@article {pmid36502540,
year = {2022},
author = {Alsaad, RKA},
title = {Past, present and future of Trichomonas vaginalis: a review study.},
journal = {Annals of parasitology},
volume = {68},
number = {3},
pages = {409-419},
doi = {10.17420/ap6803.447},
pmid = {36502540},
issn = {2299-0631},
mesh = {Male ; Female ; Humans ; *Trichomonas vaginalis/genetics ; *Trichomonas Vaginitis/diagnosis/epidemiology/parasitology ; *Trichomonas Infections/epidemiology ; Metronidazole ; Prevalence ; },
abstract = {Trichomonas vaginalis (TV) is the most common non-viral sexually transmitted infection (STI) microaerophilic protist parasite, which is the causative agent of trichomonosis. Globally, the estimated annual incidence is more than 270 million cases. It is correlated for several health problems including pelvic inflammatory disease (PID), pregnancy miscarriages, cervical carcinoma, prostatitis, prostatic adenocarcinomas, infertility, and the acquisition of human immunodeficiency virus (HIV). Most individuals infected with TV are asymptomatic. Metronidazole (MTZ) has been the treatment of choice for women. Currently, there is no effective vaccine against this pathogen despite efforts at vaccine development. Different socio-economic, demographic, behavioral, and biological factors are associated with the disease. Apart from its role as a pathogenic agent of diseases, it is also a fascinating organism with a surprisingly large genome for a parasite, i.e. larger than 160 Mb, and physiology adapted to its microaerophilic lifestyle. Particularly, the hydrogenosome, a mitochondria-derived organelle that releases hydrogen, attracted much interest in the last decades and rendered TV a model organism for eukaryotic evolution. According to the high prevalence and health consequences associated with TV, there is a requirement for improved screening programs in Iraq. The early diagnosis of asymptomatic diseases and effective treatment regimens are mandatory. Despite being highly prevalent of trichomonosis in the world, there is no review research published that solely focuses on T. vaginalis infections in Iraq.},
}

Male
Female
Humans
*Trichomonas vaginalis/genetics
*Trichomonas Vaginitis/diagnosis/epidemiology/parasitology
*Trichomonas Infections/epidemiology
Metronidazole
Prevalence

@article {pmid36508337,
year = {2022},
author = {Xu, R and Martelossi, J and Smits, M and Iannello, M and Peruzza, L and Babbucci, M and Milan, M and Dunham, JP and Breton, S and Milani, L and Nuzhdin, SV and Bargelloni, L and Passamonti, M and Ghiselli, F},
title = {Multi-tissue RNA-Seq Analysis and Long-read-based Genome Assembly Reveal Complex Sex-specific Gene Regulation and Molecular Evolution in the Manila Clam.},
journal = {Genome biology and evolution},
volume = {14},
number = {12},
pages = {},
pmid = {36508337},
issn = {1759-6653},
support = {S10 RR025496/RR/NCRR NIH HHS/United States ; S10 OD010794/OD/NIH HHS/United States ; },
mesh = {Animals ; Female ; Male ; *DNA, Mitochondrial/genetics ; RNA-Seq ; *Bivalvia/genetics ; Mitochondria/genetics ; Evolution, Molecular ; },
abstract = {The molecular factors and gene regulation involved in sex determination and gonad differentiation in bivalve molluscs are unknown. It has been suggested that doubly uniparental inheritance (DUI) of mitochondria may be involved in these processes in species such as the ubiquitous and commercially relevant Manila clam, Ruditapes philippinarum. We present the first long-read-based de novo genome assembly of a Manila clam, and a RNA-Seq multi-tissue analysis of 15 females and 15 males. The highly contiguous genome assembly was used as reference to investigate gene expression, alternative splicing, sequence evolution, tissue-specific co-expression networks, and sexual contrasting SNPs. Differential expression (DE) and differential splicing (DS) analyses revealed sex-specific transcriptional regulation in gonads, but not in somatic tissues. Co-expression networks revealed complex gene regulation in gonads, and genes in gonad-associated modules showed high tissue specificity. However, male gonad-associated modules showed contrasting patterns of sequence evolution and tissue specificity. One gene set was related to the structural organization of male gametes and presented slow sequence evolution but high pleiotropy, whereas another gene set was enriched in reproduction-related processes and characterized by fast sequence evolution and tissue specificity. Sexual contrasting SNPs were found in genes overrepresented in mitochondrial-related functions, providing new candidates for investigating the relationship between mitochondria and sex in DUI species. Together, these results increase our understanding of the role of DE, DS, and sequence evolution of sex-specific genes in an understudied taxon. We also provide resourceful genomic data for studies regarding sex diagnosis and breeding in bivalves.},
}

Animals
Female
Male
*DNA, Mitochondrial/genetics
RNA-Seq
*Bivalvia/genetics
Mitochondria/genetics
Evolution, Molecular

@article {pmid36519158,
year = {2022},
author = {Kim, S and Eom, H and Nandre, R and Choi, YJ and Lee, H and Ryu, H and Ro, HS},
title = {Comparative structural analysis on the mitochondrial DNAs from various strains of Lentinula edodes.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {1034387},
pmid = {36519158},
issn = {1664-302X},
abstract = {The evolution of mitochondria through variations in mitochondrial DNA (mtDNA) is one of the intriguing questions in eukaryotic cells. In order to assess the causes of the variations in mitochondria, the mtDNAs of the 21 strains of Lentinula edodes were assembled for this study, and analyzed together with four published mtDNA sequences. The mtDNAs were within the sizes of 117 kb ~ 122 kb. The gene number was observed consistent except for two mtDNAs, which carry a duplicated trnG1-trnG2 unit or a putative gene deletion. The size variation was largely attributed to the number of introns, repeated sequences, transposable elements (TEs), and plasmid-related sequences. Intron loss and gain were found from cox1, rnl, and rns of three mtDNAs. Loss of two introns in cox1 of KY217797.1 reduced its size by 2.7 kb, making it the smallest cox1 gene (8.4 kb) among the cox1s of the 25 mtDNAs, whereas gain of a Group II intron (2.65 kb) and loss of a Group I intron (1.7 kb) in cox1 of MF774813.1 resulted in the longest cox1 (12 kb). In rnl of L. edodes, we discovered four intron insertion consensus sequences which were unique to basidiomycetes but not ascomycetes. Differential incorporation of introns was the primary cause of the rnl size polymorphism. Homing endonucleases (HEGs) were suggestively involved in the mobilization of the introns because all of the introns have HEG genes of the LAGRIDADG or GIY-YIG families with the conserved HEG cleavage sites. TEs contributed to 11.04% of the mtDNA size in average, of which 7.08% was LTR-retrotransposon and 3.96% was DNA transposon, whereas the repeated sequences covered 4.6% of the mtDNA. The repeat numbers were variable in a strain-dependent manner. Both the TEs and repeated sequences were mostly found in the intronic and intergenic regions. Lastly, two major deletions were found in the plasmid-related sequence regions (pol2-pol3 and pol1-atp8) in the five mtDNAs. Particularly, the 6.8 kb-long deletion at pol2-pol3 region made MF774813.1 the shortest mtDNA of all. Our results demonstrate that mtDNA is a dynamic molecule that persistently evolves over a short period of time by insertion/deletion and repetition of DNA segments at the strain level.},
}

@article {pmid36520311,
year = {2023},
author = {Marszalek, J and Craig, EA and Tomiczek, B},
title = {J-Domain Proteins Orchestrate the Multifunctionality of Hsp70s in Mitochondria: Insights from Mechanistic and Evolutionary Analyses.},
journal = {Sub-cellular biochemistry},
volume = {101},
number = {},
pages = {293-318},
pmid = {36520311},
issn = {0306-0225},
mesh = {*Saccharomyces cerevisiae Proteins/metabolism ; HSP70 Heat-Shock Proteins/genetics/metabolism ; Mitochondria/genetics/metabolism ; Molecular Chaperones/genetics/metabolism ; Mitochondrial Proteins/genetics/metabolism ; },
abstract = {Mitochondrial J-domain protein (JDP) co-chaperones orchestrate the function of their Hsp70 chaperone partner(s) in critical organellar processes that are essential for cell function. These include folding, refolding, and import of mitochondrial proteins, maintenance of mitochondrial DNA, and biogenesis of iron-sulfur cluster(s) (FeS), prosthetic groups needed for function of mitochondrial and cytosolic proteins. Consistent with the organelle's endosymbiotic origin, mitochondrial Hsp70 and the JDPs' functioning in protein folding and FeS biogenesis clearly descended from bacteria, while the origin of the JDP involved in protein import is less evident. Regardless of their origin, all mitochondrial JDP/Hsp70 systems evolved unique features that allowed them to perform mitochondria-specific functions. Their modes of functional diversification and specialization illustrate the versatility of JDP/Hsp70 systems and inform our understanding of system functioning in other cellular compartments.},
}

*Saccharomyces cerevisiae Proteins/metabolism
HSP70 Heat-Shock Proteins/genetics/metabolism
Mitochondria/genetics/metabolism
Molecular Chaperones/genetics/metabolism
Mitochondrial Proteins/genetics/metabolism

@article {pmid36523555,
year = {2022},
author = {Hogg, DW and Reid, AL and Dodsworth, TL and Chen, Y and Reid, RM and Xu, M and Husic, M and Biga, PR and Slee, A and Buck, LT and Barsyte-Lovejoy, D and Locke, M and Lovejoy, DA},
title = {Skeletal muscle metabolism and contraction performance regulation by teneurin C-terminal-associated peptide-1.},
journal = {Frontiers in physiology},
volume = {13},
number = {},
pages = {1031264},
pmid = {36523555},
issn = {1664-042X},
abstract = {Skeletal muscle regulation is responsible for voluntary muscular movement in vertebrates. The genes of two essential proteins, teneurins and latrophilins (LPHN), evolving in ancestors of multicellular animals form a ligand-receptor pair, and are now shown to be required for skeletal muscle function. Teneurins possess a bioactive peptide, termed the teneurin C-terminal associated peptide (TCAP) that interacts with the LPHNs to regulate skeletal muscle contractility strength and fatigue by an insulin-independent glucose importation mechanism in rats. CRISPR-based knockouts and siRNA-associated knockdowns of LPHN-1 and-3 in the C2C12 mouse skeletal cell line shows that TCAP stimulates an LPHN-dependent cytosolic Ca[2+] signal transduction cascade to increase energy metabolism and enhance skeletal muscle function via increases in type-1 oxidative fiber formation and reduce the fatigue response. Thus, the teneurin/TCAP-LPHN system is presented as a novel mechanism that regulates the energy requirements and performance of skeletal muscle.},
}

@article {pmid36527364,
year = {2023},
author = {Knoop, V},
title = {C-to-U and U-to-C: RNA editing in plant organelles and beyond.},
journal = {Journal of experimental botany},
volume = {74},
number = {7},
pages = {2273-2294},
doi = {10.1093/jxb/erac488},
pmid = {36527364},
issn = {1460-2431},
mesh = {*RNA Editing ; Uridine/genetics/metabolism ; *Organelles/genetics/metabolism ; Plants/genetics/metabolism ; Chloroplasts/metabolism ; RNA, Plant/genetics/metabolism ; Plant Proteins/metabolism ; },
abstract = {The genomes in the two energy-converting organelles of plant cells, chloroplasts and mitochondria, contain numerous 'errors' that are corrected at the level of RNA transcript copies. The genes encoded in the two endosymbiotic organelles would not function properly if their transcripts were not altered by site-specific cytidine-to-uridine (C-to-U) exchanges and by additional reverse U-to-C exchanges in hornworts, lycophytes, and ferns. These peculiar processes of plant RNA editing, re-establishing genetic information that could alternatively be present at the organelle genome level, has spurred much research over >30 years. Lately new studies have revealed numerous interesting insights, notably on the biochemical machinery identifying specific pyrimidine nucleobases for conversion from C to U and vice versa. Here, I will summarize prominent research findings that lately have contributed to our better understanding of these phenomena introducing an added layer of information processing in plant cells. Some of this recent progress is based on the successful functional expression of plant RNA editing factors in bacteria and mammalian cells. These research approaches have recapitulated natural processes of horizontal gene transfer through which some protist lineages seem to have acquired plant RNA editing factors and adapted them functionally for their own purposes.},
}

*RNA Editing
Uridine/genetics/metabolism
*Organelles/genetics/metabolism
Plants/genetics/metabolism
Chloroplasts/metabolism
RNA, Plant/genetics/metabolism
Plant Proteins/metabolism

@article {pmid36545736,
year = {2023},
author = {He, L and Maheshwari, A},
title = {Mitochondria in Early Life.},
journal = {Current pediatric reviews},
volume = {19},
number = {4},
pages = {395-416},
doi = {10.2174/1573396319666221221110728},
pmid = {36545736},
issn = {1875-6336},
support = {R01 DK120309/DK/NIDDK NIH HHS/United States ; },
mesh = {Humans ; *Epigenesis, Genetic ; *Mitochondria/genetics/metabolism ; Signal Transduction ; },
abstract = {Mitochondria are highly-dynamic, membrane-bound organelles that generate most of the chemical energy needed to power the biochemical reactions in eukaryotic cells. These organelles also communicate with the nucleus and other cellular structures to help maintain somatic homeostasis, allow cellular adaptation to stress, and help maintain the developmental trajectory. Mitochondria also perform numerous other functions to support metabolic, energetic, and epigenetic regulation in our cells. There is increasing information on various disorders caused by defects in intrinsic mitochondrial or supporting nuclear genes, on different organ systems. In this review, we have summarized the ultrastructural morphology, structural components, our current understanding of the evolution, biogenesis, dynamics, function, clinical manifestations of mitochondrial dysfunction, and future possibilities. The implications of deficits in mitochondrial dynamics and signaling for embryo viability and offspring health are also explored. We present information from our own clinical and laboratory research in conjunction with information collected from an extensive search in the databases PubMed, EMBASE, and Scopus.},
}

Humans
*Epigenesis, Genetic
*Mitochondria/genetics/metabolism
Signal Transduction

@article {pmid36555867,
year = {2022},
author = {Malnick, SDH and Alin, P and Somin, M and Neuman, MG},
title = {Fatty Liver Disease-Alcoholic and Non-Alcoholic: Similar but Different.},
journal = {International journal of molecular sciences},
volume = {23},
number = {24},
pages = {},
pmid = {36555867},
issn = {1422-0067},
mesh = {Humans ; *Non-alcoholic Fatty Liver Disease/metabolism ; *Carcinoma, Hepatocellular/metabolism ; *Metabolic Syndrome/metabolism ; *Liver Neoplasms/metabolism ; Liver/metabolism ; *Liver Diseases, Alcoholic/metabolism ; Liver Cirrhosis/metabolism ; Ethanol/metabolism ; },
abstract = {In alcohol-induced liver disease (ALD) and in non-alcoholic fatty liver disease (NAFLD), there are abnormal accumulations of fat in the liver. This phenomenon may be related to excessive alcohol consumption, as well as the combination of alcohol consumption and medications. There is an evolution from simple steatosis to steatohepatitis, fibrosis and cirrhosis leading to hepatocellular carcinoma (HCC). Hepatic pathology is very similar regarding non-alcoholic fatty liver disease (NAFLD) and ALD. Initially, there is lipid accumulation in parenchyma and progression to lobular inflammation. The morphological changes in the liver mitochondria, perivenular and perisinusoidal fibrosis, and hepatocellular ballooning, apoptosis and necrosis and accumulation of fibrosis may lead to the development of cirrhosis and HCC. Medical history of ethanol consumption, laboratory markers of chronic ethanol intake, AST/ALT ratio on the one hand and features of the metabolic syndrome on the other hand, may help in estimating the contribution of alcohol intake and the metabolic syndrome, respectively, to liver steatosis.},
}

Humans
*Non-alcoholic Fatty Liver Disease/metabolism
*Carcinoma, Hepatocellular/metabolism
*Metabolic Syndrome/metabolism
*Liver Neoplasms/metabolism
Liver/metabolism
*Liver Diseases, Alcoholic/metabolism
Liver Cirrhosis/metabolism
Ethanol/metabolism

@article {pmid36563715,
year = {2023},
author = {Shukla, P and Mukherjee, S and Patil, A and Joshi, B},
title = {Molecular characterization of variants in mitochondrial DNA encoded genes using next generation sequencing analysis and mitochondrial dysfunction in women with PCOS.},
journal = {Gene},
volume = {855},
number = {},
pages = {147126},
doi = {10.1016/j.gene.2022.147126},
pmid = {36563715},
issn = {1879-0038},
mesh = {Humans ; Female ; DNA, Mitochondrial/genetics ; High-Throughput Nucleotide Sequencing/methods ; *Polycystic Ovary Syndrome/genetics ; Mitochondria/genetics ; RNA, Transfer ; *Genome, Mitochondrial ; },
abstract = {Emerging studies indicates mitochondrial dysfunction and involvement of mitochondrial DNA (mtDNA) variants in the pathogenesis of polycystic ovary syndrome (PCOS). Cumulative effect of mtDNA rare variants are now gaining considerable interest apart from common variants in the pathogenesis of complex diseases. Rare variants may modify the effect of polymorphism or in combination with the common variants may affect the risk of disease. With the evolution of high throughput sequencing techniques, which can be utilized to identify common as well as rare variants along with heteroplasmy levels, comprehensive characterization of the mtDNA variants is possible. Till date, few studies reported common mtDNA variants using traditional sequencing techniques but rare variants in mtDNA encoding genes remain unexplored in women with PCOS. These mtDNA variants may be responsible for mitochondrial dysfunction and may contribute in PCOS pathogenesis. In this study we determined mtDNA copy number, a biomarker of mitochondrial dysfunction and first time analysed variants in mtDNA encoded genes in women with PCOS using mitochondrial Next Generation sequencing (NGS) approach and compared allele frequency from mitochondrial 1000 genome dataset. Variant annotation and prioritization was done using highly automated pipeline, MToolBox that excludes reads mapped from nuclear mitochondrial DNA sequences (NumtS) to identify unique mtDNA reads. The present study identified significant reduction in mtDNA copy number in women with PCOS compared to non-PCOS women. A total of unique 214 prioritized common to rare variants were identified in mtDNA encoded genes, 183 variants in OXPHOS complexes, 14 variants in MT-tRNA and 17 variants in MT-rRNA genes that may be involved in mitochondrial dysfunction in PCOS. Numerous variants were heteroplasmic, pathogenic in nature and occurred in evolutionary conserved region. Heteroplasmic variants were more frequently occurred in MT-CO3 gene. Non-synonymous variants were more than synonymous variants and mainly occurred in OXPHOS complex I and IV. Few variants were found to be associated with diseases in MITOMAP database. The study provides a better understanding towards pathogenesis of PCOS from novel aspects focusing on mitochondrial genetic defects as underlying cause for contributing mitochondrial dysfunction in women with PCOS.},
}

Humans
Female
DNA, Mitochondrial/genetics
High-Throughput Nucleotide Sequencing/methods
*Polycystic Ovary Syndrome/genetics
Mitochondria/genetics
RNA, Transfer
*Genome, Mitochondrial

@article {pmid36574824,
year = {2023},
author = {Baião, GC and Schneider, DI and Miller, WJ and Klasson, L},
title = {Multiple introgressions shape mitochondrial evolutionary history in Drosophila paulistorum and the Drosophila willistoni group.},
journal = {Molecular phylogenetics and evolution},
volume = {180},
number = {},
pages = {107683},
doi = {10.1016/j.ympev.2022.107683},
pmid = {36574824},
issn = {1095-9513},
support = {P 28255/FWF_/Austrian Science Fund FWF/Austria ; },
mesh = {Animals ; *Drosophila/genetics ; Phylogeny ; Nucleic Acid Hybridization ; *Hybridization, Genetic ; },
abstract = {Hybridization and the consequent introgression of genomic elements is an important source of genetic diversity for biological lineages. This is particularly evident in young clades in which hybrid incompatibilities are still incomplete and mixing between species is more likely to occur. Drosophila paulistorum, a representative of the Neotropical Drosophila willistoni subgroup, is a classic model of incipient speciation. The species is divided into six semispecies that show varying degrees of pre- and post-mating incompatibility with each other. In the present study, we investigate the mitochondrial evolutionary history of D. paulistorum and the willistoni subgroup. For that, we perform phylogenetic and comparative analyses of the complete mitochondrial genomes and draft nuclear assemblies of 25 Drosophila lines of the willistoni and saltans species groups. Our results show that the mitochondria of D. paulistorum are polyphyletic and form two non-sister clades that we name α and β. Identification and analyses of nuclear mitochondrial insertions further reveal that the willistoni subgroup has an α-like mitochondrial ancestor and strongly suggest that both the α and β mitochondria of D. paulistorum were acquired through introgression from unknown fly lineages of the willistoni subgroup. We also uncover multiple mitochondrial introgressions across D. paulistorum semispecies and generate novel insight into the evolution of the species.},
}

Animals
*Drosophila/genetics
Phylogeny
Nucleic Acid Hybridization
*Hybridization, Genetic

@article {pmid36601706,
year = {2023},
author = {Kashinina, NV and Lushchekina, AA and Sorokin, PA and Tarasyan, KK and Kholodova, MV},
title = {The modern state of the European saiga population (Saiga tatarica tatarica): mtDNA, DRB3 MHC gene, and microsatellite diversity.},
journal = {Integrative zoology},
volume = {18},
number = {4},
pages = {661-676},
doi = {10.1111/1749-4877.12704},
pmid = {36601706},
issn = {1749-4877},
mesh = {Animals ; *DNA, Mitochondrial/genetics ; *Antelopes/genetics ; Mitochondria/genetics ; Alleles ; },
}

Animals
*DNA, Mitochondrial/genetics
*Antelopes/genetics
Mitochondria/genetics
Alleles

@article {pmid36605941,
year = {2022},
author = {Locatelli, AG and Cenci, S},
title = {Autophagy and longevity: Evolutionary hints from hyper-longevous mammals.},
journal = {Frontiers in endocrinology},
volume = {13},
number = {},
pages = {1085522},
pmid = {36605941},
issn = {1664-2392},
mesh = {Animals ; Mice ; *Longevity/genetics ; *Aging/genetics/metabolism ; Autophagy/physiology ; Saccharomyces cerevisiae ; Mammals ; },
abstract = {Autophagy is a fundamental multi-tasking adaptive cellular degradation and recycling strategy. Following its causal implication in age-related decline, autophagy is currently among the most broadly studied and challenged mechanisms within aging research. Thanks to these efforts, new cellular nodes interconnected with this phylogenetically ancestral pathway and unexpected roles of autophagy-associated genetic products are unveiled daily, yet the history of functional adaptations of autophagy along its evolutive trail is poorly understood and documented. Autophagy is traditionally studied in canonical and research-wise convenient model organisms such as yeast and mice. However, unconventional animal models endowed with extended longevity and exemption from age-related diseases offer a privileged perspective to inquire into the role of autophagy in the evolution of longevity. In this mini review we retrace the appearance and functions evolved by autophagy in eukaryotic cells and its protective contribution in the pathophysiology of aging.},
}

Animals
Mice
*Longevity/genetics
*Aging/genetics/metabolism
Autophagy/physiology
Saccharomyces cerevisiae
Mammals

@article {pmid36605953,
year = {2022},
author = {Wu, CS and Chen, CI and Chaw, SM},
title = {Plastid phylogenomics and plastome evolution in the morning glory family (Convolvulaceae).},
journal = {Frontiers in plant science},
volume = {13},
number = {},
pages = {1061174},
pmid = {36605953},
issn = {1664-462X},
abstract = {Convolvulaceae, the morning glories or bindweeds, is a large family containing species of economic value, including crops, traditional medicines, ornamentals, and vegetables. However, not only are the phylogenetic relationships within this group still debated at the intertribal and intergeneric levels, but also plastid genome (plastome) complexity within Convolvulaceae is not well surveyed. We gathered 78 plastomes representing 17 genera across nine of the 12 Convolvulaceae tribes. Our plastid phylogenomic trees confirm the monophyly of Convolvulaceae, place the genus Jacquemontia within the subfamily Dicranostyloideae, and suggest that the tribe Merremieae is paraphyletic. In contrast, positions of the two genera Cuscuta and Erycibe are uncertain as the bootstrap support of the branches leading to them is moderate to weak. We show that nucleotide substitution rates are extremely variable among Convolvulaceae taxa and likely responsible for the topological uncertainty. Numerous plastomic rearrangements are detected in Convolvulaceae, including inversions, duplications, contraction and expansion of inverted repeats (IRs), and losses of genes and introns. Moreover, integrated foreign DNA of mitochondrial origin was found in the Jacquemontia plastome, adding a rare example of gene transfer from mitochondria to plastids in angiosperms. In the IR of Dichondra, we discovered an extra copy of rpl16 containing a direct repeat of ca. 200 bp long. This repeat was experimentally demonstrated to trigger effective homologous recombination, resulting in the coexistence of intron-containing and -lacking rpl16 duplicates. Therefore, we propose a hypothetical model to interpret intron loss accompanied by invasion of direct repeats at appropriate positions. Our model complements the intron loss model driven by retroprocessing when genes have lost introns but contain abundant RNA editing sites adjacent to former splicing sites.},
}

@article {pmid36610569,
year = {2023},
author = {Ji, X and Tian, Y and Liu, W and Lin, C and He, F and Yang, J and Miao, W and Li, Z},
title = {Mitochondrial characteristics of the powdery mildew genus Erysiphe revealed an extraordinary evolution in protein-coding genes.},
journal = {International journal of biological macromolecules},
volume = {230},
number = {},
pages = {123153},
doi = {10.1016/j.ijbiomac.2023.123153},
pmid = {36610569},
issn = {1879-0003},
mesh = {*Erysiphe ; Phylogeny ; *Ascomycota/genetics ; Plants/microbiology ; Plant Diseases/genetics/microbiology ; },
abstract = {The genus Erysiphe was an obligate parasite causing powdery mildew disease on a wide range of higher plants. However, the knowledge of their mitogenome architecture for lifestyle adaptability was scarce. Here, we assembled the first complete mitogenome (190,559 bp in size) for rubber tree powdery mildew pathogen Erysiphe quercicola. Comparable analysis of the Erysiphe mitogenomes exhibited conserved gene content, genome organization and codon usage bias, but extensive dynamic intron gain/loss events were presented between Erysiphe species. The phylogeny of the Ascomycota species constructed in the phylogenetic analysis showed genetic divergences of the Erysiphe species. Compared with other distant saprophytic and plant pathogenic fungi, Erysiphe had a flat distribution of evolutionary pressures on fungal standard protein-coding genes (PCGs). The Erysiphe PCGs had the highest mean selection pressure. In particular, Erysiphe's cox1, nad1, cob and rps3 genes had the most elevated selection pressures among corresponding PCGs across fungal genera. Altogether, the investigations provided a novel insight into the potential evolutionary pattern of the genus Erysiphe to adapt obligate biotrophic lifestyle and promoted the understanding of the high plasticity and population evolution of fungal mitogenomes.},
}

