@article {pmid38053364,
year = {2023},
author = {Camus, MF and Inwongwan, S},
title = {Mitonuclear interactions modulate nutritional preference.},
journal = {Biology letters},
volume = {19},
number = {12},
pages = {20230375},
pmid = {38053364},
issn = {1744-957X},
mesh = {Animals ; Genotype ; *Mitochondria/genetics ; Haplotypes ; Drosophila/genetics ; *Life History Traits ; DNA, Mitochondrial/genetics ; Cell Nucleus/genetics ; },
abstract = {In nature, organisms are faced with constant nutritional options which fuel key life-history traits. Studies have shown that species can actively make nutritional decisions based on internal and external cues. Metabolism itself is underpinned by complex genomic interactions involving components from both nuclear and mitochondrial genomes. Products from these two genomes must coordinate how nutrients are extracted, used and recycled. Given the complicated nature of metabolism, it is not well understood how nutritional choices are affected by mitonuclear interactions. This is under the rationale that changes in genomic interactions will affect metabolic flux and change physiological requirements. To this end we used a large Drosophila mitonuclear genetic panel, comprising nine isogenic nuclear genomes coupled to nine mitochondrial haplotypes, giving a total of 81 different mitonuclear genotypes. We use a capillary-based feeding assay to screen this panel for dietary preference between carbohydrate and protein. We find significant mitonuclear interactions modulating nutritional choices, with these epistatic interactions also being dependent on sex. Our findings support the notion that complex genomic interactions can place a constraint on metabolic flux. This work gives us deeper insights into how key metabolic interactions can have broad implications on behaviour.},
}

Animals
Genotype
*Mitochondria/genetics
Haplotypes
Drosophila/genetics
*Life History Traits
DNA, Mitochondrial/genetics
Cell Nucleus/genetics

@article {pmid38052127,
year = {2023},
author = {Fernández Miyakawa, ME and Casanova, NA and Kogut, MH},
title = {How did antibiotic growth promoters increase growth and feed efficiency in poultry?.},
journal = {Poultry science},
volume = {103},
number = {2},
pages = {103278},
doi = {10.1016/j.psj.2023.103278},
pmid = {38052127},
issn = {1525-3171},
abstract = {It has been hypothesized that reducing the bioenergetic costs of gut inflammation as an explanation for the effect of antibiotic growth promoters (AGPs) on animal efficiency, framing some observations but not explaining the increase in growth rate or the prevention of infectious diseases. The host's ability to adapt to alterations in environmental conditions and to maintain health involves managing all physiological interactions that regulate homeostasis. Thus, metabolic pathways are vital in regulating physiological health as the energetic demands of the host guides most biological functions. Mitochondria are not only the metabolic heart of the cell because of their role in energy metabolism and oxidative phosphorylation, but also a central hub of signal transduction pathways that receive messages about the health and nutritional states of cells and tissues. In response, mitochondria direct cellular and tissue physiological alterations throughout the host. The endosymbiotic theory suggests that mitochondria evolved from prokaryotes, emphasizing the idea that these organelles can be affected by some antibiotics. Indeed, therapeutic levels of several antibiotics can be toxic to mitochondria, but subtherapeutic levels may improve mitochondrial function and defense mechanisms by inducing an adaptive response of the cell, resulting in mitokine production which coordinates an array of adaptive responses of the host to the stressor(s). This adaptive stress response is also observed in several bacteria species, suggesting that this protective mechanism has been preserved during evolution. Concordantly, gut microbiome modulation by subinhibitory concentration of AGPs could be the result of direct stimulation rather than inhibition of determined microbial species. In eukaryotes, these adaptive responses of the mitochondria to internal and external environmental conditions, can promote growth rate of the organism as an evolutionary strategy to overcome potential negative conditions. We hypothesize that direct and indirect subtherapeutic AGP regulation of mitochondria functional output can regulate homeostatic control mechanisms in a manner similar to those involved with disease tolerance.},
}

@article {pmid38047232,
year = {2023},
author = {Charrasse, S and Poquillon, T and Saint-Omer, C and Pastore, M and Bordignon, B and Frye, RE and Reynes, C and Racine, V and Aouacheria, A},
title = {Quantitative assessment of mitochondrial morphology relevant for studies on cellular health and environmental toxicity.},
journal = {Computational and structural biotechnology journal},
volume = {21},
number = {},
pages = {5609-5619},
pmid = {38047232},
issn = {2001-0370},
abstract = {Mitochondria are essential organelles that play crucial roles in cellular energy metabolism, calcium signaling and apoptosis. Their importance in tissue homeostasis and stress responses, combined to their ability to transition between various structural and functional states, make them excellent organelles for monitoring cellular health. Quantitative assessment of mitochondrial morphology can therefore provide valuable insights into environmentally-induced cell damage. High-content screening (HCS) provides a powerful tool for analyzing organelles and cellular substructures. We developed a fully automated and miniaturized HCS wet-plus-dry pipeline (MITOMATICS) exploiting mitochondrial morphology as a marker for monitoring cellular health or damage. MITOMATICS uses an in-house, proprietary software (MitoRadar) to enable fast, exhaustive and cost-effective analysis of mitochondrial morphology and its inherent diversity in live cells. We applied our pipeline and big data analytics software to assess the mitotoxicity of selected chemicals, using the mitochondrial uncoupler CCCP as an internal control. Six different pesticides (inhibiting complexes I, II and III of the mitochondrial respiratory chain) were tested as individual compounds and five other pesticides present locally in Occitanie (Southern France) were assessed in combination to determine acute mitotoxicity. Our results show that the assayed pesticides exhibit specific signatures when used as single compounds or chemical mixtures and that they function synergistically to impact mitochondrial architecture. Study of environment-induced mitochondrial damage has the potential to open new fields in mechanistic toxicology, currently underexplored by regulatory toxicology and exposome research. Such exploration could inform health policy guidelines and foster pharmacological intervention, water, air and soil pollution control and food safety.},
}

@article {pmid38047014,
year = {2023},
author = {Kobayashi, G},
title = {Buried treasure in a public repository: Mining mitochondrial genes of 32 annelid species from sequence reads deposited in the Sequence Read Archive (SRA).},
journal = {PeerJ},
volume = {11},
number = {},
pages = {e16446},
pmid = {38047014},
issn = {2167-8359},
mesh = {Humans ; Animals ; Genes, Mitochondrial ; Phylogeny ; *Annelida ; DNA, Mitochondrial/genetics ; *Polychaeta/genetics ; },
abstract = {BACKGROUND: The mitochondrial genomes (mitogenomes) of metazoans generally include the same set of protein-coding genes, which ensures the homology of mitochondrial genes between species. The mitochondrial genes are often used as reference data for species identification based on genetic data (DNA barcoding). The need for such reference data has been increasing due to the application of environmental DNA (eDNA) analysis for environmental assessments. Recently, the number of publicly available sequence reads obtained with next-generation sequencing (NGS) has been increasing in the public database (the NCBI Sequence Read Archive, SRA). Such freely available NGS reads would be promising sources for assembling mitochondrial protein-coding genes (mPCGs) of organisms whose mitochondrial genes are not available in GenBank. The present study aimed to assemble annelid mPCGs from raw data deposited in the SRA.

METHODS: The recent progress in the classification of Annelida was briefly introduced. In the present study, the mPCGs of 32 annelid species of 19 families in clitellates and allies in Sedentaria (echiurans and polychaetes) were newly assembled from the reads deposited in the SRA. Assembly was performed with a recently published pipeline mitoRNA, which includes cycles of Bowtie2 mapping and Trinity assembly. Assembled mPCGs were deposited in GenBank as Third Party Data (TPA) data. A phylogenetic tree was reconstructed with maximum likelihood (ML) analysis, together with other mPCGs deposited in GenBank.

RESULTS AND DISCUSSION: mPCG assembly was largely successful except for Travisia forbesii; only four genes were detected from the assembled contigs of the species probably due to the reads targeting its parasite. Most genes were largely successfully obtained, whereas atp8, nad2, and nad4l were only successful in 22-24 species. The high nucleotide substitution rates of these genes might be relevant to the failure in the assembly although nad6, which showed a similarly high substitution rate, was successfully assembled. Although the phylogenetic positions of several lineages were not resolved in the present study, the phylogenetic relationships of some polychaetes and leeches that were not inferred by transcriptomes were well resolved probably due to a more dense taxon sampling than previous phylogenetic analyses based on transcriptomes. Although NGS data are generally better sources for resolving phylogenetic relationships of both higher and lower classifications, there are ensuring needs for specific loci of the mitochondrial genes for analyses that do not require high resolutions, such as DNA barcoding, eDNA, and phylogenetic analysis among lower taxa. Assembly from publicly available NGS reads would help design specific primers for the mitochondrial gene sequences of species, whose mitochondrial genes are hard to amplify by Sanger sequencing using universal primers.},
}

Humans
Animals
Genes, Mitochondrial
Phylogeny
*Annelida
DNA, Mitochondrial/genetics
*Polychaeta/genetics

@article {pmid38042216,
year = {2023},
author = {Kong, D and Gan, Z and Li, X},
title = {Phylogenetic relationships and adaptation in deep-sea carideans revealed by mitogenomes.},
journal = {Gene},
volume = {},
number = {},
pages = {148054},
doi = {10.1016/j.gene.2023.148054},
pmid = {38042216},
issn = {1879-0038},
abstract = {The deep-sea environment is characterized by extreme and inhospitable conditions, including oxygen depletion, low temperatures, high pressure, absence of light, and limited food availability. Mitochondria and mitogenomes play a crudial role in aerobic respiration to generate energy for eukaryotes. Here, using the Illumina Hiseq 4000 platform, we performed mitogenome sequencing for five deep-sea caridean species: Lebbeus shinkaiae, Lebbeus Formosus, Glyphocrangon regalis, Heterocarpus dorsalis, and Heterocarpus laevigatus, and five deep-sea caridean mitogenomes were assembled and identified. Each of the five mitogenomes contained 13 protein-coding genes, 2 rRNAs and 22 tRNAs. Specific elements, such as tandem repeats and AT-rich sequences, were observed in the control regions of Lebbeus formosus and Lebbeus shinkaiae, potentially take a role in regulating mitochondrial genome replication and transcription. The gene order of all obtained mitogenomes follows caridean ancestral type organization. Phylogenetic analysis shows a robustly supported phylogenetic tree for the infraorder Caridea. The monophyly of the families included in this study was strongly supported. This study supports the monophyly of Oplophoroidea, but rejects the monophyletic status of Nematocarcinoidea, Crangonoidea, and Alpheoidea. At the genus level, Plesionika is polyphyletic and Rimicaris is paraphyletic in our analysis. Furthermore, Paralebbeus may be considered invalid and synonymous with Lebbeus. Positive selection analysis reveals evidence for adaptive changes in the mitogenome of different deep-sea caridean lineages. Nine residues located in cox1, cox3, atp6, nad1, nad2, nad4, nad5, nad6 and cytb were determined to have undergone positive selection. Mitogenome of different deep-sea lineages experienced different positive selection, and the lineage represented by Alvinocarididae living in deep-sea hydrothermal vents experienced the strongest positive selection. This study provides valuable insights into the adaptive evolution of deep-sea shrimps at the mitochondrial, highlighting the mitogenomic strategy that contribute to their unique adaptations in the deep-sea environment.},
}

@article {pmid36736695,
year = {2023},
author = {Fähnrich, A and Stephan, I and Hirose, M and Haarich, F and Awadelkareem, MA and Ibrahim, S and Busch, H and Wohlers, I},
title = {North and East African mitochondrial genetic variation needs further characterization towards precision medicine.},
journal = {Journal of advanced research},
volume = {54},
number = {},
pages = {59-76},
doi = {10.1016/j.jare.2023.01.021},
pmid = {36736695},
issn = {2090-1224},
mesh = {Humans ; *DNA, Mitochondrial/genetics ; *East African People/genetics ; Genetic Variation/genetics ; Haplotypes ; Phylogeny ; Precision Medicine ; Sequence Analysis, DNA ; *North African People/genetics ; },
abstract = {INTRODUCTION: Mitochondria are maternally inherited cell organelles with their own genome, and perform various functions in eukaryotic cells such as energy production and cellular homeostasis. Due to their inheritance and manifold biological roles in health and disease, mitochondrial genetics serves a dual purpose of tracing the history as well as disease susceptibility of human populations across the globe. This work requires a comprehensive catalogue of commonly observed genetic variations in the mitochondrial DNAs for all regions throughout the world. So far, however, certain regions, such as North and East Africa have been understudied.

OBJECTIVES: To address this shortcoming, we have created the most comprehensive quality-controlled North and East African mitochondrial data set to date and use it for characterizing mitochondrial genetic variation in this region.

METHODS: We compiled 11 published cohorts with novel data for mitochondrial genomes from 159 Sudanese individuals. We combined these 641 mitochondrial sequences with sequences from the 1000 Genomes (n = 2504) and the Human Genome Diversity Project (n = 828) and used the tool haplocheck for extensive quality control and detection of in-sample contamination, as well as Nanopore long read sequencing for haplogroup validation of 18 samples.

RESULTS: Using a subset of high-coverage mitochondrial sequences, we predict 15 potentially novel haplogroups in North and East African subjects and observe likely phylogenetic deviations from the established PhyloTree reference for haplogroups L0a1 and L2a1.

CONCLUSION: Our findings demonstrate common hitherto unexplored variants in mitochondrial genomes of North and East Africa that lead to novel phylogenetic relationships between haplogroups present in these regions. These observations call for further in-depth population genetic studies in that region to enable the prospective use of mitochondrial genetic variation for precision medicine.},
}

Humans
*DNA, Mitochondrial/genetics
*East African People/genetics
Genetic Variation/genetics
Haplotypes
Phylogeny
Precision Medicine
Sequence Analysis, DNA
*North African People/genetics

@article {pmid38036853,
year = {2023},
author = {Ando, R and Shimozono, S and Ago, H and Takagi, M and Sugiyama, M and Kurokawa, H and Hirano, M and Niino, Y and Ueno, G and Ishidate, F and Fujiwara, T and Okada, Y and Yamamoto, M and Miyawaki, A},
title = {StayGold variants for molecular fusion and membrane-targeting applications.},
journal = {Nature methods},
volume = {},
number = {},
pages = {},
pmid = {38036853},
issn = {1548-7105},
support = {JP15dm0207001//Japan Agency for Medical Research and Development (AMED)/ ; JP21am0101070//Japan Agency for Medical Research and Development (AMED)/ ; 21H05041//Ministry of Education, Culture, Sports, Science and Technology (MEXT)/ ; 21H05041//Ministry of Education, Culture, Sports, Science and Technology (MEXT)/ ; 21H05041//Ministry of Education, Culture, Sports, Science and Technology (MEXT)/ ; 19H05794, 19H05795//Ministry of Education, Culture, Sports, Science and Technology (MEXT)/ ; JPM JCR20E2//MEXT | JST | Core Research for Evolutional Science and Technology (CREST)/ ; },
abstract = {Although StayGold is a bright and highly photostable fluorescent protein, its propensity for obligate dimer formation may hinder applications in molecular fusion and membrane targeting. To attain monovalent as well as bright and photostable labeling, we engineered tandem dimers of StayGold to promote dispersibility. On the basis of the crystal structure of this fluorescent protein, we disrupted the dimerization to generate a monomeric variant that offers improved photostability and brightness compared to StayGold. We applied the new monovalent StayGold tools to live-cell imaging experiments using spinning-disk laser-scanning confocal microscopy or structured illumination microscopy. We achieved cell-wide, high-spatiotemporal resolution and sustained imaging of dynamic subcellular events, including the targeting of endogenous condensin I to mitotic chromosomes, the movement of the Golgi apparatus and its membranous derivatives along microtubule networks, the distribution of cortical filamentous actin and the remolding of cristae membranes within mobile mitochondria.},
}

@article {pmid38019044,
year = {2023},
author = {Osiewacz, HD},
title = {Impact of Mitochondrial Architecture, Function, Redox Homeostasis, and Quality Control on Organismic Aging: Lessons from a Fungal Model System.},
journal = {Antioxidants & redox signaling},
volume = {},
number = {},
pages = {},
doi = {10.1089/ars.2023.0487},
pmid = {38019044},
issn = {1557-7716},
abstract = {SIGNIFICANCE: Mitochondria are eukaryotic organelles with various essential functions. They are both, the source as well as the targets of reactive oxygen species (ROS). Different branches of a mitochondrial quality control system (mQCS), like ROS balancing, degradation of damaged proteins, or whole mitochondria can mitigate the adverse effects of ROS stress. However, the capacity of mQCS is limited. Overwhelming this capacity leads to dysfunctions and aging. Strategies to interfere into mitochondria-dependent human aging with the aim to increase the healthy period of life, the healthspan, rely on the precise knowledge of mitochondrial functions. Experimental models like Podospora anserina, a filamentous fungus with a clear mitochondrial aging etiology, proved to be instrumental to reach this goal.

RECENT ADVANCES: Investigations of the P. anserina mQCS revealed that it is constituted by a complex network of different branches. Moreover, mitochondrial architecture and lipid homeostasis emerged to affect aging.

CRITICAL ISSUES: The regulation of the mQCS is only incompletely understood. Details about the involved signaling molecules and interacting pathways remain to be elucidated. Moreover, most of the currently generated experimental data were generated in well-controlled experiments which do not reflect the constantly changing natural life conditions and bear the danger to miss relevant aspects leading to incorrect conclusions.

FUTURE DIRECTIONS: In P. anserina, the precise impact of redox signaling as well as of molecular damaging for aging remains to be defined. Moreover, natural fluctuation of environmental conditions needs to be considered to generate a realistic picture of aging mechanisms as they developed during evolution.},
}

@article {pmid38007160,
year = {2023},
author = {Gao, X and Feng, B and Du, C and Hou, C and Jin, S and Tang, D and Zhu, J and Lv, Y},
title = {Expression dynamics indicate the involvement of SPG7 in the reproduction and spermiogenesis of Phascolosoma esculenta.},
journal = {Gene},
volume = {895},
number = {},
pages = {148028},
doi = {10.1016/j.gene.2023.148028},
pmid = {38007160},
issn = {1879-0038},
abstract = {Spastic paraplegia 7 (SPG7) is an m-AAA protease subunit involved in mitochondrial morphology and physiology. However, its function in animal reproduction is yet to be evaluated. In this study, its molecular features, subcellular localization, and expression dynamics were investigated to analyze its potential function in the reproduction of male Phascolosoma esculenta, an economically important marine species in China. The full-length cDNA of P. esculenta spg7 (Pe-spg7) measures 3053 bp and encodes an 853-amino acid protein (Pe-SPG7). Pe-SPG7 includes two transmembrane domains, an AAA domain and a proteolytic domain. Amino acid sequence alignment revealed that SPG7 was conserved during evolution. The mRNA and protein expression of spg7 indicated its involvement in reproduction. Its expression was the highest in coelomic fluid, where spermatids develop, and it was significantly higher in the breeding stage than in the nonbreeding stage. SPG7 was mainly found in the mitochondria of spermatids in the coelomic fluid, indicating that it functions in this organelle in spermatids. Immunofluorescence experiments showed that SPG7 was expressed and colocalized in the mitochondria during spermiogenesis, suggesting its involvement in P. esculenta spermiogenesis. Therefore, SPG7 may participate in spermiogenesis by functioning in the mitochondria and regulate the reproduction of male P. esculenta. This study provided insights into the function of SPG7 in animal reproduction and P. esculenta gametogenesis.},
}

@article {pmid37935058,
year = {2023},
author = {Smith, CH and Mejia-Trujillo, R and Breton, S and Pinto, BJ and Kirkpatrick, M and Havird, JC},
title = {Mitonuclear Sex Determination? Empirical Evidence from Bivalves.},
journal = {Molecular biology and evolution},
volume = {40},
number = {11},
pages = {},
pmid = {37935058},
issn = {1537-1719},
support = {1R35GM142836/NH/NIH HHS/United States ; },
mesh = {Female ; Animals ; *Bivalvia/genetics ; DNA, Mitochondrial/genetics ; Mitochondria/genetics ; Genes, Mitochondrial ; *RNA, Small Untranslated ; },
abstract = {Genetic elements encoded in nuclear DNA determine the sex of an individual in many animals. In certain bivalve lineages that possess doubly uniparental inheritance (DUI), mitochondrial DNA (mtDNA) has been hypothesized to contribute to sex determination. In these cases, females transmit a female mtDNA to all offspring, while male mtDNA (M mtDNA) is transmitted only from fathers to sons. Because M mtDNA is inherited in the same way as Y chromosomes, it has been hypothesized that mtDNA may be responsible for sex determination. However, the role of mitochondrial and nuclear genes in sex determination has yet to be validated in DUI bivalves. In this study, we used DNA, RNA, and mitochondrial short noncoding RNA (sncRNA) sequencing to explore the role of mitochondrial and nuclear elements in the sexual development pathway of the freshwater mussel Potamilus streckersoni (Bivalvia: Unionida). We found that the M mtDNA sheds a sncRNA partially within a male-specific mitochondrial gene that targets a pathway hypothesized to be involved in female development and mitophagy. RNA-seq confirmed the gene target was significantly upregulated in females, supporting a direct role of mitochondrial sncRNAs in gene silencing. These findings support the hypothesis that M mtDNA inhibits female development. Genome-wide patterns of genetic differentiation and heterozygosity did not support a nuclear sex-determining region, although we cannot reject that nuclear factors are involved with sex determination. Our results provide further evidence that mitochondrial loci contribute to diverse, nonrespiratory functions and additional insights into an unorthodox sex-determining system.},
}

Female
Animals
*Bivalvia/genetics
DNA, Mitochondrial/genetics
Mitochondria/genetics
Genes, Mitochondrial
*RNA, Small Untranslated

@article {pmid38006556,
year = {2024},
author = {Duplouy, A},
title = {Validating a Mitochondrial Sweep Accompanying the Rapid Spread of a Maternally Inherited Symbiont.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2739},
number = {},
pages = {239-247},
pmid = {38006556},
issn = {1940-6029},
abstract = {Maternally inherited symbiotic bacteria that interfere with the reproduction of their hosts can contribute to selective sweeps of mitochondrial haplotypes through hitch-hiking or coordinate inheritance of cytoplasmic bacteria and host mitochondria. The sweep will be manifested by genetic variations of mitochondrial genomic DNA of symbiont-infected hosts relative to their uninfected counterparts. In particular, at the population level, infected specimens will show a reduced mitochondrial DNA polymorphism compared to that in the nuclear DNA. This may challenge the use of mitochondrial DNA sequences as neutral genetic markers, as the mitochondrial patterns will reflect the evolutionary history of parasitism, rather than the sole evolutionary history of the host. Here, I describe a detailed step-by-step procedure to infer the occurrence and timing of symbiont-induced mitochondrial sweeps in host species.},
}

@article {pmid38002320,
year = {2023},
author = {Nusir, A and Sinclair, P and Kabbani, N},
title = {Mitochondrial Proteomes in Neural Cells: A Systematic Review.},
journal = {Biomolecules},
volume = {13},
number = {11},
pages = {},
pmid = {38002320},
issn = {2218-273X},
abstract = {Mitochondria are ancient endosymbiotic double membrane organelles that support a wide range of eukaryotic cell functions through energy, metabolism, and cellular control. There are over 1000 known proteins that either reside within the mitochondria or are transiently associated with it. These mitochondrial proteins represent a functional subcellular protein network (mtProteome) that is encoded by mitochondrial and nuclear genomes and significantly varies between cell types and conditions. In neurons, the high metabolic demand and differential energy requirements at the synapses are met by specific modifications to the mtProteome, resulting in alterations in the expression and functional properties of the proteins involved in energy production and quality control, including fission and fusion. The composition of mtProteomes also impacts the localization of mitochondria in axons and dendrites with a growing number of neurodegenerative diseases associated with changes in mitochondrial proteins. This review summarizes the findings on the composition and properties of mtProteomes important for mitochondrial energy production, calcium and lipid signaling, and quality control in neural cells. We highlight strategies in mass spectrometry (MS) proteomic analysis of mtProteomes from cultured cells and tissue. The research into mtProteome composition and function provides opportunities in biomarker discovery and drug development for the treatment of metabolic and neurodegenerative disease.},
}

@article {pmid37999092,
year = {2023},
author = {Liu, SP and Yin, HD and Li, WJ and Qin, ZH and Yang, Y and Huang, ZZ and Zong, L and Liu, XK and Du, Z and Fan, WL and Zhang, YQ and Zhang, D and Zhang, YE and Liu, XY and Yang, D and Ge, SQ},
title = {The Morphological Transformation of the Thorax during the Eclosion of Drosophila melanogaster (Diptera: Drosophilidae).},
journal = {Insects},
volume = {14},
number = {11},
pages = {},
pmid = {37999092},
issn = {2075-4450},
support = {32270460//National Science Foundation of China/ ; 2021xjkk0605//Third Xinjiang Scientific Expedition Program/ ; },
abstract = {The model organism Drosophila melanogaster, as a species of Holometabola, undergoes a series of transformations during metamorphosis. To deeply understand its development, it is crucial to study its anatomy during the key developmental stages. We describe the anatomical systems of the thorax, including the endoskeleton, musculature, nervous ganglion, and digestive system, from the late pupal stage to the adult stage, based on micro-CT and 3D visualizations. The development of the endoskeleton causes original and insertional changes in muscles. Several muscles change their shape during development in a non-uniform manner with respect to both absolute and relative size; some become longer and broader, while others shorten and become narrower. Muscular shape may vary during development. The number of muscular bundles also increases or decreases. Growing muscles are probably anchored by the tissues in the stroma. Some muscles and tendons are absent in the adult stage, possibly due to the hardened sclerites. Nearly all flight muscles are present by the third day of the pupal stage, which may be due to the presence of more myofibers with enough mitochondria to support flight power. There are sexual differences in the same developmental period. In contrast to the endodermal digestive system, the functions of most thoracic muscles change in the development from the larva to the adult in order to support more complex locomotion under the control of a more structured ventral nerve cord based on the serial homology proposed herein.},
}

@article {pmid37996801,
year = {2023},
author = {Song, Y and Du, X and Li, A and Fan, A and He, L and Sun, Z and Niu, Y and Qiao, Y},
title = {Assembly and analysis of the complete mitochondrial genome of Forsythia suspensa (Thunb.) Vahl.},
journal = {BMC genomics},
volume = {24},
number = {1},
pages = {708},
pmid = {37996801},
issn = {1471-2164},
support = {20210302123390//the Basic Research Program of Shanxi Province/ ; 2023//Shanxi Province Modern Agricultural Chinese Herbal Medicine Industry Technology System Project/ ; CXGC2023041//Shanxi Agricultural University Science and Technology Innovation Promotion Project/ ; },
abstract = {BACKGROUND: Forsythia suspensa (Thunb.) Vahl is a valuable ornamental and medicinal plant. Although the nuclear and chloroplast genomes of F. suspensa have been published, its complete mitochondrial genome sequence has yet to be reported. In this study, the genomic DNA of F. suspensa yellowish leaf material was extracted, sequenced by using a mixture of Illumina Novaseq6000 short reads and Oxford Nanopore PromethION long reads, and the sequencing data were assembled and annotated.

