in P. occultum and "A. fulgidus," and 25 to over 100 times less abundant in the others. The level of lipoic acid was up to 20 times lower in H. volcanii, Methanobacterium thermoautotrophicum, and Thermococcus celer. It was over two orders of magnitude lower among the remaining organisms. With the exception of "A. fulgidus," lipoic acid, pantothenic acid, and pyridoxine were more abundant in the members of the methanogen-halophile branch of the archaebacteria than in the sulfur-metabolizing branch.},
}
@article {pmid3137214,
year = {1988},
author = {Schneider, GJ and Hasekorn, R},
title = {RNA polymerase subunit homology among cyanobacteria, other eubacteria and archaebacteria.},
journal = {Journal of bacteriology},
volume = {170},
number = {9},
pages = {4136-4140},
pmid = {3137214},
issn = {0021-9193},
support = {GM 21823/GM/NIGMS NIH HHS/United States ; },
mesh = {Archaea/*enzymology/genetics/immunology ; Bacteria/*enzymology ; Biological Evolution ; Cross Reactions ; Cyanobacteria/*enzymology/genetics/immunology ; DNA-Directed RNA Polymerases/*analysis/genetics/immunology ; Electrophoresis, Polyacrylamide Gel ; Escherichia coli/*enzymology/genetics/immunology ; Immunoassay ; },
abstract = {RNA polymerase purified from vegetative cells of the cyanobacterium Anabaena sp. strain PCC 7120 contains a dissociable sigma factor and a core of five subunits: the beta', beta, and two alpha subunits characteristic of all eubacteria and an additional 66,000-molecular-weight polypeptide called gamma. Fifteen of fifteen strains of unicellular and filamentous cyanobacteria tested contained a serologically related gamma protein. Antiserum to gamma reacted with Escherichia coli beta' and the A subunit of RNA polymerase of the archaebacterium Sulfolobus acidocaldarius. Thus the evolution of the RNA polymerase beta' subunit has followed different paths in three groups of procaryotes: cyanobacteria, other eubacteria, and archaebacteria.},
}
@article {pmid2465484,
year = {1988},
author = {Londei, P and Altamura, S and Sanz, JL and Amils, R},
title = {Aminoglycoside-induced mistranslation in thermophilic archaebacteria.},
journal = {Molecular &amp; general genetics : MGG},
volume = {214},
number = {1},
pages = {48-54},
pmid = {2465484},
issn = {0026-8925},
mesh = {Anti-Bacterial Agents/*pharmacology ; Archaea/*drug effects/genetics ; Bacteria/*drug effects ; Hexosamines/pharmacology ; Phylogeny ; Polyribonucleotides/genetics ; Protein Biosynthesis/*drug effects ; *Protein Synthesis Inhibitors ; RNA, Bacterial/drug effects/genetics ; RNA, Ribosomal/drug effects/genetics ; Species Specificity ; Streptomycin/pharmacology ; Structure-Activity Relationship ; },
abstract = {The effect of selected aminoglycoside antibiotics on the translational accuracy of poly(U) programmed ribosomes derived from the thermophilic archaebacteria Thermoplasma acidophilum, Sulfolobus solfataricus, Thermococcus celer and Desulfurococcus mobilis has been determined. Under optimum temperature and ionic conditions for polyphenylalanine synthesis, the four species investigated are found to be markedly diverse in their response to the miscoding-inducing action of aminoglycoside antibiotics. T. acidophilum is sensitive to all of the compounds tested except streptomycin; S. solfataricus responds to paromomycin and to hygromycin B; T. celer is only affected by neomycin, and D. mobilis is refractory to all drugs. The only feature shared by the four species under study, and by all archaebacteria so far investigated, is their complete insensitivity to streptomycin. The structural and phylogenetic implications of the remarkable diversity encountered among archaebacterial ribosomes in their susceptibility to aminoglycosides are discussed.},
}
@article {pmid3412892,
year = {1988},
author = {Allmansberger, R and Knaub, S and Klein, A},
title = {Conserved elements in the transcription initiation regions preceding highly expressed structural genes of methanogenic archaebacteria.},
journal = {Nucleic acids research},
volume = {16},
number = {15},
pages = {7419-7436},
pmid = {3412892},
issn = {0305-1048},
mesh = {Base Composition ; Base Sequence ; DNA, Bacterial/genetics ; Euryarchaeota/*genetics ; Free Radicals ; *Genes, Bacterial ; Hydroxides ; Molecular Sequence Data ; Nucleic Acid Conformation ; Oxidoreductases/*genetics ; Promoter Regions, Genetic ; *Regulatory Sequences, Nucleic Acid ; *Transcription, Genetic ; },
abstract = {The sequences of the intergenic regions of the strongly expressed genes encoding methyl CoM reductase in three different methanogenic archaebacteria were determined and the 5'-ends of the transcripts were mapped. After alignment, consensus sequences were found which are located both upstream and downstream of the transcription starts. They correspond, in part, to those previously characterized as putative elements of archaebacterial promoter sequences. In addition, bending of the DNA in front of the transcription start sites was shown in two cases and a characteristic common DNA structure immediately downstream of the 5'-end of the transcript was discovered. This structure was also found in the corresponding regions of previously described genes in methanogens. Our results suggest that both sequence and structural information may have roles in the initiation of transcription of protein encoding genes of these archaebacteria.},
}
@article {pmid3133361,
year = {1988},
author = {Morris, CJ and Reeve, JN},
title = {Conservation of structure in the human gene encoding argininosuccinate synthetase and the argG genes of the archaebacteria Methanosarcina barkeri MS and Methanococcus vannielii.},
journal = {Journal of bacteriology},
volume = {170},
number = {7},
pages = {3125-3130},
pmid = {3133361},
issn = {0021-9193},
mesh = {Amino Acid Sequence ; Archaea/enzymology/*genetics ; Argininosuccinate Synthase/*genetics ; Bacteria/*genetics ; Base Sequence ; Carbamoyl-Phosphate Synthase (Glutamine-Hydrolyzing)/genetics ; Chromosomes, Human ; Cloning, Molecular ; DNA, Bacterial/genetics ; Euryarchaeota/enzymology/*genetics ; Exons ; *Genes, Bacterial ; Humans ; Ligases/*genetics ; Molecular Sequence Data ; Repetitive Sequences, Nucleic Acid ; },
abstract = {The DNA sequences of the argG genes of Methanosarcina barkeri MS and Methanococcus vannielii were determined. The polypeptide products of these methanogen genes have amino acid sequences which are 50% identical to each other and 38% identical to the amino acid sequence encoded by the exons of the human argininosuccinate synthetase gene. Introns in the human chromosomal gene separate regions which encode amino acids conserved in both the archaebacterial and human gene products. An open reading frame immediately upstream of argG in Methanosarcina barkeri MS codes for an amino acid sequence which is 45 and 31% identical to the sequences of the large subunits of carbamyl phosphate synthetase in Escherichia coli and Saccharomyces cerevisiae, respectively. If this gene encodes carbamyl phosphate synthetase in Methanosarcina barkeri, this is the first example, in an archaebacterium, of physical linkage of genes that encode enzymes which catalyze reactions in the same amino acid biosynthetic pathway.},
}
@article {pmid3150420,
year = {1988},
author = {Koga, Y and Nishihara, M},
title = {[Lipids of archaebacteria--heptad hypothesis].},
journal = {Seikagaku. The Journal of Japanese Biochemical Society},
volume = {60},
number = {6},
pages = {424-435},
pmid = {3150420},
issn = {0037-1017},
mesh = {Archaea/*metabolism ; Bacteria/*metabolism ; Lipids/*analysis ; },
}
@article {pmid3131139,
year = {1988},
author = {Zillig, W and Palm, P and Reiter, WD and Gropp, F and Pühler, G and Klenk, HP},
title = {Comparative evaluation of gene expression in archaebacteria.},
journal = {European journal of biochemistry},
volume = {173},
number = {3},
pages = {473-482},
doi = {10.1111/j.1432-1033.1988.tb14023.x},
pmid = {3131139},
issn = {0014-2956},
mesh = {Archaea/*genetics ; Bacteria/*genetics ; *Gene Expression Regulation ; },
abstract = {Gene organization, gene structure, especially regarding transcription and translation signals, and the structure of essential components of the gene expression machinery of archaebacteria are compared with those of eubacteria and eukaryotes. Many features of the genetic machinery of archaebacteria are shared either with eubacteria or with eukaryotes. For example, the translation signals including ribosome-binding sites are the same as in eubacteria, but the consensus sequence of archaebacterial promoters closely resembles that of the eukaryotic polymerase II promoters. Archaebacterial genes can be organized in transcription units resembling those of eubacteria. But the sequences of several protein components of the genetic machinery have strikingly more homology with those of their eukaryotic than with those of their eubacterial correspondents. The sequences of the large components of DNA-dependent RNA polymerases of archaebacteria closely resemble those of the eukaryotic RNA polymerases II and, somewhat less, III. In a dendrogram calculated from percentage homology data, the eukaryotic RNA polymerase I component A shares a branching point with the eubacterial component. The implications of these findings for the origin and the evolution of the eukaryotic ancestry are discussed.},
}
@article {pmid2834336,
year = {1988},
author = {Schallenberg, J and Moes, M and Truss, M and Reiser, W and Thomm, M and Stetter, KO and Klein, A},
title = {Cloning and physical mapping of RNA polymerase genes from Methanobacterium thermoautotrophicum and comparison of homologies and gene orders with those of RNA polymerase genes from other methanogenic archaebacteria.},
journal = {Journal of bacteriology},
volume = {170},
number = {5},
pages = {2247-2253},
pmid = {2834336},
issn = {0021-9193},
mesh = {Archaea/enzymology/*genetics ; Bacteria/*genetics ; Base Sequence ; Chromosome Mapping ; Cloning, Molecular ; DNA Restriction Enzymes ; DNA, Bacterial/genetics ; DNA-Directed RNA Polymerases/*genetics ; Deoxyribonuclease EcoRI ; Euryarchaeota/enzymology/*genetics ; Genes ; Genes, Bacterial ; Immunoassay ; Molecular Sequence Data ; Nucleic Acid Hybridization ; Phylogeny ; Plasmids ; Sequence Homology, Nucleic Acid ; },
abstract = {The structural genes encoding the four largest subunits of RNA polymerase, A, B', B", and C, were physically mapped in Methanobacterium thermoautotrophicum Winter. The genes formed a cluster in the order B", B', A, C and had a common orientation. DNA hybridization experiments yielded different degrees of homology between RNA polymerase gene sequences of different species of Methanobacterium and Methanococcus voltae. No homology was detectable between Methanobacterium thermoautotrophicum and Methanosarcina barkeri. From Southern hybridization experiments in which probes of the four genes from Methanobacterium thermoautotrophicum Winter and restriction digests of the genomic DNAs of the different methanogens were used, a common gene order of the RNA polymerase genes could be deduced.},
}
@article {pmid3347494,
year = {1988},
author = {Sioud, M and Baldacci, G and de Recondo, AM and Forterre, P},
title = {Novobiocin induces positive supercoiling of small plasmids from halophilic archaebacteria in vivo.},
journal = {Nucleic acids research},
volume = {16},
number = {4},
pages = {1379-1391},
pmid = {3347494},
issn = {0305-1048},
mesh = {DNA, Superhelical/drug effects ; Halobacterium/*genetics ; Novobiocin/*pharmacology ; Nucleic Acid Hybridization ; Osmolar Concentration ; Plasmids/*drug effects ; },
abstract = {The halophilic archaebacterium Halobacterium strain GRB harbours a multicopy plasmid of 1.7 kb which is negatively supercoiled. After addition of novobiocin to culture medium all 1.7 kb plasmid molecules become positively supercoiled. Positive supercoiling occurs at the same dose of novobiocin inhibiting the eubacterial DNA gyrase in vitro. Novobiocin also induces positive supercoiling of pHV2, a 6.3 kb plasmid from Halobacterium volcanii. These results indicate the existence of a mechanism producing positive superturns in halobacteria. The 1.7 kb plasmid from Halobacterium GRB could be used to produce high amounts of pure positively supercoiled DNA for biophysical and biochemical studies.},