*Erysiphe
Phylogeny
*Ascomycota/genetics
Plants/microbiology
Plant Diseases/genetics/microbiology

@article {pmid36613565,
year = {2022},
author = {Bottoni, P and Gionta, G and Scatena, R},
title = {Remarks on Mitochondrial Myopathies.},
journal = {International journal of molecular sciences},
volume = {24},
number = {1},
pages = {},
pmid = {36613565},
issn = {1422-0067},
mesh = {Humans ; *Mitochondria/genetics/metabolism ; *Mitochondrial Myopathies/genetics ; Cell Respiration ; Oxidative Phosphorylation ; NAD/metabolism ; Reactive Oxygen Species/metabolism ; },
abstract = {Mitochondrial myopathies represent a heterogeneous group of diseases caused mainly by genetic mutations to proteins that are related to mitochondrial oxidative metabolism. Meanwhile, a similar etiopathogenetic mechanism (i.e., a deranged oxidative phosphorylation and a dramatic reduction of ATP synthesis) reveals that the evolution of these myopathies show significant differences. However, some physiological and pathophysiological aspects of mitochondria often reveal other potential molecular mechanisms that could have a significant pathogenetic role in the clinical evolution of these disorders, such as: i. a deranged ROS production both in term of signaling and in terms of damaging molecules; ii. the severe modifications of nicotinamide adenine dinucleotide (NAD)+/NADH, pyruvate/lactate, and α-ketoglutarate (α-KG)/2- hydroxyglutarate (2-HG) ratios. A better definition of the molecular mechanisms at the basis of their pathogenesis could improve not only the clinical approach in terms of diagnosis, prognosis, and therapy of these myopathies but also deepen the knowledge of mitochondrial medicine in general.},
}

Humans
*Mitochondria/genetics/metabolism
*Mitochondrial Myopathies/genetics
Cell Respiration
Oxidative Phosphorylation
NAD/metabolism
Reactive Oxygen Species/metabolism

@article {pmid36629021,
year = {2023},
author = {Fang, YK and Vaitová, Z and Hampl, V},
title = {A mitochondrion-free eukaryote contains proteins capable of import into an exogenous mitochondrion-related organelle.},
journal = {Open biology},
volume = {13},
number = {1},
pages = {220238},
pmid = {36629021},
issn = {2046-2441},
mesh = {*Eukaryota/metabolism ; *Protozoan Proteins/metabolism ; Organelles/chemistry/metabolism ; Mitochondria/metabolism ; Protein Transport ; },
abstract = {The endobiotic flagellate Monocercomonoides exilis is the only known eukaryote to have lost mitochondria and all its associated proteins in its evolutionary past. This final stage of the mitochondrial evolutionary pathway may serve as a model to explain events at their very beginning such as the initiation of protein import. We have assessed the capability of proteins from this eukaryote to enter emerging mitochondria using a specifically designed in vitro assay. Hydrogenosomes (reduced mitochondria) of Trichomonas vaginalis were incubated with a soluble protein pool derived from a cytosolic fraction of M. exilis, and proteins entering hydrogenosomes were subsequently detected by mass spectrometry. The assay detected 19 specifically and reproducibly imported proteins, and in 14 cases the import was confirmed by the overexpression of their tagged version in T. vaginalis. In most cases, only a small portion of the signal reached the hydrogenosomes, suggesting specific but inefficient transport. Most of these proteins represent enzymes of carbon metabolism, and none exhibited clear signatures of proteins targeted to hydrogenosomes or mitochondria, which is consistent with their inefficient import. The observed phenomenon may resemble a primaeval type of protein import which might play a role in the establishment of the organelle and shaping of its proteome in the initial stages of endosymbiosis.},
}

*Eukaryota/metabolism
*Protozoan Proteins/metabolism
Organelles/chemistry/metabolism
Mitochondria/metabolism
Protein Transport

@article {pmid36632145,
year = {2023},
author = {Borges, DGF and Carvalho, DS and Bomfim, GC and Ramos, PIP and Brzozowski, J and Góes-Neto, A and Andrade, R and El-Hani, C},
title = {On the origin of mitochondria: a multilayer network approach.},
journal = {PeerJ},
volume = {11},
number = {},
pages = {e14571},
pmid = {36632145},
issn = {2167-8359},
mesh = {Phylogeny ; *Mitochondria/genetics ; Biological Evolution ; *Alphaproteobacteria/genetics ; Genes, Mitochondrial ; },
abstract = {BACKGOUND: The endosymbiotic theory is widely accepted to explain the origin of mitochondria from a bacterial ancestor. While ample evidence supports the intimate connection of Alphaproteobacteria to the mitochondrial ancestor, pinpointing its closest relative within sampled Alphaproteobacteria is still an open evolutionary debate. Many different phylogenetic methods and approaches have been used to answer this challenging question, further compounded by the heterogeneity of sampled taxa, varying evolutionary rates of mitochondrial proteins, and the inherent biases in each method, all factors that can produce phylogenetic artifacts. By harnessing the simplicity and interpretability of protein similarity networks, herein we re-evaluated the origin of mitochondria within an enhanced multilayer framework, which is an extension and improvement of a previously developed method.

METHODS: We used a dataset of eight proteins found in mitochondria (N = 6 organisms) and bacteria (N = 80 organisms). The sequences were aligned and resulting identity matrices were combined to generate an eight-layer multiplex network. Each layer corresponded to a protein network, where nodes represented organisms and edges were placed following mutual sequence identity. The Multi-Newman-Girvan algorithm was applied to evaluate community structure, and bifurcation events linked to network partition allowed to trace patterns of divergence between studied taxa.

RESULTS: In our network-based analysis, we first examined the topology of the 8-layer multiplex when mitochondrial sequences disconnected from the main alphaproteobacterial cluster. The resulting topology lent firm support toward an Alphaproteobacteria-sister placement for mitochondria, reinforcing the hypothesis that mitochondria diverged from the common ancestor of all Alphaproteobacteria. Additionally, we observed that the divergence of Rickettsiales was an early event in the evolutionary history of alphaproteobacterial clades.

CONCLUSION: By leveraging complex networks methods to the challenging question of circumscribing mitochondrial origin, we suggest that the entire Alphaproteobacteria clade is the closest relative to mitochondria (Alphaproteobacterial-sister hypothesis), echoing recent findings based on different datasets and methodologies.},
}

Phylogeny
*Mitochondria/genetics
Biological Evolution
*Alphaproteobacteria/genetics
Genes, Mitochondrial

@article {pmid36634192,
year = {2023},
author = {Osipova, E and Barsacchi, R and Brown, T and Sadanandan, K and Gaede, AH and Monte, A and Jarrells, J and Moebius, C and Pippel, M and Altshuler, DL and Winkler, S and Bickle, M and Baldwin, MW and Hiller, M},
title = {Loss of a gluconeogenic muscle enzyme contributed to adaptive metabolic traits in hummingbirds.},
journal = {Science (New York, N.Y.)},
volume = {379},
number = {6628},
pages = {185-190},
doi = {10.1126/science.abn7050},
pmid = {36634192},
issn = {1095-9203},
mesh = {Animals ; *Birds/genetics/metabolism ; Energy Metabolism/genetics ; *Flight, Animal/physiology ; *Gluconeogenesis/genetics ; *Adaptation, Physiological/genetics ; *Fructose-Bisphosphatase/genetics ; *Muscle, Skeletal/enzymology ; },
abstract = {Hummingbirds possess distinct metabolic adaptations to fuel their energy-demanding hovering flight, but the underlying genomic changes are largely unknown. Here, we generated a chromosome-level genome assembly of the long-tailed hermit and screened for genes that have been specifically inactivated in the ancestral hummingbird lineage. We discovered that FBP2 (fructose-bisphosphatase 2), which encodes a gluconeogenic muscle enzyme, was lost during a time period when hovering flight evolved. We show that FBP2 knockdown in an avian muscle cell line up-regulates glycolysis and enhances mitochondrial respiration, coincident with an increased mitochondria number. Furthermore, genes involved in mitochondrial respiration and organization have up-regulated expression in hummingbird flight muscle. Together, these results suggest that FBP2 loss was likely a key step in the evolution of metabolic muscle adaptations required for true hovering flight.},
}

Animals
*Birds/genetics/metabolism
Energy Metabolism/genetics
*Flight, Animal/physiology
*Gluconeogenesis/genetics
*Adaptation, Physiological/genetics
*Fructose-Bisphosphatase/genetics
*Muscle, Skeletal/enzymology

@article {pmid36638953,
year = {2023},
author = {Gnocchi, D and Sabbà, C and Mazzocca, A},
title = {Lactic acid fermentation: A maladaptive mechanism and an evolutionary throwback boosting cancer drug resistance.},
journal = {Biochimie},
volume = {208},
number = {},
pages = {180-185},
doi = {10.1016/j.biochi.2023.01.005},
pmid = {36638953},
issn = {1638-6183},
mesh = {Humans ; *Lactic Acid/metabolism ; Fermentation ; Glycolysis ; Mitochondria/metabolism ; *Neoplasms/drug therapy/genetics/metabolism ; Drug Resistance, Neoplasm/genetics ; },
abstract = {After four decades of research primarily focused on tumour genetics, the importance of metabolism in tumour biology is receiving renewed attention. Cancer cells undergo energy, biosynthetic and metabolic rewiring, which involves several pathways with a prevalent change from oxidative phosphorylation (OXPHOS) to lactic acid fermentation, known as the Warburg effect. During carcinogenesis, microenvironmental changes can trigger the transition from OXPHOS to lactic acid fermentation, an ancient form of energy supply, mimicking the behaviour of certain anaerobic unicellular organisms according to "atavistic" models of cancer. However, the role of this transition as a mechanism of cancer drug resistance is unclear. Here, we hypothesise that the metabolic rewiring of cancer cells to fermentation can be triggered, enhanced, and sustained by exposure to chronic or high-dose chemotherapy, thereby conferring resistance to drug therapy. We try to expand on the idea that metabolic reprogramming from OXPHOS to lactate fermentation in drug-resistant tumour cells occurs as a general phenotypic mechanism in any type of cancer, regardless of tumour cell heterogeneity, biodiversity, and genetic characteristics. This metabolic response may therefore represent a common feature in cancer biology that could be exploited for therapeutic purposes to overcome chemotherapy resistance, which is currently a major challenge in cancer treatment.},
}

Humans
*Lactic Acid/metabolism
Fermentation
Glycolysis
Mitochondria/metabolism
*Neoplasms/drug therapy/genetics/metabolism
Drug Resistance, Neoplasm/genetics

@article {pmid36644898,
year = {2023},
author = {He, W and Xiang, K and Chen, C and Wang, J and Wu, Z},
title = {Master graph: an essential integrated assembly model for the plant mitogenome based on a graph-based framework.},
journal = {Briefings in bioinformatics},
volume = {24},
number = {1},
pages = {},
doi = {10.1093/bib/bbac522},
pmid = {36644898},
issn = {1477-4054},
mesh = {Animals ; *Genome, Mitochondrial ; DNA, Mitochondrial/genetics ; Biological Evolution ; Mitochondria/genetics ; Plants/genetics ; Phylogeny ; },
abstract = {Unlike the typical single circular structure of most animal mitochondrial genomes (mitogenome), the drastic structural variation of plant mitogenomes is a result of a mixture of molecules of various sizes and structures. Obtaining the full panoramic plant mitogenome is still considered a roadblock in evolutionary biology. In this study, we developed a graph-based sequence assembly toolkit (GSAT) to construct the pan-structural landscape of plant mitogenome with high-quality mitochondrial master graphs (MMGs) for model species including rice (Oryza sativa) and thale cress (Arabidopsis thaliana). The rice and thale cress MMGs have total lengths of 346 562 and 358 041 bp, including 9 and 6 contigs and 12 and 8 links, respectively, and could be further divided into 6 and 3 minimum master circles and 4 and 2 minimum secondary circles separately. The nuclear mitochondrial DNA segments (NUMTs) in thale cress strongly affected the frequency evaluation of the homologous structures in the mitogenome, while the effects of NUMTs in rice were relatively weak. The mitochondrial plastid DNA segments (MTPTs) in both species had no effects on the assessment of the MMGs. All potential recombinant structures were evaluated, and the findings revealed that all, except for nuclear-homologous structures, MMG structures are present at a much higher frequency than non-MMG structures are. Investigations of potential circular and linear molecules further supported multiple dominant structures in the mitogenomes and could be completely summarized in the MMG. Our study provided an efficient and accurate model for assembling and applying graph-based plant mitogenomes to assess their pan-structural variations.},
}

Animals
*Genome, Mitochondrial
DNA, Mitochondrial/genetics
Biological Evolution
Mitochondria/genetics
Plants/genetics
Phylogeny

@article {pmid36646908,
year = {2023},
author = {Muñoz-Gómez, SA},
title = {Energetics and evolution of anaerobic microbial eukaryotes.},
journal = {Nature microbiology},
volume = {8},
number = {2},
pages = {197-203},
pmid = {36646908},
issn = {2058-5276},
mesh = {*Eukaryota ; Anaerobiosis ; *Mitochondria/metabolism ; Eukaryotic Cells/metabolism ; Fermentation ; },
abstract = {Mitochondria and aerobic respiration have been suggested to be required for the evolution of eukaryotic cell complexity. Aerobic respiration is several times more energetically efficient than fermentation. Moreover, aerobic respiration occurs at internalized mitochondrial membranes that are not constrained by a sublinear scaling with cell volume. However, diverse and complex anaerobic eukaryotes (for example, free-living and parasitic unicellular, and even small multicellular, eukaryotes) that exclusively rely on fermentation for energy generation have evolved repeatedly from aerobic ancestors. How do fermenting eukaryotes maintain their cell volumes and complexity while relying on such a low energy-yielding process? Here I propose that reduced rates of ATP generation in fermenting versus respiring eukaryotes are compensated for by longer cell cycles that satisfy lifetime energy demands. A literature survey and growth efficiency calculations show that fermenting eukaryotes divide approximately four to six times slower than aerobically respiring counterparts with similar cell volumes. Although ecological advantages such as competition avoidance offset lower growth rates and yields in the short term, fermenting eukaryotes inevitably have fewer physiological and ecological possibilities, which ultimately constrain their long-term evolutionary trajectories.},
}

*Eukaryota
Anaerobiosis
*Mitochondria/metabolism
Eukaryotic Cells/metabolism
Fermentation

@article {pmid36648250,
year = {2023},
author = {Graham, AM and Barreto, FS},
title = {Myxozoans (Cnidaria) do not Retain Key Oxygen-Sensing and Homeostasis Toolkit Genes.},
journal = {Genome biology and evolution},
volume = {15},
number = {1},
pages = {},
pmid = {36648250},
issn = {1759-6653},
mesh = {Animals ; *Cnidaria/metabolism ; Oxygen/metabolism ; *Myxozoa/genetics ; Hypoxia/genetics ; Homeostasis ; Hypoxia-Inducible Factor 1, alpha Subunit ; },
abstract = {For aerobic organisms, both the hypoxia-inducible factor pathway and the mitochondrial genomes are key players in regulating oxygen homeostasis. Recent work has suggested that these mechanisms are not as highly conserved as previously thought, prompting more surveys across animal taxonomic levels, which would permit testing of hypotheses about the ecological conditions facilitating evolutionary loss of such genes. The Phylum Cnidaria is known to harbor wide variation in mitochondrial chromosome morphology, including an extreme example, in the Myxozoa, of mitochondrial genome loss. Because myxozoans are obligate endoparasites, frequently encountering hypoxic environments, we hypothesize that variation in environmental oxygen availability could be a key determinant in the evolution of metabolic gene networks associated with oxygen-sensing, hypoxia-response, and energy production. Here, we surveyed genomes and transcriptomes across 46 cnidarian species for the presence of HIF pathway members, as well as for an assortment of hypoxia, mitochondrial, and stress-response toolkit genes. We find that presence of the HIF pathway, as well as number of genes associated with mitochondria, hypoxia, and stress response, do not vary in parallel to mitochondrial genome morphology. More interestingly, we uncover evidence that myxozoans have lost the canonical HIF pathway repression machinery, potentially altering HIF pathway functionality to work under the specific conditions of their parasitic lifestyles. In addition, relative to other cnidarians, myxozoans show loss of large proportions of genes associated with the mitochondrion and involved in response to hypoxia and general stress. Our results provide additional evidence that the HIF regulatory machinery is evolutionarily labile and that variations in the canonical system have evolved in many animal groups.},
}

Animals
*Cnidaria/metabolism
Oxygen/metabolism
*Myxozoa/genetics
Hypoxia/genetics
Homeostasis
Hypoxia-Inducible Factor 1, alpha Subunit

@article {pmid36651963,
year = {2023},
author = {Moreira, F and Arenas, M and Videira, A and Pereira, F},
title = {Evolution of TOP1 and TOP1MT Topoisomerases in Chordata.},
journal = {Journal of molecular evolution},
volume = {91},
number = {2},
pages = {192-203},
pmid = {36651963},
issn = {1432-1432},
mesh = {Animals ; *DNA, Mitochondrial/genetics ; *Chordata/genetics ; DNA Topoisomerases, Type I/genetics/chemistry/metabolism ; Mitochondria/genetics ; Cell Nucleus/genetics ; },
abstract = {Type IB topoisomerases relax the torsional stress associated with DNA metabolism in the nucleus and mitochondria and constitute important molecular targets of anticancer drugs. Vertebrates stand out among eukaryotes by having two Type IB topoisomerases acting specifically in the nucleus (TOP1) and mitochondria (TOP1MT). Despite their major importance, the origin and evolution of these paralogues remain unknown. Here, we examine the molecular evolutionary processes acting on both TOP1 and TOP1MT in Chordata, taking advantage of the increasing number of available genome sequences. We found that both TOP1 and TOP1MT evolved under strong purifying selection, as expected considering their essential biological functions. Critical active sites, including those associated with resistance to anticancer agents, were found particularly conserved. However, TOP1MT presented a higher rate of molecular evolution than TOP1, possibly related with its specialized activity on the mitochondrial genome and a less critical role in cells. We could place the duplication event that originated the TOP1 and TOP1MT paralogues early in the radiation of vertebrates, most likely associated with the first round of vertebrate tetraploidization (1R). Moreover, our data suggest that cyclostomes present a specialized mitochondrial Type IB topoisomerase. Interestingly, we identified two missense mutations replacing amino acids in the Linker region of TOP1MT in Neanderthals, which appears as a rare event when comparing the genome of both species. In conclusion, TOP1 and TOP1MT differ in their rates of evolution, and their evolutionary histories allowed us to better understand the evolution of chordates.},
}

Animals
*DNA, Mitochondrial/genetics
*Chordata/genetics
DNA Topoisomerases, Type I/genetics/chemistry/metabolism
Mitochondria/genetics
Cell Nucleus/genetics

@article {pmid36656997,
year = {2023},
author = {Opazo, JC and Vandewege, MW and Hoffmann, FG and Zavala, K and Meléndez, C and Luchsinger, C and Cavieres, VA and Vargas-Chacoff, L and Morera, FJ and Burgos, PV and Tapia-Rojas, C and Mardones, GA},
title = {How Many Sirtuin Genes Are Out There? Evolution of Sirtuin Genes in Vertebrates With a Description of a New Family Member.},
journal = {Molecular biology and evolution},
volume = {40},
number = {2},
pages = {},
pmid = {36656997},
issn = {1537-1719},
mesh = {Animals ; *Sirtuins/genetics ; *Sirtuin 3/genetics ; Evolution, Molecular ; Vertebrates/genetics ; Phylogeny ; Mammals ; },
abstract = {Studying the evolutionary history of gene families is a challenging and exciting task with a wide range of implications. In addition to exploring fundamental questions about the origin and evolution of genes, disentangling their evolution is also critical to those who do functional/structural studies to allow a deeper and more precise interpretation of their results in an evolutionary context. The sirtuin gene family is a group of genes that are involved in a variety of biological functions mostly related to aging. Their duplicative history is an open question, as well as the definition of the repertoire of sirtuin genes among vertebrates. Our results show a well-resolved phylogeny that represents an improvement in our understanding of the duplicative history of the sirtuin gene family. We identified a new sirtuin gene family member (SIRT3.2) that was apparently lost in the last common ancestor of amniotes but retained in all other groups of jawed vertebrates. According to our experimental analyses, elephant shark SIRT3.2 protein is located in mitochondria, the overexpression of which leads to an increase in cellular levels of ATP. Moreover, in vitro analysis demonstrated that it has deacetylase activity being modulated in a similar way to mammalian SIRT3. Our results indicate that there are at least eight sirtuin paralogs among vertebrates and that all of them can be traced back to the last common ancestor of the group that existed between 676 and 615 millions of years ago.},
}

Animals
*Sirtuins/genetics
*Sirtuin 3/genetics
Evolution, Molecular
Vertebrates/genetics
Phylogeny
Mammals

@article {pmid36657651,
year = {2023},
author = {Moreno-Carmona, M and Montaña-Lozano, P and Prada Quiroga, CF and Baeza, JA},
title = {Comparative analysis of mitochondrial genomes reveals family-specific architectures and molecular features in scorpions (Arthropoda: Arachnida: Scorpiones).},
journal = {Gene},
volume = {859},
number = {},
pages = {147189},
doi = {10.1016/j.gene.2023.147189},
pmid = {36657651},
issn = {1879-0038},
mesh = {Humans ; Animals ; Scorpions/genetics ; *Arachnida/genetics ; *Genome, Mitochondrial/genetics ; Phylogeny ; Mitochondria/genetics ; RNA, Transfer/genetics ; },
abstract = {Scorpions are a group of arachnids with great evolutionary success that comprise more than 2,000 described species. Mitochondrial genomes have been little studied in this clade. We describe and compare different scorpion mitochondrial genomes and analyze their architecture and molecular characteristics. We assembled eight new scorpion mitochondrial genomes from transcriptomic datasets, annotated them, predicted the secondary structures of tRNAs, and compared the nucleotide composition, codon usage, and relative synonymous codon usage of 16 complete scorpion mitochondrial genomes. Lastly, we provided a phylogeny based on all mitochondrial protein coding genes. We characterized the mitogenomes in detail and reported particularities such as dissimilar synteny in the family Buthidae compared to other scorpions, unusual tRNA secondary structures, and unconventional start and stop codons in all scorpions. Our comparative analysis revealed that scorpion mitochondrial genomes exhibit different architectures and features depending on taxonomic identity. We highlight the parvorder Buthida, particularly the family Buthidae, as it invariably exhibited different mitogenome features such as synteny, codon usage, and AT-skew compared to the parvorder Iurida that included the rest of the scorpion families we analyzed in this study. Our results provide a better understanding of the evolution of mitogenome features and phylogenetic relationships in scorpions.},
}

Humans
Animals
Scorpions/genetics
*Arachnida/genetics
*Genome, Mitochondrial/genetics
Phylogeny
Mitochondria/genetics
RNA, Transfer/genetics

@article {pmid36659315,
year = {2017},
author = {Ye, LQ and Zhao, H and Zhou, HJ and Ren, XD and Liu, LL and Otecko, NO and Wang, ZB and Yang, MM and Zeng, L and Hu, XT and Yao, YG and Zhang, YP and Wu, DD},
title = {The RNA editome of Macaca mulatta and functional characterization of RNA editing in mitochondria.},
journal = {Science bulletin},
volume = {62},
number = {12},
pages = {820-830},
doi = {10.1016/j.scib.2017.05.021},
pmid = {36659315},
issn = {2095-9281},
abstract = {RNA editing was first discovered in mitochondrial RNA molecular. However, whether adenosine-to-inosine (A-to-I) RNA editing has functions in nuclear genes involved in mitochondria remains elusive. Here, we retrieved 707,246 A-to-I RNA editing sites in Macaca mulatta leveraging massive transcriptomes of 30 different tissues and genomes of nine tissues, together with the reported data, and found that A-to-I RNA editing occurred frequently in nuclear genes that have functions in mitochondria. The mitochondrial structure, the level of ATP production, and the expression of some key genes involved in mitochondrial function were dysregulated after knocking down the expression of ADAR1 and ADAR2, the key genes encoding the enzyme responsible for RNA editing. When investigating dynamic changes of RNA editing during brain development, an amino-acid-changing RNA editing site (I234/V) in MFN1, a mediator of mitochondrial fusion, was identified to be significantly correlated with age, and could influence the function of MFN1. When studying transcriptomes of brain disorder, we found that dysregulated RNA editing sites in autism were also enriched within genes having mitochondrial functions. These data indicated that RNA editing had a significant function in mitochondria via their influence on nuclear genes.},
}

@article {pmid36670920,
year = {2022},
author = {Cruz-Gregorio, A and Aranda-Rivera, AK and Aparicio-Trejo, OE and Medina-Campos, ON and Sciutto, E and Fragoso, G and Pedraza-Chaverri, J},
title = {GK-1 Induces Oxidative Stress, Mitochondrial Dysfunction, Decreased Membrane Potential, and Impaired Autophagy Flux in a Mouse Model of Breast Cancer.},
journal = {Antioxidants (Basel, Switzerland)},
volume = {12},
number = {1},
pages = {},
pmid = {36670920},
issn = {2076-3921},
support = {IN218822//National Autonomous University of Mexico/ ; IN200922//National Autonomous University of Mexico/ ; 302961//Consejo Nacional de Ciencia y Tecnología/ ; A1-S-7495//Consejo Nacional de Ciencia y Tecnología/ ; 5000-9105//Programa de Apoyo a la Investigación y el Posgrado (PAIP), Facultd de Química, UNAM/ ; },
abstract = {Breast cancer (BC) is the second most common cancer worldwide in women. During the last decades, the mortality due to breast cancer has progressively decreased due to early diagnosis and the emergence of more effective new treatments. However, human epidermal growth factor receptor 2 (HER2) and triple-negative breast cancer (TNBC) remain with poor prognoses. In our research group, we are proposing the GK-1 immunomodulatory peptide as a new alternative for immunotherapy of these aggressive tumors. GK-1 reduced the growth rate of established tumors and effectively reduced lung metastasis in the 4T1 experimental murine model of breast cancer. Herein, the effect of GK-1 on the redox state, mitochondrial metabolism, and autophagy of triple-negative tumors that can be linked to cancer evolution was studied. GK-1 decreased catalase activity, reduced glutathione (GSH) content and GSH/oxidized glutathione (GSSG) ratio while increased hydrogen peroxide (H2O2) production, GSSG, and protein carbonyl content, inducing oxidative stress (OS) in tumoral tissues. This imbalance between reactive oxygen species (ROS) and antioxidants was related to mitochondrial dysfunction and uncoupling, characterized by reduced mitochondrial respiratory parameters and dissipation of mitochondrial membrane potential (ΔΨm), respectively. Furthermore, GK-1 likely affected autophagy flux, confirmed by elevated levels of p62, a marker of autophagy flux. Overall, the induction of OS, dysfunction, and uncoupling of the mitochondria and the reduction of autophagy could be molecular mechanisms that underlie the reduction of the 4T1 breast cancer induced by GK-1.},
}