RESULT: The F. suspensa mitochondrial genome was obtained in the length of 535,692 bp with a circular structure, and the GC content was 44.90%. The genome contains 60 genes, including 36 protein-coding genes, 21 tRNA genes, and three rRNA genes. We further analyzed RNA editing of the protein-coding genes, relative synonymous codon usage, and sequence repeats based on the genomic data. There were 25 homologous sequences between F. suspensa mitochondria and chloroplast genome, which involved the transfer of 8 mitochondrial genes, and 9473 homologous sequences between mitochondrial and nuclear genomes. Analysis of the nucleic acid substitution rate, nucleic acid diversity, and collinearity of protein-coding genes of the F. suspensa mitochondrial genome revealed that the majority of genes may have undergone purifying selection, exhibiting a slower rate of evolution and a relatively conserved structure. Analysis of the phylogenetic relationships among different species revealed that F. suspensa was most closely related to Olea europaea subsp. Europaea.

CONCLUSION: In this study, we sequenced, assembled, and annotated a high-quality F. suspensa mitochondrial genome. The results of this study will enrich the mitochondrial genome data of Forsythia, lay a foundation for the phylogenetic development of Forsythia, and promote the evolutionary analysis of Oleaceae species.},
}

@article {pmid37994879,
year = {2023},
author = {Záhonová, K and Füssy, Z and Stairs, CW and Leger, MM and Tachezy, J and Čepička, I and Roger, AJ and Hampl, V},
title = {Comparative analysis of mitochondrion-related organelles in anaerobic amoebozoans.},
journal = {Microbial genomics},
volume = {9},
number = {11},
pages = {},
doi = {10.1099/mgen.0.001143},
pmid = {37994879},
issn = {2057-5858},
mesh = {Anaerobiosis ; *Mitochondria/genetics ; *Eukaryota ; Iron ; Sulfates ; },
abstract = {Archamoebae comprises free-living or endobiotic amoebiform protists that inhabit anaerobic or microaerophilic environments and possess mitochondrion-related organelles (MROs) adapted to function anaerobically. We compared in silico reconstructed MRO proteomes of eight species (six genera) and found that the common ancestor of Archamoebae possessed very few typical components of the protein translocation machinery, electron transport chain and tricarboxylic acid cycle. On the other hand, it contained a sulphate activation pathway and bacterial iron-sulphur (Fe-S) assembly system of MIS-type. The metabolic capacity of the MROs, however, varies markedly within this clade. The glycine cleavage system is widely conserved among Archamoebae, except in Entamoeba, probably owing to its role in catabolic function or one-carbon metabolism. MRO-based pyruvate metabolism was dispensed within subgroups Entamoebidae and Rhizomastixidae, whereas sulphate activation could have been lost in isolated cases of Rhizomastix libera, Mastigamoeba abducta and Endolimax sp. The MIS (Fe-S) assembly system was duplicated in the common ancestor of Mastigamoebidae and Pelomyxidae, and one of the copies took over Fe-S assembly in their MRO. In Entamoebidae and Rhizomastixidae, we hypothesize that Fe-S cluster assembly in both compartments may be facilitated by dual localization of the single system. We could not find evidence for changes in metabolic functions of the MRO in response to changes in habitat; it appears that such environmental drivers do not strongly affect MRO reduction in this group of eukaryotes.},
}

Anaerobiosis
*Mitochondria/genetics
*Eukaryota
Iron
Sulfates

@article {pmid37995039,
year = {2023},
author = {Lee, YJ and Uh, YR and Kim, YM and Kim, CM and Jang, CS},
title = {Characterization and comparative analysis of the complete organelle genomes of three red macroalgae species (Neoporphyra dentata, Neoporphyra seriata, and Neopyropia yezoensis) and development of molecular makers for their identification.},
journal = {Genes & genomics},
volume = {},
number = {},
pages = {},
pmid = {37995039},
issn = {2092-9293},
support = {20210656//Korea Institute of Marine Science and Technology promotion/ ; },
abstract = {BACKGROUND: Many species of red algae belonging to the phylum Rhodophyta are consumed by humans as raw materials for nutrition and medicine. As the seaweed market grows, the importance of the laver species has increased. The classification of red algal species has changed significantly, and the accuracy of this classification has improved significantly in recent years. Here, we report the complete circular genomes of the chloroplasts (cp) and mitochondria (mt) of three laver species (Neoporphyra dentata, Neoporphyra seriata, and Neopyropia yezoensis).

OBJECTIVE: This study aims to assemble, annotate, and characterize the organization of the organelle genomes of three laver species, conduct comparative genomic studies, and develop molecular markers based on SNPs.

METHODS: We analyzed organelle genome structures, repeat sequences, sequence divergence, gene rearrangements, and phylogenetic relationships of three laver species.

RESULTS: The chloroplast genomes of the three species contained an average of 212 protein-coding genes (PCGs), while the mitochondrial genomes contained an average of 25 PCGs. We reconstructed the phylogenetic trees based on both chloroplast and mitochondrial genomes using 201 and 23 PCGs (in cp and mt genomes, respectively) shared in the class Bangiophyceae (and five species of Florideophyceae class used as an outgroup). In addition, 12 species-specific molecular markers were developed for qRT-PCR analysis.

CONCLUSIONS: This is the first report of Neoporphyra seriata complete organellar genomes. With the results, this study provides useful genetic information regarding taxonomic discrepancies, the reconstruction of phylogenetic trees, and the evolution of red algae. Moreover, the species-specific markers can be used as fast and easy methods to identify a target species.},
}

@article {pmid37988339,
year = {2023},
author = {Kang, N and Hu, H},
title = {Adaptive evidence of mitochondrial genes in Pteromalidae and Eulophidae (Hymenoptera: Chalcidoidea).},
journal = {PloS one},
volume = {18},
number = {11},
pages = {e0294687},
pmid = {37988339},
issn = {1932-6203},
mesh = {Animals ; *Hymenoptera/genetics ; Genes, Mitochondrial ; Phylogeny ; Bayes Theorem ; Ecosystem ; Ultraviolet Rays ; Mitochondrial Proteins/genetics ; *Genome, Mitochondrial ; },
abstract = {Pteromalidae and Eulophidae are predominant and abundant taxa within Chalcidoidea (Hymenoptera: Apocrita). These taxa are found in diverse ecosystems, ranging from basin deserts (200 m) to alpine grasslands (4500 m). Mitochondria, cellular powerhouses responsible for energy production via oxidative phosphorylation, are sensitive to various environmental factors such as extreme cold, hypoxia, and intense ultraviolet radiation characteristic of alpine regions. Whether the molecular evolution of mitochondrial genes in these parasitoids corresponds to changes in the energy requirements and alpine environmental adaptations remains unknown. In this study, we performed a comparative analysis of mitochondrial protein-coding genes from 11 alpine species of Pteromalidae and Eulophidae, along with 18 lowland relatives, including 16 newly sequenced species. We further examined the codon usage preferences (RSCU, ENC-GC3s, neutrality, and PR2 bias plot) in these mitochondrial protein-coding sequences and conducted positive selection analysis based on their Bayesian phylogenetic relationships, and identified positive selection sites in the ATP6, ATP8, COX1, COX3, and CYTB genes, emphasizing the crucial role of mitochondrial gene adaptive evolution in the adaptation of Pteromalidae and Eulophidae to alpine environments. The phylogenetically independent contrast (PIC) analysis results verified the ω ratio of 13 PCGs from Pteromalidae and Eulophidae increased with elevation, and results from generalized linear model confirm that ATP6, ATP8, COX3, and ND1 are closely correlated with temperature-related environmental factors. This research not only enriched the molecular data of endemic alpine species but also underscores the significance of mitochondrial genes in facilitating the adaptation of these minor parasitoids to plateau habitats.},
}

Animals
*Hymenoptera/genetics
Genes, Mitochondrial
Phylogeny
Bayes Theorem
Ecosystem
Ultraviolet Rays
Mitochondrial Proteins/genetics
*Genome, Mitochondrial

@article {pmid37978174,
year = {2023},
author = {Mahendrarajah, TA and Moody, ERR and Schrempf, D and Szánthó, LL and Dombrowski, N and Davín, AA and Pisani, D and Donoghue, PCJ and Szöllősi, GJ and Williams, TA and Spang, A},
title = {ATP synthase evolution on a cross-braced dated tree of life.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {7456},
pmid = {37978174},
issn = {2041-1723},
mesh = {Phylogeny ; *Bacteria/genetics ; *Archaea/genetics ; Mitochondria/genetics ; Adenosine Triphosphate ; Evolution, Molecular ; Eukaryota/genetics ; Biological Evolution ; },
abstract = {The timing of early cellular evolution, from the divergence of Archaea and Bacteria to the origin of eukaryotes, is poorly constrained. The ATP synthase complex is thought to have originated prior to the Last Universal Common Ancestor (LUCA) and analyses of ATP synthase genes, together with ribosomes, have played a key role in inferring and rooting the tree of life. We reconstruct the evolutionary history of ATP synthases using an expanded taxon sampling set and develop a phylogenetic cross-bracing approach, constraining equivalent speciation nodes to be contemporaneous, based on the phylogenetic imprint of endosymbioses and ancient gene duplications. This approach results in a highly resolved, dated species tree and establishes an absolute timeline for ATP synthase evolution. Our analyses show that the divergence of ATP synthase into F- and A/V-type lineages was a very early event in cellular evolution dating back to more than 4 Ga, potentially predating the diversification of Archaea and Bacteria. Our cross-braced, dated tree of life also provides insight into more recent evolutionary transitions including eukaryogenesis, showing that the eukaryotic nuclear and mitochondrial lineages diverged from their closest archaeal (2.67-2.19 Ga) and bacterial (2.58-2.12 Ga) relatives at approximately the same time, with a slightly longer nuclear stem-lineage.},
}

Phylogeny
*Bacteria/genetics
*Archaea/genetics
Mitochondria/genetics
Adenosine Triphosphate
Evolution, Molecular
Eukaryota/genetics
Biological Evolution

@article {pmid37958068,
year = {2023},
author = {Hui, M and Zhang, Y and Wang, A and Sha, Z},
title = {The First Genome Survey of the Snail Provanna glabra Inhabiting Deep-Sea Hydrothermal Vents.},
journal = {Animals : an open access journal from MDPI},
volume = {13},
number = {21},
pages = {},
pmid = {37958068},
issn = {2076-2615},
support = {XDA22050302 and XDB42000000//the Strategic Priority Research Program of the Chinese Academy of Sciences/ ; 42025603//National Science Foundation for Distinguished Young Scholars/ ; LSKJ202203104//the Science and Technology Innovation Project of Laoshan Laboratory/ ; },
abstract = {The snail P. glabra is an endemic species in deep-sea chemosynthetic ecosystems of the Northwest Pacific Ocean. To obtain more genetic information on this species and provide the basis for subsequent whole-genome map construction, a genome survey was performed on this snail from the hydrothermal vent of Okinawa Trough. The genomic size of P. glabra was estimated to be 1.44 Gb, with a heterozygosity of 1.91% and a repeated sequence content of 69.80%. Based on the sequencing data, a draft genome of 1.32 Gb was assembled. Transposal elements (TEs) accounted for 40.17% of the entire genome, with DNA transposons taking the highest proportion. It was found that most TEs were inserted in the genome recently. In the simple sequence repeats, the dinucleotide motif was the most enriched microsatellite type, accounting for 53% of microsatellites. A complete mitochondrial genome of P. glabra with a total length of 16,268 bp was assembled from the sequencing data. After comparison with the published mitochondrial genome of Provanna sp. from a methane seep, 331 potential single nucleotide polymorphism (SNP) sites were identified in protein-coding genes (PCGs). Except for the cox1 gene, nad2, nad4, nad5, and cob genes are expected to be candidate markers for population genetic and phylogenetic studies of P. glabra and other deep-sea snails. Compared with shallow-water species, three mitochondrial genes of deep-sea gastropods exhibited a higher evolutionary rate, indicating strong selection operating on mitochondria of deep-sea species. This study provides insights into the genome characteristics of P. glabra and supplies genomic resources for further studies on the adaptive evolution of the snail in extreme deep-sea chemosynthetic environments.},
}

@article {pmid37929337,
year = {2023},
author = {Ibrahim, MK and Haria, A and Mehta, NV and Degani, MS},
title = {Antimicrobial potential of quaternary phosphonium salt compounds: a review.},
journal = {Future medicinal chemistry},
volume = {15},
number = {22},
pages = {2113-2141},
doi = {10.4155/fmc-2023-0188},
pmid = {37929337},
issn = {1756-8927},
mesh = {Phylogeny ; Microbial Sensitivity Tests ; *Anti-Infective Agents/pharmacology/chemistry ; Anti-Bacterial Agents/pharmacology/chemistry ; Mitochondria ; Quaternary Ammonium Compounds/chemistry ; },
abstract = {Given that mitochondrial dysregulation is a biomarker of many cancers, cationic quaternary phosphonium salt (QPS) conjugation is a widely utilized strategy for anticancer drug design. QPS-conjugated compounds exhibit greater cell permeation and accumulation in negatively charged mitochondria, and thus, show enhanced activity. Phylogenetic similarities between mitochondria and bacteria have provided a rationale for exploring the antibacterial properties of mitochondria-targeted compounds. Additionally, due to the importance of mitochondria in the survival of pathogenic microbes, including fungi and parasites, this strategy can be extended to these organisms as well. This review examines recent literature on the antimicrobial activities of various QPS-conjugated compounds and provides future directions for exploring the medicinal chemistry of these compounds.},
}

Phylogeny
Microbial Sensitivity Tests
*Anti-Infective Agents/pharmacology/chemistry
Anti-Bacterial Agents/pharmacology/chemistry
Mitochondria
Quaternary Ammonium Compounds/chemistry

@article {pmid37955101,
year = {2023},
author = {Da Costa, RT and Riggs, LM and Solesio, ME},
title = {Inorganic polyphosphate and the regulation of mitochondrial physiology.},
journal = {Biochemical Society transactions},
volume = {},
number = {},
pages = {},
doi = {10.1042/BST20230735},
pmid = {37955101},
issn = {1470-8752},
abstract = {Inorganic polyphosphate (polyP) is an ancient polymer that is well-conserved throughout evolution. It is formed by multiple subunits of orthophosphates linked together by phosphoanhydride bonds. The presence of these bonds, which are structurally similar to those found in ATP, and the high abundance of polyP in mammalian mitochondria, suggest that polyP could be involved in the regulation of the physiology of the organelle, especially in the energy metabolism. In fact, the scientific literature shows an unequivocal role for polyP not only in directly regulating oxidative a phosphorylation; but also in the regulation of reactive oxygen species metabolism, mitochondrial free calcium homeostasis, and the formation and opening of mitochondrial permeability transitions pore. All these processes are closely interconnected with the status of mitochondrial bioenergetics and therefore play a crucial role in maintaining mitochondrial and cell physiology. In this invited review, we discuss the main scientific literature regarding the regulatory role of polyP in mammalian mitochondrial physiology, placing a particular emphasis on its impact on energy metabolism. Although the effects of polyP on the physiology of the organelle are evident; numerous aspects, particularly within mammalian cells, remain unclear and require further investigation. These aspects encompass, for example, advancing the development of more precise analytical methods, unraveling the mechanism responsible for sensing polyP levels, and understanding the exact molecular mechanism that underlies the effects of polyP on mitochondrial physiology. By increasing our understanding of the biology of this ancient and understudied polymer, we could unravel new pharmacological targets in diseases where mitochondrial dysfunction, including energy metabolism dysregulation, has been broadly described.},
}

@article {pmid37944010,
year = {2023},
author = {Pegan, TM and Berv, JS and Gulson-Castillo, ER and Kimmitt, AA and Winger, BM},
title = {The pace of mitochondrial molecular evolution varies with seasonal migration distance.},
journal = {Evolution; international journal of organic evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/evolut/qpad200},
pmid = {37944010},
issn = {1558-5646},
abstract = {Animals that engage in long-distance seasonal migration experience strong selective pressures on their metabolic performance and life history, with potential consequences for molecular evolution. Species with slow life histories typically show lower rates of synonymous substitution (dS) than "fast" species. Previous research suggests long-distance seasonal migrants have a slower life history strategy than short-distance migrants, raising the possibility that rates of molecular evolution may covary with migration distance. Additionally, long-distance migrants may face strong selection on metabolically important mitochondrial genes due to their long-distance flights. Using over 1000 mitochondrial genomes, we assessed the relationship between migration distance and mitochondrial molecular evolution in 39 boreal-breeding migratory bird species. We show that migration distance correlates negatively with dS, suggesting that the slow life history associated with long-distance migration is reflected in rates of molecular evolution. Mitochondrial genes in every study species exhibited evidence of purifying selection, but the strength of selection was greater in short-distance migrants, contrary to our predictions. This result may indicate effects of selection for cold tolerance on mitochondrial evolution among species overwintering at high latitudes. Our study demonstrates that the pervasive correlation between life history and molecular evolutionary rates exists in the context of differential adaptations to seasonality.},
}

@article {pmid37954502,
year = {2022},
author = {Politis-Barber, V and Petrick, HL and Raajendiran, A and DesOrmeaux, GJ and Brunetta, HS and Dos Reis, LM and Mori, MA and Wright, DC and Watt, MJ and Holloway, GP},
title = {Ckmt1 is Dispensable for Mitochondrial Bioenergetics Within White/Beige Adipose Tissue.},
journal = {Function (Oxford, England)},
volume = {3},
number = {5},
pages = {zqac037},
pmid = {37954502},
issn = {2633-8823},
abstract = {Within brown adipose tissue (BAT), the brain isoform of creatine kinase (CKB) has been proposed to regulate the regeneration of ADP and phosphocreatine in a futile creatine cycle (FCC) that stimulates energy expenditure. However, the presence of FCC, and the specific creatine kinase isoforms regulating this theoretical model within white adipose tissue (WAT), remains to be fully elucidated. In the present study, creatine did not stimulate respiration in cultured adipocytes, isolated mitochondria or mouse permeabilized WAT. Additionally, while creatine kinase ubiquitous-type, mitochondrial (CKMT1) mRNA and protein were detected in human WAT, shRNA-mediated reductions in Ckmt1 did not decrease submaximal respiration in cultured adipocytes, and ablation of CKMT1 in mice did not alter energy expenditure, mitochondrial responses to pharmacological β3-adrenergic activation (CL 316, 243) or exacerbate the detrimental metabolic effects of consuming a high-fat diet. Taken together, these findings solidify CKMT1 as dispensable in the regulation of energy expenditure, and unlike in BAT, they do not support the presence of FCC within WAT.},
}

@article {pmid37939146,
year = {2023},
author = {Garcia, PS and Barras, F and Gribaldo, S},
title = {Components of iron-Sulfur cluster assembly machineries are robust phylogenetic markers to trace the origin of mitochondria and plastids.},
journal = {PLoS biology},
volume = {21},
number = {11},
pages = {e3002374},
pmid = {37939146},
issn = {1545-7885},
abstract = {Establishing the origin of mitochondria and plastids is key to understand 2 founding events in the origin and early evolution of eukaryotes. Recent advances in the exploration of microbial diversity and in phylogenomics approaches have indicated a deep origin of mitochondria and plastids during the diversification of Alphaproteobacteria and Cyanobacteria, respectively. Here, we strongly support these placements by analyzing the machineries for assembly of iron-sulfur ([Fe-S]) clusters, an essential function in eukaryotic cells that is carried out in mitochondria by the ISC machinery and in plastids by the SUF machinery. We assessed the taxonomic distribution of ISC and SUF in representatives of major eukaryotic supergroups and analyzed the phylogenetic relationships with their prokaryotic homologues. Concatenation datasets of core ISC proteins show an early branching of mitochondria within Alphaproteobacteria, right after the emergence of Magnetococcales. Similar analyses with the SUF machinery place primary plastids as sister to Gloeomargarita within Cyanobacteria. Our results add to the growing evidence of an early emergence of primary organelles and show that the analysis of essential machineries of endosymbiotic origin provide a robust signal to resolve ancient and fundamental steps in eukaryotic evolution.},
}

@article {pmid37931036,
year = {2023},
author = {Gu, H and Wen, J and Zhao, X and Zhang, X and Ren, X and Cheng, H and Qu, L},
title = {Evolution, Inheritance, and Strata Formation of the W Chromosome in Duck (Anas platyrhynchos).},
journal = {Genome biology and evolution},
volume = {15},
number = {11},
pages = {},
pmid = {37931036},
issn = {1759-6653},
support = {BJJQ-G01-2022//Beijing Innovation Team of the Modern Agro-industry Technology Research System for Poultry/ ; },
mesh = {Animals ; Female ; *Ducks/genetics ; *Evolution, Molecular ; Sex Chromosomes ; Birds/genetics ; Inheritance Patterns ; },
abstract = {The nonrecombining female-limited W chromosome is predicted to experience unique evolutionary processes. Difficulties in assembling W chromosome sequences have hindered the identification of duck W-linked sequences and their evolutionary footprint. To address this, we conducted three initial contig-level genome assemblies and developed a rigorous pipeline by which to successfully expand the W-linked data set, including 11 known genes and 24 newly identified genes. Our results indicate that the W chromosome expression may not be subject to female-specific selection; a significant convergent pattern of upregulation associated with increased female-specific selection was not detected. The genetic stability of the W chromosome is also reflected in the strong evolutionary correlation between it and the mitochondria; the complete consistency of the cladogram topology constructed from their gene sequences proves the shared maternal coevolution. By detecting the evolutionary trajectories of W-linked sequences, we have found that recombination suppression started in four distinct strata, of which three were conserved across Neognathae. Taken together, our results have revealed a unique evolutionary pattern and an independent stratum evolutionary pattern for sex chromosomes.},
}