}
@article {pmid2828337,
year = {1988},
author = {Sioud, M and Possot, O and Elie, C and Sibold, L and Forterre, P},
title = {Coumarin and quinolone action in archaebacteria: evidence for the presence of a DNA gyrase-like enzyme.},
journal = {Journal of bacteriology},
volume = {170},
number = {2},
pages = {946-953},
pmid = {2828337},
issn = {0021-9193},
mesh = {Aminocoumarins ; Anti-Bacterial Agents/pharmacology ; Archaea/*drug effects/enzymology/genetics/growth &amp; development ; Autoradiography ; Bacteria/*drug effects ; Ciprofloxacin/*pharmacology ; Coumarins/*pharmacology ; DNA Replication/drug effects ; DNA Topoisomerases, Type II/*metabolism ; Drug Interactions ; Electrophoresis, Agar Gel ; Euryarchaeota/drug effects/enzymology/growth &amp; development ; Halobacterium/drug effects/enzymology/genetics/growth &amp; development ; Novobiocin/pharmacology ; Plasmids ; },
abstract = {The action of novobiocin and coumermycin (two coumarins which interact with the gyrB subunit of eubacterial DNA gyrase) and ciprofloxacin (a fluoroquinolone which interacts with the gyrA subunit of DNA gyrase) was tested on several archaebacteria, including five methanogens, two halobacteria, and a thermoacidophile. Most strains were sensitive to doses of coumarins (0.02 to 10 micrograms/ml) which specifically inhibit DNA gyrase in eubacteria. Ciprofloxacin inhibited growth of the haloalkaliphilic strain Natronobacterium gregoryi and of the methanogen Methanosarcina barkeri. In addition, ciprofloxacin partly relieved the sensitivity to coumarins (and vice versa). Novobiocin inhibited DNA replication in Halobacterium halobium rapidly and specifically. Topological analysis has shown that the 1.7-kilobase plasmid from Halobacterium sp. strain GRB is negatively supercoiled; this plasmid was relaxed after novobiocin treatment. These results support the existence in archaebacteria of a coumarin and quinolone target related to eubacterial DNA gyrase.},
}
@article {pmid2481476,
year = {1988},
author = {Sanz, JL and Amils, R},
title = {Archaebacteria: their phylogenetic relationship with the eubacterial and eukaryotic kingdoms.},
journal = {Microbiologia (Madrid, Spain)},
volume = {4},
number = {1},
pages = {5-27},
pmid = {2481476},
issn = {0213-4101},
mesh = {Archaea/*classification/genetics/metabolism ; Bacteria/*classification ; Bacterial Proteins/genetics ; Eukaryotic Cells/analysis ; Euryarchaeota/classification ; Halobacteriaceae/classification ; Phylogeny ; RNA, Bacterial/genetics ; RNA, Ribosomal/genetics ; Ribosomal Proteins/genetics ; Sequence Homology, Nucleic Acid ; Thermoplasma/classification ; },
abstract = {In microbiology the discovery of archaebacteria ten years ago has wrought a profound change in the concepts of physiology, taxonomy, ecology, biochemistry, molecular biology, genetics and phylogeny. This review offers a concise summary of the state of the art in this field with special reference to taxonomy and ecology as well as to the different methodologies used to study the phylogeny of this unusual group of microorganisms that question many well established biological concepts.},
}
@article {pmid3151021,
year = {1988},
author = {De Rosa, M and Gambacorta, A},
title = {The lipids of archaebacteria.},
journal = {Progress in lipid research},
volume = {27},
number = {3},
pages = {153-175},
doi = {10.1016/0163-7827(88)90011-2},
pmid = {3151021},
issn = {0163-7827},
mesh = {Archaea/*analysis ; Bacteria/*analysis ; Biological Evolution ; Glyceryl Ethers/analysis ; Membrane Lipids/*analysis ; Quinones/analysis ; Spectrum Analysis ; Terpenes/analysis ; Thiophenes/analysis ; },
}
@article {pmid3150649,
year = {1988},
author = {Gulik, A and Luzatti, V and de Rosa, M and Gambacorta, A},
title = {Biradical tetraether lipids from thermoacidophilic archaebacteria.},
journal = {Advances in experimental medicine and biology},
volume = {238},
number = {},
pages = {37-45},
doi = {10.1007/978-1-4684-7908-9_4},
pmid = {3150649},
issn = {0065-2598},
mesh = {Archaea/*analysis ; Bacteria/*analysis ; Chemical Phenomena ; Chemistry, Physical ; Ethers/*isolation &amp; purification ; Glycerol/*analogs &amp; derivatives/isolation &amp; purification ; Lipid Bilayers ; Molecular Structure ; Sugar Alcohols/*isolation &amp; purification ; Temperature ; },
}
@article {pmid3149390,
year = {1988},
author = {Kamp, RM and Wittmann-Liebold, B},
title = {Ribosomal proteins from archaebacteria: high-performance liquid chromatographic purification for microsequence analysis.},
journal = {Methods in enzymology},
volume = {164},
number = {},
pages = {542-571},
doi = {10.1016/s0076-6879(88)64069-9},
pmid = {3149390},
issn = {0076-6879},
mesh = {Amino Acid Sequence ; Archaea/*analysis ; Bacteria/*analysis ; Chromatography, Gel/methods ; Chromatography, High Pressure Liquid/methods ; Chromatography, Ion Exchange/methods ; Electrophoresis, Gel, Two-Dimensional ; Indicators and Reagents ; Molecular Weight ; Ribosomal Proteins/*isolation &amp; purification ; },
}
@article {pmid3132816,
year = {1988},
author = {Danson, MJ},
title = {Archaebacteria: the comparative enzymology of their central metabolic pathways.},
journal = {Advances in microbial physiology},
volume = {29},
number = {},
pages = {165-231},
doi = {10.1016/s0065-2911(08)60348-3},
pmid = {3132816},
issn = {0065-2911},
mesh = {Archaea/*enzymology/metabolism ; Bacteria/*enzymology ; Citrate (si)-Synthase/*metabolism ; Citric Acid Cycle ; Coenzyme A Ligases/*metabolism ; Dihydrolipoamide Dehydrogenase/metabolism ; Eukaryotic Cells/enzymology ; Gluconeogenesis ; Glucose/metabolism ; Glycerol/biosynthesis ; Oxidoreductases/*metabolism ; Oxo-Acid-Lyases/*metabolism ; Pyruvates/metabolism ; Succinate-CoA Ligases/*metabolism ; },
}
@article {pmid2838639,
year = {1988},
author = {Souillard, N and Magot, M and Possot, O and Sibold, L},
title = {Nucleotide sequence of regions homologous to nifH (nitrogenase Fe protein) from the nitrogen-fixing archaebacteria Methanococcus thermolithotrophicus and Methanobacterium ivanovii: evolutionary implications.},
journal = {Journal of molecular evolution},
volume = {27},
number = {1},
pages = {65-76},
pmid = {2838639},
issn = {0022-2844},
mesh = {Amino Acid Sequence ; Archaea/enzymology/*genetics ; Bacteria/*genetics ; Base Sequence ; *Biological Evolution ; Cloning, Molecular ; DNA Restriction Enzymes ; *Genes ; *Genes, Bacterial ; Molecular Sequence Data ; Nitrogenase/*genetics ; *Oxidoreductases ; Sequence Homology, Nucleic Acid ; Species Specificity ; },
abstract = {DNA fragments bearing sequence similarity to eubacterial nif H probes were cloned from two nitrogen-fixing archaebacteria, a thermophilic methanogen, Methanococcus (Mc.) thermolithotrophicus, and a mesophilic methanogen, Methanobacterium (Mb.) ivanovii. Regions carrying similarities with the probes were sequenced. They contained several open reading frames (ORF), separated by A + T-rich regions. The largest ORFs in both regions, an 876-bp sequence in Mc. thermolithotrophicus and a 789-bp sequence in Mb. ivanovii, were assumed to be ORFsnif H. They code for polypeptides of mol. wt. 32,025 and 28,347, respectively. Both ORFsnifH were preceded by potential ribosome binding sites and followed by potential hairpin structures and by oligo-T sequences, which may act as transcription termination signals. The codon usage was similar in both ORFsnifH and was analogous to that used in the Clostridium pasteurianum nifH gene, with a preference for codons ending with A or U. The ORFnifH deduced polypeptides contained 30% sequence matches with all eubacterial nifH products already sequenced. Four cysteine residues were found at the same position in all sequences, and regions surrounding the cysteine residues are highly conserved. Comparison of all pairs of methanogenic and eubacterial nifH sequences is in agreement with a distant phylogenetic position of archaebacteria and with a very ancient origin of nif genes. However, sequence similarity between Methanobacteriales and Methanococcales is low (around 50%) as compared to that found among eubacteria, suggesting a profound divergence between the two orders of methanogens. From comparison of amino acid sequences, C. pasteurianum groups with the other eubacteria, whereas comparison of nucleotide sequences seems to bring C. pasteurianum closer to methanogens. The latter result may be due to the high A + T content of both C. pasteurianum and methanogens ORFsnif H or may come from an ancient lateral transfer between Clostridium and methanogens.},
}
@article {pmid3121311,
year = {1987},
author = {Sioud, M and Baldacci, G and Forterre, P and de Recondo, AM},
title = {Antitumor drugs inhibit the growth of halophilic archaebacteria.},
journal = {European journal of biochemistry},
volume = {169},
number = {2},
pages = {231-236},
doi = {10.1111/j.1432-1033.1987.tb13602.x},
pmid = {3121311},
issn = {0014-2956},
mesh = {Actins/analysis ; Antineoplastic Agents/*pharmacology ; Archaea/*drug effects/growth &amp; development ; Bacteria/*drug effects ; Cytochalasins/pharmacology ; DNA Damage ; Escherichia coli/drug effects/growth &amp; development ; Halobacterium/*drug effects/growth &amp; development ; Species Specificity ; Tubulin/analysis ; },
abstract = {Permeability mutants of Escherichia coli have been used to prescreen antitumor drugs. However, most compounds active against eucaryotic proteins have no effect on isofunctional proteins of eubacteria. In contrast, we show that growth of halophilic archaebacteria, procaryotes as distantly related to eubacteria as to eucaryotes, is inhibited by several drugs known to interact with tubulin, actomyosin and DNA topoisomerase II of eucaryotes. Actually, different types of evidence indicate the presence of analogous proteins in halophilic archaebacteria: (a) a yeast actin probe hybridizes with DNA restriction digests of Halobacterium halobium; (b) antibodies against tubulin and actin from chicken react in a crude extract of H. halobium with polypeptides having Mr of 55,000 and 80,000, respectively; (c) the epipodophyllotoxin VP16, a eucaryotic DNA topoisomerase II inhibitor, induces DNA strand breaks with DNA-protein covalent linkage in H. halobium as in eucaryotes. Besides the evolutionary implications, these data indicate that halophilic archaebacteria can be used to prescreen antitumor drugs active on eucaryotic proteins.},
}
@article {pmid3449743,
year = {1987},
author = {Tarasov, AL and Zviagintseva, IS and Lysenko, AM},
title = {[Nucleotide composition and homologies in the DNA of new extreme halophilic soil archaebacteria].},
journal = {Mikrobiologiia},
volume = {56},
number = {6},
pages = {938-942},
pmid = {3449743},
issn = {0026-3656},
mesh = {Base Sequence ; DNA, Bacterial/*genetics/isolation &amp; purification ; Genotype ; Halobacteriaceae/classification/*genetics ; Nucleic Acid Hybridization ; Sequence Homology, Nucleic Acid ; *Soil Microbiology ; },
abstract = {DNA nucleotide composition was studied in extreme halophilic bacteria belonging to the genera Halobacterium, Halococcus, Natronobacterium and Natronococcus. The cultures were shown to be a monolithic group of microorganisms with the content of GC pairs typical of extreme halophilic archebacteria. The difference between the content of DNA major and minor components was twice as high in Halobacterium distributus strains isolated from sulfate saline soils as compared to cultures of this species isolated from natural waters with a high salinity. DNA minor components were not found in haloalkalophilic microorganisms from soda saline soils in contrast to those from soda lakes. The results of DNA-DNA hybridization indicate that the Halobacterium genus is highly heterogeneous. The newly isolated strains of extremely halophilic H. distributus are characterized by the low homology of their DNAs both among themselves and with other species of the genus. However, the hybridization data for the collection strains H. vallismortis 1398 and H. halobium 996 from the National Collection of Microorganisms are indicative of a high homology (80-100%) which is not characteristic of cultures belonging to different species. These results as well as some phenotypical properties of H. vallismortis 1398 different from those of this species type strain support the data reported in the literature about the genetic instability of extreme halophilic archebacteria. The analysis of homologies in DNA nucleotide sequences may be used to study the taxonomy of extreme halophilic archebacteria.},