@article {pmid36671555,
year = {2023},
author = {Righetto, I and Gasparotto, M and Casalino, L and Vacca, M and Filippini, F},
title = {Exogenous Players in Mitochondria-Related CNS Disorders: Viral Pathogens and Unbalanced Microbiota in the Gut-Brain Axis.},
journal = {Biomolecules},
volume = {13},
number = {1},
pages = {},
pmid = {36671555},
issn = {2218-273X},
mesh = {Humans ; *COVID-19 ; SARS-CoV-2 ; Brain-Gut Axis ; *Central Nervous System Diseases ; *Gastrointestinal Microbiome ; Mitochondria ; },
abstract = {Billions of years of co-evolution has made mitochondria central to the eukaryotic cell and organism life playing the role of cellular power plants, as indeed they are involved in most, if not all, important regulatory pathways. Neurological disorders depending on impaired mitochondrial function or homeostasis can be caused by the misregulation of "endogenous players", such as nuclear or cytoplasmic regulators, which have been treated elsewhere. In this review, we focus on how exogenous agents, i.e., viral pathogens, or unbalanced microbiota in the gut-brain axis can also endanger mitochondrial dynamics in the central nervous system (CNS). Neurotropic viruses such as Herpes, Rabies, West-Nile, and Polioviruses seem to hijack neuronal transport networks, commandeering the proteins that mitochondria typically use to move along neurites. However, several neurological complications are also associated to infections by pandemic viruses, such as Influenza A virus and SARS-CoV-2 coronavirus, representing a relevant risk associated to seasonal flu, coronavirus disease-19 (COVID-19) and "Long-COVID". Emerging evidence is depicting the gut microbiota as a source of signals, transmitted via sensory neurons innervating the gut, able to influence brain structure and function, including cognitive functions. Therefore, the direct connection between intestinal microbiota and mitochondrial functions might concur with the onset, progression, and severity of CNS diseases.},
}

Humans
*COVID-19
SARS-CoV-2
Brain-Gut Axis
*Central Nervous System Diseases
*Gastrointestinal Microbiome
Mitochondria

@article {pmid36702320,
year = {2023},
author = {Buonvicino, D and Ranieri, G and Guasti, D and Pistolesi, A and La Rocca, AI and Rapizzi, E and Chiarugi, A},
title = {Early derangement of axonal mitochondria occurs in a mouse model of progressive but not relapsing-remitting multiple sclerosis.},
journal = {Neurobiology of disease},
volume = {178},
number = {},
pages = {106015},
doi = {10.1016/j.nbd.2023.106015},
pmid = {36702320},
issn = {1095-953X},
mesh = {Mice ; Female ; Animals ; *Multiple Sclerosis/pathology ; Hydrogen Peroxide/metabolism ; Mice, Inbred NOD ; *Encephalomyelitis, Autoimmune, Experimental/pathology ; Spinal Cord/pathology ; *Multiple Sclerosis, Relapsing-Remitting/metabolism ; Axons/pathology ; Mitochondria/metabolism ; DNA, Mitochondrial/metabolism ; },
abstract = {INTRODUCTION: Derangement of axonal mitochondrial bioenergetics occurs during progressive multiple sclerosis (PMS). However, whether this is a delayed epiphenomenon or an early causative event of disease progression waits to be understood. Answering this question might further our knowledge of mechanisms underlying neurobiology of PMS and related therapy.

METHODS: MOG35-55-immunized NOD and PLP139-151-immunized SJL female mice were adopted as models of progressive or relapsing-remitting experimental autoimmune encephalomyelitis (EAE), respectively. Multiple parameters of mitochondrial homeostasis were analyzed in the mouse spinal cord during the early asymptomatic stage, also evaluating the effects of scavenging mitochondrial reactive oxygen species with Mito-TEMPO.

RESULTS: Almost identical lumbar spinal cord immune infiltrates consisting of Th1 cells and neutrophils without B and Th17 lymphocytes occurred early upon immunization in both mouse strains. Still, only NOD mice showed axon-restricted dysregulation of mitochondrial homeostasis, with reduced mtDNA contents and increased cristae area. Increased expression of mitochondrial respiratory complex subunits Nd2, Cox1, Atp5d, Sdha also exclusively occurred in lumbar spinal cord of NOD and not SJL mice. Accordingly, in this region genes regulating mitochondrial morphology (Opa1, Mfn1, Mfn2 and Atp5j2) and mitochondriogenesis (Pgc1α, Foxo, Hif-1α and Nrf2) were induced early upon immunization. A reduced extent of mitochondrial derangement occurred in the thoracic spinal cord. Notably, the mitochondrial radical scavenger Mito-TEMPO reduced H2O2 content and prevented both mtDNA depletion and cristae remodeling, having no effects on dysregulation of mitochondrial transcriptome.

DISCUSSION: We provide here the first evidence that axonal-restricted derangement of mitochondrial homeostasis already occurs during the asymptomatic state exclusively in a mouse model of PMS. Data further our understanding of mechanisms related to EAE progression, and point to very early axonal mitochondrial dysfunction as central to the neuropathogenesis of MS evolution.},
}

Mice
Female
Animals
*Multiple Sclerosis/pathology
Hydrogen Peroxide/metabolism
Mice, Inbred NOD
*Encephalomyelitis, Autoimmune, Experimental/pathology
Spinal Cord/pathology
*Multiple Sclerosis, Relapsing-Remitting/metabolism
Axons/pathology
Mitochondria/metabolism
DNA, Mitochondrial/metabolism

@article {pmid36717448,
year = {2022},
author = {Shilovsky, GA and Putyatina, TS and Markov, AV},
title = {Evolution of Longevity as a Species-Specific Trait in Mammals.},
journal = {Biochemistry. Biokhimiia},
volume = {87},
number = {12},
pages = {1579-1599},
doi = {10.1134/S0006297922120148},
pmid = {36717448},
issn = {1608-3040},
mesh = {Animals ; *Longevity ; *Antioxidants ; Reproducibility of Results ; Aging/metabolism ; Mammals ; },
abstract = {From the evolutionary point of view, the priority problem for an individual is not longevity, but adaptation to the environment associated with the need for survival, food supply, and reproduction. We see two main vectors in the evolution of mammals. One is a short lifespan and numerous offspring ensuring reproductive success (r-strategy). The other one is development of valuable skills in order compete successfully (K-strategy). Species with the K-strategy should develop and enhance specific systems (anti-aging programs) aimed at increasing the reliability and adaptability, including lifespan. These systems are signaling cascades that provide cell repair and antioxidant defense. Hence, any arbitrarily selected long-living species should be characterized by manifestation to a different extent of the longevity-favoring traits (e.g., body size, brain development, sociality, activity of body repair and antioxidant defense systems, resistance to xenobiotics and tumor formation, presence of neotenic traits). Hereafter, we will call a set of such traits as the gerontological success of a species. Longevity is not equivalent to the evolutionary or reproductive success. This difference between these phenomena reaches its peak in mammals due to the development of endothermy and cephalization associated with the cerebral cortex expansion, which leads to the upregulated production of oxidative radicals by the mitochondria (and, consequently, accelerated aging), increase in the number of non-dividing differentiated cells, accumulation of the age-related damage in these cells, and development of neurodegenerative diseases. The article presents mathematical indicators used to assess the predisposition to longevity in different species (including the standard mortality rate and basal metabolic rate, as well as their derivatives). The properties of the evolution of mammals (including the differences between modern mammals and their ancestral forms) are also discussed.},
}

Animals
*Longevity
*Antioxidants
Reproducibility of Results
Aging/metabolism
Mammals

@article {pmid36720422,
year = {2023},
author = {Baltazar-Soares, M and Karell, P and Wright, D and Nilsson, JÅ and Brommer, JE},
title = {Bringing to light nuclear-mitochondrial insertions in the genomes of nocturnal predatory birds.},
journal = {Molecular phylogenetics and evolution},
volume = {181},
number = {},
pages = {107722},
doi = {10.1016/j.ympev.2023.107722},
pmid = {36720422},
issn = {1095-9513},
mesh = {Animals ; Phylogeny ; *Mitochondria/genetics ; DNA, Mitochondrial/genetics ; *Genome, Mitochondrial ; Birds/genetics ; Sequence Analysis, DNA ; Cell Nucleus/genetics ; },
abstract = {Mito-nuclear insertions, or NUMTs, relate to genetic material of mitochondrial origin that have been transferred to the nuclear DNA molecule. The increasing amounts of genomic data currently being produced presents an opportunity to investigate this type of patterns in genome evolution of non-model organisms. Identifying NUMTs across a range of closely related taxa allows one to generalize patterns of insertion and maintenance in autosomes, which is ultimately relevant to the understanding of genome biology and evolution. Here we collected existing pairwise genome-mitogenome data of the order Strigiformes, a group that includes all the nocturnal bird predators. We identified NUMTs by applying percent similarity thresholds after blasting mitochondrial genomes against nuclear genome assemblies. We identified NUMTsin all genomes with numbers ranging from 4 in Bubo bubo to 24 in Ciccaba nigrolineata. Statistical analyses revealed NUMT size to negatively correlate with NUMT's sequence similarity to with original mtDNA region. Lastly, characterizing these nuclear insertions of mitochondrial origin in a comparative genomics framework produced variable phylogenetic patterns, suggesting in some cases that insertions might pre-date speciation events within Strigiformes.},
}

Animals
Phylogeny
*Mitochondria/genetics
DNA, Mitochondrial/genetics
*Genome, Mitochondrial
Birds/genetics
Sequence Analysis, DNA
Cell Nucleus/genetics

@article {pmid36722300,
year = {2023},
author = {Russo, MT and Santin, A and Zuccarotto, A and Leone, S and Palumbo, A and Ferrante, MI and Castellano, I},
title = {The first genetic engineered system for ovothiol biosynthesis in diatoms reveals a mitochondrial localization for the sulfoxide synthase OvoA.},
journal = {Open biology},
volume = {13},
number = {2},
pages = {220309},
pmid = {36722300},
issn = {2046-2441},
mesh = {*Diatoms/genetics ; Genetic Engineering ; Methylhistidines ; Biological Evolution ; },
abstract = {Diatoms represent one of the most abundant groups of microalgae in the ocean and are responsible for approximately 20% of photosynthetically fixed CO2 on Earth. Due to their complex evolutionary history and ability to adapt to different environments, diatoms are endowed with striking molecular biodiversity and unique metabolic activities. Their high growth rate and the possibility to optimize their biomass make them very promising 'biofactories' for biotechnological applications. Among bioactive compounds, diatoms can produce ovothiols, histidine-derivatives, endowed with unique antioxidant and anti-inflammatory properties, and occurring in many marine invertebrates, bacteria and pathogenic protozoa. However, the functional role of ovothiols biosynthesis in organisms remains almost unexplored. In this work, we have characterized the thiol fraction of Phaeodactylum tricornutum, providing the first evidence of the presence of ovothiol B in pennate diatoms. We have used P. tricornutum to overexpress the 5-histidylcysteine sulfoxide synthase ovoA, the gene encoding the key enzyme involved in ovothiol biosynthesis and we have discovered that OvoA localizes in the mitochondria, a finding that uncovers new concepts in cellular redox biochemistry. We have also obtained engineered biolistic clones that can produce higher amount of ovothiol B compared to wild-type cells, suggesting a new strategy for the eco-sustainable production of these molecules.},
}

*Diatoms/genetics
Genetic Engineering
Methylhistidines
Biological Evolution

@article {pmid36727263,
year = {2023},
author = {Blair, C},
title = {Organellar DNA continues to provide a rich source of information in the genomics era.},
journal = {Molecular ecology},
volume = {32},
number = {9},
pages = {2144-2150},
doi = {10.1111/mec.16872},
pmid = {36727263},
issn = {1365-294X},
mesh = {Phylogeny ; *Information Sources ; *DNA, Mitochondrial/genetics ; Genomics ; Mitochondria/genetics ; DNA, Chloroplast/genetics ; Sequence Analysis, DNA ; },
abstract = {The genomics revolution continues to change how ecologists and evolutionary biologists study the evolution and maintenance of biodiversity. It is now easier than ever to generate large molecular data sets consisting of hundreds to thousands of independently evolving nuclear loci to estimate a suite of evolutionary and demographic parameters. However, any inferences will be incomplete or inaccurate if incorrect taxonomic identities and perpetuated throughout the analytical pipeline. Due to decades of research and comprehensive online databases, sequencing and analysis of mitochondrial DNA (mtDNA), chloroplast DNA (cpDNA) and select nuclear genes can provide researchers with a cost effective and simple means to verify the species identity of samples prior to subsequent phylogeographic and population genomic analysis. The addition of these sequences to genomic studies can also shed light on other important evolutionary questions such as explanations for gene tree-species tree discordance, species limits, sex-biased dispersal patterns, adaptation, and mtDNA introgression. Although the mtDNA and cpDNA genomes often should not be used exclusively to make historical inferences given their well-known limitations, the addition of these data to modern genomic studies adds little cost and effort while simultaneously providing a wealth of useful data that can have significant implications for both basic and applied research.},
}

Phylogeny
*Information Sources
*DNA, Mitochondrial/genetics
Genomics
Mitochondria/genetics
DNA, Chloroplast/genetics
Sequence Analysis, DNA

@article {pmid36732530,
year = {2023},
author = {Silva, MC and Catry, P and Bried, J and Kawakami, K and Flint, E and Granadeiro, JP},
title = {Contrasting patterns of population structure of Bulwer's petrel (Bulweria bulwerii) between oceans revealed by statistical phylogeography.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {1939},
pmid = {36732530},
issn = {2045-2322},
mesh = {Animals ; Phylogeography ; Oceans and Seas ; *Birds/genetics ; Pacific Ocean ; *Mitochondria/genetics ; DNA, Mitochondrial/genetics ; Phylogeny ; Genetic Variation ; },
abstract = {The patterns of population divergence of mid-latitude marine birds are impacted by only a few biogeographic barriers to dispersal and the effect of intrinsic factors, such as fidelity to natal colonies or wintering grounds, may become more conspicuous. Here we describe, for the first time, the phylogeographic patterns and historical demography of Bulwer's petrel Bulweria bulwerii and provide new insights regarding the drivers of species diversification in the marine environment. We sampled Bulwer's petrels from the main breeding colonies and used a statistical phylogeography approach based on surveying nuclear and mitochondrial loci (~ 9100 bp) to study its mechanisms of global diversification. We uncovered three highly differentiated groups including the Western Pacific, the Central Pacific and the Atlantic. The older divergence occurred within the Pacific Ocean, ca. 850,000 ya, and since then the W Pacific group has been evolving in isolation. Conversely, divergence between the Central Pacific and Atlantic populations occurred within the last 200,000 years. While the Isthmus of Panama is important in restricting gene flow between oceans in Bulwer's petrels, the deepest phylogeographic break is within the Pacific Ocean, where oceanographic barriers are key in driving and maintaining the remarkable structure found in this highly mobile seabird. This is in contrast with the Atlantic, where no structure was detected. Further data will provide insights regarding the extent of lineage divergence of Bulwer's petrels in the Western Pacific.},
}

Animals
Phylogeography
Oceans and Seas
*Birds/genetics
Pacific Ocean
*Mitochondria/genetics
DNA, Mitochondrial/genetics
Phylogeny
Genetic Variation

@article {pmid36734850,
year = {2023},
author = {Nord, A and Chamkha, I and Elmér, E},
title = {A whole blood approach improves speed and accuracy when measuring mitochondrial respiration in intact avian blood cells.},
journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology},
volume = {37},
number = {3},
pages = {e22766},
doi = {10.1096/fj.202201749R},
pmid = {36734850},
issn = {1530-6860},
mesh = {Animals ; *Mitochondria/metabolism ; *Cell Respiration ; Respiration ; Birds ; Blood Cells ; },
abstract = {Understanding mitochondrial biology and pathology is key to understanding the evolution of animal form and function. However, mitochondrial measurement often involves invasive, or even terminal, sampling, which can be difficult to reconcile in wild models or longitudinal studies. Non-mammal vertebrates contain mitochondria in their red blood cells, which can be exploited for minimally invasive mitochondrial measurement. Several recent bird studies have measured mitochondrial function using isolated blood cells. Isolation adds time in the laboratory and might be associated with physiological complications. We developed and validated a protocol to measure mitochondrial respiration in bird whole blood. Endogenous respiration was comparable between isolated blood cells and whole blood. However, respiration towards oxidative phosphorylation was higher in whole blood, and whole blood mitochondria were better coupled and had higher maximum working capacity. Whole blood measurement was also more reproducible than measurement on isolated cells for all traits considered. Measurements were feasible over a 10-fold range of sample volumes, although both small and large volumes were associated with changes to respiratory traits. The protocol was compatible with long-term storage: after 24 h at 5°C without agitation, all respiration traits but maximum working capacity remained unchanged, the latter decreasing by 14%. Our study suggests that whole blood measurement provides faster, more reproducible, and more biologically and physiologically relevant (mitochondrial integrity) assessment of mitochondrial respiration. We recommend future studies to take a whole blood approach unless specific circumstances require the use of isolated blood cells.},
}

Animals
*Mitochondria/metabolism
*Cell Respiration
Respiration
Birds
Blood Cells

@article {pmid36737563,
year = {2023},
author = {Rottenberg, H},
title = {The evolution of the human mitochondrial bc1 complex- adaptation for reduced rate of superoxide production?.},
journal = {Journal of bioenergetics and biomembranes},
volume = {55},
number = {1},
pages = {15-31},
pmid = {36737563},
issn = {1573-6881},
mesh = {Humans ; Cattle ; Animals ; Mice ; Sheep ; *Ubiquinone/chemistry/metabolism ; *Superoxides/metabolism ; Cytochromes b/metabolism ; Cytochromes c1/metabolism ; Oxidation-Reduction ; Primates/metabolism ; Electron Transport Complex III/metabolism ; Electron Transport ; },
abstract = {The mitochondrial bc1 complex is a major source of mitochondrial superoxide. While bc1-generated superoxide plays a beneficial signaling role, excess production of superoxide lead to aging and degenerative diseases. The catalytic core of bc1 comprises three peptides -cytochrome b, Fe-S protein, and cytochrome c1. All three core peptides exhibit accelerated evolution in anthropoid primates. It has been suggested that the evolution of cytochrome b in anthropoids was driven by a pressure to reduce the production of superoxide. In humans, the bc1 core peptides exhibit anthropoid-specific substitutions that are clustered near functionally critical sites that may affect the production of superoxide. Here we compare the high-resolution structures of bovine, mouse, sheep and human bc1 to identify structural changes that are associated with human-specific substitutions. Several cytochrome b substitutions in humans alter its interactions with other subunits. Most significantly, there is a cluster of seven substitutions, in cytochrome b, the Fe-S protein, and cytochrome c1 that affect the interactions between these proteins at the tether arm of the Fe-S protein and may alter the rate of ubiquinone oxidation and the rate of superoxide production. Another cluster of substitutions near heme bH and the ubiquinone reduction site, Qi, may affect the rate of ubiquinone reduction and thus alter the rate of superoxide production. These results are compatible with the hypothesis that cytochrome b in humans (and other anthropoid primates) evolve to reduce the rate of production of superoxide thus enabling the exceptional longevity and exceptional cognitive ability of humans.},
}

Humans
Cattle
Animals
Mice
Sheep
*Ubiquinone/chemistry/metabolism
*Superoxides/metabolism
Cytochromes b/metabolism
Cytochromes c1/metabolism
Oxidation-Reduction
Primates/metabolism
Electron Transport Complex III/metabolism
Electron Transport

@article {pmid36738170,
year = {2023},
author = {Rogers, RL and Grizzard, SL and Garner, JT},
title = {Strong, Recent Selective Sweeps Reshape Genetic Diversity in Freshwater Bivalve Megalonaias nervosa.},
journal = {Molecular biology and evolution},
volume = {40},
number = {2},
pages = {},
pmid = {36738170},
issn = {1537-1719},
support = {R35 GM133376/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; Selection, Genetic ; Fresh Water ; Genetic Variation ; *Bivalvia ; *Unionidae ; },
abstract = {Freshwater Unionid bivalves have recently faced ecological upheaval through pollution, barriers to dispersal, harvesting, and changes in fish-host prevalence. Currently, over 70% of species in North America are threatened, endangered or extinct. To characterize the genetic response to recent selective pressures, we collected population genetic data for one successful bivalve species, Megalonaias nervosa. We identify megabase-sized regions that are nearly monomorphic across the population, signals of strong, recent selection reshaping diversity across 73 Mb total. These signatures of selection are greater than is commonly seen in population genetic models. We observe 102 duplicate genes with high dN/dS on terminal branches among regions with sweeps, suggesting that gene duplication is a causative mechanism of recent adaptation in M. nervosa. Genes in sweeps reflect functional classes important for Unionid survival, including anticoagulation genes important for fish host parasitization, detox genes, mitochondria management, and shell formation. We identify sweeps in regions with no known functional impacts, suggesting mechanisms of adaptation that deserve greater attention in future work on species survival. In contrast, polymorphic transposable elements (TEs) appear to be detrimental and underrepresented among regions with sweeps. TE site frequency spectra are skewed toward singleton variants, and TEs among regions with sweeps are present at low frequency. Our work suggests that duplicate genes are an essential source of genetic novelty that has helped this species succeed in environments where others have struggled. These results suggest that gene duplications deserve greater attention in non-model population genomics, especially in species that have recently faced sudden environmental challenges.},
}

Animals
Selection, Genetic
Fresh Water
Genetic Variation
*Bivalvia
*Unionidae

@article {pmid36739562,
year = {2023},
author = {Fang, JM and Basu, S and Phu, J and Nieh, MP and LoTurco, JJ},
title = {Cellular Localization, Aggregation, and Cytotoxicity of Bicelle-Quantum Dot Nanocomposites.},
journal = {ACS applied bio materials},
volume = {6},
number = {2},
pages = {566-577},
doi = {10.1021/acsabm.2c00827},
pmid = {36739562},
issn = {2576-6422},
mesh = {Humans ; HeLa Cells ; *Quantum Dots/toxicity/chemistry ; HEK293 Cells ; *Nanocomposites/toxicity ; Sulfides ; Zinc Compounds ; },
abstract = {Bicelles are discoidal lipid nanoparticles (LNPs) in which the planar bilayer and curved rim are, respectively, composed of long- and short-chain lipids. Bicellar LNPs have a hydrophobic core, allowing hydrophobic molecules and large molecular complexes such as quantum dots (QDs) to be encapsulated. In this study, CdSe/ZnS QDs were encapsulated in bicelles made of dipalmitoyl phosphatidylcholine, dihexanoyl phosphatidylcholine, dipalmitoyl phosphatidylglycerol, and distearoyl phosphatidylethanolamine conjugated with polyethylene glycerol amine 2000 to form a well-defined bicelle-QD nanocomplex (known as NANO[2]-QD or bicelle-QD). The bicelle-QD was then incubated with Hek293t cells and HeLa cells for different periods of time to determine changes in their cellular localization. Bicelle-QDs readily penetrated Hek293t cell membranes within 15 min of incubation, localized to the cytoplasm, and associated with mitochondria and intracellular vesicles. After 1 h, the bicelle-QDs enter the cell nucleus. Large aggregates form throughout the cell after 2 h and QDs are nearly absent from the nucleus by 4 h. Previous reports have demonstrated that CdSe/ZnS QDs can be toxic to cells, and we have found that encapsulating QDs in bicelles can attenuate but did not eliminate cytotoxicity. The present research outcome demonstrates the time-resolved pathway of bicelle-encapsulated QDs in Hek293t cells, morphological evolution in cells over time, and cytotoxicity of the bicelle-QDs, providing important insight into the potential application of the nanocomplex for cellular imaging.},
}

Humans
HeLa Cells
*Quantum Dots/toxicity/chemistry
HEK293 Cells
*Nanocomposites/toxicity
Sulfides
Zinc Compounds

@article {pmid36739946,
year = {2023},
author = {Schmitz, JM and Wolters, JF and Murray, NH and Guerra, RM and Bingman, CA and Hittinger, CT and Pagliarini, DJ},
title = {Aim18p and Aim46p are chalcone isomerase domain-containing mitochondrial hemoproteins in Saccharomyces cerevisiae.},
journal = {The Journal of biological chemistry},
volume = {299},
number = {3},
pages = {102981},
pmid = {36739946},
issn = {1083-351X},
support = {R35 GM131795/GM/NIGMS NIH HHS/United States ; T32 GM008505/GM/NIGMS NIH HHS/United States ; P30 GM138396/GM/NIGMS NIH HHS/United States ; T32 HG002760/HG/NHGRI NIH HHS/United States ; P41 GM108538/GM/NIGMS NIH HHS/United States ; },
mesh = {Flavonoids/metabolism ; *Intramolecular Lyases/chemistry/metabolism ; *Saccharomyces cerevisiae/enzymology/genetics ; *Saccharomyces cerevisiae Proteins/genetics/metabolism ; },
abstract = {Chalcone isomerases (CHIs) have well-established roles in the biosynthesis of plant flavonoid metabolites. Saccharomyces cerevisiae possesses two predicted CHI-like proteins, Aim18p (encoded by YHR198C) and Aim46p (YHR199C), but it lacks other enzymes of the flavonoid pathway, suggesting that Aim18p and Aim46p employ the CHI fold for distinct purposes. Here, we demonstrate using proteinase K protection assays, sodium carbonate extractions, and crystallography that Aim18p and Aim46p reside on the mitochondrial inner membrane and adopt CHI folds, but they lack select active site residues and possess an extra fungal-specific loop. Consistent with these differences, Aim18p and Aim46p lack CHI activity and also the fatty acid-binding capabilities of other CHI-like proteins, but instead bind heme. We further show that diverse fungal homologs also bind heme and that Aim18p and Aim46p possess structural homology to a bacterial hemoprotein. Collectively, our work reveals a distinct function and cellular localization for two CHI-like proteins, introduces a new variation of a hemoprotein fold, and suggests that ancestral CHI-like proteins were hemoproteins.},
}