Animals
Female
*Ducks/genetics
*Evolution, Molecular
Sex Chromosomes
Birds/genetics
Inheritance Patterns

@article {pmid37930986,
year = {2023},
author = {Diaz-Recio Lorenzo, C and Patel, T and Arsenault-Pernet, EJ and Poitrimol, C and Jollivet, D and Martinez Arbizu, P and Gollner, S},
title = {Highly structured populations of deep-sea copepods associated with hydrothermal vents across the Southwest Pacific, despite contrasting life history traits.},
journal = {PloS one},
volume = {18},
number = {11},
pages = {e0292525},
doi = {10.1371/journal.pone.0292525},
pmid = {37930986},
issn = {1932-6203},
mesh = {Animals ; *Copepoda/genetics ; *Hydrothermal Vents ; *Life History Traits ; DNA, Mitochondrial ; Mitochondria/genetics ; Phylogeny ; Ecosystem ; },
abstract = {Hydrothermal vents are extreme environments, where abundant communities of copepods with contrasting life history traits co-exist along hydrothermal gradients. Here, we discuss how these traits may contribute to the observed differences in molecular diversity and population genetic structure. Samples were collected from vent locations across the globe including active ridges and back-arc basins and compared to existing deep-sea hydrothermal vent and shallow water data, covering a total of 22 vents and 3 non-vent sites. A total of 806 sequences of mtDNA from the Cox1 gene were used to reconstruct the phylogeny, haplotypic relationship and demography within vent endemic copepods (Dirivultidae, Stygiopontius spp.) and non-vent-endemic copepods (Ameiridae, Miraciidae and Laophontidae). A species complex within Stygiopontius lauensis was studied across five pacific back-arc basins at eight hydrothermal vent fields, with cryptic species being restricted to the basins they were sampled from. Copepod populations from the Lau, North Fiji and Woodlark basins are undergoing demographic expansion, possibly linked to an increase in hydrothermal activity in the last 10 kya. Highly structured populations of Amphiascus aff. varians 2 were also observed from the Lau to the Woodlark basins with populations also undergoing expansion. Less abundant harpacticoids exhibit little to no population structure and stable populations. This study suggests that similarities in genetic structure and demography may arise in vent-associated copepods despite having different life history traits. As structured meta-populations may be at risk of local extinction should major anthropogenic impacts, such as deep-sea mining, occur, we highlight the importance of incorporating a trait-based approach to investigate patterns of genetic connectivity and demography, particularly regarding area-based management tools and environmental management plans.},
}

Animals
*Copepoda/genetics
*Hydrothermal Vents
*Life History Traits
DNA, Mitochondrial
Mitochondria/genetics
Phylogeny
Ecosystem

@article {pmid37924024,
year = {2023},
author = {Lu, G and Wang, W and Mao, J and Li, Q and Que, Y},
title = {Complete mitogenome assembly of Selenicereus monacanthus revealed its molecular features, genome evolution, and phylogenetic implications.},
journal = {BMC plant biology},
volume = {23},
number = {1},
pages = {541},
pmid = {37924024},
issn = {1471-2229},
support = {XZ202301ZY0020N//the Science and Technology Program of Tibet Autonomous Region/ ; },
mesh = {Phylogeny ; *Genome, Mitochondrial ; Genomics ; Evolution, Molecular ; *Cactaceae/genetics ; },
abstract = {BACKGROUND: Mitochondria are the powerhouse of the cell and are critical for plant growth and development. Pitaya (Selenicereus or Hylocereus) is the most important economic crop in the family Cactaceae and is grown worldwide, however its mitogenome is unreported.

RESULTS: This study assembled the complete mitogenome of the red skin and flesh of pitaya (Selenicereus monacanthus). It is a full-length, 2,290,019 bp circular molecule encoding 59 unique genes that only occupy 2.17% of the entire length. In addition, 4,459 pairs of dispersed repeats (≥ 50 bp) were identified, accounting for 84.78% of the total length, and three repeats (394,588, 124,827, and 13,437 bp) mediating genomic recombination were identified by long read mapping and Sanger sequencing. RNA editing events were identified in all 32 protein-coding genes (PCGs), among which four sites (nad1-2, nad4L-2, atp9-copy3-223, and ccmFC-1309) were associated with the initiation or termination of PCGs. Seventy-eight homologous fragments of the chloroplast genome were identified in the mitogenome, the longest having 4,523 bp. In addition, evolutionary analyses suggest that S. monacanthus may have undergone multiple genomic reorganization events during evolution, with the loss of at least nine PCGs (rpl2, rpl10, rps2, rps3, rps10, rps11, rps14, rps19, and sdh3).

CONCLUSIONS: This study revealed the genetic basis of the S. monacanthus mitogenome, and provided a scientific basis for further research on phenotypic traits and germplasm resource development.},
}

Phylogeny
*Genome, Mitochondrial
Genomics
Evolution, Molecular
*Cactaceae/genetics

@article {pmid37917792,
year = {2023},
author = {Namasivayam, S and Sun, C and Bah, AB and Oberstaller, J and Pierre-Louis, E and Etheridge, RD and Feschotte, C and Pritham, EJ and Kissinger, JC},
title = {Massive invasion of organellar DNA drives nuclear genome evolution in Toxoplasma.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {120},
number = {45},
pages = {e2308569120},
doi = {10.1073/pnas.2308569120},
pmid = {37917792},
issn = {1091-6490},
support = {R01AI068908//HHS | NIH | NIAID | Division of Microbiology and Infectious Diseases, National Institute of Allergy and Infectious Diseases (DMID)/ ; },
mesh = {Humans ; *Toxoplasma/genetics ; Genome ; DNA, Mitochondrial/genetics ; Mitochondria/genetics ; Evolution, Molecular ; Cell Nucleus/genetics ; Sequence Analysis, DNA ; },
abstract = {Toxoplasma gondii is a zoonotic protist pathogen that infects up to one third of the human population. This apicomplexan parasite contains three genome sequences: nuclear (65 Mb); plastid organellar, ptDNA (35 kb); and mitochondrial organellar, mtDNA (5.9 kb of non-repetitive sequence). We find that the nuclear genome contains a significant amount of NUMTs (nuclear integrants of mitochondrial DNA) and NUPTs (nuclear integrants of plastid DNA) that are continuously acquired and represent a significant source of intraspecific genetic variation. NUOT (nuclear DNA of organellar origin) accretion has generated 1.6% of the extant T. gondii ME49 nuclear genome-the highest fraction ever reported in any organism. NUOTs are primarily found in organisms that retain the non-homologous end-joining repair pathway. Significant movement of organellar DNA was experimentally captured via amplicon sequencing of a CRISPR-induced double-strand break in non-homologous end-joining repair competent, but not ku80 mutant, Toxoplasma parasites. Comparisons with Neospora caninum, a species that diverged from Toxoplasma ~28 mya, revealed that the movement and fixation of five NUMTs predates the split of the two genera. This unexpected level of NUMT conservation suggests evolutionary constraint for cellular function. Most NUMT insertions reside within (60%) or nearby genes (23% within 1.5 kb), and reporter assays indicate that some NUMTs have the ability to function as cis-regulatory elements modulating gene expression. Together, these findings portray a role for organellar sequence insertion in dynamically shaping the genomic architecture and likely contributing to adaptation and phenotypic changes in this important human pathogen.},
}

Humans
*Toxoplasma/genetics
Genome
DNA, Mitochondrial/genetics
Mitochondria/genetics
Evolution, Molecular
Cell Nucleus/genetics
Sequence Analysis, DNA

@article {pmid37919084,
year = {2023},
author = {Zhang, X and Lu, YC and Wang, JL},
title = {Assembly and Characterization of the Mitochondrial Genome of Fallopia aubertii (L. Henry) Holub.},
journal = {Frontiers in bioscience (Landmark edition)},
volume = {28},
number = {10},
pages = {233},
doi = {10.31083/j.fbl2810233},
pmid = {37919084},
issn = {2768-6698},
support = {2019-ZJ-915//Natural Science Foundation of Qinghai Province Science and Technology Department/ ; 2022-JYQN-002//Foundation of Qinghai Minzu University/ ; 2021XJG17//Foundation of Qinghai Minzu University/ ; },
abstract = {BACKGROUND: Fallopia aubertii (L. Henry) Holub is a perennial semi-shrub with both ornamental and medicinal value. The mitochondrial genomes of plants contain valuable genetic traits that can be utilized for the exploitation of genetic resources. The parsing of F. aubertii mitochondrial genome can provide insight into the role of mitochondria in plant growth and development, metabolism regulation, evolution, and response to environmental stress.

METHODS: In this study, we sequenced the mitochondrial genome of F. aubertii using the Illumina NovaSeq 6000 platform and Nanopore platform. We conducted a comprehensive analysis of the mitochondrial genome of F. aubertii, which involved examining various aspects such as gene composition, repetitive sequences, RNA editing sites, phylogeny, and organelle genome homology. To achieve this, we employed several bioinformatics methods including sequence alignment analysis, repetitive sequence analysis, phylogeny analysis, and more.

RESULTS: The mitochondrial genome of F. aubertii has 64 genes, including 34 protein-coding genes (PCGs), three rRNAs, and 27 tRNAs. There were 77 short tandem repeat sequences detected in the mitochondrial genome, five tandem repeat sequences identified by Tandem Repeats Finder (TRF), and 50 scattered repeat sequences observed, including 22 forward repeat sequences and 28 palindrome repeat sequences. A total of 367 RNA coding sites were predicted in PCGs, with the highest number (33) found within ccmB. Ka/Ks values estimated for mitochondrial genes of F. aubertii and three closely related species representing Caryophyllales were less than 1 for most of the genes. The maximum likelihood evolutionary tree showed that F. aubertii and Nepenthes ×ventrata are most closely related.

CONCLUSIONS: In this study, we obtained basic information on the mitochondrial genome of F. aubertii and this study investigated repeat sequences and homologous segments, predicted RNA editing sites, and utilized the Ka/Ks ratio to estimate the selection pressure on mitochondrial genes of F. aubertii. We also discussed the systematic evolutionary position of F. aubertii based on mitochondrial genome sequences. Our study revealed variations in the sequence and structure of mitochondrial genomes in Caryophyllales. These findings are of great significance for identifying and improving valuable plant traits and serve as a reference for future molecular studies of F. aubertii.},
}

@article {pmid37903625,
year = {2024},
author = {Hacker, C and Sendra, K and Keisham, P and Filipescu, T and Lucocq, J and Salimi, F and Ferguson, S and Bhella, D and MacNeill, SA and Embley, M and Lucocq, J},
title = {Biogenesis, inheritance, and 3D ultrastructure of the microsporidian mitosome.},
journal = {Life science alliance},
volume = {7},
number = {1},
pages = {},
pmid = {37903625},
issn = {2575-1077},
mesh = {Animals ; *Fungal Proteins/metabolism ; Mitochondria/metabolism ; *Microsporidia/genetics/metabolism ; Saccharomyces cerevisiae/metabolism ; Dynamins ; Mammals/metabolism ; },
abstract = {During the reductive evolution of obligate intracellular parasites called microsporidia, a tiny remnant mitochondrion (mitosome) lost its typical cristae, organellar genome, and most canonical functions. Here, we combine electron tomography, stereology, immunofluorescence microscopy, and bioinformatics to characterise mechanisms of growth, division, and inheritance of this minimal mitochondrion in two microsporidia species (grown within a mammalian RK13 culture-cell host). Mitosomes of Encephalitozoon cuniculi (2-12/cell) and Trachipleistophora hominis (14-18/nucleus) displayed incremental/non-phasic growth and division and were closely associated with an organelle identified as equivalent to the fungal microtubule-organising centre (microsporidian spindle pole body; mSPB). The mitosome-mSPB association was resistant to treatment with microtubule-depolymerising drugs nocodazole and albendazole. Dynamin inhibitors (dynasore and Mdivi-1) arrested mitosome division but not growth, whereas bioinformatics revealed putative dynamins Drp-1 and Vps-1, of which, Vps-1 rescued mitochondrial constriction in dynamin-deficient yeast (Schizosaccharomyces pombe). Thus, microsporidian mitosomes undergo incremental growth and dynamin-mediated division and are maintained through ordered inheritance, likely mediated via binding to the microsporidian centrosome (mSPB).},
}

Animals
*Fungal Proteins/metabolism
Mitochondria/metabolism
*Microsporidia/genetics/metabolism
Saccharomyces cerevisiae/metabolism
Dynamins
Mammals/metabolism

@article {pmid37901222,
year = {2023},
author = {Brun, C and Chalet, L and Moulin, F and Bochaton, T and Ducreux, S and Paillard, M and Crola Da Silva, C},
title = {A bibliometric analysis: Ca[2+] fluxes and inflammatory phenotyping by flow cytometry in peripheral blood mononuclear cells.},
journal = {Frontiers in immunology},
volume = {14},
number = {},
pages = {1272809},
pmid = {37901222},
issn = {1664-3224},
mesh = {Humans ; *Leukocytes, Mononuclear/metabolism ; Flow Cytometry/methods ; Cell Line ; *Signal Transduction ; Inflammation/metabolism ; },
abstract = {BACKGROUND: The immune system, composed of organs, tissues, cells, and proteins, is the key to protecting the body from external biological attacks and inflammation. The latter occurs in several pathologies, such as cancers, type 1 diabetes, and human immunodeficiency virus infection. Immunophenotyping by flow cytometry is the method of choice for diagnosing these pathologies. Under inflammatory conditions, the peripheral blood mononuclear cells (PBMCs) are partially activated and generate intracellular pathways involving Ca[2+]-dependent signaling cascades leading to transcription factor expression. Ca[2+] signaling is typically studied by microscopy in cell lines but can present some limitations to explore human PBMCs, where flow cytometry can be a good alternative.

OBJECTIVE: In this review, we dived into the research field of inflammation and Ca[2+] signaling in PBMCs. We aimed to investigate the structure and evolution of this field in a physio-pathological context, and then we focused our review on flow cytometry analysis of Ca[2+] fluxes in PBMCs.

METHODS: From 1984 to 2022, 3865 articles on inflammation and Ca[2+] signaling in PBMCs were published, according to The Clarivate Web of Science (WOS) database used in this review. A bibliometric study was designed for this collection and consisted of a co-citation and bibliographic coupling analysis.

RESULTS: The co-citation analysis was performed on 133 articles: 4 clusters highlighted the global context of Ca[2+] homeostasis, including chemical probe development, identification of the leading players in Ca[2+] signaling, and the link with chemokine production in immune cell function. Next, the bibliographic coupling analysis combined 998 articles in 8 clusters. This analysis outlined the mechanisms of PBMC activation, from signal integration to cellular response. Further explorations of the bibliographic coupling network, focusing on flow cytometry, revealed 21 articles measuring cytosolic Ca[2+] in PBMCs, with only 5 since 2016. This final query showed that Ca[2+] signaling analysis in human PBMCs using flow cytometry is still underdeveloped and investigates mainly the cytosolic Ca[2+] compartment.

CONCLUSION: Our review uncovers remaining knowledge gaps of intracellular players involved in Ca[2+] signaling in PBMCs, such as reticulum and mitochondria, and presents flow cytometry as a solid option to supplement gold-standard microscopy studies.},
}

Humans
*Leukocytes, Mononuclear/metabolism
Flow Cytometry/methods
Cell Line
*Signal Transduction
Inflammation/metabolism

@article {pmid37815994,
year = {2023},
author = {Chen, YH and Miller, WB and Hay, A},
title = {Postharvest bacterial succession on cut flowers and vase water.},
journal = {PloS one},
volume = {18},
number = {10},
pages = {e0292537},
pmid = {37815994},
issn = {1932-6203},
mesh = {*Water ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; Ecosystem ; *Asteraceae ; Flowers ; Bacteria/genetics ; },
abstract = {In cut flowers, xylem occlusion or blockage by bacteria negatively affects water balance and postharvest quality. Many studies have used culture-based methods to examine bacterial populations in vase water and their effects on flower longevity. It is still unclear if and how bacterial communities at the 16S rRNA gene (16S) level change during the vase period and how such change might correlate with postharvest longevity. This study compared the sequences of 16S amplicons from 4 different types of flowers and their vase water over the course of 7 days (Rosa spp., Gerbera jamesonii, and two Lilium varieties). The relative abundance of plant chloroplast and mitochondria 16S decreased significantly over the course 7 days in all 4 flowers as bacterial diversity increased. Richness and evenness of the bacterial communities increased over time, as did the number of rare taxa and phylogenetic diversity. Bacterial communities varied with time, as well as by flower source, types, and sample location (water, stem surface, whole stem). Some taxa, such as Enterobacteriacea and Bradyhizobiaceae decreased significantly over time while others such as Pseudomonas spp. increased. For example, Pseudomonas veronii, implicated in soft rot of calla lily, increased in both whole stem samples and water samples from Gerbera jamesonii. Erwinia spp., which includes plant pathogenic species, also increased in water samples. This work highlights the dynamic and complex nature of bacterial succession in the flower vase ecosystem. More work is needed to understand if and how bacterial community structure can be managed to improve cut flower vase life.},
}

*Water
RNA, Ribosomal, 16S/genetics
Phylogeny
Ecosystem
*Asteraceae
Flowers
Bacteria/genetics

@article {pmid37818890,
year = {2023},
author = {Chen, H and Shi, BY and Du, LN and Sun, HY},
title = {Description of a New Species of Hua (Gastropoda: Semisulcospiridae) from Guizhou, China, Based on Morphology and Molecular Evidence.},
journal = {Zoological science},
volume = {40},
number = {5},
pages = {414-421},
doi = {10.2108/zs230025},
pmid = {37818890},
issn = {0289-0003},
mesh = {Female ; Animals ; *Gastropoda/anatomy & histology ; Phylogeny ; China ; Mitochondria ; },
abstract = {A new species of Hua, Hua qiannanensis sp. nov., is described from Guizhou Province, China, based on morphological and molecular evidence. The new species can be distinguished from its congeners by the following combination of characters: the smooth shell, only three smaller cusps of lateral teeth on the inner side, outer marginal teeth with eight flattened and rounded denticles, an ovipositor pore in females, and BW/H ≥ 80%, B/H = 76.8-82.3%. Molecular analysis based on partial mitochondrial COI and 16S rDNA also supports the systematic position of the new taxon.},
}

Female
Animals
*Gastropoda/anatomy & histology
Phylogeny
China
Mitochondria

@article {pmid37900311,
year = {2023},
author = {Gonzalez-Jimenez, I and Perlin, DS and Shor, E},
title = {Reactive oxidant species induced by antifungal drugs: identity, origins, functions, and connection to stress-induced cell death.},
journal = {Frontiers in cellular and infection microbiology},
volume = {13},
number = {},
pages = {1276406},
pmid = {37900311},
issn = {2235-2988},
abstract = {Reactive oxidant species (ROS) are unstable, highly reactive molecules that are produced by cells either as byproducts of metabolism or synthesized by specialized enzymes. ROS can be detrimental, e.g., by damaging cellular macromolecules, or beneficial, e.g., by participating in signaling. An increasing body of evidence shows that various fungal species, including both yeasts and molds, increase ROS production upon exposure to the antifungal drugs currently used in the clinic: azoles, polyenes, and echinocandins. However, the implications of these findings are still largely unclear due to gaps in knowledge regarding the chemical nature, molecular origins, and functional consequences of these ROS. Because the detection of ROS in fungal cells has largely relied on fluorescent probes that lack specificity, the chemical nature of the ROS is not known, and it may vary depending on the specific fungus-drug combination. In several instances, the origin of antifungal drug-induced ROS has been identified as the mitochondria, but further experiments are necessary to strengthen this conclusion and to investigate other potential cellular ROS sources, such as the ER, peroxisomes, and ROS-producing enzymes. With respect to the function of the ROS, several studies have shown that they contribute to the drugs' fungicidal activities and may be part of drug-induced programmed cell death (PCD). However, whether these "pro-death" ROS are a primary consequence of the antifungal mechanism of action or a secondary consequence of drug-induced PCD remains unclear. Finally, several recent studies have raised the possibility that ROS induction can serve an adaptive role, promoting antifungal drug tolerance and the evolution of drug resistance. Filling these gaps in knowledge will reveal a new aspect of fungal biology and may identify new ways to potentiate antifungal drug activity or prevent the evolution of antifungal drug resistance.},
}

@article {pmid37895071,
year = {2023},
author = {Olla, S and Siguri, C and Fais, A and Era, B and Fantini, MC and Di Petrillo, A},
title = {Inhibitory Effect of Quercetin on Oxidative Endogen Enzymes: A Focus on Putative Binding Modes.},
journal = {International journal of molecular sciences},
volume = {24},
number = {20},
pages = {},
pmid = {37895071},
issn = {1422-0067},
mesh = {*Quercetin/pharmacology ; Reactive Oxygen Species/metabolism ; *Antioxidants/pharmacology/metabolism ; Molecular Docking Simulation ; Oxidative Stress ; Xanthine Oxidase/metabolism ; Monoamine Oxidase/metabolism ; },
abstract = {Oxidative stress is defined as an imbalance between the production of free radicals and reactive oxygen species (ROS) and the ability of the body to neutralize them by anti-oxidant defense systems. Cells can produce ROS during physiological processes, but excessive ROS can lead to non-specific and irreversible damage to biological molecules, such as DNA, lipids, and proteins. Mitochondria mainly produce endogenous ROS during both physiological and pathological conditions. Enzymes like nicotinamide adenine dinucleotide phosphate oxidase (NOX), xanthine oxidase (XO), lipoxygenase (LOX), myeloperoxidase (MPO), and monoamine oxidase (MAO) contribute to this process. The body has enzymatic and non-enzymatic defense systems to neutralize ROS. The intake of bioactive phenols, like quercetin (Que), can protect against pro-oxidative damage by quenching ROS through a non-enzymatic system. In this study, we evaluate the ability of Que to target endogenous oxidant enzymes involved in ROS production and explore the mechanisms of action underlying its anti-oxidant properties. Que can act as a free radical scavenger by donating electrons through the negative charges in its phenolic and ketone groups. Additionally, it can effectively inhibit the activity of several endogenous oxidative enzymes by binding them with high affinity and specificity. Que had the best molecular docking results with XO, followed by MAO-A, 5-LOX, NOX, and MPO. Que's binding to these enzymes was confirmed by subsequent molecular dynamics, revealing different stability phases depending on the enzyme bound. The 500 ns simulation showed a net evolution of binding for NOX and MPO. These findings suggest that Que has potential as a natural therapy for diseases related to oxidative stress.},
}

*Quercetin/pharmacology
Reactive Oxygen Species/metabolism
*Antioxidants/pharmacology/metabolism
Molecular Docking Simulation
Oxidative Stress
Xanthine Oxidase/metabolism
Monoamine Oxidase/metabolism

@article {pmid37885664,
year = {2023},
author = {Ni, Y and Zhang, X and Li, J and Lu, Q and Chen, H and Ma, B and Liu, C},
title = {Genetic diversity of Coffea arabica L. mitochondrial genomes caused by repeat- mediated recombination and RNA editing.},
journal = {Frontiers in plant science},
volume = {14},
number = {},
pages = {1261012},
pmid = {37885664},
issn = {1664-462X},
abstract = {BACKGROUND: Coffea arabica L. is one of the most important crops widely cultivated in 70 countries across Asia, Africa, and Latin America. Mitochondria are essential organelles that play critical roles in cellular respiration, metabolism, and differentiation. C. arabica's nuclear and chloroplast genomes have been reported. However, its mitochondrial genome remained unreported. Here, we intended to sequence and characterize its mitochondrial genome to maximize the potential of its genomes for evolutionary studies, molecular breeding, and molecular marker developments.