}
@article {pmid3124853,
year = {1987},
author = {Glotz, C and Müssig, J and Gewitz, HS and Makowski, I and Arad, T and Yonath, A and Wittmann, HG},
title = {Three-dimensional crystals of ribosomes and their subunits from eu- and archaebacteria.},
journal = {Biochemistry international},
volume = {15},
number = {5},
pages = {953-960},
pmid = {3124853},
issn = {0158-5231},
support = {GM 34360/GM/NIGMS NIH HHS/United States ; },
mesh = {Archaea/*ultrastructure ; Bacteria/*ultrastructure ; Crystallization ; Escherichia coli/metabolism/ultrastructure ; Eubacterium/*ultrastructure ; Geobacillus stearothermophilus/metabolism/ultrastructure ; Halobacterium/metabolism/ultrastructure ; Microscopy, Electron ; Ribosomes/*analysis ; Thermus/metabolism/ultrastructure ; X-Ray Diffraction ; },
abstract = {Ordered three-dimensional crystals of 70S ribosomes as well as of 30S and 50S ribosomal subunits from various bacteria (E. coli, Bacillus stearothermophilus, Thermus thermophilus and Halobacterium marismortui) have been grown by vapour diffusion in hanging drops using mono- and polyalcohols. A new compact crystal form of 50S subunits has been obtained, and it is suitable for crystallographic studies at medium resolution. In addition, from one crystal form large crystals could be grown in X-ray capillaries. In all cases the crystals were obtained from functionally active ribosomal particles, and the particles from dissolved crystals retained their integrity and biological activity.},
}
@article {pmid3654579,
year = {1987},
author = {Xing, RY and Whitman, WB},
title = {Sulfometuron methyl-sensitive and -resistant acetolactate synthases of the archaebacteria Methanococcus spp.},
journal = {Journal of bacteriology},
volume = {169},
number = {10},
pages = {4486-4492},
pmid = {3654579},
issn = {0021-9193},
mesh = {Acetolactate Synthase/antagonists &amp; inhibitors/*metabolism ; Amino Acids, Branched-Chain/biosynthesis/metabolism ; Euryarchaeota/drug effects/*enzymology/growth &amp; development ; Herbicides/*pharmacology ; Kinetics ; Oxo-Acid-Lyases/*metabolism ; Sulfonylurea Compounds/*pharmacology ; },
abstract = {The herbicide sulfometuron methyl (SM) inhibited growth of some methanococci. Of 28 strains tested, the growth of 7 was completely inhibited by 0.55 mM SM. Growth of an additional 14 strains was partially inhibited, and the growth of 7 strains was unaffected by this concentration of SM. In some cases, the branched-chain amino acids protected growth. Growth inhibition was correlated with the Ki for SM of acetolactate synthase (ALS). For the enzymes from bacteria representative of the sensitive, partially resistant, and resistant methanococci (Methanococcus aeolicus, Methanococcus maripaludis, and Methanococcus voltae, respectively), the Ki for SM was 0.0012, 0.34, and greater than 1.0 mM, respectively. Inhibition was uncompetitive with respect to pyruvate. Based on these observations, ALS appeared to be the major if not the sole site of action of SM in the methanococci. The sensitivity of the ALS from these three methanococci to feedback inhibition by branched-chain amino acids was also quite different. Although all three were sensitive to feedback inhibition by valine, the Ki varied 20-fold, from 0.01 to 0.22 mM. Moreover, only the ALS from M. maripaludis was sensitive to inhibition by leucine, and the Ki was 1.8 mM. The Ki for isoleucine for the ALS from both M. maripaludis and M. voltae was about 0.1 mM. The ALS from M. aeolicus was not inhibited by isoleucine. In other respects, the ALSs from the methanococci were very similar. After dialysis, thiamine pyrophosphate but not FAD and Mg2+ was required for maximal activity, and they were all rapidly inactivated by oxygen. Although the methanococcal ALSs exhibited diverse properties, the range of catalytic and regulatory properties closely resembled those of the eubacterial enzymes.},
}
@article {pmid3301400,
year = {1987},
author = {Mankin, AS and Skripkin, EA and Kagramanova, VK},
title = {A putative internal promoter in the 16 S/23 S intergenic spacer of the rRNA operon of archaebacteria and eubacteria.},
journal = {FEBS letters},
volume = {219},
number = {2},
pages = {269-273},
doi = {10.1016/0014-5793(87)80233-8},
pmid = {3301400},
issn = {0014-5793},
mesh = {Base Sequence ; Escherichia coli/*genetics ; *Genes, Bacterial ; Halobacterium/*genetics ; Molecular Weight ; Operon ; *Promoter Regions, Genetic ; RNA, Ribosomal/genetics ; Species Specificity ; },
abstract = {The existence of the internal promoter Pi in the 16 S/23 S intergenic spacers of the rRNA operons of an eubacterium Escherichia coli and archaebacterium Halobacterium halobium is proposed. The possible functional significance of these promoters is discussed.},
}
@article {pmid2438164,
year = {1987},
author = {Vashakidze, RP and Prangishvili, DA},
title = {Simple repetitive sequences in the genomes of archaebacteria.},
journal = {FEBS letters},
volume = {216},
number = {2},
pages = {217-220},
doi = {10.1016/0014-5793(87)80692-0},
pmid = {2438164},
issn = {0014-5793},
mesh = {Archaea/*genetics ; Bacteria/*genetics ; Base Sequence ; DNA, Bacterial/*genetics ; Nucleic Acid Hybridization ; RNA, Bacterial/genetics ; *Repetitive Sequences, Nucleic Acid ; Transcription, Genetic ; },
abstract = {Stretches of simple sequences poly(dG-dT).poly(dC-dA), poly(dG-dA).poly(dC-dT), poly(dG).poly(dC) and poly(dA).poly(dT), the occurrence of which is a characteristic feature of eukaryotic genomes, are found in the genomes of archaebacteria Halobacterium halobium and Sulfolobus acidocaldarius. In S. acidocaldarius these sequences constitute a considerable portion of the genome; they belong to a class of repetitive sequences dispersed throughout the genome, being transcribed and found in RNAs of different lengths.},
}
@article {pmid3116261,
year = {1987},
author = {Leffers, H and Kjems, J and Ostergaard, L and Larsen, N and Garrett, RA},
title = {Evolutionary relationships amongst archaebacteria. A comparative study of 23 S ribosomal RNAs of a sulphur-dependent extreme thermophile, an extreme halophile and a thermophilic methanogen.},
journal = {Journal of molecular biology},
volume = {195},
number = {1},
pages = {43-61},
doi = {10.1016/0022-2836(87)90326-3},
pmid = {3116261},
issn = {0022-2836},
mesh = {Archaea/classification/*genetics ; Bacteria/*genetics ; Base Sequence ; *Biological Evolution ; Cloning, Molecular ; Euryarchaeota/genetics ; Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; Phylogeny ; RNA, Ribosomal/*genetics ; },
abstract = {The 23 S RNA genes representative of each of the main archaebacterial subkingdoms, Desulfurococcus mobilis an extreme thermophile, Halococcus morrhuae an extreme halophile and Methanobacterium thermoautotrophicum a thermophilic methanogen, were cloned and sequenced. The inferred RNA sequences were aligned with all the available 23 S-like RNAs of other archaebacteria, eubacteria/chloroplasts and the cytoplasm of eukaryotes. Universal secondary structural models containing six major structural domains were refined, and extended, using the sequence comparison approach. Much of the present structure was confirmed but six new helices were added, including one that also exists in the eukaryotic 5.8 S RNA, and extensions were made to several existing helices. The data throw doubt on whether the 5' and 3' ends of the 23 S RNA interact, since no stable helix can form in either the extreme thermophile or the methanogen RNA. A few secondary structural features, specific to the archaebacterial RNAs were identified; two of these were supported by a comparison of the archaebacterial RNA sequences, and experimentally, using chemical and ribonuclease probes. Seven tertiary structural interactions, common to all 23 S-like RNAs, were predicted within unpaired regions of the secondary structural model on the basis of co-variation of nucleotide pairs; two lie in the region of the 23 S RNA corresponding to 5.8 S RNA but they are not conserved in the latter. The flanking sequences of each of the RNAs could base-pair to form long RNA processing stems. They were not conserved in sequence but each exhibited a secondary structural feature that is common to all the archaebacterial stems for both 16 S and 23 S RNAs and constitutes a processing site. Kingdom-specific nucleotides have been identified that are associated with antibiotic binding sites at functional centres in 23 S-like RNAs: in the peptidyl transferase centre (erythromycin-domain V) the archaebacterial RNAs classify with the eukaryotic RNAs; at the elongation factor-dependent GTPase centre (thiostrepton-domain II) they fall with the eubacteria, and at the putative amino acyl tRNA site (alpha-sarcin-domain VI) they resemble eukaryotes. Two of the proposed tertiary interactions offer a structural explanation for how functional coupling of domains II and V occurs at the peptidyl transferase centre. Phylogenetic trees were constructed for the archaebacterial kingdom, and for the other two kingdoms, on the basis of the aligned 23 S-like RNA sequences.(ABSTRACT TRUNCATED AT 400 WORDS)},
}
@article {pmid3104748,
year = {1987},
author = {Jones, WJ and Nagle, DP and Whitman, WB},
title = {Methanogens and the diversity of archaebacteria.},
journal = {Microbiological reviews},
volume = {51},
number = {1},
pages = {135-177},
pmid = {3104748},
issn = {0146-0749},
mesh = {Archaea/genetics/metabolism/*physiology ; *Bacterial Physiological Phenomena ; Carbon/metabolism ; Energy Metabolism ; Euryarchaeota/*metabolism ; Lipid Metabolism ; Methane/*biosynthesis ; Ribosomes/analysis ; },
}
@article {pmid3454292,
year = {1987},
author = {Lake, JA},
title = {Prokaryotes and archaebacteria are not monophyletic: rate invariant analysis of rRNA genes indicates that eukaryotes and eocytes form a monophyletic taxon.},
journal = {Cold Spring Harbor symposia on quantitative biology},
volume = {52},
number = {},
pages = {839-846},
doi = {10.1101/sqb.1987.052.01.091},
pmid = {3454292},
issn = {0091-7451},
support = {GM-24034/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; Bacteria/*genetics ; *Cell Physiological Phenomena ; DNA, Ribosomal/*genetics ; Eubacterium/genetics ; Eukaryotic Cells/*physiology ; Euryarchaeota/genetics ; *Genes ; Halobacterium/genetics ; *Phylogeny ; RNA, Ribosomal/*genetics ; Species Specificity ; },
}
@article {pmid2441639,
year = {1987},
author = {Zillig, W},
title = {Eukaryotic traits in Archaebacteria. Could the eukaryotic cytoplasm have arisen from archaebacterial origin?.},
journal = {Annals of the New York Academy of Sciences},
volume = {503},
number = {},
pages = {78-82},
doi = {10.1111/j.1749-6632.1987.tb40599.x},
pmid = {2441639},
issn = {0077-8923},
mesh = {*Archaea/genetics ; *Bacteria/genetics ; Base Sequence ; *Biological Evolution ; *Cells/ultrastructure ; *Cytoplasm ; *Eukaryotic Cells/ultrastructure ; RNA, Bacterial ; RNA, Ribosomal ; },
}
@article {pmid2441638,
year = {1987},
author = {Doolittle, WF},
title = {The evolutionary significance of the Archaebacteria.},
journal = {Annals of the New York Academy of Sciences},
volume = {503},
number = {},
pages = {72-77},
doi = {10.1111/j.1749-6632.1987.tb40598.x},
pmid = {2441638},
issn = {0077-8923},
mesh = {*Archaea/genetics ; *Bacteria/genetics ; *Biological Evolution ; Eukaryotic Cells ; Genes, Bacterial ; Prokaryotic Cells ; RNA, Bacterial/genetics ; RNA, Ribosomal/genetics ; Symbiosis ; },
}
@article {pmid3098561,
year = {1986},
author = {Laine, B and Chartier, F and Imbert, M and Lewis, R and Sautiere, P},
title = {Primary structure of the chromosomal protein HMb from the archaebacteria Methanosarcina barkeri.},
journal = {European journal of biochemistry},
volume = {161},