Flavonoids/metabolism
*Intramolecular Lyases/chemistry/metabolism
*Saccharomyces cerevisiae/enzymology/genetics
*Saccharomyces cerevisiae Proteins/genetics/metabolism

@article {pmid36746982,
year = {2023},
author = {de Jong, MJ and Niamir, A and Wolf, M and Kitchener, AC and Lecomte, N and Seryodkin, IV and Fain, SR and Hagen, SB and Saarma, U and Janke, A},
title = {Range-wide whole-genome resequencing of the brown bear reveals drivers of intraspecies divergence.},
journal = {Communications biology},
volume = {6},
number = {1},
pages = {153},
pmid = {36746982},
issn = {2399-3642},
mesh = {Animals ; Male ; *Ursidae/genetics ; DNA, Mitochondrial/genetics ; Phylogeography ; Population Dynamics ; Mitochondria/genetics ; },
abstract = {Population-genomic studies can shed new light on the effect of past demographic processes on contemporary population structure. We reassessed phylogeographical patterns of a classic model species of postglacial recolonisation, the brown bear (Ursus arctos), using a range-wide resequencing dataset of 128 nuclear genomes. In sharp contrast to the erratic geographical distribution of mtDNA and Y-chromosomal haplotypes, autosomal and X-chromosomal multi-locus datasets indicate that brown bear population structure is largely explained by recent population connectivity. Multispecies coalescent based analyses reveal cases where mtDNA haplotype sharing between distant populations, such as between Iberian and southern Scandinavian bears, likely results from incomplete lineage sorting, not from ancestral population structure (i.e., postglacial recolonisation). However, we also argue, using forward-in-time simulations, that gene flow and recombination can rapidly erase genomic evidence of former population structure (such as an ancestral population in Beringia), while this signal is retained by Y-chromosomal and mtDNA, albeit likely distorted. We further suggest that if gene flow is male-mediated, the information loss proceeds faster in autosomes than in X chromosomes. Our findings emphasise that contemporary autosomal genetic structure may reflect recent population dynamics rather than postglacial recolonisation routes, which could contribute to mtDNA and Y-chromosomal discordances.},
}

Animals
Male
*Ursidae/genetics
DNA, Mitochondrial/genetics
Phylogeography
Population Dynamics
Mitochondria/genetics

@article {pmid36747727,
year = {2023},
author = {Espino-Sanchez, TJ and Wienkers, H and Marvin, RG and Nalder, SA and García-Guerrero, AE and VanNatta, PE and Jami-Alahmadi, Y and Blackwell, AM and Whitby, FG and Wohlschlegel, JA and Kieber-Emmons, MT and Hill, CP and Sigala, PA},
title = {Direct Tests of Cytochrome Function in the Electron Transport Chain of Malaria Parasites.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {36747727},
issn = {2692-8205},
support = {P30 GM133894/GM/NIGMS NIH HHS/United States ; T32 DK007115/DK/NIDDK NIH HHS/United States ; R25 HL108828/HL/NHLBI NIH HHS/United States ; R01 GM089778/GM/NIGMS NIH HHS/United States ; U54 DK110858/DK/NIDDK NIH HHS/United States ; R35 GM133764/GM/NIGMS NIH HHS/United States ; },
abstract = {UNLABELLED: The mitochondrial electron transport chain (ETC) of Plasmodium malaria parasites is a major antimalarial drug target, but critical cytochrome functions remain unstudied and enigmatic. Parasites express two distinct cyt c homologs (c and c -2) with unusually sparse sequence identity and uncertain fitness contributions. P. falciparum cyt c -2 is the most divergent eukaryotic cyt c homolog currently known and has sequence features predicted to be incompatible with canonical ETC function. We tagged both cyt c homologs and the related cyt c 1 for inducible knockdown. Translational repression of cyt c and cyt c 1 was lethal to parasites, which died from ETC dysfunction and impaired ubiquinone recycling. In contrast, cyt c -2 knockdown or knock-out had little impact on blood-stage growth, indicating that parasites rely fully on the more conserved cyt c for ETC function. Biochemical and structural studies revealed that both cyt c and c -2 are hemylated by holocytochrome c synthase, but UV-vis absorbance and EPR spectra strongly suggest that cyt c -2 has an unusually open active site in which heme is stably coordinated by only a single axial amino-acid ligand and can bind exogenous small molecules. These studies provide a direct dissection of cytochrome functions in the ETC of malaria parasites and identify a highly divergent Plasmodium cytochrome c with molecular adaptations that defy a conserved role in eukaryotic evolution.

SIGNIFICANCE STATEMENT: Mitochondria are critical organelles in eukaryotic cells that drive oxidative metabolism. The mitochondrion of Plasmodium malaria parasites is a major drug target that has many differences from human cells and remains poorly studied. One key difference from humans is that malaria parasites express two cytochrome c proteins that differ significantly from each other and play untested and uncertain roles in the mitochondrial electron transport chain (ETC). Our study revealed that one cyt c is essential for ETC function and parasite viability while the second, more divergent protein has unusual structural and biochemical properties and is not required for growth of blood-stage parasites. This work elucidates key biochemical properties and evolutionary differences in the mitochondrial ETC of malaria parasites.},
}

@article {pmid36748090,
year = {2023},
author = {Zhang, Y and Li, W and Bian, Y and Li, Y and Cong, L},
title = {Multifaceted roles of aerobic glycolysis and oxidative phosphorylation in hepatocellular carcinoma.},
journal = {PeerJ},
volume = {11},
number = {},
pages = {e14797},
pmid = {36748090},
issn = {2167-8359},
mesh = {Humans ; *Carcinoma, Hepatocellular/metabolism ; Oxidative Phosphorylation ; *Liver Neoplasms/metabolism ; Energy Metabolism ; Glycolysis ; },
abstract = {Liver cancer is a common malignancy with high morbidity and mortality rates. Changes in liver metabolism are key factors in the development of primary hepatic carcinoma, and mitochondrial dysfunction is closely related to the occurrence and development of tumours. Accordingly, the study of the metabolic mechanism of mitochondria in primary hepatic carcinomas has gained increasing attention. A growing body of research suggests that defects in mitochondrial respiration are not generally responsible for aerobic glycolysis, nor are they typically selected during tumour evolution. Conversely, the dysfunction of mitochondrial oxidative phosphorylation (OXPHOS) may promote the proliferation, metastasis, and invasion of primary hepatic carcinoma. This review presents the current paradigm of the roles of aerobic glycolysis and OXPHOS in the occurrence and development of hepatocellular carcinoma (HCC). Mitochondrial OXPHOS and cytoplasmic glycolysis cooperate to maintain the energy balance in HCC cells. Our study provides evidence for the targeting of mitochondrial metabolism as a potential therapy for HCC.},
}

Humans
*Carcinoma, Hepatocellular/metabolism
Oxidative Phosphorylation
*Liver Neoplasms/metabolism
Energy Metabolism
Glycolysis

@article {pmid36750641,
year = {2023},
author = {Kayastha, P and Stec, D and Sługocki, Ł and Gawlak, M and Mioduchowska, M and Kaczmarek, Ł},
title = {Integrative taxonomy reveals new, widely distributed tardigrade species of the genus Paramacrobiotus (Eutardigrada: Macrobiotidae).},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {2196},
pmid = {36750641},
issn = {2045-2322},
mesh = {Animals ; *Tardigrada/genetics ; Phylogeny ; Mitochondria/genetics ; Microscopy, Electron, Scanning ; RNA, Ribosomal, 18S/genetics ; },
abstract = {In a moss sample collected in Ribeiro Frio, Madeira, Paramacrobiotus gadabouti sp. nov. was found and described using the integrative taxonomy approach. The new species is described based on morphological and morphometric data from both phase-contrast light microscopy (PCM), as well as scanning electron microscopy (SEM). Moreover, four DNA markers, three nuclear (18S rRNA, 28S rRNA, ITS-2) and one mitochondrial (COI) markers, were used to elucidate the phylogenetic position of the new species within the family Macrobiotidae. The new species has a microplacoid that placed it within Parmacrobiotus richtersi group and exhibit richtersi-type eggs having processes terminated with cap-like structures. Paramacrobiotus gadabouti sp. nov. is most similar to Pam. alekseevi, Pam. filipi and Pam. garynahi, but differs from them mainly in details of egg morphology and morphometrics. Unlike other species from this group, which were confirmed as bisexual and showed limited distribution, Paramacrobiotus gadabouti sp. nov. is yet another parthenogenetic species with a wide distribution, demonstrating that at least some tardigrades confirm to the hypothesis of 'everything is everywhere'.},
}

Animals
*Tardigrada/genetics
Phylogeny
Mitochondria/genetics
Microscopy, Electron, Scanning
RNA, Ribosomal, 18S/genetics

@article {pmid36773750,
year = {2023},
author = {Taite, M and Fernández-Álvarez, FÁ and Braid, HE and Bush, SL and Bolstad, K and Drewery, J and Mills, S and Strugnell, JM and Vecchione, M and Villanueva, R and Voight, JR and Allcock, AL},
title = {Genome skimming elucidates the evolutionary history of Octopoda.},
journal = {Molecular phylogenetics and evolution},
volume = {182},
number = {},
pages = {107729},
doi = {10.1016/j.ympev.2023.107729},
pmid = {36773750},
issn = {1095-9513},
mesh = {Animals ; *Octopodiformes/genetics ; Phylogeny ; Bayes Theorem ; Mitochondria/genetics ; *Genome, Mitochondrial ; RNA, Transfer ; },
abstract = {Phylogenies for Octopoda have, until now, been based on morphological characters or a few genes. Here we provide the complete mitogenomes and the nuclear 18S and 28S ribosomal genes of twenty Octopoda specimens, comprising 18 species of Cirrata and Incirrata, representing 13 genera and all five putative families of Cirrata (Cirroctopodidae, Cirroteuthidae, Grimpoteuthidae, Opisthoteuthidae and Stauroteuthidae) and six families of Incirrata (Amphitretidae, Argonautidae, Bathypolypodidae, Eledonidae, Enteroctopodidae, and Megaleledonidae) which were assembled using genome skimming. Phylogenetic trees were built using Maximum Likelihood and Bayesian Inference with several alignment matrices. All mitochondrial genomes had the 'typical' genome composition and gene order previously reported for octopodiforms, except Bathypolypus ergasticus, which appears to lack ND5, two tRNA genes that flank ND5 and two other tRNA genes. Argonautoidea was revealed as sister to Octopodidae by the mitochondrial protein-coding gene dataset, however, it was recovered as sister to all other incirrate octopods with strong support in an analysis using nuclear rRNA genes. Within Cirrata, our study supports two existing classifications suggesting neither is likely in conflict with the true evolutionary history of the suborder. Genome skimming is useful in the analysis of phylogenetic relationships within Octopoda; inclusion of both mitochondrial and nuclear data may be key.},
}

Animals
*Octopodiformes/genetics
Phylogeny
Bayes Theorem
Mitochondria/genetics
*Genome, Mitochondrial
RNA, Transfer

@article {pmid36782130,
year = {2023},
author = {Zhang, S and Wang, J and He, W and Kan, S and Liao, X and Jordan, DR and Mace, ES and Tao, Y and Cruickshank, AW and Klein, R and Yuan, D and Tembrock, LR and Wu, Z},
title = {Variation in mitogenome structural conformation in wild and cultivated lineages of sorghum corresponds with domestication history and plastome evolution.},
journal = {BMC plant biology},
volume = {23},
number = {1},
pages = {91},
pmid = {36782130},
issn = {1471-2229},
support = {RCYX20200714114538196//Science, Technology, and Innovation Commission of Shenzhen Municipality/ ; 31970244//National Natural Science Foundation of China/ ; 110243160001007//Chinese Academy of Agricultural Sciences Elite Youth Program/ ; },
mesh = {*Genome, Mitochondrial/genetics ; *Sorghum/genetics ; Phylogeny ; Domestication ; Plants/genetics ; Cell Nucleus ; Evolution, Molecular ; Genome, Plant/genetics ; },
abstract = {BACKGROUND: Mitochondria are organelles within eukaryotic cells that are central to the metabolic processes of cellular respiration and ATP production. However, the evolution of mitochondrial genomes (mitogenomes) in plants is virtually unknown compared to animal mitogenomes or plant plastids, due to complex structural variation and long stretches of repetitive DNA making accurate genome assembly more challenging. Comparing the structural and sequence differences of organellar genomes within and between sorghum species is an essential step in understanding evolutionary processes such as organellar sequence transfer to the nuclear genome as well as improving agronomic traits in sorghum related to cellular metabolism.

RESULTS: Here, we assembled seven sorghum mitochondrial and plastid genomes and resolved reticulated mitogenome structures with multilinked relationships that could be grouped into three structural conformations that differ in the content of repeats and genes by contig. The grouping of these mitogenome structural types reflects the two domestication events for sorghum in east and west Africa.

CONCLUSIONS: We report seven mitogenomes of sorghum from different cultivars and wild sources. The assembly method used here will be helpful in resolving complex genomic structures in other plant species. Our findings give new insights into the structure of sorghum mitogenomes that provides an important foundation for future research into the improvement of sorghum traits related to cellular respiration, cytonuclear incompatibly, and disease resistance.},
}

*Genome, Mitochondrial/genetics
*Sorghum/genetics
Phylogeny
Domestication
Plants/genetics
Cell Nucleus
Evolution, Molecular
Genome, Plant/genetics

@article {pmid36787420,
year = {2023},
author = {Zheng, Y and Ye, Z and Xiao, Y},
title = {Subtle Structural Translation Magically Modulates the Super-Resolution Imaging of Self-Blinking Rhodamines.},
journal = {Analytical chemistry},
volume = {95},
number = {8},
pages = {4172-4179},
doi = {10.1021/acs.analchem.2c05298},
pmid = {36787420},
issn = {1520-6882},
mesh = {Rhodamines/chemistry ; *Blinking ; *Fluorescent Dyes/chemistry ; Microscopy, Fluorescence/methods ; Nanotechnology ; },
abstract = {The evolution of super-resolution imaging techniques is benefited from the ongoing competition for optimal rhodamine fluorophores. Yet, it seems blind to construct the desired rhodamine molecule matching the imaging need without the knowledge on imaging impact of even the minimum structural translation. Herein, we have designed a pair of self-blinking sulforhodamines (STMR and SRhB) with the bare distinction of methyl or ethyl substituents and engineered them with Halo protein ligands. Although the two possess similar spectral properties (λab, λfl, ϕ, etc.), they demonstrated unique single-molecule characteristics preferring to individual imaging applications. Experimentally, STMR with high emissive rates was qualified for imaging structures with rapid dynamics (endoplasmic reticulum, and mitochondria), and SRhB with prolonged on-times and photostability was suited for relatively "static" nuclei and microtubules. Using this new knowledge, the mitochondrial morphology during apoptosis and ferroptosis was first super-resolved by STMR. Our study highlights the significance of even the smallest structural modification to the modulation of super-resolution imaging performance and would provide insights for future fluorophore design.},
}

Rhodamines/chemistry
*Blinking
*Fluorescent Dyes/chemistry
Microscopy, Fluorescence/methods
Nanotechnology

@article {pmid36787792,
year = {2022},
author = {Broccard, N and Silva, NM and Currat, M},
title = {Simulated patterns of mitochondrial diversity are consistent with partial population turnover in Bronze Age Central Europe.},
journal = {American journal of biological anthropology},
volume = {177},
number = {1},
pages = {134-146},
pmid = {36787792},
issn = {2692-7691},
mesh = {*Mitochondria/genetics ; Europe ; *DNA, Mitochondrial/genetics ; Emigration and Immigration ; Biological Evolution ; DNA, Ancient ; },
abstract = {OBJECTIVES: The analysis of ancient mitochondrial DNA from osteological remains has challenged previous conclusions drawn from the analysis of mitochondrial DNA from present populations, notably by revealing an absence of genetic continuity between the Neolithic and modern populations in Central Europe. Our study investigates how to reconcile these contradictions at the mitochondrial level using a modeling approach.

MATERIALS AND METHODS: We used a spatially explicit computational framework to simulate ancient and modern DNA sequences under various evolutionary scenarios of post Neolithic demographic events and compared the genetic diversity of the simulated and observed mitochondrial sequences. We investigated which-if any-scenarios were able to reproduce statistics of genetic diversity similar to those observed, with a focus on the haplogroup N1a, associated with the spread of early Neolithic farmers.

RESULTS: Demographic fluctuations during the Neolithic transition or subsequent demographic collapses after this period, that is, due to epidemics such as plague, are not sufficient to explain the signal of population discontinuity detected on the mitochondrial DNA in Central Europe. Only a scenario involving a substantial genetic input due to the arrival of migrants after the Neolithic transition, possibly during the Bronze Age, is compatible with observed patterns of genetic diversity.

DISCUSSION: Our results corroborate paleogenomic studies, since out of the alternative hypotheses tested, the best one that was able to recover observed patterns of mitochondrial diversity in modern and ancient Central European populations was one were immigration of populations from the Pontic steppes during the Bronze Age was explicitly simulated.},
}

*Mitochondria/genetics
Europe
*DNA, Mitochondrial/genetics
Emigration and Immigration
Biological Evolution
DNA, Ancient

@article {pmid36789533,
year = {2023},
author = {Nagarajan-Radha, V and Beekman, M},
title = {G × G × E effect on phenotype expression in a non-conventional model organism, the unicellular slime mould Physarum polycephalum.},
journal = {Biology letters},
volume = {19},
number = {2},
pages = {20220494},
pmid = {36789533},
issn = {1744-957X},
mesh = {*Physarum polycephalum/genetics ; DNA, Mitochondrial/genetics ; Mitochondria/genetics ; Plasmids ; Phenotype ; },
abstract = {In metazoans, the expression of key phenotypic traits is sensitive to two- and three-way interactions between variation in mitochondrial DNA, nuclear DNA and the external environment. Whether gene-by-environment interactions affect phenotypes in single-celled eukaryotes is poorly studied, except in a few species of yeast and fungi. We developed a genetic panel of the unicellular slime mould, Physarum polycephalum containing strains differing in mitochondrial and nuclear DNA haplotypes. The panel also included two strains harbouring a selfishly replicating mitochondrial-fusion (mF) plasmid that could affect phenotype expression. We assayed movement and growth rate differences among the strains across two temperature regimes: 24° and 28°C. We found that the slime mould's growth rate, but not movement, is affected by G × G × E interactions. Predictably, mtDNA × nDNA interactions significantly affected both traits. The inter-trait correlation across the strains in each temperature regime was positive. Surprisingly, the mF plasmid had no negative effects on our chosen traits. Our study is the first to demonstrate genetic regulation of phenotype expression in a unicellular slime mould. The genetic effect on phenotypes manifests via epistatic interactions with the thermal environment, thus shedding new light on the role of G × G × E interactions in trait evolution in protists.},
}

*Physarum polycephalum/genetics
DNA, Mitochondrial/genetics
Mitochondria/genetics
Plasmids
Phenotype

@article {pmid36790104,
year = {2023},
author = {Onuț-Brännström, I and Stairs, CW and Campos, KIA and Thorén, MH and Ettema, TJG and Keeling, PJ and Bass, D and Burki, F},
title = {A Mitosome With Distinct Metabolism in the Uncultured Protist Parasite Paramikrocytos canceri (Rhizaria, Ascetosporea).},
journal = {Genome biology and evolution},
volume = {15},
number = {3},
pages = {},
pmid = {36790104},
issn = {1759-6653},
support = {MOP-42517//CIHR/Canada ; },
mesh = {Animals ; *Parasites ; *Rhizaria/genetics ; Organelles ; Mitochondria/genetics/metabolism ; Saccharomyces cerevisiae/metabolism ; },
abstract = {Ascetosporea are endoparasites of marine invertebrates that include economically important pathogens of aquaculture species. Owing to their often-minuscule cell sizes, strict intracellular lifestyle, lack of cultured representatives and minimal availability of molecular data, these unicellular parasites remain poorly studied. Here, we sequenced and assembled the genome and transcriptome of Paramikrocytos canceri, an endoparasite isolated from the European edible crab Cancer pagurus. Using bioinformatic predictions, we show that P. canceri likely possesses a mitochondrion-related organelle (MRO) with highly reduced metabolism, resembling the mitosomes of other parasites but with key differences. Like other mitosomes, this MRO is predicted to have reduced metabolic capacity and lack an organellar genome and function in iron-sulfur cluster (ISC) pathway-mediated Fe-S cluster biosynthesis. However, the MRO in P. canceri is uniquely predicted to produce ATP via a partial glycolytic pathway and synthesize phospholipids de novo through the CDP-DAG pathway. Heterologous gene expression confirmed that proteins from the ISC and CDP-DAG pathways retain mitochondrial targeting sequences that are recognized by yeast mitochondria. This represents a unique combination of metabolic pathways in an MRO, including the first reported case of a mitosome-like organelle able to synthesize phospholipids de novo. Some of these phospholipids, such as phosphatidylserine, are vital in other protist endoparasites that invade their host through apoptotic mimicry.},
}

Animals
*Parasites
*Rhizaria/genetics
Organelles
Mitochondria/genetics/metabolism
Saccharomyces cerevisiae/metabolism

@article {pmid36790303,
year = {2023},
author = {Sokolova, IM},
title = {Ectotherm mitochondrial economy and responses to global warming.},
journal = {Acta physiologica (Oxford, England)},
volume = {237},
number = {4},
pages = {e13950},
doi = {10.1111/apha.13950},
pmid = {36790303},
issn = {1748-1716},
mesh = {Reactive Oxygen Species/metabolism ; *Global Warming ; *Mitochondria/metabolism ; Energy Metabolism/physiology ; Adenosine Triphosphate/metabolism ; },
abstract = {Temperature is a key abiotic factor affecting ecology, biogeography, and evolution of species. Alterations of energy metabolism play an important role in adaptations and plastic responses to temperature shifts on different time scales. Mitochondrial metabolism affects cellular bioenergetics and redox balance making these organelles an important determinant of organismal performances such as growth, locomotion, or development. Here I analyze the impacts of environmental temperature on the mitochondrial functions (including oxidative phosphorylation, proton leak, production of reactive oxygen species(ROS), and ATP synthesis) of ectotherms and discuss the mechanisms underlying negative shifts in the mitochondrial energy economy caused by supraoptimal temperatures. Owing to the differences in the thermal sensitivity of different mitochondrial processes, elevated temperatures (beyond the species- and population-specific optimal range) cause reallocation of the electron flux and the protonmotive force (Δp) in a way that decreases ATP synthesis efficiency, elevates the relative cost of the mitochondrial maintenance, causes excessive production of ROS and raises energy cost for antioxidant defense. These shifts in the mitochondrial energy economy might have negative consequences for the organismal fitness traits such as the thermal tolerance or growth. Correlation between the thermal sensitivity indices of the mitochondria and the whole organism indicate that these traits experience similar selective pressures but further investigations are needed to establish whether there is a cause-effect relationship between the mitochondrial failure and loss of organismal performance during temperature change.},
}

Reactive Oxygen Species/metabolism
*Global Warming
*Mitochondria/metabolism
Energy Metabolism/physiology
Adenosine Triphosphate/metabolism

@article {pmid36797268,
year = {2023},
author = {Preston, AJ and Rogers, A and Sharp, M and Mitchell, G and Toruno, C and Barney, BB and Donovan, LN and Bly, J and Kennington, R and Payne, E and Iovino, A and Furukawa, G and Robinson, R and Shamloo, B and Buccilli, M and Anders, R and Eckstein, S and Fedak, EA and Wright, T and Maley, CC and Kiso, WK and Schmitt, D and Malkin, D and Schiffman, JD and Abegglen, LM},
title = {Elephant TP53-RETROGENE 9 induces transcription-independent apoptosis at the mitochondria.},
journal = {Cell death discovery},
volume = {9},
number = {1},
pages = {66},
pmid = {36797268},
issn = {2058-7716},
support = {S10 OD026959/OD/NIH HHS/United States ; U54 CA217376/CA/NCI NIH HHS/United States ; },
abstract = {Approximately 20 TP53 retrogenes exist in the African and Asian elephant genomes (Loxodonta Africana, Elephas Maximus) in addition to a conserved TP53 gene that encodes a full-length protein. Elephant TP53-RETROGENE 9 (TP53-R9) encodes a p53 protein (p53-R9) that is truncated in the middle of the canonical DNA binding domain. This C-terminally truncated p53 retrogene protein lacks the nuclear localization signals and oligomerization domain of its full-length counterpart. When expressed in human osteosarcoma cells (U2OS), p53-R9 binds to Tid1, the chaperone protein responsible for mitochondrial translocation of human p53 in response to cellular stress. Tid1 expression is required for p53-R9-induced apoptosis. At the mitochondria, p53-R9 binds to the pro-apoptotic BCL-2 family member Bax, which leads to caspase activation, cytochrome c release, and cell death. Our data show, for the first time, that expression of this truncated elephant p53 retrogene protein induces apoptosis in human cancer cells. Understanding the molecular mechanism by which the additional elephant TP53 retrogenes function may provide evolutionary insight that can be utilized for the development of therapeutics to treat human cancers.},
}

@article {pmid36806940,
year = {2023},
author = {Rivera-Colón, AG and Rayamajhi, N and Minhas, BF and Madrigal, G and Bilyk, KT and Yoon, V and Hüne, M and Gregory, S and Cheng, CHC and Catchen, JM},
title = {Genomics of Secondarily Temperate Adaptation in the Only Non-Antarctic Icefish.},
journal = {Molecular biology and evolution},
volume = {40},
number = {3},
pages = {},
pmid = {36806940},
issn = {1537-1719},
support = {//National Science Foundation/ ; },
mesh = {Animals ; Antarctic Regions ; *Adaptation, Physiological ; Fishes/genetics ; *Perciformes/genetics ; Genomics ; Antifreeze Proteins ; },
abstract = {White-blooded Antarctic icefishes, a family within the adaptive radiation of Antarctic notothenioid fishes, are an example of extreme biological specialization to both the chronic cold of the Southern Ocean and life without hemoglobin. As a result, icefishes display derived physiology that limits them to the cold and highly oxygenated Antarctic waters. Against these constraints, remarkably one species, the pike icefish Champsocephalus esox, successfully colonized temperate South American waters. To study the genetic mechanisms underlying secondarily temperate adaptation in icefishes, we generated chromosome-level genome assemblies of both C. esox and its Antarctic sister species, Champsocephalus gunnari. The C. esox genome is similar in structure and organization to that of its Antarctic congener; however, we observe evidence of chromosomal rearrangements coinciding with regions of elevated genetic divergence in pike icefish populations. We also find several key biological pathways under selection, including genes related to mitochondria and vision, highlighting candidates behind temperate adaptation in C. esox. Substantial antifreeze glycoprotein (AFGP) pseudogenization has occurred in the pike icefish, likely due to relaxed selection following ancestral escape from Antarctica. The canonical AFGP locus organization is conserved in C. esox and C. gunnari, but both show a translocation of two AFGP copies to a separate locus, previously unobserved in cryonotothenioids. Altogether, the study of this secondarily temperate species provides an insight into the mechanisms underlying adaptation to ecologically disparate environments in this otherwise highly specialized group.},
}