RESULTS: We sequenced the total DNA of C. arabica using Illumina and Nanopore platforms. We then assembled the mitochondrial genome with a hybrid strategy using Unicycler software. We found that the mitochondrial genome comprised two circular chromosomes with lengths of 867,678 bp and 153,529 bp, encoding 40 protein-coding genes, 26 tRNA genes, and three rRNA genes. We also detected 270 Simple Sequence Repeats and 34 tandem repeats in the mitochondrial genome. We found 515 high-scoring sequence pairs (HSPs) for a self-to-self similarity comparison using BLASTn. Three HSPs were found to mediate recombination by the mapping of long reads. Furthermore, we predicted 472 using deep-mt with the convolutional neural network model. Then we randomly validated 90 RNA editing events by PCR amplification and Sanger sequencing, with the majority being non-synonymous substitutions and only three being synonymous substitutions. These findings provide valuable insights into the genetic characteristics of the C. arabica mitochondrial genome, which can be helpful for future study on coffee breeding and mitochondrial genome evolution.

CONCLUSION: Our study sheds new light on the evolution of C. arabica organelle genomes and their potential use in genetic breeding, providing valuable data for developing molecular markers that can improve crop productivity and quality. Furthermore, the discovery of RNA editing events in the mitochondrial genome of C. arabica offers insights into the regulation of gene expression in this species, contributing to a better understanding of coffee genetics and evolution.},
}

@article {pmid37871810,
year = {2023},
author = {de Souza Coto, AL and Pereira, AA and Oliveira, SD and de Oliveira Moritz, MN and da Rocha, AMF and Dores-Silva, PR and da Silva, NSM and de Araújo Nogueira, AR and Gava, LM and Seraphim, TV and Borges, JC},
title = {Structural characterization of the human DjC20/HscB cochaperone in solution.},
journal = {Biochimica et biophysica acta. Proteins and proteomics},
volume = {},
number = {},
pages = {140970},
doi = {10.1016/j.bbapap.2023.140970},
pmid = {37871810},
issn = {1878-1454},
abstract = {J-domain proteins (JDPs) form a very large molecular chaperone family involved in proteostasis processes, such as protein folding, trafficking through membranes and degradation/disaggregation. JDPs are Hsp70 co-chaperones capable of stimulating ATPase activity as well as selecting and presenting client proteins to Hsp70. In mitochondria, human DjC20/HscB (a type III JDP that possesses only the conserved J-domain in some region of the protein) is involved in [FeS] protein biogenesis and assists human mitochondrial Hsp70 (HSPA9). Human DjC20 possesses a zinc-finger domain in its N-terminus, which closely contacts the J-domain and appears to be essential for its function. Here, we investigated the hDjC20 structure in solution as well as the importance of Zn[+2] for its stability. The recombinant hDjC20 was pure, folded and capable of stimulating HSPA9 ATPase activity. It behaved as a slightly elongated monomer, as attested by small-angle X-ray scattering and SEC-MALS. The presence of Zn[2+] in the hDjC20 samples was verified, a stoichiometry of 1:1 was observed, and its removal by high concentrations of EDTA and DTPA was unfeasible. However, thermal and chemical denaturation in the presence of EDTA led to a reduction in protein stability, suggesting a synergistic action between the chelating agent and denaturators that facilitate protein unfolding depending on metal removal. These data suggest that the affinity of Zn[+2] for the protein is very high, evidencing its importance for the hDjC20 structure.},
}

@article {pmid37518527,
year = {2023},
author = {Kuhara, N and Nozaki, T and Zhang, AO and Zhou, X},
title = {DNA barcoding facilitates discovery and description of two new species of the Mystacides azureus Species Group (Trichoptera: Leptoceridae) in Japan.},
journal = {Zootaxa},
volume = {5306},
number = {2},
pages = {215-231},
doi = {10.11646/zootaxa.5306.2.3},
pmid = {37518527},
issn = {1175-5334},
mesh = {Female ; Animals ; Male ; Japan ; *DNA Barcoding, Taxonomic ; Phylogeny ; *Holometabola ; Mitochondria ; },
abstract = {We examined adult specimens of the Mystacides azureus Species Group (Trichoptera: Leptoceridae) collected in Japan and confirm three species including M. azureus Linnaeus 1761 and two new species, M. rivularis and M. moritai. Males and females of the new species are described. Mystacides azureus in Japan is shown to have a considerable variation in morphology of the male tergum X. We analyzed mitochondrial COI barcodes of the genus Mystacides including these three species to confirm their species status. A maximum likelihood phylogeny based on COI barcodes shows monophyly of the new species. It also supports the hypothesis that morphological variation of the male tergum X in Japanese populations is intraspecific in only M. azureus.},
}

Female
Animals
Male
Japan
*DNA Barcoding, Taxonomic
Phylogeny
*Holometabola
Mitochondria

@article {pmid37518286,
year = {2023},
author = {Zhang, G and Gao, JJ and Takano, KT and Yafuso, M and Suwito, A and Meleng, PA and Toda, MJ},
title = {Phylogenetic classification and palm-inflorescence anthophily of the Colocasiomyia zeylanica species group (Diptera: Drosophilidae), with descriptions of five new species.},
journal = {Zootaxa},
volume = {5278},
number = {2},
pages = {201-238},
doi = {10.11646/zootaxa.5278.2.1},
pmid = {37518286},
issn = {1175-5334},
mesh = {Animals ; *Diptera ; *Drosophilidae/genetics ; Phylogeny ; Inflorescence ; Mitochondria ; },
abstract = {The zeylanica group is one of the six species groups of the anthophilic genus Colocasiomyia de Meijere in the family Drosophilidae. In addition to two known species, five morphospecies have been recognized as members of this species group but left undescribed formally. In this study, species delimitation of these putatively new species was determined by barcoding of the mitochondrial COI (cytochrome c oxydase subunit I) gene and morphological comparison. Phylogenetic relationships within the genus Colocasiomyia were inferred by a cladistic analysis of 89 morphological characters. Based on the results of these analyses, we redefined the zeylanica species group and established two subgroups within it: the zeylanica subgroup comprised of C. zeylanica, C. nepalensis, C. pinangae sp. nov., C. besaris sp. nov. and C. luciphila sp. nov., and the oligochaeta subgroup of C. oligochaeta sp. nov. and C. grimaldii sp. nov. In addition, we briefly address the anthophilic habits of drosophilid flies using palm (Arecaceae) inflorescences, especially of the zeylanica group, compiling scattered collection records from the Oriental and Papuan regions.},
}

Animals
*Diptera
*Drosophilidae/genetics
Phylogeny
Inflorescence
Mitochondria

@article {pmid37859594,
year = {2023},
author = {Waters, ER and Bezanilla, M and Vierling, E},
title = {ATAD3 Proteins: Unique Mitochondrial Proteins Essential for Life in Diverse Eukaryotic Lineages.},
journal = {Plant & cell physiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/pcp/pcad122},
pmid = {37859594},
issn = {1471-9053},
support = {IOS 1354960 MCB 2215727//National Science Foundation/ ; },
abstract = {ATAD3 proteins (ATPase family AAA domain-containing protein 3) are unique mitochondrial proteins that arose deep in the eukaryotic lineage but that are surprisingly absent from the Fungi and Amoebozoa. These ~600 amino acid proteins are anchored in the inner mitochondrial membrane and are essential in metazoans and Arabidopsis thaliana. ATAD3s comprise a C-terminal AAA+ matrix domain and an ATAD3_N domain that is located primarily in the inner membrane space but potentially extends into cytosol to interact with the ER. Sequence and structural alignments indicate ATAD3 proteins are most similar to classic chaperone unfoldases in AAA+ family, suggesting that they operate in mitochondrial protein quality control. A. thaliana has four ATAD3 genes in two distinct clades that appear first in the seed plants, and both clades are essential for viability. The four genes are generally coordinately expressed, and transcripts are highest in growing apices and imbibed seeds. Plants with disrupted ATAD3 have reduced growth, aberrant mitochondrial morphology, diffuse nucleoids and reduced oxidative phosphorylation complex I. These and other pleiotropic phenotypes are also observed in ATAD3 mutants in metazoans. Here we discuss the distribution of ATAD3 proteins as they have evolved in the plant kingdom, their unique structure, what we know about their function in plants, and the challenges in determining their essential roles in mitochondria.},
}

@article {pmid37577532,
year = {2023},
author = {Wolters, JF and LaBella, AL and Opulente, DA and Rokas, A and Hittinger, CT},
title = {Mitochondrial Genome Diversity across the Subphylum Saccharomycotina.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {37577532},
support = {R01 AI153356/AI/NIAID NIH HHS/United States ; T32 HG002760/HG/NHGRI NIH HHS/United States ; },
abstract = {Eukaryotic life depends on the functional elements encoded by both the nuclear genome and organellar genomes, such as those contained within the mitochondria. The content, size, and structure of the mitochondrial genome varies across organisms with potentially large implications for phenotypic variance and resulting evolutionary trajectories. Among yeasts in the subphylum Saccharomycotina, extensive differences have been observed in various species relative to the model yeast Saccharomyces cerevisiae, but mitochondrial genome sampling across many groups has been scarce, even as hundreds of nuclear genomes have become available. By extracting mitochondrial assemblies from existing short-read genome sequence datasets, we have greatly expanded both the number of available genomes and the coverage across sparsely sampled clades. Comparison of 353 yeast mitochondrial genomes revealed that, while size and GC content were fairly consistent across species, those in the genera Metschnikowia and Saccharomyces trended larger, while several species in the order Saccharomycetales, which includes S. cerevisiae, exhibited lower GC content. Extreme examples for both size and GC content were scattered throughout the subphylum. All mitochondrial genomes shared a core set of protein-coding genes for Complexes III, IV, and V, but they varied in the presence or absence of mitochondrially-encoded canonical Complex I genes. We traced the loss of Complex I genes to a major event in the ancestor of the orders Saccharomycetales and Saccharomycodales, but we also observed several independent losses in the orders Phaffomycetales, Pichiales, and Dipodascales. In contrast to prior hypotheses based on smaller-scale datasets, comparison of evolutionary rates in protein-coding genes showed no bias towards elevated rates among aerobically fermenting (Crabtree/Warburg-positive) yeasts. Mitochondrial introns were widely distributed, but they were highly enriched in some groups. The majority of mitochondrial introns were poorly conserved within groups, but several were shared within groups, between groups, and even across taxonomic orders, which is consistent with horizontal gene transfer, likely involving homing endonucleases acting as selfish elements. As the number of available fungal nuclear genomes continues to expand, the methods described here to retrieve mitochondrial genome sequences from these datasets will prove invaluable to ensuring that studies of fungal mitochondrial genomes keep pace with their nuclear counterparts.},
}

@article {pmid37214873,
year = {2023},
author = {Cronin, SJF and Yu, W and Hale, A and Licht-Mayer, S and Crabtree, MJ and Korecka, JA and Tretiakov, EO and Sealey-Cardona, M and Somlyay, M and Onji, M and An, M and Fox, JD and Turnes, BL and Gomez-Diaz, C and da Luz Scheffer, D and Cikes, D and Nagy, V and Weidinger, A and Wolf, A and Reither, H and Chabloz, A and Kavirayani, A and Rao, S and Andrews, N and Latremoliere, A and Costigan, M and Douglas, G and Freitas, FC and Pifl, C and Walz, R and Konrat, R and Mahad, DJ and Koslov, AV and Latini, A and Isacson, O and Harkany, T and Hallett, PJ and Bagby, S and Woolf, CJ and Channon, KM and Je, HS and Penninger, JM},
title = {Crucial neuroprotective roles of the metabolite BH4 in dopaminergic neurons.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {37214873},
support = {R01 NS112266/NS/NINDS NIH HHS/United States ; R35 NS105076/NS/NINDS NIH HHS/United States ; },
abstract = {Dopa-responsive dystonia (DRD) and Parkinson's disease (PD) are movement disorders caused by the dysfunction of nigrostriatal dopaminergic neurons. Identifying druggable pathways and biomarkers for guiding therapies is crucial due to the debilitating nature of these disorders. Recent genetic studies have identified variants of GTP cyclohydrolase-1 (GCH1), the rate-limiting enzyme in tetrahydrobiopterin (BH4) synthesis, as causative for these movement disorders. Here, we show that genetic and pharmacological inhibition of BH4 synthesis in mice and human midbrain-like organoids accurately recapitulates motor, behavioral and biochemical characteristics of these human diseases, with severity of the phenotype correlating with extent of BH4 deficiency. We also show that BH4 deficiency increases sensitivities to several PD-related stressors in mice and PD human cells, resulting in worse behavioral and physiological outcomes. Conversely, genetic and pharmacological augmentation of BH4 protects mice from genetically- and chemically induced PD-related stressors. Importantly, increasing BH4 levels also protects primary cells from PD-affected individuals and human midbrain-like organoids (hMLOs) from these stressors. Mechanistically, BH4 not only serves as an essential cofactor for dopamine synthesis, but also independently regulates tyrosine hydroxylase levels, protects against ferroptosis, scavenges mitochondrial ROS, maintains neuronal excitability and promotes mitochondrial ATP production, thereby enhancing mitochondrial fitness and cellular respiration in multiple preclinical PD animal models, human dopaminergic midbrain-like organoids and primary cells from PD-affected individuals. Our findings pinpoint the BH4 pathway as a key metabolic program at the intersection of multiple protective mechanisms for the health and function of midbrain dopaminergic neurons, identifying it as a potential therapeutic target for PD.},
}

@article {pmid37850870,
year = {2023},
author = {Nicolini, F and Ghiselli, F and Luchetti, A and Milani, L},
title = {Bivalves as emerging model systems to study the mechanisms and evolution of sex determination: a genomic point of view.},
journal = {Genome biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/gbe/evad181},
pmid = {37850870},
issn = {1759-6653},
abstract = {Bivalves are a diverse group of molluscs that have recently attained a central role in plenty of biological research fields, thanks to their peculiar life history traits. Here we propose that bivalves should be considered as emerging model systems also in sex-determination studies, since they would allow to investigate: (i) the transition between environmental and genetic sex determination, with respect to different reproductive backgrounds and sexual systems (from species with strict gonochorism to species with various forms of hermaphroditism); (ii) the genomic evolution of sex chromosomes, considering that no heteromorphic sex chromosomes are currently known and that homomorphic sex chromosomes have been identified just in few species of scallops; (iii) the putative role of mitochondria at some level of the sex determination signaling pathway, in a mechanism that may resemble the cytoplasmatic male sterility of plants; (iv) the evolutionary history of sex-determination related gene families with respect to other animal groups. In particular, we think that this last topic may lay the foundations for expanding our understanding of bivalve sex determination, as our current knowledge is quite fragmented and limited to few species. As a matter of fact, tracing the phylogenetic history and diversity of sex-determination related gene families (such as the Dmrt, Sox and Fox genes) would allow to perform more targeted functional experiments and genomic analyses, but also fostering the possibility of establishing a solid comparative framework.},
}

@article {pmid37502859,
year = {2023},
author = {Cal, K and Leyva, A and Rodríguez-Duarte, J and Ruiz, S and Santos, L and Colella, L and Ingold, M and Vilaseca, C and Galliussi, G and Ziegler, L and Peclat, TR and Bresque, M and Handy, RM and King, R and Dos Reis, LM and Espasandin, C and Breining, P and Dapueto, R and Lopez, A and Thompson, KL and Agorrody, G and DeVallance, E and Meadows, E and Lewis, SE and Barbosa, GCS and de Souza, LOL and Chichierchio, MS and Valez, V and Aicardo, A and Contreras, P and Vendelbo, MH and Jakobsen, S and Kamaid, A and Porcal, W and Calliari, A and Verdes, JM and Du, J and Wang, Y and Hollander, JM and White, TA and Radi, R and Moyna, G and Quijano, C and O'Doherty, R and Moraes-Vieira, P and Holloway, GP and Leonardi, R and Mori, MA and Camacho-Pereira, J and Kelley, EE and Duran, R and Lopez, GV and Batthyány, C and Chini, EN and Escande, C},
title = {A nitroalkene derivative of salicylate alleviates diet-induced obesity by activating creatine metabolism and non-shivering thermogenesis.},
journal = {Research square},
volume = {},
number = {},
pages = {},
pmid = {37502859},
abstract = {Obesity-related type II diabetes (diabesity) has increased global morbidity and mortality dramatically. Previously, the ancient drug salicylate demonstrated promise for the treatment of type II diabetes, but its clinical use was precluded due to high dose requirements. In this study, we present a nitroalkene derivative of salicylate, 5-(2-nitroethenyl)salicylic acid (SANA), a molecule with unprecedented beneficial effects in diet-induced obesity (DIO). SANA reduces DIO, liver steatosis and insulin resistance at doses up to 40 times lower than salicylate. Mechanistically, SANA stimulated mitochondrial respiration and increased creatine-dependent energy expenditure in adipose tissue. Indeed, depletion of creatine resulted in the loss of SANA action. Moreover, we found that SANA binds to creatine kinases CKMT1/2, and downregulation CKMT1 interferes with the effect of SANA in vivo. Together, these data demonstrate that SANA is a first-in-class activator of creatine-dependent energy expenditure and thermogenesis in adipose tissue and emerges as a candidate for the treatment of diabesity.},
}

@article {pmid37844192,
year = {2023},
author = {Borghi, F and Saiardi, A},
title = {Evolutionary perspective on mammalian inorganic polyphosphate (polyP) biology.},
journal = {Biochemical Society transactions},
volume = {},
number = {},
pages = {},
doi = {10.1042/BST20230483},
pmid = {37844192},
issn = {1470-8752},
abstract = {Inorganic polyphosphate (polyP), the polymeric form of phosphate, is attracting ever-growing attention due to the many functions it appears to perform within mammalian cells. This essay does not aim to systematically review the copious mammalian polyP literature. Instead, we examined polyP synthesis and functions in various microorganisms and used an evolutionary perspective to theorise key issues of this field and propose solutions. By highlighting the presence of VTC4 in distinct species of very divergent eucaryote clades (Opisthokonta, Viridiplantae, Discoba, and the SAR), we propose that whilst polyP synthesising machinery was present in the ancestral eukaryote, most lineages subsequently lost it during evolution. The analysis of the bacteria-acquired amoeba PPK1 and its unique polyP physiology suggests that eukaryote cells must have developed mechanisms to limit cytosolic polyP accumulation. We reviewed the literature on polyP in the mitochondria from the perspective of its endosymbiotic origin from bacteria, highlighting how mitochondria could possess a polyP physiology reminiscent of their 'bacterial' beginning that is not yet investigated. Finally, we emphasised the similarities that the anionic polyP shares with the better-understood negatively charged polymers DNA and RNA, postulating that the nucleus offers an ideal environment where polyP physiology might thrive.},
}

@article {pmid37843218,
year = {2024},
author = {Zhang, J and Zhu, Q and Wang, J and Peng, Z and Zhuang, Z and Hang, C and Li, W},
title = {Mitochondrial dysfunction and quality control lie at the heart of subarachnoid hemorrhage.},
journal = {Neural regeneration research},
volume = {19},
number = {4},
pages = {825-832},
doi = {10.4103/1673-5374.381493},
pmid = {37843218},
issn = {1673-5374},
abstract = {The dramatic increase in intracranial pressure after subarachnoid hemorrhage leads to a decrease in cerebral perfusion pressure and a reduction in cerebral blood flow. Mitochondria are directly affected by direct factors such as ischemia, hypoxia, excitotoxicity, and toxicity of free hemoglobin and its degradation products, which trigger mitochondrial dysfunction. Dysfunctional mitochondria release large amounts of reactive oxygen species, inflammatory mediators, and apoptotic proteins that activate apoptotic pathways, further damaging cells. In response to this array of damage, cells have adopted multiple mitochondrial quality control mechanisms through evolution, including mitochondrial protein quality control, mitochondrial dynamics, mitophagy, mitochondrial biogenesis, and intercellular mitochondrial transfer, to maintain mitochondrial homeostasis under pathological conditions. Specific interventions targeting mitochondrial quality control mechanisms have emerged as promising therapeutic strategies for subarachnoid hemorrhage. This review provides an overview of recent research advances in mitochondrial pathophysiological processes after subarachnoid hemorrhage, particularly mitochondrial quality control mechanisms. It also presents potential therapeutic strategies to target mitochondrial quality control in subarachnoid hemorrhage.},
}

@article {pmid37810794,
year = {2023},
author = {Rodriguez, D and Harding, SF and Sirsi, S and McNichols-O'Rourke, K and Morris, T and Forstner, MRJ and Schwalb, AN},
title = {Mitochondrial sequence data reveal population structure within Pustulosa pustulosa.},
journal = {PeerJ},
volume = {11},
number = {},
pages = {e15974},
pmid = {37810794},
issn = {2167-8359},
mesh = {Humans ; Animals ; Phylogeny ; Mitochondria ; *Bivalvia ; *Unionidae/genetics ; Texas ; Ontario ; },
abstract = {Unionid mussels are among the most imperiled group of organisms in North America, and Pustulosa pustulosa is a freshwater species with a relatively wide latitudinal distribution that extends from southern Ontario, Canada, to Texas, USA. Considerable morphological and geographic variation in the genus Pustulosa (formerly Cyclonaias) has led to uncertainty over species boundaries, and recent studies have suggested revisions to species-level classifications by synonymizing C. aurea, C. houstonensis, C. mortoni, and C. refulgens with C. pustulosa (currently P. pustulosa). Owing to its wide range and shallow phylogenetic differentiation, we analyzed individuals of P. pustulosa using mitochondrial DNA sequence data under a population genetics framework. We included 496 individuals, which were comprised of 166 samples collected during this study and 330 additional sequences retrieved from GenBank. Pairwise ΦST measures based on ND1 data suggested there may be up to five major geographic groups present within P. pustulosa. Genetic differentiation between regions within Texas was higher compared to populations from the Mississippi and Great Lakes populations, which may reflect differences in historical connectivity. Mitochondrial sequence data also revealed varying demographic histories for each major group suggesting each geographic region has also experienced differential population dynamics in the past. Future surveys should consider exploring variation within species after phylogeographic delimitation has been performed. In this study, we begin to address this need for freshwater mussels via the P. pustulosa system.},
}

Humans
Animals
Phylogeny
Mitochondria
*Bivalvia
*Unionidae/genetics
Texas
Ontario

@article {pmid37796022,
year = {2023},
author = {Usey, MM and Huet, D},
title = {ATP synthase-associated coiled-coil-helix-coiled-coil-helix (CHCH) domain-containing proteins are critical for mitochondrial function in Toxoplasma gondii.},
journal = {mBio},
volume = {},
number = {},
pages = {e0176923},
doi = {10.1128/mbio.01769-23},
pmid = {37796022},
issn = {2150-7511},
abstract = {Coiled-coil-helix-coiled-coil-helix (CHCH) domains consist of two pairs of cysteine residues that are oxidized to form disulfide bonds upon mitochondrial import. Proteins containing these domains play important roles in mitochondrial ultrastructure and in the biogenesis, function, and stability of electron transport chain complexes. Interestingly, recent investigations of the Toxoplasma gondii ATP synthase identified subunits containing CHCH domains. As CHCH domain proteins have never been found in any other ATP synthase, their role in T. gondii was unclear. Using conditional gene knockdown systems, we investigated two T. gondii ATP synthase subunits containing CHCH domains: ATPTG8 and ATPTG9. We show that these two subunits are essential for the lytic cycle as well as stability and function of the ATP synthase. Further, we illustrated that their knockdown disrupts multiple aspects of mitochondrial morphology, including ultrastructure and cristae density. Mutation of key cysteine residues in the CHCH domains also caused mis-localization of the proteins. Our work suggests that these proteins likely provide structural support to the exceptionally large T. gondii ATP synthase complex and that perturbations to the structural integrity of this complex result in deleterious downstream effects on the parasite mitochondrion. These investigations add to a growing body of work focused on the divergent aspects of the apicomplexan ATP synthase, which could ultimately uncover novel drug targets. IMPORTANCE Members of the coiled-coil-helix-coiled-coil-helix (CHCH) domain protein family are transported into the mitochondrial intermembrane space, where they play important roles in the biogenesis and function of the organelle. Unexpectedly, the ATP synthase of the apicomplexan Toxoplasma gondii harbors CHCH domain-containing subunits of unknown function. As no other ATP synthase studied to date contains this class of proteins, characterizing their function will be of broad interest to the fields of molecular parasitology and mitochondrial evolution. Here, we demonstrate that that two T. gondii ATP synthase subunits containing CHCH domains are required for parasite survival and for stability and function of the ATP synthase. We also show that knockdown disrupts multiple aspects of the mitochondrial morphology of T. gondii and that mutation of key residues in the CHCH domains caused mis-localization of the proteins. This work provides insight into the unique features of the apicomplexan ATP synthase, which could help to develop therapeutic interventions against this parasite and other apicomplexans, such as the malaria-causing parasite Plasmodium falciparum.},
}