number = {3},
pages = {681-687},
doi = {10.1111/j.1432-1033.1986.tb10493.x},
pmid = {3098561},
issn = {0014-2956},
mesh = {Amino Acid Sequence ; Archaea/*analysis ; *Archaeal Proteins ; Bacteria/*analysis ; *Bacterial Proteins ; Chemical Phenomena ; Chemistry ; Peptide Fragments/analysis ; *Ribonucleoproteins ; Terminology as Topic ; },
abstract = {The amino acid sequence of the protein HMb, a protein of 93 residues (Mr 10757) which represents the major acid-soluble component of the Methanosarcina barkeri nucleoprotein complex, has been established from automated sequence analysis of the protein and from structural data provided by peptides derived from cleavage of the protein at aspartic acid, arginine and methionine residues. The protein HMb is mainly characterized by a high amount of charged residues (15% of acidic residues and 26.8% of basic residues) which are distributed all along the polypeptide chain. The amino acid sequence of the protein HMb is not homologous to any eubacterial, archaebacterial or eukaryotic chromosomal proteins known up to now.},
}
@article {pmid3114425,
year = {1986},
author = {Lodwick, D and Ross, HN and Harris, JE and Almond, JW and Grant, WD},
title = {dam methylation in the archaebacteria.},
journal = {Journal of general microbiology},
volume = {132},
number = {11},
pages = {3055-3059},
doi = {10.1099/00221287-132-11-3055},
pmid = {3114425},
issn = {0022-1287},
mesh = {Archaea/classification/enzymology/*genetics ; Bacteria/*genetics ; DNA, Bacterial ; Electrophoresis, Agar Gel ; Methylation ; Methyltransferases/*genetics ; Phenotype ; Site-Specific DNA-Methyltransferase (Adenine-Specific) ; },
abstract = {The DNA of certain species of halophilic and methanogenic archaebacteria is dam methylated, as shown by restriction endonuclease sensitivities. The Dam+ phenotype appears to be confined to particular taxonomic groupings defined by DNA:rRNA hybridization or 16S RNA oligonucleotide cataloguing.},
}
@article {pmid2430938,
year = {1986},
author = {Dennis, PP},
title = {Molecular biology of archaebacteria.},
journal = {Journal of bacteriology},
volume = {168},
number = {2},
pages = {471-478},
pmid = {2430938},
issn = {0021-9193},
mesh = {Archaea/*genetics ; Bacteria/*genetics ; *Genes, Bacterial ; Protein Biosynthesis ; RNA, Bacterial/genetics ; RNA, Messenger/genetics ; RNA, Ribosomal/genetics ; Transcription, Genetic ; },
}
@article {pmid3093465,
year = {1986},
author = {Lin, XL and White, RH},
title = {Occurrence of coenzyme F420 and its gamma-monoglutamyl derivative in nonmethanogenic archaebacteria.},
journal = {Journal of bacteriology},
volume = {168},
number = {1},
pages = {444-448},
pmid = {3093465},
issn = {0021-9193},
mesh = {Archaea/*analysis ; Bacteria/*analysis ; Halobacteriaceae/*analysis ; Halobacterium/analysis ; Riboflavin/*analogs &amp; derivatives/analysis ; Thermoplasma/*analysis ; },
abstract = {Analysis of the fluorescent compounds extracted from six different species of halobacteria and one species each of Sulfolobus and Thermoplasma revealed the universal occurrence of coenzyme F420, (N-[N-[O-[5-(8-hydroxy-5-deazaisoalloxazin-10-yl)-2,3,4-trihydroxy -4-pentoxyhydroxyphosphinyl]-L-lactyl]-L-gamma-glutamyl]-L -glutamic acid), or its gamma-monoglutamyl derivative or both. The total amount (approximately 100 pmol/mg [dry weight]) of these compounds found in the halobacteria studied was approximately 5% of the amount previously reported for methanogenic bacteria. The amount of F420 found in the Sulfolobus and Thermoplasma strains was approximately 1% of that found in the halobacteria. The major compound in all but one of the examined strains was the gamma-monoglutamyl derivative of F420; one strain of halobacteria contained only F420. For the halobacterium-derived samples, the additional glutamic acid was shown to be linked by a gamma-glutamyl peptide bond to the terminal glutamic acid of the F420 core structure by enzymatic hydrolysis of the samples with three different gamma-glutamyltranspeptidases. The product of this enzymatic hydrolysis was F420 with one less glutamic acid in the side chain.},
}
@article {pmid3093464,
year = {1986},
author = {Conway de Macario, E and Konig, H and Macario, AJ},
title = {Immunologic distinctiveness of archaebacteria that grow in high salt.},
journal = {Journal of bacteriology},
volume = {168},
number = {1},
pages = {425-427},
pmid = {3093464},
issn = {0021-9193},
mesh = {Antibodies, Bacterial ; Antigens, Bacterial/analysis/*immunology ; Archaea/*immunology ; Bacteria/*immunology ; Cross Reactions ; Euryarchaeota/*immunology ; Halobacteriaceae/*immunology ; Halobacterium/immunology ; Sodium Chloride ; Species Specificity ; },
abstract = {The antigenic fingerprints of eight halophilic archaebacteria representing the groups recently outlined by molecular and chemical analyses were determined with calibrated antibody probes. Comparison with the antigenic fingerprints of methanogens encompassing all described families and most genera demonstrated that these two archaebacterial groups are themselves antigenically coherent but immunologically distinct.},
}
@article {pmid3098244,
year = {1986},
author = {Wais, AC},
title = {Archaebacteria: the road to the universal ancestor.},
journal = {BioEssays : news and reviews in molecular, cellular and developmental biology},
volume = {5},
number = {2},
pages = {75-78},
doi = {10.1002/bies.950050207},
pmid = {3098244},
issn = {0265-9247},
mesh = {Archaea/*genetics ; Bacteria/*genetics ; *Biological Evolution ; RNA, Ribosomal/genetics ; },
}
@article {pmid3097515,
year = {1986},
author = {Gross, DS and Garrard, WT},
title = {The ubiquitous potential Z-forming sequence of eucaryotes, (dT-dG)n . (dC-dA)n, is not detectable in the genomes of eubacteria, archaebacteria, or mitochondria.},
journal = {Molecular and cellular biology},
volume = {6},
number = {8},
pages = {3010-3013},
pmid = {3097515},
issn = {0270-7306},
support = {GM22201/GM/NIGMS NIH HHS/United States ; GM25829/GM/NIGMS NIH HHS/United States ; GM29935/GM/NIGMS NIH HHS/United States ; },
mesh = {Archaea/*genetics ; Bacteria/*genetics ; Base Sequence ; DNA/analysis ; Information Systems ; Mitochondria/*analysis ; Repetitive Sequences, Nucleic Acid ; },
abstract = {The potential Z-forming sequence (dT-dG)n . (dC-dA)n is an abundant, interspersed repeat element that is ubiquitous in eucaryotic nuclear genomes. We report that in contrast to eucaryotic nuclear DNA, the genomes of eubacteria, archaebacteria, and mitochondria lack this sequence, since even a single tract of greater than or equal to 14 base pairs in length is not detectable through either hybridization or sequence analysis. Interestingly, the phylogenetic distribution of the (dT-dG)n . (dC-dA)n repeat exhibits a striking parallel to that of (dT-dC)n . (dG-dA)n, but not to other homocopolymeric sequences such as (dC-dG)n . (dC-dG)n or (dT-dA)n . (dT-dA)n.},
}
@article {pmid3127653,
year = {1986},
author = {Morris, J and Kushner, SR and Ivarie, R},
title = {The simple repeat poly(dT-dG).poly(dC-dA) common to eukaryotes is absent from eubacteria and archaebacteria and rare in protozoans.},
journal = {Molecular biology and evolution},
volume = {3},
number = {4},
pages = {343-355},
doi = {10.1093/oxfordjournals.molbev.a040399},
pmid = {3127653},
issn = {0737-4038},
support = {CA34066/CA/NCI NIH HHS/United States ; },
mesh = {Animals ; Archaea/*genetics ; Bacteria/*genetics ; Base Sequence ; *Cell Physiological Phenomena ; *DNA/*genetics ; Eukaryota/*genetics ; Eukaryotic Cells/*physiology ; Repetitive Sequences, Nucleic Acid ; },
abstract = {Genomic DNA from a wide variety of prokaryotic and eukaryotic organisms has been assayed for the simple repeat sequence poly(dT-dG).poly(dC-dA) by Southern blotting and DNA slot blot hybridizations. Consistent with findings of others, we have found the simple alternating sequence to be present in multiple copies in all organisms in the animal kingdom (e.g., mammals, reptiles, amphibians, fish, crustaceans, insects, jellyfish, nematodes). The TG element was also found in lower eukaryotes (Saccharomyces cerevisiae, Neurospora crassa, and Dictyostelium discoideum) and at a much lower frequency in protozoans (Oxytricha fallux and Tetrahymena thermophila). The sequence was also repeated in high copy number in a higher plant (Zea mays) as well as at very high levels in a unicellular green alga (Chlamydomonas reinhardi). Although the copy number of the repeat per haploid genome was generally proportional to genome size, there was a greater-than-1,000-fold variation in the number of (TG)25/100-kb genomic DNA. By contrast, no eu-or archaebacterium--including Myxococcus xanthus, whose life cycle is very similar to that of the slime mold Dictyostelium discoideum, and Halobacter volcanii, whose genome contains other repeated sequences--was found whose genomic DNA contained this sequence in detectable amounts. A computer search also failed to find the TG element in human mitochondrial DNA.},
}
@article {pmid3086286,
year = {1986},
author = {Messner, P and Pum, D and Sára, M and Stetter, KO and Sleytr, UB},
title = {Ultrastructure of the cell envelope of the archaebacteria Thermoproteus tenax and Thermoproteus neutrophilus.},
journal = {Journal of bacteriology},
volume = {166},
number = {3},
pages = {1046-1054},
pmid = {3086286},
issn = {0021-9193},
mesh = {Archaea/*ultrastructure ; Bacteria/*ultrastructure ; Cell Membrane/*ultrastructure ; Computers ; Crystallization ; Freeze Fracturing ; Image Enhancement ; Microscopy, Electron ; },
abstract = {The ultrastructures of the regular surface layers (S-layers) of the extremely thermophilic archaebacteria Thermoproteus tenax and Thermoproteus neutrophilus were examined by freeze-etching, freeze-drying, and negative staining methods combined with optical and digital image enhancement. In both strains, a monolayer of macromolecules arranged in hexagonal arrays with center-to-center spacings of approximately 30 nm was the only component of the cell wall. The gross morphologies of the S-layer lattices of the two organisms were similar and showed the same handedness in the arrangement of the protomers of the morphological units. Striking differences were found in the anionic charge distributions on the surfaces of the two S-layer proteins as determined by labeling with polycationic ferritin. Analysis of the lattice orientation, together with the number and distribution of lattice faults on intact cells, provided a strong indication that the S-layers of both organisms have a shape-determining function.},
}
@article {pmid3013165,
year = {1986},
author = {Leichtling, BH and Rickenberg, HV and Seely, RJ and Fahrney, DE and Pace, NR},
title = {The occurrence of cyclic AMP in archaebacteria.},
journal = {Biochemical and biophysical research communications},
volume = {136},
number = {3},
pages = {1078-1082},
doi = {10.1016/0006-291x(86)90443-2},
pmid = {3013165},
issn = {0006-291X},
support = {34527//PHS HHS/United States ; AM 34554/AM/NIADDK NIH HHS/United States ; },
mesh = {Archaea/*analysis ; Bacteria/*analysis ; Cyclic AMP/*analysis ; Euryarchaeota/analysis ; Halobacterium/analysis ; Hydrogen ; },
abstract = {Cyclic AMP was found in species representative of the three major groups of the archaebacteria. In Methanobacterium thermoautotrophicum starvation for H2 led to a significant increase in cellular cAMP. The findings suggest that the occurrence of cAMP antedates the divergence of the major kingdoms of biology; the observations also imply that cAMP constitutes a very early regulatory molecule.},
}
@article {pmid3085688,
year = {1986},
author = {Thurl, S and Witke, W and Buhrow, I and Schäfer, W},
title = {Quinones from archaebacteria, II. Different types of quinones from sulphur-dependent archaebacteria.},
journal = {Biological chemistry Hoppe-Seyler},
volume = {367},
number = {3},
pages = {191-197},
doi = {10.1515/bchm3.1986.367.1.191},
pmid = {3085688},
issn = {0177-3593},
mesh = {Anaerobiosis ; Archaea/*analysis/growth &amp; development ; Bacteria/*analysis ; Mass Spectrometry ; Quinones/*isolation &amp; purification ; Species Specificity ; Sulfur/*metabolism ; },