Animals
Antarctic Regions
*Adaptation, Physiological
Fishes/genetics
*Perciformes/genetics
Genomics
Antifreeze Proteins

@article {pmid36810648,
year = {2023},
author = {Li, Y and Chen, L and Si, L and Yang, Y and Zhou, C and Yu, F and Xia, G and Wang, H},
title = {Triphenylamine-equipped 1,8-naphthaolactam: a versatile scaffold for the custom design of efficient subcellular imaging agents.},
journal = {Journal of materials chemistry. B},
volume = {11},
number = {11},
pages = {2431-2439},
doi = {10.1039/d2tb02528k},
pmid = {36810648},
issn = {2050-7518},
mesh = {*Optical Imaging ; *Mitochondria ; Amines ; },
abstract = {Fluorescence imaging has enabled much progress in biological fields, while the evolution of commercially available dyes has lagged behind their advanced applications. Herein, we launch triphenylamine-equipped 1,8-naphthaolactam (NP-TPA) as a versatile scaffold for the custom design of an efficient subcellular imaging agent (NP-TPA-Tar), given its bright and constant emissions in various states, significant Stokes shifts, and facile modifiability. The resultant four NP-TPA-Tars maintain excellent emission behavior with targeted modifications and can map the spatial distribution of lysosomes, mitochondria, endoplasmic reticulum, and plasma membrane in Hep G2 cells. Compared to its commercial counterpart, NP-TPA-Tar has a 2.8-25.2 fold increase in Stokes shift, a 1.2-1.9 fold increase in photostability, enhanced targeting capability, and comparable imaging efficiency even at low concentrations of 50 nM. This work will help to accelerate the update of current imaging agents and super-resolution and real-time imaging in biological applications.},
}

*Optical Imaging
*Mitochondria
Amines

@article {pmid36822346,
year = {2023},
author = {Cheng, A and Zhang, Y and Sun, J and Huang, D and Sulaiman, JE and Huang, X and Wu, L and Ye, W and Wu, C and Lam, H and Shi, Y and Qian, PY},
title = {Pterosin sesquiterpenoids from Pteris laeta Wall. ex Ettingsh. protect cells from glutamate excitotoxicity by modulating mitochondrial signals.},
journal = {Journal of ethnopharmacology},
volume = {308},
number = {},
pages = {116308},
doi = {10.1016/j.jep.2023.116308},
pmid = {36822346},
issn = {1872-7573},
mesh = {Reactive Oxygen Species/metabolism ; Kelch-Like ECH-Associated Protein 1/metabolism ; Glutamic Acid/metabolism ; *Pteris/metabolism ; NF-E2-Related Factor 2/metabolism ; *Sesquiterpenes/pharmacology ; Mitochondria ; Oxidative Stress ; Indans ; },
abstract = {The genus Pteris (Pteridaceae) has been used as a traditional herb for a long time. In particular, Pteris laeta Wall. ex Ettingsh. has been widely used in traditional Chinese medicine to treat nervous system diseases and some pterosin sesquiterpenes from Pteris show neuroprotective activity, but their underlying molecular mechanisms remain elusive. Therefore, to investigate the neuroprotective activity and working mechanism of pterosin sesquiterpenes from P. laeta Wall. ex Ettingsh. will provide a better understanding and guidance in using P. laeta Wall. ex Ettingsh. as a traditional Chinese medicine.

AIM OF THE STUDY: We aim to develop effective treatments for neurodegenerative diseases from pterosin sesquiterpenes by evaluating their neuroprotective activity and investigating their working mechanisms.

MATERIALS AND METHODS: Primary screening on the glutamate-induced excitotoxicity cell model was assessed by 3-(4,5-Dimethylthiazol-2-yl)-2,5-Diphenyltetrazolium Bromide (MTT) assay. Fluorescent-activated cell sorting (FACS) was used to analyze the activation level of glutamate receptors and mitochondria membrane potential after treatment. Transcriptomics and proteomics analysis was performed to identify possible targets of pterosin B. The key pathways were enriched by the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis through the Database for Annotation, Visualization, and Integrated Discovery (DAVID). The core targets were visualized by a protein-protein interaction network using STRING. The mRNA and protein expressions were evaluated using real-time quantitative polymerase chain reaction (Q-PCR) and western blot, respectively. Immunocytochemistry was performed to monitor mitochondrial and apoptotic proteins. Cellular reactive oxygen species (ROS) were measured by ROS assay, and Ca[2+] was stained with Fluo-4 AM to quantify intracellular Ca[2+] levels.

RESULTS: We found pterosin B from Pteris laeta Wall. ex Ettingsh. showed significant neuroprotective activity against glutamate excitotoxicity, enhancing cell viability from 43.8% to 105% (p-value: <0.0001). We demonstrated that pterosin B worked on the downstream signaling pathways of glutamate excitotoxicity rather than directly blocking the activation of glutamate receptors. Pterosin B restored mitochondria membrane potentials, alleviated intracellular calcium overload from 107.4% to 95.47% (p-value: 0.0006), eliminated cellular ROS by 36.55% (p-value: 0.0143), and partially secured cells from LPS-induced inflammation by increasing cell survival from 46.75% to 58.5% (p-value: 0.0114). Notably, pterosin B enhanced the expression of nuclear factor-erythroid factor 2-related factor 2 (NRF2) and heme oxygenase-1 (HO-1) by 2.86-fold (p-value: 0.0006) and 4.24-fold (p-value: 0.0012), and down-regulated Kelch-like ECH-associated protein 1 (KEAP1) expression by 2.5-fold (p-value: 0.0107), indicating that it possibly promotes mitochondrial biogenesis and mitophagy to maintain mitochondria quality control and homeostasis, and ultimately inhibits apoptotic cell death.

CONCLUSIONS: Our work revealed that pterosin B protected cells from glutamate excitotoxicity by targeting the downstream mitochondrial signals, making it a valuable candidate for developing potential therapeutic agents in treating neurodegenerative diseases.},
}

Reactive Oxygen Species/metabolism
Kelch-Like ECH-Associated Protein 1/metabolism
Glutamic Acid/metabolism
*Pteris/metabolism
NF-E2-Related Factor 2/metabolism
*Sesquiterpenes/pharmacology
Mitochondria
Oxidative Stress
Indans

@article {pmid36831240,
year = {2023},
author = {Fang, Y and Zhang, F and Zhan, Y and Lu, M and Xu, D and Wang, J and Li, Q and Zhao, L and Su, Y},
title = {RpS3 Is Required for Spermatogenesis of Drosophila melanogaster.},
journal = {Cells},
volume = {12},
number = {4},
pages = {},
pmid = {36831240},
issn = {2073-4409},
mesh = {Animals ; Male ; *Drosophila melanogaster/metabolism ; *Drosophila Proteins/metabolism ; *Ribosomal Proteins/metabolism ; Semen/metabolism ; Spermatogenesis ; },
abstract = {Ribosomal proteins (RPs) constitute the ribosome, thus participating in the protein biosynthesis process. Emerging studies have suggested that many RPs exhibit different expression levels across various tissues and function in a context-dependent manner for animal development. Drosophila melanogaster RpS3 encodes the ribosomal protein S3, one component of the 40S subunit of ribosomes. We found that RpS3 is highly expressed in the reproductive organs of adult flies and its depletion in male germline cells led to severe defects in sperm production and male fertility. Immunofluorescence staining showed that RpS3 knockdown had little effect on early germ cell differentiation, but strongly disrupted the spermatid elongation and individualization processes. Furthermore, we observed abnormal morphology and activity of mitochondrial derivatives in the elongating spermatids of RpS3-knockdown testes, which could cause the failure of axoneme elongation. We also found that RpS3 RNAi inhibited the formation of the individualization complex that takes charge of disassociating the spermatid bundle. In addition, excessive apoptotic cells were detected in the RpS3-knockdown testes, possibly to clean the defective spermatids. Together, our data demonstrated that RpS3 plays an important role in regulating spermatid elongation and individualization processes and, therefore, is required for normal Drosophila spermatogenesis.},
}

Animals
Male
*Drosophila melanogaster/metabolism
*Drosophila Proteins/metabolism
*Ribosomal Proteins/metabolism
Semen/metabolism
Spermatogenesis

@article {pmid36835385,
year = {2023},
author = {Yang, JX and Dierckxsens, N and Bai, MZ and Guo, YY},
title = {Multichromosomal Mitochondrial Genome of Paphiopedilum micranthum: Compact and Fragmented Genome, and Rampant Intracellular Gene Transfer.},
journal = {International journal of molecular sciences},
volume = {24},
number = {4},
pages = {},
pmid = {36835385},
issn = {1422-0067},
support = {U1804117//National Natural Science Foundation of China/ ; },
mesh = {*Genome, Mitochondrial ; DNA, Mitochondrial ; Mitochondria/genetics ; *Magnoliopsida/genetics ; *Orchidaceae/genetics ; Phylogeny ; },
abstract = {Orchidaceae is one of the largest families of angiosperms. Considering the large number of species in this family and its symbiotic relationship with fungi, Orchidaceae provide an ideal model to study the evolution of plant mitogenomes. However, to date, there is only one draft mitochondrial genome of this family available. Here, we present a fully assembled and annotated sequence of the mitochondrial genome (mitogenome) of Paphiopedilum micranthum, a species with high economic and ornamental value. The mitogenome of P. micranthum was 447,368 bp in length and comprised 26 circular subgenomes ranging in size from 5973 bp to 32,281 bp. The genome encoded for 39 mitochondrial-origin, protein-coding genes; 16 tRNAs (three of plastome origin); three rRNAs; and 16 ORFs, while rpl10 and sdh3 were lost from the mitogenome. Moreover, interorganellar DNA transfer was identified in 14 of the 26 chromosomes. These plastid-derived DNA fragments represented 28.32% (46,273 bp) of the P. micranthum plastome, including 12 intact plastome origin genes. Remarkably, the mitogenome of P. micranthum and Gastrodia elata shared 18% (about 81 kb) of their mitochondrial DNA sequences. Additionally, we found a positive correlation between repeat length and recombination frequency. The mitogenome of P. micranthum had more compact and fragmented chromosomes compared to other species with multichromosomal structures. We suggest that repeat-mediated homologous recombination enables the dynamic structure of mitochondrial genomes in Orchidaceae.},
}

*Genome, Mitochondrial
DNA, Mitochondrial
Mitochondria/genetics
*Magnoliopsida/genetics
*Orchidaceae/genetics
Phylogeny

@article {pmid36838260,
year = {2023},
author = {Fuerst, PA},
title = {The Status of Molecular Analyses of Isolates of Acanthamoeba Maintained by International Culture Collections.},
journal = {Microorganisms},
volume = {11},
number = {2},
pages = {},
pmid = {36838260},
issn = {2076-2607},
abstract = {Acanthamoeba is among the most ubiquitous protistan groups in nature. Knowledge of the biological diversity of Acanthamoeba comes in part from the use of strains maintained by the major microbial culture collections, ATCC and CCAP. Standard strains are vital to ensure the comparability of research. The diversity of standard strains of Acanthamoeba in the culture collections is reviewed, emphasizing the extent of genotypic studies based on DNA sequencing of the small subunit ribosomal RNA from the nucleus (18S rRNA gene; Rns) or the mitochondria (16S-like rRNA gene; rns). Over 170 different strains have been maintained at some time by culture centers. DNA sequence information is available for more than 70% of these strains. Determination of the genotypic classification of standard strains within the genus indicates that frequencies of types within culture collections only roughly mirror that from clinical or environmental studies, with significant differences in the frequency of some genotypes. Culture collections include the type of isolate from almost all named species of Acanthamoeba, allowing an evaluation of the validity of species designations. Multiple species are found to share the same Sequence Type, while multiple Sequence Types have been identified for different strains that share the same species name. Issues of sequence reliability and the possibility that a small number of standard strains have been mislabeled when studied are also examined, leading to potential problems for comparative analyses. It is important that all species have reliable genotype designations. The culture collections should be encouraged to assist in completing the molecular inventory of standard strains, while workers in the Acanthamoeba research community should endeavor to ensure that strains representative of genotypes that are missing from the culture collection are provided to the culture centers for preservation.},
}

@article {pmid36858653,
year = {2023},
author = {Degli Esposti, M},
title = {The bacterial origin of mitochondria: Incorrect phylogenies and the importance of metabolic traits.},
journal = {International review of cell and molecular biology},
volume = {374},
number = {},
pages = {1-35},
doi = {10.1016/bs.ircmb.2022.11.001},
pmid = {36858653},
issn = {1937-6448},
mesh = {Animals ; Phylogeny ; *Mitochondria ; *Eukaryota ; Oxygen ; Phenotype ; },
abstract = {This article provides an updated review on the evolution of mitochondria from bacteria, which were likely related to extant alphaproteobacteria. Particular attention is given to the timeline of oxygen history on Earth and the entwined phases of eukaryotic evolution that produced the animals that still populate our planet. Mitochondria of early-branching unicellular eukaryotes and plants appear to retain partial or vestigial traits that were directly inherited from the alphaproteobacterial ancestors of the organelles. Most of such traits define the current aerobic physiology of mitochondria. Conversely, the anaerobic traits that would be essential in the syntrophic associations postulated for the evolution of eukaryotic cells are scantly present in extant alphaproteobacteria, and therefore cannot help defining from which bacterial lineage the ancestors of mitochondria originated. This question has recently been addressed quantitatively, reaching the novel conclusion that marine bacteria related to Iodidimonas may be the living relatives of protomitochondria. Additional evidence is presented that either support or does not contrast this novel view of the bacterial origin of mitochondria.},
}

Animals
Phylogeny
*Mitochondria
*Eukaryota
Oxygen
Phenotype

@article {pmid36858654,
year = {2023},
author = {Rubio-Tomás, T and Sotiriou, A and Tavernarakis, N},
title = {The interplay between selective types of (macro)autophagy: Mitophagy and xenophagy.},
journal = {International review of cell and molecular biology},
volume = {374},
number = {},
pages = {129-157},
doi = {10.1016/bs.ircmb.2022.10.003},
pmid = {36858654},
issn = {1937-6448},
mesh = {*Macroautophagy ; *Mitophagy ; Autophagy ; DNA Damage ; Exercise ; },
abstract = {Autophagy is a physiological response, activated by a myriad of endogenous and exogenous cues, including DNA damage, perturbation of proteostasis, depletion of nutrients or oxygen and pathogen infection. Upon sensing those stimuli, cells employ multiple non-selective and selective autophagy pathways to promote fitness and survival. Importantly, there are a variety of selective types of autophagy. In this review we will focus on autophagy of bacteria (xenophagy) and autophagy of mitochondria (mitophagy). We provide a brief introduction to bulk autophagy, as well as xenophagy and mitophagy, highlighting their common molecular factors. We also describe the role of xenophagy and mitophagy in the detection and elimination of pathogens by the immune system and the adaptive mechanisms that some pathogens have developed through evolution to escape the host autophagic response. Finally, we summarize the recent articles (from the last five years) linking bulk autophagy with xenophagy and/or mitophagy in the context on developmental biology, cancer and metabolism.},
}

*Macroautophagy
*Mitophagy
Autophagy
DNA Damage
Exercise

@article {pmid36860172,
year = {2023},
author = {Cantó-Santos, J and Valls-Roca, L and Tobías, E and García-García, FJ and Guitart-Mampel, M and Esteve-Codina, A and Martín-Mur, B and Casado, M and Artuch, R and Solsona-Vilarrasa, E and Fernandez-Checa, JC and García-Ruiz, C and Rentero, C and Enrich, C and Moreno-Lozano, PJ and Milisenda, JC and Cardellach, F and Grau-Junyent, JM and Garrabou, G},
title = {Unravelling inclusion body myositis using a patient-derived fibroblast model.},
journal = {Journal of cachexia, sarcopenia and muscle},
volume = {14},
number = {2},
pages = {964-977},
pmid = {36860172},
issn = {2190-6009},
support = {PI21/00935//Instituto de Salud Carlos III/ ; PI18/00451//Instituto de Salud Carlos III/ ; PI18/00498//Instituto de Salud Carlos III/ ; //APIF Programme (University of Barcelona)/ ; //CIBERER (ISCIII-FEDER)/ ; //CD21/00019 (ISCIII- FSE+)/ ; //Serra Húnter Programme (Generalitat de Catalunya)/ ; //Torrons Vicens/ ; //PID2019-111669RB-I00/ ; //PID2020-115055RB-I00/ ; //PT17/0009/0019 (ISCIII-MINECO-FEDER)/ ; },
mesh = {Humans ; *Myositis, Inclusion Body/diagnosis/genetics/metabolism ; *Myositis ; Muscles/metabolism ; Inflammation/pathology ; Biomarkers/metabolism ; },
abstract = {BACKGROUND: Inclusion body myositis (IBM) is an inflammatory myopathy clinically characterized by proximal and distal muscle weakness, with inflammatory infiltrates, rimmed vacuoles and mitochondrial changes in muscle histopathology. There is scarce knowledge on IBM aetiology, and non-established biomarkers or effective treatments are available, partly due to the lack of validated disease models.

METHODS: We have performed transcriptomics and functional validation of IBM muscle pathological hallmarks in fibroblasts from IBM patients (n = 14) and healthy controls (n = 12), paired by age and sex. The results comprise an mRNA-seq, together with functional inflammatory, autophagy, mitochondrial and metabolic changes between patients and controls.

RESULTS: Gene expression profile of IBM vs control fibroblasts revealed 778 differentially expressed genes (P-value adj < 0.05) related to inflammation, mitochondria, cell cycle regulation and metabolism. Functionally, an increased inflammatory profile was observed in IBM fibroblasts with higher supernatant cytokine secretion (three-fold increase). Autophagy was reduced considering basal protein mediators (18.4% reduced), time-course autophagosome formation (LC3BII 39% reduced, P-value < 0.05), and autophagosome microscopic evaluation. Mitochondria displayed reduced genetic content (by 33.9%, P-value < 0.05) and function (30.2%-decrease in respiration, 45.6%-decline in enzymatic activity (P-value < 0.001), 14.3%-higher oxidative stress, 135.2%-increased antioxidant defence (P-value < 0.05), 11.6%-reduced mitochondrial membrane potential (P-value < 0.05) and 42.8%-reduced mitochondrial elongation (P-value < 0.05)). In accordance, at the metabolite level, organic acid showed a 1.8-fold change increase, with conserved amino acid profile. Correlating to disease evolution, oxidative stress and inflammation emerge as potential markers of prognosis.

CONCLUSIONS: These findings confirm the presence of molecular disturbances in peripheral tissues from IBM patients and prompt patients' derived fibroblasts as a promising disease model, which may eventually be exported to other neuromuscular disorders. We additionally identify new molecular players in IBM associated with disease progression, setting the path to deepen in disease aetiology, in the identification of novel biomarkers or in the standardization of biomimetic platforms to assay new therapeutic strategies for preclinical studies.},
}

Humans
*Myositis, Inclusion Body/diagnosis/genetics/metabolism
*Myositis
Muscles/metabolism
Inflammation/pathology
Biomarkers/metabolism

@article {pmid36883279,
year = {2023},
author = {García Pascual, B and Nordbotten, JM and Johnston, IG},
title = {Cellular and environmental dynamics influence species-specific extents of organelle gene retention.},
journal = {Proceedings. Biological sciences},
volume = {290},
number = {1994},
pages = {20222140},
pmid = {36883279},
issn = {1471-2954},
mesh = {Species Specificity ; *Mitochondria ; *Eukaryotic Cells ; Eukaryota ; },
abstract = {Mitochondria and plastids rely on many nuclear-encoded genes, but retain small subsets of the genes they need to function in their own organelle DNA (oDNA). Different species retain different numbers of oDNA genes, and the reasons for these differences are not completely understood. Here, we use a mathematical model to explore the hypothesis that the energetic demands imposed by an organism's changing environment influence how many oDNA genes it retains. The model couples the physical biology of cell processes of gene expression and transport to a supply-and-demand model for the environmental dynamics to which an organism is exposed. The trade-off between fulfilling metabolic and bioenergetic environmental demands, and retaining genetic integrity, is quantified for a generic gene encoded either in oDNA or in nuclear DNA. Species in environments with high-amplitude, intermediate-frequency oscillations are predicted to retain the most organelle genes, whereas those in less dynamic or noisy environments the fewest. We discuss support for, and insight from, these predictions with oDNA data across eukaryotic taxa, including high oDNA gene counts in sessile organisms exposed to day-night and intertidal oscillations (including plants and algae) and low counts in parasites and fungi.},
}

Species Specificity
*Mitochondria
*Eukaryotic Cells
Eukaryota

@article {pmid36883292,
year = {2023},
author = {Gaugel, SM and Hawlitschek, O and Dey, LS and Husemann, M},
title = {Evolution of mitogenomic gene order in Orthoptera.},
journal = {Insect molecular biology},
volume = {32},
number = {4},
pages = {387-399},
doi = {10.1111/imb.12838},
pmid = {36883292},
issn = {1365-2583},
mesh = {Animals ; Phylogeny ; Gene Order ; *Mitochondria/genetics ; Genomics ; *Gryllidae ; Evolution, Molecular ; },
abstract = {Mitochondrial gene order has contributed to the elucidation of evolutionary relationships in several animal groups. It generally has found its application as a phylogenetic marker for deep nodes. Yet, in Orthoptera limited research has been performed on the gene order, although the group represents one of the oldest insect orders. We performed a comprehensive study on mitochondrial genome rearrangements (MTRs) within Orthoptera in the context of mitogenomic sequence-based phylogeny. We used 280 published mitogenome sequences from 256 species, including three outgroup species, to reconstruct a molecular phylogeny. Using a heuristic approach, we assigned MTR scenarios to the edges of the phylogenetic tree and reconstructed ancestral gene orders to identify possible synapomorphies in Orthoptera. We found all types of MTRs in our dataset: inversions, transpositions, inverse transpositions, and tandem-duplication/random loss events (TDRL). Most of the suggested MTRs were in single and unrelated species. Out of five MTRs which were unique in subgroups of Orthoptera, we suggest four of them to be synapomorphies; those were in the infraorder Acrididea, in the tribe Holochlorini, in the subfamily Pseudophyllinae, and in the two families Phalangopsidae and Gryllidae or their common ancestor (leading to the relationship ((Phalangopsidae + Gryllidae) + Trigonidiidae)). However, similar MTRs have been found in distant insect lineages. Our findings suggest convergent evolution of specific mitochondrial gene orders in several species, deviant from the evolution of the mitogenome DNA sequence. As most MTRs were detected at terminal nodes, a phylogenetic inference of deeper nodes based on MTRs is not supported. Hence, the marker does not seem to aid resolving the phylogeny of Orthoptera, but adds further evidence for the complex evolution of the whole group, especially at the genetic and genomic levels. The results indicate a high demand for more research on patterns and underlying mechanisms of MTR events in Orthoptera.},
}

Animals
Phylogeny
Gene Order
*Mitochondria/genetics
Genomics
*Gryllidae
Evolution, Molecular

@article {pmid36897956,
year = {2023},
author = {Smith, CH and Pinto, BJ and Kirkpatrick, M and Hillis, DM and Pfeiffer, JM and Havird, JC},
title = {A tale of two paths: The evolution of mitochondrial recombination in bivalves with doubly uniparental inheritance.},
journal = {The Journal of heredity},
volume = {114},
number = {3},
pages = {199-206},
pmid = {36897956},
issn = {1465-7333},
support = {R01 GM116853/GM/NIGMS NIH HHS/United States ; R35 GM142836/GM/NIGMS NIH HHS/United States ; R35-GM142836/NH/NIH HHS/United States ; },
mesh = {Animals ; Female ; Male ; Phylogeny ; Mitochondria/genetics ; *Bivalvia/genetics ; DNA, Mitochondrial/genetics ; Inheritance Patterns ; *Genome, Mitochondrial ; Recombination, Genetic ; },
abstract = {In most animals, mitochondrial DNA is strictly maternally inherited and non-recombining. One exception to this pattern is called doubly uniparental inheritance (DUI), a phenomenon involving the independent transmission of female and male mitochondrial genomes. DUI is known only from the molluskan class Bivalvia. The phylogenetic distribution of male-transmitted mitochondrial DNA (M mtDNA) in bivalves is consistent with several evolutionary scenarios, including multiple independent gains, losses, and varying degrees of recombination with female-transmitted mitochondrial DNA (F mtDNA). In this study, we use phylogenetic methods to test M mtDNA origination hypotheses and infer the prevalence of mitochondrial recombination in bivalves with DUI. Phylogenetic modeling using site concordance factors supported a single origin of M mtDNA in bivalves coupled with recombination acting over long evolutionary timescales. Ongoing mitochondrial recombination is present in Mytilida and Venerida, which results in a pattern of concerted evolution of F mtDNA and M mtDNA. Mitochondrial recombination could be favored to offset the deleterious effects of asexual inheritance and maintain mitonuclear compatibility across tissues. Cardiida and Unionida have gone without recent recombination, possibly due to an extension of the COX2 gene in male mitochondrial DNA. The loss of recombination could be connected to the role of M mtDNA in sex determination or sexual development. Our results support that recombination events may occur throughout the mitochondrial genomes of DUI species. Future investigations may reveal more complex patterns of inheritance of recombinants, which could explain the retention of signal for a single origination of M mtDNA in protein-coding genes.},
}

Animals
Female
Male
Phylogeny
Mitochondria/genetics
*Bivalvia/genetics
DNA, Mitochondrial/genetics
Inheritance Patterns
*Genome, Mitochondrial
Recombination, Genetic