@article {pmid37792908,
year = {2023},
author = {Motyčková, A and Voleman, L and Najdrová, V and Arbonová, L and Benda, M and Dohnálek, V and Janowicz, N and Malych, R and Šuťák, R and Ettema, TJG and Svärd, S and Stairs, CW and Doležal, P},
title = {Adaptation of the late ISC pathway in the anaerobic mitochondrial organelles of Giardia intestinalis.},
journal = {PLoS pathogens},
volume = {19},
number = {10},
pages = {e1010773},
doi = {10.1371/journal.ppat.1010773},
pmid = {37792908},
issn = {1553-7374},
abstract = {Mitochondrial metabolism is entirely dependent on the biosynthesis of the [4Fe-4S] clusters, which are part of the subunits of the respiratory chain. The mitochondrial late ISC pathway mediates the formation of these clusters from simpler [2Fe-2S] molecules and transfers them to client proteins. Here, we characterized the late ISC pathway in one of the simplest mitochondria, mitosomes, of the anaerobic protist Giardia intestinalis that lost the respiratory chain and other hallmarks of mitochondria. In addition to IscA2, Nfu1 and Grx5 we identified a novel BolA1 homologue in G. intestinalis mitosomes. It specifically interacts with Grx5 and according to the high-affinity pulldown also with other core mitosomal components. Using CRISPR/Cas9 we were able to establish full bolA1 knock out, the first cell line lacking a mitosomal protein. Despite the ISC pathway being the only metabolic role of the mitosome no significant changes in the mitosome biology could be observed as neither the number of the mitosomes or their capability to form [2Fe-2S] clusters in vitro was affected. We failed to identify natural client proteins that would require the [2Fe-2S] or [4Fe-4S] cluster within the mitosomes, with the exception of [2Fe-2S] ferredoxin, which is itself part of the ISC pathway. The overall uptake of iron into the cellular proteins remained unchanged as also observed for the grx5 knock out cell line. The pull-downs of all late ISC components were used to build the interactome of the pathway showing specific position of IscA2 due to its interaction with the outer mitosomal membrane proteins. Finally, the comparative analysis across Metamonada species suggested that the adaptation of the late ISC pathway identified in G. intestinalis occurred early in the evolution this of supergroup of eukaryotes.},
}

@article {pmid37761909,
year = {2023},
author = {Mendivil, A and Ramírez, R and Morin, J and Ramirez, JL and Siccha-Ramirez, R and Britzke, R and Rivera, F and Ampuero, A and Oliveros, N and Congrains, C},
title = {Comparative Mitogenome Analysis of Two Native Apple Snail Species (Ampullariidae, Pomacea) from Peruvian Amazon.},
journal = {Genes},
volume = {14},
number = {9},
pages = {},
pmid = {37761909},
issn = {2073-4425},
support = {R.R. N°s 005557-2022-R (B22100301), 05753-2021-R (B21100471), 03202-R-18 (B18100781)//National University of San Marcos/ ; },
mesh = {Animals ; Peru ; Phylogeny ; *Genome, Mitochondrial/genetics ; Snails/genetics ; Mitochondria/genetics ; },
abstract = {Apple snails of the genus Pomacea Perry, 1810 (Mollusca: Caenogastropoda: Ampullariidae) are native to the Neotropics and exhibit high species diversity, holding cultural and ecological significance as an important protein source in Peru. However, most genetic studies in Pomacea have focused mostly on invasive species, especially in Southeast Asia, where they are considered important pests. In this study, we assembled and annotated the mitochondrial genomes of two Pomacea species native to the Peruvian Amazon: Pomacea reevei Ampuero & Ramírez, 2023 and Pomacea aulanieri (Deville & Hupé, 1850). The mitogenomes of P. reevei and P. aulanieri comprise 15,660 and 16,096 bp, respectively, and contain the typical 37 genes of the animal mitochondria with a large control region of 292 bp in P. reevei and 524 bp in P. aulanieri-which fall within the range of what is currently known in Pomacea. Comparisons with previously published mitogenomes in Pomacea revealed differences in the overlapping of adjacent genes, the size of certain protein-coding genes (PCGs) and the secondary structure of some tRNAs that are consistent with the phylogenetic relationships between these species. These findings provide valuable insights into the systematics and genomics of the genus Pomacea.},
}

Animals
Peru
Phylogeny
*Genome, Mitochondrial/genetics
Snails/genetics
Mitochondria/genetics

@article {pmid37761841,
year = {2023},
author = {Koshkina, O and Deniskova, T and Dotsev, A and Kunz, E and Selionova, M and Medugorac, I and Zinovieva, N},
title = {Phylogenetic Analysis of Russian Native Sheep Breeds Based on mtDNA Sequences.},
journal = {Genes},
volume = {14},
number = {9},
pages = {},
pmid = {37761841},
issn = {2073-4425},
support = {21-46-00001//RSF/ ; 075-15-2021-1037 (Internal No. 15.BRK.21.0001).//Ministry of Science and Higher Education of the Russian Federation/ ; FGGN-2022-0002//Ministry of Science and Higher Education of the Russian Federation/ ; },
mesh = {Sheep/genetics ; Animals ; *DNA, Mitochondrial/genetics ; Phylogeny ; *Mitochondria/genetics ; Animals, Domestic/genetics ; Russia ; },
abstract = {Eurasia is represented by all climatic zones and various environments. A unique breed variety of farm animals has been developed in Russia, whose territory covers a large area of the continent. A total of 69 local breeds and types of dairy, wool, and meat sheep (Ovis aries) are maintained here. However, the genetic diversity and maternal origin of these local breeds have not been comprehensively investigated. In this study, we describe the diversity and phylogeny of Russian sheep breeds inhabiting different geographical regions based on the analysis of complete sequences of mitochondrial genomes (mtDNA). Complete mtDNA sequences of the studied sheep were obtained using next-generation sequencing technology (NGS). All investigated geographical groups of sheep were characterized by high haplotype (Hd = 0.9992) and nucleotide diversity (π = 0.00378). Analysis of the AMOVA results showed that genetic diversity was majorly determined by within-population differences (77.87%). We identified 128 haplotypes in all studied sheep. Haplotypes belonged to the following haplogroups: B (64.8%), A (28.9%), C (5.5%), and D (0.8%). Haplogroup B was predominant in the western part of Russia. A high level of mtDNA polymorphism in the studied groups of local sheep indicates the presence of a significant reserve of unique genotypes in Russia, which is to be explored.},
}

Sheep/genetics
Animals
*DNA, Mitochondrial/genetics
Phylogeny
*Mitochondria/genetics
Animals, Domestic/genetics
Russia

@article {pmid37708410,
year = {2023},
author = {Khachaturyan, M and Reusch, TBH and Dagan, T},
title = {Worldwide Population Genomics Reveal Long-Term Stability of the Mitochondrial Genome Architecture in a Keystone Marine Plant.},
journal = {Genome biology and evolution},
volume = {15},
number = {9},
pages = {},
pmid = {37708410},
issn = {1759-6653},
mesh = {Humans ; Metagenomics ; *Genome, Mitochondrial ; DNA, Mitochondrial/genetics ; Mitochondria/genetics ; *Magnoliopsida/genetics ; },
abstract = {Mitochondrial genomes (mitogenomes) of flowering plants are composed of multiple chromosomes. Recombination within and between the mitochondrial chromosomes may generate diverse DNA molecules termed isoforms. The isoform copy number and composition can be dynamic within and among individual plants due to uneven replication and homologous recombination. Nonetheless, despite their functional importance, the level of mitogenome conservation within species remains understudied. Whether the ontogenetic variation translates to evolution of mitogenome composition over generations is currently unknown. Here we show that the mitogenome composition of the seagrass Zostera marina is conserved among worldwide populations that diverged ca. 350,000 years ago. Using long-read sequencing, we characterized the Z. marina mitochondrial genome and inferred the repertoire of recombination-induced configurations. To characterize the mitochondrial genome architecture worldwide and study its evolution, we examined the mitogenome in Z. marina meristematic region sampled in 16 populations from the Pacific and Atlantic oceans. Our results reveal a striking similarity in the isoform relative copy number, indicating a high conservation of the mitogenome composition among distantly related populations and within the plant germline, despite a notable variability during individual ontogenesis. Our study supplies a link between observations of dynamic mitogenomes at the level of plant individuals and long-term mitochondrial evolution.},
}

Humans
Metagenomics
*Genome, Mitochondrial
DNA, Mitochondrial/genetics
Mitochondria/genetics
*Magnoliopsida/genetics

@article {pmid37783374,
year = {2023},
author = {Igamberdiev, AU and Gordon, R},
title = {Macroevolution, differentiation trees, and the growth of coding systems.},
journal = {Bio Systems},
volume = {},
number = {},
pages = {105044},
doi = {10.1016/j.biosystems.2023.105044},
pmid = {37783374},
issn = {1872-8324},
abstract = {An open process of evolution of multicellular organisms is based on the rearrangement and growth of the program of differentiation that underlies biological morphogenesis. The maintenance of the final (adult) stable non-equilibrium state (stasis) of a developmental system determines the direction of the evolutionary process. This state is achieved via the sequence of differentiation events representable as differentiation trees. A special type of morphogenetic code, acting as a metacode governing gene expression, may include electromechanical signals appearing as differentiation waves. The excessive energy due to the incorporation of mitochondria in eukaryotic cells resulted not only in more active metabolism but also in establishing the differentiation code for interconnecting cells and forming tissues, which fueled the evolutionary process. The "invention" of "continuing differentiation" distinguishes multicellular eukaryotes from multicellular prokaryotes. The Janus-faced control, involving both top-down control by differentiation waves and bottom-up control via the mechanical consequences of cell differentiations, underlies the process of morphogenesis and results in the achievement of functional stable final states. Duplications of branches of the differentiation tree may be the basis for continuing differentiation and macroevolution, analogous to gene duplication permitting divergence of genes. Metamorphoses, if they are proven to be fusions of disparate species, may be classified according to the topology of fusions of two differentiation trees. In the process of unfolding of morphogenetic structures, microevolution can be defined as changes of the differentiation tree that preserve topology of the tree, while macroevolution represents any change that alters the topology of the differentiation tree.},
}

@article {pmid37778286,
year = {2023},
author = {Duarte Hospital, C and Tête, A and Debizet, K and Imler, J and Tomkiewicz-Raulet, C and Blanc, EB and Barouki, R and Coumoul, X and Bortoli, S},
title = {SDHi fungicides: An example of mitotoxic pesticides targeting the succinate dehydrogenase complex.},
journal = {Environment international},
volume = {180},
number = {},
pages = {108219},
doi = {10.1016/j.envint.2023.108219},
pmid = {37778286},
issn = {1873-6750},
abstract = {Succinate dehydrogenase inhibitors (SDHi) are fungicides used to control the proliferation of pathogenic fungi in crops. Their mode of action is based on blocking the activity of succinate dehydrogenase (SDH), a universal enzyme expressed by all species harboring mitochondria. The SDH is involved in two interconnected metabolic processes for energy production: the transfer of electrons in the mitochondrial respiratory chain and the oxidation of succinate to fumarate in the Krebs cycle. In humans, inherited SDH deficiencies may cause major pathologies including encephalopathies and cancers. The cellular and molecular mechanisms related to such genetic inactivation have been well described in neuroendocrine tumors, in which it induces an oxidative stress, a pseudohypoxic phenotype, a metabolic, epigenetic and transcriptomic remodeling, and alterations in the migration and invasion capacities of cancer cells, in connection with the accumulation of succinate, an oncometabolite, substrate of the SDH. We will discuss recent studies reporting toxic effects of SDHi in non-target organisms and their implications for risk assessment of pesticides. Recent data show that the SDH structure is highly conserved during evolution and that SDHi can inhibit SDH activity in mitochondria of non-target species, including humans. These observations suggest that SDHi are not specific inhibitors of fungal SDH. We hypothesize that SDHi could have toxic effects in other species, including humans. Moreover, the analysis of regulatory assessment reports shows that most SDHi induce tumors in animals without evidence of genotoxicity. Thus, these substances could have a non-genotoxic mechanism of carcinogenicity that still needs to be fully characterized and that could be related to SDH inhibition. The use of pesticides targeting mitochondrial enzymes encoded by tumor suppressor genes raises questions on the risk assessment framework of mitotoxic pesticides. The issue of SDHi fungicides is therefore a textbook case that highlights the urgent need for changes in regulatory assessment.},
}

@article {pmid36282276,
year = {2023},
author = {Wang, D and Teng, J and Ning, C and Wang, W and Liu, S and Zhang, Q and Tang, H},
title = {Mitogenome-wide association study on body measurement traits of Wenshang Barred chickens.},
journal = {Animal biotechnology},
volume = {34},
number = {7},
pages = {3154-3161},
doi = {10.1080/10495398.2022.2137035},
pmid = {36282276},
issn = {1532-2378},
mesh = {Animals ; *Chickens/genetics ; *Genome, Mitochondrial/genetics ; Phylogeny ; Phenotype ; Haplotypes/genetics ; Polymorphism, Single Nucleotide/genetics ; DNA, Mitochondrial/genetics ; },
abstract = {Mitochondria are best known for synthesizing ATP through the tricarboxylic acid cycle and oxidative phosphorylation. The cytoplasmic mitochondrial DNA (mtDNA) is important for maintaining the function. This study was designed to reveal the effect of mtDNA on chicken body measurement traits (BMTs). A population of 605 Wenshang Barred chickens were recorded BMTs, including body slope length, keel length, chest width, etc. The single-nucleotide polymorphisms (SNPs) of their mitogenomes were detected by PCR amplification and DNA sequencing. Totally 69 mutations in mitogenome were discovered, including 18 in noncoding region and 51 in coding region. By multi-sequence alignment and haplotype construction, the chickens were clustered into eight haplotypes and further three haplogroups. The association between BMTs and mtDNA SNPs, haplotypes and haplogroups were analyzed in the linear model by ASReml, respectively. Among them, the SNP mt11086 T/C in ND3 was found to significantly affect chest dept (p < .05) and was highly conservative by phylogenetic conservation analyses, which reflected the genetic effect on body size and growth of chickens. No significant association between the mitochondrial haplotypes or haplogroups and BMTs was found. The polymorphic site reflecting body size could be put into chicken breeding programs as the genetic marker.},
}

Animals
*Chickens/genetics
*Genome, Mitochondrial/genetics
Phylogeny
Phenotype
Haplotypes/genetics
Polymorphism, Single Nucleotide/genetics
DNA, Mitochondrial/genetics

@article {pmid37766465,
year = {2023},
author = {Dial, DT and Weglarz, KM and Brunet, BMT and Havill, NP and von Dohlen, CD and Burke, GR},
title = {Whole genome sequence of the Cooley spruce gall adelgid, Adelges cooleyi (Hemiptera: Sternorrhyncha: Adelgidae).},
journal = {G3 (Bethesda, Md.)},
volume = {},
number = {},
pages = {},
doi = {10.1093/g3journal/jkad224},
pmid = {37766465},
issn = {2160-1836},
abstract = {The adelgids (Adelgidae) are a small family of sap-feeding insects, which together with true aphids (Aphididae) and phylloxerans (Phylloxeridae) make up the infraorder Aphidomorpha. Some adelgid species are highly destructive to forest ecosystems, such as Adelges tsugae, A. piceae, A. laricis, Pineus pini, and P. boerneri. Despite this, there are no high-quality genomic resources for adelgids, hindering advanced genomic analyses within Adelgidae and among Aphidomorpha. Here, we used PacBio continuous long read and Illumina RNA-seq sequencing to construct a high-quality draft genome assembly for the Cooley spruce gall adelgid, Adelges cooleyi (Gillette), a gall-forming species endemic to North America. The assembled genome is 270.2 Mb in total size and has scaffold and contig N50 statistics of 14.87 Mb and 7.18 Mb, respectively. There are 24,967 predicted coding sequences, and assembly completeness is estimated at 98.1% and 99.6% with core BUSCO gene sets of Arthropoda and Hemiptera, respectively. Phylogenomic analysis using the A. cooleyi genome, three publicly available adelgid transcriptomes, four phylloxera transcriptomes, the Daktulosphaira vitifoliae (grape phylloxera) genome, four aphid genomes, and two outgroup coccoid genomes fully resolves adelgids and phylloxerans as sister taxa. The mitochondrial genome is 24 Kb, among the largest in insects sampled to date, with 39.4% composed of non-coding regions. This genome assembly is currently the only genome-scale, annotated assembly for adelgids and will be a valuable resource for understanding the ecology and evolution of Aphidomorpha.},
}

@article {pmid37760086,
year = {2023},
author = {Subczynski, WK and Pasenkiewicz-Gierula, M and Widomska, J},
title = {Protecting the Eye Lens from Oxidative Stress through Oxygen Regulation.},
journal = {Antioxidants (Basel, Switzerland)},
volume = {12},
number = {9},
pages = {},
doi = {10.3390/antiox12091783},
pmid = {37760086},
issn = {2076-3921},
support = {R01 EY015526/EY/NEI NIH HHS/United States ; },
abstract = {Molecular oxygen is a primary oxidant that is involved in the formation of active oxygen species and in the oxidation of lipids and proteins. Thus, controlling oxygen partial pressure (concentration) in the human organism, tissues, and organs can be the first step in protecting them against oxidative stress. However, it is not an easy task because oxygen is necessary for ATP synthesis by mitochondria and in many biochemical reactions taking place in all cells in the human body. Moreover, the blood circulatory system delivers oxygen to all parts of the body. The eye lens seems to be the only organ that is protected from the oxidative stress through the regulation of oxygen partial pressure. The basic mechanism that developed during evolution to protect the eye lens against oxidative damage is based on the maintenance of a very low concentration of oxygen within the lens. This antioxidant mechanism is supported by the resistance of both the lipid components of the lens membrane and cytosolic proteins to oxidation. Any disturbance, continuous or acute, in the working of this mechanism increases the oxygen concentration, in effect causing cataract development. Here, we describe the biophysical basis of the mechanism and its correlation with lens transparency.},
}

@article {pmid37752851,
year = {2023},
author = {Togashi, T and Parker, GA and Horinouchi, Y},
title = {Mitochondrial uniparental inheritance achieved after fertilization challenges the nuclear-cytoplasmic conflict hypothesis for anisogamy evolution.},
journal = {Biology letters},
volume = {19},
number = {9},
pages = {20230352},
doi = {10.1098/rsbl.2023.0352},
pmid = {37752851},
issn = {1744-957X},
abstract = {In eukaryotes, a fundamental phenomenon underlying sexual selection is the evolution of gamete size dimorphism between the sexes (anisogamy) from an ancestral gametic system with gametes of the same size in both mating types (isogamy). The nuclear-cytoplasmic conflict hypothesis has been one of the major theoretical hypotheses for the evolution of anisogamy. It proposes that anisogamy evolved as an adaptation for preventing nuclear-cytoplasmic conflict by minimizing male gamete size to inherit organelles uniparentally. In ulvophycean green algae, biparental inheritance of organelles is observed in isogamous species, as the hypothesis assumes. So we tested the hypothesis by examining whether cytoplasmic inheritance is biparental in Monostroma angicava, a slightly anisogamous ulvophycean that produces large male gametes. We tracked the fates of mitochondria in intraspecific crosses with PCR-RFLP markers. We confirmed that mitochondria are maternally inherited. However, paternal mitochondria enter the zygote, where their DNA can be detected for over 14 days. This indicates that uniparental inheritance is enforced by eliminating paternal mitochondrial DNA in the zygote, rather than by decreasing male gamete size to the minimum. Thus, uniparental cytoplasmic inheritance is achieved by an entirely different mechanism, and is unlikely to drive the evolution of anisogamy in ulvophyceans.},
}

@article {pmid37744223,
year = {2023},
author = {Suárez Menéndez, M and Rivera-León, VE and Robbins, J and Berube, M and Palsbøll, PJ},
title = {PHFinder: assisted detection of point heteroplasmy in Sanger sequencing chromatograms.},
journal = {PeerJ},
volume = {11},
number = {},
pages = {e16028},
pmid = {37744223},
issn = {2167-8359},
mesh = {Animals ; *Heteroplasmy ; Fluorescence ; *Humpback Whale ; Mitochondria ; Nucleotides ; },
abstract = {Heteroplasmy is the presence of two or more organellar genomes (mitochondrial or plastid DNA) in an organism, tissue, cell or organelle. Heteroplasmy can be detected by visual inspection of Sanger sequencing chromatograms, where it appears as multiple peaks of fluorescence at a single nucleotide position. Visual inspection of chromatograms is both consuming and highly subjective, as heteroplasmy is difficult to differentiate from background noise. Few software solutions are available to automate the detection of point heteroplasmies, and those that are available are typically proprietary, lack customization or are unsuitable for automated heteroplasmy assessment in large datasets. Here, we present PHFinder, a Python-based, open-source tool to assist in the detection of point heteroplasmies in large numbers of Sanger chromatograms. PHFinder automatically identifies point heteroplasmies directly from the chromatogram trace data. The program was tested with Sanger sequencing data from 100 humpback whales (Megaptera novaeangliae) tissue samples with known heteroplasmies. PHFinder detected most (90%) of the known heteroplasmies thereby greatly reducing the amount of visual inspection required. PHFinder is flexible and enables explicit specification of key parameters to infer double peaks (i.e., heteroplasmies).},
}

Animals
*Heteroplasmy
Fluorescence
*Humpback Whale
Mitochondria
Nucleotides

@article {pmid37748065,
year = {2023},
author = {Zhang, K and Zhao, X and Zhao, Y and Zhang, Z and Liu, Z and Liu, Z and Yu, Y and Li, J and Ma, Y and Dong, Y and Pang, X and Jin, X and Li, N and Liu, B and Wendel, JF and Zhai, J and Long, Y and Wang, T and Gong, L},
title = {Cell type-specific cytonuclear coevolution in three allopolyploid plant species.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {120},
number = {40},
pages = {e2310881120},
doi = {10.1073/pnas.2310881120},
pmid = {37748065},
issn = {1091-6490},
abstract = {Cytonuclear disruption may accompany allopolyploid evolution as a consequence of the merger of different nuclear genomes in a cellular environment having only one set of progenitor organellar genomes. One path to reconcile potential cytonuclear mismatch is biased expression for maternal gene duplicates (homoeologs) encoding proteins that target to plastids and/or mitochondria. Assessment of this transcriptional form of cytonuclear coevolution at the level of individual cells or cell types remains unexplored. Using single-cell (sc-) and single-nucleus (sn-) RNAseq data from eight tissues in three allopolyploid species, we characterized cell type-specific variations of cytonuclear coevolutionary homoeologous expression and demonstrated the temporal dynamics of expression patterns across development stages during cotton fiber development. Our results provide unique insights into transcriptional cytonuclear coevolution in plant allopolyploids at the single-cell level.},
}

@article {pmid37744141,
year = {2021},
author = {Clergeot, PH and Olson, Å},
title = {Mitonuclear Genetic Interactions in the Basidiomycete Heterobasidion parviporum Involve a Non-conserved Mitochondrial Open Reading Frame.},
journal = {Frontiers in fungal biology},
volume = {2},
number = {},
pages = {779337},
pmid = {37744141},
issn = {2673-6128},
abstract = {The mitochondrial and nuclear genomes of Eukaryotes are inherited separately and consequently follow distinct evolutionary paths. Nevertheless, the encoding of many mitochondrial proteins by the nuclear genome shows the high level of integration they have reached, which makes mitonuclear genetic interactions all the more conceivable. For each species, natural selection has fostered the evolution of coadapted alleles in both genomes, but a population-wise divergence of such alleles could lead to important phenotypic variation, and, ultimately, to speciation. In this study in the Basidiomycete Heterobasidion parviporum, we have investigated the genetic basis of phenotypic variation among laboratory-designed heterokaryons carrying the same pair of haploid nuclei, but a different mitochondrial genome. Radial growth rate data of thirteen unrelated homokaryotic parents and of their heterokaryotic offspring were combined with SNP data extracted from parental genome sequences to identify nuclear and mitochondrial loci involved in mitonuclear interactions. Two nuclear loci encoding mitochondrial proteins appeared as best candidates to engage in a genetic interaction affecting radial growth rate with a non-conserved mitochondrial open reading frame of unknown function and not reported apart from the Russulales order of Basidiomycete fungi. We believe our approach could be useful to investigate several important traits of fungal biology where mitonuclear interactions play a role, including virulence of fungal pathogens.},
}