abstract = {From the sulphur-dependent, anaerobically grown archaebacterium Sulfolobus ambivalens Caldariella quinone, CQ-6(12H) and the new Sulfolobus quinone SQ-6(12H), 6-(3,7,11,15,19,23-hexamethyltetracosyl)-5-methyl-benz[b]thioph en-4, 7-quinone have been isolated as main components. Lower homologues SQ-5-(10H), SQ-4(8H), SQ-3(6H), phylloquinone-like species CQ-6(10H), SQ-6(10H) and the menaquinone MK-6(12H) are present as minor components. The results are compared with those from Sulfolobus acidocaldarius. Thermococcus celer, Desulfurococcus mucosus and Desulfurococcus mobilis do not contain quinones in comparable amounts.},
}
@article {pmid3937542,
year = {1985},
author = {Thurl, S and Buhrow, I and Schäfer, W},
title = {Quinones from Archaebacteria, I. New types of menaquinones from the thermophilic archaebacterium Thermoproteus tenax.},
journal = {Biological chemistry Hoppe-Seyler},
volume = {366},
number = {12},
pages = {1079-1083},
doi = {10.1515/bchm3.1985.366.2.1079},
pmid = {3937542},
issn = {0177-3593},
mesh = {Archaea/*analysis ; Bacteria/*analysis ; Chromatography, Thin Layer ; Magnetic Resonance Spectroscopy ; Mass Spectrometry ; Spectrophotometry, Ultraviolet ; Vitamin K/*isolation &amp; purification ; },
abstract = {From the archaebacterium Thermoproteus tenax, strain Kra-1 a mixture of 6 quinones of menaquinone and phylloquinone type with isopentyl side chains, MK-6(12H), MK-6-(10H), MK-5(10H), MK-5(8H), MK-4(8H), MK-4(6H) and two analogous quinones, containing in addition a methyl group in the naphthoquinone system, were isolated and characterized.},
}
@article {pmid3936116,
year = {1985},
author = {Kuchino, Y},
title = {[Structural features of archaebacteria tRNAs and tRNA genes].},
journal = {Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme},
volume = {30},
number = {11},
pages = {1207-1228},
pmid = {3936116},
issn = {0039-9450},
mesh = {Archaea/*genetics ; Bacteria/*genetics ; Base Sequence ; *Genes, Bacterial ; Protein Conformation ; RNA, Transfer/*genetics ; Transcription, Genetic ; },
}
@article {pmid3934307,
year = {1985},
author = {Mancuso, CA and Odham, G and Westerdahl, G and Reeve, JN and White, DC},
title = {C15, C20, and C25 isoprenoid homologues in glycerol diether phospholipids of methanogenic archaebacteria.},
journal = {Journal of lipid research},
volume = {26},
number = {9},
pages = {1120-1125},
pmid = {3934307},
issn = {0022-2275},
mesh = {Archaea/*analysis ; Bacteria/*analysis ; Chromatography, Gas ; Chromatography, Thin Layer ; Diterpenes/analysis ; Esters ; Euryarchaeota/*analysis ; Gas Chromatography-Mass Spectrometry ; Phospholipids/*analysis ; Plasmalogens/*analysis ; Sesquiterpenes/analysis ; Species Specificity ; Terpenes/analysis ; },
abstract = {The glycerol diether phospholipids of 25 monocultures of methanogenic bacteria were isolated and degraded with hydriodic acid. The resulting alkyl iodides were converted to acetate esters and alcohols which were examined using capillary gas-liquid chromatography. The presence of C20 phytanol was observed in accordance with previous studies. Soft fragmentation by chemical ionization mass spectrometry combined with selected ion monitoring enabled the detection, for the first time, of C15 and C25 isoprenologues as components of the diether phospholipids in several strains.},
}
@article {pmid3996598,
year = {1985},
author = {Gehrmann, R and Henschen, A and Klink, F},
title = {Primary structure of elongation factor 2 around the site of ADP-ribosylation is highly conserved from archaebacteria to eukaryotes.},
journal = {FEBS letters},
volume = {185},
number = {1},
pages = {37-42},
doi = {10.1016/0014-5793(85)80736-5},
pmid = {3996598},
issn = {0014-5793},
mesh = {Adenosine Diphosphate Ribose/*metabolism ; Amino Acid Sequence ; Chromatography, Gel ; Chromatography, High Pressure Liquid ; Euryarchaeota/analysis ; Halobacterium/analysis ; Nucleoside Diphosphate Sugars/*metabolism ; Peptide Elongation Factor 2 ; Peptide Elongation Factors/isolation &amp; purification/*metabolism ; Peptide Fragments/isolation &amp; purification/metabolism ; Thermoplasma/analysis ; Trypsin/metabolism ; },
abstract = {Elongation factor 2 (EF-2) from eukaryotes and archaebacteria can be ADP-ribosylated by diphtheria toxin (DT) [(1977) Annu. Rev. Biochem. 46, 69-94; (1980) Nature 287, 250-251]. The primary structure of the ADP-ribose accepting region in EFs from the archaebacteria Thermoplasma acidophilum Halobacterium cutirubrum and Methanococcus vannielli was determined in order to elucidate the degree of conservation compared with 4 previously established eukaryotic sequences [(1971) FEBS Lett. 103, 253-255]. Within a 9-residue sequence including the site of ADP-ribosylation 5 positions were found to be occupied by the same amino acid in all the archaebacterial and eukaryotic factors studied. There were more differences among the 3 archaebacterial sequences than among the 4 eukaryotic ones.},
}
@article {pmid3928615,
year = {1985},
author = {Hamana, K and Kamekura, M and Onishi, H and Akazawa, T and Matsuzaki, S},
title = {Polyamines in photosynthetic eubacteria and extreme-halophilic archaebacteria.},
journal = {Journal of biochemistry},
volume = {97},
number = {6},
pages = {1653-1658},
doi = {10.1093/oxfordjournals.jbchem.a135223},
pmid = {3928615},
issn = {0021-924X},
mesh = {Archaea/*metabolism ; Bacteria/*metabolism ; Chromatium/metabolism ; Eubacterium/*metabolism ; Halobacteriaceae/metabolism ; Halobacterium/metabolism ; Micrococcus/metabolism ; *Photosynthesis ; Polyamines/*metabolism ; Rhodobacter sphaeroides/metabolism ; Rhodospirillum rubrum/metabolism ; },
abstract = {Qualitative and quantitative determinations of polyamines have been done in 4 photosynthetic eubacteria and 6 extreme-halophilic archaebacteria. For comparison, 5 moderate-halophilic eubacteria were also analyzed to determine their polyamine contents. Not only putrescine and spermidine but also homospermidine were found in the photosynthetic eubacteria, especially in the N2-fixing species, Rhodospirillum and Chromatium. Norspermidine, norspermine, and spermine were not detected in the phototrophic eubacteria. No appreciable amount of any polyamine was found in extreme-halophilic archaebacteria, Halobacterium and Halococcus, while moderate-halophilic eubacteria contained quite high concentrations of putrescine and spermidine and cadaverine. When arginine was incubated with cell lysates of these two archaebacteria, appreciable amounts of agmatine were produced; neither putrescine nor cadaverine was formed in the presence of ornithine or lysine. No detectable amount of spermidine was produced by the lysates on incubation with putrescine.},
}
@article {pmid3906775,
year = {1985},
author = {Oshima, T},
title = {[Evolutionary status of acids-thermophilie archaebacteria].},
journal = {Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme},
volume = {30},
number = {7 Suppl},
pages = {846-854},
pmid = {3906775},
issn = {0039-9450},
mesh = {Base Sequence ; Biological Evolution ; Cell Membrane/ultrastructure ; DNA, Bacterial/genetics ; Protein Biosynthesis ; Protein Conformation ; RNA, Ribosomal/genetics ; Thermoplasma/*analysis/genetics ; },
}
@article {pmid3922860,
year = {1985},
author = {Miketta, G},
title = {[Archaebacteria: life under extreme conditions. Interdisciplinary principle research with perspectives for a new biotechnology].},
journal = {Fortschritte der Medizin},
volume = {103},
number = {14},
pages = {84-85},
pmid = {3922860},
issn = {0015-8178},
mesh = {Archaea/*physiology ; *Bacterial Physiological Phenomena ; Bacterial Proteins/analysis ; Biological Evolution ; Phylogeny ; Research ; },
}
@article {pmid3923203,
year = {1985},
author = {Gulik, A and Luzzati, V and De Rosa, M and Gambacorta, A},
title = {Structure and polymorphism of bipolar isopranyl ether lipids from archaebacteria.},
journal = {Journal of molecular biology},
volume = {182},
number = {1},
pages = {131-149},
doi = {10.1016/0022-2836(85)90032-4},
pmid = {3923203},
issn = {0022-2836},
mesh = {Archaea/*analysis ; Bacteria/*analysis ; Chemical Phenomena ; Chemistry ; Electrons ; Fatty Alcohols ; Glycerol/analogs &amp; derivatives ; Lipid Bilayers ; Lipids/*analysis ; Mathematics ; Phospholipid Ethers ; Temperature ; Water ; X-Ray Diffraction ; },
abstract = {We describe in this work the structure and polymorphism of a variety of lipids extracted from Sulfolobus solfataricus, an extreme thermoacidophilic archaebacterium growing at about 85 degrees C and pH 2. These lipids are quite different from the usual fatty acid lipids of eukaryotes and prokaryotes: each molecule consists of two C40 omega-omega' biphytanyl residues (with 0 to 4 cyclopentane groups per residue), ether linked at both ends to two (variably substituted) glycerol or nonitol groups. Four lipid preparations were studied; the total and the polar lipid extracts, and two hydrolytic fractions, the symmetric glycerol dialkyl glycerol tetraether and the asymmetric glycerol dialkyl nonitol tetraether, as a function of water content and temperature, using X-ray scattering techniques. The main conclusions from the study of the four lipid preparations can be summarized as follows. (1) As with other lipids, a remarkable number and variety of phases are observed over a temperature-concentration range close to "physiological" conditions. The possibility is discussed that this polymorphism reflects a fundamental property of lipids, closely related to their physiological rôle. (2) As in other lipids, two types of chain conformations are observed: a disordered one (type alpha) at high temperature; at lower temperature, a more ordered packing of stiff chains, all parallel to each other (type beta'). At temperatures and degrees of hydration approaching the conditions prevailing in the living cell, the conformation is of type alpha. (3) In all the phases with chains in the alpha conformation, the unsubstituted glycerol headgroups, whose concentration is high in these lipids, segregate in the hydrocarbon matrix, away from the other polar groups. This property may have interesting biological consequences: for example, the chains of a fraction of the bipolar lipid molecules can span hydrocarbon gaps as wide as 75 A. (4) Two cubic phases are observed in the total and the polar lipid extracts, which display a remarkable degree of metastability, most unusual in lipid phase transitions involving structures with chains in the alpha conformation. This phenomenon can be explained by the interplay of the physical structure of the cubic phases (the two contain two intertwined and unconnected three-dimensional networks of rods) and the chemical structure of the lipid molecules: the two headgroups of most molecules being anchored on each of the two networks of rods, the migration of the lipid molecules is hindered by the two independent diffusion processes and by the entanglement of the chains.(ABSTRACT TRUNCATED AT 400 WORDS)},
}
@article {pmid3926756,
year = {1985},
author = {Minami, Y and Wakabayashi, S and Wada, K and Matsubara, H and Kerscher, L and Oesterhelt, D},
title = {Amino acid sequence of a ferredoxin from thermoacidophilic archaebacterium, Sulfolobus acidocaldarius. Presence of an N6-monomethyllysine and phyletic consideration of archaebacteria.},
journal = {Journal of biochemistry},
volume = {97},
number = {3},
pages = {745-753},
doi = {10.1093/oxfordjournals.jbchem.a135114},
pmid = {3926756},
issn = {0021-924X},
mesh = {Amino Acid Sequence ; Amino Acids/analysis ; Archaea/*analysis/genetics ; Bacteria/*analysis ; Bacterial Proteins/*analysis ; Biological Evolution ; Chemical Phenomena ; Chemistry ; Chymotrypsin ; Ferredoxins/*analysis ; Lysine/*analogs &amp; derivatives/analysis ; Mass Spectrometry ; Peptide Fragments ; Trypsin ; },