@article {pmid36913593,
year = {2023},
author = {Swainsbury, DJK and Hawkings, FR and Martin, EC and Musiał, S and Salisbury, JH and Jackson, PJ and Farmer, DA and Johnson, MP and Siebert, CA and Hitchcock, A and Hunter, CN},
title = {Cryo-EM structure of the four-subunit Rhodobacter sphaeroides cytochrome bc1 complex in styrene maleic acid nanodiscs.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {120},
number = {12},
pages = {e2217922120},
pmid = {36913593},
issn = {1091-6490},
support = {BB/M000265/1//UKRI | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; BB/V006630/1//UKRI | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; },
mesh = {*Rhodobacter sphaeroides/chemistry ; Cytochromes c ; Cytochromes b ; Styrene ; Cryoelectron Microscopy ; Quinones ; Lipids ; Electron Transport Complex III ; Oxidation-Reduction ; Benzoquinones ; Maleates ; },
abstract = {Cytochrome bc1 complexes are ubiquinol:cytochrome c oxidoreductases, and as such, they are centrally important components of respiratory and photosynthetic electron transfer chains in many species of bacteria and in mitochondria. The minimal complex has three catalytic components, which are cytochrome b, cytochrome c1, and the Rieske iron-sulfur subunit, but the function of mitochondrial cytochrome bc1 complexes is modified by up to eight supernumerary subunits. The cytochrome bc1 complex from the purple phototrophic bacterium Rhodobacter sphaeroides has a single supernumerary subunit called subunit IV, which is absent from current structures of the complex. In this work we use the styrene-maleic acid copolymer to purify the R. sphaeroides cytochrome bc1 complex in native lipid nanodiscs, which retains the labile subunit IV, annular lipids, and natively bound quinones. The catalytic activity of the four-subunit cytochrome bc1 complex is threefold higher than that of the complex lacking subunit IV. To understand the role of subunit IV, we determined the structure of the four-subunit complex at 2.9 Å using single particle cryogenic electron microscopy. The structure shows the position of the transmembrane domain of subunit IV, which lies across the transmembrane helices of the Rieske and cytochrome c1 subunits. We observe a quinone at the Qo quinone-binding site and show that occupancy of this site is linked to conformational changes in the Rieske head domain during catalysis. Twelve lipids were structurally resolved, making contacts with the Rieske and cytochrome b subunits, with some spanning both of the two monomers that make up the dimeric complex.},
}

*Rhodobacter sphaeroides/chemistry
Cytochromes c
Cytochromes b
Styrene
Cryoelectron Microscopy
Quinones
Lipids
Electron Transport Complex III
Oxidation-Reduction
Benzoquinones
Maleates

@article {pmid36915058,
year = {2023},
author = {Zumkeller, S and Knoop, V},
title = {Categorizing 161 plant (streptophyte) mitochondrial group II introns into 29 families of related paralogues finds only limited links between intron mobility and intron-borne maturases.},
journal = {BMC ecology and evolution},
volume = {23},
number = {1},
pages = {5},
pmid = {36915058},
issn = {2730-7182},
mesh = {Introns/genetics ; *Evolution, Molecular ; *Mitochondria/genetics ; Plants/genetics ; Cell Nucleus ; },
abstract = {Group II introns are common in the two endosymbiotic organelle genomes of the plant lineage. Chloroplasts harbor 22 positionally conserved group II introns whereas their occurrence in land plant (embryophyte) mitogenomes is highly variable and specific for the seven major clades: liverworts, mosses, hornworts, lycophytes, ferns, gymnosperms and flowering plants. Each plant group features "signature selections" of ca. 20-30 paralogues from a superset of altogether 105 group II introns meantime identified in embryophyte mtDNAs, suggesting massive intron gains and losses along the backbone of plant phylogeny. We report on systematically categorizing plant mitochondrial group II introns into "families", comprising evidently related paralogues at different insertion sites, which may even be more similar than their respective orthologues in phylogenetically distant taxa. Including streptophyte (charophyte) algae extends our sampling to 161 and we sort 104 streptophyte mitochondrial group II introns into 25 core families of related paralogues evidently arising from retrotransposition events. Adding to discoveries of only recently created intron paralogues, hypermobile introns and twintrons, our survey led to further discoveries including previously overlooked "fossil" introns in spacer regions or e.g., in the rps8 pseudogene of lycophytes. Initially excluding intron-borne maturase sequences for family categorization, we added an independent analysis of maturase phylogenies and find a surprising incongruence between intron mobility and the presence of intron-borne maturases. Intriguingly, however, we find that several examples of nuclear splicing factors meantime characterized simultaneously facilitate splicing of independent paralogues now placed into the same intron families. Altogether this suggests that plant group II intron mobility, in contrast to their bacterial counterparts, is not intimately linked to intron-encoded maturases.},
}

Introns/genetics
*Evolution, Molecular
*Mitochondria/genetics
Plants/genetics
Cell Nucleus

@article {pmid36916992,
year = {2023},
author = {Monné, M and Cianciulli, A and Panaro, MA and Calvello, R and De Grassi, A and Palmieri, L and Mitolo, V and Palmieri, F},
title = {New Insights into the Evolution and Gene Structure of the Mitochondrial Carrier Family Unveiled by Analyzing the Frequent and Conserved Intron Positions.},
journal = {Molecular biology and evolution},
volume = {40},
number = {3},
pages = {},
pmid = {36916992},
issn = {1537-1719},
mesh = {Humans ; Introns ; Phylogeny ; *Mitochondria/genetics/metabolism ; *Membrane Transport Proteins/genetics ; Eukaryota/genetics ; Evolution, Molecular ; Conserved Sequence ; },
abstract = {Mitochondrial carriers (MCs) belong to a eukaryotic protein family of transporters that in higher organisms is called the solute carrier family 25 (SLC25). All MCs have characteristic triplicated sequence repeats forming a 3-fold symmetrical structure of a six-transmembrane α-helix bundle with a centrally located substrate-binding site. Biochemical characterization has shown that MCs altogether transport a wide variety of substrates but can be divided into subfamilies, each transporting a few specific substrates. We have investigated the intron positions in the human MC genes and their orthologs of highly diversified organisms. The results demonstrate that several intron positions are present in numerous MC sequences at the same specific points, of which some are 3-fold symmetry related. Many of these frequent intron positions are also conserved in subfamilies or in groups of subfamilies transporting similar substrates. The analyses of the frequent and conserved intron positions in MCs suggest phylogenetic relationships not only between close but also distant homologs as well as a possible involvement of the intron positions in the evolution of the substrate specificity diversification of the MC family members.},
}

Humans
Introns
Phylogeny
*Mitochondria/genetics/metabolism
*Membrane Transport Proteins/genetics
Eukaryota/genetics
Evolution, Molecular
Conserved Sequence

@article {pmid36921606,
year = {2023},
author = {Muñoz-Gómez, SA and Cadena, LR and Gardiner, AT and Leger, MM and Sheikh, S and Connell, LB and Bilý, T and Kopejtka, K and Beatty, JT and Koblížek, M and Roger, AJ and Slamovits, CH and Lukeš, J and Hashimi, H},
title = {Intracytoplasmic-membrane development in alphaproteobacteria involves the homolog of the mitochondrial crista-developing protein Mic60.},
journal = {Current biology : CB},
volume = {33},
number = {6},
pages = {1099-1111.e6},
doi = {10.1016/j.cub.2023.02.059},
pmid = {36921606},
issn = {1879-0445},
mesh = {*Mitochondrial Proteins/metabolism ; *Alphaproteobacteria/genetics/metabolism ; Mitochondrial Membranes/metabolism ; Mitochondria/metabolism ; Biological Evolution ; },
abstract = {Mitochondrial cristae expand the surface area of respiratory membranes and ultimately allow for the evolutionary scaling of respiration with cell volume across eukaryotes. The discovery of Mic60 homologs among alphaproteobacteria, the closest extant relatives of mitochondria, suggested that cristae might have evolved from bacterial intracytoplasmic membranes (ICMs). Here, we investigated the predicted structure and function of alphaproteobacterial Mic60, and a protein encoded by an adjacent gene Orf52, in two distantly related purple alphaproteobacteria, Rhodobacter sphaeroides and Rhodopseudomonas palustris. In addition, we assessed the potential physical interactors of Mic60 and Orf52 in R. sphaeroides. We show that the three α helices of mitochondrial Mic60's mitofilin domain, as well as its adjacent membrane-binding amphipathic helix, are present in alphaproteobacterial Mic60. The disruption of Mic60 and Orf52 caused photoheterotrophic growth defects, which are most severe under low light conditions, and both their disruption and overexpression led to enlarged ICMs in both studied alphaproteobacteria. We also found that alphaproteobacterial Mic60 physically interacts with BamA, the homolog of Sam50, one of the main physical interactors of eukaryotic Mic60. This interaction, responsible for making contact sites at mitochondrial envelopes, has been conserved in modern alphaproteobacteria despite more than a billion years of evolutionary divergence. Our results suggest a role for Mic60 in photosynthetic ICM development and contact site formation at alphaproteobacterial envelopes. Overall, we provide support for the hypothesis that mitochondrial cristae evolved from alphaproteobacterial ICMs and have therefore improved our understanding of the nature of the mitochondrial ancestor.},
}

*Mitochondrial Proteins/metabolism
*Alphaproteobacteria/genetics/metabolism
Mitochondrial Membranes/metabolism
Mitochondria/metabolism
Biological Evolution

@article {pmid36921696,
year = {2023},
author = {Lee, C and Ruhlman, TA and Jansen, RK},
title = {Rate accelerations in plastid and mitochondrial genomes of Cyperaceae occur in the same clades.},
journal = {Molecular phylogenetics and evolution},
volume = {182},
number = {},
pages = {107760},
doi = {10.1016/j.ympev.2023.107760},
pmid = {36921696},
issn = {1095-9513},
mesh = {Phylogeny ; Genome, Plant ; *Cyperaceae/genetics ; *Genome, Mitochondrial ; Evolution, Molecular ; *Magnoliopsida/genetics ; Plastids/genetics ; *Genome, Plastid ; },
abstract = {Cyperaceae, the second largest family in the monocot order Poales, comprises >5500 species and includes the genus Eleocharis with ∼ 250 species. A previous study of complete plastomes of two Eleocharis species documented extensive structural heteroplasmy, gene order changes, high frequency of dispersed repeats along with gene losses and duplications. To better understand the phylogenetic distribution of gene and intron content as well as rates and patterns of sequence evolution within and between mitochondrial and plastid genomes of Eleocharis and Cyperaceae, an additional 29 Eleocharis organelle genomes were sequenced and analyzed. Eleocharis experienced extensive gene loss in both genomes while loss of introns was mitochondria-specific. Eleocharis has higher rates of synonymous (dS) and nonsynonymous (dN) substitutions in the plastid and mitochondrion than most sampled angiosperms, and the pattern was distinct from other eudicot lineages with accelerated rates. Several clades showed higher dS and dN in mitochondrial genes than in plastid genes. Furthermore, nucleotide substitution rates of mitochondrial genes were significantly accelerated on the branch leading to Cyperaceae compared to most angiosperms. Mitochondrial genes of Cyperaceae exhibited dramatic loss of RNA editing sites and a negative correlation between RNA editing and dS values was detected among angiosperms. Mutagenic retroprocessing and dysfunction of DNA replication, repair and recombination genes are the most likely cause of striking rate accelerations and loss of edit sites and introns in Eleocharis and Cyperaceae organelle genomes.},
}

Phylogeny
Genome, Plant
*Cyperaceae/genetics
*Genome, Mitochondrial
Evolution, Molecular
*Magnoliopsida/genetics
Plastids/genetics
*Genome, Plastid

@article {pmid36929911,
year = {2023},
author = {Biot-Pelletier, D and Bettinazzi, S and Gagnon-Arsenault, I and Dubé, AK and Bédard, C and Nguyen, THM and Fiumera, HL and Breton, S and Landry, CR},
title = {Evolutionary Trajectories are Contingent on Mitonuclear Interactions.},
journal = {Molecular biology and evolution},
volume = {40},
number = {4},
pages = {},
pmid = {36929911},
issn = {1537-1719},
mesh = {*DNA, Mitochondrial/genetics ; Mitochondria/genetics ; Eukaryota/genetics ; Genotype ; *Genome, Mitochondrial ; Cell Nucleus/genetics ; },
abstract = {Critical mitochondrial functions, including cellular respiration, rely on frequently interacting components expressed from both the mitochondrial and nuclear genomes. The fitness of eukaryotic organisms depends on a tight collaboration between both genomes. In the face of an elevated rate of evolution in mtDNA, current models predict that the maintenance of mitonuclear compatibility relies on compensatory evolution of the nuclear genome. Mitonuclear interactions would therefore exert an influence on evolutionary trajectories. One prediction from this model is that the same nuclear genome evolving with different mitochondrial haplotypes would follow distinct molecular paths toward higher fitness. To test this prediction, we submitted 1,344 populations derived from 7 mitonuclear genotypes of Saccharomyces cerevisiae to >300 generations of experimental evolution in conditions that either select for a mitochondrial function or do not strictly require respiration for survival. Performing high-throughput phenotyping and whole-genome sequencing on independently evolved individuals, we identified numerous examples of gene-level evolutionary convergence among populations with the same mitonuclear background. Phenotypic and genotypic data on strains derived from this evolution experiment identify the nuclear genome and the environment as the main determinants of evolutionary divergence, but also show a modulating role for the mitochondrial genome exerted both directly and via interactions with the two other components. We finally recapitulated a subset of prominent loss-of-function alleles in the ancestral backgrounds and confirmed a generalized pattern of mitonuclear-specific and highly epistatic fitness effects. Together, these results demonstrate how mitonuclear interactions can dictate evolutionary divergence of populations with identical starting nuclear genotypes.},
}

*DNA, Mitochondrial/genetics
Mitochondria/genetics
Eukaryota/genetics
Genotype
*Genome, Mitochondrial
Cell Nucleus/genetics

@article {pmid36938916,
year = {2023},
author = {Jiao, J and Wang, X and Wei, C and Zhao, Y},
title = {Bioinspired Electrode for the Production and Timely Separation of Nitrile and Hydrogen.},
journal = {Small (Weinheim an der Bergstrasse, Germany)},
volume = {19},
number = {26},
pages = {e2208044},
doi = {10.1002/smll.202208044},
pmid = {36938916},
issn = {1613-6829},
support = {22102049//National Natural Science Foundation of China/ ; U22A20437//National Natural Science Foundation of China/ ; 222301420005//Joint Fund of Science and Technology R&D Plan of Henan Province/ ; },
abstract = {Replacing electrocatalytic oxygen evolution reaction (OER) with amine oxidation reaction is adopted to boost clean and environment-friendly energy source hydrogen (H2) in water. However, the electrocatalytic reaction is severely restricted by the strong adsorption of product on the catalyst surface. Inspired by the cooperation of flavin adenine dinucleotide and mitochondria membrane in biological system, the catalysis-separation complex electrodes are introduced to promote the desorption of product and hinder its readsorption by applying polytetrafluoroethylene (PTFE)-separation membrane on the one side of electrode, which is benefit for the cleanness of active sites on the catalyst surface for the continuous production and timely separation of nitrile and hydrogen. With the intermolecular force between PTFE and nitrile, the nitrile droplets can be quickly desorbed and separated from catalyst surface of anode, and the size of nitrile droplets on the catalyst surface is only 0.23% to that without PTFE. As a result, the current at 1.49 VRHE from the catalyst with PTFE membrane is about 33 times to that of catalyst without PTFE after long-term operation. Moreover, the cathode with PTFE membrane also achieves the rapid desorption of H2 bubbles and stable cathodic current because of the strong absorption of PTFE to H2 .},
}

@article {pmid36939357,
year = {2023},
author = {Macher, JN and Coots, NL and Poh, YP and Girard, EB and Langerak, A and Muñoz-Gómez, SA and Sinha, SD and Jirsová, D and Vos, R and Wissels, R and Gile, GH and Renema, W and Wideman, JG},
title = {Single-Cell Genomics Reveals the Divergent Mitochondrial Genomes of Retaria (Foraminifera and Radiolaria).},
journal = {mBio},
volume = {14},
number = {2},
pages = {e0030223},
pmid = {36939357},
issn = {2150-7511},
mesh = {Animals ; *Foraminifera/genetics ; *Genome, Mitochondrial ; Phylogeny ; Codon, Terminator ; *Rhizaria/genetics ; Genomics ; Eukaryota/genetics ; Amino Acids/genetics ; DNA, Mitochondrial/genetics ; },
abstract = {Mitochondria originated from an ancient bacterial endosymbiont that underwent reductive evolution by gene loss and endosymbiont gene transfer to the nuclear genome. The diversity of mitochondrial genomes published to date has revealed that gene loss and transfer processes are ongoing in many lineages. Most well-studied eukaryotic lineages are represented in mitochondrial genome databases, except for the superphylum Retaria-the lineage comprising Foraminifera and Radiolaria. Using single-cell approaches, we determined two complete mitochondrial genomes of Foraminifera and two nearly complete mitochondrial genomes of radiolarians. We report the complete coding content of an additional 14 foram species. We show that foraminiferan and radiolarian mitochondrial genomes contain a nearly fully overlapping but reduced mitochondrial gene complement compared to other sequenced rhizarians. In contrast to animals and fungi, many protists encode a diverse set of proteins on their mitochondrial genomes, including several ribosomal genes; however, some aerobic eukaryotic lineages (euglenids, myzozoans, and chlamydomonas-like algae) have reduced mitochondrial gene content and lack all ribosomal genes. Similar to these reduced outliers, we show that retarian mitochondrial genomes lack ribosomal protein and tRNA genes, contain truncated and divergent small and large rRNA genes, and contain only 14 or 15 protein-coding genes, including nad1, -3, -4, -4L, -5, and -7, cob, cox1, -2, and -3, and atp1, -6, and -9, with forams and radiolarians additionally carrying nad2 and nad6, respectively. In radiolarian mitogenomes, a noncanonical genetic code was identified in which all three stop codons encode amino acids. Collectively, these results add to our understanding of mitochondrial genome evolution and fill in one of the last major gaps in mitochondrial sequence databases. IMPORTANCE We present the reduced mitochondrial genomes of Retaria, the rhizarian lineage comprising the phyla Foraminifera and Radiolaria. By applying single-cell genomic approaches, we found that foraminiferan and radiolarian mitochondrial genomes contain an overlapping but reduced mitochondrial gene complement compared to other sequenced rhizarians. An alternative genetic code was identified in radiolarian mitogenomes in which all three stop codons encode amino acids. Collectively, these results shed light on the divergent nature of the mitochondrial genomes from an ecologically important group, warranting further questions into the biological underpinnings of gene content variability and genetic code variation between mitochondrial genomes.},
}

Animals
*Foraminifera/genetics
*Genome, Mitochondrial
Phylogeny
Codon, Terminator
*Rhizaria/genetics
Genomics
Eukaryota/genetics
Amino Acids/genetics
DNA, Mitochondrial/genetics

@article {pmid36944988,
year = {2023},
author = {Yu, X and Wei, P and Chen, Z and Li, X and Zhang, W and Yang, Y and Liu, C and Zhao, S and Li, X and Liu, X},
title = {Comparative analysis of the organelle genomes of three Rhodiola species provide insights into their structural dynamics and sequence divergences.},
journal = {BMC plant biology},
volume = {23},
number = {1},
pages = {156},
pmid = {36944988},
issn = {1471-2229},
support = {XZ202001YD0028C//Local Development Funds of Science and Technology Department of Tibet/ ; 413100105//Plateau Ecology Youth Innovative Fund of Wuhan University/ ; },
mesh = {*Rhodiola/genetics ; Phylogeny ; *Genome, Plastid ; Tibet ; Mitochondria/genetics ; *Genome, Mitochondrial/genetics ; Evolution, Molecular ; },
abstract = {BACKGROUND: Plant organelle genomes are a valuable resource for evolutionary biology research, yet their genome architectures, evolutionary patterns and environmental adaptations are poorly understood in many lineages. Rhodiola species is a type of flora mainly distributed in highland habitats, with high medicinal value. Here, we assembled the organelle genomes of three Rhodiola species (R. wallichiana, R. crenulata and R. sacra) collected from the Qinghai-Tibet plateau (QTP), and compared their genome structure, gene content, structural rearrangements, sequence transfer and sequence evolution rates.

RESULTS: The results demonstrated the contrasting evolutionary pattern between plastomes and mitogenomes in three Rhodiola species, with the former possessing more conserved genome structure but faster evolutionary rates of sequence, while the latter exhibiting structural diversity but slower rates of sequence evolution. Some lineage-specific features were observed in Rhodiola mitogenomes, including chromosome fission, gene loss and structural rearrangement. Repeat element analysis shows that the repeats occurring between the two chromosomes may mediate the formation of multichromosomal structure in the mitogenomes of Rhodiola, and this multichromosomal structure may have recently formed. The identification of homologous sequences between plastomes and mitogenomes reveals several unidirectional protein-coding gene transfer events from chloroplasts to mitochondria. Moreover, we found that their organelle genomes contained multiple fragments of nuclear transposable elements (TEs) and exhibited different preferences for TEs insertion type. Genome-wide scans of positive selection identified one gene matR from the mitogenome. Since the matR is crucial for plant growth and development, as well as for respiration and stress responses, our findings suggest that matR may participate in the adaptive response of Rhodiola species to environmental stress of QTP.

CONCLUSION: The study analyzed the organelle genomes of three Rhodiola species and demonstrated the contrasting evolutionary pattern between plastomes and mitogenomes. Signals of positive selection were detected in the matR gene of Rhodiola mitogenomes, suggesting the potential role of this gene in Rhodiola adaptation to QTP. Together, the study is expected to enrich the genomic resources and provide valuable insights into the structural dynamics and sequence divergences of Rhodiola species.},
}

*Rhodiola/genetics
Phylogeny
*Genome, Plastid
Tibet
Mitochondria/genetics
*Genome, Mitochondrial/genetics
Evolution, Molecular

@article {pmid36948134,
year = {2023},
author = {Celik, A and Orfany, A and Dearling, J and Del Nido, PJ and McCully, JD and Bakar-Ates, F},
title = {Mitochondrial transplantation: Effects on chemotherapy in prostate and ovarian cancer cells in vitro and in vivo.},
journal = {Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie},
volume = {161},
number = {},
pages = {114524},
doi = {10.1016/j.biopha.2023.114524},
pmid = {36948134},
issn = {1950-6007},
mesh = {Male ; Female ; Humans ; Animals ; Mice ; Prostate/pathology ; Apoptosis ; Cell Line, Tumor ; *Ovarian Neoplasms/pathology ; Mitochondria ; Cisplatin/pharmacology ; Drug Resistance, Neoplasm ; *Antineoplastic Agents/pharmacology/therapeutic use ; },
abstract = {Prostate and ovarian cancers affect the male and female reproductive organs and are among the most common cancers in developing countries. Previous studies have demonstrated that cancer cells have a high rate of aerobic glycolysis that is present in nearly all invasive human cancers and persists even under normoxic conditions. Aerobic glycolysis has been correlated with chemotherapeutic resistance and tumor aggressiveness. These data suggest that mitochondrial dysfunction may confer a significant proliferative advantage during the somatic evolution of cancer. In this study we investigated the effect of direct mitochondria transplantation on cancer cell proliferation and chemotherapeutic sensitivity in prostate and ovarian cancer models, both in vitro and in vivo. Our results show that the transplantation of viable, respiration competent mitochondria has no effect on cancer cell proliferation but significantly decreases migration and alters cell cycle checkpoints. Our results further demonstrate that mitochondrial transplantation significantly increases chemotherapeutic sensitivity, providing similar apoptotic levels with low-dose chemotherapy as that achieved with high-dose chemotherapy. These results suggest that mitochondria transplantation provides a novel approach for early prostate and ovarian cancer therapy, significantly increasing chemotherapeutic sensitivity in in vitro and in vivo murine models.},
}

Male
Female
Humans
Animals
Mice
Prostate/pathology
Apoptosis
Cell Line, Tumor
*Ovarian Neoplasms/pathology
Mitochondria
Cisplatin/pharmacology
Drug Resistance, Neoplasm
*Antineoplastic Agents/pharmacology/therapeutic use

@article {pmid36948470,
year = {2023},
author = {Cayuela, H and Gaillard, JM and Vieira, C and Ronget, V and Gippet, JMW and Conde García, T and Marais, GAB and Lemaître, JF},
title = {Sex differences in adult lifespan and aging rate across mammals: A test of the 'Mother Curse hypothesis'.},
journal = {Mechanisms of ageing and development},
volume = {212},
number = {},
pages = {111799},
doi = {10.1016/j.mad.2023.111799},
pmid = {36948470},
issn = {1872-6216},
mesh = {Humans ; Animals ; Female ; Male ; *Longevity/genetics ; *Mothers ; Sex Characteristics ; Aging ; DNA, Mitochondrial/genetics ; Drosophila ; Mammals ; },
abstract = {In many animal species, including humans, males have shorter lifespan and show faster survival aging than females. This differential increase in mortality between sexes could result from the accumulation of deleterious mutations in the mitochondrial genome of males due to the maternal mode of mtDNA inheritance. To date, empirical evidence supporting the existence of this mechanism - called the Mother Curse hypothesis - remains largely limited to a few study cases in humans and Drosophila. In this study, we tested whether the Mother Curse hypothesis accounts for sex differences in lifespan and aging rate across 128 populations of mammals (60 and 68 populations studied in wild and captive conditions, respectively) encompassing 104 species. We found that adult lifespan decreases with increasing mtDNA neutral substitution rate in both sexes in a similar way in the wild - but not in captivity. Moreover, the aging rate marginally increased with neutral substitution rate in males and females in the wild. Overall, these results indicate that the Mother Curse hypothesis is not supported across mammals. We further discuss the implication of these findings for our understanding of the evolution of sex differences in mortality and aging.},
}

Humans
Animals
Female
Male
*Longevity/genetics
*Mothers
Sex Characteristics
Aging
DNA, Mitochondrial/genetics
Drosophila
Mammals