@article {pmid37735485,
year = {2023},
author = {Sidorczuk, K and Mackiewicz, P and Pietluch, F and Gagat, P},
title = {Characterization of signal and transit peptides based on motif composition and taxon-specific patterns.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {15751},
pmid = {37735485},
issn = {2045-2322},
support = {2018/31/N/NZ2/01338//Narodowym Centrum Nauki/ ; 2019/35/N/NZ8/03366//Narodowym Centrum Nauki/ ; 2017/26/D/NZ8/00444//Narodowym Centrum Nauki/ ; },
abstract = {Targeting peptides or presequences are N-terminal extensions of proteins that encode information about their cellular localization. They include signal peptides (SP), which target proteins to the endoplasmic reticulum, and transit peptides (TP) directing proteins to the organelles of endosymbiotic origin: chloroplasts and mitochondria. TPs were hypothesized to have evolved from antimicrobial peptides (AMPs), which are responsible for the host defence against microorganisms, including bacteria, fungi and viruses. In this study, we performed comprehensive bioinformatic analyses of amino acid motifs of targeting peptides and AMPs using a curated set of experimentally verified proteins. We identified motifs frequently occurring in each type of presequence showing specific patterns associated with their amino acid composition, and investigated their position within the presequence. We also compared motif patterns among different taxonomic groups and identified taxon-specific features, providing some evolutionary insights. Considering the functional relevance and many practical applications of targeting peptides and AMPs, we believe that our analyses will prove useful for their design, and better understanding of protein import mechanism and presequence evolution.},
}

@article {pmid37406344,
year = {2023},
author = {Lamb, IM and Okoye, IC and Mather, MW and Vaidya, AB},
title = {Unique Properties of Apicomplexan Mitochondria.},
journal = {Annual review of microbiology},
volume = {77},
number = {},
pages = {541-560},
doi = {10.1146/annurev-micro-032421-120540},
pmid = {37406344},
issn = {1545-3251},
support = {R01 AI028398/AI/NIAID NIH HHS/United States ; R01 AI100569/AI/NIAID NIH HHS/United States ; R01 AI154499/AI/NIAID NIH HHS/United States ; },
mesh = {Animals ; Mitochondria/genetics/metabolism ; *Toxoplasma/metabolism ; Biological Evolution ; *Malaria ; },
abstract = {Apicomplexan parasites constitute more than 6,000 species infecting a wide range of hosts. These include important pathogens such as those causing malaria and toxoplasmosis. Their evolutionary emergence coincided with the dawn of animals. Mitochondrial genomes of apicomplexan parasites have undergone dramatic reduction in their coding capacity, with genes for only three proteins and ribosomal RNA genes present in scrambled fragments originating from both strands. Different branches of the apicomplexans have undergone rearrangements of these genes, with Toxoplasma having massive variations in gene arrangements spread over multiple copies. The vast evolutionary distance between the parasite and the host mitochondria has been exploited for the development of antiparasitic drugs, especially those used to treat malaria, wherein inhibition of the parasite mitochondrial respiratory chain is selectively targeted with little toxicity to the host mitochondria. We describe additional unique characteristics of the parasite mitochondria that are being investigated and provide greater insights into these deep-branching eukaryotic pathogens.},
}

Animals
Mitochondria/genetics/metabolism
*Toxoplasma/metabolism
Biological Evolution
*Malaria

@article {pmid37715276,
year = {2023},
author = {Leal-Dutra, CA and Yuen, LM and Guedes, BAM and Contreras-Serrano, M and Marques, PE and Shik, JZ},
title = {Evidence that the domesticated fungus Leucoagaricus gongylophorus recycles its cytoplasmic contents as nutritional rewards to feed its leafcutter ant farmers.},
journal = {IMA fungus},
volume = {14},
number = {1},
pages = {19},
pmid = {37715276},
issn = {2210-6340},
support = {ERC-2017-STG-757810/ERC_/European Research Council/International ; },
abstract = {Leafcutter ants farm a fungal cultivar (Leucoagaricus gongylophorus) that converts inedible vegetation into food that sustains colonies with up to millions of workers. Analogous to edible fruits of crops domesticated by humans, L. gongylophorus has evolved specialized nutritional rewards-swollen hyphal cells called gongylidia that package metabolites and are consumed by ant farmers. Yet, little is known about how gongylidia form, and thus how fungal physiology and ant provisioning collectively govern farming performance. We explored the process of gongylidium formation using advanced microscopy to image the cultivar at scales of nanometers, and both in vitro experiments and in silico analyses to examine the mechanisms of gongylidia formation when isolated from ant farmers. We first used transmission electron, fluorescence, and confocal microscopy imaging to see inside hyphal cells. This imaging showed that the cultivar uses a process called autophagy to recycle its own cellular material (e.g. cytosol, mitochondria) and then shuttles the resulting metabolites into a vacuole whose continual expansion displaces other organelles and causes the gongylidium cell's bulging bulb-like appearance. We next used scanning electron microscopy and light microscopy to link this intracellular rearrangement to the external branching patterns of gongylidium cells as they clump together into edible bundles called staphyla. We next confirmed that autophagy plays a critical role in gongylidium formation both: (1) in vitro as gongylidium suppression occurred when isolated fungal cultures were grown on media with autophagy inhibitors, and (2) in silico as differential transcript expression (RNA-seq) analyses showed upregulation of multiple autophagy gene isoforms in gongylidia relative to undifferentiated hyphae. While autophagy is a ubiquitous and often highly derived process across the tree of life, our study reveals a new role for autophagy as a mechanism of functional integration between ant farmers and their fungal crop, and potentially as a signifier of higher-level homeostasis between uniquely life-time committed ectosymbionts.},
}

@article {pmid37685874,
year = {2023},
author = {Maffeo, B and Panuzzo, C and Moraca, A and Cilloni, D},
title = {A Leukemic Target with a Thousand Faces: The Mitochondria.},
journal = {International journal of molecular sciences},
volume = {24},
number = {17},
pages = {},
doi = {10.3390/ijms241713069},
pmid = {37685874},
issn = {1422-0067},
abstract = {In the era of personalized medicine greatly improved by molecular diagnosis and tailor-made therapies, the survival rate of acute myeloid leukemia (AML) at 5 years remains unfortunately low. Indeed, the high heterogeneity of AML clones with distinct metabolic and molecular profiles allows them to survive the chemotherapy-induced changes, thus leading to resistance, clonal evolution, and relapse. Moreover, leukemic stem cells (LSCs), the quiescent reservoir of residual disease, can persist for a long time and activate the recurrence of disease, supported by significant metabolic differences compared to AML blasts. All these points highlight the relevance to develop combination therapies, including metabolism inhibitors to improve treatment efficacy. In this review, we summarized the metabolic differences in AML blasts and LSCs, the molecular pathways related to mitochondria and metabolism are druggable and targeted in leukemia therapies, with a distinct interest for Venetoclax, which has revolutionized the therapeutic paradigms of several leukemia subtype, unfit for intensive treatment regimens.},
}

@article {pmid37664184,
year = {2023},
author = {Mendoza-Hoffmann, F and Yang, L and Buratto, D and Brito-Sánchez, J and Garduño-Javier, G and Salinas-López, E and Uribe-Álvarez, C and Ortega, R and Sotelo-Serrano, O and Cevallos, MÁ and Ramírez-Silva, L and Uribe-Carvajal, S and Pérez-Hernández, G and Celis-Sandoval, H and García-Trejo, JJ},
title = {Inhibitory to non-inhibitory evolution of the ζ subunit of the F1FO-ATPase of Paracoccus denitrificans and α-proteobacteria as related to mitochondrial endosymbiosis.},
journal = {Frontiers in molecular biosciences},
volume = {10},
number = {},
pages = {1184200},
pmid = {37664184},
issn = {2296-889X},
abstract = {Introduction: The ζ subunit is a potent inhibitor of the F1FO-ATPase of Paracoccus denitrificans (PdF1FO-ATPase) and related α-proteobacteria different from the other two canonical inhibitors of bacterial (ε) and mitochondrial (IF1) F1FO-ATPases. ζ mimics mitochondrial IF1 in its inhibitory N-terminus, blocking the PdF1FO-ATPase activity as a unidirectional pawl-ratchet and allowing the PdF1FO-ATP synthase turnover. ζ is essential for the respiratory growth of P. denitrificans, as we showed by a Δζ knockout. Given the vital role of ζ in the physiology of P. denitrificans, here, we assessed the evolution of ζ across the α-proteobacteria class. Methods: Through bioinformatic, biochemical, molecular biology, functional, and structural analyses of several ζ subunits, we confirmed the conservation of the inhibitory N-terminus of ζ and its divergence toward its C-terminus. We reconstituted homologously or heterologously the recombinant ζ subunits from several α-proteobacteria into the respective F-ATPases, including free-living photosynthetic, facultative symbiont, and intracellular facultative or obligate parasitic α-proteobacteria. Results and discussion: The results show that ζ evolved, preserving its inhibitory function in free-living α-proteobacteria exposed to broad environmental changes that could compromise the cellular ATP pools. However, the ζ inhibitory function was diminished or lost in some symbiotic α-proteobacteria where ζ is non-essential given the possible exchange of nutrients and ATP from hosts. Accordingly, the ζ gene is absent in some strictly parasitic pathogenic Rickettsiales, which may obtain ATP from the parasitized hosts. We also resolved the NMR structure of the ζ subunit of Sinorhizobium meliloti (Sm-ζ) and compared it with its structure modeled in AlphaFold. We found a transition from a compact ordered non-inhibitory conformation into an extended α-helical inhibitory N-terminus conformation, thus explaining why the Sm-ζ cannot exert homologous inhibition. However, it is still able to inhibit the PdF1FO-ATPase heterologously. Together with the loss of the inhibitory function of α-proteobacterial ε, the data confirm that the primary inhibitory function of the α-proteobacterial F1FO-ATPase was transferred from ε to ζ and that ζ, ε, and IF1 evolved by convergent evolution. Some key evolutionary implications on the endosymbiotic origin of mitochondria, as most likely derived from α-proteobacteria, are also discussed.},
}

@article {pmid37662149,
year = {2023},
author = {Liu, H and Hou, Z and Xu, L and Ma, Q and Wei, M and Tembrock, LR and Zhang, S and Wu, Z},
title = {Comparative analysis of organellar genomes between diploid and tetraploid Chrysanthemum indicum with its relatives.},
journal = {Frontiers in plant science},
volume = {14},
number = {},
pages = {1228551},
pmid = {37662149},
issn = {1664-462X},
abstract = {Chrysanthemum indicum, a species native to Eastern Asia is well known as one of the progenitor species of the cultivated Chrysanthemum which is grown for its ornamental and medicinal value. Previous genomic studies on Chrysanthemum have largely ignored the dynamics of plastid genome (plastome) and mitochondria genome (mitogenome) evolution when analyzing this plant lineage. In this study, we sequenced and assembled the plastomes and mitogenomes of diploid and tetraploid C. indicum as well as the morphologically divergent variety C. indicum var. aromaticum. We used published data from 27 species with both plastome and mitogenome complete sequences to explore differences in sequence evolution between the organellar genomes. The size and structure of organellar genome between diploid and tetraploid C. indicum were generally similar but the tetraploid C. indicum and C. indicum var. aromaticum were found to contain unique sequences in the mitogenomes which also contained previously undescribed open reading frames (ORFs). Across Chrysanthemum mitogenome structure varied greatly but sequences transferred from plastomes in to the mitogenomes were conserved. Finally, differences observed between mitogenome and plastome gene trees may be the result of the difference in the rate of sequence evolution between genes in these two genomes. In total the findings presented here greatly expand the resources for studying Chrysanthemum organellar genome evolution with possible applications to conservation, breeding, and gene banking in the future.},
}

@article {pmid37661814,
year = {2023},
author = {Konaka, H and Kato, Y and Hirano, T and Tsujimoto, K and Park, J and Koba, T and Aoki, W and Matsuzaki, Y and Taki, M and Koyama, S and Itotagawa, E and Jo, T and Hirayama, T and Kawai, T and Ishii, KJ and Ueda, M and Yamaguchi, S and Akira, S and Morita, T and Maeda, Y and Nishide, M and Nishida, S and Shima, Y and Narazaki, M and Takamatsu, H and Kumanogoh, A},
title = {Secretion of mitochondrial DNA via exosomes promotes inflammation in Behçet's syndrome.},
journal = {The EMBO journal},
volume = {},
number = {},
pages = {e112573},
doi = {10.15252/embj.2022112573},
pmid = {37661814},
issn = {1460-2075},
support = {J200705023//Japan Agency for Medical Research and Development (AMED)/ ; J200705710//Japan Agency for Medical Research and Development (AMED)/ ; J200705049//Japan Agency for Medical Research and Development (AMED)/ ; Jp18cm016335//Japan Agency for Medical Research and Development (AMED)/ ; JP18cm059042//Japan Agency for Medical Research and Development (AMED)/ ; 15K09550//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 18K08386//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JP18H05282//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 22H03111//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; //MEXT | JST | Center of Innovation Program (COI)/ ; JPMJCR16G2//MEXT | JST | Core Research for Evolutional Science and Technology (CREST)/ ; 15652237//MEXT | JST | Core Research for Evolutional Science and Technology (CREST)/ ; //Mitsubishi Foundation (The Mitsubishi Foundation)/ ; //Naito Foundation ()/ ; },
abstract = {Mitochondrial DNA (mtDNA) leakage into the cytoplasm can occur when cells are exposed to noxious stimuli. Specific sensors recognize cytoplasmic mtDNA to promote cytokine production. Cytoplasmic mtDNA can also be secreted extracellularly, leading to sterile inflammation. However, the mode of secretion of mtDNA out of cells upon noxious stimuli and its relevance to human disease remain unclear. Here, we show that pyroptotic cells secrete mtDNA encapsulated within exosomes. Activation of caspase-1 leads to mtDNA leakage from the mitochondria into the cytoplasm via gasdermin-D. Caspase-1 also induces intraluminal membrane vesicle formation, allowing for cellular mtDNA to be taken up and secreted as exosomes. Encapsulation of mtDNA within exosomes promotes a strong inflammatory response that is ameliorated upon exosome biosynthesis inhibition in vivo. We further show that monocytes derived from patients with Behçet's syndrome (BS), a chronic systemic inflammatory disorder, show enhanced caspase-1 activation, leading to exosome-mediated mtDNA secretion and similar inflammation pathology as seen in BS patients. Collectively, our findings support that mtDNA-containing exosomes promote inflammation, providing new insights into the propagation and exacerbation of inflammation in human inflammatory diseases.},
}

@article {pmid37208299,
year = {2023},
author = {Dapper, AL and Diegel, AE and Wade, MJ},
title = {Relative rates of evolution of male-beneficial nuclear compensatory mutations and male-harming Mother's Curse mitochondrial alleles.},
journal = {Evolution; international journal of organic evolution},
volume = {77},
number = {9},
pages = {1945-1955},
doi = {10.1093/evolut/qpad087},
pmid = {37208299},
issn = {1558-5646},
support = {//U.S. Department of Agriculture/ ; //National Science Foundation/ ; },
abstract = {Mother's Curse alleles represent a significant source of potential male fitness defects. The maternal inheritance of mutations with the pattern of sex-specific fitness effects, s♀>0>s♂, allows Mother's Curse alleles to spread through a population even though they reduce male fitness. Although the mitochondrial genomes of animals contain only a handful of protein-coding genes, mutations in many of these genes have been shown to have a direct effect on male fertility. The evolutionary process of nuclear compensation is hypothesized to counteract the male-limited mitochondrial defects that spread via Mother's Curse. Here we use population genetic models to investigate the evolution of compensatory autosomal nuclear mutations that act to restore the loss of fitness caused by mitochondrial mutation pressures. We derive the rate of male fitness deterioration by Mother's Curse and the rate of restoration by nuclear compensatory evolution. We find that the rate of nuclear gene compensation is many times slower than that of its deterioration by cytoplasmic mutation pressure, resulting in a significant lag in the recovery of male fitness. Thus, the numbers of nuclear genes capable of restoring male mitochondrial fitness defects must be large in order to sustain male fitness in the face of mutation pressures.},
}

@article {pmid37644003,
year = {2023},
author = {French, CM and Bertola, LD and Carnaval, AC and Economo, EP and Kass, JM and Lohman, DJ and Marske, KA and Meier, R and Overcast, I and Rominger, AJ and Staniczenko, PPA and Hickerson, MJ},
title = {Global determinants of insect mitochondrial genetic diversity.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {5276},
pmid = {37644003},
issn = {2041-1723},
support = {DBI 2104147//National Science Foundation (NSF)/ ; DEB 1745562//National Science Foundation (NSF)/ ; },
mesh = {Animals ; *Insecta/genetics ; *Mitochondria ; DNA, Mitochondrial/genetics ; Biodiversity ; Genetic Variation ; },
abstract = {Understanding global patterns of genetic diversity is essential for describing, monitoring, and preserving life on Earth. To date, efforts to map macrogenetic patterns have been restricted to vertebrates, which comprise only a small fraction of Earth's biodiversity. Here, we construct a global map of predicted insect mitochondrial genetic diversity from cytochrome c oxidase subunit 1 sequences, derived from open data. We calculate the mitochondrial genetic diversity mean and genetic diversity evenness of insect assemblages across the globe, identify their environmental correlates, and make predictions of mitochondrial genetic diversity levels in unsampled areas based on environmental data. Using a large single-locus genetic dataset of over 2 million globally distributed and georeferenced mtDNA sequences, we find that mitochondrial genetic diversity evenness follows a quadratic latitudinal gradient peaking in the subtropics. Both mitochondrial genetic diversity mean and evenness positively correlate with seasonally hot temperatures, as well as climate stability since the last glacial maximum. Our models explain 27.9% and 24.0% of the observed variation in mitochondrial genetic diversity mean and evenness in insects, respectively, making an important step towards understanding global biodiversity patterns in the most diverse animal taxon.},
}

Animals
*Insecta/genetics
*Mitochondria
DNA, Mitochondrial/genetics
Biodiversity
Genetic Variation

@article {pmid37638880,
year = {2023},
author = {Gupta, SV and Campos, L and Schmidt, KH},
title = {Mitochondrial superoxide dismutase Sod2 suppresses nuclear genome instability during oxidative stress.},
journal = {Genetics},
volume = {},
number = {},
pages = {},
doi = {10.1093/genetics/iyad147},
pmid = {37638880},
issn = {1943-2631},
abstract = {Oxidative stress can damage DNA and thereby contribute to genome instability. To avoid an imbalance or overaccumulation of reactive oxygen species (ROS), cells are equipped with antioxidant enzymes that scavenge excess ROS. Cells lacking the RecQ-family DNA helicase Sgs1, which contributes to homology-dependent DNA break repair and chromosome stability, are known to accumulate ROS, but the origin and consequences of this oxidative stress phenotype are not fully understood. Here, we show that the sgs1 mutant exhibits elevated mitochondrial superoxide, increased mitochondrial mass, and accumulation of recombinogenic DNA lesions that can be suppressed by antioxidants. Increased mitochondrial mass in the sgs1Δ mutant is accompanied by increased mitochondrial branching, which was also inducible in wildtype cells by replication stress. Superoxide dismutase Sod2 genetically interacts with Sgs1 in the suppression of nuclear chromosomal rearrangements under paraquat-induced oxidative stress. PQ-induced chromosome rearrangements in the absence of Sod2 are promoted by Rad51 recombinase and the polymerase subunit Pol32. Finally, dependence of chromosomal rearrangements on the Rev1/Pol ζ mutasome suggests that under oxidative stress successful DNA synthesis during DNA break repair depends on translesion DNA synthesis.},
}

@article {pmid37636868,
year = {2023},
author = {Le Cam, S and Brémaud, J and Malkócs, T and Kreckelbergh, E and Becquet, V and Dubillot, E and Garcia, P and Breton, S and Pante, E},
title = {LAMP-based molecular sexing in a gonochoric marine bivalve (Macoma balthica rubra) with divergent sex-specific mitochondrial genomes.},
journal = {Ecology and evolution},
volume = {13},
number = {8},
pages = {e10320},
pmid = {37636868},
issn = {2045-7758},
abstract = {Taking advantage of the unique system of doubly uniparental inheritance (DUI) of mitochondria, we developed a reliable molecular method to sex individuals of the marine bivalve Macoma balthica rubra. In species with DUI (~100 known bivalves), both sexes transmit their mitochondria: males bear both a male- and female-type mitogenome, while females bear only the female type. Male and female mitotypes are sufficiently divergent to reliably PCR-amplify them specifically. Loop-mediated isothermal amplification (LAMP) is a precise, economical and portable alternative to PCR for molecular sexing and we demonstrate its application in this context. We used 154 individuals sampled along the Atlantic coast of France and sexed microscopically by gonad examination to test for the congruence among gamete type, PCR sexing and LAMP sexing. We show an exact match among the sexing results from these three methods using the male and female mt-cox1 genes. DUI can be disrupted in inter-specific hybrids, causing unexpected distribution of mitogenomes, such as homoplasmic males or heteroplasmic females. To our knowledge, DUI disruption at the intra-specific scale has never been tested. We applied our sexing protocol to control for unexpected heteroplasmy caused by hybridization between divergent genetic lineages and found no evidence of disruption in the mode of mitochondrial inheritance in M. balthica rubra. We propose LAMP as a useful tool to accelerate eco-evolutionary studies of DUI. It offers the opportunity to investigate the potential role of, previously unaccounted-for, sex-specific patterns such as sexual selection or sex-specific dispersal bias in the evolution of free-spawning benthic species.},
}

@article {pmid37636259,
year = {2023},
author = {Fiedler, L and Middendorf, M and Bernt, M},
title = {Fully automated annotation of mitochondrial genomes using a cluster-based approach with de Bruijn graphs.},
journal = {Frontiers in genetics},
volume = {14},
number = {},
pages = {1250907},
pmid = {37636259},
issn = {1664-8021},
abstract = {A wide range of scientific fields, such as forensics, anthropology, medicine, and molecular evolution, benefits from the analysis of mitogenomic data. With the development of new sequencing technologies, the amount of mitochondrial sequence data to be analyzed has increased exponentially over the last few years. The accurate annotation of mitochondrial DNA is a prerequisite for any mitogenomic comparative analysis. To sustain with the growth of the available mitochondrial sequence data, highly efficient automatic computational methods are, hence, needed. Automatic annotation methods are typically based on databases that contain information about already annotated (and often pre-curated) mitogenomes of different species. However, the existing approaches have several shortcomings: 1) they do not scale well with the size of the database; 2) they do not allow for a fast (and easy) update of the database; and 3) they can only be applied to a relatively small taxonomic subset of all species. Here, we present a novel approach that does not have any of these aforementioned shortcomings, (1), (2), and (3). The reference database of mitogenomes is represented as a richly annotated de Bruijn graph. To generate gene predictions for a new user-supplied mitogenome, the method utilizes a clustering routine that uses the mapping information of the provided sequence to this graph. The method is implemented in a software package called DeGeCI (De Bruijn graph Gene Cluster Identification). For a large set of mitogenomes, for which expert-curated annotations are available, DeGeCI generates gene predictions of high conformity. In a comparative evaluation with MITOS2, a state-of-the-art annotation tool for mitochondrial genomes, DeGeCI shows better database scalability while still matching MITOS2 in terms of result quality and providing a fully automated means to update the underlying database. Moreover, unlike MITOS2, DeGeCI can be run in parallel on several processors to make use of modern multi-processor systems.},
}