abstract = {The amino acid sequence of a ferredoxin from a thermoacidophilic archaebacterium, Sulfolobus acidocaldarius, was determined by a combination of various conventional methods to be as follows: Gly-Ile-Asp-Pro-Tyr-Arg-Thr-His-Lys-Pro-Val-Val-Gly-Asp-Ser-Ser-Gly-His- Lys-Ile -Tyr-Gly-Pro-Val-Glu-Ser-Pro-Lys(Me)-Val-Leu-Gly-Val-His-Gly-Thr-Ile-Val -Gly-Va l-Asp-Phe-Asp-Leu-Cys-Ile-Ala-Asp-Gly-Ser-Cys-Ile-Thr-Ala-Cys-Pro-Val-As n-Val-P he-Gln-Trp-Tyr-Glu-Thr-Pro-Gly-His-Pro-Ala-Ser-Glu-Lys-Lys-Ala-Asp-Pro-V al-Asn- Glu-Gln-Ala-Cys-Ile-Phe-Cys-Met-Ala-Cys-Val-Asn-Val-Cys-Pro-Val-Ala-Ala- Ile-Asp -Val-Lys-Pro-Pro. It was composed of 103 amino acid residues giving a molecular weight of 10,908 excluding Fe and S atoms. This ferredoxin contained an N6-monomethyllysine residue at position 29 which was determined by a comparison of the elution profile of the acid hydrolysates of the protein and peptides on an amino acid analyzer with three methyl derivatives of lysine and also by field desorption mass spectrometry of a purified peptide. The ferredoxin has only 7 cysteine residues, which probably participate in constructing the Fe-S clusters of this ferredoxin, indicating the presence of a unique chelate structure. Comparison of this ferredoxin with other archaebacterial ferredoxins indicated that the archaebacteria might have multiple origins in an evolutionary tree.},
}
@article {pmid3919306,
year = {1985},
author = {Kelly, DP},
title = {Crossroads for archaebacteria.},
journal = {Nature},
volume = {313},
number = {6005},
pages = {734},
doi = {10.1038/313734a0},
pmid = {3919306},
issn = {0028-0836},
mesh = {Archaea/*physiology ; *Bacterial Physiological Phenomena ; Biological Evolution ; },
}
@article {pmid3927820,
year = {1985},
author = {Lake, JA},
title = {Evolving ribosome structure: domains in archaebacteria, eubacteria, eocytes and eukaryotes.},
journal = {Annual review of biochemistry},
volume = {54},
number = {},
pages = {507-530},
doi = {10.1146/annurev.bi.54.070185.002451},
pmid = {3927820},
issn = {0066-4154},
mesh = {Animals ; Archaea/ultrastructure ; Binding Sites ; *Biological Evolution ; Eukaryotic Cells/ultrastructure ; Peptide Elongation Factors/metabolism ; Peptide Initiation Factors/metabolism ; Peptidyl Transferases/metabolism ; Prokaryotic Cells/ultrastructure ; Protein Biosynthesis ; RNA, Messenger/metabolism ; RNA, Transfer/metabolism ; Ribosomes/metabolism/*ultrastructure ; },
}
@article {pmid3922682,
year = {1985},
author = {Zillig, W and Schnabel, R and Stetter, KO},
title = {Archaebacteria and the origin of the eukaryotic cytoplasm.},
journal = {Current topics in microbiology and immunology},
volume = {114},
number = {},
pages = {1-18},
doi = {10.1007/978-3-642-70227-3_1},
pmid = {3922682},
issn = {0070-217X},
mesh = {Archaea/*classification/genetics/physiology ; Bacteria/*classification ; *Biological Evolution ; Cytoplasm/physiology ; DNA-Directed RNA Polymerases/genetics/immunology ; Eukaryotic Cells/physiology ; Species Specificity ; },
}
@article {pmid3919890,
year = {1985},
author = {Perbal, B and Kohiyama, M},
title = {[Existence of sequences homologous to the V-MYB oncogene in the genome of archaebacteria].},
journal = {Comptes rendus de l'Academie des sciences. Serie III, Sciences de la vie},
volume = {300},
number = {5},
pages = {177-180},
pmid = {3919890},
issn = {0764-4469},
mesh = {Archaea/*genetics ; Bacteria/*genetics ; DNA, Bacterial/*analysis ; Genes, Bacterial ; Nucleic Acid Hybridization ; *Oncogenes ; },
abstract = {The presence of DNA sequences homologous to the v-myb oncogene in the genome of both halophilic and methanogenic archaebacteria was revealed after hybridization of restriction fragments with cloned probes. No myb-related sequences were detected in the DNA from S. acidocaldarius.},
}
@article {pmid2580942,
year = {1985},
author = {Ross, HN and Grant, WD},
title = {Nucleic acid studies on halophilic archaebacteria.},
journal = {Journal of general microbiology},
volume = {131},
number = {1},
pages = {165-173},
doi = {10.1099/00221287-131-1-165},
pmid = {2580942},
issn = {0022-1287},
mesh = {Archaea/*classification ; Bacteria/*classification ; Base Composition ; DNA, Bacterial ; Halobacterium/classification ; *Nucleic Acid Hybridization ; Plasmids ; RNA, Bacterial ; RNA, Ribosomal ; },
abstract = {DNA-16S rRNA hybridization studies of archaebacterial halophiles revealed nine major groups. High (greater than 45%) DNA-DNA homologies were found only within DNA-rRNA groups. The DNA-DNA homology between the type strains of Halobacterium halobium, Hb. salinarium and Hb. cutirubrum was greater than 70%. The implications for the taxonomy of the extreme halophiles are discussed.},
}
@article {pmid6209167,
year = {1984},
author = {Schmid, G and Strobel, O and Stöffler-Meilicke, M and Stöffler, G and Böck, A},
title = {A ribosomal protein that is immunologically conserved in archaebacteria, eubacteria and eukaryotes.},
journal = {FEBS letters},
volume = {177},
number = {2},
pages = {189-194},
doi = {10.1016/0014-5793(84)81281-8},
pmid = {6209167},
issn = {0014-5793},
mesh = {Archaea/*genetics ; Ascomycota/*genetics ; Bacteria/*genetics ; Epitopes/*analysis ; Escherichia coli/genetics ; *Phylogeny ; Ribosomal Proteins/*analysis/immunology ; Saccharomyces cerevisiae/*genetics ; Species Specificity ; Xylariales/*genetics ; },
abstract = {A ribosomal protein which exhibits cross-reaction between organisms belonging to the eubacterial, archaebacterial and eukaryotic groups was studied by immunoblotting analysis. It was identified as the equivalent of the E. coli ribosomal protein L2.},
}
@article {pmid6427011,
year = {1984},
author = {Sanz, JL and Amils, R},
title = {Sensitivity of thermoacidophilic archaebacteria to alpha-sarcin.},
journal = {FEBS letters},
volume = {171},
number = {1},
pages = {63-66},
doi = {10.1016/0014-5793(84)80460-3},
pmid = {6427011},
issn = {0014-5793},
mesh = {Animals ; Archaea/*drug effects/growth &amp; development ; Aspergillus ; Bacteria/*drug effects ; Base Sequence ; Chloroplasts/metabolism ; *Endoribonucleases ; Fungal Proteins/*toxicity ; Humans ; Mice ; Mitochondria/metabolism ; Mitochondria, Liver/metabolism ; RNA, Ribosomal/metabolism ; Rats ; Ribosomes/drug effects/metabolism ; Saccharomyces cerevisiae/metabolism ; Species Specificity ; Temperature ; Xenopus ; },
abstract = {The protein synthesis machinery of Sulfolobus solfataricus , a thermoacidophilic archaebacterium, is insensitive to most of the known antibiotics that interfere with elongation. alpha-Sarcin, a cytotoxic protein, inhibits protein synthesis on eukaryotic systems by cleaving a specific sequence of the large rRNA. alpha-Sarcin is capable of inhibiting protein synthesis on S. solfataricus producing a fragment under conditions similar to those which produce it in yeast ribosomes. This result suggests the presence on S. solfataricus of the sequence necessary for the enzymatic hydrolysis promoted by alpha-sarcin.},
}
@article {pmid6426463,
year = {1984},
author = {Danson, MJ and Eisenthal, R and Hall, S and Kessell, SR and Williams, DL},
title = {Dihydrolipoamide dehydrogenase from halophilic archaebacteria.},
journal = {The Biochemical journal},
volume = {218},
number = {3},
pages = {811-818},
pmid = {6426463},
issn = {0264-6021},
mesh = {Archaea/*enzymology ; Bacteria/*enzymology ; Chromatography, Gel ; Dihydrolipoamide Dehydrogenase/antagonists &amp; inhibitors/*metabolism ; Halobacterium/*enzymology ; Iodoacetates/pharmacology ; Iodoacetic Acid ; Kinetics ; Molecular Weight ; Temperature ; },
abstract = {Dihydrolipoamide dehydrogenase has been discovered in the halophilic archaebacteria for the first time. The enzyme from both classical and alkaliphilic halobacteria has been investigated. (1) The enzyme specifically catalysed the stoichiometric oxidation of dihydrolipoamide by NAD+. Enzymic activity was optimal at 2 M-NaCl and was remarkably resistant to thermal denaturation. (2) The relative molecular masses (Mr) of the native enzyme from the various species of halobacteria were determined to be within the range 112000-120000. (3) The enzyme exhibited a hyperbolic dependence of catalytic activity on both dihydrolipoamide and NAD+ concentrations. From these steady-state kinetic measurements the dissociation constant (Ks) of dihydrolipoamide was determined to be 57 (+/- 5) microM. (4) The enzyme was only susceptible to inactivation by iodoacetic acid in the presence of its reducing ligands, dihydrolipoamide or NADH. The rate of inactivation followed a hyperbolic dependence on the concentration of dihydrolipoamide, from which the Ks of this substrate was calculated to be 55 (+/- 7) microM. Together with the steady-state kinetic data, the pattern of inactivations is consistent with the involvement in catalysis of a reversibly reducible disulphide bond, as has been found in dihydrolipoamide dehydrogenase from non-archaebacterial species. In eubacterial and eukaryotic organisms, dihydrolipoamide dehydrogenase functions in the 2-oxo acid dehydrogenase complexes. These multienzyme systems have not been detected in the archaebacteria, and, in the context of this apparent absence, the possible function and evolutionary significance of archaebacterial dihydrolipoamide dehydrogenase are discussed.},
}
@article {pmid6202564,
year = {1984},
author = {Schnabel, H and Schnabel, R and Yeats, S and Tu, J and Gierl, A and Neumann, H and Zillig, W},
title = {Genome organization and transcription in archaebacteria.},
journal = {Folia biologica},
volume = {30 Spec No},
number = {},
pages = {2-6},
pmid = {6202564},
issn = {0015-5500},
mesh = {Archaea/*genetics ; Bacteria/*genetics ; Bacteriophages/genetics ; DNA, Bacterial/metabolism ; DNA, Viral ; DNA-Directed RNA Polymerases/metabolism ; *Genes, Bacterial ; Genes, Viral ; Halobacterium/genetics ; Plasmids ; RNA, Bacterial/genetics ; RNA, Ribosomal/genetics ; *Transcription, Genetic ; },
abstract = {The genome organization of the archaebacteria is investigated in three model systems: a) rRNA genes of various archaebacteria, b) a plasmid of 15.6 kb from Sulfolobus acidocaldarius which exists in free or integrated form, c) the 59 kb genome of phage phi H of Halobacterium halobium as a model for the unusual structural variability of DNA in this organism. Several variants of this phage have been isolated, their genomes differ by several insertions, a deletion, and an inversion. The frequent inversion and circularization of a 12 kb segment of DNA appears to be linked to the presence of two copies of an IS element at its flanks. DNA-dependent RNA polymerases have been isolated from a large number of archaebacteria including representatives of 4 families of the novel order Thermoproteales . As shown by immunological methods, they are closely related to those of eukaryotes. Two different types of RNA polymerase exist in the two main branches of the archaebacteria. The role of one component of the enzyme of Thermoplasma acidophilum was elucidated using an in vitro transcription system.},
}
@article {pmid6193425,
year = {1983},
author = {Rogers, J},
title = {Introns in archaebacteria.},
journal = {Nature},
volume = {304},
number = {5928},
pages = {685},
doi = {10.1038/304685a0},
pmid = {6193425},
issn = {0028-0836},
mesh = {Archaea/*genetics ; Bacteria/*genetics ; *Base Sequence ; Escherichia coli/genetics ; RNA, Bacterial/genetics ; RNA, Transfer/genetics ; Species Specificity ; },
}
@article {pmid6407755,
year = {1983},
author = {Lake, JA},
title = {Evolving ribosome structure: domains in archaebacteria, eubacteria, and eucaryotes.},
journal = {Cell},
volume = {33},
number = {2},
pages = {318-319},
doi = {10.1016/0092-8674(83)90412-9},
pmid = {6407755},
issn = {0092-8674},
mesh = {Animals ; Archaea/ultrastructure ; Eubacterium/ultrastructure ; Eukaryotic Cells/ultrastructure ; *Models, Structural ; Protein Biosynthesis ; Ribosomes/*analysis ; },
}
@article {pmid6406834,
year = {1983},
author = {Prangishvili, DA},
title = {[Molecular biology of archaebacteria].},
journal = {Molekuliarnaia biologiia},
volume = {17},
number = {2},
pages = {234-248},
pmid = {6406834},
issn = {0026-8984},
mesh = {Archaea/*genetics ; Bacteria/*genetics ; Base Sequence ; Molecular Weight ; RNA, Ribosomal/*genetics ; Species Specificity ; },
abstract = {In the process of phylogenetic studies, based on the comparative analysis of sequences of 16S (18S) rRNA, C. Woese and collaborators discovered that some microorganisms, which previously had been described as bacteria, form a group named archaebacteria, differing from other bacteria as well as from eukaryotes to the same extent as the latter differ from each other. A review of the work leading to that result, as well as characteristics of archaebacteria with emphasis on their biochemistry and molecular biology, is presented.},