@article {pmid36949187,
year = {2023},
author = {Mühleip, A and Flygaard, RK and Baradaran, R and Haapanen, O and Gruhl, T and Tobiasson, V and Maréchal, A and Sharma, V and Amunts, A},
title = {Structural basis of mitochondrial membrane bending by the I-II-III2-IV2 supercomplex.},
journal = {Nature},
volume = {615},
number = {7954},
pages = {934-938},
pmid = {36949187},
issn = {1476-4687},
support = {MR/M00936X/1/MRC_/Medical Research Council/United Kingdom ; MR/T032154/1/MRC_/Medical Research Council/United Kingdom ; },
mesh = {*Cryoelectron Microscopy ; Electron Transport ; *Electron Transport Complex III/chemistry/metabolism/ultrastructure ; *Electron Transport Complex IV/chemistry/metabolism/ultrastructure ; *Mitochondria/chemistry/enzymology/metabolism/ultrastructure ; *Mitochondrial Membranes/chemistry/enzymology/metabolism/ultrastructure ; *Electron Transport Complex II/chemistry/metabolism/ultrastructure ; *Electron Transport Complex I/chemistry/metabolism/ultrastructure ; Protein Multimerization ; Protein Subunits/chemistry/metabolism ; Molecular Dynamics Simulation ; Binding Sites ; Evolution, Molecular ; },
abstract = {Mitochondrial energy conversion requires an intricate architecture of the inner mitochondrial membrane[1]. Here we show that a supercomplex containing all four respiratory chain components contributes to membrane curvature induction in ciliates. We report cryo-electron microscopy and cryo-tomography structures of the supercomplex that comprises 150 different proteins and 311 bound lipids, forming a stable 5.8-MDa assembly. Owing to subunit acquisition and extension, complex I associates with a complex IV dimer, generating a wedge-shaped gap that serves as a binding site for complex II. Together with a tilted complex III dimer association, it results in a curved membrane region. Using molecular dynamics simulations, we demonstrate that the divergent supercomplex actively contributes to the membrane curvature induction and tubulation of cristae. Our findings highlight how the evolution of protein subunits of respiratory complexes has led to the I-II-III2-IV2 supercomplex that contributes to the shaping of the bioenergetic membrane, thereby enabling its functional specialization.},
}

*Cryoelectron Microscopy
Electron Transport
*Electron Transport Complex III/chemistry/metabolism/ultrastructure
*Electron Transport Complex IV/chemistry/metabolism/ultrastructure
*Mitochondria/chemistry/enzymology/metabolism/ultrastructure
*Mitochondrial Membranes/chemistry/enzymology/metabolism/ultrastructure
*Electron Transport Complex II/chemistry/metabolism/ultrastructure
*Electron Transport Complex I/chemistry/metabolism/ultrastructure
Protein Multimerization
Protein Subunits/chemistry/metabolism
Molecular Dynamics Simulation
Binding Sites
Evolution, Molecular

@article {pmid36951086,
year = {2023},
author = {Sloan, DB and DeTar, RA and Warren, JM},
title = {Aminoacyl-tRNA Synthetase Evolution within the Dynamic Tripartite Translation System of Plant Cells.},
journal = {Genome biology and evolution},
volume = {15},
number = {4},
pages = {},
pmid = {36951086},
issn = {1759-6653},
mesh = {Animals ; *Amino Acyl-tRNA Synthetases/genetics/metabolism ; Plant Cells/metabolism ; Amino Acid Sequence ; Cytosol/metabolism ; RNA, Transfer/genetics/metabolism ; },
abstract = {Eukaryotes maintain separate protein translation systems for nuclear and organellar genes, including distinct sets of tRNAs and aminoacyl-tRNA synthetases (aaRSs). In animals, mitochondrial-targeted aaRSs are expressed at lower levels and are less conserved in sequence than cytosolic aaRSs involved in translation of nuclear mRNAs, likely reflecting lower translational demands in mitochondria. In plants, translation is further complicated by the presence of plastids, which share most aaRSs with mitochondria. In addition, plant mitochondrial tRNA pools have a dynamic history of gene loss and functional replacement by tRNAs from other compartments. To investigate the consequences of these distinctive features of translation in plants, we analyzed sequence evolution in angiosperm aaRSs. In contrast to previously studied eukaryotic systems, we found that plant organellar and cytosolic aaRSs exhibit only a small difference in expression levels, and organellar aaRSs are slightly more conserved than cytosolic aaRSs. We hypothesize that these patterns result from high translational demands associated with photosynthesis in mature chloroplasts. We also investigated aaRS evolution in Sileneae, an angiosperm lineage with extensive mitochondrial tRNA replacement and aaRS retargeting. We predicted positive selection for changes in aaRS sequence resulting from these recent changes in subcellular localization and tRNA substrates but found little evidence for accelerated sequence divergence. Overall, the complex tripartite translation system in plant cells appears to have imposed more constraints on the long-term evolutionary rates of organellar aaRSs compared with other eukaryotic lineages, and plant aaRS protein sequences appear largely robust to more recent perturbations in subcellular localization and tRNA interactions.},
}

Animals
*Amino Acyl-tRNA Synthetases/genetics/metabolism
Plant Cells/metabolism
Amino Acid Sequence
Cytosol/metabolism
RNA, Transfer/genetics/metabolism

@article {pmid36964263,
year = {2023},
author = {Jablonski, D and Ribeiro-Júnior, MA and Simonov, E and Šoltys, K and Meiri, S},
title = {A new, rare, small-ranged, and endangered mountain snake of the genus Elaphe from the Southern Levant.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {4839},
pmid = {36964263},
issn = {2045-2322},
mesh = {Animals ; Phylogeny ; *Colubridae ; Mitochondria/genetics ; Lebanon ; Syria ; DNA, Mitochondrial/genetics ; },
abstract = {The genus Elaphe Fitzinger, 1833 includes 17 species of charismatic, large-sized, non-venomous, Eurasian snakes. In the Western Palearctic, the genus is represented by three species from the Elaphe quatuorlineata group ranging from the Apennine peninsula to Central Asia. The southernmost population of this group is distributed in the mountains of the Southern Levant, with more than 400 km gap to other Elaphe populations. This population has been known to science for only 50 years and is virtually unstudied due to its extreme rarity. We studied these snakes' morphological and genetic variation from the three countries where they are known to occur, i.e., Israel (Hermon, the Israeli-controlled Golan Heights), Lebanon, and Syria. We used nine mitochondrial and nuclear genes, complete mitogenome sequences, and a comprehensive morphological examination including published data, our own field observations, and museum specimens, to study its relationship to other species in the group. The three currently recognized species of the group (E. quatuorlineata, E. sauromates, E. urartica), and the Levant population, form four deeply divergent, strongly supported clades. Three of these clades correspond to the abovementioned species while the Southern Levant clade, which is genetically and morphologically distinct from all named congeners, is described here as a new species, Elaphe druzei sp. nov. The basal divergence of this group is estimated to be the Late Miocene with subsequent radiation from 5.1 to 3.9 Mya. The revealed biogeography of the E. quatuorlineata group supports the importance of the Levant as a major center of endemism and diversity of biota in Eurasia. The new species is large-sized and is one of the rarest snakes in the Western Palearctic. Because of its small mountain distribution range, in an area affected by land use and climate change, the new Elaphe urgently needs strict protection. Despite political issues, we hope this will be based on the cooperation of all countries where the new species occurs.},
}

Animals
Phylogeny
*Colubridae
Mitochondria/genetics
Lebanon
Syria
DNA, Mitochondrial/genetics

@article {pmid36965057,
year = {2023},
author = {Speijer, D},
title = {How mitochondria showcase evolutionary mechanisms and the importance of oxygen.},
journal = {BioEssays : news and reviews in molecular, cellular and developmental biology},
volume = {45},
number = {6},
pages = {e2300013},
doi = {10.1002/bies.202300013},
pmid = {36965057},
issn = {1521-1878},
mesh = {*Biological Evolution ; *Oxygen/metabolism ; Eukaryota/metabolism ; Bacteria/genetics/metabolism ; Mitochondria/metabolism ; },
abstract = {Darwinian evolution can be simply stated: natural selection of inherited variations increasing differential reproduction. However, formulated thus, links with biochemistry, cell biology, ecology, and population dynamics remain unclear. To understand interactive contributions of chance and selection, higher levels of biological organization (e.g., endosymbiosis), complexities of competing selection forces, and emerging biological novelties (such as eukaryotes or meiotic sex), we must analyze actual examples. Focusing on mitochondria, I will illuminate how biology makes sense of life's evolution, and the concepts involved. First, looking at the bacterium - mitochondrion transition: merging with an archaeon, it lost its independence, but played a decisive role in eukaryogenesis, as an extremely efficient aerobic ATP generator and internal ROS source. Second, surveying later mitochondrion adaptations and diversifications illustrates concepts such as constructive neutral evolution, dynamic interactions between endosymbionts and hosts, the contingency of life histories, and metabolic reprogramming. Without oxygen, mitochondria disappear; with (intermittent) oxygen diversification occurs in highly complex ways, especially upon (temporary) phototrophic substrate supply. These expositions show the Darwinian model to be a highly fruitful paradigm.},
}

*Biological Evolution
*Oxygen/metabolism
Eukaryota/metabolism
Bacteria/genetics/metabolism
Mitochondria/metabolism

@article {pmid36966978,
year = {2023},
author = {Edera, AA and Howell, KA and Nevill, PG and Small, I and Sanchez-Puerta, MV},
title = {Evolution of cox2 introns in angiosperm mitochondria and efficient splicing of an elongated cox2i691 intron.},
journal = {Gene},
volume = {869},
number = {},
pages = {147393},
doi = {10.1016/j.gene.2023.147393},
pmid = {36966978},
issn = {1879-0038},
mesh = {Introns/genetics ; *Magnoliopsida/genetics ; Mitochondria/genetics ; RNA Splicing ; Base Sequence ; },
abstract = {In angiosperms, the mitochondrial cox2 gene harbors up to two introns, commonly referred to as cox2i373 and cox2i691. We studied the cox2 from 222 fully-sequenced mitogenomes from 30 angiosperm orders and analyzed the evolution of their introns. Unlike cox2i373, cox2i691 shows a distribution among plants that is shaped by frequent intron loss events driven by localized retroprocessing. In addition, cox2i691 exhibits sporadic elongations, frequently in domain IV of introns. Such elongations are poorly related to repeat content and two of them showed the presence of LINE transposons, suggesting that increasing intron size is very likely due to nuclear intracelular DNA transfer followed by incorporation into the mitochondrial DNA. Surprisingly, we found that cox2i691 is erroneously annotated as absent in 30 mitogenomes deposited in public databases. Although each of the cox2 introns is ∼1.5 kb in length, a cox2i691 of 4.2 kb has been reported in Acacia ligulata (Fabaceae). It is still unclear whether its unusual length is due to a trans-splicing arrangement or the loss of functionality of the interrupted cox2. Through analyzing short-read RNA sequencing of Acacia with a multi-step computational strategy, we found that the Acacia cox2 is functional and its long intron is spliced in cis in a very efficient manner despite its length.},
}

Introns/genetics
*Magnoliopsida/genetics
Mitochondria/genetics
RNA Splicing
Base Sequence

@article {pmid36971557,
year = {2023},
author = {Shaliutina-Loginova, A and Francetic, O and Doležal, P},
title = {Bacterial Type II Secretion System and Its Mitochondrial Counterpart.},
journal = {mBio},
volume = {14},
number = {2},
pages = {e0314522},
pmid = {36971557},
issn = {2150-7511},
mesh = {*Type II Secretion Systems/metabolism ; Bacterial Proteins/genetics/metabolism ; Gram-Negative Bacteria/metabolism ; Periplasm/metabolism ; Bacterial Secretion Systems/metabolism ; },
abstract = {Over the billions of years that bacteria have been around, they have evolved several sophisticated protein secretion nanomachines to deliver toxins, hydrolytic enzymes, and effector proteins into their environments. Of these, the type II secretion system (T2SS) is used by Gram-negative bacteria to export a wide range of folded proteins from the periplasm across the outer membrane. Recent findings have demonstrated that components of the T2SS are localized in mitochondria of some eukaryotic lineages, and their behavior is consistent with the presence of a mitochondrial T2SS-derived system (miT2SS). This review focuses on recent advances in the field and discusses open questions concerning the function and evolution of miT2SSs.},
}

*Type II Secretion Systems/metabolism
Bacterial Proteins/genetics/metabolism
Gram-Negative Bacteria/metabolism
Periplasm/metabolism
Bacterial Secretion Systems/metabolism

@article {pmid36977381,
year = {2023},
author = {Michels, PAM and Ginger, ML},
title = {Evolution: 'Millefoglie' origin of mitochondrial cristae.},
journal = {Current biology : CB},
volume = {33},
number = {6},
pages = {R219-R221},
doi = {10.1016/j.cub.2023.02.037},
pmid = {36977381},
issn = {1879-0445},
mesh = {*Mitochondria/genetics/metabolism ; *Mitochondrial Proteins/genetics/metabolism ; Mitochondrial Membranes/metabolism ; },
abstract = {Striated intracytoplasmic membranes in alphaproteobacteria are often reminiscent of millefoglie pastries. A new study reveals a protein complex homologous to that responsible for mitochondrial cristae formation drives intracytoplasmic membrane formation, thereby establishing bacterial ancestry for the biogenesis of mitochondrial cristae.},
}

*Mitochondria/genetics/metabolism
*Mitochondrial Proteins/genetics/metabolism
Mitochondrial Membranes/metabolism

@article {pmid36980901,
year = {2023},
author = {Hammar, F and Miller, DL},
title = {Genetic Diversity in the mtDNA of Physarum polycephalum.},
journal = {Genes},
volume = {14},
number = {3},
pages = {},
pmid = {36980901},
issn = {2073-4425},
mesh = {*Physarum polycephalum/genetics ; DNA, Mitochondrial/genetics ; Base Sequence ; Mitochondria/genetics ; Genetic Variation/genetics ; },
abstract = {The mtDNA of the myxomycete Physarum polycephalum can contain as many as 81 genes. These genes can be grouped in three different categories. The first category includes 46 genes that are classically found on the mtDNA of many organisms. However, 43 of these genes are cryptogenes that require a unique type of RNA editing (MICOTREM). A second category of gene is putative protein-coding genes represented by 26 significant open reading frames. However, these genes do not appear to be transcribed during the growth of the plasmodium and are currently unassigned since they do not have any apparent similarity to other classical mitochondrial protein-coding genes. The third category of gene is found in the mtDNA of some strains of P. polycephalum. These genes derive from a linear mitochondrial plasmid with nine significant, but unassigned, open reading frames which can integrate into the mitochondrial DNA by recombination. Here, we review the mechanism and evolution of the RNA editing necessary for cryptogene expression, discuss possible origins for the 26 unassigned open reading frames based on tentative identification of their protein product, and discuss the implications to mtDNA structure and replication of the integration of the linear mitochondrial plasmid.},
}

*Physarum polycephalum/genetics
DNA, Mitochondrial/genetics
Base Sequence
Mitochondria/genetics
Genetic Variation/genetics

@article {pmid36993903,
year = {2023},
author = {Dalle Carbonare, L and Jiménez, JC and Lichtenauer, S and van Veen, H},
title = {Plant responses to limited aeration: Advances and future challenges.},
journal = {Plant direct},
volume = {7},
number = {3},
pages = {e488},
pmid = {36993903},
issn = {2475-4455},
abstract = {Limited aeration that is caused by tissue geometry, diffusion barriers, high elevation, or a flooding event poses major challenges to plants and is often, but not exclusively, associated with low oxygen. These processes span a broad interest in the research community ranging from whole plant and crop responses, post-harvest physiology, plant morphology and anatomy, fermentative metabolism, plant developmental processes, oxygen sensing by ERF-VIIs, gene expression profiles, the gaseous hormone ethylene, and O2 dynamics at cellular resolution. The International Society for Plant Anaerobiosis (ISPA) gathers researchers from all over the world contributing to understand the causes, responses, and consequences of limited aeration in plants. During the 14th ISPA meeting, major research progress was related to the evolution of O2 sensing mechanisms and the intricate network that balances low O2 signaling. Here, the work moved beyond flooding stress and emphasized novel underexplored roles of low O2 and limited aeration in altitude adaptation, fruit development and storage, and the vegetative development of growth apices. Regarding tolerance towards flooding, the meeting stressed the relevance and regulation of developmental plasticity, aerenchyma, and barrier formation to improve internal aeration. Additional newly explored flood tolerance traits concerned resource balance, senescence, and the exploration of natural genetic variation for novel tolerance loci. In this report, we summarize and synthesize the major progress and future challenges for low O2 and aeration research presented at the conference.},
}

@article {pmid36994538,
year = {2023},
author = {Qiu, L and Dong, J and Li, X and Parey, SH and Tan, K and Orr, M and Majeed, A and Zhang, X and Luo, S and Zhou, X and Zhu, C and Ji, T and Niu, Q and Liu, S and Zhou, X},
title = {Defining honeybee subspecies in an evolutionary context warrants strategized conservation.},
journal = {Zoological research},
volume = {44},
number = {3},
pages = {483-493},
pmid = {36994538},
issn = {2095-8137},
mesh = {Bees/genetics ; Animals ; Phylogeny ; Phenotype ; *Mitochondria ; },
abstract = {Despite the urgent need for conservation consideration, strategic action plans for the preservation of the Asian honeybee, Apis cerana Fabricius, 1793, remain lacking. Both the convergent and divergent adaptations of this widespread insect have led to confusing phenotypical traits and inconsistent infraspecific taxonomy. Unclear subspecies boundaries pose a significant challenge to honeybee conservation efforts, as it is difficult to effectively prioritize conservation targets without a clear understanding of subspecies identities. Here, we investigated genome variations in 362 worker bees representing almost all populations of mainland A. cerana to understand how evolution has shaped its population structure. Whole-genome single nucleotide polymorphisms (SNPs) based on nuclear sequences revealed eight putative subspecies, with all seven peripheral subspecies exhibiting mutually exclusive monophyly and distinct genetic divergence from the widespread central subspecies. Our results demonstrated that most classic morphological traits, including body size, were related to the climatic variables of the local habitats and did not reflect the true evolutionary history of the organism. Thus, such morphological traits were not suitable for subspecific delineation. Conversely, wing vein characters showed relative independence to the environment and supported the subspecies boundaries inferred from nuclear genomes. Mitochondrial phylogeny further indicated that the present subspecies structure was a result of multiple waves of population divergence from a common ancestor. Based on our findings, we propose that criteria for subspecies delineation should be based on evolutionary independence, trait distinction, and geographic isolation. We formally defined and described eight subspecies of mainland A. cerana. Elucidation of the evolutionary history and subspecies boundaries enables a customized conservation strategy for both widespread and endemic honeybee conservation units, guiding colony introduction and breeding.},
}

Bees/genetics
Animals
Phylogeny
Phenotype
*Mitochondria

@article {pmid37021319,
year = {2023},
author = {Grosser, MR and Sites, SK and Murata, MM and Lopez, Y and Chamusco, KC and Love Harriage, K and Grosser, JW and Graham, JH and Gmitter, FG and Chase, CD},
title = {Plant mitochondrial introns as genetic markers - conservation and variation.},
journal = {Frontiers in plant science},
volume = {14},
number = {},
pages = {1116851},
pmid = {37021319},
issn = {1664-462X},
abstract = {Plant genomes are comprised of nuclear, plastid and mitochondrial components characterized by different patterns of inheritance and evolution. Genetic markers from the three genomes provide complementary tools for investigations of inheritance, genetic relationships and phenotypic contributions. Plant mitochondrial genomes are challenging for universal marker development because they are highly variable in terms of size, gene order and intergenic sequences and highly conserved with respect to protein-coding sequences. PCR amplification of introns with primers that anneal to conserved, flanking exons is effective for the development of polymorphic nuclear genome markers. The potential for plant mitochondrial intron polymorphisms to distinguish between congeneric species or intraspecific varieties has not been systematically investigated and is possibly constrained by requirements for intron secondary structure and interactions with co-evolved organelle intron splicing factors. To explore the potential for broadly applicable plant mitochondrial intron markers, PCR primer sets based upon conserved sequences flanking 11 introns common to seven angiosperm species were tested across a range of plant orders. PCR-amplified introns were screened for indel polymorphisms among a group of cross-compatible Citrus species and relatives; two Raphanus sativus mitotypes; representatives of the two Phaseolus vulgaris gene pools; and congeneric pairs of Cynodon, Cenchrus, Solanum, and Vaccinium species. All introns were successfully amplified from each plant entry. Length polymorphisms distinguishable by gel electrophoresis were common among genera but infrequent within genera. Sequencing of three introns amplified from 16 entries identified additional short indel polymorphisms and nucleotide substitutions that separated Citrus, Cynodon, Cenchrus and Vaccinium congeners, but failed to distinguish Solanum congeners or representatives of the Phaseolus vulgaris major gene pools. The ability of primer sets to amplify a wider range of plant species' introns and the presence of intron polymorphisms that distinguish congeners was confirmed by in silico analysis. While mitochondrial intron variation is limited in comparison to nuclear introns, these exon-based primer sets provide robust tools for the amplification of mitochondrial introns across a wide range of plant species wherein useful polymorphisms can be identified.},
}

@article {pmid37023388,
year = {2023},
author = {Danial, JSH and Jenner, A and Garcia-Saez, AJ and Cosentino, K},
title = {Real-Time Growth Kinetics Analysis of Macromolecular Assemblies in Cells with Single Molecule Resolution.},
journal = {The journal of physical chemistry. A},
volume = {127},
number = {15},
pages = {3490-3496},
doi = {10.1021/acs.jpca.3c00368},
pmid = {37023388},
issn = {1520-5215},
mesh = {Kinetics ; *Software ; },
abstract = {Single molecule fluorescence microscopy has the unique advantage to provide real-time information on the spatiotemporal assembly of individual protein complexes in cellular membranes. This includes the assembly of proteins into oligomer species of numerous copy numbers. However, there is a need for improved tracing analysis of the real-time growth kinetics of these assemblies in cells with single molecule resolution. Here, we present an automated analysis software to accurately measure the real-time kinetics of assembly of individual high-order oligomer complexes. Our software comes with a simple Graphical User Interface (GUI), is available as a source code and an executable, and can analyze a full data set of several hundred to thousand molecules in less than 2 minutes. Importantly, this software is suitable for the analysis of intracellular protein oligomers, whose stoichiometry is usually more difficult to quantify due to variability in signal detection in the different areas of the cell. We validated our method with simulated ground-truth data and time-lapse images of diffraction-limited oligomeric assemblies of BAX and BAK proteins on mitochondria of cells undergoing apoptosis. Our approach provides the broad community of biologists with a fast, user-friendly tool to trace the compositional evolution of macromolecular assemblies, and potentially model their growth for a deeper understanding of the structural and biophysical mechanisms underlying their functions.},
}

Kinetics
*Software

@article {pmid37029959,
year = {2023},
author = {Galindo, LJ and Prokina, K and Torruella, G and López-García, P and Moreira, D},
title = {Maturases and Group II Introns in the Mitochondrial Genomes of the Deepest Jakobid Branch.},
journal = {Genome biology and evolution},
volume = {15},
number = {4},
pages = {},
pmid = {37029959},
issn = {1759-6653},
mesh = {Humans ; Introns ; Phylogeny ; *Genome, Mitochondrial ; Eukaryota/genetics ; Eukaryotic Cells ; },
abstract = {Ophirinina is a recently described suborder of jakobid protists (Excavata) with only one described species to date, Ophirina amphinema. Despite the acquisition and analysis of massive transcriptomic and mitogenomic sequence data from O. amphinema, its phylogenetic position among excavates remained inconclusive, branching as sister group either to all Jakobida or to all Discoba. From a morphological perspective, it has not only several typical jakobid features but also unusual traits for this group, including the morphology of mitochondrial cristae (sac-shaped to flattened-curved cristae) and the presence of two flagellar vanes. In this study, we have isolated, morphologically characterized, and sequenced genome and transcriptome data of two new Ophirinina species: Ophirina chinija sp. nov. and Agogonia voluta gen. et sp. nov. Ophirina chinija differs from O. amphinema in having rounded cell ends, subapically emerging flagella and a posterior cell protrusion. The much more distantly related A. voluta has several unique ultrastructural characteristics, including sac-shaped mitochondrial cristae and a complex "B" fiber. Phylogenomic analyses with a large conserved-marker dataset supported the monophyly of Ophirina and Agogonia within the Ophirinina and, more importantly, resolved the conflicting position of ophirinids as the sister clade to all other jakobids. The characterization of the mitochondrial genomes showed that Agogonia differs from all known gene-rich jakobid mitogenomes by the presence of two group II introns and their corresponding maturase protein genes. A phylogenetic analysis of the diversity of known maturases confirmed that the Agogonia proteins are highly divergent from each other and define distant families among the prokaryotic and eukaryotic maturases. This opens the intriguing possibility that, compared to other jakobids, Ophirinina may have retained additional mitochondrial elements that may help to understand the early diversification of eukaryotes and the evolution of mitochondria.},
}

Humans
Introns
Phylogeny
*Genome, Mitochondrial
Eukaryota/genetics
Eukaryotic Cells

@article {pmid37039888,
year = {2023},
author = {Zuccoli, GS and Nascimento, JM and Moraes-Vieira, PM and Rehen, SK and Martins-de-Souza, D},
title = {Mitochondrial, cell cycle control and neuritogenesis alterations in an iPSC-based neurodevelopmental model for schizophrenia.},
journal = {European archives of psychiatry and clinical neuroscience},
volume = {273},
number = {8},
pages = {1649-1664},
pmid = {37039888},
issn = {1433-8491},
support = {2016/04912-2//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2018/14666-4//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2014/21035-0//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2015/15626-8//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2017/25588-1//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2019/00098-7//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2018/01410-1//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; },
mesh = {Adult ; Humans ; *Schizophrenia/metabolism ; *Induced Pluripotent Stem Cells/metabolism ; Cell Differentiation/genetics ; Reactive Oxygen Species/metabolism ; Proteomics ; Cell Cycle Checkpoints ; Mitochondria/metabolism ; },
abstract = {Schizophrenia is a severe psychiatric disorder of neurodevelopmental origin that affects around 1% of the world's population. Proteomic studies and other approaches have provided evidence of compromised cellular processes in the disorder, including mitochondrial function. Most of the studies so far have been conducted on postmortem brain tissue from patients, and therefore, do not allow the evaluation of the neurodevelopmental aspect of the disorder. To circumvent that, we studied the mitochondrial and nuclear proteomes of neural stem cells (NSCs) and neurons derived from induced pluripotent stem cells (iPSCs) from schizophrenia patients versus healthy controls to assess possible alterations related to energy metabolism and mitochondrial function during neurodevelopment in the disorder. Our results revealed differentially expressed proteins in pathways related to mitochondrial function, cell cycle control, DNA repair and neuritogenesis and their possible implication in key process of neurodevelopment, such as neuronal differentiation and axonal guidance signaling. Moreover, functional analysis of NSCs revealed alterations in mitochondrial oxygen consumption in schizophrenia-derived cells and a tendency of higher levels of intracellular reactive oxygen species (ROS). Hence, this study shows evidence that alterations in important cellular processes are present during neurodevelopment and could be involved with the establishment of schizophrenia, as well as the phenotypic traits observed in adult patients. Neural stem cells (NSCs) and neurons were derived from induced pluripotent stem cells (iPSCs) from schizophrenia patients and controls. Proteomic analyses were performed on the enriched mitochondrial and nuclear fractions of NSCs and neurons. Whole-cell proteomic analysis was also performed in neurons. Our results revealed alteration in proteins related to mitochondrial function, cell cycle control, among others. We also performed energy pathway analysis and reactive oxygen species (ROS) analysis of NSCs, which revealed alterations in mitochondrial oxygen consumption and a tendency of higher levels of intracellular ROS in schizophrenia-derived cells.},
}