@article {pmid37628665,
year = {2023},
author = {Havaš Auguštin, D and Šarac, J and Reidla, M and Tamm, E and Grahovac, B and Kapović, M and Novokmet, N and Rudan, P and Missoni, S and Marjanović, D and Korolija, M},
title = {Refining the Global Phylogeny of Mitochondrial N1a, X, and HV2 Haplogroups Based on Rare Mitogenomes from Croatian Isolates.},
journal = {Genes},
volume = {14},
number = {8},
pages = {},
pmid = {37628665},
issn = {2073-4425},
mesh = {Humans ; Phylogeny ; Croatia ; *Genome, Mitochondrial/genetics ; Mitochondria/genetics ; DNA, Mitochondrial/genetics ; },
abstract = {Mitochondrial DNA (mtDNA) has been used for decades as a predominant tool in population genetics and as a valuable addition to forensic genetic research, owing to its unique maternal inheritance pattern that enables the tracing of individuals along the maternal lineage across numerous generations. The dynamic interplay between evolutionary forces, primarily genetic drift, bottlenecks, and the founder effect, can exert significant influence on genetic profiles. Consequently, the Adriatic islands have accumulated a subset of lineages that exhibits remarkable absence or rarity within other European populations. This distinctive genetic composition underscores the islands' potential as a significant resource in phylogenetic research, with implications reaching beyond regional boundaries to contribute to a global understanding. In the initial attempt to expand the mitochondrial forensic database of the Croatian population with haplotypes from small isolated communities, we sequenced mitogenomes of rare haplogroups from different Croatian island and mainland populations using next-generation sequencing (NGS). In the next step and based on the obtained results, we refined the global phylogeny of haplogroup N1a, HV2, and X by analyzing rare haplotypes, which are absent from the current phylogenetic tree. The trees were based on 16 novel and 52 previously published samples, revealing completely novel branches in the X and HV2 haplogroups and a new European cluster in the ancestral N1a variant, previously believed to be an exclusively African-Asian haplogroup. The research emphasizes the importance of investigating geographically isolated populations and their unique characteristics within a global context.},
}

Humans
Phylogeny
Croatia
*Genome, Mitochondrial/genetics
Mitochondria/genetics
DNA, Mitochondrial/genetics

@article {pmid37628588,
year = {2023},
author = {Baldo, MS and Nogueira, C and Pereira, C and Janeiro, P and Ferreira, S and Lourenço, CM and Bandeira, A and Martins, E and Magalhães, M and Rodrigues, E and Santos, H and Ferreira, AC and Vilarinho, L},
title = {Leigh Syndrome Spectrum: A Portuguese Population Cohort in an Evolutionary Genetic Era.},
journal = {Genes},
volume = {14},
number = {8},
pages = {},
pmid = {37628588},
issn = {2073-4425},
mesh = {Child ; Infant ; Humans ; *Leigh Disease/genetics ; Portugal ; DNA, Mitochondrial/genetics ; Mitochondria ; Biological Evolution ; },
abstract = {Mitochondrial diseases are the most common inherited inborn error of metabolism resulting in deficient ATP generation, due to failure in homeostasis and proper bioenergetics. The most frequent mitochondrial disease manifestation in children is Leigh syndrome (LS), encompassing clinical, neuroradiological, biochemical, and molecular features. It typically affects infants but occurs anytime in life. Considering recent updates, LS clinical presentation has been stretched, and is now named LS spectrum (LSS), including classical LS and Leigh-like presentations. Apart from clinical diagnosis challenges, the molecular characterization also progressed from Sanger techniques to NGS (next-generation sequencing), encompassing analysis of nuclear (nDNA) and mitochondrial DNA (mtDNA). This upgrade resumed steps and favored diagnosis. Hereby, our paper presents molecular and clinical data on a Portuguese cohort of 40 positive cases of LSS. A total of 28 patients presented mutation in mtDNA and 12 in nDNA, with novel mutations identified in a heterogeneous group of genes. The present results contribute to the better knowledge of the molecular basis of LS and expand the clinical spectrum associated with this syndrome.},
}

Child
Infant
Humans
*Leigh Disease/genetics
Portugal
DNA, Mitochondrial/genetics
Mitochondria
Biological Evolution

@article {pmid37628587,
year = {2023},
author = {Hernández, CL},
title = {Mitochondrial DNA in Human Diversity and Health: From the Golden Age to the Omics Era.},
journal = {Genes},
volume = {14},
number = {8},
pages = {},
pmid = {37628587},
issn = {2073-4425},
mesh = {Humans ; *DNA, Mitochondrial/genetics ; *Mitochondria/genetics ; Anthropology ; Biological Evolution ; Inheritance Patterns ; },
abstract = {Mitochondrial DNA (mtDNA) is a small fraction of our hereditary material. However, this molecule has had an overwhelming presence in scientific research for decades until the arrival of high-throughput studies. Several appealing properties justify the application of mtDNA to understand how human populations are-from a genetic perspective-and how individuals exhibit phenotypes of biomedical importance. Here, I review the basics of mitochondrial studies with a focus on the dawn of the field, analysis methods and the connection between two sides of mitochondrial genetics: anthropological and biomedical. The particularities of mtDNA, with respect to inheritance pattern, evolutionary rate and dependence on the nuclear genome, explain the challenges of associating mtDNA composition and diseases. Finally, I consider the relevance of this single locus in the context of omics research. The present work may serve as a tribute to a tool that has provided important insights into the past and present of humankind.},
}

Humans
*DNA, Mitochondrial/genetics
*Mitochondria/genetics
Anthropology
Biological Evolution
Inheritance Patterns

@article {pmid37634556,
year = {2023},
author = {Theriault, JE and Shaffer, C and Dienel, GA and Sander, CY and Hooker, JM and Dickerson, BC and Barrett, LF and Quigley, KS},
title = {A Functional Account of Stimulation-based Aerobic Glycolysis and its Role in Interpreting BOLD Signal Intensity Increases in Neuroimaging Experiments.},
journal = {Neuroscience and biobehavioral reviews},
volume = {},
number = {},
pages = {105373},
doi = {10.1016/j.neubiorev.2023.105373},
pmid = {37634556},
issn = {1873-7528},
abstract = {In aerobic glycolysis, oxygen is abundant, and yet cells metabolize glucose without using it, decreasing their ATP per glucose yield by 15-fold. During task-based stimulation, aerobic glycolysis occurs in localized brain regions, presenting a puzzle: why produce ATP inefficiently when, all else being equal, evolution should favor the efficient use of metabolic resources? The answer is that all else is not equal. We propose that a tradeoff exists between efficient ATP production and the efficiency with which ATP is spent to transmit information. Aerobic glycolysis, despite yielding little ATP per glucose, may support neuronal signaling in thin (< 0.5µm), information-efficient axons. We call this the efficiency tradeoff hypothesis. This tradeoff has potential implications for interpretations of task-related BOLD "activation" observed in fMRI. We hypothesize that BOLD "activation" may index local increases in aerobic glycolysis, which support signaling in thin axons carrying "bottom-up" information, or "prediction error"-i.e., the BIAPEM (BOLD increases approximate prediction error metabolism) hypothesis. Finally, we explore implications of our hypotheses for human brain evolution, social behavior, and mental disorders.},
}

@article {pmid37629135,
year = {2023},
author = {Cai, H and Ren, Y and Du, J and Liu, L and Long, L and Yang, M},
title = {Analysis of the RNA Editing Sites and Orthologous Gene Function of Transcriptome and Chloroplast Genomes in the Evolution of Five Deutzia Species.},
journal = {International journal of molecular sciences},
volume = {24},
number = {16},
pages = {},
doi = {10.3390/ijms241612954},
pmid = {37629135},
issn = {1422-0067},
support = {No.21326301D//Province Key Research and Development Program of Hebei/ ; },
abstract = {In this study, the chloroplast genomes and transcriptomes of five Deutzia genus species were sequenced, characterized, combined, and analyzed. A phylogenetic tree was constructed, including 32 other chloroplast genome sequences of Hydrangeoideae species. The results showed that the five Deutzia chloroplast genomes were typical circular genomes 156,860-157,025 bp in length, with 37.58-37.6% GC content. Repeat analysis showed that the Deutzia species had 41-45 scattered repeats and 199-201 simple sequence repeats. Comparative genomic and pi analyses indicated that the genomes are conservative and that the gene structures are stable. According to the phylogenetic tree, Deutzia species appear to be closely related to Kirengeshoma palmata and Philadelphus. By combining chloroplast genomic and transcriptomic analyses, 29-31 RNA editing events and 163-194 orthologous genes were identified. The ndh, rpo, rps, and atp genes had the most editing sites, and all RNA editing events were of the C-to-U type. Most of the orthologous genes were annotated to the chloroplast, mitochondria, and nucleus, with functions including energy production and conversion, translation, and protein transport. Genes related to the biosynthesis of monoterpenoids and flavonoids were also identified from the transcriptome of Deutzia spp. Our results will contribute to further studies of the genomic information and potential uses of the Deutzia spp.},
}

@article {pmid37629077,
year = {2023},
author = {Zalewska, A and Antonowicz, B and Szulimowska, J and Zieniewska-Siemieńczuk, I and Leśniewska, B and Borys, J and Zięba, S and Kostecka-Sochoń, P and Żendzian-Piotrowska, M and Lo Giudice, R and Lo Giudice, G and Żukowski, P and Maciejczyk, M},
title = {Mitochondrial Redox Balance of Fibroblasts Exposed to Ti-6Al-4V Microplates Subjected to Different Types of Anodizing.},
journal = {International journal of molecular sciences},
volume = {24},
number = {16},
pages = {},
doi = {10.3390/ijms241612896},
pmid = {37629077},
issn = {1422-0067},
support = {B.SUB.23.309//Medical University in Bialystok/ ; },
abstract = {Despite the high biocompatibility of titanium and its alloys, the need to remove titanium implants is increasingly being debated due to the potential for adverse effects associated with long-term retention. Therefore, new solutions are being sought to enhance the biocompatibility of titanium implants. One of them is to increase the thickness of the passive layer of the implant made of titanium dioxide. We were the first to evaluate the effect of hard-anodized (type II) Ti-6Al-4V alloy discs on the cytotoxicity, mitochondrial function, and redox balance of fibroblasts mitochondria compared to standard-anodized (type III) and non-anodized discs. The study used fibroblasts obtained from human gingival tissue. The test discs were applied to the bottom of 12-well plates. Cells were cultured for 24 h and 7, 14, and 21 days and mitochondria were isolated. We demonstrated the occurrence of oxidative stress in the mitochondria of fibroblasts of all tested groups, regardless of the presence and type of anodization. Type II anodization prevented changes in complex II activity (vs. control). The lowest degree of citrate synthase inhibition occurred in mitochondria exposed to titanium discs with type II anodization. In the last phase of culture, the presence of type II anodization reduced the degree of cytochrome c oxidase inhibition compared to the other tests groups and the control group, and prevented apoptosis. Throughout the experiment, the release of titanium, aluminium, and vanadium ions from titanium discs with a hard-anodized passive layer was higher than from the other titanium discs, but decreased with time. The obtained results proved the existence of dysfunction and redox imbalance in the mitochondria of fibroblasts exposed to hard-anodized titanium discs, suggesting the need to search for new materials perhaps biodegradable in tissues of the human body.},
}

@article {pmid37386734,
year = {2023},
author = {Arnqvist, G and Rowe, L},
title = {Ecology, the pace-of-life, epistatic selection and the maintenance of genetic variation in life-history genes.},
journal = {Molecular ecology},
volume = {32},
number = {17},
pages = {4713-4724},
doi = {10.1111/mec.17062},
pmid = {37386734},
issn = {1365-294X},
support = {AdG-294333//FP7 Ideas: European Research Council/ ; //Natural Sciences and Engineering Research Council of Canada/ ; 2018-00705//Svenska Forskningsrådet Formas/ ; //Uppsala Universitet/ ; 2019-03611//Vetenskapsrådet/ ; },
mesh = {*Polymorphism, Genetic ; Selection, Genetic ; Biological Evolution ; Alleles ; *Life History Traits ; Models, Genetic ; Genetic Variation ; Epistasis, Genetic ; },
abstract = {Evolutionary genetics has long struggled with understanding how functional genes under selection remain polymorphic in natural populations. Taking as a starting point that natural selection is ultimately a manifestation of ecological processes, we spotlight an underemphasized and potentially ubiquitous ecological effect that may have fundamental effects on the maintenance of genetic variation. Negative frequency dependency is a well-established emergent property of density dependence in ecology, because the relative profitability of different modes of exploiting or utilizing limiting resources tends to be inversely proportional to their frequency in a population. We suggest that this may often generate negative frequency-dependent selection (NFDS) on major effect loci that affect rate-dependent physiological processes, such as metabolic rate, that are phenotypically manifested as polymorphism in pace-of-life syndromes. When such a locus under NFDS shows stable intermediate frequency polymorphism, this should generate epistatic selection potentially involving large numbers of loci with more minor effects on life-history (LH) traits. When alternative alleles at such loci show sign epistasis with a major effect locus, this associative NFDS will promote the maintenance of polygenic variation in LH genes. We provide examples of the kind of major effect loci that could be involved and suggest empirical avenues that may better inform us on the importance and reach of this process.},
}

*Polymorphism, Genetic
Selection, Genetic
Biological Evolution
Alleles
*Life History Traits
Models, Genetic
Genetic Variation
Epistasis, Genetic

@article {pmid37603398,
year = {2023},
author = {Ratliffe, J and Kataura, T and Otten, EG and Korolchuk, VI},
title = {The evolution of selective autophagy as a mechanism of oxidative stress response: The evolutionarily acquired ability of selective autophagy receptors to respond to oxidative stress is beneficial for human longevity.},
journal = {BioEssays : news and reviews in molecular, cellular and developmental biology},
volume = {},
number = {},
pages = {e2300076},
doi = {10.1002/bies.202300076},
pmid = {37603398},
issn = {1521-1878},
support = {EP/W524700/1//EPSRC PhD studentship/ ; BB/M023389/1//BBSRC/ ; BB/R008167/2//BBSRC/ ; //The International Medical Research Foundation/ ; //Uehara Memorial Foundation/ ; },
abstract = {Ageing is associated with a decline in autophagy and elevated reactive oxygen species (ROS), which can breach the capacity of antioxidant systems. Resulting oxidative stress can cause further cellular damage, including DNA breaks and protein misfolding. This poses a challenge for longevous organisms, including humans. In this review, we hypothesise that in the course of human evolution selective autophagy receptors (SARs) acquired the ability to sense and respond to localised oxidative stress. We posit that in the vicinity of protein aggregates and dysfunctional mitochondria oxidation of key cysteine residues in SARs induces their oligomerisation which initiates autophagy. The degradation of damaged cellular components thus could reduce ROS production and restore redox homeostasis. This evolutionarily acquired function of SARs may represent one of the biological adaptations that contributed to longer lifespan. Inversely, loss of this mechanism can lead to age-related diseases associated with impaired autophagy and oxidative stress.},
}

@article {pmid37602330,
year = {2023},
author = {Das, P and Pal, S and Das, N and Chakraborty, K and Chatterjee, K and Mal, S and Choudhuri, T},
title = {Endogenous PTEN acts as the key determinant for mTOR inhibitor sensitivity by inducing the stress-sensitized PTEN-mediated death axis in KSHV-associated malignant cells.},
journal = {Frontiers in molecular biosciences},
volume = {10},
number = {},
pages = {1062462},
pmid = {37602330},
issn = {2296-889X},
abstract = {As a part of viral cancer evolution, KSHV-infected human endothelial cells exert a unique transcriptional program via upregulated mTORC1 signaling. This event makes them sensitive to mTOR inhibitors. Master transcriptional regulator PTEN acts as the prime regulator of mTOR and determining factor for mTOR inhibitory drug resistance and sensitivity. PTEN is post-translationally modified in KSHV-associated cell lines and infected tissues. Our current study is an attempt to understand the functional role of upstream modulator PTEN in determining the sensitivity of mTOR inhibitors against KSHV-infected cells in an in vitro stress-responsive model. Our analysis shows that, despite phosphorylation, endogenous levels of intact PTEN in different KSHV-infected cells compared to normal and non-infected cells are quite high. Genetic overexpression of intact PTEN showed functional integrity of this gene in the infected cells in terms of induction of a synchronized cell death process via cell cycle regulation and mitochondria-mediated apoptosis. PTEN overexpression enhanced the mTOR inhibitory drug activity, the silencing of which hampers the process against KSHV-infected cells. Additionally, we have shown that endogenous PTEN acts as a stress balancer molecule inside KSHV-infected cells and can induce stress-sensitized death program post mTOR inhibitor treatment, lined up in the ATM-chk2-p53 axis. Moreover, autophagic regulation was found as a major regulator in mTOR inhibitor-induced PTEN-mediated death axis from our study. The current work critically intersected the PTEN-mediated stress balancing mechanism where autophagy has been utilized as a part of the KSHV stress management system and is specifically fitted and switched toward autophagy-mediated apoptosis directing toward a therapeutic perspective.},
}

@article {pmid37599162,
year = {2023},
author = {Braun, HP and Klusch, N},
title = {Promotion of oxidative phosphorylation by complex I-anchored carbonic anhydrases?.},
journal = {Trends in plant science},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tplants.2023.07.007},
pmid = {37599162},
issn = {1878-4372},
abstract = {The mitochondrial NADH-dehydrogenase complex of the respiratory chain, known as complex I, includes a carbonic anhydrase (CA) module attached to its membrane arm on the matrix side in protozoans, algae, and plants. Its physiological role is so far unclear. Recent electron cryo-microscopy (cryo-EM) structures show that the CA module may directly provide protons for translocation across the inner mitochondrial membrane at complex I. CAs can have a central role in adjusting the proton concentration in the mitochondrial matrix. We suggest that CA anchoring in complex I represents the original configuration to secure oxidative phosphorylation (OXPHOS) in the context of early endosymbiosis. After development of 'modern mitochondria' with pronounced cristae structures, this anchoring became dispensable, but has been retained in protozoans, algae, and plants.},
}

@article {pmid37596708,
year = {2023},
author = {Golik, P},
title = {RNA processing and degradation mechanisms shaping the mitochondrial transcriptome of budding yeasts.},
journal = {IUBMB life},
volume = {},
number = {},
pages = {},
doi = {10.1002/iub.2779},
pmid = {37596708},
issn = {1521-6551},
abstract = {Yeast mitochondrial genes are expressed as polycistronic transcription units that contain RNAs from different classes and show great evolutionary variability. The promoters are simple, and transcriptional control is rudimentary. Posttranscriptional mechanisms involving RNA maturation, stability, and degradation are thus the main force shaping the transcriptome and determining the expression levels of individual genes. Primary transcripts are fragmented by tRNA excision by RNase P and tRNase Z, additional processing events occur at the dodecamer site at the 3' end of protein-coding sequences. groups I and II introns are excised in a self-splicing reaction that is supported by protein splicing factors encoded by the nuclear genes, or by the introns themselves. The 3'-to-5' exoribonucleolytic complex called mtEXO is the main RNA degradation activity involved in RNA turnover and processing, supported by an auxiliary 5'-to-3' exoribonuclease Pet127p. tRNAs and, to a lesser extent, rRNAs undergo several different base modifications. This complex gene expression system relies on the coordinated action of mitochondrial and nuclear genes and undergoes rapid evolution, contributing to speciation events. Moving beyond the classical model yeast Saccharomyces cerevisiae to other budding yeasts should provide important insights into the coevolution of both genomes that constitute the eukaryotic genetic system.},
}

@article {pmid37453661,
year = {2023},
author = {Dreishpoon, MB and Bick, NR and Petrova, B and Warui, DM and Cameron, A and Booker, SJ and Kanarek, N and Golub, TR and Tsvetkov, P},
title = {FDX1 regulates cellular protein lipoylation through direct binding to LIAS.},
journal = {The Journal of biological chemistry},
volume = {299},
number = {9},
pages = {105046},
doi = {10.1016/j.jbc.2023.105046},
pmid = {37453661},
issn = {1083-351X},
abstract = {Ferredoxins are a family of iron-sulfur (Fe-S) cluster proteins that serve as essential electron donors in numerous cellular processes that are conserved through evolution. The promiscuous nature of ferredoxins as electron donors enables them to participate in many metabolic processes including steroid, heme, vitamin D, and Fe-S cluster biosynthesis in different organisms. However, the unique natural function(s) of each of the two human ferredoxins (FDX1 and FDX2) are still poorly characterized. We recently reported that FDX1 is both a crucial regulator of copper ionophore-induced cell death and serves as an upstream regulator of cellular protein lipoylation, a mitochondrial lipid-based post-translational modification naturally occurring on four mitochondrial enzymes that are crucial for TCA cycle function. Here we show that FDX1 directly regulates protein lipoylation by binding the lipoyl synthase (LIAS) enzyme promoting its functional binding to the lipoyl carrier protein GCSH and not through indirect regulation of cellular Fe-S cluster biosynthesis. Metabolite profiling revealed that the predominant cellular metabolic outcome of FDX1 loss of function is manifested through the regulation of the four lipoylation-dependent enzymes ultimately resulting in loss of cellular respiration and sensitivity to mild glucose starvation. Transcriptional profiling established that FDX1 loss-of-function results in the induction of both compensatory metabolism-related genes and the integrated stress response, consistent with our findings that FDX1 loss-of-function is conditionally lethal. Together, our findings establish that FDX1 directly engages with LIAS, promoting its role in cellular protein lipoylation, a process essential in maintaining cell viability under low glucose conditions.},
}

@article {pmid37587350,
year = {2023},
author = {Merchant, A and Ramirez, BI and Reyes, MN and Van, D and Martinez-Colin, M and Ojo, DO and Mazuca, EL and De La O, HJ and Glenn, AM and Lira, CG and Ehsan, H and Yu, E and Kaneko, G},
title = {Genomic loss of the HSP70cA gene in the vertebrate lineage.},
journal = {Cell stress & chaperones},
volume = {},
number = {},
pages = {},
pmid = {37587350},
issn = {1466-1268},
abstract = {Metazoan 70 kDa heat shock protein (HSP70) genes have been classified into four lineages: cytosolic A (HSP70cA), cytosolic B (HSP70cB), endoplasmic reticulum (HSP70er), and mitochondria (HSP70m). Because previous studies have identified no HSP70cA genes in vertebrates, we hypothesized that this gene was lost on the evolutionary path to vertebrates. To test this hypothesis, the present study conducted a comprehensive database search followed by phylogenetic and synteny analyses. HSP70cA genes were found in invertebrates and in two of the three subphyla of Chordata, Cephalochordata (lancelets) and Tunicata (tunicates). However, no HSP70cA gene was found in the genomes of Craniata (another subphylum of Chordata; lamprey, hagfish, elephant shark, and coelacanth), suggesting the loss of the HSP70cA gene in the early period of vertebrate evolution. Synteny analysis using available genomic resources indicated that the synteny around the HSP70 genes was generally conserved between tunicates but was largely different between tunicates and lamprey. These results suggest the presence of dynamic chromosomal rearrangement in early vertebrates that possibly caused the loss of the HSP70cA gene in the vertebrate lineage.},
}

@article {pmid37584544,
year = {2023},
author = {Yang, C and Li, X and Zhou, J and Gao, C},
title = {Autophagy contributes to positive feedback regulation of SnRK1 signaling in plants.},
journal = {Autophagy},
volume = {},
number = {},
pages = {},
doi = {10.1080/15548627.2023.2247741},
pmid = {37584544},
issn = {1554-8635},
abstract = {SnRK1 (SNF1-related protein kinase 1) is a plant ortholog of yeast Snf1 and mammalian adenosine monophosphate-activated protein kinase (AMPK) that acts as a positive regulator of macroautophagy/autophagy. However, whether and how the autophagy pathway modulates SnRK1 activity remains elusive. Recently, we identified a clade of plant-specific FLZ (FCS-like zinc finger) proteins as novel ATG8 (autophagy related 8)-interacting partners in Arabidopsis thaliana. These AtFLZs, which mainly localize on the surface of mitochondria, can inhibit SnRK1 signaling by repressing the T-loop phosphorylation of its catalytic α subunits, thereby negatively regulating carbon starvation-induced autophagy and plant tolerance to energy deprivation. Upon energy starvation, autophagy is activated to mediate the degradation of these AtFLZs, thus relieving their repression of SnRK1. More importantly, the ATG8-FLZ-SnRK1 regulatory axis appears to be functionally conserved during seed plant evolution. These findings highlight the positive role of autophagy in SnRK1 signaling activation under energy-limiting conditions in plants.},
}