}
@article {pmid6402493,
year = {1983},
author = {Pappenheimer, AM and Dunlop, PC and Adolph, KW and Bodley, JW},
title = {Occurrence of diphthamide in archaebacteria.},
journal = {Journal of bacteriology},
volume = {153},
number = {3},
pages = {1342-1347},
pmid = {6402493},
issn = {0021-9193},
support = {GM 26832/GM/NIGMS NIH HHS/United States ; },
mesh = {Adenosine Diphosphate Ribose/metabolism ; Archaea/*analysis ; Bacteria/*analysis ; Histidine/*analogs &amp; derivatives/analysis ; Peptide Elongation Factor 2 ; Peptide Elongation Factors/metabolism ; Protein Processing, Post-Translational ; },
abstract = {We examined the nature of the diphtheria toxin fragment A recognition site in the protein synthesis translocating factor present in cell-free preparations from the archaebacteria Thermoplasma acidophilum and Halobacterium halobium. In agreement with earlier work (M. Kessel and F. Klink, Nature (London) 287:250-251, 1980), we found that extracts from these organisms contain a protein factor which is a substrate for the ADP-ribosylation reaction catalyzed by diphtheria toxin fragment A. However, the rate of the reaction was approximately 1,000 times slower than that typically observed with eucaryotic elongation factor 2. We also demonstrated the presence of diphthine (the deamidated form of diphthamide, i.e., 2-[3-carboxyamide-3-(trimethylammonio)propyl]histidine) in acid hydrolysates of H. halobium protein in amounts comparable to those found in hydrolysates of similar preparations from eucaryotic cells (Saccharomyces cerevisiae and HeLa). Diphthine could not be detected in hydrolysates of protein from the eubacterium Escherichia coli. Whereas both archaebacterial and eucaryotic elongation factors contain diphthamide, they differ importantly in other respects.},
}
@article {pmid6401847,
year = {1983},
author = {Fischer, F and Zillig, W and Stetter, KO and Schreiber, G},
title = {Chemolithoautotrophic metabolism of anaerobic extremely thermophilic archaebacteria.},
journal = {Nature},
volume = {301},
number = {5900},
pages = {511-513},
doi = {10.1038/301511a0},
pmid = {6401847},
issn = {0028-0836},
mesh = {Anaerobiosis ; Archaea/*genetics ; Bacteria/*genetics ; Carbon Dioxide ; Energy Metabolism ; Hydrogen/metabolism ; Sulfur/metabolism ; },
abstract = {Several types of extremely thermophilic archaebacteria have recently been isolated from solfataric water holes, hot springs and hot sea floors. It has been shown that some of them can live using sulphur respiration of reduced carbon substrates as a source of energy, a type of metabolism previously described for the eubacterium Desulfuromonas. We report here that several extremely thermophilic archaebacteria can live with carbon dioxide as their sole carbon source, obtaining energy from the oxidation of hydrogen by sulphur, producing hydrogen sulphide. They are thus capable of a new type of anaerobic, purely chemolithoautotrophic metabolism, a possible primaeval mode of life.},
}
@article {pmid6420842,
year = {1983},
author = {Lake, JA},
title = {Ribosome evolution: the structural bases of protein synthesis in archaebacteria, eubacteria, and eukaryotes.},
journal = {Progress in nucleic acid research and molecular biology},
volume = {30},
number = {},
pages = {163-194},
doi = {10.1016/s0079-6603(08)60686-8},
pmid = {6420842},
issn = {0079-6603},
mesh = {Archaea/genetics ; Bacteria/*genetics ; *Biological Evolution ; Escherichia coli/genetics ; Eukaryotic Cells/physiology ; Models, Structural ; Prokaryotic Cells/physiology ; *Protein Biosynthesis ; Ribosomal Proteins/*genetics ; Ribosomes/*metabolism ; },
}
@article {pmid6310116,
year = {1983},
author = {Gliozzi, A and Rolandi, R and De Rosa, M and Gambacorta, A},
title = {Monolayer black membranes from bipolar lipids of archaebacteria and their temperature-induced structural changes.},
journal = {The Journal of membrane biology},
volume = {75},
number = {1},
pages = {45-56},
pmid = {6310116},
issn = {0022-2631},
mesh = {Archaea/*ultrastructure ; Bacteria/*ultrastructure ; Biological Evolution ; Cell Membrane/ultrastructure ; Chemical Phenomena ; Chemistry, Physical ; Electric Conductivity ; Ion Channels ; Membrane Fluidity ; Membrane Lipids/physiology ; Membrane Potentials ; Temperature ; Valinomycin/pharmacology ; },
abstract = {The membrane of Caldariella acidophila, an extreme thermophilic archaebacterium, is characterized by unusual bipolar complex lipids. They consist of two nonequivalent polar heads, linked by a C40 alkylic component. The molecular organization of these lipids in the plasma membrane is still a matter of study. In this paper, we present current-voltage measurements on artificial bipolar lipid membranes, indicating that molecules are indeed organized as a covalently bound bilayer, in which each molecule is completely stretched and spans its entire thickness. Furthermore, conformational transitions of these artificial membranes (which could be formed only above 70 degrees C from a lipid/squalene dispersion) are analyzed in the 80 to 15 degrees C temperature range. Abrupt variations in capacitance and valinomycin-induced conductance seem to indicate the occurrence of at least two structural changes. Measurements are also extended to different solvent systems. Results are consistent with the picture of a monolayer bipolar lipid membrane in which few solvent molecules align themselves parallel to the lipophilic chains. The amount of solvent as well as the temperature at which conformational transitions occur, depend on the solvent system in which the lipid is dispersed.},
}
@article {pmid6816594,
year = {1982},
author = {Kerscher, L and Nowitzki, S and Oesterhelt, D},
title = {Thermoacidophilic archaebacteria contain bacterial-type ferredoxins acting as electron acceptors of 2-oxoacid:ferredoxin oxidoreductases.},
journal = {European journal of biochemistry},
volume = {128},
number = {1},
pages = {223-230},
doi = {10.1111/j.1432-1033.1982.tb06955.x},
pmid = {6816594},
issn = {0014-2956},
mesh = {Amino Acids/isolation &amp; purification ; Archaea/*enzymology ; Bacteria/*enzymology ; Electron Transport ; Ferredoxins/*physiology ; Free Radicals ; Halobacterium/enzymology ; Ketone Oxidoreductases/*metabolism ; Oxidation-Reduction ; Pyruvate Synthase ; Thermoplasma/enzymology ; },
abstract = {Thermoplasma acidophilum and Sulfolobus acidocaldarius contain coenzyme A-acylating 2-oxoacid:ferredoxin oxidoreductases similar to those found in halophilic archaebacteria. A common feature of these enzymes is the formation of a free radical intermediate in the course of the catalytic cycle. The electron-accepting ferredoxins and a similar protein from Desulfurococcus mobilis have been purified and characterized. In contrast to the [2Fe-2S] ferredoxin of Halobacterium halobium, the ferredoxins of thermoacidophilic archaebacteria most likely contain two [4Fe-4S]2 + (2 + .1 +) clusters per molecule. Properties of these proteins are compared with respect to the evolution of archaebacteria.},
}
@article {pmid6178978,
year = {1982},
author = {Kuchino, Y and Ihara, M and Yabusaki, Y and Nishimura, S},
title = {Initiator tRNAs from archaebacteria show common unique sequence characteristics.},
journal = {Nature},
volume = {298},
number = {5875},
pages = {684-685},
doi = {10.1038/298684a0},
pmid = {6178978},
issn = {0028-0836},
mesh = {Archaea/*genetics ; Bacteria/*genetics ; Base Sequence ; Biological Evolution ; Peptide Chain Initiation, Translational ; RNA, Bacterial/*genetics ; RNA, Transfer/*genetics ; },
}
@article {pmid6800790,
year = {1982},
author = {Prangishvilli, D and Zillig, W and Gierl, A and Biesert, L and Holz, I},
title = {DNA-dependent RNA polymerase of thermoacidophilic archaebacteria.},
journal = {European journal of biochemistry},
volume = {122},
number = {3},
pages = {471-477},
doi = {10.1111/j.1432-1033.1982.tb06461.x},
pmid = {6800790},
issn = {0014-2956},
mesh = {Archaea/*enzymology ; Bacteria/*enzymology ; Chemical Phenomena ; Chemistry ; DNA-Directed RNA Polymerases/*isolation &amp; purification ; Molecular Weight ; Temperature ; Transcription, Genetic ; },
abstract = {The component compositions of the DNA-dependent RNA polymerases of the extremely thermophilic, anaerobic sulfur-respiring archaebacteria Thermoproteus tenax and Desulfurococcus mucosus strongly resemble each other but also that of the RNA polymerase of Sulfolobus acidocaldarius suggesting that both organisms belong to the same novel order Thermoproteales, which together with the order represented by Sulfolobus, forms the thermoacidophilic branch of archaebacteria. The component pattern of the RNA polymerase of Thermoplasma acidophilum, which does not belong to this branch, also appears homologous. The archaebacterial type of the DNA-dependent RNA polymerase is thus characterized by 9-10 components yielding a characteristic pattern which resembles that of yeast RNA polymerase A(I). In contrast to the alpha subunit of eubacterial RNA polymerases, the third largest component of archaebacterial RNA polymerases, although similar in size, is present only one per enzyme monomer. The polymerases of T. tenax and D. mucosus, like those previously isolated from other archaebacteria, are completely resistant against 100 microgram/ml rifampicin and streptolydigin. The RNA polymerases of both organisms are highly thermostable. The enzyme from D. mucosus transcribes selectively and almost completely the H strand of phase T7 DNA.},
}
@article {pmid6800415,
year = {1982},
author = {Gliozzi, A and Rolandi, R and De Rosa, M and Gambacorta, A},
title = {Artificial black membranes from bipolar lipids of thermophilic Archaebacteria.},
journal = {Biophysical journal},
volume = {37},
number = {2},
pages = {563-566},
pmid = {6800415},
issn = {0006-3495},
mesh = {Archaea/*analysis ; Bacteria/*analysis ; Electric Conductivity ; Membrane Lipids/*analysis ; Membrane Potentials ; *Membranes, Artificial ; Sodium Chloride ; Temperature ; },
abstract = {The membrane of thermophilic archaebacteria is characterized by the presence of unusual isoprenoid bipolar lipids. The molecular organization of these lipids is still a matter of study. Important information could come from forming artificial black membranes. Black films can be formed from n-alkane or squalene dispersions of bipolar lipids extracted from the membrane of Caldariella acidophila. Membrane formation occurred only above a critical temperature (approximately 70 degrees C) corresponding to the physiological one. At lower temperatures, special solvent systems (n-alkanes or squalene, butanol and n-alkanes or squalene, butanol chloroform) were required. To characterize the physical parameters of these membranes, conductance and capacitance measurements were performed. Conductance was in the range of 10(-8) - 10(-7) omega -1 cm -2 , where specific capacitance at T = 72 degrees C was Cs = 0.685 +/- 0.004 microF/cm2 and Cs = 0.658 +/- 0.08 microF/cm2, corresponding to a dielectric thickness of 27 and 29 A for squalene and dodecane dispersions, respectively. Capacitance was shown to vary as the square of membrane potential, as usual in lipid bilayers. Values of the proportionality constant alpha have been compared to those of solvent-containing and solvent-free bilayers. The behavior of capacitance as a function of temperature is also shown by lowering temperature; the occurrence of complex structural changes was indicated. All the experimental data suggest that the presence of solvent is very low. Two possible molecular configurations of the films are discussed.},
}
@article {pmid6178834,
year = {1982},
author = {Tu, JK and Prangishvilli, D and Huber, H and Wildgruber, G and Zillig, W and Stetter, KO},
title = {Taxonomic relations between archaebacteria including 6 novel genera examined by cross hybridization of DNAs and 16S rRNAs.},
journal = {Journal of molecular evolution},
volume = {18},
number = {2},