Adult
Humans
*Schizophrenia/metabolism
*Induced Pluripotent Stem Cells/metabolism
Cell Differentiation/genetics
Reactive Oxygen Species/metabolism
Proteomics
Cell Cycle Checkpoints
Mitochondria/metabolism

@article {pmid37042115,
year = {2023},
author = {Metcalfe, NB and Bellman, J and Bize, P and Blier, PU and Crespel, A and Dawson, NJ and Dunn, RE and Halsey, LG and Hood, WR and Hopkins, M and Killen, SS and McLennan, D and Nadler, LE and Nati, JJH and Noakes, MJ and Norin, T and Ozanne, SE and Peaker, M and Pettersen, AK and Przybylska-Piech, A and Rathery, A and Récapet, C and Rodríguez, E and Salin, K and Stier, A and Thoral, E and Westerterp, KR and Westerterp-Plantenga, MS and Wojciechowski, MS and Monaghan, P},
title = {Solving the conundrum of intra-specific variation in metabolic rate: A multidisciplinary conceptual and methodological toolkit: New technical developments are opening the door to an understanding of why metabolic rate varies among individual animals of a species: New technical developments are opening the door to an understanding of why metabolic rate varies among individual animals of a species.},
journal = {BioEssays : news and reviews in molecular, cellular and developmental biology},
volume = {45},
number = {6},
pages = {e2300026},
doi = {10.1002/bies.202300026},
pmid = {37042115},
issn = {1521-1878},
support = {MC_UU_00014/4/MRC_/Medical Research Council/United Kingdom ; RG/17/12/33167/BHF_/British Heart Foundation/United Kingdom ; },
mesh = {Animals ; Humans ; *Basal Metabolism ; Phenotype ; },
abstract = {Researchers from diverse disciplines, including organismal and cellular physiology, sports science, human nutrition, evolution and ecology, have sought to understand the causes and consequences of the surprising variation in metabolic rate found among and within individual animals of the same species. Research in this area has been hampered by differences in approach, terminology and methodology, and the context in which measurements are made. Recent advances provide important opportunities to identify and address the key questions in the field. By bringing together researchers from different areas of biology and biomedicine, we describe and evaluate these developments and the insights they could yield, highlighting the need for more standardisation across disciplines. We conclude with a list of important questions that can now be addressed by developing a common conceptual and methodological toolkit for studies on metabolic variation in animals.},
}

Animals
Humans
*Basal Metabolism
Phenotype

@article {pmid37044183,
year = {2023},
author = {Chen, H and Huang, L and Yu, J and Miao, Y and Liu, C},
title = {Mitochondrial genome of Artemisia argyi L. suggested conserved mitochondrial protein-coding genes among genera Artemisia, Tanacetum and Chrysanthemum.},
journal = {Gene},
volume = {871},
number = {},
pages = {147427},
doi = {10.1016/j.gene.2023.147427},
pmid = {37044183},
issn = {1879-0038},
mesh = {Humans ; *Genome, Mitochondrial ; *Artemisia/genetics ; *Tanacetum/genetics ; *Chrysanthemum/genetics ; Phylogeny ; Mitochondria/genetics ; Mitochondrial Proteins/genetics ; },
abstract = {BACKGROUND: Artemisia argyi L., also known as mugwort, is a perennial herb whose leaves are commonly used as a source of traditional medicines. However, the evolution and structure of the mitochondrial genome (mitogenome) in A. argyi remain unclear. In this study, the mitogenome of A. argyi was assembled and characterized for the first time.

RESULTS: The mitogenome of A. argyi was a circular molecule of 229,354 bp. It encodes 56 genes, including 33 protein-coding genes (PCGs), 20 tRNA genes, and three rRNA genes, and three pseudogenes. Five trans-spliced introns were observed in three PCGs namely, nad1, nad2 and nad5. Repeat analysis identified 65 SSRs, 14 tandem repeats, and 167 dispersed repeats. The A. argyi mitogenome contains 12 plastid transfer sequences from 79 bp to 2552 bp. Five conserved MTPTs were identified in all 18 Asteraceae species. Comparison of mitogenome between A. argyi and one Artemisia specie and two Chrysanthemum species showed 14 conserved gene clusters. Phylogenetic analysis with organelle genomes of A. argyi and 18 other Anthemideae plants showed inconsistent phylogenetic trees, which implied that the evolutionary rates of PCGs and rrna genes derived from mitochondrion and plastid were incongruent. The Ka/Ks ratio of the 27 shared protein-coding genes in the 18 Anthemideae species are all less than 1 indicating that these genes were under the effect of purifying selection. Lastly, a total of 568 RNA editing sites in PCGs were further identified. The average editing frequency of non-synonymous changes was significantly higher than that of synonymous changes (one-sample Student's t-test, p-values ≤ 0.05) in three tissues (root, leaf and stem).

CONCLUSIONS: In this study, the gene content, genome size, genome comparison, mitochondrial plastid sequences, dN/dS analysis of mitochondrial protein-coding genes, and RNA-editing events in A. argyi mitogenome were determined, providing insights into the phylogenetic relationships of Asteraceae plant.},
}

Humans
*Genome, Mitochondrial
*Artemisia/genetics
*Tanacetum/genetics
*Chrysanthemum/genetics
Phylogeny
Mitochondria/genetics
Mitochondrial Proteins/genetics

@article {pmid37045318,
year = {2022},
author = {Hasan, ME and Hasan, A and Béarez, P and Shen, KN and Chang, CW and Tran, TTV and Golani, D and Al-Saboonchi, A and Siddiqui, PJA and Durand, JD},
title = {Planiliza lauvergnii (Eydoux & Souleyet, 1850), a senior synonym of Planiliza affinis (Günther, 1861) with a re-evaluation of keeled back mullets (Mugiliformes: Mugilidae).},
journal = {Zootaxa},
volume = {5194},
number = {4},
pages = {497-518},
doi = {10.11646/zootaxa.5194.4.2},
pmid = {37045318},
issn = {1175-5334},
mesh = {Animals ; *Smegmamorpha ; Phylogeny ; Fishes/genetics ; Biological Evolution ; Mitochondria ; },
abstract = {The taxonomic status of the keeled back mullets (Teleostei: Mugilidae) has been reinvestigated. Two nominal mugilid species having keeled backs from East Asia: Mugil lauvergnii Eydoux & Souleyet, 1850 and Mugil affinis Günther, 1861 have been re-evaluated through examination of the holotypes and fresh specimens. Comparison of morpho-meristic characters of the holotypes shows that both species are identical. Phylogenetic analysis based on mitochondrial cytochrome c oxidase 1 (CO1) confirmed morphological data by highlighting presence of a single clade from East Asia. Mugil lauvergnii (=Planiliza lauvergnii) is thus the sole keeled back mullet from East Asia and a senior synonym of Mugil affinis (=Planiliza affinis). The taxonomic status of two other keeled back mullets, Planiliza carinata and P. klunzingeri, is also contentious due to their similar morphology. Meristic and morphometric variation as well as sequence divergence between the two species are limited but phylogenetic analyses delineate well-supported clades consistent with biogeography and currently accepted taxonomy. Planiliza carinata and P. klunzingeri share a recent common ancestor in a Maximum Likelihood tree, with separate distribution ranges while P. lauvergnii formed a paraphyletic lineage. Based on present findings, we suggest maintenance of the taxonomic distinction of P. klunzingeri and P. carinata and discuss its evolutionary significance.},
}

Animals
*Smegmamorpha
Phylogeny
Fishes/genetics
Biological Evolution
Mitochondria

@article {pmid37063179,
year = {2023},
author = {Tyszka, AS and Bretz, EC and Robertson, HM and Woodcock-Girard, MD and Ramanauskas, K and Larson, DA and Stull, GW and Walker, JF},
title = {Characterizing conflict and congruence of molecular evolution across organellar genome sequences for phylogenetics in land plants.},
journal = {Frontiers in plant science},
volume = {14},
number = {},
pages = {1125107},
pmid = {37063179},
issn = {1664-462X},
abstract = {Chloroplasts and mitochondria each contain their own genomes, which have historically been and continue to be important sources of information for inferring the phylogenetic relationships among land plants. The organelles are predominantly inherited from the same parent, and therefore should exhibit phylogenetic concordance. In this study, we examine the mitochondrion and chloroplast genomes of 226 land plants to infer the degree of similarity between the organelles' evolutionary histories. Our results show largely concordant topologies are inferred between the organelles, aside from four well-supported conflicting relationships that warrant further investigation. Despite broad patterns of topological concordance, our findings suggest that the chloroplast and mitochondrial genomes evolved with significant differences in molecular evolution. The differences result in the genes from the chloroplast and the mitochondrion preferentially clustering with other genes from their respective organelles by a program that automates selection of evolutionary model partitions for sequence alignments. Further investigation showed that changes in compositional heterogeneity are not always uniform across divergences in the land plant tree of life. These results indicate that although the chloroplast and mitochondrial genomes have coexisted for over 1 billion years, phylogenetically, they are still evolving sufficiently independently to warrant separate models of evolution. As genome sequencing becomes more accessible, research into these organelles' evolution will continue revealing insight into the ancient cellular events that shaped not only their history, but the history of plants as a whole.},
}

@article {pmid37070190,
year = {2023},
author = {Schönherr, S and Weissensteiner, H and Kronenberg, F and Forer, L},
title = {Haplogrep 3 - an interactive haplogroup classification and analysis platform.},
journal = {Nucleic acids research},
volume = {51},
number = {W1},
pages = {W263-W268},
pmid = {37070190},
issn = {1362-4962},
mesh = {Humans ; Phylogeny ; *Software ; *DNA, Mitochondrial/genetics ; Mitochondria/genetics ; Biological Evolution ; },
abstract = {Over the last decade, Haplogrep has become a standard tool for haplogroup classification in the field of human mitochondrial DNA and is widely used by medical, forensic, and evolutionary researchers. Haplogrep scales well for thousands of samples, supports many file formats and provides an intuitive graphical web interface. Nevertheless, the currently available version has limitations when applying it to large biobank-scale data. In this paper, we present a major upgrade to the software by adding (a) haplogroup summary statistics and variant annotations from various publicly available genome databases, (b) an interface to connect new phylogenetic trees, (c) a new state-of-the-art web framework managing large scale data, (d) algorithmic adaptions to improve FASTA classification using BWA-specific alignment rules and (e) a pre-classification quality control step for VCF samples. These improvements will give researchers the opportunity to classify thousands of samples as usual but providing additional ways to investigate the dataset directly in the browser. The web service and its documentation can be accessed freely without any registration at https://haplogrep.i-med.ac.at.},
}

Humans
Phylogeny
*Software
*DNA, Mitochondrial/genetics
Mitochondria/genetics
Biological Evolution

@article {pmid37071674,
year = {2023},
author = {Libby, E and Kempes, CP and Okie, JG},
title = {Metabolic compatibility and the rarity of prokaryote endosymbioses.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {120},
number = {17},
pages = {e2206527120},
pmid = {37071674},
issn = {1091-6490},
mesh = {Phylogeny ; *Symbiosis/genetics ; *Prokaryotic Cells/metabolism ; Eukaryota/genetics ; Eukaryotic Cells/metabolism ; Biological Evolution ; },
abstract = {The evolution of the mitochondria was a significant event that gave rise to the eukaryotic lineage and most large complex life. Central to the origins of the mitochondria was an endosymbiosis between prokaryotes. Yet, despite the potential benefits that can stem from a prokaryotic endosymbiosis, their modern occurrence is exceptionally rare. While many factors may contribute to their rarity, we lack methods for estimating the extent to which they constrain the appearance of a prokaryotic endosymbiosis. Here, we address this knowledge gap by examining the role of metabolic compatibility between a prokaryotic host and endosymbiont. We use genome-scale metabolic flux models from three different collections (AGORA, KBase, and CarveMe) to assess the viability, fitness, and evolvability of potential prokaryotic endosymbioses. We find that while more than half of host-endosymbiont pairings are metabolically viable, the resulting endosymbioses have reduced growth rates compared to their ancestral metabolisms and are unlikely to gain mutations to overcome these fitness differences. In spite of these challenges, we do find that they may be more robust in the face of environmental perturbations at least in comparison with the ancestral host metabolism lineages. Our results provide a critical set of null models and expectations for understanding the forces that shape the structure of prokaryotic life.},
}

Phylogeny
*Symbiosis/genetics
*Prokaryotic Cells/metabolism
Eukaryota/genetics
Eukaryotic Cells/metabolism
Biological Evolution

@article {pmid37072481,
year = {2023},
author = {Christinaki, AC and Theelen, B and Zania, A and Coutinho, SDA and Cabañes, JF and Boekhout, T and Kouvelis, VN},
title = {Co-evolution of large inverted repeats and G-quadruplex DNA in fungal mitochondria may facilitate mitogenome stability: the case of Malassezia.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {6308},
pmid = {37072481},
issn = {2045-2322},
mesh = {Humans ; *Malassezia/genetics ; Phylogeny ; *Genome, Mitochondrial/genetics ; *G-Quadruplexes ; Mitochondria/genetics ; DNA ; },
abstract = {Mitogenomes are essential due to their contribution to cell respiration. Recently they have also been implicated in fungal pathogenicity mechanisms. Members of the basidiomycetous yeast genus Malassezia are an important fungal component of the human skin microbiome, linked to various skin diseases, bloodstream infections, and they are increasingly implicated in gut diseases and certain cancers. In this study, the comparative analysis of Malassezia mitogenomes contributed to phylogenetic tree construction for all species. The mitogenomes presented significant size and gene order diversity which correlates to their phylogeny. Most importantly, they showed the inclusion of large inverted repeats (LIRs) and G-quadruplex (G4) DNA elements, rendering Malassezia mitogenomes a valuable test case for elucidating the evolutionary mechanisms responsible for this genome diversity. Both LIRs and G4s coexist and convergently evolved to provide genome stability through recombination. This mechanism is common in chloroplasts but, hitherto, rarely found in mitogenomes.},
}

Humans
*Malassezia/genetics
Phylogeny
*Genome, Mitochondrial/genetics
*G-Quadruplexes
Mitochondria/genetics
DNA

@article {pmid37074804,
year = {2023},
author = {Mcguire, JA and Huang, X and Reilly, SB and Iskandar, DT and Wang-Claypool, CY and Werning, S and Chong, RA and Lawalata, SZS and Stubbs, AL and Frederick, JH and Brown, RM and Evans, BJ and Arifin, U and Riyanto, A and Hamidy, A and Arida, E and Koo, MS and Supriatna, J and Andayani, N and Hall, R},
title = {Species Delimitation, Phylogenomics, and Biogeography of Sulawesi Flying Lizards: A Diversification History Complicated by Ancient Hybridization, Cryptic Species, and Arrested Speciation.},
journal = {Systematic biology},
volume = {72},
number = {4},
pages = {885-911},
pmid = {37074804},
issn = {1076-836X},
support = {S10 RR027303/RR/NCRR NIH HHS/United States ; S10 RR029668/RR/NCRR NIH HHS/United States ; },
mesh = {Animals ; Phylogeny ; Indonesia ; *Lizards/genetics ; Phylogeography ; Genetics, Population ; Genetic Speciation ; },
abstract = {The biota of Sulawesi is noted for its high degree of endemism and for its substantial levels of in situ biological diversification. While the island's long period of isolation and dynamic tectonic history have been implicated as drivers of the regional diversification, this has rarely been tested in the context of an explicit geological framework. Here, we provide a tectonically informed biogeographical framework that we use to explore the diversification history of Sulawesi flying lizards (the Draco lineatus Group), a radiation that is endemic to Sulawesi and its surrounding islands. We employ a framework for inferring cryptic speciation that involves phylogeographic and genetic clustering analyses as a means of identifying potential species followed by population demographic assessment of divergence-timing and rates of bi-directional migration as means of confirming lineage independence (and thus species status). Using this approach, phylogenetic and population genetic analyses of mitochondrial sequence data obtained for 613 samples, a 50-SNP data set for 370 samples, and a 1249-locus exon-capture data set for 106 samples indicate that the current taxonomy substantially understates the true number of Sulawesi Draco species, that both cryptic and arrested speciations have taken place, and that ancient hybridization confounds phylogenetic analyses that do not explicitly account for reticulation. The Draco lineatus Group appears to comprise 15 species-9 on Sulawesi proper and 6 on peripheral islands. The common ancestor of this group colonized Sulawesi ~11 Ma when proto-Sulawesi was likely composed of two ancestral islands, and began to radiate ~6 Ma as new islands formed and were colonized via overwater dispersal. The enlargement and amalgamation of many of these proto-islands into modern Sulawesi, especially during the past 3 Ma, set in motion dynamic species interactions as once-isolated lineages came into secondary contact, some of which resulted in lineage merger, and others surviving to the present. [Genomics; Indonesia; introgression; mitochondria; phylogenetics; phylogeography; population genetics; reptiles.].},
}

Animals
Phylogeny
Indonesia
*Lizards/genetics
Phylogeography
Genetics, Population
Genetic Speciation

@article {pmid37077029,
year = {2023},
author = {Park, D and Yu, Y and Kim, JH and Lee, J and Park, J and Hong, K and Seo, JK and Lim, C and Min, KT},
title = {Suboptimal Mitochondrial Activity Facilitates Nuclear Heat Shock Responses for Proteostasis and Genome Stability.},
journal = {Molecules and cells},
volume = {46},
number = {6},
pages = {374-386},
pmid = {37077029},
issn = {0219-1032},
mesh = {Humans ; *Proteostasis ; Reactive Oxygen Species/metabolism ; *Heat-Shock Response/genetics ; HSP70 Heat-Shock Proteins/metabolism ; Mitochondria/metabolism ; Nuclear Proteins/metabolism ; Genomic Instability ; },
abstract = {Thermal stress induces dynamic changes in nuclear proteins and relevant physiology as a part of the heat shock response (HSR). However, how the nuclear HSR is fine-tuned for cellular homeostasis remains elusive. Here, we show that mitochondrial activity plays an important role in nuclear proteostasis and genome stability through two distinct HSR pathways. Mitochondrial ribosomal protein (MRP) depletion enhanced the nucleolar granule formation of HSP70 and ubiquitin during HSR while facilitating the recovery of damaged nuclear proteins and impaired nucleocytoplasmic transport. Treatment of the mitochondrial proton gradient uncoupler masked MRP-depletion effects, implicating oxidative phosphorylation in these nuclear HSRs. On the other hand, MRP depletion and a reactive oxygen species (ROS) scavenger non-additively decreased mitochondrial ROS generation during HSR, thereby protecting the nuclear genome from DNA damage. These results suggest that suboptimal mitochondrial activity sustains nuclear homeostasis under cellular stress, providing plausible evidence for optimal endosymbiotic evolution via mitochondria-to-nuclear communication.},
}

Humans
*Proteostasis
Reactive Oxygen Species/metabolism
*Heat-Shock Response/genetics
HSP70 Heat-Shock Proteins/metabolism
Mitochondria/metabolism
Nuclear Proteins/metabolism
Genomic Instability

@article {pmid37082671,
year = {2023},
author = {Ibodeng, GO and Uche, IN and Mokua, R and Galo, M and Odigwe, B and Galeas, JN and Dasgupta, S},
title = {A snapshot of lung cancer: where are we now?-a narrative review.},
journal = {Annals of translational medicine},
volume = {11},
number = {6},
pages = {261},
pmid = {37082671},
issn = {2305-5839},
abstract = {BACKGROUND AND OBJECTIVE: The global impact of cancer and cancer-related deaths has been a huge challenge and continues to be a setback in the health sector and beyond even in recent times. Cancer is the second leading cause of death globally with lung cancer (LC) being the second most prevalent malignancy and the leading cause of mortality amongst cancers in men and women worldwide. LC still constitutes a major burden despite recent advances in diagnostic and treatment tools. In this article, we review the trends in LC with an emphasis on non-small cell LC. We aimed to identify nuclear and mitochondrial genetic alterations, microbiome dysbiosis, and their significance in non-small cell LC tumorigenesis as well as its relevance in the future management of LCs.

METHODS: We identified studies for this review by searching the PubMed, Cochrane, Education Resources Information Center (ERIC), and Surveillance, Epidemiology, and End Results (SEER) databases for English-Language articles published from January 1, 2000 through to July 30, 2022, using keywords: lung cancer, non-small cell lung cancer, early detection, treatment, mitochondria, microbiome and epigenetics.

KEY CONTENT AND FINDINGS: This review will highlight the genomic environment, mitochondrial and nuclear alterations that play a role in the etiopathogenesis of LC and its application in the progression as well as management of the disease. We also elaborate on current molecular tumor biomarkers and their therapeutic targets.

CONCLUSIONS: LC remains the leading cause of cancer-related deaths globally with poor prognosis despite available treatment options and even recent advances in both diagnostic tools and management guidelines. Human nuclear and mitochondrial alterations clearly play a role in tumorigenesis and progressive genomic evolution is crucial in the early carcinogenesis of LC which is strongly influenced by host immune surveillance. It is imperative that more research and clinical trials be undertaken to appreciate an in-depth understanding of LC from the molecular level to facilitate the discovery of more targeted therapy and overall better management of LC.},
}

@article {pmid37100315,
year = {2023},
author = {Françoso, E and Zuntini, AR and Ricardo, PC and Santos, PKF and de Souza Araujo, N and Silva, JPN and Gonçalves, LT and Brito, R and Gloag, R and Taylor, BA and Harpur, BA and Oldroyd, BP and Brown, MJF and Arias, MC},
title = {Rapid evolution, rearrangements and whole mitogenome duplication in the Australian stingless bees Tetragonula (Hymenoptera: Apidae): A steppingstone towards understanding mitochondrial function and evolution.},
journal = {International journal of biological macromolecules},
volume = {242},
number = {Pt 1},
pages = {124568},
doi = {10.1016/j.ijbiomac.2023.124568},
pmid = {37100315},
issn = {1879-0003},
mesh = {Animals ; Australia ; *Bees/genetics ; *Genome, Mitochondrial/genetics ; Mitochondria/genetics ; Phylogeny ; },
abstract = {The extreme conservation of mitochondrial genomes in metazoans poses a significant challenge to understanding mitogenome evolution. However, the presence of variation in gene order or genome structure, found in a small number of taxa, can provide unique insights into this evolution. Previous work on two stingless bees in the genus Tetragonula (T. carbonaria and T. hockingsi) revealed highly divergent CO1 regions between them and when compared to the bees from the same tribe (Meliponini), indicating rapid evolution. Using mtDNA isolation and Illumina sequencing, we elucidated the mitogenomes of both species. In both species, there has been a duplication of the whole mitogenome to give a total genome size of 30,666 bp in T. carbonaria; and 30,662 bp in T. hockingsi. These duplicated genomes present a circular structure with two identical and mirrored copies of all 13 protein coding genes and 22 tRNAs, with the exception of a few tRNAs that are present as single copies. In addition, the mitogenomes are characterized by rearrangements of two block of genes. We believe that rapid evolution is present in the whole Indo-Malay/Australasian group of Meliponini but is extraordinarily elevated in T. carbonaria and T. hockingsi, probably due to founder effect, low effective population size and the mitogenome duplication. All these features - rapid evolution, rearrangements, and duplication - deviate significantly from the vast majority of the mitogenomes described so far, making the mitogenomes of Tetragonula unique opportunities to address fundamental questions of mitogenome function and evolution.},
}

Animals
Australia
*Bees/genetics
*Genome, Mitochondrial/genetics
Mitochondria/genetics
Phylogeny

@article {pmid37107622,
year = {2023},
author = {Li, X and Zhe, M and Huang, Y and Fan, W and Yang, J and Zhu, A},
title = {The Evolution of Mitochondrial Genomes between Two Cymbidium Sister Species: Dozens of Circular Chromosomes and the Maintenance and Deterioration of Genome Synteny.},
journal = {Genes},
volume = {14},
number = {4},
pages = {},
pmid = {37107622},
issn = {2073-4425},
mesh = {*Genome, Mitochondrial/genetics ; Synteny ; Introns ; Chromosomes ; *Orchidaceae ; },
abstract = {Plant mitochondrial genomes (mitogenomes) exhibit fluid genome architectures, which could lead to the rapid erosion of genome synteny over a short evolutionary time scale. Among the species-rich orchid family, the leafy Cymbidium lancifolium and leafless Cymbidium macrorhizon are sister species with remarkable differences in morphology and nutritional physiology. Although our understanding of the evolution of mitochondria is incomplete, these sister taxa are ideal for examining this subject. In this study, the complete mitogenomes of C. lancifolium and C. macrorhizon, totaling 704,244 bp and 650,751 bp, respectively, were assembled. In the 2 mitogenomes, 38 protein-coding genes, 18 cis- and 6 trans-spliced introns, and approximately 611 Kb of homologous sequences are identical; overall, they have 99.4% genome-wide similarity. Slight variations in the mitogenomes of C. lancifolium and C. macrorhizon in repeat content (21.0 Kb and 21.6 Kb, respectively) and mitochondrial DNA of plastid origin (MIPT; 38.2 Kb and 37.5 Kb, respectively) were observed. The mitogenome architectures of C. lancifolium and C. macrorhizon are complex and comprise 23 and 22 mini-circular chromosomes, respectively. Pairwise comparisons indicate that the two mitogenomes are largely syntenic, and the disparity in chromosome numbers is likely due to repeat-mediated rearrangements among different chromosomes. Notably, approximately 93.2 Kb C. lancifolium mitochondrial sequences lack any homology in the C. macrorhizon mitogenome, indicating frequent DNA gains and losses, which accounts mainly for the size variation. Our findings provide unique insights into mitogenome evolution in leafy and leafless plants of sister species and shed light on mitogenome dynamics during the transition from mixotrophy to mycoheterotrophy.},
}

*Genome, Mitochondrial/genetics
Synteny
Introns
Chromosomes
*Orchidaceae