@article {pmid37481145,
year = {2023},
author = {DeCicco, LH and DeRaad, DA and Ostrow, EN and Moyle, RG},
title = {A complete species-level phylogeny of the Erythrura parrotfinches (Aves: Estrildidae).},
journal = {Molecular phylogenetics and evolution},
volume = {187},
number = {},
pages = {107883},
doi = {10.1016/j.ympev.2023.107883},
pmid = {37481145},
issn = {1095-9513},
mesh = {Animals ; Phylogeny ; *Passeriformes/genetics ; DNA ; Genes, Mitochondrial ; Mitochondria/genetics ; DNA, Mitochondrial/genetics ; Sequence Analysis, DNA ; },
abstract = {Identifying species boundaries and phylogenetic relationships among groups of closely related species provides a necessary framework for understanding how biodiversity evolves in natural systems. Here we present a complete phylogeny of the avian genus Erythrura (family Estrildidae) commonly known as parrotfinches, which includes species threatened by habitat loss and the pet trade. Using both mitogenome and reduced-representation genome-wide nuclear DNA sequence data, we reconstructed the evolutionary history of the group by sampling all 12 recognized species, four of which had not previously been studied in a phylogenetic context. We included intra-species geographic sampling that allowed us to comment on species limits in some taxa. We recovered the Gouldian Finch (Chloebia gouldiae) of Australia which has often been placed in the monotypic genus Chloebia, as being sister to a clade comprising all Erythrura species. In addition, we recovered a well-supported clade comprising eight species distributed throughout the Pacific Island eco-region, whereas those species occurring in continental southeast Asia, the Greater Sundas, and the Philippines, were recovered as earlier branching lineages. Of note was the early branching of the Fiji-endemic E. kleinschmidti which corroborates its unique phenotype. We also found a deep phylogenetic split (8.59% corrected, 7.89% uncorrected divergence in the mitochondrial gene ND2) between the Java and Philippine populations of E. hyperythra, indicating unrecognized species-level diversity within this taxon. In contrast, genome-wide nuclear data suggested that the New Guinea endemic species E. papuana is embedded within the widespread species E. trichroa in all phylogenetic reconstructions, corroborating previously published mitochondrial data that suggested a similar pattern. By generating a phylogenetic hypothesis for the relationships among all species of Erythrura parrotfinches, we provide a framework for better understanding the extant diversity and evolutionary history of this group.},
}

Animals
Phylogeny
*Passeriformes/genetics
DNA
Genes, Mitochondrial
Mitochondria/genetics
DNA, Mitochondrial/genetics
Sequence Analysis, DNA

@article {pmid37582787,
year = {2023},
author = {Meadows, JRS and Kidd, JM and Wang, GD and Parker, HG and Schall, PZ and Bianchi, M and Christmas, MJ and Bougiouri, K and Buckley, RM and Hitte, C and Nguyen, AK and Wang, C and Jagannathan, V and Niskanen, JE and Frantz, LAF and Arumilli, M and Hundi, S and Lindblad-Toh, K and Ginja, C and Agustina, KK and André, C and Boyko, AR and Davis, BW and Drögemüller, M and Feng, XY and Gkagkavouzis, K and Iliopoulos, G and Harris, AC and Hytönen, MK and Kalthoff, DC and Liu, YH and Lymberakis, P and Poulakakis, N and Pires, AE and Racimo, F and Ramos-Almodovar, F and Savolainen, P and Venetsani, S and Tammen, I and Triantafyllidis, A and vonHoldt, B and Wayne, RK and Larson, G and Nicholas, FW and Lohi, H and Leeb, T and Zhang, YP and Ostrander, EA},
title = {Genome sequencing of 2000 canids by the Dog10K consortium advances the understanding of demography, genome function and architecture.},
journal = {Genome biology},
volume = {24},
number = {1},
pages = {187},
pmid = {37582787},
issn = {1474-760X},
support = {R01GM140135/GM/NIGMS NIH HHS/United States ; R24GM082910/GM/NIGMS NIH HHS/United States ; Intramural Program/HG/NHGRI NIH HHS/United States ; ERC-2013-StG-337574-UNDEAD/ERC_/European Research Council/International ; ERC-2019-StG-853272-PALAEOFARM/ERC_/European Research Council/International ; },
abstract = {BACKGROUND: The international Dog10K project aims to sequence and analyze several thousand canine genomes. Incorporating 20 × data from 1987 individuals, including 1611 dogs (321 breeds), 309 village dogs, 63 wolves, and four coyotes, we identify genomic variation across the canid family, setting the stage for detailed studies of domestication, behavior, morphology, disease susceptibility, and genome architecture and function.

RESULTS: We report the analysis of > 48 M single-nucleotide, indel, and structural variants spanning the autosomes, X chromosome, and mitochondria. We discover more than 75% of variation for 239 sampled breeds. Allele sharing analysis indicates that 94.9% of breeds form monophyletic clusters and 25 major clades. German Shepherd Dogs and related breeds show the highest allele sharing with independent breeds from multiple clades. On average, each breed dog differs from the UU_Cfam_GSD_1.0 reference at 26,960 deletions and 14,034 insertions greater than 50 bp, with wolves having 14% more variants. Discovered variants include retrogene insertions from 926 parent genes. To aid functional prioritization, single-nucleotide variants were annotated with SnpEff and Zoonomia phyloP constraint scores. Constrained positions were negatively correlated with allele frequency. Finally, the utility of the Dog10K data as an imputation reference panel is assessed, generating high-confidence calls across varied genotyping platform densities including for breeds not included in the Dog10K collection.

CONCLUSIONS: We have developed a dense dataset of 1987 sequenced canids that reveals patterns of allele sharing, identifies likely functional variants, informs breed structure, and enables accurate imputation. Dog10K data are publicly available.},
}

@article {pmid37565789,
year = {2023},
author = {Yang, Y and Oldenkott, B and Ramanathan, S and Lesch, E and Takenaka, M and Schallenberg-Rüdinger, M and Knoop, V},
title = {DYW cytidine deaminase domains have a long-range impact on RNA recognition by the PPR array of chimeric plant C-to-U RNA editing factors and strongly affect target selection.},
journal = {The Plant journal : for cell and molecular biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/tpj.16412},
pmid = {37565789},
issn = {1365-313X},
support = {SCHA 1952/2-2//Deutsche Forschungsgemeinschaft/ ; },
abstract = {The protein factors for the specific C-to-U RNA editing events in plant mitochondria and chloroplasts possess unique arrays of RNA-binding pentatricopeptide repeats (PPRs) linked to carboxy-terminal cytidine deaminase DYW domains via the extension motifs E1 and E2. The E1 and E2 motifs have distant similarities to tetratricopeptide repeats known to mediate protein-protein interactions but their precise function is unclear. Here, we investigate the tolerance of PPR56 and PPR65, two functionally characterized RNA editing factors of the moss Physcomitrium patens, for the creation of chimeras by variably replacing their C-terminal protein regions. Making use of a heterologous RNA editing assay system in Escherichia coli we find that heterologous DYW domains can strongly restrict or widen the spectrum of off-targets in the bacterial transcriptome for PPR56. Surprisingly, our data suggest that these changes are not only caused by the preference of a given heterologous DYW domain for the immediate sequence environment of the cytidine to be edited but also by a long-range impact on the nucleotide selectivity of the upstream PPRs.},
}

@article {pmid37556561,
year = {2023},
author = {Raval, PK and Martin, WF and Gould, SB},
title = {Mitochondrial evolution: Gene shuffling, endosymbiosis, and signaling.},
journal = {Science advances},
volume = {9},
number = {32},
pages = {eadj4493},
pmid = {37556561},
issn = {2375-2548},
mesh = {*Symbiosis/genetics ; *Mitochondria/genetics ; Eukaryotic Cells/metabolism ; Genes, Mitochondrial ; Phylogeny ; Biological Evolution ; Evolution, Molecular ; },
abstract = {Genes for cardiolipin and ceramide synthesis occur in some alphaproteobacterial genomes. They shed light on mitochondrial origin and signaling in the first eukaryotic cells.},
}

*Symbiosis/genetics
*Mitochondria/genetics
Eukaryotic Cells/metabolism
Genes, Mitochondrial
Phylogeny
Biological Evolution
Evolution, Molecular

@article {pmid37557975,
year = {2023},
author = {Weaver, RJ and McDonald, AE},
title = {Mitochondrial alternative oxidase across the tree of life: Presence, absence, and putative cases of lateral gene transfer.},
journal = {Biochimica et biophysica acta. Bioenergetics},
volume = {},
number = {},
pages = {149003},
doi = {10.1016/j.bbabio.2023.149003},
pmid = {37557975},
issn = {1879-2650},
abstract = {The alternative oxidase (AOX) is a terminal oxidase in the electron transport system that plays a role in mitochondrial bioenergetics. The past 20 years of research shows AOX has a wide yet patchy distribution across the tree of life. AOX has been suggested to have a role in stress tolerance, growth, and development in plants, but less is known about its function in other groups, including animals. In this study, we analyzed the taxonomic distribution of AOX across >2800 species representatives from prokaryotes and eukaryotes and developed a standardized workflow for finding and verifying the authenticity of AOX sequences. We found that AOX is limited to proteobacteria among prokaryotes, but is widely distributed in eukaryotes, with the highest prevalence in plants, fungi, and protists. AOX is present in many invertebrates, but is absent in others including most arthropods, and is absent from vertebrates. We found aberrant AOX sequences associated with some animal groups. Some of these aberrant AOXs were contaminants, but we also found putative cases of lateral gene transfer of AOX from fungi and protists to nematodes, springtails, fungus gnats, and rotifers. Our findings provide a robust and detailed analysis of the distribution of AOX and a method for identifying and verifying putative AOX sequences, which will be useful as more sequence data becomes available on public repositories.},
}

@article {pmid37558671,
year = {2023},
author = {Kuhle, B and Hirschi, M and Doerfel, LK and Lander, GC and Schimmel, P},
title = {Structural basis for a degenerate tRNA identity code and the evolution of bimodal specificity in human mitochondrial tRNA recognition.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {4794},
pmid = {37558671},
issn = {2041-1723},
support = {GM125908//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; NS095892//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; GM142196//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; S10OD021634//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; GM125908//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; },
abstract = {Animal mitochondrial gene expression relies on specific interactions between nuclear-encoded aminoacyl-tRNA synthetases and mitochondria-encoded tRNAs. Their evolution involves an antagonistic interplay between strong mutation pressure on mtRNAs and selection pressure to maintain their essential function. To understand the molecular consequences of this interplay, we analyze the human mitochondrial serylation system, in which one synthetase charges two highly divergent mtRNA[Ser] isoacceptors. We present the cryo-EM structure of human mSerRS in complex with mtRNA[Ser(UGA)], and perform a structural and functional comparison with the mSerRS-mtRNA[Ser(GCU)] complex. We find that despite their common function, mtRNA[Ser(UGA)] and mtRNA[Ser(GCU)] show no constrain to converge on shared structural or sequence identity motifs for recognition by mSerRS. Instead, mSerRS evolved a bimodal readout mechanism, whereby a single protein surface recognizes degenerate identity features specific to each mtRNA[Ser]. Our results show how the mutational erosion of mtRNAs drove a remarkable innovation of intermolecular specificity rules, with multiple evolutionary pathways leading to functionally equivalent outcomes.},
}

@article {pmid37551058,
year = {2023},
author = {Huynh, SD and Melonek, J and Colas des Francs-Small, C and Bond, CS and Small, I},
title = {A unique C-terminal domain contributes to the molecular function of Restorer-of-fertility proteins in plant mitochondria.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.19166},
pmid = {37551058},
issn = {1469-8137},
support = {CE140100008//Australian Research Council/ ; LP200100547//Australian Research Council/ ; },
abstract = {Restorer-of-fertility (Rf) genes encode pentatricopeptide repeat (PPR) proteins that are targeted to mitochondria where they specifically bind to transcripts that induce cytoplasmic male sterility and repress their expression. In searching for a molecular signature unique to this class of proteins, we found that a majority of known Rf proteins have a distinct domain, which we called RfCTD (Restorer-of-fertility C-terminal domain), and its presence correlates with the ability to induce cleavage of the mitochondrial RNA target. A screen of 219 angiosperm genomes from 123 genera using a sequence profile that can quickly and accurately identify RfCTD sequences revealed considerable variation in RFL/RfCTD gene numbers across flowering plants. We observed that plant genera with bisexual flowers have significantly higher numbers of RFL genes compared to those with unisexual flowers, consistent with a role of these proteins in restoration of male fertility. We show that removing the RfCTD from the RFL protein RNA PROCESSING FACTOR 2-nad6 prevented cleavage of its RNA target, the nad6 transcript, in Arabidopsis thaliana mitochondria. We provide a simple way of identifying putative Rf candidates in genome sequences, new insights into the molecular mode of action of Rf proteins and the evolution of fertility restoration in flowering plants.},
}

@article {pmid37548336,
year = {2023},
author = {Ryan, K and Greenway, R and Landers, J and Arias-Rodriguez, L and Tobler, M and Kelley, JL},
title = {Selection on standing genetic variation mediates convergent evolution in extremophile fish.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {},
doi = {10.1111/mec.17081},
pmid = {37548336},
issn = {1365-294X},
support = {W911NF-15-1-0175//Army Research Office/ ; W911NF-16-1-0225//Army Research Office/ ; IOS-1931657//National Science Foundation/ ; IOS-2311366//National Science Foundation/ ; },
abstract = {Hydrogen sulfide is a toxic gas that disrupts numerous biological processes, including energy production in the mitochondria, yet fish in the Poecilia mexicana species complex have independently evolved sulfide tolerance several times. Despite clear evidence for convergence at the phenotypic level in these fishes, it is unclear if the repeated evolution of hydrogen sulfide tolerance is the result of similar genomic changes. To address this gap, we used a targeted capture approach to sequence genes associated with sulfide processes and toxicity from five sulfidic and five nonsulfidic populations in the species complex. By comparing sequence variation in candidate genes to a reference set, we identified similar population structure and differentiation, suggesting that patterns of variation in most genes associated with sulfide processes and toxicity are due to demographic history and not selection. But the presence of tree discordance for a subset of genes suggests that several loci are evolving divergently between ecotypes. We identified two differentiation outlier genes that are associated with sulfide detoxification in the mitochondria that have signatures of selection in all five sulfidic populations. Further investigation into these regions identified long, shared haplotypes among sulfidic populations. Together, these results reveal that selection on standing genetic variation in putatively adaptive genes may be driving phenotypic convergence in this species complex.},
}

@article {pmid37538245,
year = {2023},
author = {Zhang, H and Li, X and Fan, W and Pandovski, S and Tian, Y and Dillin, A},
title = {Inter-tissue communication of mitochondrial stress and metabolic health.},
journal = {Life metabolism},
volume = {2},
number = {1},
pages = {},
pmid = {37538245},
issn = {2755-0230},
support = {R01 AG059566/AG/NIA NIH HHS/United States ; R01 ES021667/ES/NIEHS NIH HHS/United States ; },
abstract = {Mitochondria function as a hub of the cellular metabolic network. Mitochondrial stress is closely associated with aging and a variety of diseases, including neurodegeneration and cancer. Cells autonomously elicit specific stress responses to cope with mitochondrial stress to maintain mitochondrial homeostasis. Interestingly, mitochondrial stress responses may also be induced in a non-autonomous manner in cells or tissues that are not directly experiencing such stress. Such non-autonomous mitochondrial stress responses are mediated by secreted molecules called mitokines. Due to their significant translational potential in improving human metabolic health, there has been a surge in mitokine-focused research. In this review, we summarize the findings regarding inter-tissue communication of mitochondrial stress in animal models. In addition, we discuss the possibility of mitokine-mediated intercellular mitochondrial communication originating from bacterial quorum sensing.},
}

@article {pmid37522604,
year = {2023},
author = {Chukaew, T and Isomura, N and Mezaki, T and Matsumoto, H and Kitano, YF and Nozawa, Y and Tachikawa, H and Fukami, H},
title = {Molecular Phylogeny and Taxonomy of the Coral Genus Cyphastrea (Cnidaria, Scleractinia, Merulinidae) in Japan, With the First Records of Two Species.},
journal = {Zoological science},
volume = {40},
number = {4},
pages = {326-340},
doi = {10.2108/zs230009},
pmid = {37522604},
issn = {0289-0003},
mesh = {Animals ; Phylogeny ; *Anthozoa/genetics ; Japan ; DNA, Ribosomal/genetics ; Mitochondria/genetics ; Sequence Analysis, DNA ; },
abstract = {The scleractinian coral genus Cyphastrea is widely distributed in the Indo-Pacific region and is common from the subtropical to the warm-temperate regions in Japan. Three new species in this genus have recently been reported from south-eastern Australia or the Red Sea. However, taxonomic and species diversity have been little studied so far in Japan. In this study, we analyzed 112 specimens of Cyphastrea collected from the subtropical to the warm-temperate regions in Japan to clarify the species diversity in the country. This analysis was based on skeletal morphological and molecular analyses using three genetic markers of the nuclear 28S rDNA, histone H3 gene, and the mitochondrial noncoding intergenic region between COI and tRNAmet. The molecular phylogenetic trees showed that our specimens are separated mainly into four clades. Considering the morphological data with the molecular phylogenetic relationships, we confirmed a total of nine species, including two species, C. magna and C. salae, recorded for the first time in Japan. Although eight out of nine species were genetically included within Cyphastrea, one species, C. agassizi, was genetically distant from all other species and was closely related to the genus Leptastrea, suggesting the return of this species to the genus to which it was originally ascribed. Two newly recorded species were reciprocally monophyletic, while the other six species (excluding C. agassizi) clustered in two clades without forming species-specific lineages, including three polyphyletic species. Thus, the species boundary between species in Cyphastrea remains unclear in most species using these three sequenced loci.},
}

Animals
Phylogeny
*Anthozoa/genetics
Japan
DNA, Ribosomal/genetics
Mitochondria/genetics
Sequence Analysis, DNA

@article {pmid37518710,
year = {2023},
author = {Russell, PJC and Pateman, JE and Gagarina, AV and Lukhtanov, VA},
title = {Investigations into the Melitaea ornata species complex in the Levant: M. telona and the newly erected species Melitaea klili Benyamini, 2021 (Lepidoptera: Nymphalidae).},
journal = {Zootaxa},
volume = {5285},
number = {1},
pages = {187-195},
doi = {10.11646/zootaxa.5285.1.9},
pmid = {37518710},
issn = {1175-5334},
mesh = {Male ; Animals ; *Butterflies/genetics ; Phylogeny ; DNA, Mitochondrial/genetics ; Mitochondria/genetics ; Genes, Mitochondrial ; DNA Barcoding, Taxonomic ; },
abstract = {Melitaea klili Benyamini, 2021 was recently described from Israel as a species closely related to M. telona Fruhstorfer, 1908, but different in phenology, ecological preferences and with an allopatric distribution. Here, based on comparative examinations of mitochondrial DNA-barcodes, male genitalia and larval behaviour under laboratory conditions, we synonymize M. klili with M. telona. The COI barcodes of M. klili were found to be identical to those of M. telona. Analysis of 658 bp fragment of the mitochondrial gene COI demonstrated that the minimum uncorrected p-distance between M. ornata and M. telona was 1.98%. This value is remarkably less than the 3% threshold traditionally accepted as a species boundary in DNA barcoding studies. The morphological differences between these taxa are minimal. In fact, M. ornata and M. telona represent two phylogenetic lineages, the taxonomic status of which (separate species or subspecies of the same species) is intermediate and debatable.},
}

Male
Animals
*Butterflies/genetics
Phylogeny
DNA, Mitochondrial/genetics
Mitochondria/genetics
Genes, Mitochondrial
DNA Barcoding, Taxonomic

@article {pmid37518493,
year = {2023},
author = {Tomimori, Y and Matsui, M and Okawa, H and Nishikawa, K and Tanabe, S and Kamasaka, R},
title = {Reassessment of species delimitation using nuclear markers in three lentic-breeding salamanders from the Chugoku District of Japan (Amphibia: Caudata: Hynobiidae).},
journal = {Zootaxa},
volume = {5293},
number = {1},
pages = {145-160},
doi = {10.11646/zootaxa.5293.1.6},
pmid = {37518493},
issn = {1175-5334},
mesh = {Animals ; *Urodela/genetics ; Phylogeny ; Japan ; *DNA, Mitochondrial/genetics ; Mitochondria/genetics ; },
abstract = {Hynobius akiensis sensu lato has recently been split into three species based on short sequence analyses of cyt-b gene of mtDNA and without data of nuclear DNA, and strange sympatric distribution in some areas has been indicated in two species. We analyzed nuclear DNA marker (SNPs) and complete sequence of cyt-b in H. akiensis sensu lato to reassess species delimitation and genetic introgression among species. As a result, we found two lineages with discordant mitochondrial and nuclear DNA in some areas. Of H. akiensis sensu lato, each of the two contains the type locality of two species recently reported (H. sumidai and H. geiyoensis), and the use of these names has been previously advocated. However, their sympatric distribution was rejected based on nuclear DNA data, which we consider is more reliable than mtDNA. We thus clarify geographic boundary of these two species and revise the species delimitations.},
}

Animals
*Urodela/genetics
Phylogeny
Japan
*DNA, Mitochondrial/genetics
Mitochondria/genetics

@article {pmid37515372,
year = {2023},
author = {Fernández-Moncada, I and Rodrigues, RS and Fundazuri, UB and Bellocchio, L and Marsicano, G},
title = {Type-1 cannabinoid receptors and their ever-expanding roles in brain energy processes.},
journal = {Journal of neurochemistry},
volume = {},
number = {},
pages = {},
doi = {10.1111/jnc.15922},
pmid = {37515372},
issn = {1471-4159},
support = {//INSERM/ ; Micabra, ERC-2017-AdG-786467//the European Research Council/ ; DRM20101220445//Fondation pour la Recherche Medicale/ ; ALTF87-2018//EMBO/ ; //the Human Frontiers Science Program/ ; 17219710//Region Aquitaine/ ; CanBrain, AAP2022A-2021-16763610//Region Aquitaine/ ; ANR-19-CE14-0039//French State/Agence Nationale de la Recherche/ ; ERA-Net Neuron CanShank, ANR-21-NEU2-0001-04//French State/Agence Nationale de la Recherche/ ; MitObesity, ANR 18-CE14-0029-01//French State/Agence Nationale de la Recherche/ ; CaCoVi, ANR 18-CE16-0001-02//French State/Agence Nationale de la Recherche/ ; GPR BRAIN_2030//University of Bordeaux's IdEx "Investments for the Future" program/ ; },
abstract = {The brain requires large quantities of energy to sustain its functions. At the same time, the brain is isolated from the rest of the body, forcing this organ to develop strategies to control and fulfill its own energy needs. Likely based on these constraints, several brain-specific mechanisms emerged during evolution. For example, metabolically specialized cells are present in the brain, where intercellular metabolic cycles are organized to separate workload and optimize the use of energy. To orchestrate these strategies across time and space, several signaling pathways control the metabolism of brain cells. One of such controlling systems is the endocannabinoid system, whose main signaling hub in the brain is the type-1 cannabinoid (CB1) receptor. CB1 receptors govern a plethora of different processes in the brain, including cognitive function, emotional responses, or feeding behaviors. Classically, the mechanisms of action of CB1 receptors on brain function had been explained by its direct targeting of neuronal synaptic function. However, new discoveries have challenged this view. In this review, we will present and discuss recent data about how a small fraction of CB1 receptors associated to mitochondrial membranes (mtCB1), are able to exert a powerful control on brain functions and behavior. mtCB1 receptors impair mitochondrial functions both in neurons and astrocytes. In the latter cells, this effect is linked to an impairment of astrocyte glycolytic function, resulting in specific behavioral outputs. Finally, we will discuss the potential implications of (mt)CB1 expression on oligodendrocytes and microglia metabolic functions, with the aim to encourage interdisciplinary approaches to better understand the role of (mt)CB1 receptors in brain function and behavior.},
}