pages = {109-114},
pmid = {6178834},
issn = {0022-2844},
mesh = {Archaea/*genetics ; Bacteria/*genetics ; *DNA, Bacterial ; Drug Stability ; Hot Temperature ; *Nucleic Acid Hybridization ; *RNA, Bacterial ; *RNA, Ribosomal ; Species Specificity ; },
abstract = {DNAs from 16 species of archaebacteria including 6 novel isolates were hybridized with 16S rRNAs from 7 species representing different orders or groups of the urkingdom of archaebacteria. The yields, normalized for the number of genes per microgram of DNA, and the temperature stabilities of all hybrids were determined and related to each other. A taxonomic tree constructed from such fractional stability data reveals the same major divisions as that derived from comparative cataloging of 16S rRNA sequences. The extreme halophiles appear however as a distinct order besides the three known divisions of methanogens. The methanogens, the halophiles and Thermoplasma form one of two clearly recognizable branches of the archaebacterial urkingdom. The order represented by Sulfolobus and the related novel order Thermoproteales form the other branch. Three novel genera, Thermoproteus, Desulfurococcus and the "stiff filaments" represent three families of this order. The extremely thermophilic methanogen Methanothermus fervidus belongs to the Methanobacteriales. SN1, a methanogen from Italy, appears as another species of the genus Methanococcus. Another novel methanogen, M3, represents a genus or family of the order Methanomicrobiales.},
}
@article {pmid6792708,
year = {1981},
author = {Conway de Macario, E and Wolin, MJ and Macario, AJ},
title = {Immunology of archaebacteria that produce methane gas.},
journal = {Science (New York, N.Y.)},
volume = {214},
number = {4516},
pages = {74-75},
doi = {10.1126/science.6792708},
pmid = {6792708},
issn = {0036-8075},
support = {NIAID AI-12461/AI/NIAID NIH HHS/United States ; },
mesh = {Antigens, Bacterial/*analysis ; Archaea/classification/*immunology ; Bacteria/*immunology ; Euryarchaeota/classification/*immunology ; Species Specificity ; },
abstract = {The antigenic map of 17 methanogenic bacteria representing the entire range of available species was determined by multiple assay with antibody probes. Four major clusters of antigenically related strains coincide with the females proposed on the basis of 16S ribosomal RNA analysis. Immunological mapping uncovered relationships not yet shown by other methods and allowed identification and classification of two new bacterial isolates.},
}
@article {pmid6791033,
year = {1981},
author = {Zillig, W and Tu, J and Holz, I},
title = {Thermoproteales--a third order of thermoacidophilic archaebacteria.},
journal = {Nature},
volume = {293},
number = {5827},
pages = {85-86},
doi = {10.1038/293085a0},
pmid = {6791033},
issn = {0028-0836},
mesh = {Archaea/*classification/genetics ; Bacteria/*classification ; DNA-Directed RNA Polymerases/genetics ; RNA, Ribosomal/genetics ; Transcription, Genetic ; },
}
@article {pmid6167563,
year = {1981},
author = {Schmid, G and Böck, A},
title = {Immunological comparison of ribosomal proteins from archaebacteria.},
journal = {Journal of bacteriology},
volume = {147},
number = {2},
pages = {282-288},
pmid = {6167563},
issn = {0021-9193},
mesh = {Antigens, Bacterial/analysis ; Bacteria/immunology ; Bacterial Proteins/*immunology ; Cross Reactions ; Epitopes ; Euryarchaeota/*immunology ; Gram-Negative Chemolithotrophic Bacteria/*immunology ; Halobacterium/*immunology ; Isoelectric Point ; Ribosomal Proteins/*immunology ; Saccharomyces cerevisiae/immunology ; },
abstract = {Antisera were raised in rabbits against ribosomal proteins of Methanobacterium bryantii and used to analyze immunological relationships to ribosomes from other archaebacteria, from eubacteria, and from yeasts. Cross-reaction could be detected within the methanogens and with a member of the extreme halophiles; the degree of immunological similarity reflected the relationship delineated by 16S ribosomal ribonucleic acid oligonucleotide analysis (Fox et al., Science 209:457-463, 1980). With the methods and the anti-total-protein sera employed, there was no detectable cross-reaction with ribosomal proteins or ribosomes from Sulfolobus sp., eubacteria, or yeast.},
}
@article {pmid6168919,
year = {1981},
author = {Kandler, O},
title = {[Archaebacteria and phylogeny of organisms].},
journal = {Die Naturwissenschaften},
volume = {68},
number = {4},
pages = {183-192},
pmid = {6168919},
issn = {0028-1042},
mesh = {Archaea/*genetics ; Bacteria/*genetics ; Base Sequence ; DNA-Directed RNA Polymerases/genetics ; Lipids/analysis ; *Phylogeny ; RNA, Bacterial/*genetics ; RNA, Ribosomal/*genetics ; Ribosomal Proteins/genetics ; Species Specificity ; },
abstract = {The determination of the sequence similarity of the ribosomal 16S RNA of many bacteria and a few higher organisms has shown that the methanogenic, halophilic, and acido-thermophilic organisms are phylogenetically separated from the kingdoms of the Eubacteria and Eukaryotes thus representing a third kingdom called "Archaebacteria". Many biochemical and molecular biological features support this conclusion.},
}
@article {pmid6161309,
year = {1981},
author = {Woese, CR and Gupta, R},
title = {Are archaebacteria merely derived 'prokaryotes'?.},
journal = {Nature},
volume = {289},
number = {5793},
pages = {95-96},
doi = {10.1038/289095a0},
pmid = {6161309},
issn = {0028-0836},
mesh = {Archaea/*genetics ; Bacteria/*genetics ; Bacterial Proteins/genetics ; *Biological Evolution ; *Cell Physiological Phenomena ; Eukaryotic Cells/physiology ; Prokaryotic Cells/*physiology ; RNA, Bacterial/genetics ; },
abstract = {The archaebacteria are a group of prokaryotes which seem as distinct from the true bacteria (eubacteria) as they are from eukaryotes. The evidence on which this conclusion rests is of two types: genotypic (quantitative)--that is, comparative sequence studies, and phenotypic (qualitative)--that is, differences in various organismal characteristics. The differences between archaebacteria and true bacteria are so great, both quantitatively and qualitatively, that the two bacterial groups should be considered as representing separate primary lines of descent, each tracing directly back to the universal ancestor. Furthermore, this ancestor itself seems not to be a prokaryote; rather it was a far simpler type of organism, one properly called a progenote. If this is true, the discovery of archaebacteria marks a major advance in the biologist's attempts to understand the basis for the evolution of the cell.},
}
@article {pmid6159535,
year = {1980},
author = {Van Valen, LM and Maiorana, VC},
title = {The archaebacteria and eukaryotic origins.},
journal = {Nature},
volume = {287},
number = {5779},
pages = {248-250},
doi = {10.1038/287248a0},
pmid = {6159535},
issn = {0028-0836},
mesh = {Archaea/*classification/genetics/physiology ; Bacteria/*classification ; *Biological Evolution ; Cells/*cytology ; Energy Metabolism ; Eukaryotic Cells/*cytology ; Phylogeny ; RNA, Bacterial/genetics ; RNA, Ribosomal/genetics ; },
abstract = {Critical analysis of the phylogeny of prokaryotes is in its infancy. Woese and others have made the startling proposal that methane-producing bacteria and a few others form a phyletically unified group, the Archaebacteria, as old and as diverse (although not now as numerous) as all other bacteria. The only critique of this proposal is inadequate. Here we present an alternative view, that the Archaebacteria were derived from other bacteria and contain the ancestor of a cell which engulfed others, eventually to become the first eukaryote.},
}
@article {pmid458874,
year = {1979},
author = {Tornabene, TG and Langworthy, TA and Holzer, G and Oró, J},
title = {Squalenes, phytanes and other isoprenoids as major neutral lipids of methanogenic and thermoacidophilic "archaebacteria".},
journal = {Journal of molecular evolution},
volume = {13},
number = {1},
pages = {73-83},
pmid = {458874},
issn = {0022-2844},
mesh = {Cell Wall/analysis ; Diterpenes/*analysis ; Euryarchaeota/*analysis ; Lipids/*analysis ; Species Specificity ; Squalene/*analysis ; Temperature ; Terpenes/*analysis ; },
abstract = {The neutral lipids of nine species of methanogenic bacteria including five methanobacilli, two methanococci, a methanospirillum, one methanosarcina as well as two thermoacidophilic bacteria, Thermoplasma and Sulfolobus, were analyzed. The major components were C30, C25 and/or C20 acylic isoprenoid hydrocarbons with a continuous range of hydroisoprenoid homologues. The range of acyclic isoprenoids detected were from C14 to C30. Apart from Methanosarcina barkeri, squalene and/or hydrosqualene derivetives were the predominant components in all species studied. The components of Methanosarcina barkeri were a family of C25 homologues. The distribution of the neutral lipid components and their specific variations in relative intensities emphasized the differences between the test organisms while the generic nature of the isoprenoid hydrocarbons demonstrated similarities between the diverse bacteria. The neutral lipid compositions from these bacteria, many of which exist in environmental conditions like those described for the various evolutionary stages of the archean ecology, resemble the isoprenoid distribution isolated from ancient sediments and petroleum. Therefore, these finding may have major implications to biological and biogeochemical evolution.},
}
@article {pmid758677,
year = {1979},
author = {Tornabene, TG and Langworthy, TA},
title = {Diphytanyl and dibiphytanyl glycerol ether lipids of methanogenic archaebacteria.},
journal = {Science (New York, N.Y.)},
volume = {203},
number = {4375},
pages = {51-53},
doi = {10.1126/science.758677},
pmid = {758677},
issn = {0036-8075},
mesh = {Biological Evolution ; Ethers/analysis ; Euryarchaeota/*analysis/classification/genetics ; Glycerol/analogs &amp; derivatives/analysis ; Lipids/*analysis ; Mass Spectrometry ; },
abstract = {The lipids of nine different methanogenic bacterial strains are comprised of diphytanyl glycerol diethers, previously known only in extremely halophilic bacterial, as well as dibiphytanyl diglycerol tetraethers, known formerly only in the extremely thermoacidophilic bacteria Thermoplasma and Sulfolobus. Of the methanogens examined from four representative taxonomic groups, Methanobacterium and Methanospirillum contained both types of isopranyl ethers in nearly equal proportions, whereas the coccal forms, Methanosarcina and Methanococcus, possessed diphytanyl glycerol diethers, but with only a trace of or no dibiphytanyl diglycerol tetraethers. The occurrence of both types of isopranyl glycerol ethers in methanogenic bacteria supports the proposal that they have a close genealogical relationship to the extremely halophilic and thermoacidophilic bacteria.},
}
@article {pmid691075,
year = {1978},
author = {Woese, CR and Magrum, LJ and Fox, GE},
title = {Archaebacteria.},
journal = {Journal of molecular evolution},
volume = {11},
number = {3},
pages = {245-251},
pmid = {691075},
issn = {0022-2844},
mesh = {Bacteria/classification/*genetics ; Cell Wall/analysis ; Eukaryotic Cells/physiology ; Euryarchaeota/analysis/classification/*genetics ; Lipids/analysis ; Phylogeny ; Protein Biosynthesis ; },
abstract = {Experimental work published elsewhere has shown that the Archaebacteria encompass several distinct subgroups including methanogens, extreme halophiles, and various thermoacidophiles. The common characteristics of Archaebacteria known to date are these: (1) the presence of characteristic tRNAs and ribosomal RNAs; (2) the absence of peptidoglycan cell walls, with in many cases, replacement by a largely proteinaceous coat; (3) the occurrence of ether linked lipids built from phytanyl chains and (4) in all cases known so far, their occurrence only in unusual habitats. These organisms contain a number of 'eucaryotic features' in addition to their many bacterial attributes. This is interpreted as a strong indication that the Archaebacteria, while not actually eucaryotic, do indeed represents a third separate, line of descent as originally proposed.},
}